diff --git a/README.md b/README.md index 4d89ad5..3436249 100644 --- a/README.md +++ b/README.md @@ -1 +1,22 @@ # pyudv + +pyudv is a python package allowing to read and process UDV data. The main modules are: + +- `pyudv.read_mfprof`, which helps you read binary files from Met-Flow UDVs +- `pyudv.probes`, which helps you plot the various probes, calculate the intersection points, etc .. +- `pyudv.velocity`, which helps you reconstruct 2D velocity fields from the various probes measurements +- `pyudv.amplitude`, which helps you infer concentration from amplitude measurements + +> [!WARNING] +> Although tested, this is still in development, use with caution. Feedbacks welcome. + +### Installation + +#### User only + +Using `pip3 install --upgrade https://github.com/cgadal-pythonpackages/pyudv/tarball/master` + +#### If code or development + +- clone the repository, e.g. `git clone https://github.com/cgadal-pythonpackages/pyudv` +- `cd pyudv && pip3 install -e ./` will install in editable mode. \ No newline at end of file diff --git a/docs/_autosummary/pyudv.amplitude.direct_models.alpha_w.rst b/docs/_autosummary/pyudv.amplitude.direct_models.alpha_w.rst deleted file mode 100644 index 7f1cd5e..0000000 --- a/docs/_autosummary/pyudv.amplitude.direct_models.alpha_w.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.amplitude.direct\_models.alpha\_w -======================================= - -.. currentmodule:: pyudv.amplitude.direct_models - -.. autofunction:: alpha_w - -.. _sphx_glr_backreferences_pyudv.amplitude.direct_models.alpha_w: - -.. minigallery:: pyudv.amplitude.direct_models.alpha_w - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.amplitude.direct_models.correction_factor.rst b/docs/_autosummary/pyudv.amplitude.direct_models.correction_factor.rst deleted file mode 100644 index ca16d75..0000000 --- a/docs/_autosummary/pyudv.amplitude.direct_models.correction_factor.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.amplitude.direct\_models.correction\_factor -================================================= - -.. currentmodule:: pyudv.amplitude.direct_models - -.. autofunction:: correction_factor - -.. _sphx_glr_backreferences_pyudv.amplitude.direct_models.correction_factor: - -.. minigallery:: pyudv.amplitude.direct_models.correction_factor - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.amplitude.direct_models.create_MSvoltage.rst b/docs/_autosummary/pyudv.amplitude.direct_models.create_MSvoltage.rst deleted file mode 100644 index 801d83c..0000000 --- a/docs/_autosummary/pyudv.amplitude.direct_models.create_MSvoltage.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.amplitude.direct\_models.create\_MSvoltage -================================================ - -.. currentmodule:: pyudv.amplitude.direct_models - -.. autofunction:: create_MSvoltage - -.. _sphx_glr_backreferences_pyudv.amplitude.direct_models.create_MSvoltage: - -.. minigallery:: pyudv.amplitude.direct_models.create_MSvoltage - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.amplitude.direct_models.cumulative_trapezoid.rst b/docs/_autosummary/pyudv.amplitude.direct_models.cumulative_trapezoid.rst deleted file mode 100644 index a6de9c7..0000000 --- a/docs/_autosummary/pyudv.amplitude.direct_models.cumulative_trapezoid.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.amplitude.direct\_models.cumulative\_trapezoid -==================================================== - -.. currentmodule:: pyudv.amplitude.direct_models - -.. autofunction:: cumulative_trapezoid - -.. _sphx_glr_backreferences_pyudv.amplitude.direct_models.cumulative_trapezoid: - -.. minigallery:: pyudv.amplitude.direct_models.cumulative_trapezoid - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.amplitude.direct_models.near_field_theoretical.rst b/docs/_autosummary/pyudv.amplitude.direct_models.near_field_theoretical.rst deleted file mode 100644 index db93b88..0000000 --- a/docs/_autosummary/pyudv.amplitude.direct_models.near_field_theoretical.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.amplitude.direct\_models.near\_field\_theoretical -======================================================= - -.. currentmodule:: pyudv.amplitude.direct_models - -.. autofunction:: near_field_theoretical - -.. _sphx_glr_backreferences_pyudv.amplitude.direct_models.near_field_theoretical: - -.. minigallery:: pyudv.amplitude.direct_models.near_field_theoretical - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.amplitude.direct_models.rst b/docs/_autosummary/pyudv.amplitude.direct_models.rst deleted file mode 100644 index bb47fa9..0000000 --- a/docs/_autosummary/pyudv.amplitude.direct_models.rst +++ /dev/null @@ -1,38 +0,0 @@ -pyudv.amplitude.direct\_models -============================== - -.. automodule:: pyudv.amplitude.direct_models - - - - - - - - - - - - .. rubric:: Functions - - .. autosummary:: - :toctree: - :template: custom-function-template.rst - :nosignatures: - - alpha_w - correction_factor - create_MSvoltage - cumulative_trapezoid - near_field_theoretical - sound_velocity - - - - - - - - - - \ No newline at end of file diff --git a/docs/_autosummary/pyudv.amplitude.direct_models.sound_velocity.rst b/docs/_autosummary/pyudv.amplitude.direct_models.sound_velocity.rst deleted file mode 100644 index ce32cb9..0000000 --- a/docs/_autosummary/pyudv.amplitude.direct_models.sound_velocity.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.amplitude.direct\_models.sound\_velocity -============================================== - -.. currentmodule:: pyudv.amplitude.direct_models - -.. autofunction:: sound_velocity - -.. _sphx_glr_backreferences_pyudv.amplitude.direct_models.sound_velocity: - -.. minigallery:: pyudv.amplitude.direct_models.sound_velocity - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.amplitude.inversion.correction_factor.rst b/docs/_autosummary/pyudv.amplitude.inversion.correction_factor.rst deleted file mode 100644 index 13f0652..0000000 --- a/docs/_autosummary/pyudv.amplitude.inversion.correction_factor.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.amplitude.inversion.correction\_factor -============================================ - -.. currentmodule:: pyudv.amplitude.inversion - -.. autofunction:: correction_factor - -.. _sphx_glr_backreferences_pyudv.amplitude.inversion.correction_factor: - -.. minigallery:: pyudv.amplitude.inversion.correction_factor - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.amplitude.inversion.explicit_inversion.rst b/docs/_autosummary/pyudv.amplitude.inversion.explicit_inversion.rst deleted file mode 100644 index f1a6536..0000000 --- a/docs/_autosummary/pyudv.amplitude.inversion.explicit_inversion.