From e4f9f07d82c0bf4767d426afc7216829f2b2e966 Mon Sep 17 00:00:00 2001 From: Gabriel Torregrosa Date: Fri, 19 Apr 2024 16:56:17 +0200 Subject: [PATCH 1/5] Docker and vectorfield tiff added --- README.md | 5 +++++ docker/dockerfile | 6 ++++++ src/registrationtools/time_registration.py | 14 ++++++++++---- 3 files changed, 21 insertions(+), 4 deletions(-) create mode 100644 docker/dockerfile diff --git a/README.md b/README.md index 481c13c..1e19b57 100644 --- a/README.md +++ b/README.md @@ -27,6 +27,11 @@ Then, to install the whole thing, it is necessary to first install blockmatching conda install vt -c morpheme +or, + + conda install vt-python -n morpheme -c morpheme -c conda-forge + + Then, you can install the 3D-registration library either directly via pip: pip install 3D-registration diff --git a/docker/dockerfile b/docker/dockerfile new file mode 100644 index 0000000..77e2a4a --- /dev/null +++ b/docker/dockerfile @@ -0,0 +1,6 @@ +BASE continuumio/miniconda3:24.3.0-0 + +RUN conda install vt-python -n morpheme -c morpheme -c conda-forge +RUN pip install SimpleITK +RUN pip install scikit-image +RUN pip install git+https://github.com/gatocor/registration-tools \ No newline at end of file diff --git a/src/registrationtools/time_registration.py b/src/registrationtools/time_registration.py index 54a6c04..5002a02 100644 --- a/src/registrationtools/time_registration.py +++ b/src/registrationtools/time_registration.py @@ -414,12 +414,18 @@ def __produce_trsf(self, params: Tuple[trsf_parameters, int, int, bool]): p.trsf_folder, "t%06d-%06d.klb" % (t_flo, t_ref) ) ) + elif p.keep_vectorfield: + print( + "The vectorfield cannot be stored in klb format without pyklb being installed. It will be stored in a .tif format." + ) + res_trsf = ( + " -composition-with-initial -res-trsf " + + os.path.join( + p.trsf_folder, "t%06d-%06d.tif" % (t_flo, t_ref) + ) + ) else: res_trsf = "" - if p.keep_vectorfield: - print( - "The vectorfield cannot be stored without pyklb being installed" - ) call( self.path_to_bin + "blockmatching -ref " From 6cb86bb4dbc7829babe50a2418809d77e0534d24 Mon Sep 17 00:00:00 2001 From: Gabriel Torregrosa Date: Fri, 19 Apr 2024 17:53:30 +0200 Subject: [PATCH 2/5] Docker working --- README.md | 2 +- docker/dockerfile | 6 ++-- docker/environment.yml | 75 ++++++++++++++++++++++++++++++++++++++++++ environment.yml | 75 ++++++++++++++++++++++++++++++++++++++++++ 4 files changed, 155 insertions(+), 3 deletions(-) create mode 100644 docker/environment.yml create mode 100644 environment.yml diff --git a/README.md b/README.md index 1e19b57..d8b8922 100644 --- a/README.md +++ b/README.md @@ -29,7 +29,7 @@ Then, to install the whole thing, it is necessary to first install blockmatching or, - conda install vt-python -n morpheme -c morpheme -c conda-forge + conda install vt-python -c morpheme -c conda-forge Then, you can install the 