diff --git a/.gitattributes b/.gitattributes index 47a9831f0..c4b8d507a 100644 --- a/.gitattributes +++ b/.gitattributes @@ -11,7 +11,11 @@ pygimli/_version.py export-subst *.sh text # Declare files that will always have CRLF line endings on checkout. -# *.sln text eol=crlf +*.py text eol=crlf +*.md text eol=crlf +*.rst text eol=crlf +*.bib text eol=crlf +*.txt text eol=crlf # Denote all files that are truly binary and should not be modified. *.png binary diff --git a/.github/ISSUE_TEMPLATE/bug.yml b/.github/ISSUE_TEMPLATE/bug.yml new file mode 100644 index 000000000..228accab4 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug.yml @@ -0,0 +1,107 @@ +name: Bug Report +description: Please use this form to file a bug report. +labels: ["bug"] +body: + - type: markdown + attributes: + value: Thanks for taking the time to fill out this bug report! To facilitate efficient support, please fill out all the information applicable to your issue. + - type: markdown + attributes: + value: "### Problem description" + - type: textarea + id: problem-description + attributes: + label: Problem description + description: Please provide a general description of the issue here. + - type: markdown + attributes: + value: "### Your environment" + - type: textarea + id: environment-report + attributes: + label: Your environment + description: Please provide the output of `print(pygimli.Report())` here. If that does not work, please fill out the information on operating system, Python version and pyGIMLi version below. + render: shell + - type: dropdown + id: os + attributes: + label: Operating System + description: Which operating system are you using? + options: + - Windows + - Mac + - Linux + - type: dropdown + id: python-version + attributes: + label: Which Python version are you using? + options: + - 3.15 + - 3.14 + - 3.13 + - 3.12 + - 3.11 + - 3.10 + - 3.9 + - type: input + id: way-of-installation + attributes: + label: Way of installation + description: Please describe your way of installing pyGIMLi, e.g. Conda package, manual compilation from source etc. + - type: dropdown + id: pygimli-version + attributes: + label: Which version of PyGIMLI are you using? + description: Output of `print(pygimli.__version__)` + options: + - 1.5.4 + - 1.5.3 + - 1.5.2 + - 1.5.1 + - 1.5.0 + - type: textarea + id: environment-additional + attributes: + label: Additional information on the environment + description: If you have additional information on the environment or installation that did not fit the forms above, please enter it here. + - type: markdown + attributes: + value: "### Reproducing the issue" + - type: textarea + id: reproduce-steps + attributes: + label: Steps to reproduce the issue + description: If there are specific steps necessary to reproduce the issue, please describe them here. + - type: textarea + id: reproduce-code + attributes: + label: Code to reproduce the issue + description: Please provide the code that produces the error in the form of a minimal reproducible example. Alternatively, you can also attach the code as a file in the field below. + render: shell + - type: textarea + id: reproduce-data + attributes: + label: Additional data to reproduce the issue + description: Please provide additional data that is necessary to reproduce the error, e.g. data files, additional code or Python dependencies. + - type: markdown + attributes: + value: "### Expected behavior" + - type: textarea + id: expected + attributes: + label: Expected behavior + description: Tell us what should happen or what you want to achieve. + - type: markdown + attributes: + value: "### Actual behavior" + - type: textarea + id: actual-text + attributes: + label: Actual behavior + description: Please tell us what happens instead of the expected behavior. + - type: textarea + id: actual-output + attributes: + label: Output of your script + description: If applicable, please provide the output of your script that shows the actual behavior. + render: shell diff --git a/.github/ISSUE_TEMPLATE/feature-request.yml b/.github/ISSUE_TEMPLATE/feature-request.yml new file mode 100644 index 000000000..90ce411b8 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature-request.yml @@ -0,0 +1,9 @@ +name: Feature Request +description: Please use this form to propose a new feature for pyGIMLi. +labels: ["feature request"] +body: +- type: textarea + id: feature-request + attributes: + label: Feature Request + description: Please provide details on the feature request here. \ No newline at end of file diff --git a/.github/ISSUE_TEMPLATE/question.yml b/.github/ISSUE_TEMPLATE/question.yml new file mode 100644 index 000000000..77e5599cb --- /dev/null +++ b/.github/ISSUE_TEMPLATE/question.yml @@ -0,0 +1,9 @@ +name: Question +description: Please use this form if you expect that your issue is rather a question than a problem with the code. +labels: ["question"] +body: +- type: textarea + id: question + attributes: + label: Question + description: Please provide details on your issue or question. \ No newline at end of file diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 45659460a..d4dfcb77f 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -60,25 +60,28 @@ jobs: working-directory: build run: xvfb-run make doc # xvfb is necessary for headless display of pyvista plots merging: - name: Merging dev into master + name: Automerging runs-on: self-hosted needs: docs if: github.ref == 'refs/heads/dev' # Only merge from dev steps: - - name: Merge into master - uses: devmasx/merge-branch@master - with: - type: now - target_branch: master - github_token: ${{ secrets.GITHUB_TOKEN }} + - name: Merge dev -> master (with rebase) + working-directory: source + run: | + git config --local user.email "actions@github.com" + git config --local user.name "GitHub Actions" + git remote set-url origin https://florian-wagner:${{ secrets.SECRET }}@github.com/gimli-org/gimli.git + git fetch + git rebase origin/master + git push origin HEAD:master --force-with-lease upload-html: name: Upload HTML to dev.pygimli.org runs-on: self-hosted needs: docs if: github.ref == 'refs/heads/dev' # Only merge from dev steps: - - name: Merge into master + - name: Uploading built html files working-directory: build run: rsync -avP --delete doc/html/ /var/www/html - - + + diff --git a/.gitignore b/.gitignore index fa5c1d7c9..ba28ed3ba 100644 --- a/.gitignore +++ b/.gitignore @@ -14,6 +14,9 @@ doc/_static/usecases/original/ *.ipynb *.ipynb_checkpoints* +doc/user-guide/*_files +doc/user-guide/*.html + # Customizations *.log *.pdf @@ -110,4 +113,4 @@ pygimli/core/libgimli.dll.back pygimli/core/_pygimli_.pyd.back pygimli/core/_pygimli_.so.dSYM/ pygimli/VERSION -synth.ves \ No newline at end of file +synth.ves diff --git a/.jenkins.sh b/.jenkins.sh index 9845d828b..3896229a0 100644 --- a/.jenkins.sh +++ b/.jenkins.sh @@ -80,8 +80,8 @@ export PYVISTA_OFF_SCREEN=true export PYTHONPATH=`pwd`/../trunk:$PYTHONPATH OMP_THREAD_LIMIT=4 python -c "import pygimli; print(pygimli.Report()); pygimli.test(show=False, abort=True, htmlreport=\"build_tests.html\", devTests=True)" -# Build documentation -make clean-gallery +#Build documentation +#make clean-gallery # TMP for fast Jenkins builds make doc # = doxygen, sphinxapi, sphinxpdf, sphinxhtml end=$(date +"%s") echo "Ending automatic build #$BUILD_NUMBER". diff --git a/AUTHORS.md b/AUTHORS.md new file mode 100644 index 000000000..5f352ed3d --- /dev/null +++ b/AUTHORS.md @@ -0,0 +1,17 @@ +- [Carsten Rücker](https://orcid.org/0000-0002-8231-9861) + + *Berlin University of Technology, Department of Applied Geophysics, Berlin, Germany* + + + +- [Thomas Günther](https://orcid.org/0000-0001-5409-0273) + + *TU Bergakademie Freiberg, Electromagnetics and potential methods working group, Freiberg, Germany* + + + +- [Florian Wagner](https://orcid.org/0000-0001-7407-9741) + + *RWTH Aachen University, Geophysical Imaging and Monitoring (GIM), Aachen, Germany* + + \ No newline at end of file diff --git a/AUTHORS.rst b/AUTHORS.rst deleted file mode 100644 index d7d2db53a..000000000 --- a/AUTHORS.rst +++ /dev/null @@ -1,31 +0,0 @@ -* `Carsten Rücker `_ - - *Berlin University of Technology, Department of Applied Geophysics, Berlin, Germany* - - carsten@pygimli.org - -* `Thomas Günther `_ - - *Leibniz Institute for Applied Geophysics, Hannover, Germany* - - thomas@pygimli.org - -* `Florian Wagner `_ - - *RWTH Aachen University, Geophysical Imaging and Monitoring (GIM), Aachen, Germany* - - florian@pygimli.org - -* Friedrich Dinsel - - *Berlin University of Technology, Department of Applied Geophysics, Berlin, Germany* - - friedrich@pygimli.org - -* `Maximilian Weigand `_ - - *University of Bonn, Department of Geophysics, Bonn, Germany* - -* `Andrea Balza `_ - - *RWTH Aachen University, Geophysical Imaging and Monitoring (GIM), Aachen, Germany* diff --git a/CITATION.md b/CITATION.md new file mode 100644 index 000000000..2bd202fa1 --- /dev/null +++ b/CITATION.md @@ -0,0 +1,29 @@ +# Citing pyGIMLi + +If you use pyGIMLi for your work, please cite [this paper](http://www.sciencedirect.com/science/article/pii/S0098300417300584/pdfft?md5=44253eaacd5490e3fb32210671672496&pid=1-s2.0-S0098300417300584-main.pdf) as: + +> Rücker, C., Günther, T., Wagner, F.M., 2017. pyGIMLi: An open-source library +> for modelling and inversion in geophysics, Computers and Geosciences, 109, +> 106-123, doi: 10.1016/j.cageo.2017.07.011. + +```{raw} html +
+``` + +Scripts to reproduce the figures in the paper can be found at +. + +BibTeX code: + +```bibtex +@article{Ruecker2017, + title = {{pyGIMLi}: An open-source library for modelling and inversion in geophysics}, + journal = {Computers and Geosciences}, + volume = {109}, + pages = {106--123}, + year = {2017}, + doi = {10.1016/j.cageo.2017.07.011}, + url = {https://www.sciencedirect.com/science/article/pii/S0098300417300584}, + author = {R\"ucker, C. and G\"unther, T. and Wagner, F. M.} +} +``` diff --git a/CITATION.rst b/CITATION.rst deleted file mode 100644 index b80f0b7f0..000000000 --- a/CITATION.rst +++ /dev/null @@ -1,30 +0,0 @@ -Citing pyGIMLi --------------- - -If you use pyGIMLi for your work, please cite `this paper `_ as: - - Rücker, C., Günther, T., Wagner, F.M., 2017. pyGIMLi: An open-source library - for modelling and inversion in geophysics, Computers and Geosciences, 109, - 106-123, doi: 10.1016/j.cageo.2017.07.011. - -.. raw:: html - -
- -Scripts to reproduce the figures in the paper can be found at -https://cg17.pygimli.org. - -BibTeX code: - -.. code-block:: bibtex - - @article{Ruecker2017, - title = {{pyGIMLi}: An open-source library for modelling and inversion in geophysics}, - journal = {Computers and Geosciences}, - volume = {109}, - pages = {106--123}, - year = {2017}, - doi = {10.1016/j.cageo.2017.07.011}, - url = {https://www.sciencedirect.com/science/article/pii/S0098300417300584}, - author = {R\"ucker, C. and G\"unther, T. and Wagner, F. M.} - } diff --git a/CMakeLists.txt b/CMakeLists.txt index 158687aa5..91b027a0f 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -668,17 +668,6 @@ if (SPHINX_FOUND AND NOT SKIP_SPHINX) add_subdirectory(doc EXCLUDE_FROM_ALL) message(STATUS "Search recursive for related doc files from here: " ${CMAKE_SOURCE_DIR}) - file(GLOB DOCFILES LIST_DIRECTORIES false - RELATIVE "${CMAKE_SOURCE_DIR}" - "*.rst") - message(STATUS "DOCFILES: " ${DOCFILES}) - - file(GLOB DFILES LIST_DIRECTORIES false - RELATIVE "${CMAKE_SOURCE_DIR}" - "*.md") - message(STATUS "MDFILES: " ${DFILES}) - list(APPEND DOCFILES ${DFILES}) - set (RECDOCTYPES "*.rst" "*.md" "*.png" "*.svg" "*.bib" "paper/*.py") foreach (DTYPE ${RECDOCTYPES}) @@ -689,27 +678,6 @@ if (SPHINX_FOUND AND NOT SKIP_SPHINX) message(STATUS "Append DOC files: (${DTYPE}) " ${DFILES}) list(APPEND DOCFILES ${DFILES}) endforeach() - # message(STATUS "RSTFILES: " ${DFILES}) - - # file(GLOB_RECURSE DFILES LIST_DIRECTORIES false - # RELATIVE "${CMAKE_SOURCE_DIR}" "${CMAKE_SOURCE_DIR}" "./doc/*.md") - # message(STATUS "MDFILES: " ${DFILES}) - # list(APPEND DOCFILES ${DFILES}) - - # file(GLOB_RECURSE DFILES LIST_DIRECTORIES false - # RELATIVE "${CMAKE_SOURCE_DIR}" "${CMAKE_SOURCE_DIR}" "./doc/*.png") - # message(STATUS "PNGFILES: " ${DFILES}) - # list(APPEND DOCFILES ${DFILES}) - - # file(GLOB_RECURSE DFILES LIST_DIRECTORIES false - # RELATIVE "${CMAKE_SOURCE_DIR}" "${CMAKE_SOURCE_DIR}" "./doc/*.bib") - # message(STATUS "BIBFILES: " ${DFILES}) - # list(APPEND DOCFILES ${DFILES}) - - # file(GLOB_RECURSE PYFILES LIST_DIRECTORIES false - # RELATIVE "${CMAKE_SOURCE_DIR}" "${CMAKE_SOURCE_DIR}" "doc/paper/*.py") - # message(STATUS "PYFILES: " ${PYFILES}) - # list(APPEND DOCFILES ${PYFILES}) set(RSTFILES ${DOCFILES} CACHE INTERNAL "RST source file that we need to copy") diff --git a/COPYING.rst b/COPYING.rst deleted file mode 100644 index ba8230c06..000000000 --- a/COPYING.rst +++ /dev/null @@ -1,204 +0,0 @@ -License -======= - - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. Definitions. - - "License" shall mean the terms and conditions for use, reproduction, - and distribution as defined by Sections 1 through 9 of this document. - - "Licensor" shall mean the copyright owner or entity authorized by - the copyright owner that is granting the License. - - "Legal Entity" shall mean the union of the acting entity and all - other entities that control, are controlled by, or are under common - control with that entity. For the purposes of this definition, - "control" means (i) the power, direct or indirect, to cause the - direction or management of such entity, whether by contract or - otherwise, or (ii) ownership of fifty percent (50%) or more of the - outstanding shares, or (iii) beneficial ownership of such entity. - - "You" (or "Your") shall mean an individual or Legal Entity - exercising permissions granted by this License. - - "Source" form shall mean the preferred form for making modifications, - including but not limited to software source code, documentation - source, and configuration files. - - "Object" form shall mean any form resulting from mechanical - transformation or translation of a Source form, including but - not limited to compiled object code, generated documentation, - and conversions to other media types. - - "Work" shall mean the work of authorship, whether in Source or - Object form, made available under the License, as indicated by a - copyright notice that is included in or attached to the work - (an example is provided in the Appendix below). - - "Derivative Works" shall mean any work, whether in Source or Object - form, that is based on (or derived from) the Work and for which the - editorial revisions, annotations, elaborations, or other modifications - represent, as a whole, an original work of authorship. For the purposes - of this License, Derivative Works shall not include works that remain - separable from, or merely link (or bind by name) to the interfaces of, - the Work and Derivative Works thereof. - - "Contribution" shall mean any work of authorship, including - the original version of the Work and any modifications or additions - to that Work or Derivative Works thereof, that is intentionally - submitted to Licensor for inclusion in the Work by the copyright owner - or by an individual or Legal Entity authorized to submit on behalf of - the copyright owner. For the purposes of this definition, "submitted" - means any form of electronic, verbal, or written communication sent - to the Licensor or its representatives, including but not limited to - communication on electronic mailing lists, source code control systems, - and issue tracking systems that are managed by, or on behalf of, the - Licensor for the purpose of discussing and improving the Work, but - excluding communication that is conspicuously marked or otherwise - designated in writing by the copyright owner as "Not a Contribution." - - "Contributor" shall mean Licensor and any individual or Legal Entity - on behalf of whom a Contribution has been received by Licensor and - subsequently incorporated within the Work. - - 2. Grant of Copyright License. Subject to the terms and conditions of - this License, each Contributor hereby grants to You a perpetual, - worldwide, non-exclusive, no-charge, royalty-free, irrevocable - copyright license to reproduce, prepare Derivative Works of, - publicly display, publicly perform, sublicense, and distribute the - Work and such Derivative Works in Source or Object form. - - 3. Grant of Patent License. Subject to the terms and conditions of - this License, each Contributor hereby grants to You a perpetual, - worldwide, non-exclusive, no-charge, royalty-free, irrevocable - (except as stated in this section) patent license to make, have made, - use, offer to sell, sell, import, and otherwise transfer the Work, - where such license applies only to those patent claims licensable - by such Contributor that are necessarily infringed by their - Contribution(s) alone or by combination of their Contribution(s) - with the Work to which such Contribution(s) was submitted. If You - institute patent litigation against any entity (including a - cross-claim or counterclaim in a lawsuit) alleging that the Work - or a Contribution incorporated within the Work constitutes direct - or contributory patent infringement, then any patent licenses - granted to You under this License for that Work shall terminate - as of the date such litigation is filed. - - 4. Redistribution. You may reproduce and distribute copies of the - Work or Derivative Works thereof in any medium, with or without - modifications, and in Source or Object form, provided that You - meet the following conditions: - - (a) You must give any other recipients of the Work or - Derivative Works a copy of this License; and - - (b) You must cause any modified files to carry prominent notices - stating that You changed the files; and - - (c) You must retain, in the Source form of any Derivative Works - that You distribute, all copyright, patent, trademark, and - attribution notices from the Source form of the Work, - excluding those notices that do not pertain to any part of - the Derivative Works; and - - (d) If the Work includes a "NOTICE" text file as part of its - distribution, then any Derivative Works that You distribute must - include a readable copy of the attribution notices contained - within such NOTICE file, excluding those notices that do not - pertain to any part of the Derivative Works, in at least one - of the following places: within a NOTICE text file distributed - as part of the Derivative Works; within the Source form or - documentation, if provided along with the Derivative Works; or, - within a display generated by the Derivative Works, if and - wherever such third-party notices normally appear. The contents - of the NOTICE file are for informational purposes only and - do not modify the License. You may add Your own attribution - notices within Derivative Works that You distribute, alongside - or as an addendum to the NOTICE text from the Work, provided - that such additional attribution notices cannot be construed - as modifying the License. - - You may add Your own copyright statement to Your modifications and - may provide additional or different license terms and conditions - for use, reproduction, or distribution of Your modifications, or - for any such Derivative Works as a whole, provided Your use, - reproduction, and distribution of the Work otherwise complies with - the conditions stated in this License. - - 5. Submission of Contributions. Unless You explicitly state otherwise, - any Contribution intentionally submitted for inclusion in the Work - by You to the Licensor shall be under the terms and conditions of - this License, without any additional terms or conditions. - Notwithstanding the above, nothing herein shall supersede or modify - the terms of any separate license agreement you may have executed - with Licensor regarding such Contributions. - - 6. Trademarks. This License does not grant permission to use the trade - names, trademarks, service marks, or product names of the Licensor, - except as required for reasonable and customary use in describing the - origin of the Work and reproducing the content of the NOTICE file. - - 7. Disclaimer of Warranty. Unless required by applicable law or - agreed to in writing, Licensor provides the Work (and each - Contributor provides its Contributions) on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or - implied, including, without limitation, any warranties or conditions - of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A - PARTICULAR PURPOSE. You are solely responsible for determining the - appropriateness of using or redistributing the Work and assume any - risks associated with Your exercise of permissions under this License. - - 8. Limitation of Liability. In no event and under no legal theory, - whether in tort (including negligence), contract, or otherwise, - unless required by applicable law (such as deliberate and grossly - negligent acts) or agreed to in writing, shall any Contributor be - liable to You for damages, including any direct, indirect, special, - incidental, or consequential damages of any character arising as a - result of this License or out of the use or inability to use the - Work (including but not limited to damages for loss of goodwill, - work stoppage, computer failure or malfunction, or any and all - other commercial damages or losses), even if such Contributor - has been advised of the possibility of such damages. - - 9. Accepting Warranty or Additional Liability. While redistributing - the Work or Derivative Works thereof, You may choose to offer, - and charge a fee for, acceptance of support, warranty, indemnity, - or other liability obligations and/or rights consistent with this - License. However, in accepting such obligations, You may act only - on Your own behalf and on Your sole responsibility, not on behalf - of any other Contributor, and only if You agree to indemnify, - defend, and hold each Contributor harmless for any liability - incurred by, or claims asserted against, such Contributor by reason - of your accepting any such warranty or additional liability. - - END OF TERMS AND CONDITIONS - - APPENDIX: How to apply the Apache License to your work. - - To apply the Apache License to your work, attach the following - boilerplate notice, with the fields enclosed by brackets "[]" - replaced with your own identifying information. (Don't include - the brackets!) The text should be enclosed in the appropriate - comment syntax for the file format. We also recommend that a - file or class name and description of purpose be included on the - same "printed page" as the copyright notice for easier - identification within third-party archives. - - Copyright [yyyy] [name of copyright owner] - - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License. diff --git a/INSTALLATION.md b/INSTALLATION.md new file mode 100644 index 000000000..5f8f15d7a --- /dev/null +++ b/INSTALLATION.md @@ -0,0 +1,197 @@ +(installation)= +# Installation + +```{raw} html +

+ + + + + + + + + + + + + + +


+``` + +On all platforms, we recommend to install pyGIMLi via the conda package manager +contained in the Anaconda Python distribution. For details on how to install +Anaconda, see [this page](https://docs.anaconda.com/anaconda/install/). + +Note that Anaconda comes with many (great) packages, many of which you likely +will not use. If you want to save space, you can install the [light-weight +version Miniconda](https://docs.anaconda.com/free/miniconda/miniconda-install/). + +:::{note} +After installing Anaconda or Miniconda, make sure that you have at least +version 23.10.0 of conda (`conda --version`). +::: + +% TODO: Temporarily disabled. PDF needs to update version automatically. + +% A **step-by-step guide for Windows users** can be found `here + +% `_. + +To avoid conflicts with other packages, we recommend to install pyGIMLi in a +separate environment. Here we call this environment `pg`, but you can give +it any name. Note that this environment has to be created only once. + +Open a terminal (Linux & Mac) or the Anaconda Prompt (Windows) and type: + +```bash +conda create -n pg -c gimli -c conda-forge "pygimli>=1.5.0" +``` + +If you want to use pyGIMLi from the command line, you have to activate the +environment. You can put this line in your `~/.bashrc` file so that it is +activated automatically if you open a terminal. + +```bash +conda activate pg +``` + +After that you can use pyGIMLi with your text editor of choice and a terminal. + + +## Using pip + +*Currently only available for linux and windows.* + +pyGIMLi can be also installed using the default python installer using `pip`. If you don't use a conda environment we encurage the use of a virtual environment. + +```bash +python -m venv .venv --promp=pg +.venv/bin/activate # for linux +#or for windows +.venv/Scripts/activate +``` +Its maybe not a bad idea to keep evironments if you have a working toolchain and test new pygimli version in a new virtual environment first. + + +To install pygimli using `pip`: + +```bash +pip install pygimli +``` + +To update pygimli using `pip`: + +```bash +pip install -U pygimli +``` + +Find available version: + +```bash +pip index versions pygimli +``` + +To install a specific version using `pip`: + +```bash +pip install pygimli==$version +``` + + +## Usage with Spyder or JupyterLab + +Depending on your preferences, you can also install third-party software such as +the MATLAB-like integrated development environment (): + +```bash +conda install -c conda-forge spyder +``` + +Or alternatively, the web-based IDE JupyterLab (): + +```bash +conda install -c conda-forge jupyterlab +``` + +If you do one of the above steps in the `pg` environment, then it will +automatically find pyGIMLi. But you may not want to install JupyterLab or +Spyder for every different environment. To use your existing JupyterLab +installation in the `base` environment with pyGIMLi in the `pg` environment, +follow these steps: + +```bash +conda activate pg +conda install ipykernel +conda activate base +conda install -c conda-forge nb_conda_kernels +jupyter lab +``` + +## pyGIMLi on Google Colab + +Even though still experimental, pyGIMLi can be run on Google Colab without any +installation on your own computer. Just create a new Notebook and install the +pyGIMLi package via pip: + + !pip install pygimli tetgen + +It turns out that there are some packages preinstalled that lead to some +incompatibl numpy version, so you might have to uninstall them first. + +.. code:: python + + !pip uninstall -y numba tensorflow pytensor thinc + !pip install pygimli tetgen + +## Staying up-to-date + +Update your pyGIMLi installation from time to time, if want to have the newest +functionality. + +```bash +conda update -c gimli -c conda-forge pygimli +``` + +If something went wrong and you are running an old, not further +supported Python version, consider a fresh install in a new clean environment. +The only drawback of using conda is that you are bound to the rhythm in which we +update the conda packages. In order to work with the latest Python codes you +should create an environment with the latest pyGIMLi C++ core only, + +```bash +conda create -n pgcore -c gimli -c conda-forge pgcore +``` + +retrieve the source code by git + +```bash +git clone https://github.com/gimli-org/gimli +cd gimli +``` + +and install pygimli as a development package using conda + +```bash +conda develop . +``` + +or using pip + +```bash +pip install --no-build-isolation --no-deps -e . +``` + +Alternatively you could set the `PYTHONPATH` variable, but you would have to care +for dependencies by yourself. + +Later you can just update the pyGIMLi code by + +```bash +git pull +``` + +Only if you need recent changes to the C++ core, you have to compile +pyGIMLi using your systems toolchain as described in + diff --git a/INSTALLATION.rst b/INSTALLATION.rst deleted file mode 100644 index 026270a04..000000000 --- a/INSTALLATION.rst +++ /dev/null @@ -1,158 +0,0 @@ -Installation -============ - -.. raw:: html - -

- - - - - - - - - - - - - - -


- - -On all platforms, we recommend install pyGIMLi via the conda package manager -and the cleanest way is to create a new environment. -Besides large installers like `Anaconda `_ -that come with many (great) packages, you can save space and install a -light-weight installer like -`Miniconda `_ -or `Miniforge `_. - -.. note:: - - After installing Anaconda or Miniconda, make sure that you have at least - version 23.10.0 of conda (`conda --version`). - -.. TODO: Temporarily disabled. PDF needs to update version automatically. -.. A **step-by-step guide for Windows users** can be found `here -.. `_. - -To avoid conflicts with other packages, we recommend to install pyGIMLi in a -separate environment. Here we call this environment `pg`, but you can give -it any name. Note that this environment has to be created only once. - -Open a terminal (Linux & Mac) or the Anaconda Prompt (Windows) and type: - -.. code-block:: bash - - conda create -n pg -c gimli -c conda-forge "pygimli>=1.5.0" - -If you want to use pyGIMLi from the command line, you have to activate the -environment. You can put this line in your `~/.bashrc` file so that it is -activated automatically if you open a terminal. - -.. code-block:: bash - - conda activate pg - -After that you can use pyGIMLi with your text editor of choice and a terminal. - -Usage with Spyder or JupyterLab -------------------------------- - -Depending on your preferences, you can also install third-party software such as -the MATLAB-like integrated development environment (https://www.spyder-ide.org): - -.. code-block:: bash - - conda install -c conda-forge spyder - -Or alternatively, the web-based IDE JupyterLab (https://jupyterlab.readthedocs.io): - -.. code-block:: bash - - conda install -c conda-forge jupyterlab - -If you do one of the above steps in the `pg` environment, then it will -automatically find pyGIMLi. But you may not want to install JupyterLab or -Spyder for every different environment. To use your existing JupyterLab -installation in the `base` environment with pyGIMLi in the `pg` environment, -follow these steps: - -.. code-block:: bash - - conda activate pg - conda install ipykernel - conda activate base - conda install -c conda-forge nb_conda_kernels - jupyter lab - -pyGIMLi on Google Colab ------------------------ -pyGIMLi can be run on Google Colab without any installation on your own -computer. Just create a new Notebook and install pyGIMLi via pip: - -.. code:: python - - !pip install pygimli tetgen - -It turns out that there are some packages preinstalled that lead to some -incompatibl numpy version, so you might have to uninstall them first. - -.. code:: python - - !pip uninstall -y numba tensorflow pytensor thinc - !pip install pygimli tetgen - -Staying up-to-date ------------------- - -Update your pyGIMLi installation from time to time, if want to have the newest -functionality. - -.. code-block:: bash - - conda update -c gimli -c conda-forge pygimli - -If there something went wrong and you are running an old, not further -supported python version, consider a fresh install in a new clean environment. -The only drawback of using conda is that you are bound to the rhythm in which we -update the conda packages. In order to work with the latest Python codes you -should create an environment with the latest pyGIMLi C++ core only, - -.. code-block:: bash - - conda create -n pgcore -c gimli -c conda-forge pgcore - -retrieve the source code by git - -.. code-block:: bash - - git clone https://github.com/gimli-org/gimli - cd gimli - -and install pygimli as a development package using conda - -.. code-block:: bash - - conda develop . - -or using pip - -.. code-block:: bash - - pip install --no-build-isolation --no-deps -e . - -Alternatively you could set the PYTHONPATH variable but you would have to care -for dependencies by yourself. - -Later you can just update the pygimli code by - -.. code-block:: bash - - git pull - -Only if you need recent changes to the C++ core, you have to compile -pyGIMLi using your systems toolchain as described in -https://www.pygimli.org/compilation.html#sec-build diff --git a/ISSUE_TEMPLATE.md b/ISSUE_TEMPLATE.md deleted file mode 100644 index a8f004931..000000000 --- a/ISSUE_TEMPLATE.md +++ /dev/null @@ -1,36 +0,0 @@ -### Problem description - -Please describe your issue here. - -### Your environment - -Please provide the output of `print(pygimli.Report())` here. If that does not -work, please give provide some additional information on your: - -**Operating system**: e.g. Windows, Linux or Mac? -**Python version**: e.g. 3.9, 3.10, etc.? -**pyGIMLi version**: Output of `print(pygimli.__version__)` -**Way of installation**: e.g. Conda package, manual compilation from source, etc. - -### Steps to reproduce - -Tell us how to reproduce this issue. Ideally, you could paste the code that produces the error: - -```python -import pygimli as pg -... -``` - -### Expected behavior - -Tell us what should happen or what you want to achieve. - -### Actual behavior - -Tell us what happens instead and/or provide the output of your script. - -``` -Paste your script output here. -``` - -> If possible, please add one or more labels to your issue, e.g. if you expect that your issue is rather a question than a problem with the code, please add the label "question". \ No newline at end of file diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 000000000..c5bb2d296 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,203 @@ +# License + +> Apache License +> Version 2.0, January 2004 +> http://www.apache.org/licenses/ + +TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + +1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + +2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + +3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + +4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + +5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + +6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + +7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + +8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + +9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + +END OF TERMS AND CONDITIONS + +APPENDIX: How to apply the Apache License to your work. + + To apply the Apache License to your work, attach the following + boilerplate notice, with the fields enclosed by brackets "[]" + replaced with your own identifying information. (Don't include + the brackets!) The text should be enclosed in the appropriate + comment syntax for the file format. We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + +Copyright [yyyy] [name of copyright owner] + +Licensed under the Apache License, Version 2.0 (the "License"); +you may not use this file except in compliance with the License. +You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. \ No newline at end of file diff --git a/README.rst b/README.rst deleted file mode 100644 index 5598c070d..000000000 --- a/README.rst +++ /dev/null @@ -1,107 +0,0 @@ -About pyGIMLi -============= - -Introduction ------------- - -pyGIMLi is an open-source library for -:ref:`modelling` and -:ref:`inversion` and in geophysics. The -object-oriented library provides management for structured and unstructured -meshes in 2D and 3D, finite-element and finite-volume solvers, various -geophysical forward operators, as well as Gauss-Newton based frameworks for -constrained, joint and fully-coupled inversions with flexible regularization. - -What is pyGIMLi suited for? - -* analyze, visualize and invert geophysical data in a reproducible manner -* forward modelling of (geo)physical problems on complex 2D and 3D geometries -* inversion with flexible controls on a-priori information and regularization -* combination of different methods in constrained, joint and fully-coupled inversions -* teaching applied geophysics (e.g. in combination with `Jupyter notebooks `_) - -What is pyGIMLi **NOT** suited for? - -* for people that expect a ready-made GUI for interpreting their data - -.. _sec:authors: - -Authors -------- - -.. raw:: html - -

- - - -

- -.. .. image:: https://img.shields.io/github/contributors/gimli-org/gimli.svg?style=flat-square - :target: https://github.com/gimli-org/gimli/graphs/contributors - -We gratefully acknowledge all contributors to the pyGIMLi open-source project and look forward to `your contribution `_! - -.. include:: ../AUTHORS.rst - -.. _sec:about_gimli_inversion: - -Inversion ---------- - -One main task of pyGIMli is to carry out inversion, i.e. error-weighted -minimization, for given forward routines and data. Various types of -regularization on meshes (1D, 2D, 3D) with regular or irregular arrangement are -available. There is flexible control of all inversion parameters. The default -inversion framework is based on the generalized Gauss-Newton method. - -Please see :ref:`tut:inversion` for examples and more -details. - -.. _sec:about_gimli_modelling: - -Modelling ---------- - -pyGIMLi comes with various geophysical forward operators, which can directly be -used for a given problem. In addition, abstract finite-element and finite-volume -interfaces are available to solve custom PDEs on a given mesh. See -:mod:`pygimli.physics` for a collection of forward operators and -:mod:`pygimli.solver` for the solver interface. - -The modelling capabilities of pyGIMLi include: - -* 1D, 2D, 3D discretizations -* linear and quadratic shape functions (automatic shape function generator for possible higher order) -* Triangle, Quads, Tetrahedron, Prism and Hexahedron, mixed meshes -* solver for elliptic problems (Helmholtz-type PDE) - -Please see :ref:`tut:modelling` for examples and more details. - -License -------- -pyGIMLi is distributed under the terms of the **Apache 2.0** license. Details on -the license agreement can be found `here -`_. - - -Credits -------- - -We use or link some third-party software (beside the usual tool stack: cmake, gcc, boost, python, numpy, scipy, matplotlib) and are grateful for all the work made by the authors of these awesome open-source tools: - -* libkdtree++: Maybe abandoned, mirror: https://github.com/nvmd/libkdtree - -* meshio: https://github.com/nschloe/meshio - -* pyplusplus: https://pypi.org/project/pyplusplus/ - -* pyvista: https://docs.pyvista.org/ - -* suitesparse, umfpack: https://people.engr.tamu.edu/davis/suitesparse.html - -* Tetgen: http://wias-berlin.de/software/index.jsp?id=TetGen&lang=1 - -* Triangle: https://www.cs.cmu.edu/~quake/triangle.html - - diff --git a/core/src/regionManager.cpp b/core/src/regionManager.cpp index 9900fa92e..c1f99da9c 100644 --- a/core/src/regionManager.cpp +++ b/core/src/regionManager.cpp @@ -494,7 +494,7 @@ void Region::fillBoundarySize(RVector & vec, Index boundStart){ void Region::setTransModel(Trans< RVector > & tM){ if (isBackground_){ - // log(Warning, "Region Nr:", marker_, " is background and should not get a model transformation."); + // log(Warning, "Region Nr:", marker_, " is background and should not get a model transformation."); return; } @@ -506,7 +506,7 @@ void Region::setTransModel(Trans< RVector > & tM){ void Region::setModelTransStr_(const std::string & val){ if (isBackground_){ - // log(Warning, "Region Nr:", marker_, " is background and should not get a model transformation."); + // log(Warning, "Region Nr:", marker_, " is background and should not get a model transformation."); return; } transString_ = val; @@ -613,6 +613,7 @@ void RegionManager::clear(){ if (mesh_) { delete mesh_; mesh_ = NULL; } } + void RegionManager::setMesh(const Mesh & mesh, bool holdRegionInfos){ if (!holdRegionInfos){ @@ -633,7 +634,7 @@ void RegionManager::setMesh(const Mesh & mesh, bool holdRegionInfos){ mesh_->createNeighborInfos(); if (verbose_) { std::cout << swatch.duration(true) << " s " << std::endl; - std::cout << "analysing mesh ... "; + std::cout << "analyzing mesh ... "; } //** looking for and create regions @@ -644,7 +645,7 @@ void RegionManager::setMesh(const Mesh & mesh, bool holdRegionInfos){ bool singleOnly = false; if (regions.size() > 50){ singleOnly = true; - log(Info,"More than 50 regions, so we assume single regions only."); + log(Info, "More than 50 regions, so we assume single regions only."); } std::map < int, std::vector< Cell * > > markerCellVectorMap; @@ -707,6 +708,7 @@ Region * RegionManager::createRegion_(SIndex marker, const Mesh & mesh, SIndex c Region * region = NULL; if (regionMap_.count(marker) == 0){ + // __MS(marker) region = new Region(marker, mesh, cellMarker, this); regionMap_.insert(std::make_pair(marker, region)); } else { @@ -946,7 +948,7 @@ void RegionManager::fillConstraints(RSparseMapMatrix & C){ cID += x.second->constraintCount(); // __MS(cID) } - + // __MS(interRegionConstraints_.size()) if (interRegionConstraints_.size() > 0){ if (verbose_) std::cout << "Creating inter region constraints." << std::endl; @@ -955,9 +957,9 @@ void RegionManager::fillConstraints(RSparseMapMatrix & C){ for (auto & it : this->interRegionConstraints_){ std::pair< SIndex, SIndex > ab = it.first; - + double cWeight = it.second; - + // if (verbose_) { // std::cout << "\t" << i << ": " // << ab.first << "< (" << cWeight << ") >" diff --git a/dependencies.rst b/dependencies.rst deleted file mode 100644 index 669357fe7..000000000 --- a/dependencies.rst +++ /dev/null @@ -1,53 +0,0 @@ -.. _sec:install_pre: - -Prerequisites -------------- - -To build pyGIMLi from source, the following tools are required: - -* subversion, git, mercurial, wget, tar -* cmake >= 2.8.10 -* gcc >= 4.4 -* >=Python-3.5 | >=Python-2.7 -* numpy-dev -* >=matplotlib-3.0 -* >=clang++-3.6.0 (3.7.0, 3.8.0) -* libclang-3.7-dev -* >=llvm-3.6.0 (3.7.0, 3.8.0) -* libz-dev -* python-setuptools - - tested on: - - * gentoo x86_64: gcc-4.4.5, gcc-4.5.3, gcc-4.5.4, gcc-4.9.2 gcc-5.3.0 - * Debian 3.2.46-1 x86_64: gcc-4.7.2 - * Ubuntu 16.04 LTS with gcc-5.4.0 - * Arch Linux gcc-5.2.0 - * CentOS - * MinGW32: gcc-4.6.2/4, gcc-4.7.2, gcc-5.2.0 - * MinGW64: gcc-4.5.4, gcc-5.2.0, gcc-6.3.0, gcc-7.1.0 - -Optional Prerequisites -...................... - -These tools can be installed system-wide with your native package manager (i.e. -apt-get). If not found, the provided build scripts will automatically download -and compile the necessary components. - -* libboost >=1.46 (python) (1.46, 1.48, 1.49, 1.51, 1.52, 1.53, 1.57) -* blas and lapack for suitesparse (system or auto via cmake) -* SuiteSparse (http://faculty.cse.tamu.edu/davis/suitesparse.html) -* cppunit -* procps -* triangle (http://www.cs.cmu.edu/~quake/triangle.html) - -Prerequisites automatically installed by the installer -...................................................... - -These tools are required to create the Python bindings and are likely to be -outdated in your distribution and should therefore not be installed -system-wide. The build scripts will install them automatically. - -* castxml -* pygccxml -* pyplusplus diff --git a/dev_requirements.txt b/dev_requirements.txt index ab00d4b6d..b77416151 100644 --- a/dev_requirements.txt +++ b/dev_requirements.txt @@ -18,10 +18,6 @@ pygccxml==2.5.0 # needed to run matplotlib>=3.7,<3.9 -# useful to run -ipython -jupytext - # optional, but strongly recommended #scipy<1.14 # for numpy 1 scipy>=1.14 # for numpy 2 @@ -31,7 +27,7 @@ pyvista[all]>=0.44 # for numpy 2 pyqt5 tqdm -# needed to build docu +# needed to build docu (after doc reworks) sphinx>=3.1 sphinxcontrib-bibtex sphinxcontrib-programoutput @@ -40,8 +36,15 @@ sphinx-gallery sphinx-design pydata-sphinx-theme bibtexparser +jupytext +myst_nb +linkify-it-py + +# optional, but strongly recommended +scooby +ipython -# needed for testing +# for testing pytest meshio diff --git a/doc/BUILD_LINUX.rst b/doc/BUILD_LINUX.rst index ff67f33d9..53ff99f8b 100644 --- a/doc/BUILD_LINUX.rst +++ b/doc/BUILD_LINUX.rst @@ -51,6 +51,7 @@ tweaking** Curl installer .............. +(Probably outdated.) If you are not using Anaconda, you can build pyGIMLi from source in the current directory via: diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt index 088a7bf10..1a1107ef3 100644 --- a/doc/CMakeLists.txt +++ b/doc/CMakeLists.txt @@ -95,7 +95,7 @@ add_custom_target(sphinxhtml ALL ${SPHINX_EXECUTABLE} -v -D abort_on_example_error=1 -T - -b html + -b dirhtml -c "${SPHINX_BUILD_DIR}/doc" -d "${SPHINX_CACHE_DIR}/html" "${SPHINX_BUILD_DIR}/doc" @@ -116,7 +116,7 @@ add_custom_target(sphinxhtml-nogallery ALL -D abort_on_example_error=1 -D plot_gallery=0 -T - -b html + -b dirhtml -c "${SPHINX_BUILD_DIR}/doc" -d "${SPHINX_CACHE_DIR}/html" "${SPHINX_BUILD_DIR}/doc" diff --git a/doc/Makefile b/doc/Makefile index a5a297a29..988c304cb 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -44,7 +44,7 @@ help: @echo " xml to make Docutils-native XML files" @echo " pseudoxml to make pseudoxml-XML files for display purposes" -auto: api +auto: # Used to auto-update website in local build. Requires sphinx-autobuild. sphinx-autobuild --delay 2 --ignore "pygimliapi/*" --ignore "pygimliapi/_generated/*" --ignore "*gallery.html" --ignore "*.examples" --ignore "*.ipynb" --ignore "*.zip" --ignore "*.pickle" . _build/html -D plot_gallery=0 @@ -68,12 +68,12 @@ gallery: python ./sidebar_gallery.py html-nogallery: api - $(SPHINXBUILD) -D plot_gallery=0 -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + $(SPHINXBUILD) -D plot_gallery=0 -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/html @echo @echo "Build finished without gallery. The HTML pages are in $(BUILDDIR)/html." html: api - $(SPHINXBUILD) -v -D abort_on_example_error=True -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + $(SPHINXBUILD) -v -D abort_on_example_error=True -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/html @echo @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." @@ -82,11 +82,6 @@ spelling: api @echo @echo "Spellcheck finished." -dirhtml: - $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml - @echo - @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." - singlehtml: $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml @echo @@ -103,7 +98,7 @@ json: @echo "Build finished; now you can process the JSON files." htmlhelp: - $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + $(SPHINXBUILD) -b dirhtmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp @echo @echo "Build finished; now you can run HTML Help Workshop with the" \ ".hhp project file in $(BUILDDIR)/htmlhelp." @@ -180,3 +175,7 @@ pseudoxml: $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml @echo @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." + +serve: + cd $(BUILDDIR)/html + python -m http.server diff --git a/doc/_static/css/custom.css b/doc/_static/css/custom.css index a683e5259..23be5cdf4 100644 --- a/doc/_static/css/custom.css +++ b/doc/_static/css/custom.css @@ -186,4 +186,8 @@ table.doc-index td, table th { [data-theme=dark] .bd-header-announcement { background: #7a7d16; + } + +.xref.std.std-ref { + visibility: hidden; } \ No newline at end of file diff --git a/doc/_templates/navbar-nav.html b/doc/_templates/navbar-nav.html deleted file mode 100644 index 9bdadc62e..000000000 --- a/doc/_templates/navbar-nav.html +++ /dev/null @@ -1,25 +0,0 @@ - \ No newline at end of file diff --git a/doc/_templates/sidebar.html b/doc/_templates/sidebar.html index 2e74cd136..56ba76b8f 100644 --- a/doc/_templates/sidebar.html +++ b/doc/_templates/sidebar.html @@ -22,7 +22,7 @@
  • Code diff --git a/doc/about.rst b/doc/about.rst deleted file mode 100644 index 0768eda7e..000000000 --- a/doc/about.rst +++ /dev/null @@ -1,3 +0,0 @@ -.. _sec:GIMLi: - -.. include:: ../README.rst diff --git a/doc/about/authors.md b/doc/about/authors.md new file mode 100644 index 000000000..10798d3b0 --- /dev/null +++ b/doc/about/authors.md @@ -0,0 +1,18 @@ +# Authors +## Core Development Team +```{include} ../../AUTHORS.md +``` + +The core developers have also written the main [pyGIMLi publication](#citation). + +## Contributors + + + + +We gratefully acknowledge all contributors to the pyGIMLi open-source project and look forward to [your contribution](https://pygimli.org/contrib.html)! + + + + + diff --git a/doc/about/citation.md b/doc/about/citation.md new file mode 100644 index 000000000..3db5f7333 --- /dev/null +++ b/doc/about/citation.md @@ -0,0 +1,12 @@ +(citation)= + +```{include} ../../CITATION.md +``` +```{rubric} Other studies and extended abstracts about pyGIMLi +``` + +```{eval-rst} +.. bibliography:: libgimli.bib + :style: mystyle + :all: +``` \ No newline at end of file diff --git a/doc/about/index.md b/doc/about/index.md new file mode 100644 index 000000000..fd3f6d0a8 --- /dev/null +++ b/doc/about/index.md @@ -0,0 +1,78 @@ +(about)= + +# About pyGIMLi + +pyGIMLi is an open-source library for [modelling](#modelling) and +[inversion](#inversion) and in geophysics. The object-oriented library provides +management for structured and unstructured meshes in 2D and 3D, finite-element +and finite-volume solvers, various geophysical forward operators, as well as +Gauss-Newton based frameworks for constrained, joint and fully-coupled +inversions with flexible regularization. + +## Main capabilities +What is pyGIMLi suited for? + +- analyze, visualize and invert geophysical data in a reproducible manner +- forward modelling of (geo)physical problems on complex 2D and 3D geometries +- inversion with flexible controls on a-priori information and regularization +- combination of different methods in constrained, joint and fully-coupled inversions +- teaching applied geophysics (e.g. in combination with [Jupyter notebooks](http://jupyter-notebook.readthedocs.io/en/latest/notebook.html#notebook-documents)) + +What is pyGIMLi **NOT** suited for? + +- for people that expect a ready-made GUI for interpreting their data + +(inversion)= +### Inversion + +One main task of pyGIMli is to carry out inversion, i.e. error-weighted +minimization, for given forward routines and data. Various types of +regularization on meshes (1D, 2D, 3D) with regular or irregular arrangement are +available. There is flexible control of all inversion parameters. The default +inversion framework is based on the generalized Gauss-Newton method. + +Please see {ref}`tut:inversion` for examples and more +details. + +(modelling)= +### Modelling + +pyGIMLi comes with various geophysical forward operators, which can directly be +used for a given problem. In addition, abstract finite-element and finite-volume +interfaces are available to solve custom PDEs on a given mesh. See +{mod}`pygimli.physics` for a collection of forward operators and +{mod}`pygimli.solver` for the solver interface. + +The modelling capabilities of pyGIMLi include: + +- 1D, 2D, 3D discretizations +- linear and quadratic shape functions (automatic shape function generator for possible higher order) +- Triangle, Quads, Tetrahedron, Prism and Hexahedron, mixed meshes +- solver for elliptic problems (Helmholtz-type PDE) + +Please see {ref}`tut:modelling` for examples and more details. + +## License + +pyGIMLi is distributed under the terms of the **Apache 2.0** license. Details on +the license agreement can be found [here](#license). + +## Credits + +We use or link some third-party software (beside the usual tool stack: cmake, gcc, boost, python, numpy, scipy, matplotlib) and are grateful for all the work made by the authors of these awesome open-source tools: + +- libkdtree++: Maybe abandoned, mirror: +- meshio: +- pyplusplus: +- pyvista: +- suitesparse, umfpack: +- Tetgen: +- Triangle: + +:::{toctree} +:hidden: + +authors +citation +license +::: \ No newline at end of file diff --git a/doc/about/introduction.md b/doc/about/introduction.md new file mode 100644 index 000000000..e10b99d01 --- /dev/null +++ b/doc/about/introduction.md @@ -0,0 +1 @@ +# Introduction diff --git a/doc/libgimli.bib b/doc/about/libgimli.bib similarity index 100% rename from doc/libgimli.bib rename to doc/about/libgimli.bib diff --git a/doc/about/license.md b/doc/about/license.md new file mode 100644 index 000000000..0f6d2b46d --- /dev/null +++ b/doc/about/license.md @@ -0,0 +1,5 @@ +(license)= + +```{include} ../../LICENSE.md +``` + diff --git a/doc/citation.rst b/doc/citation.rst deleted file mode 100644 index 65ae68a78..000000000 --- a/doc/citation.rst +++ /dev/null @@ -1,9 +0,0 @@ -.. _sec:citation: - -.. include:: ../CITATION.rst - -.. rubric:: Other studies and extended abstracts about pyGIMLi - -.. bibliography:: libgimli.bib - :style: mystyle - :all: diff --git a/doc/community/contribute.md b/doc/community/contribute.md new file mode 100644 index 000000000..24a19e7e9 --- /dev/null +++ b/doc/community/contribute.md @@ -0,0 +1,144 @@ +(sec-contributing)= + +# How to contribute + +As an open-source project, pyGIMLi always welcomes contributions from the +community. Here, we offer guidance for 4 different ways of contributing with +increasing levels of required coding proficiency (A-D). + +## A. Submit a bug report + +If you experience issues with pyGIMLi or miss a certain feature, please [open a +new issue on GitHub](https://github.com/gimli-org/gimli/issues). To do so, +you need to [create a GitHub account](https://github.com/join). + +## B. Send us your example + +We are constantly looking for interesting usage examples of pyGIMLi. If you have +used the package and would like to contribute your work to the {ref}`chapt:examples`, you can send us your example. +Make sure that your Python script is documented according to the [sphinx-gallery syntax](https://sphinx-gallery.github.io/stable/tutorials/plot_parse.html#sphx-glr-tutorials-plot-parse-py). + +## C. Quickly edit the documentation + +If you would like to edit a typo or improve the documentation on our website, you can submit fixes to the +documentation page by clicking on "Improve this page" under the quick links menu on every page in the right sidebar. +This will direct you to the Github page to make the edits directly on the ".rst" using Github (you will need a Github account, see step A). +Once you make your edits, fill out the fields under "Commit changes" (make sure to provide a good overview of the changes you have made). +Note that you will make changes to a new branch under your fork since you will not have access to make changes in the existing branch. +Once you click "Commit changes" this automatically creates a pull request which we will review and then merge, if everything is good to go! + +If you would like to contribute to the API or make changes offline to the files under `doc`, see following *Contribute to Code* and *Documentation* for more information. + +## D. Contribute to code + +:::{note} +To avoid redundant work, please [contact us](mailto:mail@pygimli.org) +or check the [current issues](https://github.com/gimli-org/gimli/issues) +before you start working on a non-trivial feature. +::: + +The preferred way to contribute to the pygimli code base is via a pull request +(PR) on GitHub. The general concept is explained [here](https://guides.github.com/introduction/flow) and involves the following steps: + +### 1. Fork and clone the repository + +If you are a first-time contributor, you need [a GitHub account](https://github.com/join) and your own copy ("fork") of the code. To do so, go +to and click the "Fork button" in the upper +right corner. This will create an identical copy of the complete code base under +your username on the GitHub server. You can navigate to this repository and clone it to your local disk: + +```bash +git clone https://github.com/YOUR_USERNAME/gimli +``` + +### 2. Prepare your environment + +To install the neccesary Python requirements on your computer, we recommend the Anaconda Python distribution and the conda package manager. +The cloned and forked repository contains an *environment.yml* file with the specification for all package requirements to build +and test pyGIMLi. This file should exist in the directory where you have cloned the repository. In order to create a separate environment +where you will work, run the following command in the same directory of the repository in your terminal: + +```bash +conda env create # Creates the environment (only once) +conda activate pgdev # Activates it (everytime you want to work in it) +conda develop . # Installs your git-version of pygimli (only once) +python -c "import pygimli; pygimli.test()" # Make sure that everything works (also after adding new code) +``` + +You will need to do the last step (`conda activate pgdev`) everytime you start a terminal or put it in your `.bashrc`. `(pgdev)` should appear before your terminal location. + +### 3. Create a feature branch + +Go to the source folder and create a feature branch to hold your changes. It is +advisable to give it a sensible name such as `adaptive_meshes`. + +```bash +cd gimli +git checkout -b adaptive_meshes +``` + +### 4. Start making your changes + +Go nuts! Add and modify files and regularly commit your changes with meaningful +commit messages. Remember that you are working in your own personal copy and in +case you break something, you can always go back. While coding, we encourage you +to follow a few {ref}`sec:Coding_rules`. + +```bash +git add new_file1 new_file2 modified_file1 +git commit -m "Implemented adaptive meshes." +``` + +### 5. Test your code + +Make sure that everything works as expected. New functions should always contain +a docstring with a test: + +```python +def sum(a, b): + """Return the sum of `a` and `b`. + + Examples + -------- + >>> a = 1 + >>> b = 2 + >>> sum(a,b) + 3 + """ + return a + b +``` + +When you run `pg.test()` the docstring test will be evaluated. See also the +section on {ref}`sec:testing`. + +### 6. Documentation + +We use sphinx to build the web pages from these sources. To edit HTML file, navigate to the doc folder in the repository. +Once you have made edits. Run the following commands on your terminal. + +```bash +make html +``` + +The process should build all of the documentation so it may take some time to complete. When it finishes, the last line should state: + +```bash +Build finished. The HTML pages are in _build/html. +``` + +### 7. Submit a pull request + +Once you implemented a functioning new feature, make sure your GitHub repository +contains all your commits: + +```bash +git push origin adaptive_meshes +``` + +After pushing, you can go to GitHub and you will see a green PR button. Describe +your changes in more detail. Once reviewed by the core developers, your PR will +be merged to the main repository. + +:::{note} +Please see for additional notes on coding rules, testing, etc. +::: diff --git a/doc/community/development/cheatsheet.md b/doc/community/development/cheatsheet.md new file mode 100644 index 000000000..2b10250d6 --- /dev/null +++ b/doc/community/development/cheatsheet.md @@ -0,0 +1,102 @@ +# Cheatsheet + ++++ + +```{contents} Table of Content +:depth: 3 +``` + ++++ + +## Citations + ++++ + +{cite}`Seigel1959` did something great + ++++ + +## Evaluate code + +```{code-cell} ipython3 +import pygimli as pg +mesh = pg.createGrid(20,5) +data = pg.x(mesh) +pg.show(mesh, data) +``` + +## Some Markdown features + +### Math + +Since Pythagoras, we know that $a^2 + b^2 = c^2$ + +$$ +(a + b)^2 = (a + b)(a + b) \\ + = a^2 + 2ab + b^2 +$$ (mymath2) + +The equation {eq}"mymath2" is also a quadratic equation. + +Some **text-like stuff**! + +:::{admonition} Here's my title +:class: tip + +Here's my admonition content. + +::: + +### Tables + +:::{table} Table caption +:widths: auto +:align: center + +| foo | bar | +| --- | --- | +| baz | bim | +::: + +### Typography + +**strong**, _emphasis_, `literal text`, \*escaped symbols\* + +### Footnotes + +A longer footnote definition.