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.amplitude.inversion.explicit\_inversion -============================================= - -.. currentmodule:: pyudv.amplitude.inversion - -.. autofunction:: explicit_inversion - -.. _sphx_glr_backreferences_pyudv.amplitude.inversion.explicit_inversion: - -.. minigallery:: pyudv.amplitude.inversion.explicit_inversion - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.amplitude.inversion.rst b/docs/_autosummary/pyudv.amplitude.inversion.rst deleted file mode 100644 index 0f290f3..0000000 --- a/docs/_autosummary/pyudv.amplitude.inversion.rst +++ /dev/null @@ -1,34 +0,0 @@ -pyudv.amplitude.inversion -========================= - -.. automodule:: pyudv.amplitude.inversion - - - - - - - - - - - - .. rubric:: Functions - - .. autosummary:: - :toctree: - :template: custom-function-template.rst - :nosignatures: - - correction_factor - explicit_inversion - - - - - - - - - - \ No newline at end of file diff --git a/docs/_autosummary/pyudv.amplitude.rst b/docs/_autosummary/pyudv.amplitude.rst deleted file mode 100644 index cf72804..0000000 --- a/docs/_autosummary/pyudv.amplitude.rst +++ /dev/null @@ -1,34 +0,0 @@ -pyudv.amplitude -=============== - -.. automodule:: pyudv.amplitude - - - - .. rubric:: Modules - - .. autosummary:: - :toctree: - :template: custom-module-template.rst - :recursive: - - pyudv.amplitude.direct_models - pyudv.amplitude.inversion - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/docs/_autosummary/pyudv.helpers.create_arboresence.rst b/docs/_autosummary/pyudv.helpers.create_arboresence.rst deleted file mode 100644 index fb225e8..0000000 --- a/docs/_autosummary/pyudv.helpers.create_arboresence.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.helpers.create\_arboresence -================================= - -.. currentmodule:: pyudv.helpers - -.. autofunction:: create_arboresence - -.. _sphx_glr_backreferences_pyudv.helpers.create_arboresence: - -.. minigallery:: pyudv.helpers.create_arboresence - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.helpers.moving_std.rst b/docs/_autosummary/pyudv.helpers.moving_std.rst deleted file mode 100644 index 9973968..0000000 --- a/docs/_autosummary/pyudv.helpers.moving_std.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.helpers.moving\_std -========================= - -.. currentmodule:: pyudv.helpers - -.. autofunction:: moving_std - -.. _sphx_glr_backreferences_pyudv.helpers.moving_std: - -.. minigallery:: pyudv.helpers.moving_std - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.helpers.moving_std1d.rst b/docs/_autosummary/pyudv.helpers.moving_std1d.rst deleted file mode 100644 index 2995d6d..0000000 --- a/docs/_autosummary/pyudv.helpers.moving_std1d.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.helpers.moving\_std1d -=========================== - -.. currentmodule:: pyudv.helpers - -.. autofunction:: moving_std1d - -.. _sphx_glr_backreferences_pyudv.helpers.moving_std1d: - -.. minigallery:: pyudv.helpers.moving_std1d - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.helpers.rst b/docs/_autosummary/pyudv.helpers.rst deleted file mode 100644 index daf2262..0000000 --- a/docs/_autosummary/pyudv.helpers.rst +++ /dev/null @@ -1,37 +0,0 @@ -pyudv.helpers -============= - -.. automodule:: pyudv.helpers - - - - - - - - - - - - .. rubric:: Functions - - .. autosummary:: - :toctree: - :template: custom-function-template.rst - :nosignatures: - - create_arboresence - moving_std - moving_std1d - uniform_filter - uniform_filter1d - - - - - - - - - - \ No newline at end of file diff --git a/docs/_autosummary/pyudv.helpers.uniform_filter.rst b/docs/_autosummary/pyudv.helpers.uniform_filter.rst deleted file mode 100644 index 2b56c54..0000000 --- a/docs/_autosummary/pyudv.helpers.uniform_filter.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.helpers.uniform\_filter -============================= - -.. currentmodule:: pyudv.helpers - -.. autofunction:: uniform_filter - -.. _sphx_glr_backreferences_pyudv.helpers.uniform_filter: - -.. minigallery:: pyudv.helpers.uniform_filter - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.helpers.uniform_filter1d.rst b/docs/_autosummary/pyudv.helpers.uniform_filter1d.rst deleted file mode 100644 index 0d14e97..0000000 --- a/docs/_autosummary/pyudv.helpers.uniform_filter1d.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.helpers.uniform\_filter1d -=============================== - -.. currentmodule:: pyudv.helpers - -.. autofunction:: uniform_filter1d - -.. _sphx_glr_backreferences_pyudv.helpers.uniform_filter1d: - -.. minigallery:: pyudv.helpers.uniform_filter1d - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.probes.Probe.plot_probe.rst b/docs/_autosummary/pyudv.probes.Probe.plot_probe.rst deleted file mode 100644 index 477a1d6..0000000 --- a/docs/_autosummary/pyudv.probes.Probe.plot_probe.rst +++ /dev/null @@ -1,6 +0,0 @@ -pyudv.probes.Probe.plot\_probe -============================== - -.. currentmodule:: pyudv.probes - -.. automethod:: Probe.plot_probe \ No newline at end of file diff --git a/docs/_autosummary/pyudv.probes.Probe.rst b/docs/_autosummary/pyudv.probes.Probe.rst deleted file mode 100644 index d7ddd24..0000000 --- a/docs/_autosummary/pyudv.probes.Probe.rst +++ /dev/null @@ -1,24 +0,0 @@ -pyudv.probes.Probe -================== - -.. currentmodule:: pyudv.probes - -.. autoclass:: Probe - :show-inheritance: - :inherited-members: - :special-members: __call__, __add__, __mul__ - - - - .. rubric:: Methods - - .. autosummary:: - :toctree: - - ~Probe.plot_probe - - - - - - \ No newline at end of file diff --git a/docs/_autosummary/pyudv.probes.compute_vertical_axis.rst b/docs/_autosummary/pyudv.probes.compute_vertical_axis.rst deleted file mode 100644 index 8cc3960..0000000 --- a/docs/_autosummary/pyudv.probes.compute_vertical_axis.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.probes.compute\_vertical\_axis -==================================== - -.. currentmodule:: pyudv.probes - -.. autofunction:: compute_vertical_axis - -.. _sphx_glr_backreferences_pyudv.probes.compute_vertical_axis: - -.. minigallery:: pyudv.probes.compute_vertical_axis - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.probes.probe_crossing_point.rst b/docs/_autosummary/pyudv.probes.probe_crossing_point.rst deleted file mode 100644 index 27be701..0000000 --- a/docs/_autosummary/pyudv.probes.probe_crossing_point.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.probes.probe\_crossing\_point -=================================== - -.. currentmodule:: pyudv.probes - -.. autofunction:: probe_crossing_point - -.. _sphx_glr_backreferences_pyudv.probes.probe_crossing_point: - -.. minigallery:: pyudv.probes.probe_crossing_point - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.probes.rst b/docs/_autosummary/pyudv.probes.rst deleted file mode 100644 index 2192c12..0000000 --- a/docs/_autosummary/pyudv.probes.rst +++ /dev/null @@ -1,44 +0,0 @@ -pyudv.probes -============ - -.. automodule:: pyudv.probes - - - - - - - - - - - - .. rubric:: Functions - - .. autosummary:: - :toctree: - :template: custom-function-template.rst - :nosignatures: - - compute_vertical_axis - probe_crossing_point - sketch_probes - - - - - - .. rubric:: Classes - - .. autosummary:: - :toctree: - :template: custom-class-template.rst - :nosignatures: - - Probe - - - - - - \ No newline at end of file diff --git a/docs/_autosummary/pyudv.probes.sketch_probes.rst b/docs/_autosummary/pyudv.probes.sketch_probes.rst deleted file mode 100644 index 6d8aeb0..0000000 --- a/docs/_autosummary/pyudv.probes.sketch_probes.