3D-registration library either directly via pip: diff --git a/docker/dockerfile b/docker/dockerfile index 77e2a4a..ccef43a 100644 --- a/docker/dockerfile +++ b/docker/dockerfile @@ -1,6 +1,8 @@ -BASE continuumio/miniconda3:24.3.0-0 +FROM continuumio/miniconda3:22.11.1 -RUN conda install vt-python -n morpheme -c morpheme -c conda-forge +RUN apt-get update +COPY environment.yml . +RUN conda env create -f environment.yml RUN pip install SimpleITK RUN pip install scikit-image RUN pip install git+https://github.com/gatocor/registration-tools \ No newline at end of file diff --git a/docker/environment.yml b/docker/environment.yml new file mode 100644 index 0000000..4d1f862 --- /dev/null +++ b/docker/environment.yml @@ -0,0 +1,75 @@ +name: registrationtools +channels: + - morpheme + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1=conda_forge + - _openmp_mutex=4.5=2_gnu + - bzip2=1.0.8=hd590300_5 + - ca-certificates=2024.2.2=hbcca054_0 + - ld_impl_linux-64=2.40=h41732ed_0 + - libblas=3.9.0=22_linux64_openblas + - libcblas=3.9.0=22_linux64_openblas + - libffi=3.4.2=h7f98852_5 + - libgcc-ng=13.2.0=h807b86a_5 + - libgfortran-ng=13.2.0=h69a702a_5 + - libgfortran5=13.2.0=ha4646dd_5 + - libgomp=13.2.0=h807b86a_5 + - liblapack=3.9.0=22_linux64_openblas + - libnsl=2.0.1=hd590300_0 + - libopenblas=0.3.27=pthreads_h413a1c8_0 + - libsqlite=3.45.3=h2797004_0 + - libstdcxx-ng=13.2.0=h7e041cc_5 + - libuuid=2.38.1=h0b41bf4_0 + - libxcrypt=4.4.36=hd590300_1 + - libzlib=1.2.13=hd590300_5 + - ncurses=6.4.20240210=h59595ed_0 + - numpy=1.26.4=py39h474f0d3_0 + - openssl=3.2.1=hd590300_1 + - pip=24.0=pyhd8ed1ab_0 + - pybind11=2.12.0=py39h7633fee_0 + - pybind11-global=2.12.0=py39h7633fee_0 + - python=3.9.19=h0755675_0_cpython + - python_abi=3.9=4_cp39 + - readline=8.2=h8228510_1 + - setuptools=69.5.1=pyhd8ed1ab_0 + - tk=8.6.13=noxft_h4845f30_101 + - vt=1.0.0=h3fd9d12_0 + - vt-python=1.1.0=py39h3fd9d12_5 + - wheel=0.43.0=pyhd8ed1ab_1 + - xtensor=0.24.0=h4bd325d_0 + - xtensor-python=0.26.0=py39h5472131_1 + - xtl=0.7.4=h4bd325d_0 + - xz=5.2.6=h166bdaf_0 + - zlib=1.2.13=hd590300_5 + - pip: + - 3d-registration==0.5.2 + - contourpy==1.2.1 + - cycler==0.12.1 + - ensure==1.0.4 + - fonttools==4.51.0 + - h5py==3.11.0 + - imageio==2.34.0 + - importlib-resources==6.4.0 + - kiwisolver==1.4.5 + - lazy-loader==0.4 + - matplotlib==3.8.4 + - networkx==3.2.1 + - packaging==24.0 + - pandas==2.2.2 + - patsy==0.5.6 + - pillow==10.3.0 + - pyparsing==3.1.2 + - python-dateutil==2.9.0.post0 + - pytz==2024.1 + - scikit-image==0.22.0 + - scipy==1.13.0 + - simpleitk==2.3.1 + - six==1.16.0 + - statsmodels==0.14.2 + - tifffile==2024.4.18 + - transforms3d==0.4.1 + - tzdata==2024.1 + - zipp==3.18.1 +prefix: /homes/users/gtorregrosa/miniconda3/envs/morpheme diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..4d1f862 --- /dev/null +++ b/environment.yml @@ -0,0 +1,75 @@ +name: registrationtools +channels: + - morpheme + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1=conda_forge + - _openmp_mutex=4.5=2_gnu + - bzip2=1.0.8=hd590300_5 + - ca-certificates=2024.2.2=hbcca054_0 + - ld_impl_linux-64=2.40=h41732ed_0 + - libblas=3.9.0=22_linux64_openblas + - libcblas=3.9.0=22_linux64_openblas + - libffi=3.4.2=h7f98852_5 + - libgcc-ng=13.2.0=h807b86a_5 + - libgfortran-ng=13.2.0=h69a702a_5 + - libgfortran5=13.2.0=ha4646dd_5 + - libgomp=13.2.0=h807b86a_5 + - liblapack=3.9.0=22_linux64_openblas + - libnsl=2.0.1=hd590300_0 + - libopenblas=0.3.27=pthreads_h413a1c8_0 + - libsqlite=3.45.3=h2797004_0 + - libstdcxx-ng=13.2.0=h7e041cc_5 + - libuuid=2.38.1=h0b41bf4_0 + - libxcrypt=4.4.36=hd590300_1 + - libzlib=1.2.13=hd590300_5 + - ncurses=6.4.20240210=h59595ed_0 + - numpy=1.26.4=py39h474f0d3_0 + - openssl=3.2.1=hd590300_1 + - pip=24.0=pyhd8ed1ab_0 + - pybind11=2.12.0=py39h7633fee_0 + - pybind11-global=2.12.0=py39h7633fee_0 + - python=3.9.19=h0755675_0_cpython + - python_abi=3.9=4_cp39 + - readline=8.2=h8228510_1 + - setuptools=69.5.1=pyhd8ed1ab_0 + - tk=8.6.13=noxft_h4845f30_101 + - vt=1.0.0=h3fd9d12_0 + - vt-python=1.1.0=py39h3fd9d12_5 + - wheel=0.43.0=pyhd8ed1ab_1 + - xtensor=0.24.0=h4bd325d_0 + - xtensor-python=0.26.0=py39h5472131_1 + - xtl=0.7.4=h4bd325d_0 + - xz=5.2.6=h166bdaf_0 + - zlib=1.2.13=hd590300_5 + - pip: + - 3d-registration==0.5.2 + - contourpy==1.2.1 + - cycler==0.12.1 + - ensure==1.0.4 + - fonttools==4.51.0 + - h5py==3.11.0 + - imageio==2.34.0 + - importlib-resources==6.4.0 + - kiwisolver==1.4.5 + - lazy-loader==0.4 + - matplotlib==3.8.4 + - networkx==3.2.1 + - packaging==24.0 + - pandas==2.2.2 + - patsy==0.5.6 + - pillow==10.3.0 + - pyparsing==3.1.2 + - python-dateutil==2.9.0.post0 + - pytz==2024.1 + - scikit-image==0.22.0 + - scipy==1.13.0 + - simpleitk==2.3.1 + - six==1.16.0 + - statsmodels==0.14.2 + - tifffile==2024.4.18 + - transforms3d==0.4.1 + - tzdata==2024.1 + - zipp==3.18.1 +prefix: /homes/users/gtorregrosa/miniconda3/envs/morpheme From d4f4e3e5ab99d6c7fca212cb1da7bf089df0339b Mon Sep 17 00:00:00 2001 From: Gabriel Torregrosa Date: Mon, 1 Jul 2024 14:13:19 +0200 Subject: [PATCH 3/5] Add docker --- docker/README.md | 76 ++++++++++++++++++ docker/build.sh | 6 ++ docker/dockerfile | 10 +-- docker/environment.yaml | 170 ++++++++++++++++++++++++++++++++++++++++ docker/environment.yml | 75 ------------------ environment.yml | 1 - 6 files changed, 257 insertions(+), 81 deletions(-) create mode 100644 docker/README.md create mode 100755 docker/build.sh create mode 100644 docker/environment.yaml delete mode 100644 docker/environment.yml diff --git a/docker/README.md b/docker/README.md new file mode 100644 index 0000000..a01998a --- /dev/null +++ b/docker/README.md @@ -0,0 +1,76 @@ +# Registrationtools docker + +The dockerfile makes an image that contains a set of relevant packages for image registration