[^mylongdef] + +[^mylongdef]: This is the _**footnote definition**_. + + That continues for all indented lines + + - even other block elements + + Plus any preceding unindented lines, +that are not separated by a blank line + +This is not part of the footnote. + +### Cards + +:::{card} Card Title +Header +^^^ +Card content + ++++ + +Footer +::: + +### Tabs + +::::{tab-set} + +:::{tab-item} Label1 +Content 1 +::: + +:::{tab-item} Label2 +Content 2 +::: diff --git a/doc/community/development/dependencies.md b/doc/community/development/dependencies.md new file mode 100644 index 000000000..d9a81a536 --- /dev/null +++ b/doc/community/development/dependencies.md @@ -0,0 +1,60 @@ +(sec-install-pre)= + +# Dependencies + +To build pyGIMLi from source, the following tools are required: + +- subversion, git, mercurial, wget, tar + +- cmake >= 2.8.10 + +- gcc >= 4.4 + +- \>=Python-3.5 | >=Python-2.7 + +- numpy-dev + +- \>=matplotlib-3.0 + +- \>=clang++-3.6.0 (3.7.0, 3.8.0) + +- libclang-3.7-dev + +- \>=llvm-3.6.0 (3.7.0, 3.8.0) + +- libz-dev + +- python-setuptools + + > tested on: + > + > - gentoo x86_64: gcc-4.4.5, gcc-4.5.3, gcc-4.5.4, gcc-4.9.2 gcc-5.3.0 + > - Debian 3.2.46-1 x86_64: gcc-4.7.2 + > - Ubuntu 16.04 LTS with gcc-5.4.0 + > - Arch Linux gcc-5.2.0 + > - CentOS + > - MinGW32: gcc-4.6.2/4, gcc-4.7.2, gcc-5.2.0 + > - MinGW64: gcc-4.5.4, gcc-5.2.0, gcc-6.3.0, gcc-7.1.0 + +## Optional Prerequisites + +These tools can be installed system-wide with your native package manager (i.e. +apt-get). If not found, the provided build scripts will automatically download +and compile the necessary components. + +- libboost >=1.46 (python) (1.46, 1.48, 1.49, 1.51, 1.52, 1.53, 1.57) +- blas and lapack for suitesparse (system or auto via cmake) +- SuiteSparse () +- cppunit +- procps +- triangle () + +## Prerequisites automatically installed by the installer + +These tools are required to create the Python bindings and are likely to be +outdated in your distribution and should therefore not be installed +system-wide. The build scripts will install them automatically. + +- castxml +- pygccxml +- pyplusplus diff --git a/doc/community/development/guidelines.md b/doc/community/development/guidelines.md new file mode 100644 index 000000000..631f5a868 --- /dev/null +++ b/doc/community/development/guidelines.md @@ -0,0 +1,368 @@ +(sec-coding-guidelines)= + +# Developer guidelines + +## Contributing to the code + +:::{note} +These steps are only relevant if you have write privileges to the main +GitHub repository. The general contribution guidelines can be found in +\_sec:contributing:. +::: + +1. Clone the GIMLi repository: + + > ```bash + > git clone https://github.com/gimli-org/gimli gimli-src && cd gimli-src + > ``` + +You should be on the master branch by default. Check by calling *git status*. +GIMLi encourages developers to keep the *master branch* clean. So please use the +default development branch called *dev*. Save [this +script](https://gist.github.com/florian-wagner/0be0b09bbabec6791ed3) in +.git/hooks for automatic warnings in case you are about to push to the master +branch. + +2. Checkout the dev branch: + + > ```bash + > git checkout dev + > ``` + +3. Make changes in your favorite editor. + +4. Add new files to the staging area: + + > ```bash + > git add new_file1 new_file2 + > ``` + +5. Make a commit with a *meaningful* message: + + > ```bash + > git commit -a -m "ADD: important new feature." + > ``` + > + > Make use of the prefixes in the table below to categorize commits. + +6. Pull the latest developments from GitHub using automatic rebase: + +> For more info see: +> +> > ```bash +> > git pull --rebase +> > ``` + +You can set the rebase behavior on default with: + +> ```bash +> git config --global branch.autosetuprebase always +> ``` + +7. Push to the origin development branch: + + > ```bash + > git push origin dev + > ``` + +Note that if you are on the `dev` branch, a `git push` should suffice, but the +command above is more explicit about the branch which should be pushed. + +8. Show available tags and branches: + + > ```bash + > git tag + > git branch + > ``` + +9. If you plan bigger changes or developments create an own branch for it: + + > ```bash + > git branch my_new_test_branch + > git checkout my_new_test_branch + > ``` + +Work on your code in branch `my_new_test_branch` and test it. +If you are happy with your results merge them back +into the dev branch and delete the branch. + +> ```bash +> git checkout dev +> git merge my_new_test_branch +> git branch -d my_new_test_branch +> ``` + +## Branches + +| Branch name | Description | Purpose | CI (Jenkins) Current behavior | CI (Jenkins) Wishlist | Rules | +| ----------- | ----------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------- | +| dev | Main development branch | This is where new versions are developed and pull requests are merged to. | Build and test, on success generate and merge to master | Test pull requests, build nightly conda packages for test channel | Run pg.test() and make doc before pushing. Tag related issues in commit message. | +| release | Latest release | This is where releases are "staged". This usually means creating a git tag and manually merging dev into release. Hot fixes and website typos can be directly committed here. | Start in empty workspace, build, test and create documentation after each push. On success, merge into master and update . | Test "backward compatibility" (e.g., run example scripts from last release with this version). Test on Mac and Windows, too. | Make sure the tag is annotated and the version string is following the principles described below. | +| master | Latest tested dev | Make sure that if people checkout the repository, they always have a working version. | (represented by ) | Build pgcore (if necessary) and pygimli conda packages for release. | Never push anything to master! | +| - | Feature branches | Larger endeavors and major restructuring should happen in dedicated feature branches (or forks), which are eventually merged to dev. This can also be useful if you want to give write access to others to jointly work on a feature. | Automatic testing can be requested (). | | Start feature branch from dev. Inform other developers about your develpment (to avoid conflicts and redundant work). | + +## Commit messages + +Please prepend your commit messages with one of the following prefixes depending on the nature of the commit: + +| **Prefix** | **Meaning** | +| ---------- | -------------------------------------------------------------------- | +| **ADD:** | Addition of new functionality | +| **API:** | API change (argument orders or renames) | +| **BLD:** | Changes to pyGIMLi's build pipeline | +| **CI:** | Continuous integration (i.e., Jenkins related) | +| **CLN:** | Clean up, refactoring or typo correction | +| **DEF:** | Change of default behavior | +| **DEP:** | Deprecation | +| **DOC:** | Improve documentation (i.e., docstrings or website) | +| **ENH:** | Enhancement, e.g. due to more flexibility by new (keyword) arguments | +| **FIX:** | Fixing a bug | +| **REL:** | Release (setting tags, updating version strings, etc.) | +| **STY:** | Coding style improvement (PEP8, PEP257) | +| **TST:** | New or improved test | + +:::{note} +The tags **API, ENH, ADD, FIX** are relevant for creating the changelog later. +::: + +## Version numbering + +Following the PEP conventions, pygimli holds a `__version__` string. + +```python +import pygimli as pg +print(pg.__version__) +v1.4.1-0-g76a4848-modified +``` + +This string consists of: + +> \<*Last git tag*>-\<*Number of commits since last tag*>-\<*last commit hash*> + +The string has a *-modified* suffix if pygimli has uncommitted changes. + +To produce a new version, type: + +```bash +git tag -a -m "First official release" "v1.0.x" # tags last commit as v1.0.x +git push --tags # pushes tags to GitHub +``` + +(sec-testing)= + +To see the commits since the last tag/release, you can use: + +```bash +git log v1.3.0...HEAD --oneline +``` + +Or to see commits between specific versions: + +```bash +git log v1.2.5...v1.2.6 --oneline +``` + +Alternatively, this information can also be obtained [via GitHub](http://github.com/gimli-org/gimli/compare/v1.4.0...v1.4.1). + +## Testing + +Run specific API examples from shell: + +```bash +python -c "import pygimli as pg; pg.test(pg.meshtools.createCircle, show=True)" +``` + +Run a specific test from shell. + +```bash +python -c "import pygimli; from pygimli.physics.petro.resistivity import *; test_Archie()" +``` + +Run all tests + +```bash +python -c "import pygimli; pygimli.test(show=True)" +``` + +Run pylint from shell to check code: + +```bash +pylint --rcfile $GIMLIROOT/.pylintrc file.py +``` + +Run prospector to check code like landscape.io do: + +```bash +prospector --profile=$GIMLIROOT/.prospector.yml file.py +``` + +Read API documentation from shell: + +```bash +python -c "import pygimli as pg; help(pg.test)" +``` + +More information on pyGIMLi's native testing function: + +```{eval-rst} +.. autofunction:: pygimli.test + +``` + +### Adding an example to the paper carousel + +1. Put a catchy figure in *doc/\_static/usecases*. It should be 750X380 px. You can use this command: + +```bash +mkdir -p converted +mogrify -path converted -format jpg -resize "750x380^" -gravity North -crop 750x380+0+0 +repage -quality 95 *.jpg +``` + +2. Add a new dictionary with additional information into *doc/paper_carousel.py*. The format should be like: + +```python +dict(img="jordi2018.jpg", + title="Improved geophysical images through geostatistical regularization", + subtitle="Jordi et al. (2018), Geophysical Journal International", + link="https://doi.org/10.1093/gji/ggy055") +``` + +(sec-coding-rules)= + +## Coding Guidelines + +- Generally we try to use PEP 8 ? +- All names should be literally and in CamelShape style. +- Classes starts with Upper-case Letters. +- Members and Methods always starts with Lower-case Letters. +- All class members (self.member) need to be initialized in the init. +- (ugly²) Do not use multi initialize in one line, e.g., a, b, c = 0, 0, 0 +- check for data types with 'if isinstance(var, type):' instead 'if type(var) == type:' + +(sec-coding-guidelines-1)= + +Use pylint or prospector to improve code quality. + +We use: (exceptions in .landscape.yml and .pylintrc) + +- pep8 +- pep257 +- pylint +- pyflakes + +We encurage to add 2 BLANKLINE between classes and methods and never use 2 BLANKLINES in the code itself. + + +### Behaviour by name for global functions: + +```python +createFOO(...) + """ Always needs to return an instance of FOO. + "" +``` + +```python +showFOO(Bar, ...) + """ Always open a window or optionally use a given Axes to show Bar as Foo.""" + return ax, cbar +``` + +```python +drawFOO(ax, Bar...) + """ Always needs an Axes ax to draw Bar as Foo. + """ + return graphics_object +``` + +```python +readFOO(fileName, *args): + """ Read object from disc. + """ + return obj +``` + +```python +importFOO(fileName, obj, *args): + """ Import object from disc into an existing object. + """ + return obj +``` + +```python +exportFOO(obj, fileName): + """ Export object to disc in foreign (FOOs) format. + """ + return true +``` + +```python +convertFOO(fooObj): + """ Convert Foo obj into gimli Obj. + """ + return gimliObj +``` + +### API Documentation and doctests + +Use the following documentation syntax or see: + + +```python +def foo(arg1:type, arg2:type=Default, *args, **kwargs) -> ReturnType: +""" Short description, i.e., one line to explain what foo does. [DOT_AT_END] + [ONE BLANKLINE] + Explain a little more verbose was foo does. Use references :cite:`Archie1942` + Use links to pygimli api :gimliapi:`GIMLI::Mesh`, `:py:mod:pygimli.manager` + for modules, `:py:func:pygimli.solver.solveFiniteElements` for functions + + Type hints can be used for arguments and return values. + + Use math. + + .. math : + a + \sigma \cdot \rho + + Explain all parameters. + + Arguments + --------- + arg1: type=Default | use links to :gimliapi:`GIMLI::Mesh` + Describe arg1. + arg2: type + Describe arg2. + + Keyword Args + ------------ + args: type + Description. + + Attributes + ---------- + For members + + Returns + ------- + type: + Describe the return value. If it is a class instance, use links to + :gimliapi:`GIMLI::Mesh` or `:py:class:pygimli.core.Mesh`. + + Examples + -------- + >>> import foo + >>> ... + >>> ... + expected output # for doctest to pass + + + See Also + -------- + average: Weighted average, + e.g., Link to tutorials :ref:`tut:Modelling_BC` assuming there + has been set an appropriate label in the tutorial. + + References + ---------- + If not in global bib file. + """ +``` + diff --git a/doc/community/development/index.md b/doc/community/development/index.md new file mode 100644 index 000000000..646a929b3 --- /dev/null +++ b/doc/community/development/index.md @@ -0,0 +1,8 @@ +# Development +:::{toctree} +:hidden: + +guidelines +cheatsheet +dependencies +::: \ No newline at end of file diff --git a/doc/community/index.md b/doc/community/index.md new file mode 100644 index 000000000..d10b25af2 --- /dev/null +++ b/doc/community/index.md @@ -0,0 +1,8 @@ +# pyGIMLi community +:::{toctree} +:hidden: + +contribute +publications +development/index +::: \ No newline at end of file diff --git a/doc/community/publications.md b/doc/community/publications.md new file mode 100644 index 000000000..12ec4a399 --- /dev/null +++ b/doc/community/publications.md @@ -0,0 +1,7 @@ +--- +orphan: true +--- + +# Publications + +// overwritten by template \ No newline at end of file diff --git a/doc/conf.py b/doc/conf.py index 787eefd79..fa2803b36 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -69,8 +69,7 @@ deps = [ "sphinxcontrib-programoutput", "sphinxcontrib-bibtex", - "sphinxcontrib-doxylink", - "bibtexparser", + "sphinxcontrib-doxylink" ] # check for p.version too @@ -95,11 +94,11 @@ # They can be extensions coming with Sphinx (named "sphinx.ext.*") # or your custom ones. extensions = [ + "myst_nb", "sphinx.ext.autodoc", "sphinx.ext.todo", "sphinx.ext.viewcode", "sphinx.ext.autosummary", - "sphinx.ext.mathjax", "sphinx.ext.intersphinx", "sphinx.ext.imgconverter", "sphinx.ext.autosectionlabel", @@ -108,6 +107,7 @@ "srclinks", "sphinxcontrib.doxylink", "sphinx_design", + # "sphinx_tippy" # "sphinxcontrib.spelling" #'sphinx.ext.pngmath', # for breath #'sphinx.ext.todo', # for breath @@ -136,13 +136,13 @@ def reset_mpl(gallery_conf, fname): join(SPHINXDOC_PATH, "tutorials"), ], "gallery_dirs": ["_examples_auto", "_tutorials_auto"], - # "reference_url": { - # "pygimli": "https://pygimli.org", - # "python": "https://docs.python.org/dev", - # "numpy": "https://numpy.org/doc/stable", - # "scipy": "https://docs.scipy.org/doc/scipy/reference", - # "matplotlib": "https://matplotlib.org/stable", - # }, + "reference_url": { + "pygimli": "https://pygimli.org", + "python": "https://docs.python.org/dev", + "numpy": "https://numpy.org/doc/stable", + "scipy": "https://docs.scipy.org/doc/scipy/reference", + "matplotlib": "https://matplotlib.org/stable", + }, # Don"t report time of fast scripts (< 10 sec) "min_reported_time": 10, # path where to store your example linker templates @@ -153,7 +153,7 @@ def reset_mpl(gallery_conf, fname): "within_subsection_order": FileNameSortKey, "remove_config_comments": True, # Only parse filenames starting with plot_ - "filename_pattern": "plot_", + "filename_pattern": "/plot_", "first_notebook_cell": ("# Checkout www.pygimli.org for more examples"), "reset_modules": (reset_mpl), # Avoid representation of mpl axis, LineCollections, etc. @@ -221,15 +221,6 @@ def reset_mpl(gallery_conf, fname): "show-inheritance": True, } -# Get mathjax -# Formulas disappear after scrolling -# mathjax_path = "https://www.pygimli.org/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML" -# Slow, but works -mathjax_path = ( - "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js" - + "?config=TeX-AMS-MML_HTMLorMML" -) - # Add any paths that contain templates here, relative to this directory. templates_path = [join(SPHINXDOC_PATH, "_templates"), join(DOC_BUILD_DIR, "_templates")] @@ -242,13 +233,13 @@ def reset_mpl(gallery_conf, fname): plot_apply_rcparams = True # if context option is used # The suffix of source filenames. -source_suffix = ".rst" +source_suffix = {'.rst': 'restructuredtext'} # The encoding of source files. source_encoding = "utf-8-sig" # The master toctree document. -master_doc = "documentation" +master_doc = "index" # General information about the project. project = "pyGIMLi" @@ -332,14 +323,23 @@ def reset_mpl(gallery_conf, fname): "footer_start": ["footer_start"], "footer_end": ["footer_end"], "pygment_light_style": "friendly", + "header_links_before_dropdown": 6, "pygment_dark_style": "native", + "icon_links": [ + { + "name": "GitHub", + "url": "https://github.com/gimli-org/gimli", + "icon": "fa-brands fa-square-github", + "type": "fontawesome", + } + ] } # Temp: SEG announcement import datetime -today = datetime.datetime.now() +current_day = datetime.datetime.now() webinar = datetime.datetime(2024, 3, 19) -if today < webinar: +if current_day < webinar: html_theme_options["announcement"] = "There will be a webinar on pyGIMLi hosted by SEG on March 19, 2024 at 4 pm CET. Register for free here." html_css_files = [ @@ -386,7 +386,7 @@ def reset_mpl(gallery_conf, fname): # Additional templates that should be rendered to pages, maps page names to # template names. -html_additional_pages = {"index": "index.html", "publist": "publications.html"} +html_additional_pages = {"index": "index.html", "community/publications": "publications.html"} # If false, no module index is generated. html_domain_indices = True @@ -674,4 +674,23 @@ def monkeypatch(self, section: str, use_admonition: bool): # os.path.abspath(join(DOC_BUILD_DIR, "../../doxygen/xml")), # } # -# breathe_default_project = "gimli" \ No newline at end of file +# breathe_default_project = "gimli" +# Settings for myst +myst_enable_extensions = [ + "amsmath", + "attrs_inline", + "colon_fence", + "deflist", + "dollarmath", + "html_admonition", + "html_image", + "linkify", + "replacements", + "smartquotes", + "substitution", +] +myst_dmath_allow_labels = True +# myst_heading_anchors = 2 +nb_execution_excludepatterns = ["*Untitled*", "_examples_auto/**/*", "_tutorials_auto/**/*"] +# nb_execution_raise_on_error = True # Important for GitHub Action +nb_execution_show_tb = True \ No newline at end of file diff --git a/doc/contrib.rst b/doc/contrib.rst deleted file mode 100644 index a2201d1db..000000000 --- a/doc/contrib.rst +++ /dev/null @@ -1,161 +0,0 @@ -.. _sec:contributing: - -Contributing -============ - -As an open-source project, pyGIMLi always welcomes contributions from the community. Here, we offer guidance for 4 different ways of contributing with -increasing levels of required coding proficiency (A-D). - -A. Submit a bug report ----------------------- - -If you experience issues with pyGIMLi or miss a certain feature, please `open a -new issue on GitHub `_. To do so, -you need to `create a GitHub account `_. - -B. Send us your example ------------------------ - -We are constantly looking for interesting usage examples of pyGIMLi. If you have -used the package and would like to contribute your work to the :ref:`chapt:examples`, you can send us your example. -Make sure that your Python script is documented according to the `sphinx-gallery syntax -`_. - -C. Quickly edit the documentation ---------------------------------- - -If you would like to edit a typo or improve the documentation on our website, you can submit fixes to the -documentation page by clicking on "Improve this page" under the quick links menu on every page in the right sidebar. -This will direct you to the Github page to make the edits directly on the ".rst" using Github (you will need a Github account, see step A). -Once you make your edits, fill out the fields under "Commit changes" (make sure to provide a good overview of the changes you have made). -Note that you will make changes to a new branch under your fork since you will not have access to make changes in the existing branch. -Once you click "Commit changes" this automatically creates a pull request which we will review and then merge, if everything is good to go! - -If you would like to contribute to the API or make changes offline to the files under `doc`, see following *Contribute to Code* and *Documentation* for more information. - - -D. Contribute to code ---------------------- - -.. note:: - - To avoid redundant work, please `contact us `_ - or check the `current issues `_ - before you start working on a non-trivial feature. - -The preferred way to contribute to the pygimli code base is via a pull request -(PR) on GitHub. The general concept is explained `here -`_ and involves the following steps: - - -1. Fork and clone the repository -++++++++++++++++++++++++++++++++ - -If you are a first-time contributor, you need `a GitHub account -`_ and your own copy ("fork") of the code. To do so, go -to https://github.com/gimli-org/gimli and click the "Fork button" in the upper -right corner. This will create an identical copy of the complete code base under -your username on the GitHub server. You can navigate to this repository and clone it to your local disk: - -.. code-block:: bash - - git clone https://github.com/YOUR_USERNAME/gimli - -2. Prepare your environment -+++++++++++++++++++++++++++ - -To install the neccesary Python requirements on your computer, we recommend the Anaconda Python distribution and the conda package manager. -The cloned and forked repository contains an *environment.yml* file with the specification for all package requirements to build -and test pyGIMLi. This file should exist in the directory where you have cloned the repository. In order to create a separate environment -where you will work, run the following command in the same directory of the repository in your terminal: - -.. code-block:: bash - - conda env create # Creates the environment (only once) - conda activate pgdev # Activates it (everytime you want to work in it) - conda develop . # Installs your git-version of pygimli (only once) - python -c "import pygimli; pygimli.test()" # Make sure that everything works (also after adding new code) - -You will need to do the last step (``conda activate pgdev``) everytime you start a terminal or put it in your ``.bashrc``. ``(pgdev)`` should appear before your terminal location. - -3. Create a feature branch -++++++++++++++++++++++++++ - -Go to the source folder and create a feature branch to hold your changes. It is -advisable to give it a sensible name such as ``adaptive_meshes``. - -.. code-block:: bash - - cd gimli - git checkout -b adaptive_meshes - -4. Start making your changes -++++++++++++++++++++++++++++ - -Go nuts! Add and modify files and regularly commit your changes with meaningful -commit messages. Remember that you are working in your own personal copy and in -case you break something, you can always go back. While coding, we encourage you -to follow a few :ref:`sec:Coding_rules`. - -.. code:: bash - - git add new_file1 new_file2 modified_file1 - git commit -m "Implemented adaptive meshes." - -5. Test your code -+++++++++++++++++ - -Make sure that everything works as expected. New functions should always contain -a docstring with a test: - -.. code:: python - - def sum(a, b): - """Return the sum of `a` and `b`. - - Examples - -------- - >>> a = 1 - >>> b = 2 - >>> sum(a,b) - 3 - """ - return a + b - -When you run ``pg.test()`` the docstring test will be evaluated. See also the -section on :ref:`sec:testing`. - -6. Documentation -++++++++++++++++ - -We use sphinx to build the web pages from these sources. To edit HTML file, navigate to the doc folder in the repository. -Once you have made edits. Run the following commands on your terminal. - -.. code:: bash - - make html - -The process should build all of the documentation so it may take some time to complete. When it finishes, the last line should state: - -.. code:: bash - - Build finished. The HTML pages are in _build/html. - - -7. Submit a pull request -++++++++++++++++++++++++ - -Once you implemented a functioning new feature, make sure your GitHub repository -contains all your commits: - -.. code:: bash - - git push origin adaptive_meshes - -After pushing, you can go to GitHub and you will see a green PR button. Describe -your changes in more detail. Once reviewed by the core developers, your PR will -be merged to the main repository. - -.. note:: - - Please see https://pygimli.org/dev for additional notes on coding rules, testing, etc. \ No newline at end of file diff --git a/doc/dev.rst b/doc/dev.rst deleted file mode 100644 index 5016e5ab7..000000000 --- a/doc/dev.rst +++ /dev/null @@ -1,385 +0,0 @@ -.. _sec:coding_guidelines: - -GitHub notes for pyGIMLi developers -=================================== - -Contributing to the code ------------------------- - -.. note:: - - These steps are only relevant if you have write privileges to the main - GitHub repository. The general contribution guidelines can be found in - _sec:contributing:. - -1. Clone the GIMLi repository: - - .. code-block:: bash - - git clone https://github.com/gimli-org/gimli gimli-src && cd gimli-src - -You should be on the master branch by default. Check by calling *git status*. -GIMLi encourages developers to keep the *master branch* clean. So please use -the default development branch called *dev*. Save `this script -`_ in .git/hooks -for automatic warnings in case you are about to push to the master branch. - -2. Checkout the dev branch: - - .. code-block:: bash - - git checkout dev - -3. Make changes in your favorite editor. - -4. Add new files to the staging area: - - .. code-block:: bash - - git add new_file1 new_file2 - -5. Make a commit with a *meaningful* message: - - .. code-block:: bash - - git commit -a -m "ADD: important new feature." - - Make use of the prefixes in the table below to categorize commits. - -6. Pull the latest developments from GitHub using automatic rebase: - - For more info see: http://kernowsoul.com/blog/2012/06/20/4-ways-to-avoid-merge-commits-in-git/ - - .. code-block:: bash - - git pull --rebase - -You can set the rebase behavior on default with: - - .. code-block:: bash - - git config --global branch.autosetuprebase always - -7. Push to the origin development branch: - - .. code-block:: bash - - git push origin dev - -Note that if you are on the `dev` branch, a `git push` should suffice, but the -command above is more explicit about the branch which should be pushed. - -8. Show available tags and branches: - - .. code-block:: bash - - git tag - git branch - -9. If you plan bigger changes or developments create an own branch for it: - - .. code-block:: bash - - git branch my_new_test_branch - git checkout my_new_test_branch - -Work on your code in branch `my_new_test_branch` and test it. -If you are happy with your results merge them back -into the dev branch and delete the branch. - - .. code-block:: bash - - git checkout dev - git merge my_new_test_branch - git branch -d my_new_test_branch - - -Branches --------- - -+--------------+----------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------+ -| Branch name | Description | Purpose | CI (Jenkins) Current behavior | CI (Jenkins) Wishlist | Rules | -+==============+============================+========================================================================================================================================================================================================================================+==================================================================================================================================================+==============================================================================================================================+========================================================================================================================+ -| dev | Main development branch | This is where new versions are developed and pull requests are merged to. | Build and test, on success generate http://dev.pygimli.org and merge to master | Test pull requests, build nightly conda packages for test channel | Run pg.test() and make doc before pushing. Tag related issues in commit message. | -+--------------+----------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------+ -| release | Latest release | This is where releases are "staged". This usually means creating a git tag and manually merging dev into release. Hot fixes and website typos can be directly committed here. | Start in empty workspace, build, test and create documentation after each push. On success, merge into master and update http://www.pygimli.org. | Test "backward compatibility" (e.g., run example scripts from last release with this version). Test on Mac and Windows, too. | Make sure the tag is annotated and the version string is following the principles described below. | -+--------------+----------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------+ -| master | Latest tested dev | Make sure that if people checkout the repository, they always have a working version. | (represented by http://dev.pygimli.org) | Build pgcore (if necessary) and pygimli conda packages for release. | Never push anything to master! | -+--------------+----------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------+ -| * | Feature branches | Larger endeavors and major restructuring should happen in dedicated feature branches (or forks), which are eventually merged to dev. This can also be useful if you want to give write access to others to jointly work on a feature. | Automatic testing can be requested (florian@pygimli.org). | | Start feature branch from dev. Inform other developers about your develpment (to avoid conflicts and redundant work). | -+--------------+----------------------------+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------+ - -Commit messages ---------------- -Please prepend your commit messages with one of the following prefixes depending on the nature of the commit: - -+------------+----------------------------------------------------------------------+ -| **Prefix** | **Meaning** | -+============+======================================================================+ -| **ADD:** | Addition of new functionality | -+------------+----------------------------------------------------------------------+ -| **API:** | API change (argument orders or renames) | -+------------+----------------------------------------------------------------------+ -| **BLD:** | Changes to pyGIMLi's build pipeline | -+------------+----------------------------------------------------------------------+ -| **CI:** | Continuous integration (i.e., Jenkins related) | -+------------+----------------------------------------------------------------------+ -| **CLN:** | Clean up, refactoring or typo correction | -+------------+----------------------------------------------------------------------+ -| **DEF:** | Change of default behavior | -+------------+----------------------------------------------------------------------+ -| **DEP:** | Deprecation | -+------------+----------------------------------------------------------------------+ -| **DOC:** | Improve documentation (i.e., docstrings or website) | -+------------+----------------------------------------------------------------------+ -| **ENH:** | Enhancement, e.g. due to more flexibility by new (keyword) arguments | -+------------+----------------------------------------------------------------------+ -| **FIX:** | Fixing a bug | -+------------+----------------------------------------------------------------------+ -| **REL:** | Release (setting tags, updating version strings, etc.) | -+------------+----------------------------------------------------------------------+ -| **STY:** | Coding style improvement (PEP8, PEP257) | -+------------+----------------------------------------------------------------------+ -| **TST:** | New or improved test | -+------------+----------------------------------------------------------------------+ - -.. note:: - - The tags **API, ENH, ADD, FIX** are relevant for creating the changelog later. - -Version numbering ------------------ - -Following the PEP conventions, pygimli holds a `__version__` string. - -.. code-block:: python - - import pygimli as pg - print(pg.__version__) - v1.4.1-0-g76a4848-modified - -This string consists of: - - <*Last git tag*>-<*Number of commits since last tag*>-<*last commit hash*> - -The string has a *-modified* suffix if pygimli has uncommitted changes. - -To produce a new version, type: - -.. code-block:: bash - - git tag -a -m "First official release" "v1.0.x" # tags last commit as v1.0.x - git push --tags # pushes tags to GitHub - -.. _sec:testing: - -To see the commits since the last tag/release, you can use: - -.. code-block:: bash - - git log v1.3.0...HEAD --oneline - -Or to see commits between specific versions: - -.. code-block:: bash - - git log v1.2.5...v1.2.6 --oneline - -Alternatively, this information can also be obtained `via GitHub `_. - -Testing -------- - -Run specific API examples from shell: - -.. code-block:: bash - - python -c "import pygimli as pg; pg.test(pg.meshtools.createCircle, show=True)" - -Run a specific test from shell. - -.. code-block:: bash - - python -c "import pygimli; from pygimli.physics.petro.resistivity import *; test_Archie()" - -Run all tests - -.. code-block:: bash - - python -c "import pygimli; pygimli.test(show=True)" - -Run pylint from shell to check code: - -.. code-block:: bash - - pylint --rcfile $GIMLIROOT/.pylintrc file.py - -Run prospector to check code like landscape.io do: - -.. code-block:: bash - - prospector --profile=$GIMLIROOT/.prospector.yml file.py - -Read API documentation from shell: - -.. code-block:: bash - - python -c "import pygimli as pg; help(pg.test)" - -More information on pyGIMLi's native testing function: - -.. autofunction:: pygimli.test - - -Adding an example to the paper carousel -....................................... - -1. Put a catchy figure in *doc/_static/usecases*. It should be 750X380 px. You can use this command: - -.. code-block:: bash - - mkdir -p converted - mogrify -path converted -format jpg -resize "750x380^" -gravity North -crop 750x380+0+0 +repage -quality 95 *.jpg - -2. Add a new dictionary with additional information into *doc/paper_carousel.py*. The format should be like: - -.. code-block:: python - - dict(img="jordi2018.jpg", - title="Improved geophysical images through geostatistical regularization", - subtitle="Jordi et al. (2018), Geophysical Journal International", - link="https://doi.org/10.1093/gji/ggy055") - - -.. _sec:Coding_rules: - -Coding Guidelines ------------------ - -* Generally we try to use PEP 8 https://www.python.org/dev/peps/pep-0008/? - -* All names should be literally and in CamelShape style. - -* Classes starts with Upper-case Letters. - -* Members and Methods always starts with Lower-case Letters. - -* All class members (self.member) need to be initialized in the init. - -* (ugly²) Do not use multi initialize in one line, e.g., a, b, c = 0, 0, 0 - -* check for data types with 'if isinstance(var, type):' instead 'if type(var) == type:' - -.. _sec:coding_guidelines: - - -Use pylint or prospector to improve code quality. - -We use: (exceptions in .landscape.yml and .pylintrc) - -* pep8 -* pep257 -* pylint -* pyflakes - -Behaviour by name for global functions: -....................................... - -.. code-block:: python - - createFOO(...) - """Always needs to return an instance of FOO."" - -.. code-block:: python - - showFOO(Bar, ...) - """Always open a window or optionally use a given Axes to show Bar as Foo.""" - return ax, cbar - -.. code-block:: python - - drawFOO(ax, Bar...) - """Always needs an Axes ax to draw Bar as Foo"" - return graphics_object - -.. code-block:: python - - readFOO(fileName, *args): - """Read object from disc.""" - return obj - -.. code-block:: python - - importFOO(fileName, obj, *args): - """Import object from disc into an existing object.""" - return obj - -.. code-block:: python - - exportFOO(obj, fileName): - """Export object to disc in foreign (FOOs) format.""" - return true - -.. code-block:: python - - convertFOO(fooObj): - """Convert Foo obj into gimli Obj""" - return gimliObj - -API Documentation and doctests -.............................. - -Use the following documentation syntax or see: -https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html - -.. code-block:: python - - def foo(arg1, arg2): - """Short description, i.e., one line to explain what foo does. [DOT_AT_END] - [ONE BLANKLINE] - Explain a little more verbose was foo does. Use references :cite:`Archie1942` - Use links to pygimli api :gimliapi:`GIMLI::Mesh`, `:py:mod:pygimli.manager` - for modules, `:py:func:pygimli.solver.solveFiniteElements` for functions - - Use math. - .. math : - a + \sigma \cdot \rho - - Explain all parameters. - - Args - ---- - arg1: type | use links to :gimliapi:`GIMLI::Mesh` - Describe arg1. - arg2: type - Describe arg2. - - Keyword Args - ------------ - args: type - Description. - - Attributes - ---------- - For members - - Returns - ------- - type: - - Examples - -------- - >>> import foo - >>> - >>> - - See Also - -------- - average : Weighted average, - e.g., Link to tutorials :ref:`tut:Modelling_BC` assuming there - has been set an appropriate label in the tutorial. - - References - ---------- - if not in global bib file - """ diff --git a/doc/doc/repro_tips_beginner.rst b/doc/doc/repro_tips_beginner.rst new file mode 100644 index 000000000..f5db9737a --- /dev/null +++ b/doc/doc/repro_tips_beginner.rst @@ -0,0 +1,15 @@ +Reproducibility tips (for beginners) +==================================== + +• Use a pinned environment (conda): + conda create -n pg -c gimli -c conda-forge pygimli + conda activate pg + +• Set random seeds in examples to stabilize results: + import numpy as np; np.random.seed(0) + +• Note OS differences (Windows vs. Linux/Mac) when paths or installers differ. + +• Link to install & contributing guides for more detail. + +References: Installation, Contributing. \ No newline at end of file diff --git a/doc/doc_notes_for_devs.txt b/doc/doc_notes_for_devs.txt deleted file mode 100644 index 5f61b25de..000000000 --- a/doc/doc_notes_for_devs.txt +++ /dev/null @@ -1,119 +0,0 @@ -.. _sec:doc_todo: - -Documentation TODO-LIST -======================= - -.. todolist:: - -Additional information ----------------------- - -.. admonition:: See also - - **Restructured Text (reST) and Sphinx CheatSheets** - - :ref:`rst-basics` - - http://docs.geoserver.org/trunk/en/docguide/sphinx.html - - http://openalea.gforge.inria.fr/doc/openalea/doc/_build/html/source/sphinx/rest_syntax.html - - http://packages.python.org/an_example_pypi_project/sphinx.html - - - **Conventions** - - PEP 8: - - http://www.python.org/dev/peps/pep-0008/ - - Numpy/Scipy Docstring convention: - - https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt#docstring-standard - - Matplotlib naming convention: - - http://matplotlib.org/1.3.0/faq/usage_faq.html#coding-styles - -**Requirements** - -Needed external extensions for building this docu - -:: - - pip install numpydoc pybtex sphinxcontrib-programoutput - -Linking to Gimli API ---------------------- - -To link to a specific class defintion the C++ API from the docs, -you can use - -:: - - See: :gimliapi:`GIMLI::Mesh` - -Which results in - -See: :gimliapi:`GIMLI::Mesh` - -Linking to Python API ---------------------- - -To link to a specific module or function in the Python API from the docs, -you can use - -:: - - See :py:func:`pygimli.meshtools.grid.appendTriangleBoundary` in :py:mod:`pygimli.meshtools` for more details. - -Which results in - -See :py:func:`pygimli.meshtools.grid.appendTriangleBoundary` in :py:mod:`pygimli.meshtools` for more details. - -.. seealso:: http://sphinx-doc.org/domains.html#cross-referencing-python-objects - -Example for a code-block: - -.. code-block:: python - - import pygimli as pg - import pybert as pb - - data = pb.DataContainerERT("bert.dat") - mesh = pg.meshtools.createParaMesh2dGrid(data.sensorPositions()) - - # set up fwd-operator - fop = pb.DCSRMultiElectrodeModelling(mesh, data) - fop.createRefinedForwardMesh() - fop.regionManager().region(0).setBackground(True) - ... # other region and fop options if needed - - # set up inversion - tD, tM = pg.RTransLog(), pg.RTransLog() - inv = pg.RInversion(data("rhoa"), fop, tD, tM) - inv.setRelativeError(data("err")) - ... # other inversion options if needed - - # perform actual inversion - model = inv.run() - - # plotting - paraMesh = f.regionManager().paraDomain() - pg.show(paraMesh, model) - -Docstring examples ------------------- - -Functions -......... - -.. autofunction:: pygimli.meshtools.mesh.readHydrus2dMesh - :noindex: -.. autofunction:: pygimli.meshtools.mesh.readGmsh - :noindex: - -Classes -....... - -.. autoclass:: pygimli.viewer.mpl.CellBrowser diff --git a/doc/documentation.rst b/doc/documentation.rst deleted file mode 100644 index 2307d9bee..000000000 --- a/doc/documentation.rst +++ /dev/null @@ -1,97 +0,0 @@ -############# -Documentation -############# - -.. only:: html - - .. list-table:: - :class: doc-index - - * - :ref:`sec:GIMLi` - - Getting started - - - :ref:`sec:design` - - Software architecture and abstraction levels - - * - :ref:`sec:install` - - How to install pyGIMLi on different platforms - - - - - - - * - `Tutorials <_tutorials_auto/index.html>`_ - - How to use pyGIMLi - - - `Examples <_examples_auto/index.html>`_ - - Interesting examples - - * - :doc:`pyGIMLi API ` - - Reference for Python modules - - - `Core API `_ - - Reference for C++ core - - * - `Publications `_ - - Research papers using pyGIMLi - - - :ref:`sec:citation` - - How to cite pyGIMLi - - * - :ref:`sec:contributing` - - Information on how to get involved - - - :ref:`sec:license` - - Terms of use and redistribution - - - ################## - Indices and tables - ################## - - .. list-table:: - :class: doc-index - - * - `Search `_ - - Search this documentation - - - :ref:`sec:glossary` - - Important terms explained - - * - :ref:`genindex` - - All functions, classes and terms - - - :ref:`sec:references` - - Publications cited in the documentation - - -.. only:: latex - - .. toctree:: - :maxdepth: 4 - - about.rst - citation.rst - design.rst - installation.rst - faq.rst - _examples_auto/index.rst - _tutorials_auto/index.rst - pygimliapi/index.rst - contrib.rst - glossary.rst diff --git a/doc/doxygen.rst b/doc/doxygen.rst deleted file mode 100644 index d15e2ad8e..000000000 --- a/doc/doxygen.rst +++ /dev/null @@ -1,6 +0,0 @@ -GIMLI Core Api -============== - - -.. doxygenindex:: - :project: gimli diff --git a/doc/examples/5_flow_transport/plot_hydrogeophysical_modeling.py b/doc/examples/5_flow_transport/plot_hydrogeophysical_modeling.py index f5c6d24eb..a159cdf1a 100644 --- a/doc/examples/5_flow_transport/plot_hydrogeophysical_modeling.py +++ b/doc/examples/5_flow_transport/plot_hydrogeophysical_modeling.py @@ -176,7 +176,7 @@ # Initialize and call the ERT manager for electrical simulation: ERT = ERTManager(verbose=False) # Run simulation for the apparent resistivities -rhoa = ERT.simulate(meshERT, res=resis, scheme=ertScheme, +rhoa = ERT.simulate(meshERT, res=resis, scheme=ertScheme, returnArray=True, verbose=False) for i in range(4): diff --git a/doc/faq.rst b/doc/faq.rst deleted file mode 100644 index 8043b3cbc..000000000 --- a/doc/faq.rst +++ /dev/null @@ -1,98 +0,0 @@ -.. _sec:faq: - -Frequently asked questions -========================== - -.. note:: - - This section is still under construction. If you have a have a question - (about GIMLi) that is not covered here, please open a `GitHub issue - `_. - -.. contents:: - :local: - :backlinks: top - -General -------- - -What is the difference between BERT and GIMLi? -.............................................. - -GIMLi is a general library for modelling and inversion in geophysics. -`BERT `_ -builds upon this framework and provides numerous high-level and user-friendly -functions and applications specifically tailored for DC resistivity studies. - -Installation ------------- - -Python 2 or Python 3? -..................... - -Short answer: Python 3. Long answer: Currently, pygimli is functionable with all -major Python versions from 3.7 on. When compiling from source, it is -important that *boost_python* is build against the same Python version you want -to use. However, many (scientific) Python projects recommend to use Python 3 for -`various reasons `_. We droped support for Python 2. In most cases you can translate your -existing Python 2 scripts to Python 3 by running `2to3 -`_. - -What do I have to do to use pygimli in Spyder? -.............................................. - -For Linux users it should be sufficient to have proper environment settings: - -.. code:: bash - - export PYTHONPATH=$PYTHONPATH:$HOME/src/gimli/gimli/python - export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/src/gimli/build/lib - export PATH=$PATH:$HOME/src/gimli/build/bin - -Note, these setting will ony affect applications that have been started from the -current console. -To make these settings permanent, make sure to add them to your *.bashrc*. - -Window users should use the conda/anaconda install which sets all appropriate paths to run pygimli in spyder. - -If this does not work, Windows users probably need to tell spyder where your manual pygimli installation can be found by an appropriate setting of -the `PYTHONPATH` in the spyder Menubar:/tools/PYTHONPATH manager. - -If you start spyder from Windows startmenu you probably need to set the -correct `PATH` somewhere in your windows personal settings. - -You can test you installation within the console via: - -.. code:: bash - - python -c 'import pygimli as pg; print(pg.version())' - -If there is something wrong with the environment settings -you get an error like this: - -.. code:: - - python: can't open file 'import pygimli as pg; print(pg.version())': - [Errno 2] No such file or directory - - -Weird findings --------------- - -My script called sip.py and nothing works -......................................... - -Rename your file to something different. One of the prerequisite library (pyQT) -import the file sip.py as module for they own and just stuck. - -Segfault on import -.................. - -Try `python -s -c "import pygimli"`. The `-s` option ensures that only system -packages are used. This avoids conflicts with local (pip) packages. - -CXXABI_1.3.9 not included in libstdc++.so.6 -........................................... -When installing conda packages on older machines, the above error may occur. If so, -check out the suggestion made -`here `_. diff --git a/doc/gimliuses.bib b/doc/gimliuses.bib index 3286ec65d..755e4a343 100644 --- a/doc/gimliuses.bib +++ b/doc/gimliuses.bib @@ -1,1444 +1,1610 @@ -% Encoding: UTF-8 - -@Article{Coscia2011, - author = {Coscia,I. and Greenhalgh, S. and Linde, N. and Doetsch, J. and Marescot, L. and G{\"u}nther, T. and Green, A.}, - journal = {Geophysics}, - title = {3{D} crosshole apparent resistivity static inversion and monitoring of a coupled river-aquifer system}, - year = {2011}, - number = {2}, - pages = {G49-59}, - volume = {76}, - doi = {10.1190/1.3553003}, - timestamp = {2010.08.09}, -} - -@Article{Guenther2012, - author = {G{\"u}nther, T. and M{\"u}ller-Petke, M.}, - journal = {Hydrology and Earth System Sciences}, - title = {{H}ydraulic properties at the {N}orth {S}ea island of {B}orkum derived from joint inversion of magnetic resonance and electrical resistivity soundings}, - year = {2012}, - number = {9}, - pages = {3279--3291}, - volume = {16}, - doi = {10.5194/hess-16-3279-2012}, - timestamp = {2016.09.14}, -} - -@Article{Costabel2014, - author = {Costabel, S. and G{\"u}nther, T.}, - journal = {Vadose Zone Journal}, - title = {{N}oninvasive {E}stimation of {W}ater {R}etention {P}arameters by {O}bserving the {C}apillary {F}ringe with {M}agnetic {R}esonance {S}ounding}, - year = {2014}, - number = {6}, - pages = {14}, - volume = {13}, - doi = {10.2136/vzj2013.09.0163}, - timestamp = {2014.06.06}, -} - -@Article{Wagner2015, - author = {Wagner, F.M. and G{\"u}nther, T. and Schmidt-Hattenberger, C. and Maurer, H.}, - journal = {Geophysics}, - title = {{C}onstructive optimization of electrode locations for target-focused resistivity monitoring}, - year = {2015}, - number = {2}, - pages = {E29--E40}, - volume = {80}, - doi = {10.1190/geo2014-0214.1}, - timestamp = {2015.01.14}, -} - -@Article{Loewer2016, - author = {Loewer, M. and Igel, J. and Wagner, N.}, - journal = {{IEEE} J. Sel. Top. Appl. Earth Observations Remote Sensing}, - title = {{S}pectral {D}ecomposition of {S}oil {E}lectrical and {D}ielectric {L}osses and {P}rediction of {I}n {S}itu {GPR} {P}erformance}, - year = {2016}, - number = {1}, - pages = {212--230}, - volume = {9}, - doi = {10.1109/jstars.2015.2424152}, - publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, - timestamp = {2016.09.14}, -} - -@InProceedings{Igel2016, - author = {Igel, J. and Stadler, S. and G{\"u}nther, T.}, - journal = {Ext. Abstr., SAGEEP, Denver, USA}, - title = {{H}igh-resolution investigation of the capillary transition zone and its influence on {GPR} signatures}, - year = {2016}, - doi = {10.1109/icgpr.2016.7572603}, - timestamp = {2016.06.28}, -} - -@Article{Costabel2016, - author = {Costabel, S. and G{\"u}nther, T. and Dlugosch, R. and M{\"u}ller-Petke, M.}, - journal = {Geophysics}, - title = {{T}orus-nuclear magnetic resonance: {Q}uasicontinuous airborne magnetic resonance profiling by using a helium-filled balloon}, - year = {2016}, - month = {jun}, - number = {4}, - pages = {WB119--WB129}, - volume = {81}, - doi = {10.1190/geo2015-0467.1}, - publisher = {Society of Exploration Geophysicists}, - timestamp = {2016.09.14}, -} - -@Article{Guenther2016, - author = {G{\"u}nther, T. and Martin, T.}, - journal = {Journal of Applied Geophysics}, - title = {{S}pectral two-dimensional inversion of frequency-domain induced polarisation data from a mining slag heap}, - year = {2016}, - pages = {436-448}, - volume = {135}, - doi = {10.1016/j.jappgeo.2016.01.008}, - timestamp = {2015.12.21}, -} - -@Article{Hupfer2016, - author = {Hupfer, S. and Martin, T. and Weller, A. and G\"{u}nther, T. and Kuhn, K. and Ngninjio, V.D.N. and Noell, U.}, - title = {{P}olarization effects of unconsolidated sulphide-sand-mixtures}, - journal = {Journal of Applied Geophysics}, - year = {2016}, - volume = {135}, - pages = {456-465}, - month = {dec}, - doi = {10.1016/j.jappgeo.2015.12.003}, - publisher = {Elsevier {BV}}, - timestamp = {2016.12.16}, -} - -@Article{Loewer2017, - author = {Loewer, M. and G\"{u}nther, T. and Igel, J. and Kruschwitz, S. and Martin, T. and Wagner, N.}, - journal = {Geophysical Journal International}, - title = {Ultra-broad-band electrical spectroscopy of soils and sediments{\textemdash}a combined permittivity and conductivity model}, - year = {2017}, - month = {jun}, - number = {3}, - pages = {1360--1373}, - volume = {210}, - doi = {10.1093/gji/ggx242}, - publisher = {Oxford University Press ({OUP})}, - timestamp = {2017.07.27}, -} - -@Article{Ronczka2017, - author = {Ronczka, M. and Hellman, K. and G\"{u}nther, T. and Wis{\'{e}}n, R. and Dahlin, T.}, - journal = {Solid Earth}, - title = {Electric resistivity and seismic refraction tomography: a challenging joint underwater survey at \"{A}sp\"{o} Hard Rock Laboratory}, - year = {2017}, - month = {jun}, - number = {3}, - pages = {671--682}, - volume = {8}, - doi = {10.5194/se-8-671-2017}, - publisher = {Copernicus {GmbH}}, - timestamp = {2017.07.27}, -} - -@Article{Hellman2017, - author = {Hellman, K. and Ronczka, M. and G\"{u}nther, T. and Wennermark, M. and R\"{u}cker, C. and Dahlin, T.}, - journal = {Journal of Applied Geophysics}, - title = {Structurally coupled inversion of {ERT} and refraction seismic data combined with cluster-based model integration}, - year = {2017}, - month = {aug}, - pages = {169--181}, - volume = {143}, - doi = {10.1016/j.jappgeo.2017.06.008}, - publisher = {Elsevier {BV}}, - timestamp = {2017.07.27}, -} - -@Article{Bergmann2017, - author = {Bergmann, P. and Schmidt-Hattenberger, C. and Labitzke, T. and Wagner, F.M. and Just, A. and Flechsig, C. and Rippe, D.}, - title = {Fluid injection monitoring using electrical resistivity tomography - five years of CO2 injection at Ketzin, Germany}, - journal = {Geophysical Prospecting}, - year = {2017}, - volume = {65}, - pages = {859-875}, - issn = {1365-2478}, - doi = {10.1111/1365-2478.12426}, - publisher = {Wiley Online Library}, - timestamp = {2016.08.24}, -} - -@Article{Boerner2017, - author = {B{\"o}rner, F. and M{\"u}ller-Huber, E. and Branka, D. and R{\"u}cker, C.}, - journal = {Near Surface Geophysics}, - title = {The effect of compaction on complex electrical resistivity of shaly sands}, - year = {2017}, - number = {6}, - pages = {633--643}, - volume = {15}, - doi = {10.3997/1873-0604.2017056}, - publisher = {European Association of Geoscientists \& Engineers}, -} - -@Article{Wagner2018, - author = {Wagner, F.M. and Wiese, B.}, - title = {Fully coupled inversion on a multi-physical reservoir model - Part II: The Ketzin CO2 storage reservoir}, - journal = {International Journal of Greenhouse Gas Control}, - year = {2018}, - volume = {75}, - pages = {273-281}, - doi = {10.1016/j.ijggc.2018.04.009}, - timestamp = {2018.02.18}, -} - -@Article{Wiese2018, - author = {Wiese, B. and Wagner, F.M. and Norden, B. and Maurer, H. and Schmidt-Hattenberger, C.}, - title = {Fully coupled inversion on a multi-physical reservoir model - Part I: Theory and concept}, - journal = {International Journal of Greenhouse Gas Control}, - year = {2018}, - volume = {75}, - pages = {262-272}, - doi = {10.1016/j.ijggc.2018.05.013}, - timestamp = {2018.02.18}, -} - -@Article{Watlet2018, - author = {Watlet, A. and Kaufmann, O. and Triantafyllou, A. and Poulain, Am. and Chambers, J. and Meldrum, P. and Wilkinson, P. and Hallet, V. and Quinif, Y. and van~Ruymbeke, M. and van~Camp, M.}, - journal = {Hydrology and Earth System Sciences}, - title = {Imaging groundwater infiltration dynamics in the karst vadose zone with long-term ERT monitoring}, - year = {2018}, - number = {2}, - pages = {1563--1592}, - volume = {22}, - doi = {10.5194/hess-22-1563-2018}, - publisher = {European Geosciences Union}, -} - -@Article{Jordi2018, - author = {Jordi, C. and Doetsch, J. and G{\"u}nther, T. and Schmelzbach, C. and Robertsson, J. O.A.}, - journal = {Geophysical Journal International}, - title = {Geostatistical regularization operators for geophysical inverse problems on irregular meshes}, - year = {2018}, - number = {2}, - pages = {1374--1386}, - volume = {213}, - doi = {10.1093/gji/ggy055}, - publisher = {Oxford University Press}, -} - -@Article{Rossi2018, - author = {Rossi, M. and Dahlin, T. and Olsson, P.-I. and G{\"u}nther, T.}, - journal = {Near Surface Geophysics}, - title = {Data acquisition, processing and filtering for reliable 3D resistivity and time-domain induced polarisation tomography in an urban area: field example of Vinsta, Stockholm}, - year = {2018}, - number = {3}, - pages = {220--229}, - volume = {16}, - doi = {10.3997/1873-0604.2018014}, - publisher = {European Association of Geoscientists \& Engineers}, -} - -@Article{Ronczka2018, - author = {Ronczka, M. and Wis{\'e}n, R. and Dahlin, T.}, - journal = {Near Surface Geophysics}, - title = {Geophysical pre-investigation for a Stockholm tunnel project: joint inversion and interpretation of geoelectric and seismic refraction data in an urban environment}, - year = {2018}, - number = {3}, - pages = {258--268}, - volume = {16}, - doi = {10.3997/1873-0604.2018009}, - publisher = {European Association of Geoscientists \& Engineers}, -} - -@Article{Skibbe2018, - author = {Skibbe, N. and G{\"u}nther, T. and M{\"u}ller-Petke, M.}, - journal = {Geophysics}, - title = {Structurally coupled cooperative inversion of magnetic resonance with resistivity soundings}, - year = {2018}, - number = {6}, - pages = {JM51--JM63}, - volume = {83}, - doi = {10.1190/geo2018-0046.1}, - publisher = {Society of Exploration Geophysicists and American Association of Petroleum~…}, -} - -@Article{Wunderlich2018, - author = {Wunderlich, T. and Fischer, P. and Wilken, D. and Hadler, H. and Erkul, E. and Mecking, R. and G{\"u}nther, T. and Heinzelmann, M. and V{\"o}tt, A. and Rabbel, W.}, - journal = {Geophysics}, - title = {Constraining electric resistivity tomography by direct push electric conductivity logs and vibracores: An exemplary study of the Fiume Morto silted riverbed (Ostia Antica, western Italy)}, - year = {2018}, - number = {3}, - pages = {B87--B103}, - volume = {83}, - doi = {10.1190/geo2016-0660.1}, - publisher = {Society of Exploration Geophysicists}, -} - -@Article{Wagner2019, - author = {Wagner, F.M. and Mollaret, C. and G{\"u}nther, T. and Kemna, A. and Hauck, C.