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.probes.sketch\_probes -=========================== - -.. currentmodule:: pyudv.probes - -.. autofunction:: sketch_probes - -.. _sphx_glr_backreferences_pyudv.probes.sketch_probes: - -.. minigallery:: pyudv.probes.sketch_probes - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.read_mfprof.amplitude_from_UVPdata.rst b/docs/_autosummary/pyudv.read_mfprof.amplitude_from_UVPdata.rst deleted file mode 100644 index 45a187a..0000000 --- a/docs/_autosummary/pyudv.read_mfprof.amplitude_from_UVPdata.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.read\_mfprof.amplitude\_from\_UVPdata -=========================================== - -.. currentmodule:: pyudv.read_mfprof - -.. autofunction:: amplitude_from_UVPdata - -.. _sphx_glr_backreferences_pyudv.read_mfprof.amplitude_from_UVPdata: - -.. minigallery:: pyudv.read_mfprof.amplitude_from_UVPdata - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.read_mfprof.amplitude_from_mfprof_reading.rst b/docs/_autosummary/pyudv.read_mfprof.amplitude_from_mfprof_reading.rst deleted file mode 100644 index e177bae..0000000 --- a/docs/_autosummary/pyudv.read_mfprof.amplitude_from_mfprof_reading.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.read\_mfprof.amplitude\_from\_mfprof\_reading -=================================================== - -.. currentmodule:: pyudv.read_mfprof - -.. autofunction:: amplitude_from_mfprof_reading - -.. _sphx_glr_backreferences_pyudv.read_mfprof.amplitude_from_mfprof_reading: - -.. minigallery:: pyudv.read_mfprof.amplitude_from_mfprof_reading - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.read_mfprof.create_variable.rst b/docs/_autosummary/pyudv.read_mfprof.create_variable.rst deleted file mode 100644 index 2599f08..0000000 --- a/docs/_autosummary/pyudv.read_mfprof.create_variable.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.read\_mfprof.create\_variable -=================================== - -.. currentmodule:: pyudv.read_mfprof - -.. autofunction:: create_variable - -.. _sphx_glr_backreferences_pyudv.read_mfprof.create_variable: - -.. minigallery:: pyudv.read_mfprof.create_variable - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.read_mfprof.filetime_to_dt.rst b/docs/_autosummary/pyudv.read_mfprof.filetime_to_dt.rst deleted file mode 100644 index 6c90172..0000000 --- a/docs/_autosummary/pyudv.read_mfprof.filetime_to_dt.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.read\_mfprof.filetime\_to\_dt -=================================== - -.. currentmodule:: pyudv.read_mfprof - -.. autofunction:: filetime_to_dt - -.. _sphx_glr_backreferences_pyudv.read_mfprof.filetime_to_dt: - -.. minigallery:: pyudv.read_mfprof.filetime_to_dt - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.read_mfprof.mfprof_to_netcdf.rst b/docs/_autosummary/pyudv.read_mfprof.mfprof_to_netcdf.rst deleted file mode 100644 index 9c30bac..0000000 --- a/docs/_autosummary/pyudv.read_mfprof.mfprof_to_netcdf.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.read\_mfprof.mfprof\_to\_netcdf -===================================== - -.. currentmodule:: pyudv.read_mfprof - -.. autofunction:: mfprof_to_netcdf - -.. _sphx_glr_backreferences_pyudv.read_mfprof.mfprof_to_netcdf: - -.. minigallery:: pyudv.read_mfprof.mfprof_to_netcdf - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.read_mfprof.read_mfprof.rst b/docs/_autosummary/pyudv.read_mfprof.read_mfprof.rst deleted file mode 100644 index cd8d537..0000000 --- a/docs/_autosummary/pyudv.read_mfprof.read_mfprof.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.read\_mfprof.read\_mfprof -=============================== - -.. currentmodule:: pyudv.read_mfprof - -.. autofunction:: read_mfprof - -.. _sphx_glr_backreferences_pyudv.read_mfprof.read_mfprof: - -.. minigallery:: pyudv.read_mfprof.read_mfprof - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.read_mfprof.rst b/docs/_autosummary/pyudv.read_mfprof.rst deleted file mode 100644 index 00e3eb7..0000000 --- a/docs/_autosummary/pyudv.read_mfprof.rst +++ /dev/null @@ -1,41 +0,0 @@ -pyudv.read\_mfprof -================== - -.. automodule:: pyudv.read_mfprof - - - - - - - - - - - - .. rubric:: Functions - - .. autosummary:: - :toctree: - :template: custom-function-template.rst - :nosignatures: - - amplitude_from_UVPdata - amplitude_from_mfprof_reading - create_variable - filetime_to_dt - mfprof_to_netcdf - read_mfprof - velocity_from_UVPdata - velocity_from_mfprof_reading - write_dictionnary - - - - - - - - - - \ No newline at end of file diff --git a/docs/_autosummary/pyudv.read_mfprof.velocity_from_UVPdata.rst b/docs/_autosummary/pyudv.read_mfprof.velocity_from_UVPdata.rst deleted file mode 100644 index c5b06c5..0000000 --- a/docs/_autosummary/pyudv.read_mfprof.velocity_from_UVPdata.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.read\_mfprof.velocity\_from\_UVPdata -========================================== - -.. currentmodule:: pyudv.read_mfprof - -.. autofunction:: velocity_from_UVPdata - -.. _sphx_glr_backreferences_pyudv.read_mfprof.velocity_from_UVPdata: - -.. minigallery:: pyudv.read_mfprof.velocity_from_UVPdata - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.read_mfprof.velocity_from_mfprof_reading.rst b/docs/_autosummary/pyudv.read_mfprof.velocity_from_mfprof_reading.rst deleted file mode 100644 index 70603fe..0000000 --- a/docs/_autosummary/pyudv.read_mfprof.velocity_from_mfprof_reading.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.read\_mfprof.velocity\_from\_mfprof\_reading -================================================== - -.. currentmodule:: pyudv.read_mfprof - -.. autofunction:: velocity_from_mfprof_reading - -.. _sphx_glr_backreferences_pyudv.read_mfprof.velocity_from_mfprof_reading: - -.. minigallery:: pyudv.read_mfprof.velocity_from_mfprof_reading - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.read_mfprof.write_dictionnary.rst b/docs/_autosummary/pyudv.read_mfprof.write_dictionnary.rst deleted file mode 100644 index 3e8852b..0000000 --- a/docs/_autosummary/pyudv.read_mfprof.write_dictionnary.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.read\_mfprof.write\_dictionnary -===================================== - -.. currentmodule:: pyudv.read_mfprof - -.. autofunction:: write_dictionnary - -.. _sphx_glr_backreferences_pyudv.read_mfprof.write_dictionnary: - -.. minigallery:: pyudv.read_mfprof.write_dictionnary - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.reconstruct_velocity.rst b/docs/_autosummary/pyudv.reconstruct_velocity.rst deleted file mode 100644 index a37c5c0..0000000 --- a/docs/_autosummary/pyudv.reconstruct_velocity.