in python. + +The relevant packages for image registration that contains are: + + - [`registrationtools`](https://github.com/GuignardLab/registration-tools): This package + - [`vt-python`](https://gitlab.inria.fr/morpheme/vt-python): Original package over which this package makes a wrapper. + - [`SimpelITK`](https://simpleitk.org/): Classical package for image registration, wrapper over the ITK package. + - [`skimage`](https://scikit-image.org/): Well-stablished package for image manipulation in python based on numpy. + +In addition to these packages, other packages are installed (e.g. numpy, matplotlib...). A list can be seen in environment.yaml. + +Constructed images are already deposited in [dsblab/registrationtools](https://hub.docker.com/repository/docker/dsblab/registrationtools), so there is not need of building the image except if you want to extend further capabilities. + +# Running the image + +## Interactive Shell + +Start the container in interactive format. + +```shell +docker run -it \ + --mount type=bind,source="$(pwd)",target=/home \ + dsblab/registrationtools:v0.1 +``` + +Activate the conda image. + +```shell +source activate registration +cd home +``` + +And now all the packages and modules will be loaded. You can start a python shell: + +```shell +python +``` + +or execute packages installed from the command line (e.g. blockmatching) + +```shell +blockmatching -h +``` + +## Script + +To execute directly a bash script simply + +```shell +docker run \ + --mount type=bind,source="$(pwd)",target=/home \ + dsblab/registrationtools:v0.1 /bin/bash -c "source activate registration: cd home; " +``` + +and a python script + +```shell +docker run \ + --mount type=bind,source="$(pwd)",target=/home \ + dsblab/registrationtools:v0.1 /bin/bash -c "source activate registration; cd home; python " +``` + +## Jupyter lab + +If you want to work interactively with a jupyter notebook. + +```shell +docker run -it \ + -p 8888:8888 \ + --mount type=bind,source="$(pwd)",target=/home \ + dsblab/registrationtools:v0.1 /bin/bash -c "jupyter lab --notebook-dir=/home --ip='*' --port=8888 --allow-root" +``` + +You can then view the Jupyter Notebook by opening http://localhost:8888 in your browser, or http://:8888 if you are using a Docker. \ No newline at end of file diff --git a/docker/build.sh b/docker/build.sh new file mode 100755 index 0000000..15ace19 --- /dev/null +++ b/docker/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +version=v0.1 + +docker build . -t dsblab/registrationtools:$version +docker push dsblab/registrationtools:$version \ No newline at end of file diff --git a/docker/dockerfile b/docker/dockerfile index ccef43a..a291c45 100644 --- a/docker/dockerfile +++ b/docker/dockerfile @@ -1,8 +1,8 @@ -FROM continuumio/miniconda3:22.11.1 +FROM continuumio/miniconda3:4.12.0 RUN apt-get update -COPY environment.yml . +COPY environment.yaml . +RUN conda install cmake make +RUN apt-get install g++ gcc -y RUN conda env create -f environment.yml -RUN pip install SimpleITK -RUN pip install scikit-image -RUN pip install git+https://github.com/gatocor/registration-tools \ No newline at end of file +RUN pip install git+https://github.com/GuignardLab/registration-tools diff --git a/docker/environment.yaml b/docker/environment.yaml new file mode 100644 index 0000000..09c83ca --- /dev/null +++ b/docker/environment.yaml @@ -0,0 +1,170 @@ +name: registration +channels: + - morpheme + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1=conda_forge + - _openmp_mutex=4.5=2_gnu + - ca-certificates=2024.6.2=hbcca054_0 + - ld_impl_linux-64=2.38=h1181459_1 + - libblas=3.9.0=22_linux64_openblas + - libcblas=3.9.0=22_linux64_openblas + - libffi=3.4.4=h6a678d5_1 + - libgcc=7.2.0=h69d50b8_2 + - libgcc-ng=13.2.0=h77fa898_13 + - libgfortran-ng=13.2.0=h69a702a_13 + - libgfortran5=13.2.0=h3d2ce59_13 + - libgomp=13.2.0=h77fa898_13 + - liblapack=3.9.0=22_linux64_openblas + - libopenblas=0.3.27=pthreads_h413a1c8_0 + - libstdcxx-ng=13.2.0=hc0a3c3a_13 + - libzlib=1.2.13=h4ab18f5_6 + - ncurses=6.4=h6a678d5_0 + - openssl=3.3.1=h4ab18f5_1 + - pip=24.0=py39h06a4308_0 + - pybind11=2.9.2=py39hf939315_1 + - pybind11-global=2.9.2=py39hf939315_1 + - python=3.9.19=h955ad1f_1 + - python_abi=3.9=2_cp39 + - readline=8.2=h5eee18b_0 + - setuptools=69.5.1=py39h06a4308_0 + - sqlite=3.45.3=h5eee18b_0 + - tk=8.6.14=h39e8969_0 + - vt=1.0.0=h3fd9d12_0 + - wheel=0.43.0=py39h06a4308_0 + - xtensor=0.24.0=h4bd325d_0 + - xtensor-python=0.26.0=py39h5472131_1 + - xtl=0.7.4=h4bd325d_0 + - xz=5.4.6=h5eee18b_1 + - zlib=1.2.13=h4ab18f5_6 + - pip: + - 3d-registration @ git+https://github.com/GuignardLab/registration-tools + - anyio==4.4.0 + - argon2-cffi==23.1.0 + - argon2-cffi-bindings==21.2.0 + - arrow==1.3.0 + - asttokens==2.4.1 + - async-lru==2.0.4 + - attrs==23.2.0 + - babel==2.15.0 + - beautifulsoup4==4.12.3 + - bleach==6.1.0 + - certifi==2024.6.2 + - cffi==1.16.0 + - charset-normalizer==3.3.2 + - comm==0.2.2 + - contourpy==1.2.1 + - cycler==0.12.1 + - debugpy==1.8.2 + - decorator==5.1.1 + - defusedxml==0.7.1 + - ensure==1.0.4 + - exceptiongroup==1.2.1 + - executing==2.0.1 + - fastjsonschema==2.20.0 + - fonttools==4.53.0 + - fqdn==1.5.1 + - h11==0.14.0 + - h5py==3.11.0 + - httpcore==1.0.5 + - httpx==0.27.0 + - idna==3.7 + - imageio==2.34.2 + - importlib-metadata==8.0.0 + - importlib-resources==6.4.0 + - ipykernel==6.29.4 + - ipython==8.18.1 + - ipywidgets==8.1.3 + - isoduration==20.11.0 + - jedi==0.19.1 + - jinja2==3.1.4 + - json5==0.9.25 + - jsonpointer==3.0.0 + - jsonschema==4.22.0 + - jsonschema-specifications==2023.12.1 + - jupyter==1.0.0 + - jupyter-client==8.6.2 + - jupyter-console==6.6.3 + - jupyter-core==5.7.2 + - jupyter-events==0.10.0 + - jupyter-lsp==2.2.5 + - jupyter-server==2.14.1 + - jupyter-server-terminals==0.5.3 + - jupyterlab==4.2.3 + - jupyterlab-pygments==0.3.0 + - jupyterlab-server==2.27.2 + - jupyterlab-widgets==3.0.11 + - kiwisolver==1.4.5 + - lab==8.2 + - lazy-loader==0.4 + - markupsafe==2.1.5 + - matplotlib==3.9.0 + - matplotlib-inline==0.1.7 + - mistune==3.0.2 + - nbclient==0.10.0 + - nbconvert==7.16.4 + - nbformat==5.10.4 + - nest-asyncio==1.6.0 + - networkx==3.2.1 + - notebook==7.2.1 + - notebook-shim==0.2.4 + - numpy==1.23.0 + - overrides==7.7.0 + - packaging==24.1 + - pandas==2.2.2 + - pandocfilters==1.5.1 + - parso==0.8.4 + - patsy==0.5.6 + - pexpect==4.9.0 + - pillow==10.3.0 + - platformdirs==4.2.2 + - prometheus-client==0.20.0 + - prompt-toolkit==3.0.47 + - psutil==6.0.0 + - ptyprocess==0.7.0 + - pure-eval==0.2.2 + - pycparser==2.22 + - pygments==2.18.0 + - pyparsing==3.1.2 + - python-dateutil==2.9.0.post0 + - python-json-logger==2.0.7 + - pytz==2024.1 + - pyyaml==6.0.1 + - pyzmq==26.0.3 + - qtconsole==5.5.2 + - qtpy==2.4.1 + - referencing==0.35.1 + - requests==2.32.3 + - rfc3339-validator==0.1.4 + - rfc3986-validator==0.1.1 + - rpds-py==0.18.1 + - scikit-image==0.24.0 + - scipy==1.13.1 + - send2trash==1.8.3 + - simplejson==3.19.2 + - six==1.16.0 + - sniffio==1.3.1 + - soupsieve==2.5 + - stack-data==0.6.3 + - statsmodels==0.14.2 + - terminado==0.18.1 + - tifffile==2024.6.18 + - tinycss2==1.3.0 + - tomli==2.0.1 + - tornado==6.4.1 + - traitlets==5.14.3 + - transforms3d==0.4.2 + - txt2tags==3.9 + - types-python-dateutil==2.9.0.20240316 + - typing-extensions==4.12.2 + - tzdata==2024.1 + - uri-template==1.3.0 + - urllib3==2.2.2 + - vtpython @ git+https://gitlab.inria.fr/morpheme/vt-python@122be17b2a25641a982649d54c17434e46989706 + - wcwidth==0.2.13 + - webcolors==24.6.0 + - webencodings==0.5.1 + - websocket-client==1.8.0 + - widgetsnbextension==4.0.11 + - zipp==3.19.2 \ No newline at end of file diff --git a/docker/environment.yml b/docker/environment.yml deleted file mode 100644 index 4d1f862..0000000 --- a/docker/environment.yml +++ /dev/null @@ -1,75 +0,0 @@ -name: registrationtools -channels: - - morpheme - - conda-forge - - defaults -dependencies: - - _libgcc_mutex=0.1=conda_forge - - _openmp_mutex=4.5=2_gnu - - bzip2=1.0.8=hd590300_5 - - ca-certificates=2024.2.2=hbcca054_0 - - ld_impl_linux-64=2.40=h41732ed_0 - - libblas=3.9.0=22_linux64_openblas - - libcblas=3.9.0=22_linux64_openblas - - libffi=3.4.2=h7f98852_5 - - libgcc-ng=13.2.0=h807b86a_5 - - libgfortran-ng=13.2.0=h69a702a_5 - - libgfortran5=13.2.0=ha4646dd_5 - - libgomp=13.2.0=h807b86a_5 - - liblapack=3.9.0=22_linux64_openblas - - libnsl=2.0.1=hd590300_0 - - libopenblas=0.3.27=pthreads_h413a1c8_0 - - libsqlite=3.45.3=h2797004_0 - - libstdcxx-ng=13.2.0=h7e041cc_5 - - libuuid=2.38.1=h0b41bf4_0 - - libxcrypt=4.4.36=hd590300_1 - - libzlib=1.2.13=hd590300_5 - - ncurses=6.4.20240210=h59595ed_0 - - numpy=1.26.4=py39h474f0d3_0 - - openssl=3.2.1=hd590300_1 - - pip=24.0=pyhd8ed1ab_0 - - pybind11=2.12.0=py39h7633fee_0 - - pybind11-global=2.12.0=py39h7633fee_0 - - python=3.9.19=h0755675_0_cpython - - python_abi=3.9=4_cp39 - - readline=8.2=h8228510_1 - - setuptools=69.5.1=pyhd8ed1ab_0 - - tk=8.6.13=noxft_h4845f30_101 - - vt=1.0.0=h3fd9d12_0 - - vt-python=1.1.0=py39h3fd9d12_5 - - wheel=0.43.0=pyhd8ed1ab_1 - - xtensor=0.24.0=h4bd325d_0 - - xtensor-python=0.26.0=py39h5472131_1 - - xtl=0.7.4=h4bd325d_0 - - xz=5.2.6=h166bdaf_0 - - zlib=1.2.13=hd590300_5 - - pip: - - 3d-registration==0.5.2 - - contourpy==1.2.1 - - cycler==0.12.1 - - ensure==1.0.4 - - fonttools==4.51.0 - - h5py==3.11.0 - - imageio==2.34.0 - - importlib-resources==6.4.0 - - kiwisolver==1.4.5 - - lazy-loader==0.4 - - matplotlib==3.8.4 - - networkx==3.2.1 - - packaging==24.0 - - pandas==2.2.2 - - patsy==0.5.6 - - pillow==10.3.0 - - pyparsing==3.1.2 - - python-dateutil==2.9.0.post0 - - pytz==2024.1 - - scikit-image==0.22.0 - - scipy==1.13.0 - - simpleitk==2.3.1 - - six==1.16.0 - - statsmodels==0.14.2 - - tifffile==2024.4.18 - - transforms3d==0.4.1 - - tzdata==2024.1 - - zipp==3.18.1 -prefix: /homes/users/gtorregrosa/miniconda3/envs/morpheme diff --git a/environment.yml b/environment.yml index 4d1f862..76ae8ac 100644 --- a/environment.yml +++ b/environment.yml @@ -72,4 +72,3 @@ dependencies: - transforms3d==0.4.1 - tzdata==2024.1 - zipp==3.18.1 -prefix: /homes/users/gtorregrosa/miniconda3/envs/morpheme From 315575c456680594550997e654d34ad389b3e9c5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gabriel=20Torregrosa=20Cort=C3=A9s?= Date: Tue, 2 Jul 2024 10:50:10 +0200 Subject: [PATCH 4/5] Update environment.yaml --- docker/environment.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docker/environment.yaml b/docker/environment.yaml index 09c83ca..cebe333 100644 --- a/docker/environment.yaml +++ b/docker/environment.yaml @@ -142,6 +142,7 @@ dependencies: - scikit-image==0.24.0 - scipy==1.13.1 - send2trash==1.8.3 + - simpleitk==2.3.1 - simplejson==3.19.2 - six==1.16.0 - sniffio==1.3.1 @@ -167,4 +168,4 @@ dependencies: - webencodings==0.5.1 - websocket-client==1.8.0 - widgetsnbextension==4.0.11 - - zipp==3.19.2 \ No newline at end of file + - zipp==3.19.2 From 8f91f980e6fff94f35a316d86d08eaa987d73459 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gabriel=20Torregrosa=20Cort=C3=A9s?= Date: Tue, 2 Jul 2024 10:50:28 +0200 Subject: [PATCH 5/5] Update dockerfile --- docker/dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/dockerfile b/docker/dockerfile index a291c45..46d4608 100644 --- a/docker/dockerfile +++ b/docker/dockerfile @@ -4,5 +4,5 @@ RUN apt-get update COPY environment.yaml . RUN conda install cmake make RUN apt-get install g++ gcc -y -RUN conda env create -f environment.yml +RUN conda env create -f environment.yaml RUN pip install git+https://github.com/GuignardLab/registration-tools