}, - title = {Quantitative imaging of water, ice, and air in permafrost systems through petrophysical joint inversion of seismic refraction and electrical resistivity data}, - journal = {Geophysical Journal International}, - year = {2019}, - volume = {219}, - number = {3}, - pages = {1866--1875}, - doi = {10.1093/gji/ggz402}, -} - -@Article{Rochlitz2019, - author = {Rochlitz, R. and Skibbe, N. and G{\"u}nther, T.}, - journal = {Geophysics}, - title = {custEM: Customizable finite-element simulation of complex controlled-source electromagnetic data}, - year = {2019}, - number = {2}, - pages = {F17--F33}, - volume = {84}, - doi = {10.1190/geo2018-0208.1}, - publisher = {Society of Exploration Geophysicists}, -} - -@Article{Pasquale2019, - author = {de~Pasquale, G. and Linde, N. and Greenwood, A.}, - journal = {Journal of Applied Geophysics}, - title = {Joint probabilistic inversion of DC resistivity and seismic refraction data applied to bedrock/regolith interface delineation}, - year = {2019}, - pages = {103839}, - volume = {170}, - doi = {10.1016/j.jappgeo.2019.103839}, - publisher = {Elsevier}, -} - -@Article{Nickschick2019, - author = {Nickschick, T. and Flechsig, C. and Mrlina, J. and Oppermann, F.k and L{\"o}big, F. and G{\"u}nther, T.}, - journal = {Solid Earth}, - title = {Large-scale electrical resistivity tomography in the Cheb Basin (Eger Rift) at an International Continental Drilling Program (ICDP) monitoring site to image fluid-related structures}, - year = {2019}, - number = {6}, - pages = {1951--1969}, - volume = {10}, - doi = {10.5194/se-10-1951-2019}, - publisher = {Copernicus GmbH}, -} - -@Article{Leger2019, - author = {L{\'e}ger, E. and Dafflon, B. and Robert, Y.}, - journal = {The Cryosphere}, - title = {A distributed temperature profiling method for assessing spatial variability in ground}, - year = {2019}, - pages = {11}, - volume = {13}, - doi = {10.5194/tc-13-2853-2019}, -} - -@Article{Assouline2019, - author = {Assouline, D. and Mohajeri, N. and Gudmundsson, A. and Scartezzini, J.-L.}, - journal = {Geothermal Energy}, - title = {A machine learning approach for mapping the very shallow theoretical geothermal potential}, - year = {2019}, - number = {1}, - pages = {19}, - volume = {7}, - doi = {10.1186/s40517-019-0135-6}, - publisher = {Springer}, -} - -@Article{LopezAlvis2019, - author = {Lopez-Alvis, J. and Hermans, T. and Nguyen, F.}, - journal = {Advances in Water Resources}, - title = {A cross-validation framework to extract data features for reducing structural uncertainty in subsurface heterogeneity}, - year = {2019}, - pages = {103427}, - volume = {133}, - doi = {10.1016/j.advwatres.2019.103427}, -} - -@Article{Pasquale2019a, - author = {de~Pasquale, G. and Linde, N. and Doetsch, J. and Holbrook, W.S.}, - journal = {Geophysical Journal International}, - title = {Probabilistic inference of subsurface heterogeneity and interface geometry using geophysical data}, - year = {2019}, - doi = {10.1093/gji/ggz055}, -} - -@Article{Ochs2020, - author = {Ochs, J. and Klitzsch, N.}, - journal = {Journal of Applied Geophysics}, - title = {Considerations regarding small-scale surface and borehole-to-surface electrical resistivity tomography}, - year = {2020}, - pages = {103862}, - volume = {172}, - doi = {10.1016/j.jappgeo.2019.103862}, - publisher = {Elsevier}, -} - -@Article{Skibbe2020, - author = {Skibbe, N. and Rochlitz, R. and G{\"u}nther, T. and M{\"u}ller-Petke, M.}, - journal = {Geophysics}, - title = {COMET: An open-source toolbox for Surface NMR}, - year = {2020}, - number = {3}, - pages = {1--56}, - volume = {85}, - doi = {10.1190/geo2019-0484.1}, -} - -@Article{Jordi2020, - author = {Jordi, C. and Doetsch, J. and G{\"u}nther, T. and Schmelzbach, C. and Maurer, H. and Robertsson, J. O.A.}, - journal = {Geophysical Journal International}, - title = {Structural joint inversion on irregular meshes}, - year = {2020}, - number = {3}, - pages = {1995--2008}, - volume = {220}, - doi = {10.1093/gji/ggz550}, - publisher = {Oxford University Press}, -} - -@Article{Whiteley2020, - author = {Whiteley, J.S. and Chambers, J.E. and Uhlemann, S. and Boyd, J. and Cimpoiasu, M.O. and Holmes, J.L. and Inauen, C.M. and Watlet, A. and Hawley-Sibbett, L.R. and Sujitapan, C. and others}, - journal = {Engineering Geology}, - title = {Landslide monitoring using seismic refraction tomography--The importance of incorporating topographic variations}, - year = {2020}, - pages = {105525}, - doi = {10.1016/j.enggeo.2020.105525}, - publisher = {Elsevier}, -} - -@Article{Clement2020, - author = {Cl{\'e}ment, R. and P{\"a}rn, J. and Maddison, M. and Henine, H. and Chaumont, C. and Tournebize, J. and Uri, V. and Espenberg, M. and G{\"u}nther, T. and Mander, {\"U}.}, - journal = {Journal of Applied Geophysics}, - title = {Frequency-domain electromagnetic induction for upscaling greenhouse gas fluxes in two hemiboreal drained peatland forests}, - year = {2020}, - pages = {103944}, - doi = {10.1016/j.jappgeo.2020.103944}, - publisher = {Elsevier}, -} - -@Article{Palacios2020, - author = {Palacios, A. and Ledo, J. J. and Linde, N. and Luquot, L. and Bellmunt, F. and Folch, A. and Marcuello, A. and Queralt, P. and Pezard, P. A. and Mart\'{\i}nez, L. and Bosch, D. and Carrera, J.}, - journal = {Hydrology and Earth System Sciences}, - title = {Time-lapse cross-hole electrical resistivity tomography ({CHERT}) for monitoring seawater intrusion dynamics in a Mediterranean aquifer}, - year = {2020}, - number = {4}, - pages = {2121--2139}, - volume = {24}, - doi = {10.5194/hess-24-2121-2020}, -} - -@Article{Klingler2020, - author = {Klingler, S. and Leven, C. and Cirpka, O.A. and Dietrich, P.}, - title = {Anomaly effect-driven optimization of direct-current geoelectric mapping surveys in large areas}, - journal = {Journal of Applied Geophysics}, - year = {2020}, - volume = {176}, - pages = {104002}, - doi = {10.1016/j.jappgeo.2020.104002}, -} - -@Article{Fediuk2020, - author = {Fediuk, A. and Wilken, D. and Wunderlich, T. and Rabbel, W.}, - title = {Physical Parameters and Contrasts of Wooden Objects in Lacustrine Environment: Ground Penetrating Radar and Geoelectrics}, - journal = {Geosciences}, - year = {2020}, - volume = {10}, - number = {4}, - issn = {2076--3263}, - article-number = {146}, - doi = {10.3390/geosciences10040146}, -} - -@Article{Peruzzo2020, - author = {Peruzzo, L. and Chou, C. and Wu, Y. and Schmutz, M. and Mary, B. and Wagner, F.M. and Petrov, P. and Newman, G. and Blancaflor, E.B. and Liu, X. and Ma, X. and Hubbard, S.}, - title = {Imaging of plant current pathways for non-invasive root Phenotyping using a newly developed electrical current source density approach}, - journal = {Plant and Soil}, - year = {2020}, - doi = {10.1007/s11104-020-04529-w}, -} - -@Article{Blazevic2020, - author = {Blazevic, L. A. and Bodet, L. and Pasquet, S. and Linde, N. and Jougnot, D. and Longuevergne, L.}, - title = {Time-Lapse Seismic and Electrical Monitoring of the Vadose Zone during A Controlled Infiltration Experiment at the Ploemeur Hydrological Observatory, France}, - journal = {Water}, - year = {2020}, - volume = {12}, - number = {5}, - issn = {2073--4441}, - article-number = {1230}, - doi = {10.3390/w12051230}, -} - -@Article{Miller2020, - author = {Miller, C. A. and Christenson, B. W. and Byrdina, S. and Vandemeulebrouck, J. and Brakenrig, T. and Britten, K. and Shanks, J. and Epstein, G.}, - journal = {Journal of Volcanology and Geothermal Research}, - title = {Snapshot of a magmatic/hydrothermal system from electrical resistivity tomography and fumarolic composition, Whakaari/White Island, New Zealand}, - year = {2020}, - issn = {0377-0273}, - pages = {106909}, - doi = {10.1016/j.jvolgeores.2020.106909}, -} - -@Article{Folch2020, - author = {Folch, A. and del Val, L. and Luquot, L. and Martínez-Pérez, L. and Bellmunt, F. and Le Lay, H. and Rodellas, V. and Ferrer, N. and Palacios, A. and Fernández, S. and Marazuela, M.A. and Diego-Feliu, M. and Pool, M. and Goyetche, T. and Ledo, J. and Pezard, P. and Bour, O. and Queralt, P. and Marcuello, A. and Garcia-Orellana, J. and Saaltink, M.W. and Vázquez-Suñé, E. and Carrera, J.}, - journal = {Journal of Hydrology}, - title = {{Combining fiber optic DTS, cross-hole ERT and time-lapse induction logging to characterize and monitor a coastal aquifer}}, - year = {2020}, - pages = {125050}, - volume = {588}, - doi = {10.1016/j.jhydrol.2020.125050}, - keywords = {Cross hole electrical resistivity tomography, Fiber optic distributed temperature sensing, Formation electrical conductivity, Sea water intrusion, Submarine groundwater discharge, Alluvial aquifer}, -} - -@Article{Costall2020, - author = {Costall, A. and Harris, B. and Teo, B. and Schaa, R. and Wagner, F. M. and Pigois, J.-P.}, - journal = {Scientific Reports}, - title = {Groundwater Throughflow and Seawater Intrusion in High Quality Coastal Aquifers}, - year = {2020}, - pages = {9866}, - volume = {10}, - doi = {10.1038/s41598-020-66516-6}, -} - -@Article{Martin2020, - author = {Martin, T. and G{\"u}nther, T. and Flores Orozco, A. and Dahlin, T.}, - journal = {Journal of Applied Geophysics}, - title = {Evaluation of spectral induced polarization field measurements in time and frequency domain}, - year = {2020}, - month = {sep}, - pages = {104141}, - volume = {180}, - doi = {10.1016/j.jappgeo.2020.104141}, - publisher = {Elsevier {BV}}, -} - -@Article{Ronczka2020, - author = {Ronczka, M. and G{\"u}nther, T. and Grinat, M. and Wiederhold, H.}, - journal = {Near Surface Geophysics}, - title = {Monitoring freshwater-saltwater interfaces with {SAMOS} - installation effects on data and inversion}, - year = {2020}, - month = {jul}, - number = {4}, - pages = {369--383}, - volume = {18}, - doi = {10.1002/nsg.12115}, - publisher = {Wiley}, -} - -@Article{Rao2020, - author = {Rao, S. and Lesparre, N. and Flores Orozco, A. and Wagner, F. and Javaux, M.}, - journal = {Plant and Soil}, - title = {Imaging plant responses to water deficit using electrical resistivity tomography}, - year = {2020}, - doi = {10.1007/s11104-020-04653-7}, -} - -@Article{Mollaret2020, - author = {Mollaret, C. and Wagner, F. and Hilbich, C. and Scapozza, C. and Hauck, C.}, - journal = {Front. Earth Sci.}, - title = {Petrophysical joint inversion applied to alpine permafrost field sites to image subsurface ice, water, air and rock contents}, - year = {2020}, - pages = {85}, - volume = {8}, - doi = {10.3389/feart.2020.00085}, - url = {https://www.frontiersin.org/articles/10.3389/feart.2020.00085/pdf}, -} - -@Article{Raab2020, - author = {Raab, T. and Weinzierl, W. and Wiese, B. and Rippe, D. and Schmidt-Hattenberger, C.}, - journal = {Advances in Geosciences}, - title = {{Development of an Electrical Resistivity Tomography Monitoring Concept for the Svelvik CO2 Field Lab, Norway}}, - year = {2020}, - pages = {41--53}, - volume = {54}, - doi = {10.5194/adgeo-54-41-2020}, - url = {https://adgeo.copernicus.org/articles/54/41/2020/}, -} - -@Article{Enemark2020, - author = {Enemark, T. and Peeters, L. and Mallants, D. and Flinchum, B. and Batelaan, O.}, - journal = {Water Resources Research}, - title = {A Systematic Approach to Hydrogeological Conceptual Model Testing, Combining Remote Sensing and Geophysical Data}, - year = {2020}, - number = {8}, - pages = {e2020WR027578}, - volume = {56}, - doi = {10.1029/2020WR027578}, - url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020WR027578}, -} - -@Article{FernandezVisentini2020, - author = {{Fernandez Visentini}, A. and Linde, N. and {Le Borgne}, T. and Dentz, M.}, - journal = {Advances in Water Resources}, - title = {Inferring geostatistical properties of hydraulic conductivity fields from saline tracer tests and equivalent electrical conductivity time-series}, - year = {2020}, - pages = {103758}, - volume = {146}, - doi = {10.1016/j.advwatres.2020.103758}, - url = {http://www.sciencedirect.com/science/article/pii/S0309170820306618}, -} - -@Article{Pacheco2020, - author = {Pacheco, M. and Plattner, A. M. and Stock, G. M. and Rood, D. H. and Pluhar, C. J.}, - journal = {Frontiers in Earth Science}, - title = {Surface Exposure Dating and Geophysical Tomography of the Royal Arches Meadow Rock Avalanche, Yosemite Valley, California}, - year = {2020}, - pages = {372}, - volume = {8}, - doi = {10.3389/feart.2020.00372}, - url = {https://www.frontiersin.org/article/10.3389/feart.2020.00372}, -} - -@Article{Saneiyan2021, - author = {Saneiyan, S. and Ntarlagiannis, D. and Colwell, F.}, - journal = {Geophysical Journal International}, - title = {Complex conductivity signatures of microbial induced calcite precipitation, field and laboratory scales}, - year = {2021}, - pages = {1811--1824}, - volume = {224}, - doi = {10.1093/gji/ggaa510}, - url = {https://doi.org/10.1093/gji/ggaa510}, -} - -@Article{Urruela2020, - author = {Urruela, A. and Rivero, L. and Casas, A. and Garcia-Artigas, R. and Sendr\'{o}s, A. and Lovera, R. and Himi, M.}, - journal = {Journal of Applied Geophysics}, - title = {Improving the resolution of investigation using {ERT} instruments with a reduced number of electrodes}, - year = {2020}, - pages = {104239}, - doi = {10.1016/j.jappgeo.2020.104239}, - url = {http://www.sciencedirect.com/science/article/pii/S0926985120306224}, -} - -@Article{Flinchum2020, - author = {Flinchum, B. A. and Banks, E. and Hatch, M. and Batelaan, O. and Peeters, L. J. M. and Pasquet, S.}, - journal = {Hydrology and Earth System Sciences}, - title = {Identifying recharge under subtle ephemeral features in a flat-lying semi-arid region using a combined geophysical approach}, - year = {2020}, - number = {9}, - pages = {4353--4368}, - volume = {24}, - doi = {10.5194/hess-24-4353-2020}, - url = {https://hess.copernicus.org/articles/24/4353/2020/}, -} - -@article{Flinchum2022, - doi = {10.3389/frwa.2021.772185}, - url = {https://doi.org/10.3389/frwa.2021.772185}, - year = {2022}, - publisher = {Frontiers Media {SA}}, - volume = {3}, - author = {Flinchum, B. A. and Holbrook, W. S. and Carr, B. J.}, - title = {What Do P-Wave Velocities Tell Us About the Critical Zone?}, - journal = {Frontiers in Water} -} - -@Article{Kordjazi2021, - author = {Kordjazi, A. and Coe, J. T. and Afanasiev, M.}, - journal = {Journal of Nondestructive Evaluation}, - title = {Nondestructive Evaluation of Drilled Shaft Construction Anomalies Using Full Waveform Tomography of Simulated Crosshole Measurements}, - year = {2021}, - number = {3}, - volume = {40}, - doi = {10.1007/s10921-020-00728-8}, -} - -@Article{Buecker2021, - author = {B{\"u}cker, M. and Flores Orozco, A. and Gallistl, J. and Steiner, M. and Aigner, L. and Hoppenbrock, J. and Glebe, R. and Morales Barrera, W. and Pita de la Paz, C. and Garc\'{\i}a Garc\'{\i}a, C. E. and Razo P\'erez, J. A. and Buckel, J. and H{\"o}rdt, A. and Schwalb, A. and P{\'e}rez, L.}, - journal = {Solid Earth}, - title = {Integrated land and water-borne geophysical surveys shed light on the sudden drying of large karst lakes in southern Mexico}, - year = {2021}, - number = {2}, - pages = {439-461}, - volume = {12}, - doi = {10.5194/se-12-439-2021}, - url = {https://se.copernicus.org/articles/12/439/2021/}, -} - -@Article{Steiner2021, - author = {Steiner, M. and Wagner, F. M. and Maierhofer, T. and Sch{\"o}ner, W. Flores Orozco, A.}, - journal = {Geophysics}, - title = {Improved estimation of ice and water contents in Alpine permafrost through constrained petrophysical joint inversion: {The Hoher Sonnblick} case study}, - year = {2021}, - doi = {10.1190/geo2020-0592.1}, -} - -@Article{Skibbe2021, - author = {Skibbe, N. and G{\"u}nther, T. and M{\"u}ller-Petke, M.}, - journal = {Geophysics}, - title = {Improved hydrogeophysical imaging by structural coupling of two-dimensional magnetic resonance and electrical resistivity tomography}, - year = {2021}, - doi = {10.1190/geo2020-0593.1}, -} - -@Article{Flinchum2021, - author = {Flinchum, B. and Peeters, L. and Munday, T. and Cahill, K.}, - journal = {Geophysics}, - title = {Improving the hydrogeologic conceptualization of a remote semiarid palaeovalley groundwater system using airborne electromagnetics, seismic refraction and reflection, and downhole nuclear magnetic resonance}, - year = {2021}, - doi = {10.1190/geo2020-0614.1}, -} - -@Article{Sabor2021, - author = {Sabor, K. and Jougnot, D. and Guerin, R. and Steck, B. and Henault, J.-M. and Apffel, L. and Vautrin, D.}, - journal = {Geophysical Journal International}, - title = {A data mining approach for improved interpretation of {ERT} inverted sections using the {DBSCAN} clustering algorithm}, - year = {2021}, - doi = {10.1093/gji/ggab023}, -} - -@Article{Martin2021, - author = {Martin, T. and G\"{u}nther, T. and Weller, A. and Kuhn, K.}, - journal = {Journal of Applied Geophysics}, - title = {Classification of slag material by spectral induced polarization laboratory and field measurements}, - year = {2021}, - doi = {10.1016/j.jappgeo.2021.104439}, -} - -@Article{Nivorlis2021, - author = {Nivorlis, A. and Rossi, M. and Dahlin, T.}, - title = {Temporal filtering and time-lapse inversion of geoelectrical data for long-term monitoring with application to a chlorinated hydrocarbon contaminated site}, - journal = {Geophysical Journal International}, - year = {2021}, - month = {10}, - volume = {228}, - number = {3}, - issn = {0956-540X}, - doi = {10.1093/gji/ggab422}, -} - -@Article{Rochlitz2021, - author = {Rochlitz, R. and Seidel, M. and B{\"o}rner, R.-U.}, - title = {Evaluation of three approaches for simulating 3-D time-domain electromagnetic data}, - journal = {Geophysical Journal International}, - volume = {227}, - number = {3}, - pages = {1980-1995}, - year = {2021}, - issn = {0956-540X}, - doi = {10.1093/gji/ggab302}, -} - -@Article{Miltenberger2021, - author = {Miltenberger, A and Uhlemann, S. and Mukerji, T. and Williams, K. and Dafflon, B. and Wang, L. and Wainwright, H.}, - title = {Probabilistic Evaluation of Geoscientific Hypotheses With Geophysical Data: Application to Electrical Resistivity Imaging of a Fractured Bedrock Zone}, - journal = {Journal of Geophysical Research: Solid Earth}, - year = {2021}, - volume = {126}, - number = {9}, - pages = {e2021JB021767}, - doi = {10.1029/2021JB021767}, - -} -@Article{Jiang2021, - author = {Jiang, L. and Tian, G. and Wang, B. and Guo, X. and He, X and Zou, A. and Chen, H and Yang, T. and El-Raouf, A. A.}, - title = {Application of three-dimensional electrical resistivity tomography in urban zones by arbitrary electrode distribution survey design}, - journal = {Journal of Applied Geophysics}, - volume = {194}, - pages = {104460}, - year = {2021}, - issn = {0926-9851}, - doi = {10.1016/j.jappgeo.2021.104460}, -} - -@Article{Whiteley2021, - author = {Whiteley, J. and Watlet, A. and Uhlemann, S. and Wilkinson, P. and Boyd, J. and Jordan, C. and Kendall, J. and Chambers, J.}, - journal = {Engineering Geology}, - title = {Rapid characterisation of landslide heterogeneity using unsupervised classification of electrical resistivity and seismic refraction surveys}, - year = {2021}, - volume = {290}, - pages = {106189}, - issn = {0013-7952}, - doi = {10.1016/j.enggeo.2021.106189}, -} - -@Article{Visentini2021, - author = {Fernandez Visentini, A. and de Anna, P. and Jougnot, D. and Le Borgne, T. and M{\'{e}}heust, Y. and Linde, N.}, - title = {Electrical Signatures of Diffusion-Limited Mixing: Insights from a Milli-fluidic Tracer Experiment}, - journal = {Transport in Porous Media}, - year = {2021}, - publisher = {Springer Science and Business Media {LLC}}, - doi = {10.1007/s11242-021-01607-0}, -} - - -@Article{Chavez2021, - author = {Chavez Olalla, J. and Winkels, T. G. and Ngan-Tillard, D. J. M. and Heimovaara, T. J.}, - title = {Geophysical tomography as a tool to estimate the geometry of soil layers: relevance for the reliability assessment of dikes}, - journal = {Georisk: Assessment and Management of Risk for Engineered Systems and Geohazards}, - year = {2021}, - pages = {1--21}, - publisher = {Taylor & Francis}, - doi = {10.1080/17499518.2021.1971252}, - url = {https://doi.org/10.1080/17499518.2021.1971252}, -} - -@Article{Jiang2021b, - author = {Jiang, L. and Wang, B. and Tian, G. and He, X. and Zou, A. and Guo, X. and Chen, H. and El-Raouf, A. A.}, - title = {Strategy for Optimization of Arbitrary Electrode Distribution for 3D Electrical Resistivity Tomography in Urban Zones}, - journal = {Pure and Applied Geophysics}, - year = {2021}, - publisher = {Springer Science and Business Media {LLC}}, - volume = {178}, - number = {9}, - pages = {3601--3618}, - doi = {10.1007/s00024-021-02848-2}, - url = {https://doi.org/10.1007/s00024-021-02848-2}, -} - -@Article{Norooz2021, - author = {Norooz, R. and Olsson, P. I. and Dahlin, T. and G\"{u}nther, T and Bernstone, C.}, - title = {A geoelectrical pre-study of \"{A}lvkarleby test embankment dam: 3D forward modelling and effects of structural constraints on the 3D inversion model of zoned embankment dams}, - journal = {Journal of Applied Geophysics}, - year = {2021}, - volume = {191}, - pages = {104355}, - issn = {0926-9851}, - doi = {10.1016/j.jappgeo.2021.104355}, -} - -@Article{Bievre2021, - author = {Bi{\`{e}}vre, G and Jongmans, D. and Lebourg, T. and Carri{\`{e}}re, S.}, - title = {Electrical resistivity monitoring of an earthslide with electrodes located outside the unstable zone (Pont-Bourquin landslide, Swiss Alps)}, - journal = {Near Surface Geophysics}, - month = {apr}, - year = {2021}, - publisher = {Wiley}, - volume = {19}, - number = {2}, - pages = {225--239}, - doi = {10.1002/nsg.12145}, -} - -@Article{Wellmann2022, - doi = {10.1130/GES02455.1}, - year = {2022}, - publisher = {Geological Society of America}, - author = {Wellmann, F. and Virgo, S. and Escallon, D. and de la Varga, M. and J\"{u}stel, A. and Wagner, F. and Kowalski, J. and Zhao, H. and Fehling, R. and Chen, Q.}, - title = {{Open AR-Sandbox}: A haptic interface for geoscience education and outreach}, - journal = {Geosphere} -} - -@Article{Ochs2021, - author = {Ochs, J. and Klitzsch, N. and Wagner, F. M.}, - doi = {10.1016/j.jappgeo.2022.104530}, - year = {2022}, - publisher = {Elsevier {BV}}, - volume = {197}, - pages = {104530}, - journal = {Journal of Applied Geophysics}, - title = {Mitigation of installation-related effects for small-scale borehole-to-surface ERT}, -} - -@Article{Guedes2022, - doi = {10.1016/j.cageo.2021.105020}, - year = {2022}, - publisher = {Elsevier {BV}}, - volume = {159}, - pages = {105020}, - author = {Jos{\'{e}}, V. and Guedes C. B. and Maciel, A. and Rocha, M. P.}, - title = {Refrapy: A Python program for seismic refraction data analysis}, - journal = {Computers {\&} Geosciences} -} - -@Article{Doyoro2022, - doi = {10.1186/s40562-022-00214-1}, - year = {2022}, - publisher = {Springer Science and Business Media {LLC}}, - volume = {9}, - number = {1}, - author = {Doyoro, Y. G. and Chang, P.-Y. and Puntu, J. M. and Lin, D.-L. and Huu, T. V. and Rahmalia, D. A. and Shie, M.-S.}, - title = {A review of open software resources in python for electrical resistivity modelling}, - journal = {Geoscience Letters} -} - -@Article{ArboledaZapata2022, - doi = {10.1016/j.jappgeo.2021.104512}, - year = {2022}, - publisher = {Elsevier {BV}}, - volume = {196}, - pages = {104512}, - author = {Arboleda-Zapata, M. and Guillemoteau, J. and Tronicke, J.}, - title = {A comprehensive workflow to analyze ensembles of globally inverted 2D electrical resistivity models}, - journal = {Journal of Applied Geophysics} -} - -@Article{Herring2022, - doi = {10.1002/ppp.2141}, - year = {2022}, - author = {Herring, T. and Lewkowicz, A. G.}, - title = {A systematic evaluation of electrical resistivity tomography for permafrost interface detection using forward modeling}, - journal = {Permafrost and Periglacial Processes} -} - -@article{Carrier2022, - title={Damage assessment of supporting pillars in an underground cave using joint inversion of electrical resistivity and {P}-wave velocity, {B}urgundy ({F}rance)}, - author={Carrier, A. and Bottelin, P. and Fabre, L. and Mathy, A.}, - journal={Pure and Applied Geophysics}, - volume={179}, - number={1}, - pages={45--67}, - year={2022}, - doi={10.1007/s00024-021-02921-w}, - publisher={Springer} -} - -@Article{gruenenbaum2023JoH, - author = {Gr\"{u}nenbaum, G\"{u}nther, T. and Greskowiak, J. and Vienken, T. and M\"{u}ller-Petke, M. and Massmann, G.}, - journal = {Journal of Hydrology}, - title = {Salinity distribution in the subterranean estuary of a meso-tidal high-energy beach characterized by {E}lectrical {R}esistivity {T}omography and direct push technology}, - year = {2023}, - pages = {129074}, - volume = {617}, - doi = {10.1016/j.jhydrol.2023.129074}, - publisher = {Elsevier {BV}}, -} - -@Article{rochlitz2023GJI, - author = {Rochlitz, R. and Becken, M. and G\"{u}nther, T.}, - journal = {Geophysical Journal International}, - title = {Three-dimensional inversion of semi-airborne electromagnetic data with a second-order finite-element forward solver}, - year = {2023}, - number = {1}, - pages = {528--545}, - volume = {234}, - doi = {10.1093/gji/ggad056}, - publisher = {Oxford University Press ({OUP})}, -} - -@Article{Moser2023, - author = {Moser, C. and Binley, A. and Flores Orozco, A.}, - doi = {10.1016/j.wasman.2023.07.006}, - issn = {0956-053X}, - journal = {Waste Management}, - pages = {208-222}, - title = {3D electrode configurations for spectral induced polarization surveys of landfills}, - volume = {169}, - year = {2023}, -} - - -@Article{su151813574, - abstract = {Seismic characterization of landslides offers the potential for developing high-resolution models on subsurface shear-wave velocity profile. However, seismic methods based on reflection processing are challenging to apply in such scenarios as a consequence of the disturbance to the often well-defined structural and stratigraphic layering by the landslide process itself. We evaluate the use of alternative seismic characterization methods based on elastic full waveform inversion (E-FWI) to probe the subsurface of a landslide complex in Majes, southern Peru, where recent agricultural development and irrigation activities have altered the hydrology and groundwater table and are thought to have contributed to increased regional landslide activities that present continuing sustainability community development challenges. We apply E-FWI to a 2D near-surface seismic data set for the purpose of better understanding the subsurface in the vicinity of a recent landslide location. We use seismic first-arrival travel-time tomography to generate the inputs required for E-FWI to generate the final high-resolution 2D compressional- and shear-wave (P- and S-wave) velocity models. At distances greater than 140 m from the cliff, the inverted models show a predominantly vertically stratified velocity structure with a low-velocity near-surface layer between 5–15 m depth. At distances closer than 140 m from the cliff, though, the models exhibit significantly reduced shear-wave velocities, stronger heterogeneity, and localized shorter wavelength structure in the top 20 m. These observations are consistent with those expected for a recent landslide complex; however, follow-on geotechnical analysis is required to confirm these assertions. Overall, the E-FWI seismic approach may be helpful for future landslide characterization projects and, when augmented with additional geophysical and geotechnical analyses, may allow for improved understanding of the hydrogeophysical properties associated with suspected ground-water-driven landslide activity.}, - author = {Yang, J. and Shragge, J. and Girard, A. J. and Gonzales, E. and Ticona, J. and Minaya, A. and Krahenbuhl, R.}, - doi = {10.3390/su151813574}, - issn = {2071-1050}, - journal = {Sustainability}, - number = {18}, - title = {Seismic Characterization of a Landslide Complex: A Case History from Majes, Peru}, - volume = {15}, - year = {2023}, -} - -@Article{Wang2022, - doi = {10.1007/s10712-022-09747-8}, - year = {2022}, - month = nov, - publisher = {Springer Science and Business Media {LLC}}, - volume = {44}, - number = {2}, - pages = {357--386}, - author = {Wang, Z. and Sun, C. and Wu, D.}, - title = {Near-surface Site Characterization Based on Joint Iterative Analysis of First-arrival and Surface-wave Data}, - journal = {Surveys in Geophysics} -} - -@Article{ArboledaZapata2023, - doi = {10.1002/esp.5695}, - year = {2023}, - month = sep, - publisher = {Wiley}, - author = {Arboleda-Zapata, M. and Guillemoteau, J. and Luc{\'{\i}}a, A. and Eberle, J. and Tronicke, J. and Korup, O.}, - title = {Tracing past extreme floods on an alluvial fan using geophysical surveying}, - journal = {Earth Surface Processes and Landforms} -} - -@Article{Carrier2023, - doi = {10.1007/s10346-023-02137-0}, - year = {2023}, - month = oct, - publisher = {Springer Science and Business Media {LLC}}, - author = {Carrier, A. and Meric, O. and Bottelin, P.}, - title = {Characterizing landslide dynamics from time-lapse time domain induced polarization and ground-based imaging: a case study of the {MontGombert} landslide (French, Alps)}, - journal = {Landslides} -} -@Comment{jabref-meta: databaseType:bibtex;} -@Article{Herring2023, - doi = {10.1002/ppp.2207}, - year = {2023}, - month = oct, - publisher = {Wiley}, - volume = {34}, - number = {4}, - pages = {494--512}, - author = {Herring, T. and Lewkowicz, A. G. and Hauck, C. and Hilbich, C. and Mollaret, C. and Oldenborger, G. A. and Uhlemann, S. and Farzamian, M. and Calmels, F. and Scandroglio, R.}, - title = {Best practices for using electrical resistivity tomography to investigate permafrost}, - journal = {Permafrost and Periglacial Processes} -} - -@Article{Pavoni2023, - author = {Pavoni, M. and Boaga, J. and Wagner, F.M. and Bast, A. and Phillips, M.}, - doi = {10.1016/j.jappgeo.2023.105097}, - journal = {Journal of Applied Geophysics}, - keywords = {Mountain permafrost, Electrical resistivity tomography (ERT), Refraction seismic tomography (RST), Joint inversion}, - pages = {105097}, - title = {Characterization of rock glaciers environments combining structurally-coupled and petrophysically-coupled joint inversions of electrical resistivity and seismic refraction datasets}, - year = {2023}, -} - -@article{Steiner2023, - doi = {10.1016/j.cageo.2023.105339}, - year = {2023}, - month = jul, - publisher = {Elsevier {BV}}, - volume = {176}, - pages = {105339}, - author = {Steiner, M. and Flores Orozco, A.}, - title = {formikoj: A flexible library for data management and processing in geophysics - Application for seismic refraction data}, - journal = {Computers {\&} Geosciences} -} - -@article{Fiolleau2023, - doi = {10.1016/j.jappgeo.2023.105090}, - year = {2023}, - month = aug, - publisher = {Elsevier {BV}}, - volume = {215}, - pages = {105090}, - author = {Fiolleau, S. and Uhlemann, S. and Wielandt, S. and Dafflon, B.}, - title = {Understanding slow-moving landslide triggering processes using low-cost passive seismic and inclinometer monitoring}, - journal = {Journal of Applied Geophysics} -} - -@article{Uecker2023, - doi = {10.3389/frwa.2023.1057725}, - year = {2023}, - month = jul, - publisher = {Frontiers Media {SA}}, - volume = {5}, - author = {Uecker, R. K. and Flinchum, B. A. and Holbrook, W. S. and Carr, B. J.}, - title = {Mapping bedrock topography: a seismic refraction survey and landscape analysis in the Laramie Range, Wyoming}, - journal = {Frontiers in Water} -} - -@article{IsunzaManrique2023, - doi = {10.1190/geo2022-0133.1}, - year = {2023}, - month = apr, - publisher = {Society of Exploration Geophysicists}, - volume = {88}, - number = {3}, - pages = {B73--B88}, - author = {Isunza Manrique, I. and Caterina, D. and Nguyen, F. and Hermans, T.}, - title = {Quantitative interpretation of geoelectric inverted data with a robust probabilistic approach}, - journal = {Geophysics} -} - -@Article{gautier2023G, - author = {Gautier, Maxime and Gautier, Stéphanie and Cattin, Rodolphe}, - journal = {GEOPHYSICS}, - title = {PyMERRY: A Python solution for an improved interpretation of electrical resistivity tomography images}, - year = {2023}, - number = {1}, - pages = {F23--F39}, - volume = {89}, - doi = {10.1190/geo2023-0105.1}, - publisher = {Society of Exploration Geophysicists}, -} - -@Article{levy2023C&G, - author = {Levy, Shiran and Laloy, Eric and Linde, Niklas}, - journal = {Computers & Geosciences}, - title = {Variational Bayesian inference with complex geostatistical priors using inverse autoregressive flows}, - year = {2023}, - issn = {0098-3004}, - month = feb, - pages = {105263}, - volume = {171}, - doi = {10.1016/j.cageo.2022.105263}, - publisher = {Elsevier BV}, -} - -@Article{levy2024C&G, - author = {Levy, Shiran and Friedli, Lea and Mariéthoz, Grégoire and Linde, Niklas}, - journal = {Computers & Geosciences}, - title = {Conditioning of multiple-point statistics simulations to indirect geophysical data}, - year = {2024}, - issn = {0098-3004}, - month = may, - pages = {105581}, - volume = {187}, - doi = {10.1016/j.cageo.2024.105581}, - publisher = {Elsevier BV}, -} - -@Article{herring2023PaPP, - author = {Herring, Teddi and Lewkowicz, Antoni G. and Hauck, Christian and Hilbich, Christin and Mollaret, Coline and Oldenborger, Greg A. and Uhlemann, Sebastian and Farzamian, Mohammad and Calmels, Fabrice and Scandroglio, Riccardo}, - journal = {Permafrost and Periglacial Processes}, - title = {Best practices for using electrical resistivity tomography to investigate permafrost}, - year = {2023}, - issn = {1099-1530}, - month = oct, - number = {4}, - pages = {494--512}, - volume = {34}, - doi = {10.1002/ppp.2207}, - publisher = {Wiley}, -} - -@Article{dimech2023SR, - author = {Dimech, Adrien and Isabelle, Anne and Sylvain, Karine and Liu, Chong and Cheng, LiZhen and Bussière, Bruno and Chouteau, Michel and Fabien-Ouellet, Gabriel and Bérubé, Charles and Wilkinson, Paul and Meldrum, Philip and Chambers, Jonathan}, - journal = {Scientific Reports}, - title = {A multiscale accuracy assessment of moisture content predictions using time-lapse electrical resistivity tomography in mine tailings}, - year = {2023}, - issn = {2045-2322}, - month = nov, - number = {1}, - volume = {13}, - doi = {10.1038/s41598-023-48100-w}, - publisher = {Springer Science and Business Media LLC}, -} - -@Article{seib2024G, - author = {Seib, Lukas and Frey, Matthis and Bossennec, Claire and Krusemark, Matthias and Burschil, Thomas and Buness, Hermann and Weydt, Leandra and Sass, Ingo}, - journal = {Geothermics}, - title = {Assessment of a medium-deep borehole thermal energy storage site in the crystalline basement: A case study of the demo site Lichtwiese Campus, Darmstadt}, - year = {2024}, - issn = {0375-6505}, - month = may, - pages = {102933}, - volume = {119}, - doi = {10.1016/j.geothermics.2024.102933}, - publisher = {Elsevier BV}, -} - -@Article{aigner2024JoAG, - author = {Aigner, Lukas and Werthmüller, Dieter and Flores Orozco, Adrián}, - journal = {Journal of Applied Geophysics}, - title = {Sensitivity analysis of inverted model parameters from transient electromagnetic measurements affected by induced polarization effects}, - year = {2024}, - issn = {0926-9851}, - month = apr, - pages = {105334}, - volume = {223}, - doi = {10.1016/j.jappgeo.2024.105334}, - publisher = {Elsevier BV}, -} - -@Article{chen2023WRR, - author = {Chen, Hang and Niu, Qifei and Mendieta, Aida and Bradford, John and McNamara, James}, - journal = {Water Resources Research}, - title = {Geophysics‐Informed Hydrologic Modeling of a Mountain Headwater Catchment for Studying Hydrological Partitioning in the Critical Zone}, - year = {2023}, - issn = {1944-7973}, - month = nov, - number = {12}, - volume = {59}, - doi = {10.1029/2023wr035280}, - publisher = {American Geophysical Union (AGU)}, -} - -@Article{navarro2023FiES, - author = {Navarro, Gonzalo and Valois, Rémi and MacDonell, Shelley and de Pasquale, Giulia and Díaz, Juan Pablo}, - journal = {Frontiers in Earth Science}, - title = {Internal structure and water routing of an ice-debris landform assemblage using multiple geophysical methods in the semiarid Andes}, - year = {2023}, - issn = {2296-6463}, - month = apr, - volume = {11}, - doi = {10.3389/feart.2023.1102620}, - publisher = {Frontiers Media SA}, -} - -@Article{ariagno2023ESPaL, - author = {Ariagno, Coline and Pasquet, Sylvain and Le Bouteiller, Caroline and van der Beek, Peter and Klotz, Sébastien}, - journal = {Earth Surface Processes and Landforms}, - title = {Seasonal dynamics of marly badlands illustrated by field records of hillslope regolith properties, Draix–Bléone Critical Zone Observatory, South‐East France}, - year = {2023}, - issn = {1096-9837}, - month = feb, - number = {8}, - pages = {1526--1539}, - volume = {48}, - doi = {10.1002/esp.5564}, - publisher = {Wiley}, -} - -@Article{flinchum2024GRL, - author = {Flinchum, B. A. and Grana, D. and Carr, B. J. and Ravichandran, N. and Eppinger, B. and Holbrook, W. S.}, - journal = {Geophysical Research Letters}, - title = {Low Vp/Vs Values as an Indicator for Fractures in the Critical Zone}, - year = {2024}, - issn = {1944-8007}, - month = jan, - number = {2}, - volume = {51}, - doi = {10.1029/2023gl105946}, - publisher = {American Geophysical Union (AGU)}, -} - -@Article{jabrane2023DiB, - author = {Jabrane, Oussama and Azzab, Driss El and Martínez-Pagán, Pedro and Martínez-Segura, Marcos A. and Mahjoub, Himi and Charroud, Mohammed}, - journal = {Data in Brief}, - title = {Contribution of Python-based BERT software for landslide monitoring using Electrical Resistivity Tomography datasets. A case study in Tghat-Fez (Morocco)}, - year = {2023}, - issn = {2352-3409}, - month = feb, - pages = {108763}, - volume = {46}, - doi = {10.1016/j.dib.2022.108763}, - publisher = {Elsevier BV}, -} - -@Article{hase2024GJI, - author = {Hase, Joost and Weigand, Maximilian and Kemna, Andreas}, - journal = {Geophysical Journal International}, - title = {A probabilistic solution to geophysical inverse problems in complex variables and its application to complex resistivity imaging}, - year = {2024}, - issn = {1365-246X}, - month = feb, - number = {1}, - pages = {456--464}, - volume = {237}, - doi = {10.1093/gji/ggae045}, - publisher = {Oxford University Press (OUP)}, -} - -@Article{zeyen2024C&G, - author = {Zeyen, Hermann and Léger, Emmanuel}, - journal = {Computers & Geosciences}, - title = {PyRefra – Refraction seismic data treatment and inversion}, - year = {2024}, - issn = {0098-3004}, - month = mar, - pages = {105556}, - volume = {185}, - doi = {10.1016/j.cageo.2024.105556}, - publisher = {Elsevier BV}, -} - -@Article{martin2023GJI, - author = {Martin, Tina and Weller, Andreas}, - journal = {Geophysical Journal International}, - title = {Superposition of induced polarization signals measured on pyrite–sand mixtures}, - year = {2023}, - issn = {1365-246X}, - month = feb, - number = {1}, - pages = {699--711}, - volume = {234}, - doi = {10.1093/gji/ggad091}, - publisher = {Oxford University Press (OUP)}, -} - -@Article{li2023MG, - author = {Li, Ang and Grana, Dario and Parsekian, Andrew D. and Carr, Brad}, - journal = {Mathematical Geosciences}, - title = {Uncertainty Quantification in Tomographic Inversion of Near-Surface Seismic Refraction Data}, - year = {2023}, - issn = {1874-8953}, - month = jul, - number = {1}, - pages = {77--101}, - volume = {56}, - doi = {10.1007/s11004-023-10083-9}, - publisher = {Springer Science and Business Media LLC}, -} - -@article{carrizo2024, - title = "Estimation of electrical conductivity models using multi-coil rigid-boom electromagnetic induction measurements", - abstract = "Electromagnetic induction measurements from multi-coil configuration instruments are used to obtain information about the electrical conductivity distribution in the subsurface. The resulting inverse problem might not have a unique and stable solution. In that case, a local inversion method can be trapped in a local minimum and lead to an incorrect solution. In this study, we evaluate the well-posedness of the inverse problem for two and three-layered electrical conductivity models. We show that for a two-layered model, uniqueness is ensured only when both in-phase and quadrature data are available from the measurements. Results from a Gauss–Newton inversion and a lookup table demonstrate that the solution space is convex. Furthermore, we demonstrate that for even a simple three-layered model, the data contained in such measurements are insufficient to reach a correct or stable solution. For models with more than 2 layers, independent prior information is necessary to solve the inverse problem. The insights from the numerical examples are applied in a field case.", - keywords = "Electromagnetic induction, Frequency domain electromagnetics, Inversion", - author = "{Carrizo Mascarell}, Maria and Dieter Werthm{\"u}ller and Evert Slob", - year = "2024", - doi = "10.1016/j.cageo.2024.105732", - volume = "193", - journal = "Computers and Geosciences", - issn = "0098-3004", - publisher = "Elsevier", -} - -@Article{Gautier2024, - author = {Gautier, Maxime and Ferry, Matthieu and Gautier, Stéphanie and Le Roux-Mallouf, Romain and Drukpa, Dowchu and Cattin, Rodolphe}, - journal = {Communications Earth & Environment}, - title = {Deformed alluvial terraces record an excess of slip over the last few centuries on the Himalayan Topographic Frontal Thrust of central Bhutan}, - year = {2024}, - issn = {2662-4435}, - month = oct, - number = {1}, - volume = {5}, - doi = {10.1038/s43247-024-01759-z}, - publisher = {Springer Science and Business Media LLC}, -} - -@Article{CongThi2024, - author = {Cong-Thi, Diep and Dieu, Linh Pham and Caterina, David and De Pauw, Xavier and Thi, Huyen Dang and Ho, Huu Hieu and Nguyen, Frédéric and Hermans, Thomas}, - journal = {Journal of Contaminant Hydrology}, - title = {Quantifying salinity in heterogeneous coastal aquifers through ERT and IP: Insights from laboratory and field investigations}, - year = {2024}, - issn = {0169-7722}, - month = mar, - pages = {104322}, - volume = {262}, - doi = {10.1016/j.jconhyd.2024.104322}, - publisher = {Elsevier BV}, -} - -@Article{Seib2024, - author = {Seib, Lukas and Frey, Matthis and Bossennec, Claire and Krusemark, Matthias and Burschil, Thomas and Buness, Hermann and Weydt, Leandra and Sass, Ingo}, - journal = {Geothermics}, - title = {Assessment of a medium-deep borehole thermal energy storage site in the crystalline basement: A case study of the demo site Lichtwiese Campus, Darmstadt}, - year = {2024}, - issn = {0375-6505}, - month = may, - pages = {102933}, - volume = {119}, - doi = {10.1016/j.geothermics.2024.102933}, - publisher = {Elsevier BV}, -} - -@Article{Skibbe2024, - author = {Skibbe, Nico and Günther, Thomas and Schwalfenberg, Kai and Meyer, Rena and Reckhardt, Anja and Greskowiak, Janek and Massmann, Gudrun and Müller-Petke, Mike}, - journal = {Journal of Hydrology}, - title = {Comparison of methods measuring electrical conductivity in coastal aquifers}, - year = {2024}, - issn = {0022-1694}, - month = nov, - pages = {131905}, - volume = {643}, - doi = {10.1016/j.jhydrol.2024.131905}, - publisher = {Elsevier BV}, -} - -@Article{AsimIbrahim2024, - author = {Asim Ibrahim, Muhammad and Afzal Butt, Nabeel and Rejkjær, Simon and Dahlin, Torleif and Madsen, Dan and Wilkens Flecknoe-Brown, Konard and G{\"u}nther, Thomas}, - journal = {Waste Management}, - title = {Early detection of deep-seated smouldering fires in wood waste storage using ERT}, - year = {2024}, - issn = {0956-053X}, - month = jun, - pages = {215--224}, - volume = {182}, - creationdate = {2024-05-25T12:16:25}, - doi = {10.1016/j.wasman.2024.04.030}, - modificationdate = {2024-05-25T12:16:25}, - owner = {Guenther.T}, - publisher = {Elsevier BV}, -} - -@Article{Norooz2024, - author = {Norooz, Reyhaneh and Nivorlis, Aristeidis and Olsson, Per-Ivar and G{\"u}nther, Thomas and Bernstone, Christian and Dahlin, Torleif}, - journal = {Journal of Civil Structural Health Monitoring}, - title = {Monitoring of {\"a}lvkarleby test embankment dam using 3D electrical resistivity tomography for detection of internal defects}, - year = {2024}, - issn = {2190-5479}, - month = mar, - creationdate = {2024-05-25T12:16:36}, - doi = {10.1007/s13349-024-00785-x}, - modificationdate = {2024-05-25T12:16:36}, - owner = {Guenther.T}, - publisher = {Springer Science and Business Media LLC}, -} - -@Article{Birnstengel2024, - author = {Birnstengel, Susann and Dietrich, Peter and Peisker, Kilian and Pohle, Marco and Hornbruch, G{\"o}tz and Bauer, Sebastian and Hu, Linwei and G{\"u}nther, Thomas and Hellwig, Olaf and Dahmke, Andreas and Werban, Ulrike}, - journal = {GEOPHYSICS}, - title = {Experimental seismic crosshole setup to investigate the application of rock-physical models at the field scale}, - year = {2024}, - issn = {1942-2156}, - month = apr, - number = {3}, - pages = {MR183--MR195}, - volume = {89}, - creationdate = {2024-05-25T12:16:51}, - doi = {10.1190/geo2022-0625.1}, - modificationdate = {2024-05-25T12:16:51}, - owner = {Guenther.T}, - publisher = {Society of Exploration Geophysicists}, -} - -@Article{Moerbe2024, - author = {M{\"o}rbe, Wiebke and Yogeshwar, Pritam and Tezkan, B{\"u}lent and Kotowski„, Philipp and Thiede„, Anneke and Steuer…, Annika and Rochlitz, Raphael and G{\"u}nther, Thomas and Brauch, Klaus and Becken„, Michael}, - journal = {GEOPHYSICS}, - title = {Large-scale 3D inversion of semi-airborne electromagnetic data - topography and induced polarization effects in a graphite exploration scenario}, - year = {2024}, - issn = {1942-2156}, - month = may, - pages = {1--54}, - creationdate = {2024-05-25T12:17:31}, - doi = {10.1190/geo2023-0471.1}, - modificationdate = {2024-05-25T12:17:31}, - owner = {Guenther.T}, - publisher = {Society of Exploration Geophysicists}, -} - -@Article{Zancanaro2024, - author = {Zancanaro, Ester and Morari, Francesco and Piccoli, Ilaria and Carrera, Alberto and Zoccarato, Claudia and Teatini, Pietro}, - journal = {Hydrological Processes}, - title = {A Novel Technique to Mitigate Saltwater Intrusion: Freshwater Recharge via Drainpipe in Permeable Paleochannels}, - year = {2024}, - issn = {1099-1085}, - month = oct, - number = {10}, - volume = {38}, - doi = {10.1002/hyp.15299}, - publisher = {Wiley}, -} - -@Article{Zhou2024, - author = {Zhou, Sheng and Yang, Yi-Xin and Cao, Jing-Jing and Meng, Long-Long and Cao, Jun-Nan and Zhang, Chi and Zhang, Shuai and Bate, B.}, - journal = {Environmental Research}, - title = {Monitoring of copper adsorption on biochar using spectral induced polarization method}, - year = {2024}, - issn = {0013-9351}, - month = jun, - pages = {118778}, - volume = {251}, - doi = {10.1016/j.envres.2024.118778}, - publisher = {Elsevier BV}, -} - -@Article{Yang2023, - author = {Yang, Yi-Xin and Zhou, Sheng and Luo, Yuan-Yuan and Chen, Jia-Kai and Chen, Ze-Jian and Cao, Jun-Nan and Zhang, Chi and Zhang, Shuai and Zhan, Liang-Tong and Chen, Yun-Min and Bate, Bate}, - journal = {Environmental Geochemistry and Health}, - title = {Monitoring the remediation of groundwater polluted by MSW landfill leachates by activated carbon and zeolite with spectral induced polarization technique}, - year = {2023}, - issn = {1573-2983}, - month = dec, - number = {1}, - volume = {46}, - doi = {10.1007/s10653-023-01796-1}, - publisher = {Springer Science and Business Media LLC}, -} - -@Article{Vella2024, - author = {Vella, Marc-Antoine and Bièvre, Grégory and Delaere, Christophe and Thiesson, Julien and Guérin, Roger and Rivera-Casanovas, Claudia and Guédron, Stéphane}, - journal = {Quaternary Science Reviews}, - title = {The hydraulic network of the pre-Hispanic city of Tiwanaku (Bolivia): New insights from the integration of canal morphology, hydrogeological and palaeoenvironmental data}, - year = {2024}, - issn = {0277-3791}, - month = jan, - pages = {108475}, - volume = {324}, - doi = {10.1016/j.quascirev.2023.108475}, - publisher = {Elsevier BV}, -} - -@Article{Danque2024, - author = {Danque, H.A. and Cannon, K.M.}, - journal = {Icarus}, - title = {Lunar polar volatile remobilization in regolith-filled craters}, - year = {2024}, - issn = {0019-1035}, - month = mar, - pages = {115953}, - volume = {411}, - doi = {10.1016/j.icarus.2024.115953}, - publisher = {Elsevier BV}, -} - -@Article{Molodtsov2024, - author = {Molodtsov, Dmitry and Kiyan, Duygu and Bean, Christopher J}, - journal = {Geophysical Journal International}, - title = {Decoupled joint inversion with variable splitting: example scheme for magnetotelluric, seismic and gravity data}, - year = {2024}, - issn = {1365-246X}, - month = aug, - number = {1}, - pages = {706--724}, - volume = {239}, - doi = {10.1093/gji/ggae292}, - publisher = {Oxford University Press (OUP)}, -} +% Encoding: UTF-8 + +@Article{Coscia2011, + author = {Coscia,I. and Greenhalgh, S. and Linde, N. and Doetsch, J. and Marescot, L. and G{\"u}nther, T. and Green, A.}, + journal = {Geophysics}, + title = {3{D} crosshole apparent resistivity static inversion and monitoring of a coupled river-aquifer system}, + year = {2011}, + number = {2}, + pages = {G49-59}, + volume = {76}, + doi = {10.1190/1.3553003}, + timestamp = {2010.08.09}, +} + +@Article{Guenther2012, + author = {G{\"u}nther, T. and M{\"u}ller-Petke, M.}, + journal = {Hydrology and Earth System Sciences}, + title = {{H}ydraulic properties at the {N}orth {S}ea island of {B}orkum derived from joint inversion of magnetic resonance and electrical resistivity soundings}, + year = {2012}, + number = {9}, + pages = {3279--3291}, + volume = {16}, + doi = {10.5194/hess-16-3279-2012}, + timestamp = {2016.09.14}, +} + +@Article{Costabel2014, + author = {Costabel, S. and G{\"u}nther, T.}, + journal = {Vadose Zone Journal}, + title = {{N}oninvasive {E}stimation of {W}ater {R}etention {P}arameters by {O}bserving the {C}apillary {F}ringe with {M}agnetic {R}esonance {S}ounding}, + year = {2014}, + number = {6}, + pages = {14}, + volume = {13}, + doi = {10.2136/vzj2013.09.0163}, + timestamp = {2014.06.06}, +} + +@Article{Wagner2015, + author = {Wagner, F.M. and G{\"u}nther, T. and Schmidt-Hattenberger, C. and Maurer, H.}, + journal = {Geophysics}, + title = {{C}onstructive optimization of electrode locations for target-focused resistivity monitoring}, + year = {2015}, + number = {2}, + pages = {E29--E40}, + volume = {80}, + doi = {10.1190/geo2014-0214.1}, + timestamp = {2015.01.14}, +} + +@Article{Loewer2016, + author = {Loewer, M. and Igel, J. and Wagner, N.}, + journal = {{IEEE} J. Sel. Top. Appl. Earth Observations Remote Sensing}, + title = {{S}pectral {D}ecomposition of {S}oil {E}lectrical and {D}ielectric {L}osses and {P}rediction of {I}n {S}itu {GPR} {P}erformance}, + year = {2016}, + number = {1}, + pages = {212--230}, + volume = {9}, + doi = {10.1109/jstars.2015.2424152}, + publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, + timestamp = {2016.09.14}, +} + +@InProceedings{Igel2016, + author = {Igel, J. and Stadler, S. and G{\"u}nther, T.}, + journal = {Ext. Abstr., SAGEEP, Denver, USA}, + title = {{H}igh-resolution investigation of the capillary transition zone and its influence on {GPR} signatures}, + year = {2016}, + doi = {10.1109/icgpr.2016.7572603}, + timestamp = {2016.06.28}, +} + +@Article{Costabel2016, + author = {Costabel, S. and G{\"u}nther, T. and Dlugosch, R. and M{\"u}ller-Petke, M.}, + journal = {Geophysics}, + title = {{T}orus-nuclear magnetic resonance: {Q}uasicontinuous airborne magnetic resonance profiling by using a helium-filled balloon}, + year = {2016}, + month = {jun}, + number = {4}, + pages = {WB119--WB129}, + volume = {81}, + doi = {10.1190/geo2015-0467.1}, + publisher = {Society of Exploration Geophysicists}, + timestamp = {2016.09.14}, +} + +@Article{Guenther2016, + author = {G{\"u}nther, T. and Martin, T.}, + journal = {Journal of Applied Geophysics}, + title = {{S}pectral two-dimensional inversion of frequency-domain induced polarisation data from a mining slag heap}, + year = {2016}, + pages = {436-448}, + volume = {135}, + doi = {10.1016/j.jappgeo.2016.01.008}, + timestamp = {2015.12.21}, +} + +@Article{Hupfer2016, + author = {Hupfer, S. and Martin, T. and Weller, A. and G\"{u}nther, T. and Kuhn, K. and Ngninjio, V.D.N. and Noell, U.}, + title = {{P}olarization effects of unconsolidated sulphide-sand-mixtures}, + journal = {Journal of Applied Geophysics}, + year = {2016}, + volume = {135}, + pages = {456-465}, + month = {dec}, + doi = {10.1016/j.jappgeo.2015.12.003}, + publisher = {Elsevier {BV}}, + timestamp = {2016.12.16}, +} + +@Article{Loewer2017, + author = {Loewer, M. and G\"{u}nther, T. and Igel, J. and Kruschwitz, S. and Martin, T. and Wagner, N.}, + journal = {Geophysical Journal International}, + title = {Ultra-broad-band electrical spectroscopy of soils and sediments{\textemdash}a combined permittivity and conductivity model}, + year = {2017}, + month = {jun}, + number = {3}, + pages = {1360--1373}, + volume = {210}, + doi = {10.1093/gji/ggx242}, + publisher = {Oxford University Press ({OUP})}, + timestamp = {2017.07.27}, +} + +@Article{Ronczka2017, + author = {Ronczka, M. and Hellman, K. and G\"{u}nther, T. and Wis{\'{e}}n, R. and Dahlin, T.}, + journal = {Solid Earth}, + title = {Electric resistivity and seismic refraction tomography: a challenging joint underwater survey at \"{A}sp\"{o} Hard Rock Laboratory}, + year = {2017}, + month = {jun}, + number = {3}, + pages = {671--682}, + volume = {8}, + doi = {10.5194/se-8-671-2017}, + publisher = {Copernicus {GmbH}}, + timestamp = {2017.07.27}, +} + +@Article{Hellman2017, + author = {Hellman, K. and Ronczka, M. and G\"{u}nther, T. and Wennermark, M. and R\"{u}cker, C. and Dahlin, T.}, + journal = {Journal of Applied Geophysics}, + title = {Structurally coupled inversion of {ERT} and refraction seismic data combined with cluster-based model integration}, + year = {2017}, + month = {aug}, + pages = {169--181}, + volume = {143}, + doi = {10.1016/j.jappgeo.2017.06.008}, + publisher = {Elsevier {BV}}, + timestamp = {2017.07.27}, +} + +@Article{Bergmann2017, + author = {Bergmann, P. and Schmidt-Hattenberger, C. and Labitzke, T. and Wagner, F.M. and Just, A. and Flechsig, C. and Rippe, D.}, + title = {Fluid injection monitoring using electrical resistivity tomography - five years of CO2 injection at Ketzin, Germany}, + journal = {Geophysical Prospecting}, + year = {2017}, + volume = {65}, + pages = {859-875}, + issn = {1365-2478}, + doi = {10.1111/1365-2478.12426}, + publisher = {Wiley Online Library}, + timestamp = {2016.08.24}, +} + +@Article{Boerner2017, + author = {B{\"o}rner, F. and M{\"u}ller-Huber, E. and Branka, D. and R{\"u}cker, C.}, + journal = {Near Surface Geophysics}, + title = {The effect of compaction on complex electrical resistivity of shaly sands}, + year = {2017}, + number = {6}, + pages = {633--643}, + volume = {15}, + doi = {10.3997/1873-0604.2017056}, + publisher = {European Association of Geoscientists \& Engineers}, +} + +@Article{Wagner2018, + author = {Wagner, F.M. and Wiese, B.}, + title = {Fully coupled inversion on a multi-physical reservoir model - Part II: The Ketzin CO2 storage reservoir}, + journal = {International Journal of Greenhouse Gas Control}, + year = {2018}, + volume = {75}, + pages = {273-281}, + doi = {10.1016/j.ijggc.2018.04.009}, + timestamp = {2018.02.18}, +} + +@Article{Wiese2018, + author = {Wiese, B. and Wagner, F.M. and Norden, B. and Maurer, H. and Schmidt-Hattenberger, C.}, + title = {Fully coupled inversion on a multi-physical reservoir model - Part I: Theory and concept}, + journal = {International Journal of Greenhouse Gas Control}, + year = {2018}, + volume = {75}, + pages = {262-272}, + doi = {10.1016/j.ijggc.2018.05.013}, + timestamp = {2018.02.18}, +} + +@Article{Watlet2018, + author = {Watlet, A. and Kaufmann, O. and Triantafyllou, A. and Poulain, Am. and Chambers, J. and Meldrum, P. and Wilkinson, P. and Hallet, V. and Quinif, Y. and van~Ruymbeke, M. and van~Camp, M.}, + journal = {Hydrology and Earth System Sciences}, + title = {Imaging groundwater infiltration dynamics in the karst vadose zone with long-term ERT monitoring}, + year = {2018}, + number = {2}, + pages = {1563--1592}, + volume = {22}, + doi = {10.5194/hess-22-1563-2018}, + publisher = {European Geosciences Union}, +} + +@Article{Jordi2018, + author = {Jordi, C. and Doetsch, J. and G{\"u}nther, T. and Schmelzbach, C. and Robertsson, J. O.A.}, + journal = {Geophysical Journal International}, + title = {Geostatistical regularization operators for geophysical inverse problems on irregular meshes}, + year = {2018}, + number = {2}, + pages = {1374--1386}, + volume = {213}, + doi = {10.1093/gji/ggy055}, + publisher = {Oxford University Press}, +} + +@Article{Rossi2018, + author = {Rossi, M. and Dahlin, T. and Olsson, P.-I. and G{\"u}nther, T.}, + journal = {Near Surface Geophysics}, + title = {Data acquisition, processing and filtering for reliable 3D resistivity and time-domain induced polarisation tomography in an urban area: field example of Vinsta, Stockholm}, + year = {2018}, + number = {3}, + pages = {220--229}, + volume = {16}, + doi = {10.3997/1873-0604.2018014}, + publisher = {European Association of Geoscientists \& Engineers}, +} + +@Article{Ronczka2018, + author = {Ronczka, M. and Wis{\'e}n, R. and Dahlin, T.}, + journal = {Near Surface Geophysics}, + title = {Geophysical pre-investigation for a Stockholm tunnel project: joint inversion and interpretation of geoelectric and seismic refraction data in an urban environment}, + year = {2018}, + number = {3}, + pages = {258--268}, + volume = {16}, + doi = {10.3997/1873-0604.2018009}, + publisher = {European Association of Geoscientists \& Engineers}, +} + +@Article{Skibbe2018, + author = {Skibbe, N. and G{\"u}nther, T. and M{\"u}ller-Petke, M.}, + journal = {Geophysics}, + title = {Structurally coupled cooperative inversion of magnetic resonance with resistivity soundings}, + year = {2018}, + number = {6}, + pages = {JM51--JM63}, + volume = {83}, + doi = {10.1190/geo2018-0046.1}, + publisher = {Society of Exploration Geophysicists and American Association of Petroleum~…}, +} + +@Article{Wunderlich2018, + author = {Wunderlich, T. and Fischer, P. and Wilken, D. and Hadler, H. and Erkul, E. and Mecking, R. and G{\"u}nther, T. and Heinzelmann, M. and V{\"o}tt, A. and Rabbel, W.