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.reconstruct\_velocity -=========================== - -.. currentmodule:: pyudv - -.. autofunction:: reconstruct_velocity - -.. _sphx_glr_backreferences_pyudv.reconstruct_velocity: - -.. minigallery:: pyudv.reconstruct_velocity - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.rst b/docs/_autosummary/pyudv.rst deleted file mode 100644 index 594d339..0000000 --- a/docs/_autosummary/pyudv.rst +++ /dev/null @@ -1,46 +0,0 @@ -pyudv -===== - -.. automodule:: pyudv - - - - .. rubric:: Modules - - .. autosummary:: - :toctree: - :template: custom-module-template.rst - :recursive: - - pyudv.amplitude - pyudv.helpers - pyudv.probes - pyudv.read_mfprof - pyudv.velocity - - - - - - - - - - .. rubric:: Functions - - .. autosummary:: - :toctree: - :template: custom-function-template.rst - :nosignatures: - - reconstruct_velocity - - - - - - - - - - \ No newline at end of file diff --git a/docs/_autosummary/pyudv.velocity.Probe.plot_probe.rst b/docs/_autosummary/pyudv.velocity.Probe.plot_probe.rst deleted file mode 100644 index 1505011..0000000 --- a/docs/_autosummary/pyudv.velocity.Probe.plot_probe.rst +++ /dev/null @@ -1,6 +0,0 @@ -pyudv.velocity.Probe.plot\_probe -================================ - -.. currentmodule:: pyudv.velocity - -.. automethod:: Probe.plot_probe \ No newline at end of file diff --git a/docs/_autosummary/pyudv.velocity.Probe.rst b/docs/_autosummary/pyudv.velocity.Probe.rst deleted file mode 100644 index fba7390..0000000 --- a/docs/_autosummary/pyudv.velocity.Probe.rst +++ /dev/null @@ -1,24 +0,0 @@ -pyudv.velocity.Probe -==================== - -.. currentmodule:: pyudv.velocity - -.. autoclass:: Probe - :show-inheritance: - :inherited-members: - :special-members: __call__, __add__, __mul__ - - - - .. rubric:: Methods - - .. autosummary:: - :toctree: - - ~Probe.plot_probe - - - - - - \ No newline at end of file diff --git a/docs/_autosummary/pyudv.velocity.compute_vertical_axis.rst b/docs/_autosummary/pyudv.velocity.compute_vertical_axis.rst deleted file mode 100644 index 54e6d20..0000000 --- a/docs/_autosummary/pyudv.velocity.compute_vertical_axis.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.velocity.compute\_vertical\_axis -====================================== - -.. currentmodule:: pyudv.velocity - -.. autofunction:: compute_vertical_axis - -.. _sphx_glr_backreferences_pyudv.velocity.compute_vertical_axis: - -.. minigallery:: pyudv.velocity.compute_vertical_axis - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.velocity.probe_crossing_point.rst b/docs/_autosummary/pyudv.velocity.probe_crossing_point.rst deleted file mode 100644 index 38c0542..0000000 --- a/docs/_autosummary/pyudv.velocity.probe_crossing_point.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.velocity.probe\_crossing\_point -===================================== - -.. currentmodule:: pyudv.velocity - -.. autofunction:: probe_crossing_point - -.. _sphx_glr_backreferences_pyudv.velocity.probe_crossing_point: - -.. minigallery:: pyudv.velocity.probe_crossing_point - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.velocity.reconstruct_velocity.rst b/docs/_autosummary/pyudv.velocity.reconstruct_velocity.rst deleted file mode 100644 index ac50482..0000000 --- a/docs/_autosummary/pyudv.velocity.reconstruct_velocity.rst +++ /dev/null @@ -1,11 +0,0 @@ -pyudv.velocity.reconstruct\_velocity -==================================== - -.. currentmodule:: pyudv.velocity - -.. autofunction:: reconstruct_velocity - -.. _sphx_glr_backreferences_pyudv.velocity.reconstruct_velocity: - -.. minigallery:: pyudv.velocity.reconstruct_velocity - :add-heading: \ No newline at end of file diff --git a/docs/_autosummary/pyudv.velocity.rst b/docs/_autosummary/pyudv.velocity.rst deleted file mode 100644 index 24a144f..0000000 --- a/docs/_autosummary/pyudv.velocity.rst +++ /dev/null @@ -1,44 +0,0 @@ -pyudv.velocity -============== - -.. automodule:: pyudv.velocity - - - - - - - - - - - - .. rubric:: Functions - - .. autosummary:: - :toctree: - :template: custom-function-template.rst - :nosignatures: - - compute_vertical_axis - probe_crossing_point - reconstruct_velocity - - - - - - .. rubric:: Classes - - .. autosummary:: - :toctree: - :template: custom-class-template.rst - :nosignatures: - - Probe - - - - - - \ No newline at end of file diff --git a/docs/_examples/_examples_jupyter.zip b/docs/_examples/_examples_jupyter.zip deleted file mode 100644 index fef68b7..0000000 Binary files a/docs/_examples/_examples_jupyter.zip and /dev/null differ diff --git a/docs/_examples/_examples_python.zip b/docs/_examples/_examples_python.zip deleted file mode 100644 index 511310f..0000000 Binary files a/docs/_examples/_examples_python.zip and /dev/null differ diff --git a/docs/_examples/images/sphx_glr_plot_direct_inversion_001.png b/docs/_examples/images/sphx_glr_plot_direct_inversion_001.png deleted file mode 100644 index 946369c..0000000 Binary files a/docs/_examples/images/sphx_glr_plot_direct_inversion_001.png and /dev/null differ diff --git a/docs/_examples/images/sphx_glr_plot_direct_inversion_002.png b/docs/_examples/images/sphx_glr_plot_direct_inversion_002.png deleted file mode 100644 index eea760d..0000000 Binary files a/docs/_examples/images/sphx_glr_plot_direct_inversion_002.png and /dev/null differ diff --git a/docs/_examples/images/sphx_glr_plot_direct_inversion_003.png b/docs/_examples/images/sphx_glr_plot_direct_inversion_003.png deleted file mode 100644 index b75ded3..0000000 Binary files a/docs/_examples/images/sphx_glr_plot_direct_inversion_003.png and /dev/null differ diff --git a/docs/_examples/images/sphx_glr_plot_read_plot_mfprof_data_001.png b/docs/_examples/images/sphx_glr_plot_read_plot_mfprof_data_001.png deleted file mode 100644 index 81073ea..0000000 Binary files a/docs/_examples/images/sphx_glr_plot_read_plot_mfprof_data_001.png and /dev/null differ diff --git a/docs/_examples/images/sphx_glr_plot_read_plot_mfprof_data_002.png b/docs/_examples/images/sphx_glr_plot_read_plot_mfprof_data_002.png deleted file mode 100644 index ab29c30..0000000 Binary files a/docs/_examples/images/sphx_glr_plot_read_plot_mfprof_data_002.png and /dev/null differ diff --git a/docs/_examples/images/sphx_glr_plot_reconstruct_velocity_001.png b/docs/_examples/images/sphx_glr_plot_reconstruct_velocity_001.png deleted file mode 100644 index e378f43..0000000 Binary files a/docs/_examples/images/sphx_glr_plot_reconstruct_velocity_001.png and /dev/null differ diff --git a/docs/_examples/images/sphx_glr_plot_reconstruct_velocity_002.png b/docs/_examples/images/sphx_glr_plot_reconstruct_velocity_002.png deleted file mode 100644 index 121b715..0000000 Binary files a/docs/_examples/images/sphx_glr_plot_reconstruct_velocity_002.png and /dev/null differ diff --git a/docs/_examples/images/thumb/sphx_glr_plot_direct_inversion_thumb.png b/docs/_examples/images/thumb/sphx_glr_plot_direct_inversion_thumb.png deleted file mode 100644 index 8353a7a..0000000 Binary files a/docs/_examples/images/thumb/sphx_glr_plot_direct_inversion_thumb.png and /dev/null differ diff --git a/docs/_examples/images/thumb/sphx_glr_plot_read_plot_mfprof_data_thumb.png b/docs/_examples/images/thumb/sphx_glr_plot_read_plot_mfprof_data_thumb.png deleted file mode 100644 index ef2e76d..0000000 Binary files a/docs/_examples/images/thumb/sphx_glr_plot_read_plot_mfprof_data_thumb.png and /dev/null differ diff --git a/docs/_examples/images/thumb/sphx_glr_plot_reconstruct_velocity_thumb.png b/docs/_examples/images/thumb/sphx_glr_plot_reconstruct_velocity_thumb.png deleted file mode 100644 index ce0701f..0000000 Binary files a/docs/_examples/images/thumb/sphx_glr_plot_reconstruct_velocity_thumb.png and /dev/null differ diff --git a/docs/_examples/index.rst b/docs/_examples/index.rst deleted file mode 100644 index ebd97d5..0000000 --- a/docs/_examples/index.rst +++ /dev/null @@ -1,96 +0,0 @@ -:orphan: - -Examples -========= - -Below is a gallery of examples demonstrating the use of several functions of pyudv. - - - -.. raw:: html - -