}, + journal = {Geophysics}, + title = {Constraining electric resistivity tomography by direct push electric conductivity logs and vibracores: An exemplary study of the Fiume Morto silted riverbed (Ostia Antica, western Italy)}, + year = {2018}, + number = {3}, + pages = {B87--B103}, + volume = {83}, + doi = {10.1190/geo2016-0660.1}, + publisher = {Society of Exploration Geophysicists}, +} + +@Article{Wagner2019, + author = {Wagner, F.M. and Mollaret, C. and G{\"u}nther, T. and Kemna, A. and Hauck, C.}, + title = {Quantitative imaging of water, ice, and air in permafrost systems through petrophysical joint inversion of seismic refraction and electrical resistivity data}, + journal = {Geophysical Journal International}, + year = {2019}, + volume = {219}, + number = {3}, + pages = {1866--1875}, + doi = {10.1093/gji/ggz402}, +} + +@Article{Rochlitz2019, + author = {Rochlitz, R. and Skibbe, N. and G{\"u}nther, T.}, + journal = {Geophysics}, + title = {custEM: Customizable finite-element simulation of complex controlled-source electromagnetic data}, + year = {2019}, + number = {2}, + pages = {F17--F33}, + volume = {84}, + doi = {10.1190/geo2018-0208.1}, + publisher = {Society of Exploration Geophysicists}, +} + +@Article{Pasquale2019, + author = {de~Pasquale, G. and Linde, N. and Greenwood, A.}, + journal = {Journal of Applied Geophysics}, + title = {Joint probabilistic inversion of DC resistivity and seismic refraction data applied to bedrock/regolith interface delineation}, + year = {2019}, + pages = {103839}, + volume = {170}, + doi = {10.1016/j.jappgeo.2019.103839}, + publisher = {Elsevier}, +} + +@Article{Nickschick2019, + author = {Nickschick, T. and Flechsig, C. and Mrlina, J. and Oppermann, F.k and L{\"o}big, F. and G{\"u}nther, T.}, + journal = {Solid Earth}, + title = {Large-scale electrical resistivity tomography in the Cheb Basin (Eger Rift) at an International Continental Drilling Program (ICDP) monitoring site to image fluid-related structures}, + year = {2019}, + number = {6}, + pages = {1951--1969}, + volume = {10}, + doi = {10.5194/se-10-1951-2019}, + publisher = {Copernicus GmbH}, +} + +@Article{Leger2019, + author = {L{\'e}ger, E. and Dafflon, B. and Robert, Y.}, + journal = {The Cryosphere}, + title = {A distributed temperature profiling method for assessing spatial variability in ground}, + year = {2019}, + pages = {11}, + volume = {13}, + doi = {10.5194/tc-13-2853-2019}, +} + +@Article{Assouline2019, + author = {Assouline, D. and Mohajeri, N. and Gudmundsson, A. and Scartezzini, J.-L.}, + journal = {Geothermal Energy}, + title = {A machine learning approach for mapping the very shallow theoretical geothermal potential}, + year = {2019}, + number = {1}, + pages = {19}, + volume = {7}, + doi = {10.1186/s40517-019-0135-6}, + publisher = {Springer}, +} + +@Article{LopezAlvis2019, + author = {Lopez-Alvis, J. and Hermans, T. and Nguyen, F.}, + journal = {Advances in Water Resources}, + title = {A cross-validation framework to extract data features for reducing structural uncertainty in subsurface heterogeneity}, + year = {2019}, + pages = {103427}, + volume = {133}, + doi = {10.1016/j.advwatres.2019.103427}, +} + +@Article{Pasquale2019a, + author = {de~Pasquale, G. and Linde, N. and Doetsch, J. and Holbrook, W.S.}, + journal = {Geophysical Journal International}, + title = {Probabilistic inference of subsurface heterogeneity and interface geometry using geophysical data}, + year = {2019}, + doi = {10.1093/gji/ggz055}, +} + +@Article{Ochs2020, + author = {Ochs, J. and Klitzsch, N.}, + journal = {Journal of Applied Geophysics}, + title = {Considerations regarding small-scale surface and borehole-to-surface electrical resistivity tomography}, + year = {2020}, + pages = {103862}, + volume = {172}, + doi = {10.1016/j.jappgeo.2019.103862}, + publisher = {Elsevier}, +} + +@Article{Skibbe2020, + author = {Skibbe, N. and Rochlitz, R. and G{\"u}nther, T. and M{\"u}ller-Petke, M.}, + journal = {Geophysics}, + title = {COMET: An open-source toolbox for Surface NMR}, + year = {2020}, + number = {3}, + pages = {1--56}, + volume = {85}, + doi = {10.1190/geo2019-0484.1}, +} + +@Article{Jordi2020, + author = {Jordi, C. and Doetsch, J. and G{\"u}nther, T. and Schmelzbach, C. and Maurer, H. and Robertsson, J. O.A.}, + journal = {Geophysical Journal International}, + title = {Structural joint inversion on irregular meshes}, + year = {2020}, + number = {3}, + pages = {1995--2008}, + volume = {220}, + doi = {10.1093/gji/ggz550}, + publisher = {Oxford University Press}, +} + +@Article{Whiteley2020, + author = {Whiteley, J.S. and Chambers, J.E. and Uhlemann, S. and Boyd, J. and Cimpoiasu, M.O. and Holmes, J.L. and Inauen, C.M. and Watlet, A. and Hawley-Sibbett, L.R. and Sujitapan, C. and others}, + journal = {Engineering Geology}, + title = {Landslide monitoring using seismic refraction tomography--The importance of incorporating topographic variations}, + year = {2020}, + pages = {105525}, + doi = {10.1016/j.enggeo.2020.105525}, + publisher = {Elsevier}, +} + +@Article{Clement2020, + author = {Cl{\'e}ment, R. and P{\"a}rn, J. and Maddison, M. and Henine, H. and Chaumont, C. and Tournebize, J. and Uri, V. and Espenberg, M. and G{\"u}nther, T. and Mander, {\"U}.}, + journal = {Journal of Applied Geophysics}, + title = {Frequency-domain electromagnetic induction for upscaling greenhouse gas fluxes in two hemiboreal drained peatland forests}, + year = {2020}, + pages = {103944}, + doi = {10.1016/j.jappgeo.2020.103944}, + publisher = {Elsevier}, +} + +@Article{Palacios2020, + author = {Palacios, A. and Ledo, J. J. and Linde, N. and Luquot, L. and Bellmunt, F. and Folch, A. and Marcuello, A. and Queralt, P. and Pezard, P. A. and Mart\'{\i}nez, L. and Bosch, D. and Carrera, J.}, + journal = {Hydrology and Earth System Sciences}, + title = {Time-lapse cross-hole electrical resistivity tomography ({CHERT}) for monitoring seawater intrusion dynamics in a Mediterranean aquifer}, + year = {2020}, + number = {4}, + pages = {2121--2139}, + volume = {24}, + doi = {10.5194/hess-24-2121-2020}, +} + +@Article{Klingler2020, + author = {Klingler, S. and Leven, C. and Cirpka, O.A. and Dietrich, P.}, + title = {Anomaly effect-driven optimization of direct-current geoelectric mapping surveys in large areas}, + journal = {Journal of Applied Geophysics}, + year = {2020}, + volume = {176}, + pages = {104002}, + doi = {10.1016/j.jappgeo.2020.104002}, +} + +@Article{Fediuk2020, + author = {Fediuk, A. and Wilken, D. and Wunderlich, T. and Rabbel, W.}, + title = {Physical Parameters and Contrasts of Wooden Objects in Lacustrine Environment: Ground Penetrating Radar and Geoelectrics}, + journal = {Geosciences}, + year = {2020}, + volume = {10}, + number = {4}, + issn = {2076--3263}, + article-number = {146}, + doi = {10.3390/geosciences10040146}, +} + +@Article{Peruzzo2020, + author = {Peruzzo, L. and Chou, C. and Wu, Y. and Schmutz, M. and Mary, B. and Wagner, F.M. and Petrov, P. and Newman, G. and Blancaflor, E.B. and Liu, X. and Ma, X. and Hubbard, S.}, + title = {Imaging of plant current pathways for non-invasive root Phenotyping using a newly developed electrical current source density approach}, + journal = {Plant and Soil}, + year = {2020}, + doi = {10.1007/s11104-020-04529-w}, +} + +@Article{Blazevic2020, + author = {Blazevic, L. A. and Bodet, L. and Pasquet, S. and Linde, N. and Jougnot, D. and Longuevergne, L.}, + title = {Time-Lapse Seismic and Electrical Monitoring of the Vadose Zone during A Controlled Infiltration Experiment at the Ploemeur Hydrological Observatory, France}, + journal = {Water}, + year = {2020}, + volume = {12}, + number = {5}, + issn = {2073--4441}, + article-number = {1230}, + doi = {10.3390/w12051230}, +} + +@Article{Miller2020, + author = {Miller, C. A. and Christenson, B. W. and Byrdina, S. and Vandemeulebrouck, J. and Brakenrig, T. and Britten, K. and Shanks, J. and Epstein, G.}, + journal = {Journal of Volcanology and Geothermal Research}, + title = {Snapshot of a magmatic/hydrothermal system from electrical resistivity tomography and fumarolic composition, Whakaari/White Island, New Zealand}, + year = {2020}, + issn = {0377-0273}, + pages = {106909}, + doi = {10.1016/j.jvolgeores.2020.106909}, +} + +@Article{Folch2020, + author = {Folch, A. and del Val, L. and Luquot, L. and Martínez-Pérez, L. and Bellmunt, F. and Le Lay, H. and Rodellas, V. and Ferrer, N. and Palacios, A. and Fernández, S. and Marazuela, M.A. and Diego-Feliu, M. and Pool, M. and Goyetche, T. and Ledo, J. and Pezard, P. and Bour, O. and Queralt, P. and Marcuello, A. and Garcia-Orellana, J. and Saaltink, M.W. and Vázquez-Suñé, E. and Carrera, J.}, + journal = {Journal of Hydrology}, + title = {{Combining fiber optic DTS, cross-hole ERT and time-lapse induction logging to characterize and monitor a coastal aquifer}}, + year = {2020}, + pages = {125050}, + volume = {588}, + doi = {10.1016/j.jhydrol.2020.125050}, + keywords = {Cross hole electrical resistivity tomography, Fiber optic distributed temperature sensing, Formation electrical conductivity, Sea water intrusion, Submarine groundwater discharge, Alluvial aquifer}, +} + +@Article{Costall2020, + author = {Costall, A. and Harris, B. and Teo, B. and Schaa, R. and Wagner, F. M. and Pigois, J.-P.}, + journal = {Scientific Reports}, + title = {Groundwater Throughflow and Seawater Intrusion in High Quality Coastal Aquifers}, + year = {2020}, + pages = {9866}, + volume = {10}, + doi = {10.1038/s41598-020-66516-6}, +} + +@Article{Martin2020, + author = {Martin, T. and G{\"u}nther, T. and Flores Orozco, A. and Dahlin, T.}, + journal = {Journal of Applied Geophysics}, + title = {Evaluation of spectral induced polarization field measurements in time and frequency domain}, + year = {2020}, + month = {sep}, + pages = {104141}, + volume = {180}, + doi = {10.1016/j.jappgeo.2020.104141}, + publisher = {Elsevier {BV}}, +} + +@Article{Ronczka2020, + author = {Ronczka, M. and G{\"u}nther, T. and Grinat, M. and Wiederhold, H.}, + journal = {Near Surface Geophysics}, + title = {Monitoring freshwater-saltwater interfaces with {SAMOS} - installation effects on data and inversion}, + year = {2020}, + month = {jul}, + number = {4}, + pages = {369--383}, + volume = {18}, + doi = {10.1002/nsg.12115}, + publisher = {Wiley}, +} + +@Article{Rao2020, + author = {Rao, S. and Lesparre, N. and Flores Orozco, A. and Wagner, F. and Javaux, M.}, + journal = {Plant and Soil}, + title = {Imaging plant responses to water deficit using electrical resistivity tomography}, + year = {2020}, + doi = {10.1007/s11104-020-04653-7}, +} + +@Article{Mollaret2020, + author = {Mollaret, C. and Wagner, F. and Hilbich, C. and Scapozza, C. and Hauck, C.}, + journal = {Front. Earth Sci.}, + title = {Petrophysical joint inversion applied to alpine permafrost field sites to image subsurface ice, water, air and rock contents}, + year = {2020}, + pages = {85}, + volume = {8}, + doi = {10.3389/feart.2020.00085}, + url = {https://www.frontiersin.org/articles/10.3389/feart.2020.00085/pdf}, +} + +@Article{Raab2020, + author = {Raab, T. and Weinzierl, W. and Wiese, B. and Rippe, D. and Schmidt-Hattenberger, C.}, + journal = {Advances in Geosciences}, + title = {{Development of an Electrical Resistivity Tomography Monitoring Concept for the Svelvik CO2 Field Lab, Norway}}, + year = {2020}, + pages = {41--53}, + volume = {54}, + doi = {10.5194/adgeo-54-41-2020}, + url = {https://adgeo.copernicus.org/articles/54/41/2020/}, +} + +@Article{Enemark2020, + author = {Enemark, T. and Peeters, L. and Mallants, D. and Flinchum, B. and Batelaan, O.}, + journal = {Water Resources Research}, + title = {A Systematic Approach to Hydrogeological Conceptual Model Testing, Combining Remote Sensing and Geophysical Data}, + year = {2020}, + number = {8}, + pages = {e2020WR027578}, + volume = {56}, + doi = {10.1029/2020WR027578}, + url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2020WR027578}, +} + +@Article{FernandezVisentini2020, + author = {{Fernandez Visentini}, A. and Linde, N. and {Le Borgne}, T. and Dentz, M.}, + journal = {Advances in Water Resources}, + title = {Inferring geostatistical properties of hydraulic conductivity fields from saline tracer tests and equivalent electrical conductivity time-series}, + year = {2020}, + pages = {103758}, + volume = {146}, + doi = {10.1016/j.advwatres.2020.103758}, + url = {http://www.sciencedirect.com/science/article/pii/S0309170820306618}, +} + +@Article{Pacheco2020, + author = {Pacheco, M. and Plattner, A. M. and Stock, G. M. and Rood, D. H. and Pluhar, C. J.}, + journal = {Frontiers in Earth Science}, + title = {Surface Exposure Dating and Geophysical Tomography of the Royal Arches Meadow Rock Avalanche, Yosemite Valley, California}, + year = {2020}, + pages = {372}, + volume = {8}, + doi = {10.3389/feart.2020.00372}, + url = {https://www.frontiersin.org/article/10.3389/feart.2020.00372}, +} + +@Article{Saneiyan2021, + author = {Saneiyan, S. and Ntarlagiannis, D. and Colwell, F.}, + journal = {Geophysical Journal International}, + title = {Complex conductivity signatures of microbial induced calcite precipitation, field and laboratory scales}, + year = {2021}, + pages = {1811--1824}, + volume = {224}, + doi = {10.1093/gji/ggaa510}, + url = {https://doi.org/10.1093/gji/ggaa510}, +} + +@Article{Urruela2020, + author = {Urruela, A. and Rivero, L. and Casas, A. and Garcia-Artigas, R. and Sendr\'{o}s, A. and Lovera, R. and Himi, M.}, + journal = {Journal of Applied Geophysics}, + title = {Improving the resolution of investigation using {ERT} instruments with a reduced number of electrodes}, + year = {2020}, + pages = {104239}, + doi = {10.1016/j.jappgeo.2020.104239}, + url = {http://www.sciencedirect.com/science/article/pii/S0926985120306224}, +} + +@Article{Flinchum2020, + author = {Flinchum, B. A. and Banks, E. and Hatch, M. and Batelaan, O. and Peeters, L. J. M. and Pasquet, S.}, + journal = {Hydrology and Earth System Sciences}, + title = {Identifying recharge under subtle ephemeral features in a flat-lying semi-arid region using a combined geophysical approach}, + year = {2020}, + number = {9}, + pages = {4353--4368}, + volume = {24}, + doi = {10.5194/hess-24-4353-2020}, + url = {https://hess.copernicus.org/articles/24/4353/2020/}, +} + +@article{Flinchum2022, + doi = {10.3389/frwa.2021.772185}, + url = {https://doi.org/10.3389/frwa.2021.772185}, + year = {2022}, + publisher = {Frontiers Media {SA}}, + volume = {3}, + author = {Flinchum, B. A. and Holbrook, W. S. and Carr, B. J.}, + title = {What Do P-Wave Velocities Tell Us About the Critical Zone?}, + journal = {Frontiers in Water} +} + +@Article{Kordjazi2021, + author = {Kordjazi, A. and Coe, J. T. and Afanasiev, M.}, + journal = {Journal of Nondestructive Evaluation}, + title = {Nondestructive Evaluation of Drilled Shaft Construction Anomalies Using Full Waveform Tomography of Simulated Crosshole Measurements}, + year = {2021}, + number = {3}, + volume = {40}, + doi = {10.1007/s10921-020-00728-8}, +} + +@Article{Buecker2021, + author = {B{\"u}cker, M. and Flores Orozco, A. and Gallistl, J. and Steiner, M. and Aigner, L. and Hoppenbrock, J. and Glebe, R. and Morales Barrera, W. and Pita de la Paz, C. and Garc\'{\i}a Garc\'{\i}a, C. E. and Razo P\'erez, J. A. and Buckel, J. and H{\"o}rdt, A. and Schwalb, A. and P{\'e}rez, L.}, + journal = {Solid Earth}, + title = {Integrated land and water-borne geophysical surveys shed light on the sudden drying of large karst lakes in southern Mexico}, + year = {2021}, + number = {2}, + pages = {439-461}, + volume = {12}, + doi = {10.5194/se-12-439-2021}, + url = {https://se.copernicus.org/articles/12/439/2021/}, +} + +@Article{Steiner2021, + author = {Steiner, M. and Wagner, F. M. and Maierhofer, T. and Sch{\"o}ner, W. Flores Orozco, A.}, + journal = {Geophysics}, + title = {Improved estimation of ice and water contents in Alpine permafrost through constrained petrophysical joint inversion: {The Hoher Sonnblick} case study}, + year = {2021}, + doi = {10.1190/geo2020-0592.1}, +} + +@Article{Skibbe2021, + author = {Skibbe, N. and G{\"u}nther, T. and M{\"u}ller-Petke, M.}, + journal = {Geophysics}, + title = {Improved hydrogeophysical imaging by structural coupling of two-dimensional magnetic resonance and electrical resistivity tomography}, + year = {2021}, + doi = {10.1190/geo2020-0593.1}, +} + +@Article{Flinchum2021, + author = {Flinchum, B. and Peeters, L. and Munday, T. and Cahill, K.}, + journal = {Geophysics}, + title = {Improving the hydrogeologic conceptualization of a remote semiarid palaeovalley groundwater system using airborne electromagnetics, seismic refraction and reflection, and downhole nuclear magnetic resonance}, + year = {2021}, + doi = {10.1190/geo2020-0614.1}, +} + +@Article{Sabor2021, + author = {Sabor, K. and Jougnot, D. and Guerin, R. and Steck, B. and Henault, J.-M. and Apffel, L. and Vautrin, D.}, + journal = {Geophysical Journal International}, + title = {A data mining approach for improved interpretation of {ERT} inverted sections using the {DBSCAN} clustering algorithm}, + year = {2021}, + doi = {10.1093/gji/ggab023}, +} + +@Article{Martin2021, + author = {Martin, T. and G\"{u}nther, T. and Weller, A. and Kuhn, K.}, + journal = {Journal of Applied Geophysics}, + title = {Classification of slag material by spectral induced polarization laboratory and field measurements}, + year = {2021}, + doi = {10.1016/j.jappgeo.2021.104439}, +} + +@Article{Nivorlis2021, + author = {Nivorlis, A. and Rossi, M. and Dahlin, T.}, + title = {Temporal filtering and time-lapse inversion of geoelectrical data for long-term monitoring with application to a chlorinated hydrocarbon contaminated site}, + journal = {Geophysical Journal International}, + year = {2021}, + month = {10}, + volume = {228}, + number = {3}, + issn = {0956-540X}, + doi = {10.1093/gji/ggab422}, +} + +@Article{Rochlitz2021, + author = {Rochlitz, R. and Seidel, M. and B{\"o}rner, R.-U.}, + title = {Evaluation of three approaches for simulating 3-D time-domain electromagnetic data}, + journal = {Geophysical Journal International}, + volume = {227}, + number = {3}, + pages = {1980-1995}, + year = {2021}, + issn = {0956-540X}, + doi = {10.1093/gji/ggab302}, +} + +@Article{Miltenberger2021, + author = {Miltenberger, A and Uhlemann, S. and Mukerji, T. and Williams, K. and Dafflon, B. and Wang, L. and Wainwright, H.}, + title = {Probabilistic Evaluation of Geoscientific Hypotheses With Geophysical Data: Application to Electrical Resistivity Imaging of a Fractured Bedrock Zone}, + journal = {Journal of Geophysical Research: Solid Earth}, + year = {2021}, + volume = {126}, + number = {9}, + pages = {e2021JB021767}, + doi = {10.1029/2021JB021767}, + +} +@Article{Jiang2021, + author = {Jiang, L. and Tian, G. and Wang, B. and Guo, X. and He, X and Zou, A. and Chen, H and Yang, T. and El-Raouf, A. A.}, + title = {Application of three-dimensional electrical resistivity tomography in urban zones by arbitrary electrode distribution survey design}, + journal = {Journal of Applied Geophysics}, + volume = {194}, + pages = {104460}, + year = {2021}, + issn = {0926-9851}, + doi = {10.1016/j.jappgeo.2021.104460}, +} + +@Article{Whiteley2021, + author = {Whiteley, J. and Watlet, A. and Uhlemann, S. and Wilkinson, P. and Boyd, J. and Jordan, C. and Kendall, J. and Chambers, J.}, + journal = {Engineering Geology}, + title = {Rapid characterisation of landslide heterogeneity using unsupervised classification of electrical resistivity and seismic refraction surveys}, + year = {2021}, + volume = {290}, + pages = {106189}, + issn = {0013-7952}, + doi = {10.1016/j.enggeo.2021.106189}, +} + +@Article{Visentini2021, + author = {Fernandez Visentini, A. and de Anna, P. and Jougnot, D. and Le Borgne, T. and M{\'{e}}heust, Y. and Linde, N.}, + title = {Electrical Signatures of Diffusion-Limited Mixing: Insights from a Milli-fluidic Tracer Experiment}, + journal = {Transport in Porous Media}, + year = {2021}, + publisher = {Springer Science and Business Media {LLC}}, + doi = {10.1007/s11242-021-01607-0}, +} + + +@Article{Chavez2021, + author = {Chavez Olalla, J. and Winkels, T. G. and Ngan-Tillard, D. J. M. and Heimovaara, T. J.}, + title = {Geophysical tomography as a tool to estimate the geometry of soil layers: relevance for the reliability assessment of dikes}, + journal = {Georisk: Assessment and Management of Risk for Engineered Systems and Geohazards}, + year = {2021}, + pages = {1--21}, + publisher = {Taylor & Francis}, + doi = {10.1080/17499518.2021.1971252}, + url = {https://doi.org/10.1080/17499518.2021.1971252}, +} + +@Article{Jiang2021b, + author = {Jiang, L. and Wang, B. and Tian, G. and He, X. and Zou, A. and Guo, X. and Chen, H. and El-Raouf, A. A.}, + title = {Strategy for Optimization of Arbitrary Electrode Distribution for 3D Electrical Resistivity Tomography in Urban Zones}, + journal = {Pure and Applied Geophysics}, + year = {2021}, + publisher = {Springer Science and Business Media {LLC}}, + volume = {178}, + number = {9}, + pages = {3601--3618}, + doi = {10.1007/s00024-021-02848-2}, + url = {https://doi.org/10.1007/s00024-021-02848-2}, +} + +@Article{Norooz2021, + author = {Norooz, R. and Olsson, P. I. and Dahlin, T. and G\"{u}nther, T and Bernstone, C.}, + title = {A geoelectrical pre-study of \"{A}lvkarleby test embankment dam: 3D forward modelling and effects of structural constraints on the 3D inversion model of zoned embankment dams}, + journal = {Journal of Applied Geophysics}, + year = {2021}, + volume = {191}, + pages = {104355}, + issn = {0926-9851}, + doi = {10.1016/j.jappgeo.2021.104355}, +} + +@Article{Bievre2021, + author = {Bi{\`{e}}vre, G and Jongmans, D. and Lebourg, T. and Carri{\`{e}}re, S.}, + title = {Electrical resistivity monitoring of an earthslide with electrodes located outside the unstable zone (Pont-Bourquin landslide, Swiss Alps)}, + journal = {Near Surface Geophysics}, + month = {apr}, + year = {2021}, + publisher = {Wiley}, + volume = {19}, + number = {2}, + pages = {225--239}, + doi = {10.1002/nsg.12145}, +} + +@Article{Wellmann2022, + doi = {10.1130/GES02455.1}, + year = {2022}, + publisher = {Geological Society of America}, + author = {Wellmann, F. and Virgo, S. and Escallon, D. and de la Varga, M. and J\"{u}stel, A. and Wagner, F. and Kowalski, J. and Zhao, H. and Fehling, R. and Chen, Q.}, + title = {{Open AR-Sandbox}: A haptic interface for geoscience education and outreach}, + journal = {Geosphere} +} + +@Article{Ochs2021, + author = {Ochs, J. and Klitzsch, N. and Wagner, F. M.}, + doi = {10.1016/j.jappgeo.2022.104530}, + year = {2022}, + publisher = {Elsevier {BV}}, + volume = {197}, + pages = {104530}, + journal = {Journal of Applied Geophysics}, + title = {Mitigation of installation-related effects for small-scale borehole-to-surface ERT}, +} + +@Article{Guedes2022, + doi = {10.1016/j.cageo.2021.105020}, + year = {2022}, + publisher = {Elsevier {BV}}, + volume = {159}, + pages = {105020}, + author = {Jos{\'{e}}, V. and Guedes C. B. and Maciel, A. and Rocha, M. P.}, + title = {Refrapy: A Python program for seismic refraction data analysis}, + journal = {Computers {\&} Geosciences} +} + +@Article{Doyoro2022, + doi = {10.1186/s40562-022-00214-1}, + year = {2022}, + publisher = {Springer Science and Business Media {LLC}}, + volume = {9}, + number = {1}, + author = {Doyoro, Y. G. and Chang, P.-Y. and Puntu, J. M. and Lin, D.-L. and Huu, T. V. and Rahmalia, D. A. and Shie, M.-S.}, + title = {A review of open software resources in python for electrical resistivity modelling}, + journal = {Geoscience Letters} +} + +@Article{ArboledaZapata2022, + doi = {10.1016/j.jappgeo.2021.104512}, + year = {2022}, + publisher = {Elsevier {BV}}, + volume = {196}, + pages = {104512}, + author = {Arboleda-Zapata, M. and Guillemoteau, J. and Tronicke, J.}, + title = {A comprehensive workflow to analyze ensembles of globally inverted 2D electrical resistivity models}, + journal = {Journal of Applied Geophysics} +} + +@Article{Herring2022, + doi = {10.1002/ppp.2141}, + year = {2022}, + author = {Herring, T. and Lewkowicz, A. G.}, + title = {A systematic evaluation of electrical resistivity tomography for permafrost interface detection using forward modeling}, + journal = {Permafrost and Periglacial Processes} +} + +@article{Carrier2022, + title={Damage assessment of supporting pillars in an underground cave using joint inversion of electrical resistivity and {P}-wave velocity, {B}urgundy ({F}rance)}, + author={Carrier, A. and Bottelin, P. and Fabre, L. and Mathy, A.}, + journal={Pure and Applied Geophysics}, + volume={179}, + number={1}, + pages={45--67}, + year={2022}, + doi={10.1007/s00024-021-02921-w}, + publisher={Springer} +} + +@Article{gruenenbaum2023JoH, + author = {Gr\"{u}nenbaum, G\"{u}nther, T. and Greskowiak, J. and Vienken, T. and M\"{u}ller-Petke, M. and Massmann, G.}, + journal = {Journal of Hydrology}, + title = {Salinity distribution in the subterranean estuary of a meso-tidal high-energy beach characterized by {E}lectrical {R}esistivity {T}omography and direct push technology}, + year = {2023}, + pages = {129074}, + volume = {617}, + doi = {10.1016/j.jhydrol.2023.129074}, + publisher = {Elsevier {BV}}, +} + +@Article{rochlitz2023GJI, + author = {Rochlitz, R. and Becken, M. and G\"{u}nther, T.}, + journal = {Geophysical Journal International}, + title = {Three-dimensional inversion of semi-airborne electromagnetic data with a second-order finite-element forward solver}, + year = {2023}, + number = {1}, + pages = {528--545}, + volume = {234}, + doi = {10.1093/gji/ggad056}, + publisher = {Oxford University Press ({OUP})}, +} + +@Article{Moser2023, + author = {Moser, C. and Binley, A. and Flores Orozco, A.}, + doi = {10.1016/j.wasman.2023.07.006}, + issn = {0956-053X}, + journal = {Waste Management}, + pages = {208-222}, + title = {3D electrode configurations for spectral induced polarization surveys of landfills}, + volume = {169}, + year = {2023}, +} + + +@Article{su151813574, + abstract = {Seismic characterization of landslides offers the potential for developing high-resolution models on subsurface shear-wave velocity profile. However, seismic methods based on reflection processing are challenging to apply in such scenarios as a consequence of the disturbance to the often well-defined structural and stratigraphic layering by the landslide process itself. We evaluate the use of alternative seismic characterization methods based on elastic full waveform inversion (E-FWI) to probe the subsurface of a landslide complex in Majes, southern Peru, where recent agricultural development and irrigation activities have altered the hydrology and groundwater table and are thought to have contributed to increased regional landslide activities that present continuing sustainability community development challenges. We apply E-FWI to a 2D near-surface seismic data set for the purpose of better understanding the subsurface in the vicinity of a recent landslide location. We use seismic first-arrival travel-time tomography to generate the inputs required for E-FWI to generate the final high-resolution 2D compressional- and shear-wave (P- and S-wave) velocity models. At distances greater than 140 m from the cliff, the inverted models show a predominantly vertically stratified velocity structure with a low-velocity near-surface layer between 5–15 m depth. At distances closer than 140 m from the cliff, though, the models exhibit significantly reduced shear-wave velocities, stronger heterogeneity, and localized shorter wavelength structure in the top 20 m. These observations are consistent with those expected for a recent landslide complex; however, follow-on geotechnical analysis is required to confirm these assertions. Overall, the E-FWI seismic approach may be helpful for future landslide characterization projects and, when augmented with additional geophysical and geotechnical analyses, may allow for improved understanding of the hydrogeophysical properties associated with suspected ground-water-driven landslide activity.}, + author = {Yang, J. and Shragge, J. and Girard, A. J. and Gonzales, E. and Ticona, J. and Minaya, A. and Krahenbuhl, R.}, + doi = {10.3390/su151813574}, + issn = {2071-1050}, + journal = {Sustainability}, + number = {18}, + title = {Seismic Characterization of a Landslide Complex: A Case History from Majes, Peru}, + volume = {15}, + year = {2023}, +} + +@Article{Wang2022, + doi = {10.1007/s10712-022-09747-8}, + year = {2022}, + month = nov, + publisher = {Springer Science and Business Media {LLC}}, + volume = {44}, + number = {2}, + pages = {357--386}, + author = {Wang, Z. and Sun, C. and Wu, D.}, + title = {Near-surface Site Characterization Based on Joint Iterative Analysis of First-arrival and Surface-wave Data}, + journal = {Surveys in Geophysics} +} + +@Article{ArboledaZapata2023, + doi = {10.1002/esp.5695}, + year = {2023}, + month = sep, + publisher = {Wiley}, + author = {Arboleda-Zapata, M. and Guillemoteau, J. and Luc{\'{\i}}a, A. and Eberle, J. and Tronicke, J. and Korup, O.}, + title = {Tracing past extreme floods on an alluvial fan using geophysical surveying}, + journal = {Earth Surface Processes and Landforms} +} + +@Article{Carrier2023, + doi = {10.1007/s10346-023-02137-0}, + year = {2023}, + month = oct, + publisher = {Springer Science and Business Media {LLC}}, + author = {Carrier, A. and Meric, O. and Bottelin, P.}, + title = {Characterizing landslide dynamics from time-lapse time domain induced polarization and ground-based imaging: a case study of the {MontGombert} landslide (French, Alps)}, + journal = {Landslides} +} +@Comment{jabref-meta: databaseType:bibtex;} +@Article{Herring2023, + doi = {10.1002/ppp.2207}, + year = {2023}, + month = oct, + publisher = {Wiley}, + volume = {34}, + number = {4}, + pages = {494--512}, + author = {Herring, T. and Lewkowicz, A. G. and Hauck, C. and Hilbich, C. and Mollaret, C. and Oldenborger, G. A. and Uhlemann, S. and Farzamian, M. and Calmels, F. and Scandroglio, R.}, + title = {Best practices for using electrical resistivity tomography to investigate permafrost}, + journal = {Permafrost and Periglacial Processes} +} + +@Article{Pavoni2023, + author = {Pavoni, M. and Boaga, J. and Wagner, F.M. and Bast, A. and Phillips, M.}, + doi = {10.1016/j.jappgeo.2023.105097}, + journal = {Journal of Applied Geophysics}, + keywords = {Mountain permafrost, Electrical resistivity tomography (ERT), Refraction seismic tomography (RST), Joint inversion}, + pages = {105097}, + title = {Characterization of rock glaciers environments combining structurally-coupled and petrophysically-coupled joint inversions of electrical resistivity and seismic refraction datasets}, + year = {2023}, +} + +@article{Steiner2023, + doi = {10.1016/j.cageo.2023.105339}, + year = {2023}, + month = jul, + publisher = {Elsevier {BV}}, + volume = {176}, + pages = {105339}, + author = {Steiner, M. and Flores Orozco, A.}, + title = {formikoj: A flexible library for data management and processing in geophysics - Application for seismic refraction data}, + journal = {Computers {\&} Geosciences} +} + +@article{Fiolleau2023, + doi = {10.1016/j.jappgeo.2023.105090}, + year = {2023}, + month = aug, + publisher = {Elsevier {BV}}, + volume = {215}, + pages = {105090}, + author = {Fiolleau, S. and Uhlemann, S. and Wielandt, S. and Dafflon, B.}, + title = {Understanding slow-moving landslide triggering processes using low-cost passive seismic and inclinometer monitoring}, + journal = {Journal of Applied Geophysics} +} + +@article{Uecker2023, + doi = {10.3389/frwa.2023.1057725}, + year = {2023}, + month = jul, + publisher = {Frontiers Media {SA}}, + volume = {5}, + author = {Uecker, R. K. and Flinchum, B. A. and Holbrook, W. S. and Carr, B. J.}, + title = {Mapping bedrock topography: a seismic refraction survey and landscape analysis in the Laramie Range, Wyoming}, + journal = {Frontiers in Water} +} + +@article{IsunzaManrique2023, + doi = {10.1190/geo2022-0133.1}, + year = {2023}, + month = apr, + publisher = {Society of Exploration Geophysicists}, + volume = {88}, + number = {3}, + pages = {B73--B88}, + author = {Isunza Manrique, I. and Caterina, D. and Nguyen, F. and Hermans, T.}, + title = {Quantitative interpretation of geoelectric inverted data with a robust probabilistic approach}, + journal = {Geophysics} +} + +@Article{gautier2023G, + author = {Gautier, Maxime and Gautier, Stéphanie and Cattin, Rodolphe}, + journal = {GEOPHYSICS}, + title = {PyMERRY: A Python solution for an improved interpretation of electrical resistivity tomography images}, + year = {2023}, + number = {1}, + pages = {F23--F39}, + volume = {89}, + doi = {10.1190/geo2023-0105.1}, + publisher = {Society of Exploration Geophysicists}, +} + +@Article{levy2023C&G, + author = {Levy, Shiran and Laloy, Eric and Linde, Niklas}, + journal = {Computers & Geosciences}, + title = {Variational Bayesian inference with complex geostatistical priors using inverse autoregressive flows}, + year = {2023}, + issn = {0098-3004}, + month = feb, + pages = {105263}, + volume = {171}, + doi = {10.1016/j.cageo.2022.105263}, + publisher = {Elsevier BV}, +} + +@Article{levy2024C&G, + author = {Levy, Shiran and Friedli, Lea and Mariéthoz, Grégoire and Linde, Niklas}, + journal = {Computers & Geosciences}, + title = {Conditioning of multiple-point statistics simulations to indirect geophysical data}, + year = {2024}, + issn = {0098-3004}, + month = may, + pages = {105581}, + volume = {187}, + doi = {10.1016/j.cageo.2024.105581}, + publisher = {Elsevier BV}, +} + +@Article{herring2023PaPP, + author = {Herring, Teddi and Lewkowicz, Antoni G. and Hauck, Christian and Hilbich, Christin and Mollaret, Coline and Oldenborger, Greg A. and Uhlemann, Sebastian and Farzamian, Mohammad and Calmels, Fabrice and Scandroglio, Riccardo}, + journal = {Permafrost and Periglacial Processes}, + title = {Best practices for using electrical resistivity tomography to investigate permafrost}, + year = {2023}, + issn = {1099-1530}, + month = oct, + number = {4}, + pages = {494--512}, + volume = {34}, + doi = {10.1002/ppp.2207}, + publisher = {Wiley}, +} + +@Article{dimech2023SR, + author = {Dimech, Adrien and Isabelle, Anne and Sylvain, Karine and Liu, Chong and Cheng, LiZhen and Bussière, Bruno and Chouteau, Michel and Fabien-Ouellet, Gabriel and Bérubé, Charles and Wilkinson, Paul and Meldrum, Philip and Chambers, Jonathan}, + journal = {Scientific Reports}, + title = {A multiscale accuracy assessment of moisture content predictions using time-lapse electrical resistivity tomography in mine tailings}, + year = {2023}, + issn = {2045-2322}, + month = nov, + number = {1}, + volume = {13}, + doi = {10.1038/s41598-023-48100-w}, + publisher = {Springer Science and Business Media LLC}, +} + +@Article{seib2024G, + author = {Seib, Lukas and Frey, Matthis and Bossennec, Claire and Krusemark, Matthias and Burschil, Thomas and Buness, Hermann and Weydt, Leandra and Sass, Ingo}, + journal = {Geothermics}, + title = {Assessment of a medium-deep borehole thermal energy storage site in the crystalline basement: A case study of the demo site Lichtwiese Campus, Darmstadt}, + year = {2024}, + issn = {0375-6505}, + month = may, + pages = {102933}, + volume = {119}, + doi = {10.1016/j.geothermics.2024.102933}, + publisher = {Elsevier BV}, +} + +@Article{aigner2024JoAG, + author = {Aigner, Lukas and Werthmüller, Dieter and Flores Orozco, Adrián}, + journal = {Journal of Applied Geophysics}, + title = {Sensitivity analysis of inverted model parameters from transient electromagnetic measurements affected by induced polarization effects}, + year = {2024}, + issn = {0926-9851}, + month = apr, + pages = {105334}, + volume = {223}, + doi = {10.1016/j.jappgeo.2024.105334}, + publisher = {Elsevier BV}, +} + +@Article{chen2023WRR, + author = {Chen, Hang and Niu, Qifei and Mendieta, Aida and Bradford, John and McNamara, James}, + journal = {Water Resources Research}, + title = {Geophysics‐Informed Hydrologic Modeling of a Mountain Headwater Catchment for Studying Hydrological Partitioning in the Critical Zone}, + year = {2023}, + issn = {1944-7973}, + month = nov, + number = {12}, + volume = {59}, + doi = {10.1029/2023wr035280}, + publisher = {American Geophysical Union (AGU)}, +} + +@Article{navarro2023FiES, + author = {Navarro, Gonzalo and Valois, Rémi and MacDonell, Shelley and de Pasquale, Giulia and Díaz, Juan Pablo}, + journal = {Frontiers in Earth Science}, + title = {Internal structure and water routing of an ice-debris landform assemblage using multiple geophysical methods in the semiarid Andes}, + year = {2023}, + issn = {2296-6463}, + month = apr, + volume = {11}, + doi = {10.3389/feart.2023.1102620}, + publisher = {Frontiers Media SA}, +} + +@Article{ariagno2023ESPaL, + author = {Ariagno, Coline and Pasquet, Sylvain and Le Bouteiller, Caroline and van der Beek, Peter and Klotz, Sébastien}, + journal = {Earth Surface Processes and Landforms}, + title = {Seasonal dynamics of marly badlands illustrated by field records of hillslope regolith properties, Draix–Bléone Critical Zone Observatory, South‐East France}, + year = {2023}, + issn = {1096-9837}, + month = feb, + number = {8}, + pages = {1526--1539}, + volume = {48}, + doi = {10.1002/esp.5564}, + publisher = {Wiley}, +} + +@Article{flinchum2024GRL, + author = {Flinchum, B. A. and Grana, D. and Carr, B. J. and Ravichandran, N. and Eppinger, B. and Holbrook, W. S.}, + journal = {Geophysical Research Letters}, + title = {Low Vp/Vs Values as an Indicator for Fractures in the Critical Zone}, + year = {2024}, + issn = {1944-8007}, + month = jan, + number = {2}, + volume = {51}, + doi = {10.1029/2023gl105946}, + publisher = {American Geophysical Union (AGU)}, +} + +@Article{jabrane2023DiB, + author = {Jabrane, Oussama and Azzab, Driss El and Martínez-Pagán, Pedro and Martínez-Segura, Marcos A. and Mahjoub, Himi and Charroud, Mohammed}, + journal = {Data in Brief}, + title = {Contribution of Python-based BERT software for landslide monitoring using Electrical Resistivity Tomography datasets. A case study in Tghat-Fez (Morocco)}, + year = {2023}, + issn = {2352-3409}, + month = feb, + pages = {108763}, + volume = {46}, + doi = {10.1016/j.dib.2022.108763}, + publisher = {Elsevier BV}, +} + +@Article{hase2024GJI, + author = {Hase, Joost and Weigand, Maximilian and Kemna, Andreas}, + journal = {Geophysical Journal International}, + title = {A probabilistic solution to geophysical inverse problems in complex variables and its application to complex resistivity imaging}, + year = {2024}, + issn = {1365-246X}, + month = feb, + number = {1}, + pages = {456--464}, + volume = {237}, + doi = {10.1093/gji/ggae045}, + publisher = {Oxford University Press (OUP)}, +} + +@Article{zeyen2024C&G, + author = {Zeyen, Hermann and Léger, Emmanuel}, + journal = {Computers & Geosciences}, + title = {PyRefra – Refraction seismic data treatment and inversion}, + year = {2024}, + issn = {0098-3004}, + month = mar, + pages = {105556}, + volume = {185}, + doi = {10.1016/j.cageo.2024.105556}, + publisher = {Elsevier BV}, +} + +@Article{martin2023GJI, + author = {Martin, Tina and Weller, Andreas}, + journal = {Geophysical Journal International}, + title = {Superposition of induced polarization signals measured on pyrite–sand mixtures}, + year = {2023}, + issn = {1365-246X}, + month = feb, + number = {1}, + pages = {699--711}, + volume = {234}, + doi = {10.1093/gji/ggad091}, + publisher = {Oxford University Press (OUP)}, +} + +@Article{li2023MG, + author = {Li, Ang and Grana, Dario and Parsekian, Andrew D. and Carr, Brad}, + journal = {Mathematical Geosciences}, + title = {Uncertainty Quantification in Tomographic Inversion of Near-Surface Seismic Refraction Data}, + year = {2023}, + issn = {1874-8953}, + month = jul, + number = {1}, + pages = {77--101}, + volume = {56}, + doi = {10.1007/s11004-023-10083-9}, + publisher = {Springer Science and Business Media LLC}, +} + +@article{carrizo2024, + title = "Estimation of electrical conductivity models using multi-coil rigid-boom electromagnetic induction measurements", + keywords = "Electromagnetic induction, Frequency domain electromagnetics, Inversion", + author = "{Carrizo Mascarell}, Maria and Dieter Werthm{\"u}ller and Evert Slob", + year = "2024", + doi = "10.1016/j.cageo.2024.105732", + volume = "193", + journal = "Computers and Geosciences", + publisher = "Elsevier", +} + +@Article{Gautier2024, + author = {Gautier, Maxime and Ferry, Matthieu and Gautier, Stéphanie and Le Roux-Mallouf, Romain and Drukpa, Dowchu and Cattin, Rodolphe}, + journal = {Communications Earth & Environment}, + title = {Deformed alluvial terraces record an excess of slip over the last few centuries on the Himalayan Topographic Frontal Thrust of central Bhutan}, + year = {2024}, + issn = {2662-4435}, + month = oct, + number = {1}, + volume = {5}, + doi = {10.1038/s43247-024-01759-z}, + publisher = {Springer Science and Business Media LLC}, +} + +@Article{CongThi2024, + author = {Cong-Thi, Diep and Dieu, Linh Pham and Caterina, David and De Pauw, Xavier and Thi, Huyen Dang and Ho, Huu Hieu and Nguyen, Frédéric and Hermans, Thomas}, + journal = {Journal of Contaminant Hydrology}, + title = {Quantifying salinity in heterogeneous coastal aquifers through ERT and IP: Insights from laboratory and field investigations}, + year = {2024}, + issn = {0169-7722}, + month = mar, + pages = {104322}, + volume = {262}, + doi = {10.1016/j.jconhyd.2024.104322}, + publisher = {Elsevier BV}, +} + +@Article{Seib2024, + author = {Seib, Lukas and Frey, Matthis and Bossennec, Claire and Krusemark, Matthias and Burschil, Thomas and Buness, Hermann and Weydt, Leandra and Sass, Ingo}, + journal = {Geothermics}, + title = {Assessment of a medium-deep borehole thermal energy storage site in the crystalline basement: A case study of the demo site Lichtwiese Campus, Darmstadt}, + year = {2024}, + issn = {0375-6505}, + month = may, + pages = {102933}, + volume = {119}, + doi = {10.1016/j.geothermics.2024.102933}, + publisher = {Elsevier BV}, +} + +@Article{Skibbe2024, + author = {Skibbe, Nico and Günther, Thomas and Schwalfenberg, Kai and Meyer, Rena and Reckhardt, Anja and Greskowiak, Janek and Massmann, Gudrun and Müller-Petke, Mike}, + journal = {Journal of Hydrology}, + title = {Comparison of methods measuring electrical conductivity in coastal aquifers}, + year = {2024}, + issn = {0022-1694}, + month = nov, + pages = {131905}, + volume = {643}, + doi = {10.1016/j.jhydrol.2024.131905}, + publisher = {Elsevier BV}, +} + +@Article{AsimIbrahim2024, + author = {Asim Ibrahim, Muhammad and Afzal Butt, Nabeel and Rejkjær, Simon and Dahlin, Torleif and Madsen, Dan and Wilkens Flecknoe-Brown, Konard and G{\"u}nther, Thomas}, + journal = {Waste Management}, + title = {Early detection of deep-seated smouldering fires in wood waste storage using ERT}, + year = {2024}, + issn = {0956-053X}, + month = jun, + pages = {215--224}, + volume = {182}, + creationdate = {2024-05-25T12:16:25}, + doi = {10.1016/j.wasman.2024.04.030}, + modificationdate = {2024-05-25T12:16:25}, + owner = {Guenther.T}, + publisher = {Elsevier BV}, +} + +@Article{Norooz2024, + author = {Norooz, Reyhaneh and Nivorlis, Aristeidis and Olsson, Per-Ivar and G{\"u}nther, Thomas and Bernstone, Christian and Dahlin, Torleif}, + journal = {Journal of Civil Structural Health Monitoring}, + title = {Monitoring of {\"a}lvkarleby test embankment dam using 3D electrical resistivity tomography for detection of internal defects}, + year = {2024}, + issn = {2190-5479}, + month = mar, + creationdate = {2024-05-25T12:16:36}, + doi = {10.1007/s13349-024-00785-x}, + modificationdate = {2024-05-25T12:16:36}, + owner = {Guenther.T}, + publisher = {Springer Science and Business Media LLC}, +} + +@Article{Birnstengel2024, + author = {Birnstengel, Susann and Dietrich, Peter and Peisker, Kilian and Pohle, Marco and Hornbruch, G{\"o}tz and Bauer, Sebastian and Hu, Linwei and G{\"u}nther, Thomas and Hellwig, Olaf and Dahmke, Andreas and Werban, Ulrike}, + journal = {GEOPHYSICS}, + title = {Experimental seismic crosshole setup to investigate the application of rock-physical models at the field scale}, + year = {2024}, + issn = {1942-2156}, + month = apr, + number = {3}, + pages = {MR183--MR195}, + volume = {89}, + creationdate = {2024-05-25T12:16:51}, + doi = {10.1190/geo2022-0625.1}, + modificationdate = {2024-05-25T12:16:51}, + owner = {Guenther.T}, + publisher = {Society of Exploration Geophysicists}, +} + +@Article{Moerbe2024, + author = {M{\"o}rbe, Wiebke and Yogeshwar, Pritam and Tezkan, B{\"u}lent and Kotowski, Philipp and Thiede, Anneke and Steuer, Annika and Rochlitz, Raphael and G{\"u}nther, Thomas and Brauch, Klaus and Becken, Michael}, + journal = {GEOPHYSICS}, + title = {Large-scale 3D inversion of semi-airborne electromagnetic data - topography and induced polarization effects in a graphite exploration scenario}, + year = {2024}, + issn = {1942-2156}, + month = may, + pages = {1--54}, + creationdate = {2024-05-25T12:17:31}, + doi = {10.1190/geo2023-0471.1}, + modificationdate = {2024-05-25T12:17:31}, + owner = {Guenther.T}, + publisher = {Society of Exploration Geophysicists}, +} + +@Article{Zancanaro2024, + author = {Zancanaro, Ester and Morari, Francesco and Piccoli, Ilaria and Carrera, Alberto and Zoccarato, Claudia and Teatini, Pietro}, + journal = {Hydrological Processes}, + title = {A Novel Technique to Mitigate Saltwater Intrusion: Freshwater Recharge via Drainpipe in Permeable Paleochannels}, + year = {2024}, + issn = {1099-1085}, + month = oct, + number = {10}, + volume = {38}, + doi = {10.1002/hyp.15299}, + publisher = {Wiley}, +} + +@Article{Zhou2024, + author = {Zhou, Sheng and Yang, Yi-Xin and Cao, Jing-Jing and Meng, Long-Long and Cao, Jun-Nan and Zhang, Chi and Zhang, Shuai and Bate, B.}, + journal = {Environmental Research}, + title = {Monitoring of copper adsorption on biochar using spectral induced polarization method}, + year = {2024}, + issn = {0013-9351}, + month = jun, + pages = {118778}, + volume = {251}, + doi = {10.1016/j.envres.2024.118778}, + publisher = {Elsevier BV}, +} + +@Article{Yang2023, + author = {Yang, Yi-Xin and Zhou, Sheng and Luo, Yuan-Yuan and Chen, Jia-Kai and Chen, Ze-Jian and Cao, Jun-Nan and Zhang, Chi and Zhang, Shuai and Zhan, Liang-Tong and Chen, Yun-Min and Bate, Bate}, + journal = {Environmental Geochemistry and Health}, + title = {Monitoring the remediation of groundwater polluted by MSW landfill leachates by activated carbon and zeolite with spectral induced polarization technique}, + year = {2023}, + issn = {1573-2983}, + month = dec, + number = {1}, + volume = {46}, + doi = {10.1007/s10653-023-01796-1}, + publisher = {Springer Science and Business Media LLC}, +} + +@Article{Vella2024, + author = {Vella, Marc-Antoine and Bièvre, Grégory and Delaere, Christophe and Thiesson, Julien and Guérin, Roger and Rivera-Casanovas, Claudia and Guédron, Stéphane}, + journal = {Quaternary Science Reviews}, + title = {The hydraulic network of the pre-Hispanic city of Tiwanaku (Bolivia): New insights from the integration of canal morphology, hydrogeological and palaeoenvironmental data}, + year = {2024}, + issn = {0277-3791}, + month = jan, + pages = {108475}, + volume = {324}, + doi = {10.1016/j.quascirev.2023.108475}, + publisher = {Elsevier BV}, +} + +@Article{Danque2024, + author = {Danque, H.A. and Cannon, K.M.}, + journal = {Icarus}, + title = {Lunar polar volatile remobilization in regolith-filled craters}, + year = {2024}, + issn = {0019-1035}, + month = mar, + pages = {115953}, + volume = {411}, + doi = {10.1016/j.icarus.2024.115953}, + publisher = {Elsevier BV}, +} + +@Article{Molodtsov2024, + author = {Molodtsov, Dmitry and Kiyan, Duygu and Bean, Christopher J}, + journal = {Geophysical Journal International}, + title = {Decoupled joint inversion with variable splitting: example scheme for magnetotelluric, seismic and gravity data}, + year = {2024}, + issn = {1365-246X}, + month = aug, + number = {1}, + pages = {706--724}, + volume = {239}, + doi = {10.1093/gji/ggae292}, + publisher = {Oxford University Press (OUP)}, +} + +@Article{Rochlitz2025, + author = {Rochlitz, Raphael and Günther, Thomas and Kotowski, Philipp Oliver and Becken, Michael}, + journal = {GEOPHYSICS}, + title = {Semi-airborne electromagnetic exploration of deep sulfide deposits with UAV-towed magnetometers - Part 2: Inversion Resolution analysis}, + year = {2025}, + issn = {1942-2156}, + month = feb, + number = {3}, + pages = {WA307--WA322}, + volume = {90}, + doi = {10.1190/geo2024-0448.1}, + publisher = {Society of Exploration Geophysicists}, +} + +@Article{Ronczka2025, + author = {Ronczka, Mathias and Günther, Thomas and Grinat, Michael and Siemon, Bernhard and Scheihing, Konstantin and Müller‐Petke, Mike}, + journal = {Near Surface Geophysics}, + title = {Multi‐scale electrical resistivity imaging and long‐term monitoring as a tool for groundwater management}, + year = {2025}, + issn = {1873-0604}, + month = apr, + doi = {10.1002/nsg.70006}, + publisher = {Wiley}, +} + +@Article{Beraus2025, + author = {Beraus, Sarah and Köhn, Daniel and Bohlen, Thomas and Burschil, Thomas and Schuster, Bennet and Buness, Hermann and Gabriel, Gerald}, + journal = {Geophysical Prospecting}, + title = {Seismic crosshole full‐waveform inversion of high‐frequency SV‐waves for glacial sediment characterization}, + year = {2025}, + issn = {1365-2478}, + month = apr, + number = {5}, + pages = {1587--1605}, + volume = {73}, + doi = {10.1111/1365-2478.70024}, + publisher = {Wiley}, +} + +@Article{Hase2024, + author = {Hase, Joost and Wagner, Florian M and Weigand, Maximilian and Kemna, Andreas}, + journal = {Geophysical Journal International}, + title = {Probabilistic geophysical inversion of complex resistivity measurements using the Hamiltonian Monte Carlo method}, + year = {2024}, + issn = {1365-246X}, + month = oct, + number = {1}, + pages = {349--361}, + volume = {240}, + doi = {10.1093/gji/ggae389}, + publisher = {Oxford University Press (OUP)}, +} + +@Article{Karaoulis2024, + author = {Karaoulis, Marios and Tsokas, Grigorios N. and Tsourlos, Panagiotis and Bogiatzis, Petros and Vargemezis, George}, + journal = {Archaeological Prospection}, + title = {3D Electrical Resistivity Tomography Using a Radial Array and Detailed Topography for Tumuli Prospection}, + year = {2024}, + issn = {1099-0763}, + month = dec, + number = {1}, + pages = {197--208}, + volume = {32}, + doi = {10.1002/arp.1966}, + publisher = {Wiley}, +} + +@Article{Helal2025, + author = {Helal, Khalid and Pugacheva, Polina and Allam, Hussien and Fath-Elbab, Mohamed and Sholqamy, Mohamed and Popovych, Olga and Schmid, Simon and Maier, Benedikt and Galal, Amr and Ramirez, Alejandro and Rupfle, Johannes and Taie, Khalid and Ali, Menna and Sessa, Clarimma and Schumacher, Thomas and Hawass, Zahi and Tayoubi, Mehdi and Grosse, Christian U. and Helal, Hany and Elkarmoty, Mohamed}, + journal = {NDT & E International}, + title = {Detection of two anomalies behind the Eastern face of the Menkaure Pyramid using a combination of non-destructive testing techniques}, + year = {2025}, + issn = {0963-8695}, + month = oct, + pages = {103331}, + volume = {155}, + doi = {10.1016/j.ndteint.2025.103331}, + publisher = {Elsevier BV}, +} + +@Article{Pasquet2025, + author = {Pasquet, Sylvain and Holbrook, W. Steven and Carr, Bradley J. and Terry, Neil and Briggs, Martin A. and Finn, Carol A. and Bedrosian, Paul A. and Auken, Esben and Pedersen, Jesper and Maurya, Pradip and Sims, Kenneth W. W.}, + journal = {Journal of Geophysical Research: Solid Earth}, + title = {Multi‐Scale Geophysical Imaging of a Hydrothermal System in Yellowstone National Park, USA}, + year = {2025}, + issn = {2169-9356}, + month = mar, + number = {4}, + volume = {130}, + doi = {10.1029/2024jb029839}, + publisher = {American Geophysical Union (AGU)}, +} + +@Article{Flinchum2025, + author = {Flinchum, B. A. and Hagan, D. and Harman, C. J.}, + journal = {Vadose Zone Journal}, + title = {Exploring the connection between critical zone structure and tree distribution in a semiarid eroding landscape with shallow seismic refraction}, + year = {2025}, + issn = {1539-1663}, + month = apr, + number = {3}, + volume = {24}, + doi = {10.1002/vzj2.70006}, + publisher = {Wiley}, +} + +@Article{Junker2025, + author = {Junker, Jonas Simon and Obermann, Anne and Voigt, Martin and Maurer, Hansruedi and Eruteya, Ovie Emmanuel and Moscariello, Andrea and Wiemer, Stefan and Zappone, Alba}, + journal = {International Journal of Greenhouse Gas Control}, + title = {Geophysical characterization of the in-situ CO2 mineral storage pilot site in Helguvik, Iceland}, + year = {2025}, + issn = {1750-5836}, + month = feb, + pages = {104320}, + volume = {141}, + doi = {10.1016/j.ijggc.2025.104320}, + publisher = {Elsevier BV}, +} + +@Article{Zhou2025, + author = {Zhou, Sheng and Yang, Yi-Xin and Meng, Long-Long and Du, Ai-Fang and Wang, Qiong and Zhang, Chi and Zhang, Shuai and Bate, Bate}, + journal = {Journal of Hazardous Materials}, + title = {Spatial delineation of AMD sources in a pyrite-rich waste rock site with spectral induced polarization method}, + year = {2025}, + issn = {0304-3894}, + month = sep, + pages = {138919}, + volume = {495}, + doi = {10.1016/j.jhazmat.2025.138919}, + publisher = {Elsevier BV}, +} + +@Article{Li2025, + author = {Li, Ang and Parsekian, Andrew D. and Grana, Dario and Carr, Bradley J.}, + journal = {GEOPHYSICS}, + title = {Quantification of measurement uncertainty in electrical resistivity tomography data and its effect on the inverted resistivity model}, + year = {2025}, + issn = {1942-2156}, + month = apr, + number = {3}, + pages = {WA275--WA291}, + volume = {90}, + doi = {10.1190/geo2024-0466.1}, + publisher = {Society of Exploration Geophysicists}, +} + +@Article{Ding2025, + author = {Ding, Yinshuai and Malehmir, Alireza}, + journal = {Geophysical Journal International}, + title = {Controlled-illumination reflection imaging of massive sulphide deposits utilizing a tunnel-to-surface acquisition setup at the Neves-Corvo mining site, Portugal}, + year = {2025}, + issn = {1365-246X}, + month = jun, + doi = {10.1093/gji/ggaf201}, + publisher = {Oxford University Press (OUP)}, +} + +@Article{Bore2025, + author = {Bore, Thierry and Shen, Yu-Jen and Serati, Mehdi and Pascal, Yoann and Al Kalbani, Muhannad and Scheuermann, Alexander and Wagner, Norman and Loewer, Markus}, + journal = {Journal of Rock Mechanics and Geotechnical Engineering}, + title = {Coaxial method to investigate broadband dielectric properties of rocks over the 5 Hz to 3 GHz frequency range}, + year = {2025}, + issn = {1674-7755}, + month = jun, + doi = {10.1016/j.jrmge.2025.04.024}, + publisher = {Elsevier BV}, +} diff --git a/doc/glossary.md b/doc/glossary.md new file mode 100644 index 000000000..cd90f7027 --- /dev/null +++ b/doc/glossary.md @@ -0,0 +1,116 @@ +(sec-glossary)= + +# Glossary + +:::{glossary} +GCC + +: The GNU Compiler Collection (GCC). Default compiler for most linux + systems. The Windows port is {term}`MinGW` See: + +FEniCS + +: The FEniCSx computing platform. + +Gmsh + +: Gmsh: a three-dimensional finite element mesh generator with built-in + pre- and post-processing facilities + {cite}`GeuzaineRemacle2009` + . + See: {py:func}`pygimli.meshtools.mesh.readGmsh` + +BERT + +: Boundless electrical resistivity tomography + +IPython + +: An improved {term}`Python` shell that integrates nicely with + {term}`Matplotlib`. See . + +Matplotlib + +: Matplotlib {term}`Python` package displays publication quality results. + It displays both 1D X-Y type plots and 2D contour plots for structured + and unstructured data. It works on all common platforms and produces + publication quality hard copies. + +MinGW + +: MinGW, a contraction of "Minimalist GNU for Windows", is a minimalist + development environment for native Microsoft Windows applications. See: + + +MSYS + +: MSYS, a contraction of "Minimal SYStem", is a Bourne Shell command line + interpreter system. Offered as an alternative to Microsoft's cmd.exe, + this provides a general purpose command line environment, which is + particularly suited to use with MinGW, for porting of many Open Source + applications to the MS-Windows platform. See: + +NumPy + +: NumPy is the fundamental package for scientific computing in Python. It + is a Python library that provides a multidimensional array object and + various functionalities related to it. + +Paraview + +: Is an open-source, multi-platform data analysis and visualization + application. See: + +Python + +: The programming language that {term}`pyGIMLi` (and your scripts) are + written in. See: + +Pylab + +: Meta-package importing several core packages such as {term}`NumPy`, + {term}`SciPy`, {term}`Matplotlib`, etc. into a single namespace. This is + usually not recommended due to possible name conflicts but provides a + quick way to get MATLAB-like functionality. + +PyVista + +: 3D visualization tool based on VTK: + +SciPy + +: Scientific Computing Tools for Python - Open-source library with many + numerical routines but the term is often used as a synonym for the + scientific python community, several conferences, and the *SciPy + Stack*, i.e. a set of core packages. + +Sphinx + +: The tools used to generate the {term}`GIMLi` documentation. See: + + +STL + +: Unstructured triangulated surface file format native to the "stereolithography" + CAD software created by 3D Systems. + +SuiteSparse + +: SuiteSparse is a single archive that contains packages for solving + large sparse problems using Sparse Cholesky factorization. + + +Triangle + +: A Two-Dimensional Quality Mesh Generator and Delaunay Triangulator. + {cite}`Shewchuk96b` + + See: {py:func}`pygimli.meshtools.mesh.readTriangle` + +Tetgen + +: A Quality Tetrahedral Mesh Generator and a 3D Delaunay Triangulator. + {cite}`Si2015` + + See: {py:func}`pygimli.meshtools.mesh.readTetgen` +::: \ No newline at end of file diff --git a/doc/glossary.rst b/doc/glossary.rst deleted file mode 100644 index 555e59965..000000000 --- a/doc/glossary.rst +++ /dev/null @@ -1,108 +0,0 @@ -.. _sec:glossary: - -Glossary -======== - -.. glossary:: - - GCC - The GNU Compiler Collection (GCC). Default compiler for most linux - systems. The Windows port is :term:`MinGW` See: http://gcc.gnu.org/ - - GIMLi - The eponymous software package. See :ref:`sec:GIMLi` - - pyGIMLi - The eponymous software package (python bindings). See :ref:`sec:GIMLi` - - libGIMLi - The eponymous software package (c++ core). See :ref:`sec:GIMLi` - - FEniCS - The FEniCSx computing platform. https://fenicsproject.org/ - - Gmsh - Gmsh: a three-dimensional finite element mesh generator with built-in - pre- and post-processing facilities - :cite:`GeuzaineRemacle2009` - http://gmsh.info/. - See: :py:func:`pygimli.meshtools.mesh.readGmsh` - - BERT - Boundless electrical resistivity tomography http://www.resistivity.net/ - - IPython - An improved :term:`Python` shell that integrates nicely with - :term:`Matplotlib`. See http://ipython.org/. - - Matplotlib - Matplotlib :term:`Python` package displays publication quality results. - It displays both 1D X-Y type plots and 2D contour plots for structured - and unstructured data. It works on all common platforms and produces - publication quality hard copies. http://matplotlib.org - - MinGW - MinGW, a contraction of "Minimalist GNU for Windows", is a minimalist - development environment for native Microsoft Windows applications. See: - http://www.mingw.org/ - - MSYS - MSYS, a contraction of "Minimal SYStem", is a Bourne Shell command line - interpreter system. Offered as an alternative to Microsoft's cmd.exe, - this provides a general purpose command line environment, which is - particularly suited to use with MinGW, for porting of many Open Source - applications to the MS-Windows platform. See: http://www.mingw.org/ - - NumPy - NumPy is the fundamental package for scientific computing in Python. It - is a Python library that provides a multidimensional array object and - various functionalities related to it. https://docs.scipy.org/doc/numpy/ - - Paraview - Is an open-source, multi-platform data analysis and visualization - application. See: http://paraview.org/ - - Python - The programming language that :term:`pyGIMLi` (and your scripts) are - written in. See: https://www.python.org/ - - Pylab - Meta-package importing several core packages such as :term:`NumPy`, - :term:`SciPy`, :term:`Matplotlib`, etc. into a single namespace. This is - usually not recommended due to possible name conflicts but provides a - quick way to get MATLAB-like functionality. - - PyVista - 3D visualization tool based on VTK: https://www.pyvista.org - - SciPy - Scientific Computing Tools for Python - Open-source library with many - numerical routines but the term is often used as a synonym for the - scientific python community, several conferences, and the *SciPy - Stack*, i.e. a set of core packages. https://scipy.org/about.html - - Sphinx - The tools used to generate the :term:`GIMLi` documentation. See: - http://sphinx-doc.org - - STL - Unstructured triangulated surface file format native to the "stereolithography" - CAD software created by 3D Systems. https://en.wikipedia.org/wiki/STL_%28file_format%29 - - - SuiteSparse - SuiteSparse is a single archive that contains packages for solving - large sparse problems using Sparse Cholesky factorization. - http://faculty.cse.tamu.edu/davis/suitesparse.html - - Triangle - A Two-Dimensional Quality Mesh Generator and Delaunay Triangulator. - :cite:`Shewchuk96b` - http://www.cs.cmu.edu/~quake/triangle.html - See: :py:func:`pygimli.meshtools.mesh.readTriangle` - - Tetgen - A Quality Tetrahedral Mesh Generator and a 3D Delaunay Triangulator. - :cite:`Si2015` - http://tetgen.org/ - See: :py:func:`pygimli.meshtools.mesh.readTetgen` diff --git a/doc/index.rst b/doc/index.rst new file mode 100644 index 000000000..49b068eeb --- /dev/null +++ b/doc/index.rst @@ -0,0 +1,10 @@ +.. toctree:: + :hidden: + + About + user-guide/index + _examples_auto/index.rst + _tutorials_auto/index.rst + pygimliapi/index.rst + Community + glossary \ No newline at end of file diff --git a/doc/installation.rst b/doc/installation.rst deleted file mode 100644 index 3a0db8f6f..000000000 --- a/doc/installation.rst +++ /dev/null @@ -1,9 +0,0 @@ -:tocdepth: 2 - -.. _sec:install: - -.. include:: ../INSTALLATION.rst - -.. note:: - - If you want to compile pyGIMLi from source, check out :ref:`sec:build`. diff --git a/doc/license.rst b/doc/license.rst deleted file mode 100644 index 38ec30d41..000000000 --- a/doc/license.rst +++ /dev/null @@ -1,4 +0,0 @@ -.. _sec:license: - -.. include:: ../COPYING.rst - diff --git a/doc/pygimliapi/index.rst b/doc/pygimliapi/index.rst index 21f0f2d19..64f313041 100644 --- a/doc/pygimliapi/index.rst +++ b/doc/pygimliapi/index.rst @@ -2,18 +2,9 @@ .. _sec:pygimliapi: -===================== -pyGIMLi API Reference -===================== - -.. only:: latex - - .. note:: - - In the following, all Python modules, functions and classes are documented. - For a reference of the C++ core library of the code, please visit: - http://pygimli.org/gimliapi/. - +========= +Reference +========= .. currentmodule:: pygimli diff --git a/doc/references.bib b/doc/references.bib index e05a8b73a..19acb9a39 100644 --- a/doc/references.bib +++ b/doc/references.bib @@ -1,600 +1,716 @@ -% Encoding: UTF-8 - -@Article{Archie1942, - Title = {{T}he {E}lectrical {R}esistivity {L}og as an {A}id in {D}etermining {S}ome {R}eservoir {C}haracteristics}, - Author = {G.E. Archie}, - Journal = {Transactions of the {AIME}}, - Year = {1942}, - - Month = {dec}, - Number = {01}, - Pages = {54--62}, - Volume = {146}, - - Doi = {10.2118/942054-g}, - Owner = {carsten}, - Publisher = {Society of Petroleum Engineers ({SPE})}, - Timestamp = {2016.07.05}, - Url = {http://dx.doi.org/10.2118/942054-g} -} - -@Article{ChenDavHag+2009, - Title = {{A}lgorithm 887: {CHOLMOD}, supernodal sparse {C}holesky factorization and update/downdate}, - Author = {Y. Chen and T. A. Davis and W. W. Hager and S. Rajamanickam}, - Journal = {ACM Trans. Math. Software}, - Year = {2009}, - Number = {3}, - Pages = {No.: 22}, - Volume = {35}, - - File = {ChenDavHag+2009.pdf:all/ChenDavHag+2009.pdf:PDF}, - Owner = {carsten}, - Timestamp = {2010.04.09} -} - -@Article{EngelhardtPit1955, - Title = {{Ü}ber die {Z}usammenhänge zwischen {P}orosität, {P}ermeabilität und {K}orngröße bei {S}anden und {S}andsteinen}, - Author = {W. v. Engelhardt and H. Pitter}, - Journal = {Heidelberger Beiträge zur Mineralogie und Petrographie}, - Year = {1955}, - Number = {6}, - Pages = {477-491}, - Volume = {2}, - - File = {EngelhardtPit1955.pdf:all/EngelhardtPit1955.pdf:PDF}, - Owner = {carsten}, - Timestamp = {2015.11.11} -} - -@Article{GeuzaineRemacle2009, - Title = {{G}msh: a three-dimensional finite element mesh generator with built-in pre- and post-processing facilities}, - Author = {Geuzaine, C. and Remacle, J.-F.}, - Journal = {International Jounral for Numerical Methods in Engineering}, - Year = {2009}, - Pages = {1309-1331}, - Volume = {79}, - - Owner = {fwagner}, - Timestamp = {2011.05.30} -} - -@Article{NordsiekWel2008, - Title = {{A} new approach to fitting induced-polarization spectra}, - Author = {Sven Nordsiek and Andreas Weller}, - Journal = {Geophysics}, - Year = {2008}, - Number = {6}, - Pages = {F235--F245}, - Volume = {73}, - - Owner = {carsten}, - Timestamp = {2011.03.17} -} - -@InCollection{Shewchuk96b, - Title = {{T}riangle: {E}ngineering a {2D} {Q}uality {M}esh {G}enerator and {D}elaunay {T}riangulator}, - Author = {Jonathan Richard Shewchuk}, - Booktitle = {Applied Computational Geometry: Towards Geometric Engineering}, - Publisher = {Springer-Verlag}, - Year = {1996}, - Editor = {Ming C. Lin and Dinesh Manocha}, - Month = may, - Note = {From the First ACM Workshop on Applied Computational Geometry}, - Pages = {203--222}, - Series = {Lecture Notes in Computer Science}, - Volume = {1148}, - - Owner = {Dlugosch.R}, - Timestamp = {2013.04.15} -} - -@Manual{tetgen, - Title = {{T}et{G}en - a quality-constrained tetrahedral mesh generator}, - - Address = {\url{http://tetgen.org}}, - Author = {H. Si}, - Organization = {Weierstrass institute, Berlin}, - Year = {2002-2008}, - - Owner = {halbmy}, - Timestamp = {2008.05.19} -} - -@Article{Si2015, - Title = {{TetGen}, a {D}elaunay-{B}ased {Q}uality {T}etrahedral {M}esh {G}enerator}, - Author = {Hang Si}, - Journal = {{ACM} Transactions on Mathematical Software}, - Year = {2015}, - - Month = {feb}, - Number = {2}, - Pages = {1--36}, - Volume = {41}, - - Doi = {10.1145/2629697}, - File = {Si2015.pdf:all/Si2015.pdf:PDF}, - Owner = {carsten}, - Publisher = {Association for Computing Machinery ({ACM})}, - Timestamp = {2015.12.03}, - Url = {http://dx.doi.org/10.1145/2629697} -} - -@TechReport{Si2004, - Title = {{T}et{G}en. {A} 3{D} {D}elaunay tetrahedral mesh generator. v.1.3}, - Author = {Hang Si}, - Institution = {WIAS}, - Year = {2004}, - Number = {4}, - Type = {Users manual}, - - File = {Si2004.pdf:all/Si2004.pdf:PDF}, - Owner = {carsten}, - Printout = {yes}, - Timestamp = {2013.08.28} -} - -@Article{SinghGup2001, - Title = {{N}ew method for fast computation of gravity and magnetic anomalies from arbitrary polyhedra}, - Author = {Bijendra Singh and D. Guptasarma}, - Journal = {Geophysics}, - Year = {2001}, - Pages = {521-526}, - Volume = {66}, - - File = {SinghGup2001.pdf:all/SinghGup2001.pdf:PDF}, - Owner = {carsten}, - Timestamp = {2013.10.10} -} - -@Article{WonBev1987, - Title = {{C}omputing the gravitational and magnetic anomalies due to a polygon: {A}lgorithms and {F}ortran subroutines}, - Author = {I. J. Won and Michael Bevis}, - Journal = {Geophysics}, - Year = {1987}, - Number = {2}, - Pages = {232-238}, - Volume = {52}, - - File = {WonBev1987.pdf:all/WonBev1987.pdf:PDF}, - Owner = {carsten}, - Timestamp = {2012.03.23} -} - -@Book{Zienkiewicz1977, - Title = {{T}he {F}inite {E}lement {M}ethod}, - Author = {O. C. Zienkiewicz}, - Publisher = {McGraw-Hill, London}, - Year = {1977}, - Edition = {3rd}, - - Owner = {carsten}, - Timestamp = {2010.03.29} -} - -@Article{PeltonWarHal1978, - author = {W.H. Pelton and S.H. Ward and P.G. Hallof and W.R. Sill and P. H. Nelson}, - title = {{M}ineral discrimination and removal of inductive coupling with multifrequency ip}, - journal = {Geophysics}, - year = {1978}, - volume = {43}, - number = {3}, - pages = {588--609}, - file = {PeltonWarHal1978.pdf:all/PeltonWarHal1978.pdf:PDF}, - groups = {SIP}, - owner = {carsten}, - timestamp = {2011.03.17}, -} - -@Article{Seigel1959, - author = {Seigel, H. O.}, - title = {Mathematical formuiation and type curves for induced polarization}, - journal = {Geophysics}, - year = {1959}, - volume = {24}, - pages = {547-565}, - owner = {carsten}, - timestamp = {2017.05.23}, -} - -@Article{RueckerGueWag2017GaG, - author = {Carsten Rücker and Thomas Günther and Florian Wagner}, - title = {{pyGIMLi}: An open-source library for modelling and inversion in geophysics}, - journal = {Computers \& Geosciences}, - year = {2017}, - owner = {Dlugosch.R}, - timestamp = {2017.07.27}, -} - -@Article{moser1991G, - author = {Moser, TJ}, - title = {{S}hortest path calculation of seismic rays}, - journal = {Geophysics}, - year = {1991}, - volume = {56}, - number = {1}, - pages = {59-67}, - issn = {0016-8033}, - doi = {10.1190/1.1442958}, - owner = {Dlugosch.R}, - timestamp = {2017.08.21}, - type = {Journal Article}, -} - -@Article{podvin1991GJI, - author = {Pascal Podvin and Isabelle Lecomte}, - title = {Finite difference computation of traveltimes in very contrasted velocity models: a massively parallel approach and its associated tools}, - journal = {Geophysical Journal International}, - year = {1991}, - volume = {105}, - number = {1}, - pages = {271--284}, - month = {apr}, - doi = {10.1111/j.1365-246x.1991.tb03461.x}, - owner = {Dlugosch.R}, - publisher = {Oxford University Press ({OUP})}, - timestamp = {2017.08.21}, - url = {https://doi.org/10.1111/j.1365-246x.1991.tb03461.x}, -} - -@Article{loewer2017GJI, - author = {M. Loewer and T. G\"{u}nther and J. Igel and S. Kruschwitz and T. Martin and N. Wagner}, - title = {Ultra-broad-band electrical spectroscopy of soils and sediments{\textemdash}a combined permittivity and conductivity model}, - journal = {Geophysical Journal International}, - year = {2017}, - volume = {210}, - number = {3}, - pages = {1360--1373}, - month = {jun}, - doi = {10.1093/gji/ggx242}, - owner = {Dlugosch.R}, - publisher = {Oxford University Press ({OUP})}, - timestamp = {2017.07.27}, - url = {https://doi.org/10.1093/gji/ggx242}, -} - -@Article{LoewerIgeWag2016, - author = {Markus Loewer and Jan Igel and Norman Wagner}, - title = {{S}pectral {D}ecomposition of {S}oil {E}lectrical and {D}ielectric {L}osses and {P}rediction of {I}n {S}itu {GPR} {P}erformance}, - journal = {{IEEE} J. Sel. Top. Appl. Earth Observations Remote Sensing}, - year = {2016}, - volume = {9}, - number = {1}, - pages = {212--230}, - doi = {10.1109/jstars.2015.2424152}, - owner = {TG}, - publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, - timestamp = {2016.09.14}, - url = {http://dx.doi.org/10.1109/JSTARS.2015.2424152}, -} - -@Article{hellman2017JoAG, - author = {Kristofer Hellman and Mathias Ronczka and Thomas G\"{u}nther and Marcus Wennermark and Carsten R\"{u}cker and Torleif Dahlin}, - title = {Structurally coupled inversion of {ERT} and refraction seismic data combined with cluster-based model integration}, - journal = {Journal of Applied Geophysics}, - year = {2017}, - volume = {143}, - pages = {169--181}, - month = {aug}, - doi = {10.1016/j.jappgeo.2017.06.008}, - owner = {Dlugosch.R}, - publisher = {Elsevier {BV}}, - timestamp = {2017.08.21}, - url = {https://doi.org/10.1016/j.jappgeo.2017.06.008}, -} - -@InProceedings{GuentherRuecker2006SAGEEP-Joint, - author = {T. G{\"u}nther and C. R{\"u}cker}, - title = {{A} new joint inversion approach applied to the combined tomography of dc resistivity and seismic refraction data.}, - booktitle = {Ext. Abstract, 19. EEGS annual meeting (SAGEEP), 02.-06.04.2006; Seattle, USA.}, - year = {2006}, - abstract = {We present a new joint inversion approach that allows for a combined inversion of independent physical parameters by exchanging structural information. The technique is based on the ideas of robust modeling. Occurring gradients of one parameter facilitate the development of gradients in the other but does not enforce this. In the presence of boundaries that can be seen by both methods it leads to sharp contrasted models. Finally, a combined image of the subsurface is obtained by cluster analysis. The technique is applied to the inversion of dc resistivity and seismic refraction data. Two synthetic data sets show how different boundary types are resolved with and without structural coupling. It is demonstrated how the quality of the inversion results is improved by the new approach.}, - doi = {10.4133/1.2923578}, - file = {GuentherRuecker2006SAGEEP-Joint.pdf:GuentherRuecker2006SAGEEP-Joint.pdf:PDF}, - owner = {Guenther.T}, - timestamp = {2017.08.21}, -} - -@InProceedings{GuentherDluHolYa2010SAGEEP, - author = {Thomas Günther and Raphael Dlugosch and Raphael Holland and Ugur Yaramanci}, - title = {{A}quifer characterization using coupled inversion of {MRS} \& {DC}/{IP} data on a hydrogeophysical test-site}, - booktitle = {Ext. Abstract, 23. EEGS annual meeting (SAGEEP), April 11-14, 2010; Keystone, CO.}, - year = {2010}, - volume = {23}, - pages = {302-307}, - abstract = {We present a new joint inversion approach that allows for a combined inversion of independent physical parameters by exchanging structural information. The technique is based on the ideas of robust modeling. Occurring gradients of one parameter facilitate the development of gradients in the other but does not enforce this. In the presence of boundaries that can be seen by both methods it leads to sharp contrasted models. Finally, a combined image of the subsurface is obtained by cluster analysis. The technique is applied to the inversion of dc resistivity and seismic refraction data. Two synthetic data sets show how different boundary types are resolved with and without structural coupling. It is demonstrated how the quality of the inversion results is improved by the new approach.}, - doi = {10.4133/1.3445447}, - file = {GuentherDluHolYa2010SAGEEP.pdf:GuentherDluHolYa2010SAGEEP.pdf:PDF}, - owner = {Guenther.T}, - timestamp = {2010.11.26}, -} - -@InProceedings{Guenther2013NSG, - author = {Thomas G{\"u}nther}, - title = {{O}n {I}nversion of {F}requency {D}omain {E}lectromagnetic {D}ata in {S}alt {W}ater {P}roblems - {S}ensitivity and {R}esolution}, - booktitle = {Ext. Abstr., 19th European Meeting of Environmental and Engineering Geophysics, Bochum, Germany}, - year = {2013}, - doi = {10.3997/2214-4609.20131387}, - file = {Guenther2013NSG.pdf:Guenther2013NSG.pdf:PDF}, - owner = {Guenther.T}, - timestamp = {2013.09.17}, -} - -@Article{jordi2018geostatistical, - author = {Jordi, C. and Doetsch, J. and G{\"u}nther, T. and Schmelzbach, C. and Robertsson, J. O.A.}, - journal = {Geophysical Journal International}, - title = {Geostatistical regularization operators for geophysical inverse problems on irregular meshes}, - year = {2018}, - number = {2}, - pages = {1374--1386}, - volume = {213}, - doi = {10.1093/gji/ggy055}, - publisher = {Oxford University Press}, -} - -@Article{gruenenbaum2023JoH, - author = {Nele Gr\"{u}nenbaum and Thomas G\"{u}nther and Janek Greskowiak and Thomas Vienken and Mike M\"{u}ller-Petke and Gudrun Massmann}, - journal = {Journal of Hydrology}, - title = {Salinity distribution in the subterranean estuary of a meso-tidal high-energy beach characterized by {E}lectrical {R}esistivity {T}omography and direct push technology}, - year = {2023}, - month = feb, - pages = {129074}, - volume = {617}, - abstract = {Understanding the interaction of terrestrial freshwater and seawater in the subterranean estuary (STE) is an important factor when considering nutrient fluxes from land to sea. State-of-the-art research describes the STE by a tide-induced upper saline recirculation cell, a freshwater discharge tube and a deep saltwater wedge. However, recent numerical modelling and shallow hydrogeochemical investigations for high-energy beaches indicate that multiple saline recirculation cells may exist and affect the land-sea interaction. Electrical Resistivity Tomography (ERT) and Direct Push (DP) technologies are common tools to explore the subsurface. Due to their sensitivity to the electrical conductivity of pore water, they permit investigating the STE. This study combines ERT and DP to image the salinity distribution within the STE of a meso-tidal, high-energy beach. We actively incorporate the DP data into the ERT inversion and use geostatistical regularization for closing the resolution gap. For the first time, our experimental results confirm the existence of several 10–20 m deep reaching upper saline recirculation cells and corresponding brackish discharge locations generated by a pronounced runnel-ridge beach system in 2019, whereas in 2021 only a single cell was displayed for a flat topography at the time.}, - creationdate = {2023-10-26T15:57:49}, - doi = {10.1016/j.jhydrol.2023.129074}, - modificationdate = {2023-10-26T15:57:49}, - owner = {Guenther.T}, - publisher = {Elsevier {BV}}, - url = {https://doi.org/10.1016/j.jhydrol.2023.129074}, -} - -@Article{rochlitz2023GJI, - author = {Rochlitz, R. and Becken, M. and G\"{u}nther, T.}, - journal = {Geophys. J. Int.}, - title = {Three-dimensional inversion of semi-airborne electromagnetic data with a second-order finite-element forward solver}, - year = {2023}, - month = {feb}, - number = {1}, - pages = {528--545}, - volume = {234}, - creationdate = {2023-10-26T15:58:01}, - doi = {10.1093/gji/ggad056}, - modificationdate = {2023-10-26T15:58:01}, - owner = {Guenther.T}, - publisher = {Oxford University Press ({OUP})}, -} - -@Article{norooz2021JoAG, - author = {Reyhaneh Norooz and Per-Ivar Olsson and Torleif Dahlin and Thomas G\"{u}nther and Christian Bernstone}, - journal = {Journal of Applied Geophysics}, - title = {A geoelectrical pre-study of \"{A}lvkarleby test embankment dam: 3D forward modelling and effects of structural constraints on the 3D inversion model of zoned embankment dams}, - year = {2021}, - month = aug, - pages = {104355}, - volume = {191}, - creationdate = {2023-10-26T15:58:15}, - doi = {10.1016/j.jappgeo.2021.104355}, - modificationdate = {2023-10-26T15:58:15}, - owner = {Guenther.T}, - publisher = {Elsevier {BV}}, - url = {https://doi.org/10.1016/j.jappgeo.2021.104355}, -} - -@Article{skibbe2021G, - author = {Nico Skibbe and Thomas G\"{u}nther and Mike M\"{u}ller-Petke}, - journal = {{GEOPHYSICS}}, - title = {Improved hydrogeophysical imaging by structural coupling of 2D magnetic resonance and electrical resistivity tomography}, - year = {2021}, - month = jun, - number = {5}, - pages = {WB77--WB88}, - volume = {86}, - creationdate = {2023-10-26T15:58:26}, - doi = {10.1190/geo2020-0593.1}, - modificationdate = {2023-10-26T15:58:26}, - owner = {Guenther.T}, - publisher = {Society of Exploration Geophysicists}, - url = {https://doi.org/10.1190/geo2020-0593.1}, -} - -@InCollection{tanner2020, - author = {David C. Tanner and Hermann Buness and Jan Igel and Thomas Günther and Gerald Gabriel and Peter Skiba and Thomas Plenefisch and Nicolai Gestermann and Thomas R. Walter}, - booktitle = {Understanding Faults}, - publisher = {Elsevier}, - title = {Chapter 3 - Fault detection}, - year = {2020}, - editor = {David Tanner and Christian Brandes}, - isbn = {978-0-12-815985-9}, - pages = {81-146}, - abstract = {This chapter focuses on the major geophysical and remote sensing methods of detecting both active and inactive faults in the Earth's crust. Each method is discussed in turn to show the uses, limitations and advantages of the method. We show examples of each method to detect faults in different geological situations.}, - creationdate = {2023-10-26T15:58:33}, - doi = {https://doi.org/10.1016/B978-0-12-815985-9.00003-5}, - keywords = {Geophysical methods, Remote sensing, Fault detection, Seismic, Ground-penetrating radar, Electrical resistivity tomography, Gravimetry, Magnetics, Seismology}, - modificationdate = {2023-10-26T15:58:33}, - owner = {Dlugosch.R}, - timestamp = {2019-10-15}, - url = {http://www.sciencedirect.com/science/article/pii/B9780128159859000035}, -} - -@Article{skibbe2020G, - author = {Nico Skibbe and Raphael Rochlitz and Thomas G\"{u}nther and Mike M\"{u}ller-Petke}, - journal = {{GEOPHYSICS}}, - title = {Coupled magnetic resonance and electrical resistivity tomography: An open-source toolbox for surface nuclear-magnetic resonance}, - year = {2020}, - month = apr, - number = {3}, - pages = {F53--F64}, - volume = {85}, - creationdate = {2023-10-26T15:58:50}, - doi = {10.1190/geo2019-0484.1}, - modificationdate = {2023-10-26T15:58:50}, - owner = {Guenther.T}, - publisher = {Society of Exploration Geophysicists}, - url = {https://doi.org/10.1190/geo2019-0484.1}, -} - -@Article{jiang2020G, - author = {Chuandong Jiang and Jan Igel and Raphael Dlugosch and Mike Müller-Petke and Thomas Günther and Julian Helms and Jörg Lang and Jutta Winsemann}, - journal = {{GEOPHYSICS}}, - title = {Magnetic resonance tomography constrained by ground-penetrating radar for improved hydrogeophysical characterisation}, - year = {2020}, - month = {aug}, - pages = {1--56}, - creationdate = {2023-10-26T15:59:03}, - doi = {10.1190/geo2020-0052.1}, - modificationdate = {2023-10-26T15:59:03}, - owner = {Dlugosch.R}, - publisher = {Society of Exploration Geophysicists}, - timestamp = {2020-08-18}, -} - -@Article{wagner2019GJI, - author = {F M Wagner and C Mollaret and T Günther and A Kemna and C Hauck}, - journal = {Geophysical Journal International}, - title = {Quantitative imaging of water, ice, and air in permafrost systems through petrophysical joint inversion of seismic refraction and electrical resistivity data}, - year = {2019}, - month = {sep}, - creationdate = {2023-10-26T15:59:18}, - doi = {10.1093/gji/ggz402}, - modificationdate = {2023-10-26T15:59:18}, - owner = {Guenther.T}, - publisher = {Oxford University Press ({OUP})}, -} - -@Article{jordi2019GJI, - author = {C Jordi and J Doetsch and T Günther and C Schmelzbach and H Maurer and J O A Robertsson}, - journal = {Geophysical Journal International}, - title = {Structural joint inversion on irregular meshes}, - year = {2019}, - month = {dec}, - number = {3}, - pages = {1995--2008}, - volume = {220}, - creationdate = {2023-10-26T15:59:32}, - doi = {10.1093/gji/ggz550}, - modificationdate = {2023-10-26T15:59:32}, - owner = {Dlugosch.R}, - publisher = {Oxford University Press ({OUP})}, - timestamp = {2020-01-15}, -} - -@Article{wunderlich2018G, - author = {Tina Wunderlich and Peter Fischer and Dennis Wilken and Hanna Hadler and Ercan Erkul and Rebekka Mecking and Thomas Günther and Michael Heinzelmann and Andreas Vött and Wolfgang Rabbel}, - journal = {{GEOPHYSICS}}, - title = {Constraining electric resistivity tomography by direct push electric conductivity logs and vibracores: {A}n exemplary study of the {F}iume {M}orto silted riverbed ({O}stia {A}ntica, western {I}taly)}, - year = {2018}, - month = {apr}, - number = {3}, - pages = {B87--B103}, - volume = {83}, - creationdate = {2023-10-26T15:59:45}, - doi = {10.1190/geo2016-0660.1}, - modificationdate = {2023-10-26T15:59:45}, - owner = {Dlugosch.R}, - publisher = {Society of Exploration Geophysicists}, - timestamp = {2018.09.17}, -} - -@Article{skibbe2018G, - author = {Nico Skibbe and Thomas Günther and Mike Müller-Petke}, - journal = {{GEOPHYSICS}}, - title = {Structurally coupled cooperative inversion of magnetic resonance with resistivity soundings}, - year = {2018}, - month = {oct}, - number = {6}, - pages = {JM51--JM63}, - volume = {83}, - creationdate = {2023-10-26T15:59:56}, - doi = {10.1190/geo2018-0046.1}, - eprint = {https://doi.org/10.1190/geo2018-0046.1}, - file = {skibbe2018G.pdf:skibbe2018G.pdf:PDF}, - modificationdate = {2023-10-26T15:59:56}, - owner = {Dlugosch.R}, - publisher = {Society of Exploration Geophysicists}, - timestamp = {2018.09.17}, - url = {https://doi.org/10.1190/geo2018-0046.1}, -} - -@Article{ronczka2015G, - author = {Mathias Ronczka and Carsten R\"{u}cker and Thomas G\"{u}nther}, - journal = {Geophysics}, - title = {{N}umerical study of long-electrode electric resistivity tomography {\textemdash} {A}ccuracy, sensitivity, and resolution}, - year = {2015}, - month = {sep}, - number = {6}, - pages = {E317--E328}, - volume = {80}, - creationdate = {2023-10-26T16:00:25}, - doi = {10.1190/geo2014-0551.1}, - modificationdate = {2023-10-26T16:00:25}, - owner = {Guenther.T}, - publisher = {Society of Exploration Geophysicists}, -} - -@Article{ronczka2020NSG, - author = {Mathias Ronczka and Thomas Günther and Michael Grinat and Helga Wiederhold}, - journal = {Near Surface Geophysics}, - title = {Monitoring freshwater-saltwater interfaces with {SAMOS} - installation effects on data and inversion}, - year = {2020}, - month = {jul}, - number = {4}, - pages = {369--383}, - volume = {18}, - creationdate = {2023-10-26T16:01:25}, - doi = {10.1002/nsg.12115}, - modificationdate = {2023-10-26T16:01:25}, - owner = {Dlugosch.R}, - publisher = {Wiley}, - timestamp = {2020-08-18}, -} - -@Article{doetsch2012JoAG, - author = {Joseph Doetsch and Niklas Linde and Mirco Pessognelli and Alan G. Green and Thomas Günther}, - journal = {Journal of Applied Geophysics}, - title = {{C}onstraining 3-{D} electrical resistance tomography with {GPR} reflection data for improved aquifer characterization}, - year = {2012}, - issn = {0926-9851}, - note = {Developments in GPR and near-surface seismics - New applications and strategies for data integration, inversion, and modelling}, - pages = {68 - 76}, - volume = {78}, - creationdate = {2023-10-26T16:01:43}, - doi = {10.1016/j.jappgeo.2011.04.008}, - keywords = {GPR}, - modificationdate = {2023-10-26T16:01:43}, - owner = {Guenther.T}, - timestamp = {2012.02.07}, - url = {http://www.sciencedirect.com/science/article/pii/S0926985111000905}, -} - -@Article{guenther2012HaESS, - author = {G\"unther, T. and M\"uller-Petke, M.}, - journal = {Hydrology and Earth System Sciences}, - title = {{H}ydraulic properties at the {N}orth {S}ea island of {B}orkum derived from joint inversion of magnetic resonance and electrical resistivity soundings}, - year = {2012}, - number = {9}, - pages = {3279--3291}, - volume = {16}, - creationdate = {2023-10-26T16:01:55}, - doi = {10.5194/hess-16-3279-2012}, - modificationdate = {2023-10-26T16:01:55}, - owner = {Guenther.T}, - timestamp = {2012.10.16}, - url = {http://www.hydrol-earth-syst-sci.net/16/3279/2012/}, -} - -@Article{ruecker2011G, - author = {Carsten R{\"u}cker and Thomas G{\"u}nther}, - journal = {Geophysics}, - title = {{T}he simulation of finite {ERT} electrodes using the complete electrode model}, - year = {2011}, - pages = {F227}, - volume = {76}, - creationdate = {2023-10-26T16:02:03}, - doi = {10.1190/1.3581356}, - modificationdate = {2023-10-26T16:02:03}, - owner = {thomas}, - printout = {yes}, - timestamp = {2011.07.14}, -} - -@Comment{jabref-meta: databaseType:bibtex;} +% Encoding: UTF-8 + +@Article{Archie1942, + Title = {{T}he {E}lectrical {R}esistivity {L}og as an {A}id in {D}etermining {S}ome {R}eservoir {C}haracteristics}, + Author = {G.E. Archie}, + Journal = {Transactions of the {AIME}}, + Year = {1942}, + + Month = {dec}, + Number = {01}, + Pages = {54--62}, + Volume = {146}, + + Doi = {10.2118/942054-g}, + Owner = {carsten}, + Publisher = {Society of Petroleum Engineers ({SPE})}, + Timestamp = {2016.07.05}, + Url = {http://dx.doi.org/10.2118/942054-g} +} + +@Article{ChenDavHag+2009, + Title = {{A}lgorithm 887: {CHOLMOD}, supernodal sparse {C}holesky factorization and update/downdate}, + Author = {Y. Chen and T. A. Davis and W. W. Hager and S. Rajamanickam}, + Journal = {ACM Trans. Math. Software}, + Year = {2009}, + Number = {3}, + Pages = {No.: 22}, + Volume = {35}, + + File = {ChenDavHag+2009.pdf:all/ChenDavHag+2009.pdf:PDF}, + Owner = {carsten}, + Timestamp = {2010.04.09} +} + +@Article{EngelhardtPit1955, + Title = {{Ü}ber die {Z}usammenhänge zwischen {P}orosität, {P}ermeabilität und {K}orngröße bei {S}anden und {S}andsteinen}, + Author = {W. v. Engelhardt and H. Pitter}, + Journal = {Heidelberger Beiträge zur Mineralogie und Petrographie}, + Year = {1955}, + Number = {6}, + Pages = {477-491}, + Volume = {2}, + + File = {EngelhardtPit1955.pdf:all/EngelhardtPit1955.pdf:PDF}, + Owner = {carsten}, + Timestamp = {2015.11.11} +} + +@Article{GeuzaineRemacle2009, + Title = {{G}msh: a three-dimensional finite element mesh generator with built-in pre- and post-processing facilities}, + Author = {Geuzaine, C. and Remacle, J.-F.}, + Journal = {International Jounral for Numerical Methods in Engineering}, + Year = {2009}, + Pages = {1309-1331}, + Volume = {79}, + + Owner = {fwagner}, + Timestamp = {2011.05.30} +} + +@Article{NordsiekWel2008, + Title = {{A} new approach to fitting induced-polarization spectra}, + Author = {Sven Nordsiek and Andreas Weller}, + Journal = {Geophysics}, + Year = {2008}, + Number = {6}, + Pages = {F235--F245}, + Volume = {73}, + + Owner = {carsten}, + Timestamp = {2011.03.17} +} + +@InCollection{Shewchuk96b, + Title = {{T}riangle: {E}ngineering a {2D} {Q}uality {M}esh {G}enerator and {D}elaunay {T}riangulator}, + Author = {Jonathan Richard Shewchuk}, + Booktitle = {Applied Computational Geometry: Towards Geometric Engineering}, + Publisher = {Springer-Verlag}, + Year = {1996}, + Editor = {Ming C. Lin and Dinesh Manocha}, + Month = may, + Note = {From the First ACM Workshop on Applied Computational Geometry}, + Pages = {203--222}, + Series = {Lecture Notes in Computer Science}, + Volume = {1148}, + + Owner = {Dlugosch.R}, + Timestamp = {2013.04.15} +} + +@Manual{tetgen, + Title = {{T}et{G}en - a quality-constrained tetrahedral mesh generator}, + + Address = {\url{http://tetgen.org}}, + Author = {H. Si}, + Organization = {Weierstrass institute, Berlin}, + Year = {2002-2008}, + + Owner = {halbmy}, + Timestamp = {2008.05.19} +} + +@Article{Si2015, + Title = {{TetGen}, a {D}elaunay-{B}ased {Q}uality {T}etrahedral {M}esh {G}enerator}, + Author = {Hang Si}, + Journal = {{ACM} Transactions on Mathematical Software}, + Year = {2015}, + + Month = {feb}, + Number = {2}, + Pages = {1--36}, + Volume = {41}, + + Doi = {10.1145/2629697}, + File = {Si2015.pdf:all/Si2015.pdf:PDF}, + Owner = {carsten}, + Publisher = {Association for Computing Machinery ({ACM})}, + Timestamp = {2015.12.03}, + Url = {http://dx.doi.org/10.1145/2629697} +} + +@TechReport{Si2004, + Title = {{T}et{G}en. {A} 3{D} {D}elaunay tetrahedral mesh generator. v.1.3}, + Author = {Hang Si}, + Institution = {WIAS}, + Year = {2004}, + Number = {4}, + Type = {Users manual}, + + File = {Si2004.pdf:all/Si2004.pdf:PDF}, + Owner = {carsten}, + Printout = {yes}, + Timestamp = {2013.08.28} +} + +@Article{SinghGup2001, + Title = {{N}ew method for fast computation of gravity and magnetic anomalies from arbitrary polyhedra}, + Author = {Bijendra Singh and D. Guptasarma}, + Journal = {Geophysics}, + Year = {2001}, + Pages = {521-526}, + Volume = {66}, + + File = {SinghGup2001.pdf:all/SinghGup2001.pdf:PDF}, + Owner = {carsten}, + Timestamp = {2013.10.10} +} + +@Article{WonBev1987, + Title = {{C}omputing the gravitational and magnetic anomalies due to a polygon: {A}lgorithms and {F}ortran subroutines}, + Author = {I. J. Won and Michael Bevis}, + Journal = {Geophysics}, + Year = {1987}, + Number = {2}, + Pages = {232-238}, + Volume = {52}, + + File = {WonBev1987.pdf:all/WonBev1987.pdf:PDF}, + Owner = {carsten}, + Timestamp = {2012.03.23} +} + +@Book{Zienkiewicz1977, + Title = {{T}he {F}inite {E}lement {M}ethod}, + Author = {O. C. Zienkiewicz}, + Publisher = {McGraw-Hill, London}, + Year = {1977}, + Edition = {3rd}, + + Owner = {carsten}, + Timestamp = {2010.03.29} +} + +@Article{PeltonWarHal1978, + author = {W.H. Pelton and S.H. Ward and P.G. Hallof and W.R. Sill and P. H. Nelson}, + title = {{M}ineral discrimination and removal of inductive coupling with multifrequency ip}, + journal = {Geophysics}, + year = {1978}, + volume = {43}, + number = {3}, + pages = {588--609}, + file = {PeltonWarHal1978.pdf:all/PeltonWarHal1978.pdf:PDF}, + groups = {SIP}, + owner = {carsten}, + timestamp = {2011.03.17}, +} + +@Article{Seigel1959, + author = {Seigel, H. O.}, + title = {Mathematical formuiation and type curves for induced polarization}, + journal = {Geophysics}, + year = {1959}, + volume = {24}, + pages = {547-565}, + owner = {carsten}, + timestamp = {2017.05.23}, +} + +@Article{RueckerGueWag2017GaG, + author = {Carsten Rücker and Thomas Günther and Florian Wagner}, + title = {{pyGIMLi}: An open-source library for modelling and inversion in geophysics}, + journal = {Computers \& Geosciences}, + year = {2017}, + owner = {Dlugosch.R}, + timestamp = {2017.07.27}, +} + +@Article{moser1991G, + author = {Moser, TJ}, + title = {{S}hortest path calculation of seismic rays}, + journal = {Geophysics}, + year = {1991}, + volume = {56}, + number = {1}, + pages = {59-67}, + issn = {0016-8033}, + doi = {10.1190/1.1442958}, + owner = {Dlugosch.R}, + timestamp = {2017.08.21}, + type = {Journal Article}, +} + +@Article{podvin1991GJI, + author = {Pascal Podvin and Isabelle Lecomte}, + title = {Finite difference computation of traveltimes in very contrasted velocity models: a massively parallel approach and its associated tools}, + journal = {Geophysical Journal International}, + year = {1991}, + volume = {105}, + number = {1}, + pages = {271--284}, + month = {apr}, + doi = {10.1111/j.1365-246x.1991.tb03461.x}, + owner = {Dlugosch.R}, + publisher = {Oxford University Press ({OUP})}, + timestamp = {2017.08.21}, + url = {https://doi.org/10.1111/j.1365-246x.1991.tb03461.x}, +} + +@Article{loewer2017GJI, + author = {M. Loewer and T. G\"{u}nther and J. Igel and S. Kruschwitz and T. Martin and N. Wagner}, + title = {Ultra-broad-band electrical spectroscopy of soils and sediments{\textemdash}a combined permittivity and conductivity model}, + journal = {Geophysical Journal International}, + year = {2017}, + volume = {210}, + number = {3}, + pages = {1360--1373}, + month = {jun}, + doi = {10.1093/gji/ggx242}, + owner = {Dlugosch.R}, + publisher = {Oxford University Press ({OUP})}, + timestamp = {2017.07.27}, + url = {https://doi.org/10.1093/gji/ggx242}, +} + +@Article{LoewerIgeWag2016, + author = {Markus Loewer and Jan Igel and Norman Wagner}, + title = {{S}pectral {D}ecomposition of {S}oil {E}lectrical and {D}ielectric {L}osses and {P}rediction of {I}n {S}itu {GPR} {P}erformance}, + journal = {{IEEE} J. Sel. Top. Appl. Earth Observations Remote Sensing}, + year = {2016}, + volume = {9}, + number = {1}, + pages = {212--230}, + doi = {10.1109/jstars.2015.2424152}, + owner = {TG}, + publisher = {Institute of Electrical {\&} Electronics Engineers ({IEEE})}, + timestamp = {2016.09.14}, + url = {http://dx.doi.org/10.1109/JSTARS.2015.2424152}, +} + +@Article{hellman2017JoAG, + author = {Kristofer Hellman and Mathias Ronczka and Thomas G\"{u}nther and Marcus Wennermark and Carsten R\"{u}cker and Torleif Dahlin}, + title = {Structurally coupled inversion of {ERT} and refraction seismic data combined with cluster-based model integration}, + journal = {Journal of Applied Geophysics}, + year = {2017}, + volume = {143}, + pages = {169--181}, + month = {aug}, + doi = {10.1016/j.jappgeo.2017.06.008}, + owner = {Dlugosch.R}, + publisher = {Elsevier {BV}}, + timestamp = {2017.08.21}, + url = {https://doi.org/10.1016/j.jappgeo.2017.06.008}, +} + +@InProceedings{GuentherRuecker2006SAGEEP-Joint, + author = {T. G{\"u}nther and C. R{\"u}cker}, + title = {{A} new joint inversion approach applied to the combined tomography of dc resistivity and seismic refraction data.}, + booktitle = {Ext. Abstract, 19. EEGS annual meeting (SAGEEP), 02.-06.04.2006; Seattle, USA.}, + year = {2006}, + abstract = {We present a new joint inversion approach that allows for a combined inversion of independent physical parameters by exchanging structural information. The technique is based on the ideas of robust modeling. Occurring gradients of one parameter facilitate the development of gradients in the other but does not enforce this. In the presence of boundaries that can be seen by both methods it leads to sharp contrasted models. Finally, a combined image of the subsurface is obtained by cluster analysis. The technique is applied to the inversion of dc resistivity and seismic refraction data. Two synthetic data sets show how different boundary types are resolved with and without structural coupling. It is demonstrated how the quality of the inversion results is improved by the new approach.}, + doi = {10.4133/1.2923578}, + file = {GuentherRuecker2006SAGEEP-Joint.pdf:GuentherRuecker2006SAGEEP-Joint.pdf:PDF}, + owner = {Guenther.T}, + timestamp = {2017.08.21}, +} + +@InProceedings{GuentherDluHolYa2010SAGEEP, + author = {Thomas Günther and Raphael Dlugosch and Raphael Holland and Ugur Yaramanci}, + title = {{A}quifer characterization using coupled inversion of {MRS} \& {DC}/{IP} data on a hydrogeophysical test-site}, + booktitle = {Ext. Abstract, 23. EEGS annual meeting (SAGEEP), April 11-14, 2010; Keystone, CO.}, + year = {2010}, + volume = {23}, + pages = {302-307}, + abstract = {We present a new joint inversion approach that allows for a combined inversion of independent physical parameters by exchanging structural information. The technique is based on the ideas of robust modeling. Occurring gradients of one parameter facilitate the development of gradients in the other but does not enforce this. In the presence of boundaries that can be seen by both methods it leads to sharp contrasted models. Finally, a combined image of the subsurface is obtained by cluster analysis. The technique is applied to the inversion of dc resistivity and seismic refraction data. Two synthetic data sets show how different boundary types are resolved with and without structural coupling. It is demonstrated how the quality of the inversion results is improved by the new approach.}, + doi = {10.4133/1.3445447}, + file = {GuentherDluHolYa2010SAGEEP.pdf:GuentherDluHolYa2010SAGEEP.pdf:PDF}, + owner = {Guenther.T}, + timestamp = {2010.11.26}, +} + +@InProceedings{Guenther2013NSG, + author = {Thomas G{\"u}nther}, + title = {{O}n {I}nversion of {F}requency {D}omain {E}lectromagnetic {D}ata in {S}alt {W}ater {P}roblems - {S}ensitivity and {R}esolution}, + booktitle = {Ext. Abstr., 19th European Meeting of Environmental and Engineering Geophysics, Bochum, Germany}, + year = {2013}, + doi = {10.3997/2214-4609.20131387}, + file = {Guenther2013NSG.pdf:Guenther2013NSG.pdf:PDF}, + owner = {Guenther.T}, + timestamp = {2013.09.17}, +} + +@Article{jordi2018geostatistical, + author = {Jordi, C. and Doetsch, J. and G{\"u}nther, T. and Schmelzbach, C. and Robertsson, J. O.A.}, + journal = {Geophysical Journal International}, + title = {Geostatistical regularization operators for geophysical inverse problems on irregular meshes}, + year = {2018}, + number = {2}, + pages = {1374--1386}, + volume = {213}, + doi = {10.1093/gji/ggy055}, + publisher = {Oxford University Press}, +} + +@Article{gruenenbaum2023JoH, + author = {Nele Gr\"{u}nenbaum and Thomas G\"{u}nther and Janek Greskowiak and Thomas Vienken and Mike M\"{u}ller-Petke and Gudrun Massmann}, + journal = {Journal of Hydrology}, + title = {Salinity distribution in the subterranean estuary of a meso-tidal high-energy beach characterized by {E}lectrical {R}esistivity {T}omography and direct push technology}, + year = {2023}, + month = feb, + pages = {129074}, + volume = {617}, + abstract = {Understanding the interaction of terrestrial freshwater and seawater in the subterranean estuary (STE) is an important factor when considering nutrient fluxes from land to sea. State-of-the-art research describes the STE by a tide-induced upper saline recirculation cell, a freshwater discharge tube and a deep saltwater wedge. However, recent numerical modelling and shallow hydrogeochemical investigations for high-energy beaches indicate that multiple saline recirculation cells may exist and affect the land-sea interaction. Electrical Resistivity Tomography (ERT) and Direct Push (DP) technologies are common tools to explore the subsurface. Due to their sensitivity to the electrical conductivity of pore water, they permit investigating the STE. This study combines ERT and DP to image the salinity distribution within the STE of a meso-tidal, high-energy beach. We actively incorporate the DP data into the ERT inversion and use geostatistical regularization for closing the resolution gap. For the first time, our experimental results confirm the existence of several 10–20 m deep reaching upper saline recirculation cells and corresponding brackish discharge locations generated by a pronounced runnel-ridge beach system in 2019, whereas in 2021 only a single cell was displayed for a flat topography at the time.}, + creationdate = {2023-10-26T15:57:49}, + doi = {10.1016/j.jhydrol.2023.129074}, + modificationdate = {2023-10-26T15:57:49}, + owner = {Guenther.T}, + publisher = {Elsevier {BV}}, + url = {https://doi.org/10.1016/j.jhydrol.2023.129074}, +} + +@Article{rochlitz2023GJI, + author = {Rochlitz, R. and Becken, M. and G\"{u}nther, T.}, + journal = {Geophys. J. Int.}, + title = {Three-dimensional inversion of semi-airborne electromagnetic data with a second-order finite-element forward solver}, + year = {2023}, + month = {feb}, + number = {1}, + pages = {528--545}, + volume = {234}, + creationdate = {2023-10-26T15:58:01}, + doi = {10.1093/gji/ggad056}, + modificationdate = {2023-10-26T15:58:01}, + owner = {Guenther.T}, + publisher = {Oxford University Press ({OUP})}, +} + +@Article{norooz2021JoAG, + author = {Reyhaneh Norooz and Per-Ivar Olsson and Torleif Dahlin and Thomas G\"{u}nther and Christian Bernstone}, + journal = {Journal of Applied Geophysics}, + title = {A geoelectrical pre-study of \"{A}lvkarleby test embankment dam: 3D forward modelling and effects of structural constraints on the 3D inversion model of zoned embankment dams}, + year = {2021}, + month = aug, + pages = {104355}, + volume = {191}, + creationdate = {2023-10-26T15:58:15}, + doi = {10.1016/j.jappgeo.2021.104355}, + modificationdate = {2023-10-26T15:58:15}, + owner = {Guenther.T}, + publisher = {Elsevier {BV}}, + url = {https://doi.org/10.1016/j.jappgeo.2021.104355}, +} + +@Article{skibbe2021G, + author = {Nico Skibbe and Thomas G\"{u}nther and Mike M\"{u}ller-Petke}, + journal = {{GEOPHYSICS}}, + title = {Improved hydrogeophysical imaging by structural coupling of 2D magnetic resonance and electrical resistivity tomography}, + year = {2021}, + month = jun, + number = {5}, + pages = {WB77--WB88}, + volume = {86}, + creationdate = {2023-10-26T15:58:26}, + doi = {10.1190/geo2020-0593.1}, + modificationdate = {2023-10-26T15:58:26}, + owner = {Guenther.T}, + publisher = {Society of Exploration Geophysicists}, + url = {https://doi.org/10.1190/geo2020-0593.1}, +} + +@InCollection{tanner2020, + author = {David C. Tanner and Hermann Buness and Jan Igel and Thomas Günther and Gerald Gabriel and Peter Skiba and Thomas Plenefisch and Nicolai Gestermann and Thomas R. Walter}, + booktitle = {Understanding Faults}, + publisher = {Elsevier}, + title = {Chapter 3 - Fault detection}, + year = {2020}, + editor = {David Tanner and Christian Brandes}, + isbn = {978-0-12-815985-9}, + pages = {81-146}, + abstract = {This chapter focuses on the major geophysical and remote sensing methods of detecting both active and inactive faults in the Earth's crust. Each method is discussed in turn to show the uses, limitations and advantages of the method. We show examples of each method to detect faults in different geological situations.}, + creationdate = {2023-10-26T15:58:33}, + doi = {https://doi.org/10.1016/B978-0-12-815985-9.00003-5}, + keywords = {Geophysical methods, Remote sensing, Fault detection, Seismic, Ground-penetrating radar, Electrical resistivity tomography, Gravimetry, Magnetics, Seismology}, + modificationdate = {2023-10-26T15:58:33}, + owner = {Dlugosch.R}, + timestamp = {2019-10-15}, + url = {http://www.sciencedirect.com/science/article/pii/B9780128159859000035}, +} + +@Article{skibbe2020G, + author = {Nico Skibbe and Raphael Rochlitz and Thomas G\"{u}nther and Mike M\"{u}ller-Petke}, + journal = {{GEOPHYSICS}}, + title = {Coupled magnetic resonance and electrical resistivity tomography: An open-source toolbox for surface nuclear-magnetic resonance}, + year = {2020}, + month = apr, + number = {3}, + pages = {F53--F64}, + volume = {85}, + creationdate = {2023-10-26T15:58:50}, + doi = {10.1190/geo2019-0484.1}, + modificationdate = {2023-10-26T15:58:50}, + owner = {Guenther.T}, + publisher = {Society of Exploration Geophysicists}, + url = {https://doi.org/10.1190/geo2019-0484.1}, +} + +@Article{jiang2020G, + author = {Chuandong Jiang and Jan Igel and Raphael Dlugosch and Mike Müller-Petke and Thomas Günther and Julian Helms and Jörg Lang and Jutta Winsemann}, + journal = {{GEOPHYSICS}}, + title = {Magnetic resonance tomography constrained by ground-penetrating radar for improved hydrogeophysical characterisation}, + year = {2020}, + month = {aug}, + pages = {1--56}, + creationdate = {2023-10-26T15:59:03}, + doi = {10.1190/geo2020-0052.1}, + modificationdate = {2023-10-26T15:59:03}, + owner = {Dlugosch.R}, + publisher = {Society of Exploration Geophysicists}, + timestamp = {2020-08-18}, +} + +@Article{wagner2019GJI, + author = {F M Wagner and C Mollaret and T Günther and A Kemna and C Hauck}, + journal = {Geophysical Journal International}, + title = {Quantitative imaging of water, ice, and air in permafrost systems through petrophysical joint inversion of seismic refraction and electrical resistivity data}, + year = {2019}, + month = {sep}, + creationdate = {2023-10-26T15:59:18}, + doi = {10.1093/gji/ggz402}, + modificationdate = {2023-10-26T15:59:18}, + owner = {Guenther.T}, + publisher = {Oxford University Press ({OUP})}, +} + +@Article{jordi2019GJI, + author = {C Jordi and J Doetsch and T Günther and C Schmelzbach and H Maurer and J O A Robertsson}, + journal = {Geophysical Journal International}, + title = {Structural joint inversion on irregular meshes}, + year = {2019}, + month = {dec}, + number = {3}, + pages = {1995--2008}, + volume = {220}, + creationdate = {2023-10-26T15:59:32}, + doi = {10.1093/gji/ggz550}, + modificationdate = {2023-10-26T15:59:32}, + owner = {Dlugosch.R}, + publisher = {Oxford University Press ({OUP})}, + timestamp = {2020-01-15}, +} + +@Article{wunderlich2018G, + author = {Tina Wunderlich and Peter Fischer and Dennis Wilken and Hanna Hadler and Ercan Erkul and Rebekka Mecking and Thomas Günther and Michael Heinzelmann and Andreas Vött and Wolfgang Rabbel}, + journal = {{GEOPHYSICS}}, + title = {Constraining electric resistivity tomography by direct push electric conductivity logs and vibracores: {A}n exemplary study of the {F}iume {M}orto silted riverbed ({O}stia {A}ntica, western {I}taly)}, + year = {2018}, + month = {apr}, + number = {3}, + pages = {B87--B103}, + volume = {83}, + creationdate = {2023-10-26T15:59:45}, + doi = {10.1190/geo2016-0660.1}, + modificationdate = {2023-10-26T15:59:45}, + owner = {Dlugosch.R}, + publisher = {Society of Exploration Geophysicists}, + timestamp = {2018.09.17}, +} + +@Article{skibbe2018G, + author = {Nico Skibbe and Thomas Günther and Mike Müller-Petke}, + journal = {{GEOPHYSICS}}, + title = {Structurally coupled cooperative inversion of magnetic resonance with resistivity soundings}, + year = {2018}, + month = {oct}, + number = {6}, + pages = {JM51--JM63}, + volume = {83}, + creationdate = {2023-10-26T15:59:56}, + doi = {10.1190/geo2018-0046.1}, + eprint = {https://doi.org/10.1190/geo2018-0046.1}, + file = {skibbe2018G.pdf:skibbe2018G.pdf:PDF}, + modificationdate = {2023-10-26T15:59:56}, + owner = {Dlugosch.R}, + publisher = {Society of Exploration Geophysicists}, + timestamp = {2018.09.17}, + url = {https://doi.org/10.1190/geo2018-0046.1}, +} + +@Article{ronczka2015G, + author = {Mathias Ronczka and Carsten R\"{u}cker and Thomas G\"{u}nther}, + journal = {Geophysics}, + title = {{N}umerical study of long-electrode electric resistivity tomography {\textemdash} {A}ccuracy, sensitivity, and resolution}, + year = {2015}, + month = {sep}, + number = {6}, + pages = {E317--E328}, + volume = {80}, + creationdate = {2023-10-26T16:00:25}, + doi = {10.1190/geo2014-0551.1}, + modificationdate = {2023-10-26T16:00:25}, + owner = {Guenther.T}, + publisher = {Society of Exploration Geophysicists}, +} + +@Article{ronczka2020NSG, + author = {Mathias Ronczka and Thomas Günther and Michael Grinat and Helga Wiederhold}, + journal = {Near Surface Geophysics}, + title = {Monitoring freshwater-saltwater interfaces with {SAMOS} - installation effects on data and inversion}, + year = {2020}, + month = {jul}, + number = {4}, + pages = {369--383}, + volume = {18}, + creationdate = {2023-10-26T16:01:25}, + doi = {10.1002/nsg.12115}, + modificationdate = {2023-10-26T16:01:25}, + owner = {Dlugosch.R}, + publisher = {Wiley}, + timestamp = {2020-08-18}, +} + +@Article{doetsch2012JoAG, + author = {Joseph Doetsch and Niklas Linde and Mirco Pessognelli and Alan G. Green and Thomas Günther}, + journal = {Journal of Applied Geophysics}, + title = {{C}onstraining 3-{D} electrical resistance tomography with {GPR} reflection data for improved aquifer characterization}, + year = {2012}, + issn = {0926-9851}, + note = {Developments in GPR and near-surface seismics - New applications and strategies for data integration, inversion, and modelling}, + pages = {68 - 76}, + volume = {78}, + creationdate = {2023-10-26T16:01:43}, + doi = {10.1016/j.jappgeo.2011.04.008}, + keywords = {GPR}, + modificationdate = {2023-10-26T16:01:43}, + owner = {Guenther.T}, + timestamp = {2012.02.07}, + url = {http://www.sciencedirect.com/science/article/pii/S0926985111000905}, +} + +@Article{guenther2012HaESS, + author = {G\"unther, T. and M\"uller-Petke, M.}, + journal = {Hydrology and Earth System Sciences}, + title = {{H}ydraulic properties at the {N}orth {S}ea island of {B}orkum derived from joint inversion of magnetic resonance and electrical resistivity soundings}, + year = {2012}, + number = {9}, + pages = {3279--3291}, + volume = {16}, + creationdate = {2023-10-26T16:01:55}, + doi = {10.5194/hess-16-3279-2012}, + modificationdate = {2023-10-26T16:01:55}, + owner = {Guenther.T}, + timestamp = {2012.10.16}, + url = {http://www.hydrol-earth-syst-sci.net/16/3279/2012/}, +} + +@Article{ruecker2011G, + author = {Carsten R{\"u}cker and Thomas G{\"u}nther}, + journal = {Geophysics}, + title = {{T}he simulation of finite {ERT} electrodes using the complete electrode model}, + year = {2011}, + pages = {F227}, + volume = {76}, + creationdate = {2023-10-26T16:02:03}, + doi = {10.1190/1.3581356}, + modificationdate = {2023-10-26T16:02:03}, + owner = {thomas}, + printout = {yes}, + timestamp = {2011.07.14}, +} + +@Article{KimKim2011, + author = {Kim, H.J. and Kim, Y.H.}, + year = {2011}, + title = {{A} unified transformation function for lower and upper bounding constraints on model parameters in electrical and electromagnetic inversion}, + journal = {J. Geophys. Eng.}, + volume = {8}, + pages = {21--26}, + doi = {10.1088/1742-2132/8/1/004}, +} + +@Article{ParkVan1991, + author = {Park, S.K. and Van, G.P.}, + year = {1991}, + title = {{I}nversion of pole-pole data for 3-d resistivity structure beneath arrays of electrodes}, + journal = {Geophysics}, + volume = {56}, + pages = {951--960}, + doi = {10.1190/1.1443128}, +} + +@Article{GuentherRueSpi2006, + author = {G{\"u}nther, T. and R{\"u}cker, C. and Spitzer, K.}, + year = {2006}, + title = {3-d modelling and inversion of {DC} resistivity data incorporating topography - {P}art {II}: {I}nversion}, + journal = {Geophys. J. Int.}, + volume = {166}, + pages = {506--517}, + doi = {10.1111/j.1365-246X.2006.03011.x}, +} + +@Article{WagnerGueSchMau2015GEO, + author = {Wagner, F.M. and G{\"u}nther, T. and Schmidt-Hattenberger, C. and Maurer, H.}, + year = {2015}, + title = {{C}onstructive optimization of electrode locations for target-focused resistivity monitoring}, + journal = {Geophysics}, + volume = {80}, + pages = {E29--E40}, + doi = {10.1190/geo2014-0214.1}, +} + +@Inproceedings{IgelStaGue2016SAGEEP, + author = {Igel, J. and Stadler, S. and Günther, T.}, + year = {2016}, + title = {{H}igh-resolution investigation of the capillary transition zone and its influence on {GPR} signatures}, + booktitle = {Ext. Abstr., SAGEEP, Denver, USA}, + doi = {10.4133/SAGEEP.29-046}, +} + +@Article{CostabelGue2014VZJ, + author = {Costabel, S. and G\"unther, T.}, + year = {2014}, + title = {{N}oninvasive {E}stimation of {W}ater {R}etention {P}arameters by {O}bserving the {C}apillary {F}ringe with {M}agnetic {R}esonance {S}ounding}, + journal = {Vadose Zone Journal}, + volume = {13}, + pages = {14}, + doi = {10.2136/vzj2013.09.0163}, +} + +@Article{GuentherMue2012HESS, + author = {G\"unther, T. and M\"uller-Petke, M.} + year = {2012}, + title = {{H}ydraulic properties at the {N}orth {S}ea island of {B}orkum derived from joint inversion of magnetic resonance and electrical resistivity soundings}, + journal = {Hydrology and Earth System Sciences}, + volume = {16}, + pages = {3279--3291}, + doi = {10.5194/hess-16-3279-2012}, +} + +@Article{BechtoldVanWei2012, + author = {Bechtold, M. and Vanderborght, J. and Weihermüller, L. and Herbst, M. and G\"unther, T. and Ippisch, O. and Kasteel, R. and Vereecken, H.}, + year = {2012}, + title = {{U}pward {T}ransport in a {T}hree-{D}imensional {H}eterogeneous {L}aboratory {S}oil under {E}vaporation {C}onditions}, + journal = {Vadose Zone Journal}, + volume = {11}, + doi = {10.2136/vzj2011.0066}, +} + +@Article{CostabelGueDluMue2016, + author = {Costabel, S. and G\"unther, T. and Dlugosch, R. and M\"uller-Petke, M.}, + year = {2016}, + title = {{T}orus-nuclear magnetic resonance: {Q}uasicontinuous airborne magnetic resonance profiling by using a helium-filled balloon}, + journal = {Geophysics}, + volume = {81}, + pages = {WB119--WB129}, + doi = {10.1190/geo2015-0467.1}, +} + +@Article{guenther2016JoAG, + author = {G{\"u}nther, T. and Martin, T.}, + year = {2016}, + title = {{S}pectral two-dimensional inversion of frequency-domain induced polarisation data from a mining slag heap}, + journal = {Journal of Applied Geophysics}, + volume = {135}, + pages = {436--448}, + doi = {10.1016/j.jappgeo.2016.01.008}, +} + +@Article{Ronczka_2016, + author = {Ronczka, M. and Hellman, K. and G{\"u}nther, T. and Wisen, R. and Dahlin, T.}, + year = {2016}, + title = {Electric resistivity and seismic refraction tomography, a challenging joint underwater survey at \"Asp\"o hard rock laboratory}, + journal = {Solid Earth Discussions}, + pages = {1--22}, + doi = {10.5194/se-2016-157}, +} + +@Article{AttwaAkcBas2014, + author = {Attwa, M. and Akca, I. and Basokur, A.T. and G\"unther, T.