- - -.. raw:: html - -
- -.. only:: html - - .. image:: /_examples/images/thumb/sphx_glr_plot_reconstruct_velocity_thumb.png - :alt: - - :ref:`sphx_glr__examples_plot_reconstruct_velocity.py` - -.. raw:: html - -
Probes and velocity reconstruction
-
- - -.. raw:: html - -
- -.. only:: html - - .. image:: /_examples/images/thumb/sphx_glr_plot_read_plot_mfprof_data_thumb.png - :alt: - - :ref:`sphx_glr__examples_plot_read_plot_mfprof_data.py` - -.. raw:: html - -
Read and plot .mfprof data
-
- - -.. raw:: html - -
- -.. only:: html - - .. image:: /_examples/images/thumb/sphx_glr_plot_direct_inversion_thumb.png - :alt: - - :ref:`sphx_glr__examples_plot_direct_inversion.py` - -.. raw:: html - -
Concentration inference from amplitude signals
-
- - -.. raw:: html - -
- - -.. toctree:: - :hidden: - - /_examples/plot_reconstruct_velocity - /_examples/plot_read_plot_mfprof_data - /_examples/plot_direct_inversion - - -.. only:: html - - .. container:: sphx-glr-footer sphx-glr-footer-gallery - - .. container:: sphx-glr-download sphx-glr-download-python - - :download:`Download all examples in Python source code: _examples_python.zip ` - - .. container:: sphx-glr-download sphx-glr-download-jupyter - - :download:`Download all examples in Jupyter notebooks: _examples_jupyter.zip ` - - -.. only:: html - - .. rst-class:: sphx-glr-signature - - `Gallery generated by Sphinx-Gallery `_ diff --git a/docs/_examples/plot_direct_inversion.ipynb b/docs/_examples/plot_direct_inversion.ipynb deleted file mode 100644 index 5102e1d..0000000 --- a/docs/_examples/plot_direct_inversion.ipynb +++ /dev/null @@ -1,79 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "\n# Concentration inference from amplitude signals\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "import matplotlib.pyplot as plt\nimport numpy as np\n\nimport pyudv.amplitude.direct_models as DM\nfrom pyudv.amplitude.inversion import explicit_inversion\nfrom pyudv.amplitude.sediment_acoustic_models import quartz_sand as quartz\n\n\ndef C_to_phi(C, rho=2.65e3):\n return C / rho\n\n\ndef phi_to_C(phi, rho=2.65e3):\n return phi * rho\n\n\nfig_width_small = 11.25" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Define the parameters for the direct model\n\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "d = 100e-6 # grain mean diameter [m]\nrho = 2.65 # grain density [g/cm3]\nrho = rho * 1e-3 / 1e-6 # grain density [kg/m3]\n\nF = 2e6 # frequency [Hz]\nT = 20 # Temperature [Celsius degrees]\na_w = DM.alpha_w(F, T) # water absorption, [m-1]\nk = 2 * np.pi * F / DM.sound_velocity(T) # wavenumber of the wave\n\nKs, Kt = 1, 1 # sediment and transducer constants\nXi = quartz.Xi(k, d / 2) # sediment attenuation constant\nrn = 0.05 # near field distance [cm]\nr = np.linspace(0.001, 12, 330) # radial coordinates [cm]\n\n# Volumic fraction of grain\nPhi = np.array([0.0001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1])" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Influence of the imposed point in the integration\n\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "# #### without near field function\npsi = DM.near_field_theoretical(r, rn) * 0 + 1 # near field function\n# defining a constant grain concentration profile\nC = Phi[:, None] * rho * (r[None, :] * 0 + 1)\nMSV = DM.create_MSvoltage(C, r, Xi, a_w, Ks, Kt, psi)\n#\nindexes = [2, 50, 150, 250, 320]\n\ncolor = []\nfig, ax = plt.subplots(\n 1, 1, figsize=(fig_width_small, fig_width_small), constrained_layout=True\n)\nfor i, phi in enumerate(Phi):\n if i == 0:\n a = plt.plot(C[i, :], r, lw=4, alpha=0.3, label=\"imposed\")\n else:\n a = plt.plot(C[i, :], r, lw=4, alpha=0.3)\n color.append(a[0].get_color())\nfor j, index in enumerate(indexes):\n C0 = C[:, index]\n r0 = r[index]\n C_inferred = explicit_inversion(MSV, r, Xi, a_w, psi, C0, r0)\n for i, phi in enumerate(Phi):\n if i == 0:\n plt.plot(\n C_inferred[i, :], r, lw=2.5 - (j + 1) / 3, label=str(r0), color=color[i]\n )\n else:\n plt.plot(C_inferred[i, :], r, lw=2.5 - (j + 1) / 3, color=color[i])\nplt.xlabel(\"Concentration~[kg/m3]\")\nplt.ylabel(\"Distance from transducer~[m]\")\nax.set_xscale(\"log\")\nplt.xlim([0.5 * C.min(), 2.5 * C.max()])\nplt.ylim([0, r.max()])\nax.invert_yaxis()\nsecax = ax.secondary_xaxis(\"top\", functions=(C_to_phi, phi_to_C))\nsecax.set_xlabel(\"Volumic fraction\")\nplt.legend(title=\"Distance of imposed concentration [mm]\")\nplt.title(\"Without near field\")\n\n# #### with near field function\npsi = DM.near_field_theoretical(r, rn) # near field function\n# defining a constant grain concentration profile\nC = Phi[:, None] * rho * (r[None, :] * 0 + 1)\nMSV = DM.create_MSvoltage(C, r[None, :], Xi, a_w, Ks, Kt, psi[None, :])\n#\ncolor = []\nfig, ax = plt.subplots(\n 1, 1, figsize=(fig_width_small, fig_width_small), constrained_layout=True\n)\nfor i, phi in enumerate(Phi):\n if i == 0:\n a = plt.plot(C[i, :], r, lw=4, alpha=0.3, label=\"imposed\")\n else:\n a = plt.plot(C[i, :], r, lw=4, alpha=0.3)\n color.append(a[0].get_color())\nfor j, index in enumerate(indexes):\n C0 = C[:, index]\n r0 = r[index]\n C_inferred = explicit_inversion(MSV, r, Xi, a_w, psi * 0 + 1, C0, r0)\n for i, phi in enumerate(Phi):\n if i == 0:\n plt.plot(\n C_inferred[i, :], r, lw=2.5 - (j + 1) / 3, label=str(r0), color=color[i]\n )\n else:\n plt.plot(C_inferred[i, :], r, lw=2.5 - (j + 1) / 3, color=color[i])\nplt.xlabel(\"Concentration~[kg/m3]\")\nplt.ylabel(\"Distance from transducer~[m]\")\nax.set_xscale(\"log\")\nplt.xlim([0.5 * C.min(), 2.5 * C.max()])\nplt.ylim([0, r.max()])\nax.invert_yaxis()\nsecax = ax.secondary_xaxis(\"top\", functions=(C_to_phi, phi_to_C))\nsecax.set_xlabel(\"Volumic fraction\")\nplt.legend(title=\"Distance of imposed concentration [mm]\")\nplt.title(\"With near field\")\n\n# #### with real type concentration profiles\npsi = DM.near_field_theoretical(r, rn) # near field function\n# C = Phi[:, None]*rho*np.exp(-r[None, :]/1) # defining an exponentially decreasing profile\n# C = Phi[:, None]*rho*np.exp(r[None, :]/10) # defining an exponentially increasing profile\nC = Phi[:, None] * rho * (r[None, :] * 0 + 1) # defining sedimentation-like profile\nC[..., :230] = 0\n#\nMSV = DM.create_MSvoltage(C, r[None, :], Xi, a_w, Ks, Kt, psi[None, :])\n#\ncolor = []\nfig, ax = plt.subplots(\n 1, 1, figsize=(fig_width_small, fig_width_small), constrained_layout=True\n)\nfor i, phi in enumerate(Phi):\n if i == 0:\n a = plt.plot(C[i, :], r, lw=4, alpha=0.3, label=\"imposed\")\n else:\n a = plt.plot(C[i, :], r, lw=4, alpha=0.3)\n color.append(a[0].get_color())\nfor j, index in enumerate(indexes):\n C0 = C[:, index]\n r0 = r[index]\n C_inferred = explicit_inversion(MSV, r, Xi, a_w, psi * 0 + 1, C0, r0)\n for i, phi in enumerate(Phi):\n if i == 0:\n plt.plot(\n C_inferred[i, :], r, lw=2.5 - (j + 1) / 3, label=str(r0), color=color[i]\n )\n else:\n plt.plot(C_inferred[i, :], r, lw=2.5 - (j + 1) / 3, color=color[i])\nplt.xlabel(\"Concentration~[kg/m3]\")\nplt.ylabel(\"Distance from transducer~[m]\")\nax.set_xscale(\"log\")\nplt.xlim([0.2 * C[:, -1].min(), 2.5 * C.max()])\nplt.ylim([0, r.max()])\nax.invert_yaxis()\nsecax = ax.secondary_xaxis(\"top\", functions=(C_to_phi, phi_to_C))\nsecax.set_xlabel(\"Volumic fraction\")\nplt.legend(title=\"Distance of imposed concentration [mm]\")\nplt.title(\"With exponential concentration profiles\")\n\n\nplt.show()" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.12" - } - }, - "nbformat": 4, - "nbformat_minor": 0 -} \ No newline at end of file diff --git a/docs/_examples/plot_direct_inversion.py b/docs/_examples/plot_direct_inversion.py deleted file mode 100644 index 9747cb5..0000000 --- a/docs/_examples/plot_direct_inversion.py +++ /dev/null @@ -1,171 +0,0 @@ -""" -============================================== -Concentration inference from amplitude signals -============================================== -""" - -import matplotlib.pyplot as plt -import numpy as np - -import pyudv.amplitude.direct_models as DM -from pyudv.amplitude.inversion import explicit_inversion -from pyudv.amplitude.sediment_acoustic_models import quartz_sand as quartz - - -def C_to_phi(C, rho=2.65e3): - return C / rho - - -def phi_to_C(phi, rho=2.65e3): - return phi * rho - - -fig_width_small = 11.25 - -# %% -# Define the parameters for the direct model -# ========================================== - -d = 100e-6 # grain mean diameter [m] -rho = 2.65 # grain density [g/cm3] -rho = rho * 1e-3 / 1e-6 # grain density [kg/m3] - -F = 2e6 # frequency [Hz] -T = 20 # Temperature [Celsius degrees] -a_w = DM.alpha_w(F, T) # water absorption, [m-1] -k = 2 * np.pi * F / DM.sound_velocity(T) # wavenumber of the wave - -Ks, Kt = 1, 1 # sediment and transducer constants -Xi = quartz.Xi(k, d / 2) # sediment attenuation constant -rn = 0.05 # near field distance [cm] -r = np.linspace(0.001, 12, 330) # radial coordinates [cm] - -# Volumic fraction of grain -Phi = np.array([0.0001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1]) - - -# %% -# Influence of the imposed point in the integration -# ================================================= - -# #### without near field function -psi = DM.near_field_theoretical(r, rn) * 0 + 1 # near field function -# defining a constant grain concentration profile -C = Phi[:, None] * rho * (r[None, :] * 0 + 1) -MSV = DM.create_MSvoltage(C, r, Xi, a_w, Ks, Kt, psi) -# -indexes = [2, 50, 150, 250, 320] - -color = [] -fig, ax = plt.subplots( - 1, 1, figsize=(fig_width_small, fig_width_small), constrained_layout=True -) -for i, phi in enumerate(Phi): - if i == 0: - a = plt.plot(C[i, :], r, lw=4, alpha=0.3, label="imposed") - else: - a = plt.plot(C[i, :], r, lw=4, alpha=0.3) - color.append(a[0].get_color()) -for j, index in enumerate(indexes): - C0 = C[:, index] - r0 = r[index] - C_inferred = explicit_inversion(MSV, r, Xi, a_w, psi, C0, r0) - for i, phi in enumerate(Phi): - if i == 0: - plt.plot( - C_inferred[i, :], r, lw=2.5 - (j + 1) / 3, label=str(r0), color=color[i] - ) - else: - plt.plot(C_inferred[i, :], r, lw=2.5 - (j + 1) / 3, color=color[i]) -plt.xlabel("Concentration~[kg/m3]") -plt.ylabel("Distance from transducer~[m]") -ax.set_xscale("log") -plt.xlim([0.5 * C.min(), 2.5 * C.max()]) -plt.ylim([0, r.max()]) -ax.invert_yaxis() -secax = ax.secondary_xaxis("top", functions=(C_to_phi, phi_to_C)) -secax.set_xlabel("Volumic fraction") -plt.legend(title="Distance of imposed concentration [mm]") -plt.title("Without near field") - -# #### with near field function -psi = DM.near_field_theoretical(r, rn) # near field function -# defining a constant grain concentration profile -C = Phi[:, None] * rho * (r[None, :] * 0 + 1) -MSV = DM.create_MSvoltage(C, r[None, :], Xi, a_w, Ks, Kt, psi[None, :]) -# -color = [] -fig, ax = plt.subplots( - 1, 1, figsize=(fig_width_small, fig_width_small), constrained_layout=True -) -for i, phi in enumerate(Phi): - if i == 0: - a = plt.plot(C[i, :], r, lw=4, alpha=0.3, label="imposed") - else: - a = plt.plot(C[i, :], r, lw=4, alpha=0.3) - color.append(a[0].get_color()) -for j, index in enumerate(indexes): - C0 = C[:, index] - r0 = r[index] - C_inferred = explicit_inversion(MSV, r, Xi, a_w, psi * 0 + 1, C0, r0) - for i, phi in enumerate(Phi): - if i == 0: - plt.plot( - C_inferred[i, :], r, lw=2.5 - (j + 1) / 3, label=str(r0), color=color[i] - ) - else: - plt.plot(C_inferred[i, :], r, lw=2.5 - (j + 1) / 3, color=color[i]) -plt.xlabel("Concentration~[kg/m3]") -plt.ylabel("Distance from transducer~[m]") -ax.set_xscale("log") -plt.xlim([0.5 * C.min(), 2.5 * C.max()]) -plt.ylim([0, r.max()]) -ax.invert_yaxis() -secax = ax.secondary_xaxis("top", functions=(C_to_phi, phi_to_C)) -secax.set_xlabel("Volumic fraction") -plt.legend(title="Distance of imposed concentration [mm]") -plt.title("With near field") - -# #### with real type concentration profiles -psi = DM.near_field_theoretical(r, rn) # near field function -# C = Phi[:, None]*rho*np.exp(-r[None, :]/1) # defining an exponentially decreasing profile -# C = Phi[:, None]*rho*np.exp(r[None, :]/10) # defining an exponentially increasing profile -C = Phi[:, None] * rho * (r[None, :] * 0 + 1) # defining sedimentation-like profile -C[..., :230] = 0 -# -MSV = DM.create_MSvoltage(C, r[None, :], Xi, a_w, Ks, Kt, psi[None, :]) -# -color = [] -fig, ax = plt.subplots( - 1, 1, figsize=(fig_width_small, fig_width_small), constrained_layout=True -) -for i, phi in enumerate(Phi): - if i == 0: - a = plt.plot(C[i, :], r, lw=4, alpha=0.3, label="imposed") - else: - a = plt.plot(C[i, :], r, lw=4, alpha=0.3) - color.append(a[0].get_color()) -for j, index in enumerate(indexes): - C0 = C[:, index] - r0 = r[index] - C_inferred = explicit_inversion(MSV, r, Xi, a_w, psi * 0 + 1, C0, r0) - for i, phi in enumerate(Phi): - if i == 0: - plt.plot( - C_inferred[i, :], r, lw=2.5 - (j + 1) / 3, label=str(r0), color=color[i] - ) - else: - plt.plot(C_inferred[i, :], r, lw=2.5 - (j + 1) / 3, color=color[i]) -plt.xlabel("Concentration~[kg/m3]") -plt.ylabel("Distance from transducer~[m]") -ax.set_xscale("log") -plt.xlim([0.2 * C[:, -1].min(), 2.5 * C.max()]) -plt.ylim([0, r.max()]) -ax.invert_yaxis() -secax = ax.secondary_xaxis("top", functions=(C_to_phi, phi_to_C)) -secax.set_xlabel("Volumic fraction") -plt.legend(title="Distance of imposed concentration [mm]") -plt.title("With exponential concentration profiles") - - -plt.show() diff --git a/docs/_examples/plot_direct_inversion.py.md5 b/docs/_examples/plot_direct_inversion.py.md5 deleted file mode 100644 index 92ec763..0000000 --- a/docs/_examples/plot_direct_inversion.py.md5 +++ /dev/null @@ -1 +0,0 @@ -e64cb93851d90dc93dee9c7f98db6cba \ No newline at end of file diff --git a/docs/_examples/plot_direct_inversion.rst b/docs/_examples/plot_direct_inversion.rst deleted file mode 100644 index c764e03..0000000 --- a/docs/_examples/plot_direct_inversion.rst +++ /dev/null @@ -1,289 +0,0 @@ - -.. DO NOT EDIT. -.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. -.