}, + year = {2014}, + title = {{S}tructure-based geoelectrical models derived from genetic algorithms: {A} case study for hydrogeological investigations along {E}lbe {R}iver coastal area, {G}ermany}, + journal = {Journal of Applied Geophysics}, + volume = {103}, + pages = {57--70}, + doi = {10.1016/j.jappgeo.2014.01.006}, +} + +@Comment{jabref-meta: databaseType:bibtex;} diff --git a/doc/references.rst b/doc/references.md similarity index 57% rename from doc/references.rst rename to doc/references.md index 7156bb63c..fcecd93e7 100644 --- a/doc/references.rst +++ b/doc/references.md @@ -1,8 +1,9 @@ -.. _sec:references: +(sec-references)= -References ----------- +# References +```{eval-rst} .. bibliography:: references.bib :style: mystyle :all: +``` \ No newline at end of file diff --git a/doc/user-guide/advanced/caching.md b/doc/user-guide/advanced/caching.md new file mode 100644 index 000000000..07f88797a --- /dev/null +++ b/doc/user-guide/advanced/caching.md @@ -0,0 +1 @@ +# Caching \ No newline at end of file diff --git a/doc/user-guide/advanced/custom-fop.md b/doc/user-guide/advanced/custom-fop.md new file mode 100644 index 000000000..1bfc9f5e5 --- /dev/null +++ b/doc/user-guide/advanced/custom-fop.md @@ -0,0 +1 @@ +# Setting up your own inversion with custom forward operator \ No newline at end of file diff --git a/doc/user-guide/advanced/hpc-parallel.md b/doc/user-guide/advanced/hpc-parallel.md new file mode 100644 index 000000000..f592867d5 --- /dev/null +++ b/doc/user-guide/advanced/hpc-parallel.md @@ -0,0 +1 @@ +# HPC & Parallel computing \ No newline at end of file diff --git a/doc/user-guide/advanced/index.md b/doc/user-guide/advanced/index.md new file mode 100644 index 000000000..86a621295 --- /dev/null +++ b/doc/user-guide/advanced/index.md @@ -0,0 +1,10 @@ + +# Advanced topics + +:::{toctree} + +custom-fop +matrices +hpc-parallel +caching +::: \ No newline at end of file diff --git a/doc/user-guide/advanced/matrices.md b/doc/user-guide/advanced/matrices.md new file mode 100644 index 000000000..9a51f3902 --- /dev/null +++ b/doc/user-guide/advanced/matrices.md @@ -0,0 +1,2 @@ + +# Matrices \ No newline at end of file diff --git a/doc/user-guide/data.md b/doc/user-guide/data.md new file mode 100644 index 000000000..6c87e4d0f --- /dev/null +++ b/doc/user-guide/data.md @@ -0,0 +1,194 @@ +--- +file_format: mystnb +kernelspec: + name: python3 +--- + +# Data + + +## What is a pyGIMLi DataContainer? + + +Data are often organized in a data container storing the individual data values as well as any description how they were obtained, e.g. the geometry of source and receivers. DataContainer is essentially a class that stores all of this information. It is different for every method and can be then filtered accordingly. It stores two primary things: sensor information and data measurements. + + +A data container holds vectors like in a dictionary, however, all of them need to have the same length defined by the .size() method. Let's first go over how you can create a DataContainer from scratch. Assume we want to create and store Vertical Electrical Sounding (VES) data. + +```{code-cell} ipython3 +:tags: [hide-cell] + +import numpy as np +import matplotlib.pyplot as plt +import pygimli as pg +from pygimli.physics import VESManager +``` + +We define logarithmically equidistant AB/2 spacings. Which is the midpoint of current electrode spacing for each measurement. + +```{code-cell} ipython3 +ab2 = np.logspace(0, 3, 11) +print(ab2) +``` + +We create an empty data container. In this case not using any method yet. + +```{code-cell} ipython3 +ves_data = pg.DataContainer() +print(ves_data) +``` + +We feed it into the data container just like in a dictionary. + +```{code-cell} ipython3 +ves_data["ab2"] = ab2 +ves_data["mn2"] = ab2 / 3 +print(ves_data) +``` + +One can also use `.showInfos()` to see the content of the data container with more wording. + +```{code-cell} ipython3 +ves_data.showInfos() +``` + +As you can see from the print out there is no sensor information. In the next subsection we will explain how to add sensor information to a data container. + ++++ + +:::{admonition} Note +:class: tip + +Data containers can also be initialized from different method managers. These have the custom names for sensors and data types of each method. For example {py:class}`pygimli.physics.ert.DataContainer` already has ['a', 'b', 'm', 'n'] entries. One can also add alias translators like C1, C2, P1, P2, so that dataERT[“P1”] will return dataERT[“m”] +::: + + +## Creating Sensors in DataContainer + + +Assume we have data associate with a transmitter, receivers and a property U. The transmitter (Tx) and receiver (Rx) positions are stored separately and we refer them with an Index (integer). Therefore we define these fields index. + +```{code-cell} ipython3 +data = pg.DataContainer() +data.registerSensorIndex("Tx") +data.registerSensorIndex("Rx") +``` + +Then we create a list of 10 sensors with a 2m spacing. We can create sensors at any moment as long as it is not in the same position of an existing sensor. + +```{code-cell} ipython3 +for x in np.arange(10): + data.createSensor([x*2, 0]) + +print(data) +``` + +We want to use all of them (and two more!) as receivers and a constant transmitter of number 2. + +```{code-cell} ipython3 +data["Rx"] = np.arange(12) +# data["Tx"] = np.arange(9) # does not work as size matters! +data["Tx"] = pg.Vector(data.size(), 2) +print(data) +``` + +:::{admonition} Note +:class: warning + +The positions under the sensor indexes must be of the same size. +::: + +If the sensor positions are given by another file (for example a GPS file), you can transform this to a NumPy array and set the sensor positions using [`.setSensorPositions()`](https://www.pygimli.org/gimliapi/classGIMLI_1_1DataContainer.html#a3c58caec5486d5390a2b6c2d8056724f) method of the DataContainer. + +## File export + +This data container can also be saved on local disk using the method `.save()` usually in a .dat format. It can then be read using `open('filename').read()`. This is also a useful way to see the data file in Python. + +```{code-cell} ipython3 +data.save("data.data") +print(open("data.data").read()) +``` + +## File format import + +Now we will go over the case if you have your own data and want to first import it using pyGIMLi and assign it to a data container. You can manually do this by importing data via Python (data must be assigned as Numpy arrays) and assign the values to the different keys in the data container. + +pyGIMLi also uses {py:func}`pygimli.load` that loads meshes and data files. It should handle most data types since it detects the headings and file extensions to get a good guess on how to load the data. + +Most methods also have the `load` function to load common data types used for the method. Such as, {py:func}`pygimli.physics.ert.load`. Method specific load functions assign the sensors if specified in the file. For a more extensive list of data imports please refer to [pybert importer package](http://resistivity.net/bert/_api/pybert.importer.html#module-pybert.importer). + + +## Processing + +To start processing the data for inversion, you can filter out and analyze the data container by applying different methods available to all types of data containers. This is done to the data container and in my cases the changes happen in place, so it is recommended to view the data in between the steps to observe what changed. + +You can check the validity of the measurements using a given condition. We can mask or unmask the data with a boolean vector. For example, below we would like to mark valid all receivers that are larger or equal to 0. + +```{code-cell} ipython3 +data.markValid(data["Rx"] >= 0) +print(data["valid"]) +print(len(data["Rx"])) +``` + +That adds a 'valid' entry to the data container that contains 1 and 0 values. You can also check the data validity by using `.checkDataValidity()`. It automatically removes values that are 0 in the valid field and writes the `invalid.data` file to your local directory. In this case it will remove the two additional values that were marked invalid. + +```{code-cell} ipython3 +data.checkDataValidity() +``` + +You can pass more information about the data set into the data container. For example, here we calculate the distance between transmitter and receiver. + +```{code-cell} ipython3 +sx = pg.x(data) +data["dist"] = np.abs(sx[data["Rx"]] - sx[data["Tx"]]) +print(data["dist"]) +``` + ++++ {"tags": ["hide-cell"]} + +You can also do some pre-processing using the validity option again. For example, here we would like to mark as **invalid** where the receiver is the same as the transmitter. + +```{code-cell} ipython3 +data.markInvalid(data["Rx"] == data["Tx"]) +``` + +then we can remove the invalid data and see the information of the remaining data. + +```{code-cell} ipython3 +data.removeInvalid() +data.showInfos() +``` + + +Below there is a table with the most useful methods, for a full list of methods of data container, please refer to [DataContainer class reference](https://www.pygimli.org/gimliapi/classGIMLI_1_1DataContainer.html) + +:::{admonition} Table of useful methods for DataContainer +:class: tip +:::{table} +:widths: auto +:align: center + +| Method | Description | +| :--- | :---: | +| [data.remove()](https://www.pygimli.org/gimliapi/classGIMLI_1_1DataContainer.html#a3d07be3931623a5ebef2bf14d06d4f50) | Remove data from index vector. Remove all data that are covered by idx. Sensors are preserved. (Inplace - DataContainer is overwritten inplace) | +| [data.add()](https://www.pygimli.org/gimliapi/classGIMLI_1_1DataContainer.html#af550aeba4f21ba26fd04c9bd3a3800ac) | Add data to this DataContainer and snap new sensor positions by tolerance snap. Data fields from this data are preserved. | +| [data.clear()](https://www.pygimli.org/gimliapi/classGIMLI_1_1DataContainer.html#ad5aa50883c00a3989aed97401592f41b) | Clear the container, remove all sensor locations and data.| +| [data.findSensorIndex()](https://www.pygimli.org/gimliapi/classGIMLI_1_1DataContainer.html#adeff1f8755b09ce80bb92b890fb0d837) | Translate a RVector into a valid IndexArray for the corresponding sensors. | +| [data.sortSensorsIndex()](https://www.pygimli.org/gimliapi/classGIMLI_1_1DataContainer.html#a3d07be3931623a5ebef2bf14d06d4f50) | Sort all data regarding there sensor indices and sensorIdxNames. Return the resulting permuation index array. | +| [data.sortSensorsX()](https://www.pygimli.org/gimliapi/classGIMLI_1_1DataContainer.html#a8d917f4e6049799bda190dfd42efef6b) | Sort all sensors regarding their increasing coordinates. Set inc flag to False to sort respective coordinate in decreasing direction.| +| [data.registerSensorIndex()](https://www.pygimli.org/gimliapi/classGIMLI_1_1DataContainer.html#a955c7c33ff8118ff9c3f5a7a78b75283) | Mark the data field entry as sensor index. | +| [data.removeUnusedSensor()](https://www.pygimli.org/gimliapi/classGIMLI_1_1DataContainer.html#a017137847f635e56a0eb5f84cbc58f5d) | Remove all unused sensors from this DataContainer and recount data sensor index entries. | +| [data.removeSensorIdx()](https://www.pygimli.org/gimliapi/classGIMLI_1_1DataContainer.html#ab0207d2be4491338818a6c67d1ed78e3) | Remove all data that contains the sensor and the sensor itself. | +::: + + + +## Visualization + +You can visualize the data in many ways depending on the physics manager. To simply view the data as a matrix you can use `pg.viewer.mpl.showDataContainerAsMatrix`. This visualizes a matrix of receivers and transmitters pairs with the associated data to plot : 'dist'. + +```{code-cell} ipython3 +pg.viewer.mpl.showDataContainerAsMatrix(data, "Rx", "Tx", 'dist') +``` + +There are various formal methods for plotting different data containers, depending on the approach used. As discussed in [Fundamentals](fundamentals.md), the primary focus here is on displaying the data container itself. Most method managers provide a .show() function specific to their method, but you can always use the main function {py:func}`pg.show`. This function automatically detects the data type and plots it accordingly. For further details on data visualization, please refer to [Data visualization](visualization.md). \ No newline at end of file diff --git a/doc/user-guide/fundamentals.md b/doc/user-guide/fundamentals.md new file mode 100644 index 000000000..d96ffd6e3 --- /dev/null +++ b/doc/user-guide/fundamentals.md @@ -0,0 +1,193 @@ +--- +file_format: mystnb +kernelspec: + name: python3 +--- + +# Fundamentals + +## Software design +In applied geophysics, a lot of research efforts are directed towards the +integration of different physical models and combined inversion approaches to +estimate multi-physical subsurface parameters. Such approaches often require +coupling of different software packages and file-based data exchange. The idea +of pyGIMLi is to present a very flexible framework for geophysical modelling and +inversion, which allows standard and customized modelling and inversion +workflows to be realized in a reproducible manner. + +The software is written in Python on top of a C++ core library, which allows a +combination of flexible scripting and numerical efficiency. pyGIMLi uses +selected external dependencies for quality constrained mesh generation in 2D +**Triangle** and 3D **Tetgen** and visualization in 2D +(**Matplotlib**) and 3D (**Paraview**) for example. For solving linear +systems we use the open-source collection **SuiteSparse**, which contains multi-frontal direct and iterative +solvers as well as reordering algorithms. + +(fig-gimliblock)= +:::{figure} _static/pg_design.png +:align: center +:class: wrap-fig +::: + + +pyGIMLi is organized in three different abstraction levels: + + +::::{tab-set} +:::{tab-item} **Application level** + +In the application level, ready-to-use method managers and frameworks are provided. Method managers (`pygimli.manager`) hold all relevant functionality related to a geophysical method. A method manager can be initialized with a data set and used to analyze and visualize this data set, create a corresponding mesh, and carry out an inversion. Various method managers are available in `pygimli.physics`. Frameworks (`pygimli.frameworks`) are generalized abstractions of standard and advanced inversions tasks such as time-lapse or joint inversion for example. Since frameworks communicate through a unified interface, they are method independent. + +::: + +:::{tab-item} **Modelling level** + +In the modelling level, users can set up customized forward operators that map discretized parameter distributions to a data vector. Once defined, it is straightforward to set up a corresponding inversion workflow or combine the forward operator with existing ones. + +::: + +:::{tab-item} **Equation level** + +The underlying equation level allows to directly access the finite element (`pygimli.solver.solveFiniteElements()`) and finite volume (`pygimli.solver.solveFiniteVolume()`) solvers to solve various partial differential equations on unstructured meshes, i.e. to approach various physical problems with possibly complex 2D and 3D geometries. + +::: +:::: + +## Module/method overview + +```{eval-rst} +.. autosummary:: + :nosignatures: + + pygimli.physics.em + pygimli.physics.ert + pygimli.physics.gravimetry + pygimli.physics.magnetics + pygimli.physics.petro + pygimli.physics.seismics + pygimli.physics.SIP + pygimli.physics.sNMR + pygimli.physics.traveltime + pygimli.physics.ves +``` + + +| method | Forward | Inverse | Dimension | +| :---------------- | :------: |:--------:|:--------:| +| {py:class}`em ` | **✓** | **✓** | *1D* | +| {py:class}`ert ` | **✓** | **✓** | *2D, 3D, 4D* | +| {py:class}`gravimetry ` | **✓** | **✓** | *2D, 3D* | +| {py:class}`magnetics ` | **✓** | **✓** | *2D, 3D* | +| {py:class}`petro ` | **✓** | **✓** | *dimensionless* | +| {py:class}`seismics ` | **✓** | **-** | "1D" | +| {py:class}`SIP ` | **✓** | **✓** | *1D, 2D* | +| {py:class}`sNMR ` | **✓** | **✓** | *1D* | +| {py:class}`traveltime ` | **✓** | **✓** | *2D, (3D)* | +| {py:class}`ves ` | **✓** | **✓** | *1D* | +::: + + +## Basic pyGIMLi classes + +```{eval-rst} +.. autosummary:: + :nosignatures: + + pygimli.Matrix + pygimli.Vector + pygimli.SparseMatrix + pygimli.BlockMatrix + pygimli.DataContainer +``` + + +```{note} + +Please add docstrings for abovementioned classes and then use autosummary function for user guide! +``` + + +| pyGIMLi class | Description | +| :---------------- | :------: | +| {py:class}` Matrix ` | All elements are stored column-wise, i.e. all rows *A[i]* are of type `pg.Vector`. This matrix is used for storing dense data (like ERT Jacobians) and doing simple algebra. | +| {py:class}` Vector ` | One dimensional array aka Vector of limited size to store data, like ERT sensitivities. | +| {py:class}`SparseMatrix ` | Used for numerical approximation of partial differential equations like finite-element or finite volume. Not typically used unless efficiency is of importance. It exists also complex-valued as pg.matrix.CSparseMatrix | +| {py:class}` BlockMatrix ` | Arbitrary matrices are combined into a logical matrix. This is of importance for inversion frameworks, e.g., concatenated Jacobian matrices during joint inversions. | +| {py:class}`DataContainer ` | Data container storing the individual data values as well as any description how they were obtained, e.g. the geometry of source and receivers. | +::: + + +## Viewer interface + +In pygimli we provide some basic post-processing routines using the matplotlib visualization framework. The main visualization call is `pygimli.viewer.show()` which is sufficient for most meshes, fields, models and streamline views. It forwards the object to be plotted to a known visualization function. `pygimli.viewer.showMesh()` is the typical call for the visualization of 2D data. + +However, the underlying `show` functions only provide an input instance and are not directly responsible for plotting the data. Depending on the data type, `pg.viewer.showMesh()` then again forwards to the following instances of `pg.viewer.mpl`: + +| **Data type** | **Draw function** | +| :---------------- | :------: | +| 2D meshes | {py:class}`drawMesh ` | +| Value per mesh cell - *model patch* | {py:class}`drawModel ` | +| Value per mesh node - *scalar field* | {py:class}`drawField ` | +| Iterable of type `[float,float]` - *vector field* | {py:class}`drawStreams ` | +| {py:class}`PosVector ` - vector field | {py:class}`drawStreams ` | +| {py:class}`Pos ` - sensor position vector | {py:class}`drawSensors ` | + + +An empty show call creates an empty ax window: + +```{code-cell} ipython3 +:tags: [hide-input] + +import pygimli as pg +import pygimli.meshtools as mt +world = mt.createWorld(start=[-10, 0], end=[10, -10], + layers=[-3, -7], worldMarker=True) +mesh = mt.createMesh(world, quality=32, area=0.2, smooth=[1, 10]) + +res = [[1,10],[2,100],[3,999]] + +cell_markers = mesh.cellMarkers() +resistivity = [res[marker-1][1] for marker in cell_markers] +nodeDta = pg.meshtools.cellDataToNodeData(mesh, resistivity) + +pg.show() +``` + +The functions `pygimli.viewer.show()` and `pygimli.viewer.showMesh()` return the matplotlib axis object as well as the colorbar object. This allows for further customization of the plot. The following example plots the mesh with cell and boundary markers as "minimal working example". The orientation of the colorscale can either be parallel to the x- (`orientation="horizontal"`) or y-axis (`orientation="vertical"`). Further customization of axes or the colorbar can be done by accessing the returned objects directly: + +```{code-cell} ipython3 +:tags: [hide-input] + +ax,cbar = pg.viewer.show(mesh, markers=True, showMesh=True, orientation="vertical") +ax.set_title("Mesh with cell and boundary markers", fontweight="bold") +ax.set_xlabel("x [m]") +ax.set_ylabel("y [m]") +``` + +If you want to plot data on top of a mesh, you can use the `data` argument. The following example shows electrical resistivities as cell data: + +```{code-cell} ipython3 +:tags: [hide-input] + +ax, cbar = pg.viewer.show(mesh, data=res, logScale=True, cMin=1, cMax=1000, orientation="vertical", label="Resistivity [$\Omega$m]") +ax.set_title("Electrical resistivities as cell data", fontweight="bold") +ax.set_xlabel("x [m]") +ax.set_ylabel("y [m]") +``` + +If you want to plot node data, this can be done with the same argument `data`. The following example shows the same electrical resistivities as node data: + +```{code-cell} ipython3 +:tags: [hide-input] + +ax, cbar = pg.viewer.show(mesh, data=nodeDta, logScale=True, cMin=1, cMax=1000, orientation = "vertical", label="Resistivity [$\Omega$m]") +ax.set_title("Electrical resistivities as node data", fontweight="bold") +ax.set_xlabel("x [m]") +ax.set_ylabel("y [m]") +``` + + +:::{admonition} Convert cell to node data +:class: info +By using the function `pg.meshtools.cellDataToNodeData()` you can convert cell data to node data. Please refer to the documentation for further details. +::: \ No newline at end of file diff --git a/doc/user-guide/getting-started/basics.md b/doc/user-guide/getting-started/basics.md new file mode 100644 index 000000000..f1f3eb9ea --- /dev/null +++ b/doc/user-guide/getting-started/basics.md @@ -0,0 +1,117 @@ +--- +file_format: mystnb +kernelspec: + name: python3 +--- + +(first-steps)= +# First steps + +The modelling as well as the inversion part of {term}`GIMLi` often requires a +spatial discretization for the domain of interest, the so called +{gimliapi}`GIMLI::Mesh`. +This tutorial shows some basic aspects of handling a mesh. + +First, the library needs to be imported. +To avoid name clashes with other libraries we suggest to `import pygimli` and +alias it to the simple abbreviation `pg`: CR + +```{code-cell} ipython3 +import pygimli as pg +``` + +Every part of the c++ namespace {gimliapi}`GIMLI` is bound to python and can +be used with the leading `pg.` + +For instance get the current version for {term}`GIMLi` with: + +```{code-cell} ipython3 +print(pg.__version__) +``` + +Now that we know the name space {gimliapi}`GIMLI`, we can create a first mesh. +A mesh is represented by a collection of nodes, cells and boundaries, +i.e., geometrical entities. + +:::{note} +A regularly spaced mesh consisting of rectangles or hexahedrons is +usually called a grid. However, a grid is just a special variant of a mesh +so GIMLi treats it the same. The only difference is how they are created. +::: + +GIMLi provides a collection of tools for mesh import, export and generation. +A simple grid generation is built-in but we also provide wrappers for +unstructured mesh generations, e.g., {term}`Triangle`, {term}`Tetgen` and +{term}`Gmsh`. To create a 2d grid you need to give two arrays/lists of sample points +in x and y direction, in that order, or just numbers. + +```{code-cell} ipython3 +grid = pg.createGrid(x=[-1.0, 0.0, 1.0, 4.0], y=[-1.0, 0.0, 1.0, 4.0]) +``` + +The returned object `grid` is an instance of {gimliapi}`GIMLI::Mesh` and +provides various methods for modification and io-operations. General +information about the grid can be printed using the simple print() function. + +```{code-cell} ipython3 +print(grid) +``` +Or you can access them manually using different methods: + +```{code-cell} ipython3 +print('Mesh: Nodes:', grid.nodeCount(), + 'Cells:', grid.cellCount(), + 'Boundaries:', grid.boundaryCount()) +``` +You can iterate through all cells of the general type {gimliapi}`GIMLI::Cell` +that also provides a lot of methods. Here we list the number of nodes and the +node ids per cell: + +```{code-cell} ipython3 +for cell in grid.cells(): + print("Cell", cell.id(), "has", cell.nodeCount(), + "nodes. Node IDs:", [n.id() for n in cell.nodes()]) + +print(type(grid.cell(0))) +``` + +To generate the input arrays `x` and `y`, you can use the +built-in {gimliapi}`GIMLI::Vector` (pre-defined with values that are type double as +`pg.Vector`), standard python lists or {term}`numpy` arrays, +which are widely compatible with {term}`GIMLi` vectors. + +```{code-cell} ipython3 +import numpy as np + +grid = pg.createGrid(x=np.linspace(-1.0, 1.0, 10), + y=1.0 - np.logspace(np.log10(1.0), np.log10(2.0), 10)) +``` + +We can find that this new `grid` contains + +```{code-cell} ipython3 +print(grid.cellCount()) +``` +rectangles of type {gimliapi}`GIMLI::Quadrangle` derived from the +base type {gimliapi}`GIMLI::Cell`, edges of type {gimliapi}`GIMLI::Edge`, +which are boundaries of the general type {gimliapi}`GIMLI::Boundary`. + +```{code-cell} ipython3 +print(grid.boundaryCount()) +``` + +The mesh can be saved and loaded in our binary mesh format `.bms`. +Or exported into `.vtk` format for 2D or 3D visualization using +{term}`Paraview`. + +However, we recommend visualizing 2-dimensional content using python scripts +that provide better exports to graphics files (e.g., png, pdf, svg). +In {term}`pygimli` we provide some basic post-processing routines using +the {term}`matplotlib` visualization framework. The main visualization call +is {py:mod}`pygimli.viewer.show` which is sufficient for most meshes, +fields, models and streamline views. + + +```{code-cell} ipython3 +pg.wait() +``` \ No newline at end of file diff --git a/doc/user-guide/getting-started/first-inversion.md b/doc/user-guide/getting-started/first-inversion.md new file mode 100644 index 000000000..744c535c8 --- /dev/null +++ b/doc/user-guide/getting-started/first-inversion.md @@ -0,0 +1,136 @@ +--- +file_format: mystnb +kernelspec: + name: python3 +--- + +(first-inversion)= +# First inversion + +This tutorial shows how to do the simplest inversion case, a curve fit, by +setting up a custom forward operator. The function to be fitted is\` + +$$ +f(x) = A \cdot e^{-x/X} +$$ + +with the two unknown coefficients A (a signal amplitude) and X (a decay rate). +Both A and X are assumed to be positive which is often the case for physical +properties. The easiest way to do this is via a logarithmic transformation of +the model vector (containing A and X) which is very easily done in pyGIMLi. + +First we import the pygimli library under a short name pg and the numerics +library numpy. Additionally we load the python plotting module of the library +matplotlib. Both are contained in most python distributions and systems. + +```{code-cell} +import numpy as np +import matplotlib.pyplot as plt +import pygimli as pg +``` + +We set up the modelling operator, i.e. to return ${\bf f}({\bf x})$ for +given model parameters A and X subsumed in a vector. In order to be able to +use operator in inversion, we derive from the abstract modelling base class. +The latter holds the main mimic of generating Jacobian and adminstrating the +model, the regularization and so on. The only function to overwrite is +**response()**. If no function **createJacobian** is provided, they are +computed by brute force (forward calculations with altered parameters). + +```{code-cell} +class ExpModelling(pg.Modelling): + """Exponential decay function modelling operator.""" + def __init__(self, xvec, verbose=False): + """Initialize with storing x values.""" + super().__init__() + self.x = xvec + + def response(self, model): + """Model response, i.e. A*exp(-x/x0).""" + return model[0] * pg.exp(-self.x / model[1]) + + def createStartModel(self, dataVals): + return pg.Vector([1.0, 3.0]) +``` + +The init function saves the x vector and defines the parameterization, i.e. +two independent parameters (a 1D mesh with 1 cell and 2 properties). +The response function computes the function using A=model[0] and X=model[1] +The function startModel defines a meaningful starting vector. There are other +methods to set the starting model as inv.setModel() but this one is a default +one for people who use the class and forget about a starting model. + +We first create an abscissa vector using numpy (note that pygimli also +provides an exp function and generate synthetic data with two arbitrary A and +X values. + +```{code-cell} +x = np.arange(0, 1, 1e-2) +data = 10.5 * np.exp(- x / 550e-3) +``` + +We define an (absolute) error level and add Gaussian noise to the data. + +```{code-cell} +error = 0.5 +data += pg.randn(*data.shape) * error +``` + +Next, an instance of the forward operator is created. We could use it for +calculating the synthetic data using f.response([10.5, 0.55]) or just +f([10.5, 0.55]). We create a real-valued (R) inversion passing the forward +operator, the data. A verbose boolean flag could be added to provide some +output the inversion, another one prints more and saves files for debugging. + +```{code-cell} +f = ExpModelling(x) +inv = pg.frameworks.MarquardtInversion(f) +``` + +We create a real-valued logarithmic transformation and apply it to the model. +Similar could be done for the data which are by default treated linearly. +We then set the error level that is used for data weighting. It can be a +float number or a vector of data length. One can also set a relative error. +Finally, we use an inversion style known as Marquardt scheme (pure local +damping with decreasing the regularization parameter subsequently) and start +with a relatively large regularization strength to avoid overshoot. +Finally run yields the coefficient vector and we plot some statistics. + +```{code-cell} +coeff = inv.run(data, absoluteError=error, verbose=True) +print(inv.relrms(), inv.chi2()) +``` + +We see that after a few iterations the absolute rms value equals the noise +level corresponding to a chi-squared misfit value of 1 as it should be the +case for synthetic data. The relative rms (in %) is less relevant here but +can be for other applications. Additionally the ranges for model and model +response are given and the objective function consisting of data misfit and +model roughness times lambda. Note that due to the local regularization the +second term does not contribute to Phi. + +We finally create a plotting figure and plot both data and model response. + +```{code-cell} +plt.figure() +plt.plot(x, data, 'x', x, inv.response, '-') +plt.grid(True) +``` + +The resulting model vector has a length of 2 and consists of the inverted A +and X values that are close to the synthetic values, being equivalent within +error bounds. + +```{code-cell} +print(coeff) +``` + +If you are interested which way the inversion took, you can have a look at +the model history. + +```{code-cell} +for model in inv.modelHistory: + print(model) + +plt.show() +``` \ No newline at end of file diff --git a/doc/user-guide/getting-started/first-modelling.md b/doc/user-guide/getting-started/first-modelling.md new file mode 100644 index 000000000..8bf83e0c8 --- /dev/null +++ b/doc/user-guide/getting-started/first-modelling.md @@ -0,0 +1,58 @@ +--- +file_format: mystnb +kernelspec: + name: python3 +--- + +(first-modelling)= +# First modelling + +This first modeling tutorial solves the stationary heat equation in 2D. The example is +taken from the pyGIMLi paper (). + +```{code-cell} ipython3 +import pygimli as pg +import pygimli.meshtools as mt +``` + +Create geometry definition for the modelling domain. + +```{code-cell} ipython3 +world = mt.createWorld(start=[-20, 0], end=[20, -16], layers=[-2, -8], + worldMarker=False) +# Create a heterogeneous block +block = mt.createRectangle(start=[-6, -3.5], end=[6, -6.0], + marker=4, boundaryMarker=10, area=0.1) +# Merge geometrical entities +geom = world + block +ax, cb = pg.show(geom, markers=True) +``` + +Create a mesh from based on the geometry definition. +When calling the {func}`pg.meshtools.createMesh` function, a quality parameter +can be forwarded to Triangle, which prescribes the minimum angle allowed in +the final mesh. + +```{code-cell} ipython3 +mesh = mt.createMesh(geom, quality=33, area=0.2, smooth=[1, 10]) +ax, _ = pg.show(mesh) +``` + +Call {py:func}`pygimli.solver.solveFiniteElements` to solve the heat +diffusion equation $\nabla\cdot(a\nabla T)=0$ with $T(bottom)=0$ +(boundary marker 4) and $T(top)=1$ (boundary marker 8), where $a$ +is the thermal diffusivity and $T$ is the temperature distribution. +We assign thermal diffusivities to the four # regions using their marker +numbers in a dictionary (a) and the fixed temperatures at the boundaries +using Dirichlet boundary conditions with the respective markers in another +dictionary (bc) + +```{code-cell} ipython3 +T = pg.solver.solveFiniteElements(mesh, + a={1: 1.0, 2: 2.0, 3: 3.0, 4:0.1}, + bc={'Dirichlet': {8: 1.0, 4: 0.0}}, verbose=True) +ax, _ = pg.show(mesh, data=T, label='Temperature $T$', + cMap="hot_r", nCols=8, contourLines=False) + +ax, _ = pg.show(geom, ax=ax, fillRegion=False) +``` \ No newline at end of file diff --git a/doc/user-guide/getting-started/how-to-continue.md b/doc/user-guide/getting-started/how-to-continue.md new file mode 100644 index 000000000..6922177bf --- /dev/null +++ b/doc/user-guide/getting-started/how-to-continue.md @@ -0,0 +1,2 @@ +(how-to-continue)= +# How to continue \ No newline at end of file diff --git a/doc/user-guide/getting-started/index.md b/doc/user-guide/getting-started/index.md new file mode 100644 index 000000000..35fcf7a2b --- /dev/null +++ b/doc/user-guide/getting-started/index.md @@ -0,0 +1,46 @@ +# Getting started + +::::{grid} 3 +:gutter: 3 + +:::{grid-item-card} Installation +:link: installation +:link-type: ref + +How to install `pyGIMLi` on your platform. +::: +:::{grid-item-card} First steps +:link: basics +:link-type: ref + +Read about the basics of using the `pyGIMLi` package. +::: +:::{grid-item-card} First modelling +:link: first-modelling +:link-type: ref + +A simple modelling example of the 2D stationary heat equation. +::: +:::{grid-item-card} First inversion +:link: first-inversion +:link-type: ref + +A simple inversion example fitting a curve. +::: +:::{grid-item-card} How to continue +:link: how-to-continue +:link-type: ref + +Additional reading material and video tutorials. +::: +:::: + +:::{toctree} +:hidden: + +installation +basics +first-modelling +first-inversion +how-to-continue +::: diff --git a/doc/user-guide/getting-started/installation.md b/doc/user-guide/getting-started/installation.md new file mode 100644 index 000000000..99b4a7806 --- /dev/null +++ b/doc/user-guide/getting-started/installation.md @@ -0,0 +1,5 @@ +```{include} ../../../INSTALLATION.md +``` +:::{note} +If you want to compile pyGIMLi from source, check out the [compilation instructions](#compilation). +::: \ No newline at end of file diff --git a/doc/user-guide/index.md b/doc/user-guide/index.md new file mode 100644 index 000000000..7232f03fd --- /dev/null +++ b/doc/user-guide/index.md @@ -0,0 +1,14 @@ +# User guide + +:::{toctree} +:numbered: + +getting-started/index +fundamentals +data +meshes +inversion +modelling +visualization +advanced/index +::: \ No newline at end of file diff --git a/doc/user-guide/inversion.md b/doc/user-guide/inversion.md new file mode 100644 index 000000000..5e7cb0854 --- /dev/null +++ b/doc/user-guide/inversion.md @@ -0,0 +1,105 @@ +# Inversion + +## Theory + +Inversion frameworks are generalized, abstract approaches to solve a specific inversion problem without specifying the appropriate geophysical methods. +This can be a specific regularization strategy, an alternative formulation of the inverse problem or algorithms of routine inversion. +It is initialized by specific forward operators or managers that provide them. + +### Gauss-Newton inversion + +The default inversion framework is based on the generalized Gauss-Newton method and is compatible with any given forward operator and thus applicable to various physical problems. +We state the inversion problem as minimization of an objective function consisting of data misfit and model constraints: + +$$ \mathbf{W}_\text{d} (\mathbf{\mathcal{F}}(\mathbf{m})-\mathbf{d}) \|^2_2 + \lambda \| \mathbf{W}_\text{m} (\mathbf{m}-\mathbf{m_0}) \|^2_2 \rightarrow\min $$ (eq:min) + +Note that we do not include inequality constraints in the minimization but use transformations to restrict parameters to reasonable ranges {cite}`{e.g., }KimKim2011`. +$\mathbf{W}_\text{d}$ is the data weighting matrix containing the inverse data errors, $\mathbf{W}_\text{m}$ is the model constraint matrix (e.g., a first-order roughness operator), and $\mathbf{m}_0$ is a reference model. +The dimensionless factor $\lambda$ scales the influence of the regularization term. +There is a wide range of different regularization methods (different kinds of smoothness and damping, mixed operators, anisotropic smoothing) +The existing ones can be used flexibly to constrain different model parameters or subsurface parts (regions), but also be extended by own functions. +The application of the Gauss-Newton scheme on minimizing {eq}`eq:min` yields the model update $\Delta\mathbf{m}^k$ in the $k^\text{th}$ iteration {cite}`ParkVan1991`: + +$$ ({\mathbf{J}}^{\text{T}}\mathbf{W_d}^{\text{T}}\mathbf{W_d}\mathbf{J} + \lambda {\mathbf{W_m}}^{\text{T}}\mathbf{W_m} +)\Delta\mathbf{m}^k =\: & +{\mathbf{J}}^{\text{T}} {\mathbf{W_d}}^{\text{T}} \mathbf{W_d}(\Delta\mathbf{d}^k) \notag \\ +−& \lambda{\mathbf{W_m}}^{\text{T}}\mathbf{W_m}(\mathbf{m}^k − \mathbf{m}^0 ) \\ +\quad\text{with}\quad \Delta \mathbf{d}^k = \mathbf{d} − \mathcal{F}(\mathbf{m}^k) +\quad\text{and}&\quad\Delta \mathbf{m}^k = \mathbf{m}^k - \mathbf{m}^{k-1}\notag +$$ + +which is solved using a conjugate-gradient least-squares solver {cite}`GuentherRueSpi2006`. +The inversion process including the region-specific regularization is sketched in Fig.~\ref{fig:InversionBase}. + +\begin{figure} +\centering\includegraphics[width=1\columnwidth]{gimli-fig-2.pdf} +\caption{Generalized inversion scheme. Already implemented (\autoref{tab:methods}) or custom forward operators can be used that provide the problem specific response function and its Jacobian. Various strategies are available to regularize the inverse problem. \label{fig:InversionBase}} +\end{figure} + +All matrices of the inversion formulation can be directly accessed from Python and thereby offer opportunities for uncertainty and resolution analysis as well as experimental design {cite}`{e.g., }WagnerGueSchMau2015GEO`. +Beyond different inversion approaches there are so-called frameworks for typical inversion (mostly regularization) tasks. +Examples that are already implemented in pyGIMLi are for example: + + * **Marquardt scheme** inversion of few independent parameters, e.g., fitting of spectra {cite}`LoewerIgeWag2016` + * **Soil-physical model reduction** incorporating soil-physical functions {cite}`IgelStaGue2016SAGEEP, CostabelGue2014VZJ` + * **Classical joint inversion** of two data sets for the same parameter like DC and EM {cite}`Guenther2013NSG` + * **Block joint inversion** of several 1D data using common layers, e.g., MRS+VES {cite}`GuentherMue2012HESS` + * **Sequential (constrained) inversion** successive independent inversion of data sets, e.g., classic time-lapse inversion {cite}`{e.g., }BechtoldVanWei2012` + * **Simultaneous constrained inversion** of data sets of data neighbored in space LCI, e.g., {cite}`CostabelGueDluMue2016`, time (full time-lapse) or frequency {cite}`guenther2016JoAG` + * **Structurally coupled cooperative inversion** of disparate data based on structural similarity (e.g., {cite}`Ronczka_2016` + * **Structure-based inversion** using layered 2D models {cite}`AttwaAkcBas2014` + + + + + + + + + + +- Gauss-Newton formulation as in the paper +- lambda +- chi^2 +- Terms should be explained in here + ++++ + +## Input data + +### Data weights / errors +### Data transforms + ++++ + +## Model parametrization + +### Mesh-free inversion (0-D) + +### Mesh inversion + +#### 1-D +#### 2-D +#### 3-D + ++++ + +## Regularization - Including prior information + +### Starting model +### Reference model +### Parameter limits +### Damping +### Smoothing +### Advanced regularization + ++++ + +## Region concept + ++++ + +## Model appraisal +### Data misfit +### Cumulative sensitivity +### Resolution diff --git a/doc/user-guide/jupytext.toml b/doc/user-guide/jupytext.toml new file mode 100644 index 000000000..486ef7717 --- /dev/null +++ b/doc/user-guide/jupytext.toml @@ -0,0 +1,2 @@ +notebook_metadata_filter="kernelspec,jupytext,-kernelspec.display_name,-jupytext.text_representation.jupytext_version" +cell_metadata_filter="all,-autoscroll,-collapsed,-scrolled,-trusted,-ExecuteTime,-editable,-slideshow" diff --git a/doc/user-guide/meshes.md b/doc/user-guide/meshes.md new file mode 100644 index 000000000..8bda50a00 --- /dev/null +++ b/doc/user-guide/meshes.md @@ -0,0 +1,488 @@ +--- +file_format: mystnb +kernelspec: + name: python3 +--- + ++++ {"raw_mimetype": ""} + +# Meshes + +This part of the user guide covers mesh-related topics, starting with a [general introduction](#basics-of-the-mesh-class) to the mesh class. Moreover, this section introduces general operations to [create](#mesh-creation) or [import](#mesh-import) meshes. Moreover, the general aspects of [visualization](#mesh-visualization) are covered within this section. + + +## Basics of the mesh class + + +We start off by looking at the general anatomy of a pyGIMLi mesh. It is represented by a collection of nodes, cells and boundaries, i.e., geometrical entities: + +```{code-cell} +:tags: [hide-input] + +import matplotlib.pyplot as plt +import pygimli as pg +import pygimli.meshtools as mt +import numpy as np + +from matplotlib.patches import Circle +from matplotlib.patheffects import withStroke + + +def circle(x, y, text=None, radius=0.15, c="blue"): + circle = Circle((x, y), radius, clip_on=False, zorder=10, linewidth=1, + edgecolor='black', facecolor=(0, 0, 0, .0125), + path_effects=[withStroke(linewidth=5, foreground='w')]) + ax.add_artist(circle) + ax.plot(x, y, color=c, marker=".") + ax.text(x, y - (radius + 0.05), text, backgroundcolor="white", + ha='center', va='top', weight='bold', color=c) + +m = pg.createGrid(4,4) + +# Create matplotlib figure and set size +fig, ax = plt.subplots(figsize=(8,8), dpi=90) +ax.set_title("The anatomy of a pyGIMLi mesh", fontweight="bold") + +# Visualize mesh with the generic pg.show command +pg.show(m, ax=ax) + +# Number all cells +for cell in m.cells(): + node = cell.allNodes()[2] + ax.text(node.x() - 0.5, node.y() - .05, "m.cell(%d)" % cell.id(), + fontsize=11, ha="center", va="top", color="grey") + +# Mark horizontal and vertical extent +circle(m.xmin(), m.xmax(), "m.xmin(),\nm.ymax() ", c="grey") +circle(m.xmin(), m.ymin(), "m.xmin(),\nm.ymin() ", c="grey") +circle(m.xmax(), m.ymin(), "m.xmax(),\nm.ymin() ", c="grey") +circle(m.xmax(), m.ymax(), "m.xmax(),\nm.ymax() ", c="grey") + +# Mark center of a cell +cid = 2 +circle(m.cell(cid).center().x(), m.cell(cid).center().y(), + "Mesh cell center") + +# Mark node +circle(m.node(1).x(), m.node(6).y(), "Mesh node position", c="green") + + +# Mark boundary center +bid = 15 +boundary_center = m.boundary(bid).center() +circle(boundary_center.x(), boundary_center.y(), + "Mesh boundary center", c="red") + +# Create boundary around cell +bid = [14,17,21,20] +bounds = [] +for i in bid: + b = m.boundaries()[i] # equivalent to mesh.boundary(17) + bounds.append(b) +for bound in bounds: + n1 = bound.allNodes()[0] + n2 = bound.allNodes()[1] + ax.plot([n1.x(), n2.x()], [n1.y(), n2.y()], "b-", lw=3, zorder=10) +ax.annotate('Mesh cell', xy=(b.center().x(), b.center().y()), + xycoords='data', xytext=(8, 25), textcoords='offset points', + weight='bold', color="blue", + arrowprops=dict(arrowstyle='->', + connectionstyle="arc", + color="blue")) + +ax.text(3.0, -0.5, "Made with matplotlib & pyGIMLi", + fontsize=10, ha="right", color='.5') +fig.tight_layout(pad=5.7) +pg.wait() +``` + +The mesh class holds either geometric definitions (piece-wise linear complex - **PLC**) or discretizations of the subsurface. It contains **nodes**, **boundaries** (edges in 2D, faces in 3D) and **cells** (triangles, quadrangles in 2D, hexahedra or tetrahedra in 3D) with associated markers and arbitrary data for nodes or cells. + + +:::{admonition} Working with meshes +:class: tip +:::{table} **General commands for accessing different entities of a mesh** +:widths: auto +:align: center + +| Function | Usage | +| :---------------- | :------: | +| `mesh.cells()` | Allows to access mesh cells | +| `mesh.cell()` | Allows to access a single cell (using the cell ID) | +| `mesh.cell().center()` | Allows to point to the center of a specific mesh cell | +| `mesh.cell().center().x()/.y()` | Allows to extract the x / y coordinate of a cell center | +| `mesh.boundaries()` | Accesses mesh boundaries | +| `mesh.boundary()` | Points to a specific boundary of the mesh (using boundary IDs) +| `mesh.boundary().center()` | Allows to point to the center of a specific mesh boundary | +| `mesh.boundary().center().x/.y` | Allows to extract x / y coordinate of a boundary +| `mesh.nodes()` | Accesses mesh nodes | +| `mesh.node()` | Refers to one specific node within the mesh | +| `mesh.node().x()/.y()` | Allows to extract x / y coordinate of a node +::: + + + +It is common practice to classify meshes into two main types - structured and unstructured. + +**Structured** meshes are meshes with implicit connectivit, exhibiting a well-known pattern in which the cells are arranged. As the cells are in a particular order, the topology of such mesh is regular. Such meshes enable easy identification of neighboring cells and points, because of their formation and structure. Often structured meshes have orthogonal quadrilateral (2D) or hexahedral (3D) elements. + +:::{admonition} Structured meshes +:class: info + +A regularly spaced mesh consisting of rectangles or hexahedrons is usually called a grid. However, a grid is just a special variant of a mesh so GIMLi treats it the same. The only difference is how they are created. +::: + +**Unstructured** meshes, as the name suggests, are more general and can randomly form any geometry shape. Unlike structured meshes, the connectivity pattern is not fixed hence unstructured meshes do not follow a uniform pattern. However, unstructured meshes are more flexible and thus allow for more complex applications. + +```{code-cell} +--- +jupyter: + source_hidden: true +--- +from pygimli.meshtools import polytools as plc + +fig, (ax1,ax2) = plt.subplots(1,2,figsize=(16,8), dpi=90) +ax1.set_title("Structured mesh", fontweight="bold") +ax2.set_title("Unstructured mesh", fontweight="bold") + +# Create geometry +world = plc.createWorld(start=[-10, 0], end=[10, -10], marker=1, + worldMarker=False) +c1 = plc.createCircle(pos=[0.0, -5.0], radius=3.0, area=.3) + +# Structured mesh +xmin, xmax = -10, 10. +zmin, zmax = -10., 0. + +xreg = np.linspace(xmin, xmax, 20) +zreg = np.linspace(zmin, zmax, 10) +m_reg = pg.meshtools.createGrid(xreg,zreg,marker=2) + +pg.show(m_reg, ax=ax1) +# Unstructured mesh +m = pg.meshtools.createMesh(world, quality=34, area=1) +pg.show(m, ax=ax2) +fig.tight_layout() +``` + + +## Mesh creation + +### Creating a regular mesh / grid in 2D + +To create a regular 2D grid, pyGIMLi offers a variety of tools that help with the task. To create a regular grid, we first of all have to create the extent of the mesh in x and z direction. For this example, we create a mesh of _20 x 10 m_ with a regular cell size of _1 x 1 m_. After defining the extent, we can simply call the pg.meshtools.createGrid() and get an overview of the number of nodes, cells and boundaries: + +```{code-cell} +xmin, xmax = -10, 10. +zmin, zmax = -10., 0. + +xreg = np.linspace(xmin, xmax, 20) +zreg = np.linspace(zmin, zmax, 10) +m_reg = pg.meshtools.createGrid(xreg,zreg,marker=2) +m_reg +``` + +To show the mesh, we can simply call the pg.show() function: + +```{code-cell} +pg.show(m_reg) +``` + +:::{admonition} Regular grids in 2D +:class: tip +:::{table} +:widths: 200px +:align: center + +| Function | Usage | +| :---------------- | :------: | +| {py:class}`createGrid ` | Creates a regular grid mesh from the provided x- and z-coordinates | +::: + + +### Creating an irregular mesh with pyGIMLi + +After covering the basics of regular grids, we want to dive into the world of irregular meshes. + +However, we first of all have to create a **geometry** that is used as underlying susurface model for the mesh creation. + +```{code-cell} +# dimensions of the world +left = -30 +right = 30 +depth = 25 + +world = mt.createWorld(start=[left, 0], + end=[right, -depth], + layers=[-5], worldMarker=False) +print(world) +pg.show(world) +``` + +:::{admonition} Region markers +:class: info + +A mesh can have different regions, which are defined by **region markers** for each cell. Region markers can be used to assign properties for forward modelling as well as to control the inversion behavior. + +For more information, see the later section on **Markers** +::: + + +We are using the mt.createWorld() function to create a world based on the gíven x- & z-coordinates. The following table lists all handy functions that can be utilized when creating a geometry in pyGIMLi: + +:::{admonition} PLC creation in pyGIMLi +:class: tip +:::{table} **General commands for geometry creations** +:widths: 200px +:align: center + +| Function | Usage | +| :---------------- | :------: | +| {py:class}`createWorld ` | Creates a PLC out of a given geometry | +| {py:class}`createCircle ` | Creates a circular PLC | +| {py:class}`createCube ` | Creates a cubic PLC | +| {py:class}`createCylinder ` | Creates a cylindric PLC | +| {py:class}`createLine ` | Creates a line polygon | +| {py:class}`createPolygon ` | Creates a polygon from a list of vertices | +| {py:class}`createRectangle ` | Creates a rectangular PLC | +::: + + +pyGIMLi has different ways to create meshes. mt.createMesh creates a mesh using Triangle, a two-dimensional constrained Delaunay mesh generator. + +The additional input parameters control the maximum triangle area and the mesh smoothness. The quality factor prescribes the minimum angles allowed in the final mesh. This can improve numerical accuracy, however, fine meshes lead to increased computational costs. Notice that we are now using showMesh which is convenient for 2D mesh visualization. + +```{code-cell} +from pygimli.viewer import showMesh + +mesh = mt.createMesh(world, + area=2.0, + quality=33, + smooth=[2, 4] # [0:no smoothing or 1:node center or 2:weighted node center, # of iter] + ) +showMesh(mesh, markers=True, showMesh=True); +``` + + +## Utilizing markers + +A mesh can have different regions, which are defined by **region markers** for each cell. Region markers can be used to assign properties for forward modelling as well as to control the inversion behavior. Moreover, a pyGIMLi mesh holds specific markers for all boundaries (outer mesh boundaries as well as interfaces between layers and boundaries around structures, see figure above). Those boundary markers are used to define specific properties or conditions on the boundaries of a mesh. They are essential for setting up boundary conditions in simulations, such as specifying fixed values or fluxes. Properly assigning boundary markers ensures accurate representation of physical boundaries and interactions in the model. + +When constructing complex geometries out of basic geometric shapes (e.g., circle, rectangle, …) we need to be careful with both the region and boundary markers. In this user guide, we explain the differences as well as the usage of both types of markers. + +### Region markers + +Let's take a closer look at the region markers of the two-layer case presented above. Every region marker of a specific mesh region has a position, which it is assigned to. By using ``, we can visualize the position in the PLC: + +```{code-cell} + +fig, ax = plt.subplots(1,1) +pg.show(world, ax=ax) +for nr, marker in enumerate(world.regionMarkers()): + print('Position marker number {}:'.format(nr + 1), marker.x(), marker.y(), + marker.z()) + ax.text(marker.x()+2,marker.y()+2, f"Region marker position {nr+1}", + fontweight="bold",fontsize=11, ha="left", va="top", color="black") + ax.scatter(marker.x(), marker.y(), s=(4 - nr) * 20, color='k') + +``` + +By default, pyGIMLi assigns unique markers to every region of the PLC, starting from 1. A marker value of 0 is assigned to a region if no region marker is found - but even if this happens, we could still manually add a marker to the specific region. For now, we want to add a polygon to the already existing 2-layer PLC. This is done using the `createPolygon()` function. Within this function, we have two adjusting variables for the region markers - *marker* and *markerPosition*. The first variable specifies the marker number and the second the position of the marker. Note, that the **position** of a region marker has to lie **within its region** to work! In this case, we specify the newly defined region to have the marker 3. The marker position is set to *[-10, -10]*. + +```{code-cell} +poly = mt.createPolygon([[left, -20], [right,-15],[right,-5],[left,-5]], isClosed=True, marker=3, markerPosition=[-10, -10]) +geometry = world + poly +fig, ax = plt.subplots(1,1) +pg.show(geometry, ax=ax) +for nr, marker in enumerate(geometry.regionMarkers()): + print('Position marker number {}:'.format(nr + 1), marker.x(), marker.y(), + marker.z()) + ax.text(marker.x()+2,marker.y()+2, f"Region marker position {nr+1}", + fontweight="bold",fontsize=11, ha="left", va="top", color="black") + ax.scatter(marker.x(), marker.y(), s=(4 - nr) * 20, color='k') +``` + +Of course it is also possible to assign the same region marker to multiple parts of your PLC. This gets especially handy as soon as you start assigning physical parameters to your meshed geometry for modelling and/or inversion purposes. For more detailed information on this matter, please take a look at the [modelling section](modelling.md) of the user guide. + +### Boundary markers +If we talk about markers in a PLC, one often forgets about the boundary markers. If you create a geometry in pyGIMLi, no matter whether it is a circle, rectangle or layered world, you need to deal with boundaries of different kinds. pyGIMLi automatically assigns numbers to the boundaries and, doing so, follows a specific pattern. In order to change the default boundary markers, please refer to the [modelling section](modelling.md) of the user guide. + +If we assume a simple rectangular world without additional layers, we have two different options on how to enumerate the boundaries: + +1) Set `createWorld(worldMarker=False)`, which leads to enumerated boundaries (*1 = left, 2=right, 3=bottom, 4=top, 5=front and 6=back*). + +2) Set `createWorld(worldMarker=True)`, which leads to the top holding the boundary marker -1 and other outer boundaries -2. + + +```{code-cell} +start = [left,0] +end = [right, -depth] +world1 = mt.createWorld(start=start, + end=end, worldMarker=False) + +world2 = mt.createWorld(start=start, + end=end, worldMarker=True) + +fig, (ax1,ax2) = plt.subplots(1,2,figsize=(16,12), dpi=90) +ax1.set_title("worldMarker = False", fontweight="bold") +ax2.set_title("worldMarker = True", fontweight="bold") + +pg.show(world1, markers=True, ax=ax1) +pg.show(world2, markers=True, ax=ax2) +``` + +Let's assume that we want to add an additional feature to our PLC, such as a rectangle. Doing so, the circle is automatically assigned a boundary marker - in this case 1. However, assuming the case where we set `worldMarker=False`, this marker is already assigned to the left boundary of the PLC (which could cause problems in any modelling application later on). So we need to adapt the boundary marker of the circle, which is simply done as follows: + +```{code-cell} + +c1 = plc.createRectangle(start=[-10,-5], end=[10,-10], marker=2) +geom1 = world1+c1 +# %% +for i in range(geom1.boundaryCount()): + if i >= 4: + geom1.boundary(i).setMarker(5) + +pg.show(geom1, markers=True) +``` + +As you can see, the boundaries around the rectangle were all changed to 5, as defined in the for-loop above. `PLC.boundaryCount()` gives us the total count of boundaries in the PLC, while `PLC.boundary().setMarker()` allows us to change a specific boundary marker. + +To see applications where the indices of the PLC / mesh boundary are utilized, please refer to the [modelling section](modelling.md) of the user guide. + +## Mesh import + +### Import options for meshes in pyGIMLi + +A broad variety of functions to import and convert different mesh types into a GIMLI mesh object exists within pyGIMLi. The following functions are the most commonly used ones: + +:::{admonition} PLC creation in pyGIMLi +:class: tip +:::{table} +:widths: 200px +:align: center + +| Function | Usage | +| :---------------- | :------: | +| {py:class}`FenicsHDF5Mesh ` | Read FEniCS mesh from .h5 format and return a GIMLI mesh object | +| {py:class}`Gmsh ` | Read GMSH ASCII file and return a GIMLI mesh object | +| {py:class}`HDF5Mesh ` | Load a mesh from HDF5 file format | +| {py:class}`Hydrus2dMesh ` | Import mesh from Hydrus 2D | +| {py:class}`Hydrus3dMesh ` | Import mesh from Hydrus 3D | +| {py:class}`MeshIO ` | Read generic meshIO mesh | +| {py:class}`STL ` | Read STL surface mesh and converts to GIMLI mesh object | +| {py:class}`Tetgen ` | Read and convert a mesh from the basic Tetgen output | +| {py:class}`Triangle ` | Read Triangle mesh | +::: + + +### Example: mesh generation using Gmsh + +When the scientific task requires a complex finite-element discretization (i.e. incorporation of structural information, usage of a complete electrode model (CEM), etc.), external meshing tools with visualization capabilities may be the option of choice for some users. In general, the bindings provided by pygimli allow to interface any external mesh generation software. For examples on how to use external meshing software, refer to the [examples section](../examples/1_meshing/) on the pyGIMLi website. + + +## Mesh modification + + +pyGIMLi provides a variety of operators to modify your mesh. The following table gives an overview of the most important functions: + +:::{admonition} Mesh modifications +:class: tip +:::{table} +:widths: 200px +:align: center + +| Function | Usage | +| :---------------- | :------: | +| {py:class}`merge2Meshes ` | Merges two meshes | +| {py:class}`mergeMeshes ` | Merges two or more meshes | +| `mesh.translate()` | Allows to translate a mesh | +| `mesh.scale()` | Scale a mesh with provided factors | +| `mesh.rotate()` | Rotate a provided mesh | +::: + + +### Merging meshes + +In some cases, the modelling domain may require different degrees of flexibility in separate mesh regions. In the following, we demonstrate this for a two-dimensional mesh consisting of a region with regularly spaced quadrilaterals and a region with unstructured triangles. + +pyGIMLi offers the possibility to merge two meshes by calling {py:class}`merge2Meshes `. + +```{code-cell} +xmin, xmax = -30, 30. +zmin, zmax = -50, -25. + +xreg = np.linspace(xmin, xmax, 30) +zreg = np.linspace(zmin, zmax, 25) + +mesh2merge = mt.createGrid(xreg, zreg, marker=3) +mergedMesh = mt.merge2Meshes(mesh,mesh2merge) +pg.show(mergedMesh, markers=True, showMesh=True) +``` + +The merged meshes appear as a singular hybrid mesh now, so we can append a triangle boundary as for non-hybrid meshes: + +```{code-cell} +mesh_append = mt.appendTriangleBoundary(mergedMesh, xbound=50., ybound=50., quality=31, smooth=True, + marker=4, isSubSurface=True, addNodes=10) + +ax, cb = pg.show(mesh_append) +``` + +When merging more than two meshes, the function {py:class}`mergeMeshes() ` can be utilized instead of {py:class}`merge2Meshes `. + + +### Translating meshes + +To perform simple changes of the meshs x- and z-coordinates, we can make use of the {py:class}`translate ` function. The following lines of code move the mesh 500 m in x and 25 m in z direction: + +```{code-cell} +translated_mesh = pg.Mesh(mesh) +translated_mesh.translate([500, 25]) +pg.show(translated_mesh) +``` + +### Scaling meshes + +Apart from moving the mesh along its axes, pyGIMLi also provides a tool to scale the mesh along specified axes - in this example, we scale along the z-axis with a factor of 2: + +```{code-cell} +scaled_mesh = pg.Mesh(mesh) +scaled_mesh.scale([1, 2]) +pg.show(scaled_mesh) +``` + +### Rotating meshes +Another valuable mesh modification tool is the mesh.rotate function. By providing a rotation angle and the rotation plane, we can adjust the orientation angle of our mesh: + +```{code-cell} +import numpy as np +rotated_mesh = pg.Mesh(mesh) +rotated_mesh.rotate([0, 0, np.deg2rad(-20)]) +pg.show(rotated_mesh) +``` + +## Mesh export + + +Suppose we want to continue working on our GIMLi mesh object in a different meshing tool - pyGIMLi provides a variety of export functions to transfer your GIMLi mesh into a different format: + +:::{admonition} Mesh export functions +:class: tip +:::{table} +:widths: 200px +:align: center + +| Function | Usage | +| :---------------- | :------: | +| {py:class}` FenicsHDF5Mesh ` | Exports GIMLi mesh in HDF5 format suitable for Fenics | +| {py:class}`HDF5Mesh ` | Writes given GIMLI::Mesh in a hdf5 format file | +| {py:class}` PLC ` | Export a piece-wise linear complex (PLC) to a .poly file (2D or 3D) | +| {py:class}`STL ` | Write STL surface mesh | +| {py:class}`STL ` | Save mesh alongside properties as vtk | +::: + +```{code-cell} +# Save rotated mesh from above as vtk file + +rotated_mesh.exportVTK('rotated_mesh.vtk') +``` diff --git a/doc/user-guide/modelling.md b/doc/user-guide/modelling.md new file mode 100644 index 000000000..6fcb56eee --- /dev/null +++ b/doc/user-guide/modelling.md @@ -0,0 +1,300 @@ +--- +file_format: mystnb +kernelspec: + name: python3 +--- + +# Modelling + +## Theory (Finite Element Analysis) +This tutorial covers the first steps into Finite Element computation +referring the *M* (Modelling) in *pyGIMLi*. + +We will not dig into deep details about the theory of the Finite Elements Analysis (FEA) here, as this can be found in several books, e.g., {cite}`Zienkiewicz1977`. + +Anyhow, there is a little need for theory to understand what it means +to use FEA for the solution of a boundary value problem. +So we start with some basics. + +Assuming Poisson's equation as a simple partial differential problem +to be solved for the sought scalar field $ u(\mathbf{r}) $ within +a modelling domain ${r}\in\Omega`$ +with a non-zero right-hand side function $ f $. + +$$ +- \Delta u = f \quad{\mathrm{in}}\quad~\Omega \\ + u = g \quad{\mathrm{on}}\quad\partial\Omega\ +$$ + +The Laplace operator $ `\Delta = \nabla\cdot\nabla` $ given by the divergence +of the gradient, is the sum of the second partial derivatives of the field +$`u(\mathbf{r})`$ with respect to the Cartesian coordinates +in 1D space $ \mathbf{r} = (x) $, in 2D $ {r} = (x, y) $, or 3D +space $ \mathbf{r} = (x, y, z) $. +On the boundary $ \partial\Omega $ of the domain, we want +known values of $ u=g $ as so called Dirichlet boundary conditions. + +A common approach to solve this problem is the method of weighted residuals. +The base assumption states that an approximated solution $ u_h\approx u$ will +only satisfy the differential equation with a rest $ R $ : $\Delta u_h + f = R $. If we choose some weighting functions $ w $, +we can try to minimize the resulting residuum over our modelling domain as: + + +$$ \int_{\Omega} R w = 0\; $$ + +which leads to: + + + +$$ \int_{\Omega} - \Delta u_h w = \int_{\Omega} f w\ $$ + +It is preferable to eliminate the second derivative in the Laplace operator, +either due to integration by parts or by applying the product rule and +Gauss's law. +This leads to the so called weak formulation: + + +$$ \int_{\Omega} \nabla u_h \nabla w - \int_{\partial \Omega}\mathbf{n}\nabla u_h w = \int_{\Omega} f w $$ + +$$ \int_{\Omega} \nabla u_h \nabla w = \int_{\Omega} f w + \int_{\partial \Omega}\frac{\partial u_h}{\partial\mathbf{n}} w\ $$ + +We can solve these integrals after choosing an appropriate basis +for an approximate solution $ u_h $ as: + +$$ u_h = \sum_i \mathrm{u}_i N_i\quad\text{with}\quad i = 0\ldots\mathcal{N}\ $$ + +The latter fundamental FEA relation discretizes the continuous solution $ u_h $ +into a discrete values $ \mathrm{u} = \{\mathrm{u}_i\} $ for a number of $ i = 0\ldots\mathcal{N} $ discrete points, usually called nodes. + +The basis functions $ N_i $ can be understood as interpolation rules for +the discrete solution between adjacent nodes and will be chosen later. + +Now we can set the unknown weighting functions to be the same as the basis +functions $ w=N_j $ with $ j=0\ldots\mathcal{N} $ (Galerkin method) + +$$ \int_{\Omega} \sum_i \mathrm{u}_i \nabla N_i \nabla N_j = \int_{\Omega} f_j N_j + \int_{\partial \Omega} h N_j + \quad \text{with}\quad h = \frac{\partial u}{\partial \mathbf{n}} +$$ + +this can be rewritten with $h=0$ as: + + +$$ \mathrm{A} \mathrm{u} = \mathrm{b} $$ +$$ \text{with } +\mathrm{A} = \{\mathrm{a}_{i,j}\} = \int_{\Omega}\nabla N_i \nabla N_j \quad\text{known as 'Stiffness matrix'} $$ + +$$ \mathrm{b} = \{\mathrm{b}_j\} = \int_{\Omega} f_j N_j \quad\text{known as 'Load vector'} $$ + + +The solution of this linear system of equations leads to the +discrete solution $ \mathrm{u} = \{\mathrm{u}_i\} $ for all +$ i=1\ldots\mathcal{N}`$ nodes inside the modelling domain. + +For the practical part, the choice of the nodes is crucial. If we choose too +little, the accuracy of the sought solution might be too small. If we choose too +many, the dimension of the system matrix will be too large, which leads to +higher memory consumption and calculation times. + +To define the nodes, we discretize our modelling domain into cells, or the +eponymous elements. Cells are basic geometric shapes like triangles or +hexahedrons and are constructed from the nodes and collected in a mesh. For more details, refer to the [Meshes](meshes.md) section of the user guide. In summary, the discrete +solutions of the differential equation using FEA on a specific mesh are defined +on the node positions of the mesh. + +To complete the solution for the small example, we still need to apply the boundary condition $u=g$ which is known as the Dirichlet condition. Setting +explicit values for our solution is not covered by the general Galerkin weighted +residuum method but we can solve it algebraically. We reduce the linear system +of equations by the known solutions $g={g_k}$ for all $k$ nodes on +the affected boundary elements: + +$$ \mathrm{A_D}\cdot\mathrm{u} = \mathrm{b_D} \\ + \text{with } \mathrm{A_D} = \{\mathrm{a}_{i,j}\}\quad\forall i, j ~\notin~ k ~\text{and}~1~\text{for}~i,j \in k\\ + \mathrm{b_D} = \{\mathrm{b}_j\} - \mathrm{A}\cdot\mathrm{g}\quad\forall j \notin k~\text{and}~g_k~\text{for}~j \in k $$ + +Now we have all parts together to assemble $\mathrm{A_D}$ and +$\mathrm{b_D}$ and finally solve the given boundary value problem. + +It is usually a good idea to test a numerical approach with known solutions. +To keep things simple we create a modelling problem from the reverse direction. +We choose a solution, calculate the right hand side function +and select the domain geometry suitable for nice Dirichlet values. + +$$ u(x,y) = \operatorname{sin}(x)\operatorname{sin}(y) $$ + $$ - \Delta u = f(x,y) = 2 \operatorname{sin}(x)\operatorname{sin}(y) $$ + $$ \Omega \in I\!R^2 \quad \text{on}\quad 0 \leq x \leq 2\pi,~~ 0 \leq y \leq 2\pi $$ + $$ u = g = 0 \quad \text{on}\quad \partial \Omega $$ + +We now can solve the Poison equation applying the FEA capabilities of pygimli +and compare the resulting approximate solution $\mathrm{u}$ +with our known exact solution $u(x,y)$. + +## Parameterizing a mesh with physical properties +```{code-cell} +:tags: [hide-cell] + +import numpy as np +import pygimli as pg + +from pygimli.solver import solve +from pygimli.viewer import show +from pygimli.viewer.mpl import drawStreams +import pygimli.meshtools as mt +``` + +We can parametrize a mesh that has been made with different physical properties depending on the region. For example, we have the following polygons created as PLC and created a mesh from this: + +Create geometry definition for the modelling domain. worldMarker=True indicates the default boundary conditions for the ERT. Here we are also creating layers at `y=-10` and `y=-30`. This will make a world with 3 different markers for the 3 distinct layers. + +```{code-cell} +world = mt.createWorld(start=[-50, 0], end=[50, -50], layers=[-10, -30],worldMarker=True) +``` + +Create some heterogeneous circular anomaly and assign the following markers: + +```{code-cell} +block_1 = mt.createCircle(pos=[-5, -3.], radius=[4, 1], marker=4, + boundaryMarker=10, area=0.1) +block_2 = mt.createCircle(pos=[10, -3.], radius=[4, 1], marker=5, + boundaryMarker=10, area=0.1) +``` +Merge geometry definition into a Piecewise Linear Complex (PLC) and plot it using `pg.show`, you can pass markers=True to get a look at how your regions are numbered. Also, you can set `boundaryMarkers=True` to analyze the boundary markers which will be explained in the next section. + +```{code-cell} +geom = world + block_1 + block_2 +pg.show(geom, markers=True, boundaryMarkers=False) +``` + +Create a mesh for the finite element modelling with appropriate mesh quality. + +```{code-cell} +mesh = mt.createMesh(geom, quality=34) +``` + +You can also print the amount of markers that are in the mesh by using the following commands: + +```{code-cell} +number_of_cellmarkers = list(set(mesh.cellMarkers())) +print(number_of_cellmarkers) +``` + +Create a map to set resistivity values in the appropriate regions + [[regionNumber, resistivity], [regionNumber, resistivity], [...] + +```{code-cell} +rhomap = [[1, 100.], + [2, 75.], + [3, 50.], + [4, 150.], + [5, 25]] +``` + +Here we assigned a different resistivity value to each part of the mesh using its cell markers and we can view the resistivity distribution with the following command: + +```{code-cell} +pg.show(mesh, data=rhomap, label=pg.unit('res'), markers=True) +``` +We will now show the different options to set boundary conditions and get these ready to then simulate and model the data. + +## Boundary conditions (BC) + +:::{admonition} Definition of Boundary Conditions +:class: tip + +- Boundary marker (-1) : surface boundary conditions - `pg.core.MARKER_BOUND_HOMOGEN_NEUMANN` +- Boundary marker (-2) : mixed-boundary conditions - `pg.core.MARKER_BOUND_MIXED` +- Boundary marker ( >= 1 ) : no-flow boundaries +::: + + +As shown in [meshes section](meshes.md) of the user guide, pyGIMLi automatically assigns boundaries when using `mt.createWorld()`. However, you can assign BCs to different elements of your PLC or mesh. + +There are different ways of specifying BCs. They can be maps from markers to values, explicit functions or implicit (lambda) functions. We use the example of the Poisson equation on the unit square and specify different boundary conditions on the four sides. + +- The boundary 1 (left) and 2 (right) are directly mapped to the values 1 and 2. +- On side 3 (top) a lambda function 3+x is used (p is the boundary position and p[0] its x coordinate). +- On side 4 (bottom) a function uDirichlet is used that simply returns 4 in this example but can compute anything as a function of the individual boundaries b. + + +```{code-cell} +def uDirichlet(boundary): + """Return a solution value for a given boundary. + Scalar values are applied to all nodes of the boundary.""" + return 4.0 + +dirichletBC = {1: 1, # left + 2: 2.0, # right + 3: lambda boundary: 3.0 + boundary.center()[0], # bottom + 4: uDirichlet} # top +``` + +The boundary conditions are passed using the BC keyword dictionary `dirichletBC`. + +```{code-cell} +grid = pg.createGrid(x=np.linspace(-1.0, 1.0, 21), + y=np.linspace(-1.0, 1.0, 21)) +u = solve(grid, f=1., bc={'Dirichlet': dirichletBC}) + +# Note that showMesh returns the created figure ax and the created colorBar. +ax, cbar = show(grid, data=u, label='Solution $u$') + +show(grid, ax=ax) + +ax.text(1.02, 0, '$u=2$', va='center', ha='left', rotation='vertical') +ax.text(-1.01, 0, '$u=1$', va='center', ha='right', rotation='vertical') +ax.text(0, 1.01, '$u=4$', ha='center') +ax.text(0, -1.01, '$u=3+x$', ha='center', va='top') + +ax.set_title('$\\nabla\cdot(1\\nabla u)=1$') + +ax.set_xlim([-1.1, 1.1]) # some boundary for the text +ax.set_ylim([-1.1, 1.1]) +``` + + +Alternatively we can define the gradients of the solution on the boundary, i.e., Neumann type BC. This is done with another dictionary {marker: value} and passed by the bc dictionary. + +```{code-cell} +neumannBC = {1: -0.5, # left + 4: 2.5} # bottom + +dirichletBC = {3: 1.0} # top + +u = solve(grid, f=0., bc={'Dirichlet': dirichletBC, 'Neumann': neumannBC}) +``` + +Note that on boundary 2 (right) has no BC explicitly applied leading to default (natural) BC that are of homogeneous Neumann type $\frac{\partial u}{\partial n}=0$ + + +```{code-cell} +ax = show(grid, data=u, filled=True, orientation='vertical', + label='Solution $u$', + levels=np.linspace(min(u), max(u), 14), hold=True)[0] + +# Instead of the grid we now want to add streamlines to show the gradients of +# the solution (i.e., the flow direction). +drawStreams(ax, grid, u) +ax.text(0.0, 1.01, '$u=1$', + horizontalalignment='center') # top -- 3 +ax.text(-1.0, 0.0, '$\partial u/\partial n=-0.5$', + va='center', ha='right', rotation='vertical') # left -- 1 +ax.text(0.0, -1.01, '$\partial u/\partial n=2.5$', + ha='center', va='top') # bot -- 4 +ax.text(1.01, 0.0, '$\partial u/\partial n=0$', + va='center', ha='left', rotation='vertical') # right -- 2 + +ax.set_title('$\\nabla\cdot(1\\nabla u)=0$') + +ax.set_xlim([-1.1, 1.1]) +ax.set_ylim([-1.1, 1.1]) +``` + +Its also possible to force single nodes to fixed values too. + +```{code-cell} +u = solve(grid, f=1., bc={'Node': [grid.findNearestNode([0.0, 0.0]), 1.0]}) +np.testing.assert_approx_equal(u[grid.findNearestNode([0.0, 0.0])], 1.0, significant=10) + +ax, _ = pg.show(grid, u, logScale=False, label='Solution $u$',) +_ = pg.show(grid, ax=ax) +``` + diff --git a/doc/user-guide/visualization.md b/doc/user-guide/visualization.md new file mode 100644 index 000000000..be8db7e7d --- /dev/null +++ b/doc/user-guide/visualization.md @@ -0,0 +1,176 @@ +--- +file_format: mystnb +kernelspec: + name: python3 +--- + +# Visualization + +As presented in the [Fundamentals](fundamentals.md), pyGIMLi offers some basic post-processing routines for plotting. For 2D and 3D visualizations, we rely on [Matplotlib](https://matplotlib.org/g) and [pyVista](https://docs.pyvista.org/), respectively, and provide the following frameworks: + +```{eval-rst} +.. autosummary:: + :nosignatures: + + pygimli.viewer.mpl + pygimli.viewer.pv +``` + +In the following, we will give a brief overview on the most important aspects on visualizing your plots as well as performing simple (cosmetic) changes. + +## Plotting in 2D + +For plotting in 2D, the method `pygimli.viewer.showMesh()` is called, which creates an axis object and plots a 2D mesh, if provided with node or cell data. As already discussed in the [fundamentals](visualization.md) section, the type of data determines the appropriate draw method. + +[This matplotlib glossary](https://matplotlib.org/stable/api/axes_api.html) comprehends all possible adjustments that you can apply to plots based on `pg.show()`. In the following table, we summarized the most relevant functions: + +```{eval-rst} +.. autosummary:: + :nosignatures: + + matplotlib.axes.Axes.text + matplotlib.axes.Axes.arrow + matplotlib.axes.Axes.axis + matplotlib.axes.Axes.set_axis_off + matplotlib.axes.Axes.set_axis_on + matplotlib.axes.Axes.invert_xaxis + matplotlib.axes.Axes.invert_yaxis + matplotlib.axes.Axes.set_xlim + matplotlib.axes.Axes.set_ylim + matplotlib.axes.Axes.set_xlabel + matplotlib.axes.Axes.set_ylabel + matplotlib.axes.Axes.set_title + matplotlib.axes.Axes.legend + matplotlib.axes.Axes.set_aspect + matplotlib.axes.Axes.set_adjustable + matplotlib.axes.Axes.set_xticks + matplotlib.axes.Axes.set_yticks + matplotlib.axes.Axes.sharex + matplotlib.axes.Axes.sharey + +``` + + +### Plotting meshes and models + +As described in the [Fundamentals](fundamentals.md) section, `pygimli.viewer.show()` and `pygimli.viewer.showMesh()` utilize a variety of drawing functions, depending on the input data provided. In the following, we will take a look at how to manually access the necessary drawing functions to plot an empty mesh, as well as cell-based and node-based data. + +```{code-cell} +:tags: [hide-input] +import numpy as np +import matplotlib.pyplot as plt +import pygimli as pg +from pygimli.viewer import mpl +import pygimli.meshtools as mt +``` + +To visualize a grid or a triangular mesh in 2D, we can simply make use of the `pygimli.viewer.show()` function, which refers to `pygimli.viewer.mpl.drawMesh()`: + +```{code-cell} +n = np.linspace(1, 2, 10) +mesh = pg.createGrid(x=n, y=n) +fig, ax = plt.subplots() +mpl.drawMesh(ax, mesh) +plt.show() +``` + +If we now want to plot cell-based values on top of our mesh, `pygimli.viewer.show()` links to the function `pygimli.viewer.mpl.drawModel()`: + +```{code-cell} +mx = pg.x(mesh.cellCenter()) +my = pg.y(mesh.cellCenter()) +data = np.cos(1.5 * mx) * np.sin(1.5 * my) +fig, ax = plt.subplots() +mpl.drawModel(ax, mesh, data) +plt.show() +``` + +Simliarly, for scalar field values, the function `pygimli.viewer.mpl.drawField()` is utilized: + +```{code-cell} +nx = pg.x(mesh.positions()) +ny = pg.y(mesh.positions()) +data = np.cos(1.5 * nx) * np.sin(1.5 * ny) +fig, ax = plt.subplots() +mpl.drawField(ax, mesh, data) +plt.show() +``` + +pyGIMLi also allows to plot vector field streamlines with `pygimli.viewer.mpl.drawStreams`, as in the following example. Every cell contains only one streamline and every new stream line starts in the center of a cell. + +```{code-cell} +fig, ax = plt.subplots() +mpl.drawStreams(ax, mesh, data, color='red') +mpl.drawStreams(ax, mesh, data, dropTol=0.9) +mpl.drawStreams(ax, mesh, pg.solver.grad(mesh, data), + color='green', quiver=True) +ax.set_aspect('equal') +``` + +A more specific case is the visualization of sensor positions, which is also covered by a drawing function within the visualization framework of pyGIMLi. By providing a list of sensor positions to plot as [x,y] pairs, the function `pygimli.viewer.mpl.drawSensors()`draws the sensor positions as dots with a given diameter. + +```{code-cell} +sensors = np.random.rand(5, 2) +fig, ax = pg.plt.subplots() +mpl.drawSensors(ax, sensors, diam=0.02, coords=[0, 1]) +ax.set_aspect('equal') +pg.wait() +``` + + +## Plotting in 3D + +For plotting in 3D, pyGIMLi utilizes the `pygimli.viewer.pv` module, which leverages the capabilities of pyVista for rendering. The primary function for visualizing 3D meshes is `pygimli.viewer.pv.drawMesh()`, which can handle various types of 3D data, including cell-based and node-based data. Similar to 2D plotting, the type of data provided determines the appropriate drawing method. As for the 2D plots, we can fine-tune the 3D plots by referring to the [`pyvista.Plotter` functions](https://docs.pyvista.org/api/plotting/_autosummary/pyvista.plotter) +The following examples demonstrate how to plot 3D meshes, cell data, and streamlines, as well as how to create slices through the mesh for detailed analysis. + +### Plotting meshes and models in 3D + +Plotting meshes using pyVista is straightforward with pyGIMLi. The `pygimli.viwer.pv.drawMesh()` function is called to visualize 3D meshes and models, leveraging pyVista's powerful rendering capabilities. + +```{code-cell} +from pygimli.viewer import pv +plc = mt.createCube(size=[40, 20, 15], marker=1, boundaryMarker=0) +cube = mt.createCube(size=[15, 15, 8], marker=2, boundaryMarker=0) +geom = plc + cube + +mesh = mt.createMesh(geom, area=4) +pg.show(mesh, style='wireframe', showMesh=True) +``` + +To visualize cell-based values in a 3D mesh created with pyVista, `pg.show` makes use of the `pygimli.viewer.pv.drawModel()` function, which draws a given mesh together with provided values: + +```{code-cell} +mx = pg.x(mesh.cellCenter()) +my = pg.y(mesh.cellCenter()) +mz = pg.z(mesh.cellCenter()) + +data = mx + +pg.show(mesh, data, label="Cell position x (m)") +``` + + +As for the 2D section, pyVista also allows to plot streams by taking vector field of gradient data per cell. The according function is utilized in the example below: + +```{code-cell} + +ax, _ = pg.show(mesh, alpha=0.3, hold=True, colorBar=False) +pv.drawStreamLines(ax, mesh, data, radius=.1, source_radius=10) +ax.show() +``` + +Creating slices in a 3D plot allows for detailed analysis of the internal structure of the mesh. The `pygimli.viewer.pv.drawSlice()` function can be used to create and visualize these slices, specifying the normal vector and cell values to be displayed. + +```{code-cell} +ax, _ = pg.show(mesh, alpha=0.3, hold=True, colorBar=False) +pv.drawSlice(ax, mesh, normal=[0,1,0], data=data, label="Cell position x") +ax.show() +``` + +If you want to take a look at more practical applications and examples that fully use the plotting capabilities of pyGIMLi, please refer to the [examples section](../examples/). + +## External plotting + +If you ever encounter the situation that the plotting capabilities of pyGIMLi are too limited for your need and you want to use more powerful programs such as Paraview, you can easily export meshes and models from pyGIMLi. + +The **VTK format** can save values along with the mesh, point data like voltage under POINT_DATA and cell data like velocity under CELL_DATA. It is particularly suited to save inversion results including the inversion domain in one file. \ No newline at end of file diff --git a/environment.yml b/environment.yml index 7b8f124a4..fd3230ae2 100644 --- a/environment.yml +++ b/environment.yml @@ -10,7 +10,7 @@ dependencies: - sphinx >= 3.1 - pytest - numpy - - scipy + - scipy >= 1.14 - pytest-cov - pytest-html - sphinx-gallery @@ -18,11 +18,16 @@ dependencies: - sphinxcontrib-programoutput - sphinxcontrib-spelling - sphinxcontrib-doxylink + - sphinx-autobuild - bibtexparser - - pyvista[all,trame]>=0.42 + - pyvista[all,trame]>=0.44 - meshio - - tetgen - scooby + - tdqm - sphinx-design - pydata-sphinx-theme - + - myst-nb + - jupytext + - trame-vtk + - conda-build + - linkify-it-py \ No newline at end of file diff --git a/pygimli/core/mesh.py b/pygimli/core/mesh.py index ce3eed86f..a06ed6410 100644 --- a/pygimli/core/mesh.py +++ b/pygimli/core/mesh.py @@ -772,6 +772,8 @@ def __Mesh__populate__(self, prop:str, value): self[prop] = parseMapToCellArray(value, self) elif len(value) == self.cellCount(): self[prop] = value + elif len(value) > max(self.cellMarkers()): # cell marker indexing + self[prop] = np.array(value)[self.cellMarkers()] else: raise Exception("Length mismatch!") diff --git a/pygimli/frameworks/inversion.py b/pygimli/frameworks/inversion.py index e896ef289..f6df10284 100644 --- a/pygimli/frameworks/inversion.py +++ b/pygimli/frameworks/inversion.py @@ -14,11 +14,13 @@ class InversionBase(object): - """Inversion base class for all inversions. + """ Inversion base class for all inversions. New inversion frame not using RInversion anymore. """ def __init__(self, fop=None, **kwargs): + """ Initialize inversion base class. + """ self._debug = kwargs.pop('debug', False) self._verbose = kwargs.pop('verbose', False) self._preStep = None @@ -49,66 +51,85 @@ def __init__(self, fop=None, **kwargs): self.lineSearchMethod = None # auto inter-quad # self.minTau/maxTau + @property def fop(self): - """Forward operator.""" + """ Forward operator. + """ return self._fop + @fop.setter def fop(self, f): - """Set forward operator.""" + """ Set forward operator. + """ self.setForwardOperator(f) + def setForwardOperator(self, fop): - """Set forward operator.""" + """ Set forward operator. + """ self._fop = fop # we need to initialize the regionmanager by calling it once self._fop.regionManager() + @property def verbose(self): - """Verbosity level.""" + """ Verbosity level. + """ return self._verbose + @verbose.setter def verbose(self, v): - """Set verbosity level for both forward operator and inversion.""" + """ Set verbosity level for both forward operator and inversion. + """ self._verbose = v self.fop.setVerbose(self._verbose) + @property def dataTrans(self): - """Data transformation.""" + """ Data transformation. + """ return self._dataTrans + @dataTrans.setter def dataTrans(self, dt): - """Set data transformation.""" + """ Set data transformation. + """ if isinstance(dt, str): dt = str2Trans(dt) self._dataTrans = dt + @property def modelTrans(self): - """Model transformation.""" + """ Model transformation. + """ return self.fop.modelTrans + @modelTrans.setter def modelTrans(self, mt): - """Set model transformation.""" + """ Set model transformation. + """ if isinstance(mt, str): mt = str2Trans(mt) self.fop.modelTrans = mt # self._modelTrans # ???? + def convertStartModel(self, model): - """Convert scalar or array into startmodel vector. + """ Convert scalar or array into startmodel vector. Use valid range or self.fop.parameterCount, if possible. - Attributes - ---------- + Arguments + --------- model: float|int|array|None starting model value or array """ @@ -126,13 +147,23 @@ def convertStartModel(self, model): format(len(model), self.fop.parameterCount)) return None + @property def model(self): - """The last active (i.e. current) model.""" + """ The last active, i.e., current model. + """ return self._model + @model.setter def model(self, m): + """ Set model. + + Arguments + --------- + m: [float,] + Model used as current model. + """ if self._model is not None: assert len(self._model) == len(m), "Model size mismatch!" @@ -141,48 +172,64 @@ def model(self, m): self._jacobianOutdated = True self._response = None # not known + @property # not sure if we need it def response(self): - """Return last forward response.""" + """ Return last forward response. + """ if self._response is None: self._response = self.fop.response(self.model) return self._response + @response.setter def response(self, v): - """Set response vector from outside (e.g. postprocessing).""" + """ Set response vector from outside (e.g. postprocessing). + """ + # does this even make sense? visualization is Manager's job assert len(self.dataVals) == len(v), "Response size not matching." self._response = v + @property def dataVals(self): - """Data vector (deprecated).""" + """ Data vector (deprecated). + """ + # why deprecated? whats the alternative? + if self._dataVals is None: + pg.critical("No data. Inversion framework needs data values to run") + return self._dataVals + @dataVals.setter def dataVals(self, d): - """Set mandatory data values. + """ Set mandatory data values. Values == 0.0 will be set to tolerance """ + # also deprecated? whats the alternative? + if d is None: + pg.critical("Data values can't be set to None") self._dataVals = d - if self._dataVals is None: - pg._y(d) - pg.critical("Inversion framework needs data values to run") @property def errorVals(self): - """Errors vector (deprecated).""" + """ Errors vector (deprecated). + """ + # why deprecated? whats the alternative? return self._errorVals + @errorVals.setter def errorVals(self, d): - """Set mandatory error values. + """ Set mandatory error values. - Values == 0.0. Will be set to Tolerance + Values == 0.0 will be set to tolerance. """ + # also deprecated? whats the alternative? self._errorVals = d if self._errorVals is None: @@ -195,22 +242,42 @@ def errorVals(self, d): "Found zero error values. Setting them to fallback value of 1") pg.core.fixZero(self._errorVals, 1) + def echoStatus(self): - """Echo inversion status (model, response, rms, chi^2, phi).""" - pass + """ Echo inversion status (model, response, rms, chi^2, phi). + """ + # implementation? - def setPostStep(self, p): - """Set a function to be called after each iteration. - The function is called with p(IterationNumber, self).""" + def setPostStep(self, p:callable): + """ Set a function to be called after each iteration. + + Arguments + --------- + p: callable + Function to be called after each iteration. + called with `p(IterationNumber:int, self:InversionBase)` + + """ self._postStep = p - def setPreStep(self, p): - """Set a function to be called before each iteration.""" + + def setPreStep(self, p:callable): + """ Set a function to be called before each iteration. + + Arguments + --------- + p: callable + Function to be called before each iteration. + called with `p(IterationNumber:int, self:InversionBase)` + """ self._preStep = p + + def setData(self, data): - """Set data.""" + """ Set data. + """ # QUESTION_ISNEEDED if isinstance(data, pg.DataContainer): raise Exception("should not be here .. its Managers job") @@ -218,12 +285,16 @@ def setData(self, data): else: self.dataVals = data + def chi2(self, response=None): - """Chi-squared misfit (mean of squared error-weighted misfit).""" + """ Chi-squared misfit (mean of squared error-weighted misfit). + """ return self.phiData(response) / len(self.dataVals) + def phiData(self, response=None): - """Data objective function (sum of suqred error-weighted misfit).""" + """ Data objective function (sum of squared error-weighted misfit). + """ if response is None: response = self.response @@ -233,8 +304,10 @@ def phiData(self, response=None): return pg.math.dot(dData, dData) + def roughness(self, model=None, weighted=True): - """Return (weighted) roughness vector.""" + """ Return (weighted) roughness vector. + """ if model is None: model or self.model @@ -245,16 +318,20 @@ def roughness(self, model=None, weighted=True): else: return pureRoughness + def phiModel(self, model=None): - """Model objective function (norm of regularization term).""" + """ Model objective function (norm of regularization term). + """ if model is None: model = self.model rough = self.roughness(model, weighted=True) return pg.math.dot(rough, rough) + def phi(self, model=None, response=None): - """Total objective function (phiD + lambda * phiM).""" + """ Total objective function (phiD + lambda * phiM). + """ if response is None: response = self.response @@ -264,16 +341,20 @@ def phi(self, model=None, response=None): else: return phiD + self.phiModel(model) * self.lam + def relrms(self): - """Relative root-mean-square misfit of the last run.""" + """ Relative root-mean-square misfit of the last run. + """ return pg.math.rrms(self.data, self.response) + def absrms(self): - """Absolute root-mean-square misfit of the last run.""" + """ Absolute root-mean-square misfit of the last run. + """ return pg.math.rms(self.data, self.response) def setRegularization(self, *args, **kwargs): - """Set regularization properties for the inverse problem. + """ Set regularization properties for the inverse problem. This can be for specific regions (args) or all regions (no args). @@ -316,8 +397,9 @@ def setRegularization(self, *args, **kwargs): if len(kwargs) > 0: self.fop.setRegionProperties(*args, **kwargs) + def setInterRegionConstraint(self, region1, region2, strength): - """Set constraints between neighboring regions. + """ Set constraints between neighboring regions. Parameters ---------- @@ -329,8 +411,9 @@ def setInterRegionConstraint(self, region1, region2, strength): self.fop.regionManager().setInterRegionConstraint( region1, region2, strength) + def setInterfaceConstraint(self, marker, strength): - """Set regularization strength on specific interface. + """ Set regularization strength on specific interface. Parameters ---------- @@ -342,12 +425,16 @@ def setInterfaceConstraint(self, marker, strength): self.fop.regionManager().setInterfaceConstraint( marker, strength) + def setConstraintWeights(self, cWeight): - """Set weighting factors for the invidual rows of the C matrix.""" + """ Set weighting factors for the individual rows of the C matrix. + """ self.cWeight = cWeight + def reset(self): - """Reset function currently called at beginning of every inversion.""" + """ Reset function currently called at beginning of every inversion. + """ # FW: Note that this is called at the beginning of run. I therefore # removed the startingModel here to allow explicitly set starting # models by the user. @@ -358,12 +445,18 @@ def reset(self): self._dataVals = None self._errorVals = None + def oneStep(self): - """Carry out one iteration step (e.g. good for coupling etc.).""" + """ Carry out one iteration step (e.g. good for coupling etc.). + """ dModel = self.modelUpdate() - print("dM: ", dModel) + if self.verbose is True: + print("dM: ", dModel) tau, responseLS = lineSearch(self, dModel) - print("tau: ", tau) + + if self.verbose is True: + print("tau: ", tau) + pg.debug(f"tau={tau}") if tau >= 0.95: # practically 1 tau = 1 @@ -374,8 +467,9 @@ def oneStep(self): else: # compute new response self.response = self.fop.response(self.model) + def run(self, dataVals, errorVals=None, **kwargs): - """Run inversion. + """ Run inversion. The inversion will always start from the starting model taken from the forward operator. @@ -581,11 +675,11 @@ def run(self, dataVals, errorVals=None, **kwargs): def jacobianMatrix(self, error_weighted=False, numpy_matrix=False): - """Jacobian matrix of the inverse (data/model-transformed) problem. + """ Jacobian matrix of the inverse (data/model-transformed) problem. - Whereas the forward operator holds the jacobian matrix of the forward, + Whereas the forward operator holds the Jacobian matrix of the forward, i.e. the intrinsic (untransformed) problem, this function returns the - jacobian of the (transformed) inverse problem, i.e. taking model and + Jacobian of the (transformed) inverse problem, i.e. taking model and data transformations into account by using their inner derivatives. Parameters @@ -609,19 +703,24 @@ def jacobianMatrix(self, error_weighted=False, numpy_matrix=False): return pg.matrix.MultLeftRightMatrix(self.fop.jacobian(), tData, tModel) + def residual(self): - """Residual vector (data-reponse)/error using data transform.""" + """ Residual vector (data-reponse)/error using data transform. + """ return (self.dataTrans.fwd(self.dataVals) - self.dataTrans.fwd(self.response)) / \ self.dataTrans.error(self.response, self.errorVals) def dataGradientFormal(self): # formal but restricted to existent J - """Data gradient from jacobian and residual, i.e. J^T * dData.""" + """ Data gradient from Jacobian and residual, i.e. J^T * dData. + """ return -self.jacobianMatrix(error_weighted=True).transMult( self.residual()) + def dataGradient(self, error_weighted=True): # also works for fop.STy - """Data gradient from jacobian and residual, i.e. J^T * dData.""" + """ Data gradient from jacobian and residual, i.e. J^T * dData. + """ tData = self.dataTrans.deriv(self.response) if error_weighted: tData /= self.dataTrans.error(self.response, self.errorVals) @@ -629,8 +728,10 @@ def dataGradient(self, error_weighted=True): # also works for fop.STy return self.fop.STy(-self.residual()*tData) / \ self.modelTrans.deriv(self.model) + def modelGradient(self): - """Model gradient, i.e. C^T * C * (m - m0).""" + """ Model gradient, i.e. C^T * C * (m - m0). + """ # self.inv.checkConstraints() # not necessary? if isinstance(self.cWeight, (float, int)): C = pg.matrix.ScaledMatrix(self.fop.constraints(), self.cWeight) @@ -639,18 +740,30 @@ def modelGradient(self): return C.transMult(C.mult(self.modelTrans(self.model))) + def gradient(self): - """Gradient of the objective function.""" + """ Gradient of the objective function. + """ return self.dataGradient() + self.modelGradient() * self.lam class GaussNewtonInversion(InversionBase): - """Gauss-Newton based inversion.""" + """ Gauss-Newton based inversion. + """ def __init__(self, fop=None, **kwargs): + """ Initialize Gauss-Newton inversion. + + Arguments + --------- + fop : ForwardOperator + Forward operator to be used for the inversion. + """ super().__init__(fop=fop, **kwargs) + def modelUpdate(self): - """Compute (full) model update from inverse .""" + """ Compute (full) model update from inverse. + """ pg.verbose("Running LSQR inversion step!") model = self.model if len(self.response) != len(self.dataVals): @@ -662,11 +775,13 @@ def modelUpdate(self): tM = self.modelTrans nData = len(self.dataVals) self.A = pg.BlockMatrix() # to be filled with scaled J and C matrices - # part 1: data part + + ### part 1: data part self.JJ = self.jacobianMatrix(error_weighted=True) self.mat1 = self.A.addMatrix(self.JJ) self.A.addMatrixEntry(self.mat1, 0, 0) - # part 2: normal constraints + + ### part 2: normal constraints # self.checkConstraints() self.C = self.fop.constraints() self.leftC = pg.Vector(self.C.rows(), 1.0) @@ -675,7 +790,8 @@ def modelUpdate(self): self.leftC, self.rightC) self.mat2 = self.A.addMatrix(self.CC) self.A.addMatrixEntry(self.mat2, nData, 0, sqrt(self.lam)) - # % part 3: parameter constraints + + ### part 3: parameter constraints if self.G is not None: self.rightG = 1.0 / tM.deriv(model) self.GG = pg.matrix.MultRightMatrix(self.G, self.rightG) @@ -702,6 +818,7 @@ class DescentInversion(InversionBase): def __init__(self, **kwargs): super().__init__(**kwargs) + def modelUpdate(self): """The negative gradient of objective function as search direction.""" if self.fop.STy.__doc__ is pg.Modelling.STy.__doc__: # original @@ -1110,40 +1227,48 @@ def minDPhi(self, dPhi): @property def lam(self): - """Return regularization strength.""" + """ Return regularization strength. + """ return self._lam @lam.setter def lam(self, lam): - """Set regularization strength.""" + """ Set regularization strength. + """ self._lam = lam self.inv.setLambda(lam) def setDeltaPhiStop(self, it): - """Define minimum relative decrease in objective function to stop.""" + """ Define minimum relative decrease in objective function to stop. + """ self.inv.setDeltaPhiAbortPercent(it) @pg.renamed(setDeltaPhiStop) def setDeltaChiStop(self, it): - """Set data fit change level (deprecated).""" + """ Set data fit change level (deprecated). + """ self.setDeltaPhiStop(it) def echoStatus(self): - """Echo inversion status (model, response, rms, chi^2, phi).""" + """ Echo inversion status (model, response, rms, chi^2, phi). + """ self.inv.echoStatus() def setPostStep(self, p): - """Set a function to be called after each iteration. + """ Set a function to be called after each iteration. - The function is called with p(IterationNumber, self).""" + The function is called with p(IterationNumber, self). + """ self._postStep = p def setPreStep(self, p): - """Set a function to be called before each iteration.""" + """ Set a function to be called before each iteration. + """ self._preStep = p def setData(self, data): - """Set data.""" + """ Set data. + """ # QUESTION_ISNEEDED if isinstance(data, pg.DataContainer): raise Exception("should not be here .. its Managers job") @@ -1152,11 +1277,13 @@ def setData(self, data): self.dataVals = data def chi2(self, response=None): - """Chi-squared misfit (mean of squared error-weighted misfit).""" + """ Chi-squared misfit (mean of squared error-weighted misfit). + """ return self.phiData(response) / len(self.dataVals) def phiData(self, response=None): - """Data objective function (sum of suqred error-weighted misfit).""" + """ Data objective function (sum of suqred error-weighted misfit). + """ if response is None: response = self.response @@ -1167,7 +1294,8 @@ def phiData(self, response=None): return pg.math.dot(dData, dData) def phiModel(self, model=None): - """Model objective function (norm of regularization term).""" + """ Model objective function (norm of regularization term). + """ if model is None: model = self.model @@ -1175,7 +1303,8 @@ def phiModel(self, model=None): return pg.math.dot(rough, rough) def phi(self, model=None, response=None): - """Total objective function (phiD + lambda * phiM).""" + """ Total objective function (phiD + lambda * phiM). + """ phiD = self.phiData(response) if self.inv.localRegularization(): return phiD @@ -1183,15 +1312,17 @@ def phi(self, model=None, response=None): return phiD + self.phiModel(model) * self.inv.getLambda() def relrms(self): - """Relative root-mean-square misfit of the last run.""" + """ Relative root-mean-square misfit of the last run. + """ return self.inv.relrms() def absrms(self): - """Absolute root-mean-square misfit of the last run.""" + """ Absolute root-mean-square misfit of the last run. + """ return self.inv.absrms() def setRegularization(self, *args, **kwargs): - """Set regularization properties for the inverse problem. + """ Set regularization properties for the inverse problem. This can be for specific regions (args) or all regions (no args). @@ -1235,7 +1366,7 @@ def setRegularization(self, *args, **kwargs): self.fop.setRegionProperties(*args, **kwargs) def setInterRegionConstraint(self, region1, region2, strength): - """Set constraints between neighboring regions. + """ Set constraints between neighboring regions. Parameters ---------- @@ -1248,7 +1379,7 @@ def setInterRegionConstraint(self, region1, region2, strength): region1, region2, strength) def setInterfaceConstraint(self, marker, strength): - """Set regularization strength on specific interface. + """ Set regularization strength on specific interface. Parameters ---------- @@ -1261,11 +1392,12 @@ def setInterfaceConstraint(self, marker, strength): marker, strength) def setConstraintWeights(self, cWeight): - """Set weighting factors for the invidual rows of the C matrix.""" + """ Set weighting factors for the invidual rows of the C matrix. + """ self.inv.setCWeight(cWeight) def run(self, dataVals, errorVals=None, **kwargs): - """Run inversion. + """ Run inversion. The inversion will always start from the starting model taken from the forward operator. @@ -1511,7 +1643,7 @@ def run(self, dataVals, errorVals=None, **kwargs): return self.model def showProgress(self, style='all'): - r"""Show inversion progress after every iteration. + r""" Show inversion progress after every iteration. Can show models if `drawModel` method exists. The default fallback is plotting the :math:`\chi^2` fit as a function of iterations. Called if @@ -1533,7 +1665,7 @@ def showProgress(self, style='all'): for other_ax in ax.figure.axes: # pg._y(type(other_ax).mro()) if type(other_ax).mro()[0] == type(ax): - # only clear Axes not Colorbars + # only clear axes not the colorbars other_ax.clear() self.fop.drawModel(ax, self.inv.model()) @@ -1576,11 +1708,11 @@ def showProgress(self, style='all'): pg.plt.pause(0.05) def jacobianMatrix(self, error_weighted=False, numpy_matrix=False): - """Jacobian matrix of the inverse (data/model-transformed) problem. + """ Jacobian matrix of the inverse (data/model-transformed) problem. - Whereas the forward operator holds the jacobian matrix of the forward, + Whereas the forward operator holds the Jacobian matrix of the forward, i.e. the intrinsic (untransformed) problem, this function returns the - jacobian of the (transformed) inverse problem, i.e. taking model and + Jacobian of the (transformed) inverse problem, i.e. taking model and data transformations into account by using their inner derivatives. Parameters @@ -1609,23 +1741,27 @@ def jacobianMatrix(self, error_weighted=False, numpy_matrix=False): tData, tModel) def residual(self): - """Residual vector (data-reponse)/error using data transform.""" + """ Residual vector (data-reponse)/error using data transform. + """ return (self.dataTrans(self.dataVals) - self.dataTrans(self.response)) / \ self.dataTrans.error(self.response, self.errorVals) def dataGradient(self): - """Data gradient from jacobian and residual, i.e. J^T * dData.""" + """ Data gradient from jacobian and residual, i.e. J^T * dData. + """ return -self.jacobianMatrix(error_weighted=True).transMult(self.residual()) def modelGradient(self): - """Model gradient, i.e. C^T * C * (m - m0).""" + """ Model gradient, i.e. C^T * C * (m - m0). + """ # self.inv.checkConstraints() # not necessary? C = pg.matrix.MultLeftMatrix(self.fop.constraints(), self.inv.cWeight()) return C.transMult(C.mult(self.modelTrans(self.model))) def gradient(self): - """Gradient of the objective function.""" + """ Gradient of the objective function. + """ return self.dataGradient() + self.modelGradient() * self.lam # END OF REMOVAL upon pg 1.6 @@ -1636,7 +1772,8 @@ def gradient(self): class MarquardtInversion(Inversion): - """Marquardt scheme, i.e. local damping with decreasing strength.""" + """ Marquardt scheme, i.e. local damping with decreasing strength. + """ def __init__(self, fop=None, **kwargs): super().__init__(fop, **kwargs) diff --git a/pygimli/frameworks/linesearch.py b/pygimli/frameworks/linesearch.py index 93b20f449..82cdd600a 100644 --- a/pygimli/frameworks/linesearch.py +++ b/pygimli/frameworks/linesearch.py @@ -13,6 +13,25 @@ def tauVector(taumin=0.01, taumax=1, logScale=False, n=21): else: return np.linspace(taumin, taumax, n) +def lineSearchArmijo(inv, dM, tau=100, c=1e-4, tauFactor=0.8): + """Line search using Armijos rule, typical for Steepest Descent. + + Start with a "largish" value alpha and decrease it by a factor until the + Armijo rul is fulfilled (c is a small constant between 0 and 1): + + Phi(m+tau*m) <= Phi(m) + c alpha v^T dM + + where n is the negative normed gradient, i.e. -dM/norm(dM) + """ + v = -dM / np.linalg.norm(dM) + Elim = inv.phi() + sum(v*dM) * c * tau + while Enew > Elim: + newModel = inv.modelTrans.update(inv.model, v*tau) + newResponse = inv.fop.response(newModel) + Enew = inv.phi(newModel, newResponse) + tau *= tauFactor + + return tau/tauFactor, newResponse def lineSearchExact(inv, dM, taus=None, show=False, **kwargs): """Line search by exact forward response. diff --git a/pygimli/frameworks/methodManager.py b/pygimli/frameworks/methodManager.py index b4aabf18c..03dad06bd 100644 --- a/pygimli/frameworks/methodManager.py +++ b/pygimli/frameworks/methodManager.py @@ -770,8 +770,7 @@ def applyMesh(self, mesh, ignoreRegionManager=False, **kwargs): self.fop.setMesh(mesh, ignoreRegionManager=ignoreRegionManager) - def invert(self, data=None, mesh=None, startModel=None, - **kwargs): + def invert(self, data=None, mesh=None, startModel=None, **kwargs): """Run the full inversion. Parameters diff --git a/pygimli/frameworks/modelling.py b/pygimli/frameworks/modelling.py index 1ce47348d..e7879e8e9 100644 --- a/pygimli/frameworks/modelling.py +++ b/pygimli/frameworks/modelling.py @@ -45,7 +45,7 @@ class Modelling(pg.core.ModellingBase): Todo ---- - * Docu: + * Doc: - describe members (model transformation, dictionary of region properties) * think about splitting all mesh related into MeshModelling @@ -59,7 +59,6 @@ class Modelling(pg.core.ModellingBase): - initialize both with initDataSpace(), initModelSpace * createJacobian should also return J """ - def __init__(self, **kwargs): """Initialize. @@ -71,10 +70,10 @@ def __init__(self, **kwargs): modelTrans : [pg.trans.TransLog()] - Parameters - ---------- - **kwargs : - fop : Modelling + Keyword Arguments + ----------------- + **kwargs: + fop: Modelling """ self._fop = None # pg.frameworks.Modelling .. not needed .. remove it @@ -93,42 +92,52 @@ def __init__(self, **kwargs): self.modelTrans = pg.trans.TransLog() # Model transformation operator + def __hash__(self): - """Create a hash for Method Manager.""" + """ Create a hash for Method Manager. + """ # ^ pg.utils.dirHash(self._regionProperties) if self._data is not None: return pg.utils.strHash(str(type(self))) ^ hash(self._data) else: return pg.utils.strHash(str(type(self))) + def Sx(self, x): - """Right-hand side multiplication of Jacobian J*x. + """ Right-hand side multiplication of Jacobian J*x. By default, uses self.jacobian().mult(x) Overwrite for efficient use with gradient-type inversion. """ return self.jacobian().mult(x) + def STy(self, y): - """Right-hand side multiplication of Jacobian J.T*y. + """ Right-hand side multiplication of Jacobian J.T*y. By default, uses self.jacobian().transMult(x) Overwrite for efficient use with gradient-type inversion. """ return self.jacobian().transMult(y) + def __call__(self, *args, **kwargs): - """Call forward operator.""" + """ Call forward operator. + """ return self.response(*args, **kwargs) + @property def fop(self): - """Forward operator.""" + """ Forward operator. + """ return self._fop + @fop.setter def fop(self, fop): - """Set forward operator.""" + """ Set forward operator. + """ if fop is not None: if not isinstance(fop, pg.frameworks.Modelling): pg.critical('Forward operator needs to be an instance of ' @@ -136,29 +145,39 @@ def fop(self, fop): self._fop = fop + @property def data(self): - """Return data.""" + """ Return data. + """ return self._data + @data.setter def data(self, d): - """Set data (short property setter).""" + """ Set data (short property setter). + """ self.setData(d) + def setData(self, data): - """Set data (actual version).""" + """ Set data (actual version). + """ if isinstance(data, pg.DataContainer): self.setDataContainer(data) else: self._data = data + def setDataPost(self, data): - """Called when the dataContainer has been set sucessfully.""" + """ Called when the dataContainer has been set successfully. + """ pass + def setDataContainer(self, data): - """Set Data container.""" + """ Set Data container. + """ if self.fop is not None: pg.critical('in use?') self.fop.setData(data) @@ -168,17 +187,21 @@ def setDataContainer(self, data): self.setDataPost(self.data) + @property def modelTrans(self): - """Return model transformation.""" + """ Return model transformation. + """ self._applyRegionProperties() if self.regionManager().haveLocalTrans(): return self.regionManager().transModel() return self._modelTrans + @modelTrans.setter def modelTrans(self, tm): - """Set model transformation.""" + """ Set model transformation. + """ if isinstance(tm, str): if tm.lower() == "log": tm = pg.trans.TransLog() @@ -189,8 +212,10 @@ def modelTrans(self, tm): self._modelTrans = tm + def regionManager(self): - """Region manager.""" + """ Region manager. + """ self._regionManagerInUse = True # initialize RM if necessary super().regionManager() @@ -198,29 +223,37 @@ def regionManager(self): self._applyRegionProperties() return super().regionManager() + @property def parameterCount(self): - """Return parameter count.""" + """ Return parameter count. + """ pC = self.regionManager().parameterCount() if pC == 0: pg.warn("Parameter count is 0") return pC + def ensureContent(self): - """Whatever this is.""" + """ Whatever this is. + """ pass + def initModelSpace(self, **kwargs): """TODO.""" pass + def createDefaultStartModel(self, dataVals): - """Create the default startmodel as the median of the data values.""" + """ Create the default startmodel as the median of the data values. + """ pg.critical("'don't use me") + def createStartModel(self, dataVals=None): - """Create the default startmodel as the median of the data values. + """ Create the default startmodel as the median of the data values. Overwriting might be a good idea. Its used by inversion to create a valid startmodel if there are @@ -234,13 +267,17 @@ def createStartModel(self, dataVals=None): sm = self.regionManager().createStartModel() return sm + def clearRegionProperties(self): - """Clear all region parameter.""" + """ Clear all region parameter. + """ self._regionChanged = True self._regionProperties = {} + def regionProperties(self, regionNr=None): - """Return dictionary of all properties for region number regionNr.""" + """ Return dictionary of all properties for region number regionNr. + """ if regionNr is None: return self._regionProperties @@ -250,6 +287,7 @@ def regionProperties(self, regionNr=None): print(self._regionProperties) pg.error("no region for region #:", regionNr) + def setRegionProperties(self, regionNr, **kwargs): """Set region properties. regionNr can be '*' for all regions. @@ -567,35 +605,28 @@ def drawData(self, ax, data, err=None, label=None, **kwargs): class MeshModelling(Modelling): """Modelling class with a mesh discretization.""" - def __init__(self, **kwargs): super().__init__(**kwargs) self._axs = None self._meshNeedsUpdate = True - self._baseMesh = None + self._baseMesh = None ## keep a copy of the original mesh # optional p2 refinement for forward task self._refineP2 = False self._refineH2 = True self._pd = None self._C = None # custom Constraints matrix + def __hash__(self): - """Unique hash for caching.""" + """ Unique hash for caching. + """ return super().__hash__() ^ hash(self.mesh()) - @property - def mesh(self): - """Return mesh.""" - pg._r("inuse ?") - if self._fop is not None: - pg._r("inuse ?") - return self._fop.mesh - else: - return self.mesh() @property def paraDomain(self): - """Return parameter (inverse) mesh.""" + """ Return parameter (inverse) mesh. + """ # We need our own copy here because its possible that we want to use # the mesh after the fop was deleted if not self.mesh(): @@ -604,6 +635,7 @@ def paraDomain(self): self._pd = pg.Mesh(self.regionManager().paraDomain()) return self._pd + def setCustomConstraints(self, C): """ Set custom constraints matrix for lazy evaluation. @@ -611,8 +643,10 @@ def setCustomConstraints(self, C): """ self._C = C + def createConstraints(self): - """Create constraint matrix.""" + """ Create constraint matrix. + """ # just ensure there is valid mesh # self.mesh() @@ -646,8 +680,10 @@ def createConstraints(self): return self.constraints() + def paraModel(self, model): - """Return parameter model, i.e. model mapped back with cell markers.""" + """ Return parameter model, i.e. model mapped back with cell markers. + """ mod = model[self.paraDomain.cellMarkers()] if isinstance(mod, np.ndarray): mod = pg.Vector(mod) @@ -656,8 +692,9 @@ def paraModel(self, model): mod.isParaModel = True return mod + def ensureContent(self): - """Internal function to ensure there is a valid initialized mesh. + """ Internal function to ensure there is a valid initialized mesh. Initialization means the cell marker are recounted and/or there was a mesh refinement or boundary enlargement, all to fit the needs for the @@ -666,15 +703,17 @@ def ensureContent(self): # Need to call this once to be sure the mesh is initialized when needed self.mesh() + def setMeshPost(self, mesh): - """Interface to be called when the mesh has been set successfully. + """ Interface to be called when the mesh has been set successfully. Might be overwritten by child classes. """ pass + def createRefinedFwdMesh(self, mesh): - """Refine the current mesh for higher accuracy. + """ Refine the current mesh for higher accuracy. This is called automatic when accessing self.mesh() so it ensures any effect of changing region properties (background, single). @@ -691,8 +730,10 @@ def createRefinedFwdMesh(self, mesh): pg.info("Mesh for forward task:", m) return m + def createFwdMesh_(self): - """Create forward mesh.""" + """ Create forward mesh. + """ pg.info("Creating forward mesh from region infos.") m = pg.Mesh(self.regionManager().mesh()) @@ -717,8 +758,10 @@ def createFwdMesh_(self): pg.info('Set custom constraints matrix.') self.setConstraints(self._C) + def mesh(self): - """Returns the currently used mesh.""" + """ Returns the currently used mesh. + """ self._applyRegionProperties() if self._regionManagerInUse and self._regionChanged is True: @@ -726,8 +769,11 @@ def mesh(self): return super().mesh() + def setMesh(self, mesh, ignoreRegionManager=False): - """Set mesh and specify whether region manager can be ignored.""" + """ Set mesh and specify whether region manager can be ignored. + """ + # pg._b('setMesh', id(mesh), mesh, ignoreRegionManager) # keep a copy, just in case self._baseMesh = mesh @@ -737,12 +783,7 @@ def setMesh(self, mesh, ignoreRegionManager=False): # Modelling without region manager if ignoreRegionManager is True or not self._regionManagerInUse: self._regionManagerInUse = False - if self.fop is not None: - pg.critical('in use?') - self.fop.setMesh(mesh, ignoreRegionManager=True) - else: - super(Modelling, self).setMesh(mesh, ignoreRegionManager=True) - pass + super(Modelling, self).setMesh(mesh, ignoreRegionManager=True) self.setMeshPost(mesh) return @@ -752,8 +793,10 @@ def setMesh(self, mesh, ignoreRegionManager=False): self.regionManager().setMesh(mesh) self.setDefaultBackground() + def setDefaultBackground(self): - """Set the lowest region to background if several exist.""" + """ Set the lowest region to background if several exist. + """ regionIds = self.regionManager().regionIdxs() pg.info("Found {} regions.".format(len(regionIds))) if len(regionIds) > 1: @@ -762,6 +805,7 @@ def setDefaultBackground(self): "(marker={0})".format(bk)) self.setRegionProperties(bk, background=True) + def drawModel(self, ax, model, **kwargs): """Draw the model as mesh-based distribution.""" mod = None diff --git a/pygimli/frameworks/timelapse.py b/pygimli/frameworks/timelapse.py index a1086c430..abdde8b5a 100644 --- a/pygimli/frameworks/timelapse.py +++ b/pygimli/frameworks/timelapse.py @@ -19,6 +19,7 @@ def __init__(self, modellingOperator, scalef=1.0, **ini): self.nf = 0 self.nm = 0 + def setData(self, data, modellingOperator=None, **ini): """Distribute the data containers amongst the fops.""" modellingOperator = modellingOperator or self.modellingOperator @@ -30,6 +31,7 @@ def setData(self, data, modellingOperator=None, **ini): # fopi.setData(pg.Vector(datai)) self.fops.append(fopi) + def setMeshPost(self, mesh): """Set mesh to all forward operators.""" for fop in self.fops: @@ -37,15 +39,19 @@ def setMeshPost(self, mesh): self.prepareJacobian() + + def setDefaultBackground(self): """Set the default background behaviour.""" - regionIds = self.regionManager().regionIdxs() - pg.info("Found {} regions.".format(len(regionIds))) - if len(regionIds) > 1: - bk = pg.sort(regionIds)[0] - pg.info("Region with smallest marker ({0}) " - "set to background".format(bk)) - self.setRegionProperties(bk, background=True) + super().setDefaultBackground() + # regionIds = self.regionManager().regionIdxs() + # pg.info("Found {} regions.".format(len(regionIds))) + # if len(regionIds) > 1: + # bk = pg.sort(regionIds)[0] + # pg.info("Region with smallest marker ({0}) " + # "set to background".format(bk)) + # self.setRegionProperties(bk, background=True) + @property def parameterCount(self): diff --git a/pygimli/meshtools/mesh.py b/pygimli/meshtools/mesh.py index 6aa533232..406ac1dd3 100644 --- a/pygimli/meshtools/mesh.py +++ b/pygimli/meshtools/mesh.py @@ -2,15 +2,13 @@ """General mesh generation and maintenance.""" import os - import numpy as np - import pygimli as pg def createMesh(poly, quality=32, area=0.0, smooth=None, switches=None, verbose=False, **kwargs): - """Create a mesh for a given PLC or point list. + r"""Create a mesh for a given PLC or point list. The mesh is created by :term:`triangle` or :term:`tetgen` if the pgGIMLi support for these mesh generators is installed. @@ -24,7 +22,7 @@ def createMesh(poly, quality=32, area=0.0, smooth=None, switches=None, Parameters ---------- poly: :gimliapi:`GIMLI::Mesh` or list or ndarray - * 2D or 3D gimli mesh that contains the PLC. + * 2D or 3D GIMli mesh that contains the PLC. * 2D mesh needs edges * 3D mesh needs a plc and tetgen as system component * List of x y pairs [[x0, y0], ... ,[xN, yN]] @@ -46,7 +44,7 @@ def createMesh(poly, quality=32, area=0.0, smooth=None, switches=None, 1: node center 2: weighted node center - If smooth is just set to True then [1, 4] is choosen. + If smooth is just set to True then [1, 4] is chosen. switches: str Set additional triangle command switches. @@ -96,8 +94,8 @@ def createMesh(poly, quality=32, area=0.0, smooth=None, switches=None, pg.critical("No nodes in poly to create a valid mesh") if switches is None: - # -D Conforming delaunay - # -F Uses Steven Fortune's sweepline algorithm + # -D Conforming Delaunay + # -F Uses Steven Fortune's sweep line algorithm switches = 'pzeA' if area > 0: diff --git a/pygimli/meshtools/polytools.py b/pygimli/meshtools/polytools.py index e15fc64c1..547a39b70 100644 --- a/pygimli/meshtools/polytools.py +++ b/pygimli/meshtools/polytools.py @@ -352,7 +352,7 @@ def createWorld(start, end, marker=1, area=0., layers=None, worldMarker=True, world = createCube(size=pg.Pos(end)-pg.Pos(start), pos=(pg.Pos(end)+pg.Pos(start))/2.0, - area=area, **kwargs) + area=area, marker=marker, **kwargs) for i, b in enumerate(world.boundaries()): if worldMarker is True: @@ -1158,6 +1158,7 @@ def createParaMeshSurface(sensors, paraBoundary=None, boundary=-1, """ if hasattr(sensors, 'sensors'): sensors = sensors.sensors() + sensors = np.asarray(sensors) if paraBoundary is None: @@ -1203,7 +1204,11 @@ def createParaMeshSurface(sensors, paraBoundary=None, boundary=-1, paraRect.node(i).setMarker((i % 4 + 5) * 10) # create surface mesh of sensors and with maximal and parameter extent - surfacePLC = boundaryRect + paraRect + sensors[:, 0:2] + if boundary == 0: + surfacePLC = paraRect + sensors[:, 0:2] + else: + surfacePLC = boundaryRect + paraRect + sensors[:, 0:2] + surface = pg.meshtools.createMesh(surfacePLC, quality=surfaceMeshQuality) # interpolate topography to surface diff --git a/pygimli/physics/ert/__init__.py b/pygimli/physics/ert/__init__.py index ac719e540..9b9526015 100644 --- a/pygimli/physics/ert/__init__.py +++ b/pygimli/physics/ert/__init__.py @@ -25,7 +25,8 @@ from .ertScheme import createData from .processing import (uniqueERTIndex, generateDataFromUniqueIndex, reciprocalIndices, fitReciprocalErrorModel, - reciprocalProcessing) + reciprocalProcessing, combineMultipleData, + removeDuplicates) from .timelapse import TimelapseERT from .crosshole import CrossholeERT from pygimli.physics.ves import VESManager # backward compatibility diff --git a/pygimli/physics/ert/ertIPManager.py b/pygimli/physics/ert/ertIPManager.py index baae3d768..b0ae61024 100644 --- a/pygimli/physics/ert/ertIPManager.py +++ b/pygimli/physics/ert/ertIPManager.py @@ -62,7 +62,7 @@ def invertFDIP(self, ipdata="ip", **kwargs): if max(ipdata) > 3.15: # mrad ipdata /= 1000 - if iperr >= 1: + if np.max(iperr) >= 1: iperr /= 1000 complexData = pg.utils.toComplex(data["rhoa"], ipdata) diff --git a/pygimli/physics/ert/ertModelling.py b/pygimli/physics/ert/ertModelling.py index 87972a630..26fc5e49b 100644 --- a/pygimli/physics/ert/ertModelling.py +++ b/pygimli/physics/ert/ertModelling.py @@ -111,32 +111,40 @@ def __init__(self, sr=True, verbose=False): self._conjImag = False # the imaginary parts are flipped for log trans + def setVerbose(self, v): - """Set verbosity.""" + """ Set verbosity. + """ super().setVerbose(v) self._core.setVerbose(v) + def setDefaultBackground(self): - """Set the default background behaviour.""" + """ Set the default background behavior. + """ # if self.complex(): # deactivated, do it by hand # self.regionManager().addRegion(3, self._baseMesh, 2) + super().setDefaultBackground() + # regionIds = self.regionManager().regionIdxs() + # pg.info("Found {} regions.".format(len(regionIds))) - regionIds = self.regionManager().regionIdxs() - pg.info("Found {} regions.".format(len(regionIds))) + # if len(regionIds) > 1: + # bk = pg.sort(regionIds)[0] + # pg.info(f"(ERTModelling) Region with smallest marker ({bk}) " + # "set to background.") + # self.setRegionProperties(bk, background=True) - if len(regionIds) > 1: - bk = pg.sort(regionIds)[0] - pg.info(f"(ERTModelling) Region with smallest marker ({bk}) " - "set to background.") - self.setRegionProperties(bk, background=True) @property def parameterCount(self): - """Return number of parameters.""" + """ Return number of parameters. + """ return self.regionManager().parameterCount() * (1 + self.complex()) + def createConstraints(self, C=None): - """Create constraint matrix (special type for this).""" + """ Create constraint matrix (special type for this). + """ super().createConstraints() # standard C if self.complex(): if C is not None: @@ -150,8 +158,10 @@ def createConstraints(self, C=None): self.C = pg.matrix.RepeatDMatrix(self.C1, 2) self.setConstraints(self.C) + def createStartModel(self, dataVals): - """Create Starting model for ERT inversion.""" + """ Create Starting model for ERT inversion. + """ if self.complex(): dataC = pg.utils.toComplex(dataVals) nModel = self.parameterCount // 2 diff --git a/pygimli/physics/ert/importData.py b/pygimli/physics/ert/importData.py index 0b3bdcdd2..ee6e187ff 100644 --- a/pygimli/physics/ert/importData.py +++ b/pygimli/physics/ert/importData.py @@ -130,20 +130,29 @@ def getNonEmptyRow(i, comment='#'): header['ipDT'] = np.array(ipline[2:-2], dtype=float) header['ipGateT'] = np.cumsum(np.hstack((header['ipDelay'], header['ipDT']))) - data = pg.DataContainerERT() data.resize(nData) if typ == 9 or typ == 10: raise Exception("Don't know how to read:" + str(typ)) + row = getNonEmptyRow(it, comment=';') if typ in [11, 12, 13]: # mixed array res = pg.Vector(nData, 0.0) ip = pg.Vector(nData, 0.0) + err = pg.Vector(nData, 0.0) + iperr = pg.Vector(nData, 0.0) specIP = [] + hasErr = False + if row.startswith("Error"): + hasErr = True + row = getNonEmptyRow(it, comment=';') + header['ipErrType'] = getNonEmptyRow(it, comment=';') + for i in range(nData): - vals = getNonEmptyRow(it, comment=';').replace(',', ' ').split() + row = getNonEmptyRow(it, comment=';') + vals = row.replace(',', ' ').split() # row starts with 4 if int(vals[0]) == 4: @@ -179,6 +188,12 @@ def getNonEmptyRow(i, comment='#'): ip[i] = float(vals[ipCol]) if 'ipNumGates' in header: specIP.append(vals[ipCol:]) + if hasErr: + ipCol = int(vals[0])*2+3 + err[i] = float(vals[ipCol]) + if hasIP: + ipErrCol = int(vals[0])*2+4 + iperr[i] = float(vals[ipCol]) data.createFourPointData(i, eaID, ebID, emID, enID) @@ -195,6 +210,12 @@ def getNonEmptyRow(i, comment='#'): A[A < -1000] = -999 for i in range(header['ipNumGates']): data.set('ip'+str(i+1), A[:, i]) + + if hasErr: + data["err"] = err + if hasIP: + data["iperr"] = iperr + else: # not type 11-13 # amount of values per column per typ nntyp = [0, 3, 3, 4, 3, 3, 4, 4, 3, 0, 0, 8, 10] @@ -284,19 +305,24 @@ def getNonEmptyRow(i, comment='#'): if hasIP: data.set('ip', dataBody[nn - 1]) - row = getNonEmptyRow(it, comment=';') - if row.lower().startswith('topography'): + try: row = getNonEmptyRow(it, comment=';') - - istopo = int(row) - if istopo: - ntopo = int(getNonEmptyRow(it, comment=';')) - ap = data.additionalPoints() - for i in range(ntopo): - strs = getNonEmptyRow(it, comment=';').replace(',', ' ').split() - ap.push_back(pg.Pos([float(s) for s in strs])) - - data.setAdditionalPoints(ap) + if row.lower().startswith('topography'): + row = getNonEmptyRow(it, comment=';') + + istopo = int(row) + if istopo: + header["foundTopo"] = 1 + ntopo = int(getNonEmptyRow(it, comment=';')) + ap = data.additionalPoints() + for i in range(ntopo): + strs = getNonEmptyRow(it, comment=';').replace(',', ' ').split() + ap.push_back(pg.Pos([float(s) for s in strs])) + + data.setAdditionalPoints(ap) + + except StopIteration: + header["foundTopo"] = 0 data.sortSensorsX() data.sortSensorsIndex() diff --git a/pygimli/physics/ert/processing.py b/pygimli/physics/ert/processing.py index ca293dfb3..ad6bb425a 100644 --- a/pygimli/physics/ert/processing.py +++ b/pygimli/physics/ert/processing.py @@ -58,14 +58,15 @@ def generateDataFromUniqueIndex(ind, data=None, nI=None): scheme.resize(0) # make sure all data are deleted scheme.resize(len(ind)) nmba = np.zeros([len(ind), 4], dtype=int) + ind1 = ind.copy() for i in range(4): - col = ind % nI - ind -= col - ind = ind // nI + col = ind1 % nI + ind1 -= col + ind1 = ind1 // nI nmba[:, i] = col for i, tok in enumerate("nmba"): - scheme[tok] = nmba[:, i] - 1 + scheme[tok] = pg.IVector(nmba[:, i]) - 1 scheme["valid"] = 1 return scheme @@ -284,6 +285,46 @@ def getReciprocals(data, change=False, remove=False): data.removeInvalid() +def removeDuplicates(data, mode:str="average"): + """Remove duplicate rows from an ERT datacontainer. + + Parameters + ---------- + data : ERTDataContainer + The data container from which duplicates should be removed. + mode : str, optional + The method to handle duplicates, choose between + - "average" + - "first" + - "last" + - "minerr" + - "weighted" + """ + ind = uniqueERTIndex(data) + tokens = ["u", "i", "r", "rhoa", "err", "ip", "iperr"] + for i in np.unique(ind): + fi = np.nonzero(ind == i)[0] + if len(fi) > 1: + f0 = fi[0] + data["valid"][f0] = True + for ff in fi[1:]: + data["valid"][ff] = False + + if mode == "average": + for tok in tokens: + data[tok][f0] = np.mean(data[tok][fi]) + else: + ff = f0 + if mode == "last": + ff = fi[-1] + elif mode == "minerr": + ff = fi[np.argmin(data["err"][fi])] + for tok in tokens: + data[tok][f0] = data[tok][ff] + + data.removeInvalid() + + def extractReciprocals(fwd, bwd): """Extract reciprocal data from forward/backward DataContainers.""" nMax = max(fwd.sensorCount(), bwd.sensorCount()) @@ -313,7 +354,29 @@ def extractReciprocals(fwd, bwd): return rec, both def combineMultipleData(DATA): - """Combine multiple data containers into data/err matrices.""" + """Combine multiple data containers into data/err matrices. + + Generates a unified data container and a data matrices + Non-existing data are filled with NaN values. + + Parameters + ---------- + DATA : list of DataContainerERT + data contea + + Returns + ------- + data : pg.DataContainerERT + ERT data container with quadrupols from all input data + RHOA : np.array of size data.size() x len(DATA) + apparent resistivity data matrix + ERR : np.array (same size) + relative error matrix + IP : np.array(same size) + induced polarization data matrix + IPERR : np.array(same size) + induced polarization error matrix + """ assert hasattr(DATA, '__iter__'), "DATA should be DataContainers or str!" if isinstance(DATA[0], str): # read in if strings given DATA = [pg.DataContainerERT(data) for data in DATA] @@ -325,7 +388,9 @@ def combineMultipleData(DATA): scheme = generateDataFromUniqueIndex(uI, DATA[0]) uI = uniqueERTIndex(scheme) #, unify=False) R = np.ones([scheme.size(), len(DATA)]) * np.nan + IP = R.copy() ERR = np.zeros_like(R) + IPERR = R.copy() if not scheme.haveData('k'): # just do that only once scheme['k'] = createGeometricFactors(scheme) # check numerical @@ -339,6 +404,8 @@ def combineMultipleData(DATA): R[ii, i] = di['r'] ERR[ii, i] = di['err'] + IP[ii, i] = di['ip'] + IPERR[ii, i] = di['iperr'] RHOA = np.abs(np.reshape(scheme['k'], [-1, 1]) * R) - return scheme, RHOA, ERR + return scheme, RHOA, ERR, IP, IPERR diff --git a/pygimli/physics/ert/timelapse.py b/pygimli/physics/ert/timelapse.py index 8fe337bb4..3cda65219 100644 --- a/pygimli/physics/ert/timelapse.py +++ b/pygimli/physics/ert/timelapse.py @@ -15,6 +15,27 @@ # class TimelapseERT(Timelapse) +def guessDateTime(fname, delimiter="_", fmt="%Y%m%d-%H%M%S"): + """Guess date and time from filename.""" + parts = fname.split(delimiter) + dtstr = None + for part in parts: + if len(part) == 8 and part.startswith("20"): + dstr = part + elif len(part) == 6: + tstr = part + elif len(part) == 15: + dtstr = part.copy() + + if dtstr is None: + if dstr is not None and tstr is not None: + dtstr = "-".join([dstr, tstr]) + else: + return None + + mydate = datetime.strptime(dtstr, fmt) + return mydate + class TimelapseERT(): """Class for crosshole ERT data manipulation. @@ -71,7 +92,7 @@ def __init__(self, filename=None, **kwargs): if np.any(self.DATA): if isinstance(self.DATA[0], pg.DataContainerERT): - self.data, self.DATA, self.ERR = combineMultipleData(self.DATA) + self.data, self.DATA, self.ERR, *_ = combineMultipleData(self.DATA) self.mask() if "name" in kwargs: @@ -108,8 +129,13 @@ def load(self, filename, **kwargs): self.times = np.array( [datetime.fromisoformat(s) for s in timestr]) elif "*" in filename: - DATA = [ert.load(fname) for fname in glob(filename)] - self.data, self.DATA, self.ERR = combineMultipleData(DATA) + fnames = glob(filename) + DATA = [ert.load(fname) for fname in fnames] + if guessDateTime(fnames[0]) is not None: + self.times = [guessDateTime(fname) for fname in fnames] + + self.data, self.DATA, self.ERR, self.IP, self.IPERR = \ + combineMultipleData(DATA) self.name = filename[:-4].replace("*", "All") @@ -273,13 +299,15 @@ def showData(self, v="rhoa", t=None, **kwargs): return self.data.show(v, **kwargs) - def showTimeline(self, ax=None, **kwargs): + def showTimeline(self, what="rho", ax=None, **kwargs): """Show data timeline. Parameters ---------- ax : mpl.Axes|None matplotlib axes to plot (otherwise new) + what : str ["rhoa"] + define what to plot a, b, m, n : int tokens to extract data from """ @@ -297,14 +325,26 @@ def showTimeline(self, ax=None, **kwargs): kwargs.pop(k) abmn = [self.data[tok] for tok in "abmn"] + DATA = self.DATA + ylabel = "resistivity (Ohmm)" + if what.lower() == "ip": + DATA = self.IP + ylabel = "IP" + elif what.lower() == "err": + DATA = self.ERR * 100 + ylabel = "error (%)" + elif what.lower() == "iperr": + DATA = self.IPERR + ylabel = "IP error" + for i in np.nonzero(good)[0]: lab1 = lab + " ".join([str(tt[i]) for tt in abmn]) - ax.semilogy(self.times, self.DATA[i, :], "x-", label=lab1, **kwargs) + ax.semilogy(self.times, DATA[i, :], "x-", label=lab1, **kwargs) ax.grid(True) ax.legend() ax.set_xlabel("time") - ax.set_ylabel("resistivity (Ohmm)") + ax.set_ylabel(ylabel) return ax def fitReciprocalErrorModel(self, **kwargs): @@ -605,8 +645,9 @@ def generateRatioPDF(self, **kwargs): for i, model in enumerate(self.models[1:]): ax = fig.subplots() pg.show(self.pd, model/basemodel, ax=ax, **kwargs) - ax.set_title(str(i)+": " + self.times[i+1].isoformat(" ", "minutes") + "/" + - self.times[i].isoformat(" ", "minutes")) + cmpi = i if creep else 0 + ax.set_title(str(i+1)+": " + self.times[i+1].isoformat(" ", "minutes") + "/" + + self.times[cmpi].isoformat(" ", "minutes")) fig.savefig(pdf, format='pdf') fig.clf() if creep: diff --git a/pygimli/physics/ert/visualization.py b/pygimli/physics/ert/visualization.py index 3e6da5f2f..8a3eeb85f 100644 --- a/pygimli/physics/ert/visualization.py +++ b/pygimli/physics/ert/visualization.py @@ -216,9 +216,12 @@ def drawERTData(ax, data, vals=None, **kwargs): The used Colorbar or None """ if vals is None: - vals = data['rhoa'] + vals = 'rhoa' + + if isinstance(vals, str): + vals = data[vals].array() - valid = data.get("valid").array().astype("bool") + valid = data.get("valid").array().astype(bool) vals = ma.array(vals, mask=~valid) ind = kwargs.pop('ind', None) diff --git a/pygimli/physics/gravimetry/MagneticsModelling.py b/pygimli/physics/gravimetry/MagneticsModelling.py index 58e7fa77e..d338c91bb 100644 --- a/pygimli/physics/gravimetry/MagneticsModelling.py +++ b/pygimli/physics/gravimetry/MagneticsModelling.py @@ -5,25 +5,32 @@ class MagneticsModelling(pg.frameworks.MeshModelling): - """Magnetics modelling operator using Holstein (2007).""" - - def __init__(self, mesh=None, points=None, cmp=["TFA"], igrf=[50, 13]): - """Setup forward operator. + """ Magnetics modelling operator using Holstein (2007). + """ + def __init__(self, mesh=None, points=None, cmp=["TFA"], igrf=[0, 0, 50000]): + """ Setup forward operator. Parameters ---------- - mesh : pygimli:mesh - tetrahedral or hexahedral mesh - points : list|array of (x, y, z) - measuring points - cmp : list of str - component of: gx, gy, gz, TFA, Bx, By, Bz, Bxy, Bxz, Byy, Byz, Bzz - igrf : list|array of size 3 or 7 - international geomagnetic reference field, either - [D, I, H, X, Y, Z, F] - declination, inclination, horizontal field, - X/Y/Z components, total field OR - [X, Y, Z] - X/Y/Z components - [lat, lon] - latitude, longitude (automatic IGRF) + mesh: pygimli:mesh + Tetrahedral or hexahedral mesh. + + points: list|array of (x, y, z) + Measuring points. + + cmp: [str,] + Component of: gx, gy, gz, TFA, Bx, By, Bz, Bxy, Bxz, Byy, Byz, Bzz + + igrf: list|array of size 3 or 7 + International geomagnetic reference field. + either: + + * [D, I, H, X, Y, Z, F] - declination, + inclination, horizontal field, X/Y/Z components, total field OR + * [X, Y, Z] - X/Y/Z + components OR + * [lat, lon] - latitude, + longitude (automatic by pyIGRF) """ # check if components do not contain g! super().__init__() @@ -34,19 +41,27 @@ def __init__(self, mesh=None, points=None, cmp=["TFA"], igrf=[50, 13]): self.components = cmp self.igrf = None + if hasattr(igrf, "__iter__"): if len(igrf) == 2: # lat lon - import pyIGRF + pyIGRF = pg.optImport('pyIGRF', requiredFor="use igrf support" + f" for {self.__class__.__name__}. " + "Please install pyIGRF with: pip install pyIGRF") + self.igrf = pyIGRF.igrf_value(*igrf) - else: + else: # 3 (x,y,z) or 7 (T,H,X,Y,Z,D,I) self.igrf = igrf + self.kernel = None self.J = pg.matrix.BlockMatrix() + if self.mesh_ is not None: self.setMesh(self.mesh_) + def computeKernel(self): - """Compute the kernel.""" + """ Compute the kernel. + """ points = np.column_stack([self.sensorPositions[:, 1], self.sensorPositions[:, 0], -np.abs(self.sensorPositions[:, 2])]) @@ -65,19 +80,63 @@ def computeKernel(self): self.J.recalcMatrixSize() self.setJacobian(self.J) - # better move the latter to - # self.createKernel - - # def setMesh(self, mesh): - # self.createKernel(mesh) def response(self, model): - """Compute forward response.""" + """ Compute forward response. + + Arguments + --------- + model: array-like + Model parameters. + """ if self.kernel is None: self.computeKernel() return self.J.dot(model) + def createJacobian(self, model): - """Do nothing as this is a linear problem.""" + """ Do nothing as this is a linear problem. + + Abstract method to create the Jacobian matrix. + Need to be implemented in derived classes. + + Arguments + --------- + model: array-like + Model parameters. + """ + # any defaults possible? + + +class RemanentMagneticsModelling(MagneticsModelling): + def __init__(self, mesh, points, cmp=["Bx", "By", "Bz"], igrf=[0, 0, 50000]): + self.mesh_ = mesh + self.mesh_["marker"] = 0 + super().__init__(mesh=self.mesh_, points=points, igrf=igrf, cmp=cmp) + self.magX = MagneticsModelling(self.mesh_, points, igrf=[1, 0, 0], cmp=cmp) + self.magX.computeKernel() + self.magY = MagneticsModelling(self.mesh_, points, igrf=[0, 1, 0], cmp=cmp) + self.magY.computeKernel() + self.magZ = MagneticsModelling(self.mesh_, points, igrf=[0, 0, 1], cmp=cmp) + self.magZ.computeKernel() + self.m1 = pg.Mesh(self._baseMesh) + self.m2 = pg.Mesh(self._baseMesh) + self.regionManager().addRegion(1, self.m1, 0) + self.regionManager().addRegion(2, self.m2, 0) + self.J = pg.matrix.hstack([self.magX.jacobian(), + self.magY.jacobian(), + self.magZ.jacobian()]) + self.J.recalcMatrixSize() + self.setJacobian(self.J) + + def createJacobian(self, model): + """Do nothing.""" pass + + def response(self, model): + """Add together all three responses.""" + modelXYZ = np.reshape(model, [3, -1]) + return (self.magX.response(modelXYZ[0]) + + self.magY.response(modelXYZ[1]) + + self.magZ.response(modelXYZ[2])) * 4e-7 * np.pi * 1e9 diff --git a/pygimli/physics/gravimetry/__init__.py b/pygimli/physics/gravimetry/__init__.py index 0cbf61646..5ea2cc7e6 100644 --- a/pygimli/physics/gravimetry/__init__.py +++ b/pygimli/physics/gravimetry/__init__.py @@ -18,7 +18,7 @@ from . gravMagModelling import solveGravimetry, GravityModelling2D from . kernel import SolveGravMagHolstein -from . MagneticsModelling import MagneticsModelling +from . MagneticsModelling import MagneticsModelling, RemanentMagneticsModelling from . magneticsManager import MagManager from . GravityModelling import GravityModelling #from . MagneticsModelling import gravMagBoundaryHolstein diff --git a/pygimli/physics/gravimetry/kernel.py b/pygimli/physics/gravimetry/kernel.py index 32ddb1c94..7403b873c 100644 --- a/pygimli/physics/gravimetry/kernel.py +++ b/pygimli/physics/gravimetry/kernel.py @@ -38,7 +38,7 @@ def SolveGravMagHolstein(mesh, pnts, cmp, igrf=None): # , foot=np.inf): B_tens = None kernel = np.zeros((mesh.cellCount(), len(pnts), len(cmp))) - if igrf: + if np.any(igrf): if len(igrf) == 3: # an X, Y, Z vector F = np.linalg.norm(igrf) fakt = F / (4*np.pi) diff --git a/pygimli/physics/gravimetry/magneticsManager.py b/pygimli/physics/gravimetry/magneticsManager.py index 02f54328a..26123ce32 100644 --- a/pygimli/physics/gravimetry/magneticsManager.py +++ b/pygimli/physics/gravimetry/magneticsManager.py @@ -2,7 +2,6 @@ # -*- coding: utf-8 -*- """Method Manager for Magnetics.""" import numpy as np -import matplotlib.pyplot as plt import pygimli as pg import pygimli.meshtools as mt @@ -13,10 +12,11 @@ class MagManager(MeshMethodManager): - """Magnetics Manager.""" - + """ Magnetics Manager. + """ def __init__(self, data=None, **kwargs): - """Create Magnetics Manager instance.""" + """ Create Magnetics Manager instance. + """ self.DATA = kwargs.pop("DATA", None) self.x = kwargs.pop("x", None) self.y = kwargs.pop("y", None) @@ -38,13 +38,15 @@ def __init__(self, data=None, **kwargs): if self.mesh_ is not None: self.setMesh(self.mesh_) + def showData(self, cmp=None, **kwargs): - """Show data.""" + """ Show data. + """ cmp = cmp or self.cmp nc = 2 if len(cmp) > 1 else 1 nr = (len(cmp)+1) // 2 - fig, ax = plt.subplots(nr, nc, sharex=True, sharey=True, squeeze=False, - figsize=(7, len(self.cmp)*1+3)) + fig, ax = pg.plt.subplots(nr, nc, sharex=True, sharey=True, + squeeze=False, figsize=(7, len(self.cmp)*1+3)) axs = np.atleast_1d(ax.flat) kwargs.setdefault("cmap", "bwr") for i, c in enumerate(cmp): @@ -58,8 +60,29 @@ def showData(self, cmp=None, **kwargs): return ax - def createGrid(self, dx=50, depth=800, bnd=0): - """Create a grid.""" + + def createGrid(self, dx:float=50, depth:float=800, bnd:float=0): + """ Create a grid. + + TODO + ---- + * check default values, make them more sensible + and depending on data + + Arguments + --------- + dx: float=50 + Grid spacing in x and y direction. + depth: float=800 + Depth of the grid in z direction. + bnd: float=0 + Boundary distance to extend the grid in x and y direction. + + Returns + ------- + mesh: :gimliapi:`GIMLI::Mesh` + Created 3D structured grid. + """ x = np.arange(min(self.x)-bnd, max(self.x)+bnd+.1, dx) y = np.arange(min(self.y)-bnd, max(self.y)+bnd+.1, dx) z = np.arange(-depth, .1, dx) @@ -67,10 +90,39 @@ def createGrid(self, dx=50, depth=800, bnd=0): self.fop.setMesh(self.mesh_) return self.mesh_ - def createMesh(self, bnd=0, area=1e5, depth=800, quality=1.3, addPLC=None, addPoints=True): - """Create an unstructured mesh.""" - geo = mt.createCube(start=[min(self.x)-bnd, min(self.x)-bnd, -depth], end=[max(self.x)+bnd, max(self.y)+bnd, 0]) - if addPoints: + + def createMesh(self, bnd:float=0, area:float=1e5, depth:float=800, + quality:float=1.3, addPLC:pg.Mesh=None, addPoints:bool=True): + """ Create an unstructured 3D mesh. + + TODO + ---- + * check default values, make them more sensible + and depending on data + + Arguments + --------- + bnd: float=0 + Boundary distance to extend the mesh in x and y direction. + area: float=1e5 + Maximum area constraint for cells. + depth: float=800 + Depth of the mesh in z direction. + quality: float=1.3 + Quality factor for mesh generation. + addPLC: :gimliapi:`GIMLI::Mesh` + PLC mesh to add to the mesh. + addPoints: bool=True + Add points from self.x and self.y to the mesh. + + Returns + ------- + mesh: :gimliapi:`GIMLI::Mesh` + Created 3D unstructured mesh. + """ + geo = mt.createCube(start=[min(self.x)-bnd, min(self.x)-bnd, -depth], + end=[max(self.x)+bnd, max(self.y)+bnd, 0]) + if addPoints is True: for xi, yi in zip(self.x, self.y): geo.createNode([xi, yi, 0]) if addPLC: @@ -80,56 +132,69 @@ def createMesh(self, bnd=0, area=1e5, depth=800, quality=1.3, addPLC=None, addPo self.fop.setMesh(self.mesh_) return self.mesh_ - def createForwardOperator(self, **kwargs): - """Create forward operator (computationally extensive!).""" + + def createForwardOperator(self): + """ Create forward operator (computationally extensive!). + """ points = np.column_stack([self.x, self.y, -np.abs(self.z)]) self.fwd = MagneticsModelling(points=points, cmp=self.cmp, igrf=self.igrf) return self.fwd + def inversion(self, noise_level=2, noisify=False, **kwargs): """Run Inversion (requires mesh and FOP). - Parameters - ---------- - noise_level : float|array + Arguments + --------- + noise_level: float|array absolute noise level (absoluteError) - noisify : bool + noisify: bool add noise before inversion - relativeError : float|array [0.01] + relativeError: float|array [0.01] relative error to stabilize very low data - depthWeighting : bool [True] + depthWeighting: bool [True] apply depth weighting after Li&Oldenburg (1996) - z0 : float + z0: float skin depth for depth weighting - mul : array + mul: array multiply constraint weight with - standard inversion keyword arguments - .................................... - C(,cType) : int|Matrix|[float, float, float] - constraint order, matrix or correlation lengths - limits : [float, float] - lower and upper parameter limits - symlogThreshold : float [0] - threshold for symlog data trans (0 = linear) - startModel : float|array - starting model (typically homogeneous) - lam : float + Keyword arguments + ----------------- + startModel: float|array=0.001 + Starting model (typically homogeneous) + relativeError: float=0.001 + Relative error to stabilize very low data. + lam: float=10 regularization strength - robustData, blockyModel : bool - L1 norm on data misfit and model roughness - maxIter : int - maximum iteration number + verbose: bool=True + Be verbose + symlogThreshold: float [0] + Threshold for symlog data trans. + limits: [float, float] + Lower and upper parameter limits. + C: int|Matrix|[float, float, float] [1] + Constraint order. + C(,cType): int|Matrix|[float, float, float]=C + Constraint order, matrix or correlation lengths. + z0: float=25 + Skin depth for depth weighting. + depthWeighting: bool=True + Apply depth weighting after Li&Oldenburg (1996). + mul: float=1 + Multiply depth weighting constraint weight with this factor. + **kwargs: + Additional keyword arguments for the inversion. Returns ------- - model : array - model vector (also saved in self.inv.model) + model: np.array + Model vector (also saved in self.inv.model). """ - datavec = np.concatenate([self.DATA[c] for c in self.cmp]) + dataVec = np.concatenate([self.DATA[c] for c in self.cmp]) if noisify: - datavec += np.random.randn(len(datavec)) * noise_level + dataVec += np.random.randn(len(dataVec)) * noise_level # self.inv_ = pg.Inversion(fop=self.fwd, verbose=True) self.inv.setForwardOperator(self.fwd) @@ -137,6 +202,7 @@ def inversion(self, noise_level=2, noisify=False, **kwargs): kwargs.setdefault("relativeError", 0.001) kwargs.setdefault("lam", 10) kwargs.setdefault("verbose", True) + thrs = kwargs.pop("symlogThreshold", 0) if thrs > 0: self.inv.dataTrans = pg.trans.TransSymLog(thrs) @@ -145,6 +211,7 @@ def inversion(self, noise_level=2, noisify=False, **kwargs): self.inv.setRegularization(limits=limits) C = kwargs.pop("C", 1) cType = kwargs.pop("cType", C) + if hasattr(C, "__iter__"): self.inv.setRegularization(correlationLengths=C) cType = -1 @@ -166,30 +233,78 @@ def inversion(self, noise_level=2, noisify=False, **kwargs): dw *= kwargs.pop("mul", 1) self.inv.setConstraintWeights(dw) - model = self.inv.run(datavec, absoluteError=noise_level, **kwargs) + model = self.inv.run(dataVec, absoluteError=noise_level, **kwargs) return model + def showDataFit(self): - """Show data, model response and misfit.""" + """ Show data, model response and misfit. + """ nc = len(self.cmp) - _, ax = pg.plt.subplots(ncols=3, nrows=nc, figsize=(12, 3*nc), sharex=True, sharey=True, squeeze=False) + _, ax = pg.plt.subplots(ncols=3, nrows=nc, figsize=(12, 3*nc), + sharex=True, sharey=True, squeeze=False) vals = np.reshape(self.inv.dataVals, [nc, -1]) mm = np.max(np.abs(vals)) resp = np.reshape(self.inv.response, [nc, -1]) errs = np.reshape(self.inv.errorVals, [nc, -1]) # relative! misf = (vals - resp) / np.abs(errs * vals) - fkw = dict(cmap="bwr", vmin=-mm, vmax=mm) - mkw = dict(cmap="bwr", vmin=-3, vmax=3) + fkw = {'cmap':"bwr", 'vmin':-mm, 'vmax':mm} + mkw = {'cmap':"bwr", 'vmin':-3, 'vmax':3} for i in range(nc): ax[i, 0].scatter(self.x, self.y, c=vals[i], **fkw) ax[i, 1].scatter(self.x, self.y, c=resp[i], **fkw) ax[i, 2].scatter(self.x, self.y, c=misf[i], **mkw) - def show3DModel(self, label=None, trsh=0.025, synth=None, invert=False, - position="yz", elevation=10, azimuth=25, zoom=1.2, **kwargs): - """Standard 3D view.""" + + def show3DModel(self, label:str=None, trsh:float=0.025, + synth:pg.Mesh=None, invert:bool=False, + position:str="yz", elevation:float=10, azimuth:float=25, + zoom:float=1.2, **kwargs): + """ Standard 3D view. + + Arguments + --------- + label: str='sus' + Label for the mesh data to visualize. + + trsh: float=0.025 + Threshold for the mesh data to visualize. + synth: :gimliapi:`GIMLI::Mesh`=None + Synthetic model to visualize in wireframe. + invert: bool=False + Invert the threshold filter. + position: str="yz" + Camera position, e.g. "yz", "xz", "xy". + elevation: float=10 + Camera elevation angle. + azimuth: float=25 + Camera azimuth angle. + zoom: float=1.2 + Camera zoom factor. + + Keyword arguments + ----------------- + cMin: float=0.001 + Minimum color value for the mesh data. + cMax: float=None + Maximum color value for the mesh data. If None, it is set to the + maximum value of the mesh data. + cMap: str="Spectral_r" + Colormap for the mesh data visualization. + logScale: bool=False + Use logarithmic scale for the mesh data visualization. + **kwargs: + Additional keyword arguments for the pyvista plot. + + Returns + ------- + pl: pyvista Plotter + Plot widget with the 3D model visualization. + """ if label is None: + ## ever happen that this is a string? label = self.inv.model + if not isinstance(label, str): self.mesh_["sus"] = np.array(label) label = "sus" @@ -198,17 +313,18 @@ def show3DModel(self, label=None, trsh=0.025, synth=None, invert=False, kwargs.setdefault("cMax", max(self.mesh_[label])) kwargs.setdefault("cMap", "Spectral_r") kwargs.setdefault("logScale", False) + flt = None pl, _ = pg.show(self.mesh_, style="wireframe", hold=True, alpha=0.1) # mm = [min(self.mesh_[label]), min(self.mesh_[label])] if trsh > 0: - flt = {"threshold": dict(value=trsh, scalars=label, invert=invert)} + flt = {"threshold": {'value':trsh, 'scalars':label,'invert':invert}} pv.drawModel(pl, self.mesh_, label=label, style="surface", filter=flt, **kwargs) pv.drawMesh(pl, self.mesh_, label=label, style="surface", **kwargs, - filter={"slice": dict(normal=[-1, 0, 0], origin=[0, 0, 0])}) + filter={"slice": {'normal':[-1, 0, 0], 'origin':[0, 0, 0]}}) if synth: pv.drawModel(pl, synth, style="wireframe") diff --git a/pygimli/physics/traveltime/TravelTimeManager.py b/pygimli/physics/traveltime/TravelTimeManager.py index 2c4c8cc96..39119fe4a 100644 --- a/pygimli/physics/traveltime/TravelTimeManager.py +++ b/pygimli/physics/traveltime/TravelTimeManager.py @@ -492,9 +492,11 @@ def saveResult(self, folder=None, size=(16, 10), verbose=False, **kwargs): np.savetxt(os.path.join(path, 'chi.txt'), self.inv.chi2History) - fig, ax = pg.plt.subplots() - self.showResult(ax=ax, cov=self.standardizedCoverage(), **kwargs) - fig.set_size_inches(size) - fig.savefig(os.path.join(path, 'velocity.pdf'), bbox_inches='tight') - pg.plt.close(fig) + if m.dim() == 2: + fig, ax = pg.plt.subplots() + self.showResult(ax=ax, cov=self.standardizedCoverage(), **kwargs) + fig.set_size_inches(size) + fig.savefig(os.path.join(path, 'velocity.pdf'), bbox_inches='tight') + pg.plt.close(fig) + return path diff --git a/pygimli/physics/traveltime/tt.py b/pygimli/physics/traveltime/tt.py index 4aaca2a5f..ff7469a04 100644 --- a/pygimli/physics/traveltime/tt.py +++ b/pygimli/physics/traveltime/tt.py @@ -52,3 +52,6 @@ def show(data, **kwargs): else: drawFirstPicks(ax, data, tt=kwargs.pop("t", None), **kwargs) # drawTravelTimeData(ax, data, **kwargs) + cBar = None + + return ax, cBar \ No newline at end of file diff --git a/pygimli/physics/ves/vesModelling.py b/pygimli/physics/ves/vesModelling.py index dbf6a800f..fc25bd10c 100644 --- a/pygimli/physics/ves/vesModelling.py +++ b/pygimli/physics/ves/vesModelling.py @@ -11,23 +11,27 @@ class VESModelling(Block1DModelling): Attributes ---------- - ab2 : + ab2 : array-like Half distance between the current electrodes A and B. - mn2 : + mn2 : array-like Half distance between the potential electrodes M and N. Only used for input (feeding am etc.) or plotting. - am : + am : array-like Part of data basis. Distances between A and M electrodes. A is first current, M is first potential electrode. - bm : + bm : array-like Part of data basis. Distances between B and M electrodes. B is second current, M is first potential electrode. - an : + an : array-like Part of data basis. Distances between A and N electrodes. A is first current, N is second potential electrode. - bn : + bn : array-like Part of data basis. Distances between B and N electrodes. B is second current, N is second potential electrode. + nLayers : int [4] + number of layers, i.e. the parameter number is nLayers*2-1 + nPara : int [] + number of parameters per layer """ def __init__(self, ab2=None, mn2=None, **kwargs): diff --git a/pygimli/setup.py.in b/pygimli/setup.py.in index 1deb4b58f..2777b5f89 100644 --- a/pygimli/setup.py.in +++ b/pygimli/setup.py.in @@ -40,7 +40,7 @@ setup( include_package_data=True, license="Apache 2.0", keywords=["inversion", "modelling", "geophysics"], - install_requires=['pgcore>=@PGCORE_VERSION_WHL@', + install_requires=['pgcore>=@PGCORE_VERSION_WHL@', '<2' 'numpy>=2.1', 'matplotlib>=3.7', 'scipy>=1.14', diff --git a/pygimli/testing/test_FEM.py b/pygimli/testing/test_FEM.py index bad084522..7840ecec3 100644 --- a/pygimli/testing/test_FEM.py +++ b/pygimli/testing/test_FEM.py @@ -256,11 +256,12 @@ def _testP1_(mesh, show=False, followP2=True): _testP1_(pg.createGrid(x=np.linspace(-0.04, 0.04, 11), y=np.linspace(-0.4, 0, 11))) # 3D reg quad - _testP1_(pg.createGrid(x=np.linspace(-2, 2, 11), - y=np.linspace( 0, 1, 11), - z=np.linspace( 0, 1, 11)), - followP2=False - ) + # _testP1_(pg.createGrid(x=np.linspace(-2, 2, 11), + # y=np.linspace( 0, 1, 11), + # z=np.linspace( 0, 1, 11)), + # followP2=False + # ) + #return # check why P2 fails here, # 2D tri diff --git a/pygimli/testing/test_MeshGenerator.py b/pygimli/testing/test_MeshGenerator.py index ea99f5749..68b28bf82 100644 --- a/pygimli/testing/test_MeshGenerator.py +++ b/pygimli/testing/test_MeshGenerator.py @@ -71,6 +71,12 @@ def test_createGrid(self): # print(mesh) # self.assertEqual(mesh.cellCount(), 10.0) + # test also RValue conversion to correct arrays signed arrays + x = np.arange(-10, 11) + self.assertEqual(pg.createGrid(x,x,x).bb(), + [pg.Pos(-10.0, -10.0, -10.0), + pg.Pos(10.0, 10.0, 10.0)]) + def test_createMesh1D(self): diff --git a/pygimli/testing/test_misc.py b/pygimli/testing/test_misc.py index fa665bf34..acb9a0997 100644 --- a/pygimli/testing/test_misc.py +++ b/pygimli/testing/test_misc.py @@ -41,9 +41,9 @@ def test_Trans(self): f.add(pg.trans.TransLog(), 5) f.add(pg.trans.TransLog(), 5) - np.testing.assert_array_equal(f.at(0).fwd(np.ones(10)*10), + np.testing.assert_array_equal(f.at(0).fwd(np.ones(10)*10), np.log(np.ones(10)*10)) - np.testing.assert_array_equal(f.fwd(np.ones(10)*10), + np.testing.assert_array_equal(f.fwd(np.ones(10)*10), np.log(np.ones(10)*10)) # tm2 = pg.trans.TransLog() # tc.add(tm2, 5, 10) @@ -53,6 +53,7 @@ def test_Trans(self): #fop._modelTrans = pg.trans.TransLog() + def test_DataContainerFilter(self): """ """ @@ -64,10 +65,10 @@ def test_DataContainerFilter(self): data.markInvalid(pg.core.IndexArray(np.arange(5, dtype="long"))) self.assertEqual(data('valid'), [0.0, 0.0, 0.0, 0.0, 0.0]) - + data.markValid(np.arange(5, dtype="long")) self.assertEqual(data('valid'), [1.0, 1.0, 1.0, 1.0, 1.0]) - + data.markInvalid(range(5)) self.assertEqual(data('valid'), [0.0, 0.0, 0.0, 0.0, 0.0]) @@ -75,32 +76,34 @@ def test_DataContainerFilter(self): data.markValid(pg.Vector(x) > 2.0) self.assertEqual(data('valid'), [0.0, 0.0, 0.0, 1.0, 1.0]) - + data.markValid(pg.BVector(x < 2.0)) self.assertEqual(data('valid'), [1.0, 1.0, 0.0, 1.0, 1.0]) data.markInvalid(pg.find(x > 3.0)) self.assertEqual(data('valid'), [1.0, 1.0, 0.0, 1.0, 0.0]) - + data.markInvalid(x < 1.0) self.assertEqual(data('valid'), [0.0, 1.0, 0.0, 1.0, 0.0]) + def test_DataContainerSensors(self): data = pg.DataContainer() - + sensors = [[x, 0.0] for x in range(5)] data.setSensorPositions(sensors) data.setSensorPositions(data.sensors()[::-1]) - + self.assertEqual(data.sensor(0), [4., 0.0, 0.0]) self.assertEqual(data.sensor(4), [0., 0.0, 0.0]) + def test_DataContainerIndex(self): data = pg.DataContainer() data['b'] = np.ones(2) * 3.14 np.testing.assert_array_equal(data['b'], np.ones(2)*3.14) self.assertEqual(type(data['b']), type(pg.Vector())) - + data['b'][0] = 1.0 self.assertEqual(data['b'][0], 1.0) @@ -110,17 +113,19 @@ def test_DataContainerIndex(self): self.assertEqual(type(data['a']), type(np.array(1))) self.assertEqual(data['a'].dtype, 'int') data['a'][0] = 1.0 # will not work for sensorIndex until its changed in the datacontainer as IndexArray - + data['a'] = np.ones(2)*1.2 np.testing.assert_array_equal(data['a'], np.ones(2)) self.assertEqual(type(data['a']), type(np.array(1))) self.assertEqual(data['a'].dtype, 'int') + def test_Operators(self): t = pg.Vector(10, 1.0) self.assertEqual(len(t == 1.0), len(t > 0)) self.assertEqual(len(t == 1.0), len(t == 1)) + def test_Int64Problem(self): data = pg.DataContainerERT() data.createFourPointData(0, 0, 1, 2, 3) @@ -146,6 +151,7 @@ def test_Int64Problem(self): self.assertEqual(sum(data('m')), 9*2) self.assertEqual(sum(data('n')), 9*3) + def test_PosConstMember(self): p1 = pg.Pos(1.0, 0.0, 0.0) p2 = pg.Pos(0.0, 1.0, 0.0) @@ -153,12 +159,13 @@ def test_PosConstMember(self): p3 = p1.cross(p2) self.assertEqual(p3, pg.Pos(0.0, 0.0, 1.0)) + def test_Hash(self): v1 = pg.Vector(10, 2.) v2 = pg.Vector(10, 2.) self.assertFalse(pg.Vector(1, 0.).hash() == pg.Vector(2, 0.).hash()) - + self.assertEqual(v1.hash(), v2.hash()) self.assertEqual(hash(v1), hash(v2)) v2[2] = 3. @@ -167,10 +174,14 @@ def test_Hash(self): self.assertTrue(v1.hash() == v2.hash()) self.assertEqual(v1.hash(), pg.Vector(10, 2.).hash()) + self.assertEqual(pg.utils.valHash([1, 0, 0])== + pg.utils.valHash([0, 1, 0]), False) + + def test_HashData(self): d1 = pg.DataContainerERT() d2 = pg.DataContainerERT() - + self.assertEqual(d1.hash(), d2.hash()) d1.createSensor([1.0, 0.0]) d2.createSensor([2.0, 0.0]) @@ -203,15 +214,15 @@ def test_HashMesh(self): m2.node(0).setPos([1.0, 0.0]) self.assertTrue(m1.hash() == m2.hash()) - - # does not work .. need time to implement + + # does not work .. need time to implement # def test_DataContainerWrite(self): # data = pg.DataContainer() # data.save('test.dat') # fi = open('test2.dat', 'w') # data.write(fi) # fi.close() - + def test_DataTypes(self): pg.core.showSizes() diff --git a/pygimli/utils/__init__.py b/pygimli/utils/__init__.py index 0797e2f2a..6ce4b9592 100644 --- a/pygimli/utils/__init__.py +++ b/pygimli/utils/__init__.py @@ -18,7 +18,7 @@ from .complex import (isComplex, toComplex, toPolar, squeezeComplex, toRealMatrix, KramersKronig) -from .cache import (cache, strHash, noCache) +from .cache import (cache, strHash, noCache, valHash) from .geostatistics import (computeInverseRootMatrix, covarianceMatrix, generateGeostatisticalModel) from .gps import GKtoUTM, findUTMZone, getProjection, getUTMProjection, readGPX diff --git a/pygimli/utils/cache.py b/pygimli/utils/cache.py index e59fea45f..599cd8c70 100644 --- a/pygimli/utils/cache.py +++ b/pygimli/utils/cache.py @@ -5,55 +5,87 @@ Input supports python base types and all pg.core objects with .hash() method. Output supports DataContainerERT, ... -TODO: - - * Output types: - numpy.ndarray, pg.Mesh. pg.Vector, pg.Matrix - To use just add the decorator. +``` @pg.cache def myLongRunningStuff(*args, **kwargs): #... return results +``` + +To use the cache without the decorator, you can call it also like this: +`pg.cache(myLongRunningStuff)(*args, **kwargs)` + """ import sys import os +import traceback import inspect import hashlib import json import time import numpy as np - import pygimli as pg __NO_CACHE__ = False -def noCache(c): +def noCache(c:bool=True): + """ Set the caching to noCache mode. + + This will disable the caching mechanism and all decorated functions + """ global __NO_CACHE__ __NO_CACHE__ = c -def strHash(string): - return int(hashlib.sha224(string.encode()).hexdigest()[:16], 16) -def valHash(a): - +def strHash(s: str) -> int: + """ Create a hash value for the given string. + + Uses sha224 to create a 16 byte hash value. + + Arguments + --------- + s: str + The string to hash. + + Returns + ------- + hash: int + The hash value of the string. + """ + return int(hashlib.sha224(s.encode()).hexdigest()[:16], 16) + + +def valHash(a:any)-> int: + """ Create a hash value for the given value. + + Arguments + --------- + a: any + The value to hash. Can be a string, int, list, numpy array or any + other object. Logs an error if the type is not supported. + Returns + ------- + hash: int + The hash value of the value. + """ if isinstance(a, str): return strHash(a) elif isinstance(a, int): return a elif isinstance(a, list): hsh = 0 - for item in a: - hsh = hsh ^ valHash(item) + for i, item in enumerate(a): + hsh = hsh ^ valHash(str(i)+str(item)) return hsh elif isinstance(a, np.ndarray): if a.ndim == 1: return hash(pg.Vector(a)) elif a.ndim == 2: - # convert to RVector to use memcopy + # convert to RVector to use mem copy return hash(pg.Vector(a.reshape((1,a.shape[0]*a.shape[1]))[0])) else: print(a) @@ -61,16 +93,34 @@ def valHash(a): return hash(a) + class Cache(object): - def __init__(self, hashValue): + """ Cache class to store and restore data. + + This class is used to store and restore data in a cache. + """ + def __init__(self, hashValue:int): + """ Initialize the cache with a hash value. + + Arguments + --------- + hashValue: int + The hash value of the function and its arguments. + """ self._value = None self._hash = hashValue self._name = CacheManager().cachingPath(str(self._hash)) self._info = None self.restore() + @property def info(self): + """ Return the cache info dictionary. + + This dictionary contains information about the cache like type, file, + date, duration, restored count, code info, version, args and kwargs. + """ if self._info is None: self._info = {'type': '', 'file': '', @@ -84,16 +134,37 @@ def info(self): } return self._info + @info.setter def info(self, i): + """ Set the cache info dictionary. + + Arguments + --------- + i: dict + The cache info dictionary to set. + """ self._info = i + @property def value(self): + """ Return the cached value. + """ return self._value + @value.setter def value(self, v): + """ Set the cached value and store it in the cache. + + Arguments + --------- + v: any + The value to cache. Can be a DataContainerERT, Mesh, RVector, + ndarray or any other object with either a save method or can be + pickled. + """ self.info['type'] = str(type(v).__name__) # if len(self.info['type']) != 1: @@ -117,19 +188,24 @@ def value(self, v): v.save(self._name) else: np.save(self._name, v, allow_pickle=True) - # pg.warn('ascii save of type', self.info['type'], 'might by dangerous') + # pg.warn('ascii save of type', self.info['type'], + # 'might by dangerous') # v.save(self._name) self._value = v pg.info('Cache stored:', self._name) + def updateCacheInfo(self): + """ Update the cache info dictionary and save it to a json file. + """ with open(self._name + '.json', 'w') as of: json.dump(self.info, of, sort_keys=False, indent=4, separators=(',', ': ')) def restore(self): - """Read data from json infos""" + """ Restore cache from json infos. + """ if os.path.exists(self._name + '.json'): # Fricking mpl kills locale setting to system default .. this went @@ -144,7 +220,7 @@ def restore(self): # pg.error('only single return caches supported for now.') #pg._y(pg.pf(self.info)) - + if self.info['type'] == 'DataContainerERT': self._value = pg.DataContainerERT(self.info['file'], removeInvalid=False) @@ -178,36 +254,66 @@ def restore(self): self._name, self.info['codeinfo'])) else: # default try numpy - pg.warn('Could not restore cache of type {0}.'.format(self.info['type'])) + pg.warn('Could not restore cache of type ' + f'{self.info["type"]}.') pg.debug("Restoring cache took:", pg.dur(), "s") - except Exception as e: - import traceback + except BaseException as e: traceback.print_exc(file=sys.stdout) print(self.info) - pg.error('Cache restoring failed.') + pg.error('Cache restoring failed:', e) + -#@pg.singleton class CacheManager(object): + """ Cache manager to handle caching of functions and data. + + This class is a singleton and should be accessed via the instance method. + It provides methods to create unique cache paths, hash functions and + cache function calls. + + TODO + ---- + * Unify singleton handling + """ __instance = None __has_init = False def __new__(cls): + """ Create a new instance of the CacheManager. + """ if cls.__instance is None: cls.__instance = object.__new__(cls) return cls.__instance + def __init__(self): + """ Initialize the CacheManager just once. + """ if not self.__has_init: self._caches = {} self.__has_init = True + @staticmethod def instance(cls): + """ Get the singleton instance of the CacheManager. + """ return cls.__instance__ - def cachingPath(self, fName): - """Create a path name for the cache""" + + def cachingPath(self, fName:str): + """ Create a full path name for the cache. + + Arguments + --------- + fName: str + The name of the file to cache. + + Returns + ------- + path: str + The full path to the cache file. + """ if pg.rc["globalCache"]: path = pg.getCachePath() else: @@ -216,17 +322,46 @@ def cachingPath(self, fName): os.mkdir(path) return os.path.join(path, fName) - def functInfo(self, funct): - """Return unique info string about the called function.""" - return funct.__code__.co_filename + ":" + funct.__qualname__ - def hash(self, funct, *args, **kwargs): - """"Create a hash value""" + def funcInfo(self, func): + """ Return unique info string about the called function. + + Arguments + --------- + func: function + The function to get the info from. + + Returns + ------- + info: str + A string containing the file name and the qualified name of the + function. + """ + return func.__code__.co_filename + ":" + func.__qualname__ + + + def hash(self, func, *args, **kwargs): + """ Create a hash value. + + Arguments + --------- + func: function + The function to hash. + *args: any + The positional arguments of the function. + **kwargs: any + The keyword arguments of the function. + + Returns + ------- + hash: int + A unique hash value for the function and its arguments. + """ pg.tic() - functInfo = self.functInfo(funct) - funcHash = strHash(functInfo) + funcInfo = self.funcInfo(func) + funcHash = strHash(funcInfo) versionHash = strHash(pg.versionStr()) - codeHash = strHash(inspect.getsource(funct)) + codeHash = strHash(inspect.getsource(func)) argHash = 0 for i, a in enumerate(args): @@ -240,47 +375,86 @@ def hash(self, funct, *args, **kwargs): argHash = argHash ^ (valHash(k + str(v))) else: argHash = argHash ^ valHash(k) ^ valHash(v) - + pg.debug("Hashing took:", pg.dur(), "s") return funcHash ^ versionHash ^ codeHash ^ argHash - def cache(self, funct, *args, **kwargs): - """ Create a unique cache """ - hashVal = self.hash(funct, *args, **kwargs) - - cached = Cache(hashVal) - cached.info['codeinfo'] = self.functInfo(funct) - cached.info['version'] = pg.versionStr() - cached.info['args'] = str(args) - cached.info['kwargs'] = str(kwargs) - - return cached - -def cache(funct): - """Cache decorator.""" + def cache(self, func, *args, **kwargs): + """ Create a unique cache. + + Arguments + --------- + func: function + The function to cache. + *args: any + The positional arguments of the function. + **kwargs: any + The keyword arguments of the function. + + Returns + ------- + c: Cache + A Cache object containing the cached value, info and hash value. + """ + hashVal = self.hash(func, *args, **kwargs) + + c = Cache(hashVal) + c.info['codeinfo'] = self.funcInfo(func) + c.info['version'] = pg.versionStr() + c.info['args'] = str(args) + c.info['kwargs'] = str(kwargs) + + return c + + +def cache(func): + """ Cache decorator. + + This decorator caches the return value of the function and stores it in a + Cache object. If the function is called again with the same arguments, + the cached value is returned instead of calling the function again. + If the cache is not found, the function is called and the result is stored + in the cache. + + This can be used without using the decorator by calling: + `pg.cache(func)(*args, **kwargs)` + + Arguments + --------- + func: function + The function to cache. + + Returns + ------- + wrapper: function + A wrapper function that caches the return value of the function. + """ def wrapper(*args, **kwargs): nc = kwargs.pop('skipCache', False) - + if any(('--noCache' in sys.argv, '-N' in sys.argv, nc is True, __NO_CACHE__)): - return funct(*args, **kwargs) - - cache = CacheManager().cache(funct, *args, **kwargs) - if cache.value is not None: - return cache.value - else: - # pg.tic will not work because there is only one global __swatch__ - sw = pg.Stopwatch(True) - rv = funct(*args, **kwargs) - cache.info['date'] = time.time() - cache.info['dur'] = sw.duration() - try: - cache.value = rv - except Exception as e: - print(e) - pg.warn("Can't cache:", rv) - return rv + return func(*args, **kwargs) + + c = CacheManager().cache(func, *args, **kwargs) + if c.value is not None: + return c.value + + # pg.tic will not work because there is only one global __swatch__ + sw = pg.Stopwatch(True) + rv = func(*args, **kwargs) + c.info['date'] = time.time() + c.info['dur'] = sw.duration() + try: + c.value = rv + except Exception as e: + print(e) + pg.warn("Can't cache:", rv) + return rv + + wrapper.__name__ = func.__name__ + wrapper.__doc__ = func.__doc__ return wrapper diff --git a/pygimli/utils/sparseMat2Numpy.py b/pygimli/utils/sparseMat2Numpy.py index e31535833..4c7798a9b 100644 --- a/pygimli/utils/sparseMat2Numpy.py +++ b/pygimli/utils/sparseMat2Numpy.py @@ -102,27 +102,29 @@ def sparseMatrix2csr(A): Matrix to convert into. """ #optImport(scipy.sparse, requiredFor="toCRS_matrix") + shape=(A.rows(), A.cols()) + from scipy.sparse import csr_matrix if isinstance(A, pg.matrix.CSparseMapMatrix): C = pg.matrix.CSparseMatrix(A) return csr_matrix((C.vecVals().array(), C.vecRowIdx(), - C.vecColPtr()), dtype=complex) + C.vecColPtr()), shape=shape, dtype=complex) if isinstance(A, pg.matrix.SparseMapMatrix): C = pg.matrix.SparseMatrix(A) return csr_matrix((C.vecVals().array(), C.vecRowIdx(), - C.vecColPtr())) - elif isinstance(A, pg.matrix.SparseMatrix): + C.vecColPtr()), shape=shape) + if isinstance(A, pg.matrix.SparseMatrix): return csr_matrix((A.vecVals().array(), A.vecRowIdx(), - A.vecColPtr())) - elif isinstance(A, pg.matrix.CSparseMatrix): + A.vecColPtr()), shape=shape) + if isinstance(A, pg.matrix.CSparseMatrix): csr = csr_matrix((A.vecVals().array(), A.vecRowIdx(), - A.vecColPtr()), dtype=complex) + A.vecColPtr()), shape=shape, dtype=complex) return csr - elif isinstance(A, pg.matrix.BlockMatrix): + if isinstance(A, pg.matrix.BlockMatrix): M = A.sparseMapMatrix() return sparseMatrix2csr(M) diff --git a/pygimli/viewer/mpl/boreholes.py b/pygimli/viewer/mpl/boreholes.py index ae3ca8bf8..0f7e8b6e2 100644 --- a/pygimli/viewer/mpl/boreholes.py +++ b/pygimli/viewer/mpl/boreholes.py @@ -148,8 +148,19 @@ def _build_common_colormap(self): self.cmin = min(self.class_id) self.cmax = max(self.class_id) - def plot(self, ax, plot_thickness=1.0, do_legend=True, **legend_kwargs): - """Plot the boreholes on the specified axis.""" + def plot(self, ax, plot_thickness=1.0, do_legend=True, **kwargs): + """Plot the boreholes on the specified axis. + + Parameters + ---------- + ax : matplotlib.Axes + plot_thickness : float [1.0] + width (in m) for borehole columns + do_legend : bool + draw a legend for the geological units + **kwargs : keyword arguments passed to legend + fontsize, markerscale, (s. matplotlib.legend) + """ self._build_common_colormap() for b in self.boreholes: @@ -157,10 +168,19 @@ def plot(self, ax, plot_thickness=1.0, do_legend=True, **legend_kwargs): cmin=self.cmin, cmax=self.cmax, cm=self.cm) if do_legend: - self.add_legend(ax, self.cm, **legend_kwargs) + self.add_legend(ax, self.cm, **kwargs) def add_legend(self, ax, cmap, **legend_kwargs): - """Add a legend to the plot.""" + """Add a legend to the plot. + + Parameters + ---------- + ax : matplotlib.axes + cmap : matplotlib.colormap + + Keyword arguments passed to ax.legend: + fontsize, markerscale + """ leg = create_legend(ax, cmap, np.arange(cmap.N), self.common_unique) extra = dict(bbox_to_anchor=(0.9, 0.05, 0.1, 0.1), ncol=cmap.N / 2, @@ -168,6 +188,7 @@ def add_legend(self, ax, cmap, **legend_kwargs): columnspacing=1.0, loc='center right', markerscale=0.7, framealpha=1.0, borderpad=0.5, handleheight=0.5, frameon=True) - legend_kwargs.update(extra) + + extra.update(legend_kwargs) + ax.legend(handles=leg, **extra) - ax.legend(handles=leg, **legend_kwargs) diff --git a/pygimli/viewer/mpl/colorbar.py b/pygimli/viewer/mpl/colorbar.py index 0f56a2f4d..01e97f3c3 100644 --- a/pygimli/viewer/mpl/colorbar.py +++ b/pygimli/viewer/mpl/colorbar.py @@ -175,9 +175,9 @@ def updateColorBar(cbar, gci=None, cMin=None, cMax=None, cMap=None, # logScale, ', nCols:', nCols, nLevs, ', label:', label, levels) if gci is not None: - if min(gci.get_array()) < 1e12: - norm = mpl.colors.Normalize(vmin=min(gci.get_array()), - vmax=max(gci.get_array())) + if np.min(gci.get_array().any()) < 1e12: + norm = mpl.colors.Normalize(vmin=np.min(gci.get_array()), + vmax=np.max(gci.get_array())) gci.set_norm(norm) if cbar is not None: @@ -461,7 +461,8 @@ def setCbarLevels(cbar, cMin=None, cMax=None, nLevs=5, levels=None): cbar.ax.figure.draw_without_rendering() #cbar._draw_all() # work but dunno how long this will exists except: - cbar.draw_all() # removed by mpl-3.8 + #cbar.draw_all() # removed by mpl-3.8 + cbar._draw_all() # necessary since mpl 3.0 cbar.ax.minorticks_off() diff --git a/pygimli/viewer/mpl/dataview.py b/pygimli/viewer/mpl/dataview.py index 64d3ae9e0..0eb02b227 100644 --- a/pygimli/viewer/mpl/dataview.py +++ b/pygimli/viewer/mpl/dataview.py @@ -555,7 +555,7 @@ def showDataContainerAsMatrix(data, x=None, y=None, v=None, **kwargs): yToken = '' mul = kwargs.pop('mul', 10**int(np.ceil(np.log10(data.sensorCount())))) plus = kwargs.pop('plus', 1) # add 1 to count - verbose = kwargs.get('verbose', True) + verbose = kwargs.get('verbose', False) if isinstance(x, str): xToken = x x = data(x) diff --git a/pygimli/viewer/showmesh.py b/pygimli/viewer/showmesh.py index b5b24f4f2..b3d6041f4 100644 --- a/pygimli/viewer/showmesh.py +++ b/pygimli/viewer/showmesh.py @@ -36,7 +36,7 @@ def show(obj=None, data=None, **kwargs): Syntactic sugar to show a obj with data. Forwards to a known visualization for obj. Typical is :py:mod:`pygimli.viewer.showMesh` or - :py:mod:`pygimli.viewer.mayaview.showMesh3D` to show most of the typical 2D + :py:mod:`pygimli.viewer.pv.showMesh3D` to show most of the typical 2D and 3D content. See tutorials and examples for usage hints. An empty show call creates an empty ax window. @@ -96,6 +96,14 @@ def show(obj=None, data=None, **kwargs): from pygimli.physics.ert import showERTData return showERTData(obj, vals=kwargs.pop('vals', data), **kwargs) + if isinstance(obj, pg.DataContainer): # some other + if obj.isSensorIndex("s") and obj.isSensorIndex("g"): + from pygimli.viewer.mpl import showDataContainerAsMatrix + if data is None and obj.haveData("t"): + data = "t" + + return showDataContainerAsMatrix(obj, "s", "g", data) + # try to interpret obj as matrices if isinstance(obj, pg.core.MatrixBase) or (isinstance(obj, np.ndarray) and obj.ndim == 2): @@ -337,7 +345,9 @@ def showMesh(mesh, data=None, block=False, colorBar=None, showBoundary = True elif isinstance(data, pg.core.stdVectorRVector3): drawSensors(ax, data, **kwargs) - elif isinstance(data, pg.PosVector): + elif isinstance(data, pg.PosVector) \ + or hasattr(data, 'ndim') and data.ndim == 2 \ + and (data.shape[1] == 2 or data.shape[1] == 3): drawStreams(ax, mesh, data, **kwargs) else: # check for map like data=[[marker, val], ....] @@ -347,9 +357,16 @@ def showMesh(mesh, data=None, block=False, colorBar=None, if hasattr(data[0], '__len__') and not \ isinstance(data, np.ma.core.MaskedArray) and not \ - isinstance(data[0], str): + isinstance(data[0], str) and not \ + (len(data) == 1 or len(data[0] == 0)): + if len(data) == 2: # [u,v] x N data = np.array(data).T + + if len(data) == 1: # 1xM matrix + return showMesh(np.ravel(data), **kwargs) + if data.shape[1] == 1: # Mx1 matrix + return showMesh(np.ravel(data), **kwargs) if data.shape[1] == 2: # N x [u,v] drawStreams(ax, mesh, data, **kwargs) elif data.shape[1] == 3: # N x [u,v,w]