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: -.. "_examples/plot_direct_inversion.py" -.. LINE NUMBERS ARE GIVEN BELOW. - -.. only:: html - - .. note:: - :class: sphx-glr-download-link-note - - :ref:`Go to the end ` - to download the full example code - -.. rst-class:: sphx-glr-example-title - -.. _sphx_glr__examples_plot_direct_inversion.py: - - -============================================== -Concentration inference from amplitude signals -============================================== - -.. GENERATED FROM PYTHON SOURCE LINES 6-25 - -.. code-block:: default - - - import matplotlib.pyplot as plt - import numpy as np - - import pyudv.amplitude.direct_models as DM - from pyudv.amplitude.inversion import explicit_inversion - from pyudv.amplitude.sediment_acoustic_models import quartz_sand as quartz - - - def C_to_phi(C, rho=2.65e3): - return C / rho - - - def phi_to_C(phi, rho=2.65e3): - return phi * rho - - - fig_width_small = 11.25 - - - - - - - - -.. GENERATED FROM PYTHON SOURCE LINES 26-28 - -Define the parameters for the direct model -========================================== - -.. GENERATED FROM PYTHON SOURCE LINES 28-47 - -.. code-block:: default - - - d = 100e-6 # grain mean diameter [m] - rho = 2.65 # grain density [g/cm3] - rho = rho * 1e-3 / 1e-6 # grain density [kg/m3] - - F = 2e6 # frequency [Hz] - T = 20 # Temperature [Celsius degrees] - a_w = DM.alpha_w(F, T) # water absorption, [m-1] - k = 2 * np.pi * F / DM.sound_velocity(T) # wavenumber of the wave - - Ks, Kt = 1, 1 # sediment and transducer constants - Xi = quartz.Xi(k, d / 2) # sediment attenuation constant - rn = 0.05 # near field distance [cm] - r = np.linspace(0.001, 12, 330) # radial coordinates [cm] - - # Volumic fraction of grain - Phi = np.array([0.0001, 0.002, 0.005, 0.01, 0.02, 0.05, 0.1]) - - - - - - - - - -.. GENERATED FROM PYTHON SOURCE LINES 48-50 - -Influence of the imposed point in the integration -================================================= - -.. GENERATED FROM PYTHON SOURCE LINES 50-172 - -.. code-block:: default - - - # #### without near field function - psi = DM.near_field_theoretical(r, rn) * 0 + 1 # near field function - # defining a constant grain concentration profile - C = Phi[:, None] * rho * (r[None, :] * 0 + 1) - MSV = DM.create_MSvoltage(C, r, Xi, a_w, Ks, Kt, psi) - # - indexes = [2, 50, 150, 250, 320] - - color = [] - fig, ax = plt.subplots( - 1, 1, figsize=(fig_width_small, fig_width_small), constrained_layout=True - ) - for i, phi in enumerate(Phi): - if i == 0: - a = plt.plot(C[i, :], r, lw=4, alpha=0.3, label="imposed") - else: - a = plt.plot(C[i, :], r, lw=4, alpha=0.3) - color.append(a[0].get_color()) - for j, index in enumerate(indexes): - C0 = C[:, index] - r0 = r[index] - C_inferred = explicit_inversion(MSV, r, Xi, a_w, psi, C0, r0) - for i, phi in enumerate(Phi): - if i == 0: - plt.plot( - C_inferred[i, :], r, lw=2.5 - (j + 1) / 3, label=str(r0), color=color[i] - ) - else: - plt.plot(C_inferred[i, :], r, lw=2.5 - (j + 1) / 3, color=color[i]) - plt.xlabel("Concentration~[kg/m3]") - plt.ylabel("Distance from transducer~[m]") - ax.set_xscale("log") - plt.xlim([0.5 * C.min(), 2.5 * C.max()]) - plt.ylim([0, r.max()]) - ax.invert_yaxis() - secax = ax.secondary_xaxis("top", functions=(C_to_phi, phi_to_C)) - secax.set_xlabel("Volumic fraction") - plt.legend(title="Distance of imposed concentration [mm]") - plt.title("Without near field") - - # #### with near field function - psi = DM.near_field_theoretical(r, rn) # near field function - # defining a constant grain concentration profile - C = Phi[:, None] * rho * (r[None, :] * 0 + 1) - MSV = DM.create_MSvoltage(C, r[None, :], Xi, a_w, Ks, Kt, psi[None, :]) - # - color = [] - fig, ax = plt.subplots( - 1, 1, figsize=(fig_width_small, fig_width_small), constrained_layout=True - ) - for i, phi in enumerate(Phi): - if i == 0: - a = plt.plot(C[i, :], r, lw=4, alpha=0.3, label="imposed") - else: - a = plt.plot(C[i, :], r, lw=4, alpha=0.3) - color.append(a[0].get_color()) - for j, index in enumerate(indexes): - C0 = C[:, index] - r0 = r[index] - C_inferred = explicit_inversion(MSV, r, Xi, a_w, psi * 0 + 1, C0, r0) - for i, phi in enumerate(Phi): - if i == 0: - plt.plot( - C_inferred[i, :], r, lw=2.5 - (j + 1) / 3, label=str(r0), color=color[i] - ) - else: - plt.plot(C_inferred[i, :], r, lw=2.5 - (j + 1) / 3, color=color[i]) - plt.xlabel("Concentration~[kg/m3]") - plt.ylabel("Distance from transducer~[m]") - ax.set_xscale("log") - plt.xlim([0.5 * C.min(), 2.5 * C.max()]) - plt.ylim([0, r.max()]) - ax.invert_yaxis() - secax = ax.secondary_xaxis("top", functions=(C_to_phi, phi_to_C)) - secax.set_xlabel("Volumic fraction") - plt.legend(title="Distance of imposed concentration [mm]") - plt.title("With near field") - - # #### with real type concentration profiles - psi = DM.near_field_theoretical(r, rn) # near field function - # C = Phi[:, None]*rho*np.exp(-r[None, :]/1) # defining an exponentially decreasing profile - # C = Phi[:, None]*rho*np.exp(r[None, :]/10) # defining an exponentially increasing profile - C = Phi[:, None] * rho * (r[None, :] * 0 + 1) # defining sedimentation-like profile - C[..., :230] = 0 - # - MSV = DM.create_MSvoltage(C, r[None, :], Xi, a_w, Ks, Kt, psi[None, :]) - # - color = [] - fig, ax = plt.subplots( - 1, 1, figsize=(fig_width_small, fig_width_small), constrained_layout=True - ) - for i, phi in enumerate(Phi): - if i == 0: - a = plt.plot(C[i, :], r, lw=4, alpha=0.3, label="imposed") - else: - a = plt.plot(C[i, :], r, lw=4, alpha=0.3) - color.append(a[0].get_color()) - for j, index in enumerate(indexes): - C0 = C[:, index] - r0 = r[index] - C_inferred = explicit_inversion(MSV, r, Xi, a_w, psi * 0 + 1, C0, r0) - for i, phi in enumerate(Phi): - if i == 0: - plt.plot( - C_inferred[i, :], r, lw=2.5 - (j + 1) / 3, label=str(r0), color=color[i] - ) - else: - plt.plot(C_inferred[i, :], r, lw=2.5 - (j + 1) / 3, color=color[i]) - plt.xlabel("Concentration~[kg/m3]") - plt.ylabel("Distance from transducer~[m]") - ax.set_xscale("log") - plt.xlim([0.2 * C[:, -1].min(), 2.5 * C.max()]) - plt.ylim([0, r.max()]) - ax.invert_yaxis() - secax = ax.secondary_xaxis("top", functions=(C_to_phi, phi_to_C)) - secax.set_xlabel("Volumic fraction") - plt.legend(title="Distance of imposed concentration [mm]") - plt.title("With exponential concentration profiles") - - - plt.show() - - - -.. rst-class:: sphx-glr-horizontal - - - * - - .. image-sg:: /_examples/images/sphx_glr_plot_direct_inversion_001.png - :alt: Without near field - :srcset: /_examples/images/sphx_glr_plot_direct_inversion_001.png - :class: sphx-glr-multi-img - - * - - .. image-sg:: /_examples/images/sphx_glr_plot_direct_inversion_002.png - :alt: With near field - :srcset: /_examples/images/sphx_glr_plot_direct_inversion_002.png - :class: sphx-glr-multi-img - - * - - .. image-sg:: /_examples/images/sphx_glr_plot_direct_inversion_003.png - :alt: With exponential concentration profiles - :srcset: /_examples/images/sphx_glr_plot_direct_inversion_003.png - :class: sphx-glr-multi-img - - -.. rst-class:: sphx-glr-script-out - - .. code-block:: none - - /home/cyril/Documents/Work/Research/Codes/python_libs/custom/pyudv/pyudv/amplitude/inversion.py:12: RuntimeWarning: divide by zero encountered in divide - return f / (B - 4 * Xi * integral) - /home/cyril/Documents/Work/Research/Codes/python_libs/custom/pyudv/pyudv/amplitude/inversion.py:42: RuntimeWarning: invalid value encountered in divide - B = constant_MSV / C0_expanded + 4 * Xi * constant_int - - - - - -.. rst-class:: sphx-glr-timing - - **Total running time of the script:** ( 0 minutes 3.661 seconds) - - -.. _sphx_glr_download__examples_plot_direct_inversion.py: - -.. only:: html - - .. container:: sphx-glr-footer sphx-glr-footer-example - - - - - .. container:: sphx-glr-download sphx-glr-download-python - - :download:`Download Python source code: plot_direct_inversion.py ` - - .. container:: sphx-glr-download sphx-glr-download-jupyter - - :download:`Download Jupyter notebook: plot_direct_inversion.ipynb ` - - -.. only:: html - - .. rst-class:: sphx-glr-signature - - `Gallery generated by Sphinx-Gallery `_ diff --git a/docs/_examples/plot_direct_inversion_codeobj.pickle b/docs/_examples/plot_direct_inversion_codeobj.pickle deleted file mode 100644 index e22afce..0000000 Binary files a/docs/_examples/plot_direct_inversion_codeobj.pickle and /dev/null differ diff --git a/docs/_examples/plot_read_plot_mfprof_data.ipynb b/docs/_examples/plot_read_plot_mfprof_data.ipynb deleted file mode 100644 index e3eb427..0000000 --- a/docs/_examples/plot_read_plot_mfprof_data.ipynb +++ /dev/null @@ -1,43 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "\n# Read and plot .mfprof data\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "import matplotlib.colors as colors\nimport matplotlib.pyplot as plt\nimport numpy as np\n\nfrom pyudv.read_mfprof import (\n amplitude_from_mfprof_reading,\n read_mfprof,\n velocity_from_mfprof_reading,\n)\n\n#\npath_data = \"src/data_sample.mfprof\"\n\n# #### Loading data\nData, Parameters, Info, Units = read_mfprof(path_data)\nAmplitude_data = amplitude_from_mfprof_reading(Data, Parameters)\nVelocity_data = velocity_from_mfprof_reading(Data, Parameters)\ntime = Data[\"profileTime\"]\nz_coordinates = Data[\"DistanceAlongBeam\"] * 1e2\nindmax_time = np.argwhere(Data[\"transducer\"] == 0)[1][0] - 1\nindmax_z = -1\nind_bottom = 572\n\n# #### plotting velocity\ndivnorm = colors.TwoSlopeNorm(vcenter=0, vmin=-0.2, vmax=0.2)\nfig, ax = plt.subplots(1, 1, constrained_layout=True)\nc = ax.pcolormesh(\n time[:indmax_time],\n z_coordinates[:indmax_z],\n Velocity_data[:indmax_z, :indmax_time],\n cmap=\"PuOr\",\n norm=divnorm,\n rasterized=True,\n shading=\"auto\",\n)\nax.axhline(y=z_coordinates[ind_bottom], color=\"k\", lw=\"0.5\", ls=\"--\")\nax.invert_yaxis()\nfig.colorbar(c, label=\"Velocity [m/s]\")\nax.set_xlabel(\"Time [s]\")\nax.set_ylabel(\"DistanceAlongBeam [cm]\")\n# fig.draw_without_rendering()\nplt.savefig(\"plots/Spatio_temporal_velocity.pdf\", dpi=600)\nplt.show()\n\n# #### plotting amplitude\ndivnorm = colors.TwoSlopeNorm(vcenter=0, vmin=-0.1, vmax=0.1)\nfig, ax = plt.subplots(1, 1, constrained_layout=True)\nc = ax.pcolormesh(\n time[:indmax_time],\n z_coordinates[:indmax_z],\n Amplitude_data[:indmax_z, :indmax_time],\n rasterized=True,\n shading=\"auto\",\n cmap=\"PuOr\",\n norm=divnorm,\n)\nax.axhline(y=z_coordinates[ind_bottom], color=\"k\", lw=\"0.5\", ls=\"--\")\nax.invert_yaxis()\nfig.colorbar(c, label=\"Amplitude [V]\")\nax.set_xlabel(\"Time [s]\")\nax.set_ylabel(\"DistanceAlongBeam [cm]\")\nplt.savefig(\"plots/Spatio_temporal_amplitude.pdf\", dpi=600)\nplt.show()" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.12" - } - }, - "nbformat": 4, - "nbformat_minor": 0 -} \ No newline at end of file diff --git a/docs/_examples/plot_read_plot_mfprof_data.py b/docs/_examples/plot_read_plot_mfprof_data.py deleted file mode 100644 index 8c6b60a..0000000 --- a/docs/_examples/plot_read_plot_mfprof_data.py +++ /dev/null @@ -1,69 +0,0 @@ -""" -========================== -Read and plot .mfprof data -========================== -""" - -import matplotlib.colors as colors -import matplotlib.pyplot as plt -import numpy as np - -from pyudv.read_mfprof import ( - amplitude_from_mfprof_reading, - read_mfprof, - velocity_from_mfprof_reading, -) - -# -path_data = "src/data_sample.mfprof" - -# #### Loading data -Data, Parameters, Info, Units = read_mfprof(path_data) -Amplitude_data = amplitude_from_mfprof_reading(Data, Parameters) -Velocity_data = velocity_from_mfprof_reading(Data, Parameters) -time = Data["profileTime"] -z_coordinates = Data["DistanceAlongBeam"] * 1e2 -indmax_time = np.argwhere(Data["transducer"] == 0)[1][0] - 1 -indmax_z = -1 -ind_bottom = 572 - -# #### plotting velocity -divnorm = colors.TwoSlopeNorm(vcenter=0, vmin=-0.2, vmax=0.2) -fig, ax = plt.subplots(1, 1, constrained_layout=True) -c = ax.pcolormesh( - time[:indmax_time], - z_coordinates[:indmax_z], - Velocity_data[:indmax_z, :indmax_time], - cmap="PuOr", - norm=divnorm, - rasterized=True, - shading="auto", -) -ax.axhline(y=z_coordinates[ind_bottom], color="k", lw="0.5", ls="--") -ax.invert_yaxis() -fig.colorbar(c, label="Velocity [m/s]") -ax.set_xlabel("Time [s]") -ax.set_ylabel("DistanceAlongBeam [cm]") -# fig.draw_without_rendering() -plt.savefig("plots/Spatio_temporal_velocity.pdf", dpi=600) -plt.show() - -# #### plotting amplitude -divnorm = colors.TwoSlopeNorm(vcenter=0, vmin=-0.1, vmax=0.1) -fig, ax = plt.subplots(1, 1, constrained_layout=True) -c = ax.pcolormesh( - time[:indmax_time], - z_coordinates[:indmax_z], - Amplitude_data[:indmax_z, :indmax_time], - rasterized=True, - shading="auto", - cmap="PuOr", - norm=divnorm, -) -ax.axhline(y=z_coordinates[ind_bottom], color="k", lw="0.5", ls="--") -ax.invert_yaxis() -fig.colorbar(c, label="Amplitude [V]") -ax.set_xlabel("Time [s]") -ax.set_ylabel("DistanceAlongBeam [cm]") -plt.savefig("plots/Spatio_temporal_amplitude.pdf", dpi=600) -plt.show() diff --git a/docs/_examples/plot_read_plot_mfprof_data.py.md5 b/docs/_examples/plot_read_plot_mfprof_data.py.md5 deleted file mode 100644 index 939c6be..0000000 --- a/docs/_examples/plot_read_plot_mfprof_data.py.md5 +++ /dev/null @@ -1 +0,0 @@ -52bdb84aa34da29b0801b00a7d51fc57 \ No newline at end of file diff --git a/docs/_examples/plot_read_plot_mfprof_data.rst b/docs/_examples/plot_read_plot_mfprof_data.rst deleted file mode 100644 index 1e7cb5d..0000000 --- a/docs/_examples/plot_read_plot_mfprof_data.rst +++ /dev/null @@ -1,145 +0,0 @@ - -.. DO NOT EDIT. -.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. -.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: -.. "_examples/plot_read_plot_mfprof_data.py" -.. LINE NUMBERS ARE GIVEN BELOW. - -.. only:: html - - .. note:: - :class: sphx-glr-download-link-note - - :ref:`Go to the end ` - to download the full example code - -.. rst-class:: sphx-glr-example-title - -.. _sphx_glr__examples_plot_read_plot_mfprof_data.py: - - -========================== -Read and plot .mfprof data -========================== - -.. GENERATED FROM PYTHON SOURCE LINES 6-70 - - - -.. rst-class:: sphx-glr-horizontal - - - * - - .. image-sg:: /_examples/images/sphx_glr_plot_read_plot_mfprof_data_001.png - :alt: plot read plot mfprof data - :srcset: /_examples/images/sphx_glr_plot_read_plot_mfprof_data_001.png - :class: sphx-glr-multi-img - - * - - .. image-sg:: /_examples/images/sphx_glr_plot_read_plot_mfprof_data_002.png - :alt: plot read plot mfprof data - :srcset: /_examples/images/sphx_glr_plot_read_plot_mfprof_data_002.png - :class: sphx-glr-multi-img - - - - - -.. code-block:: default - - - import matplotlib.colors as colors - import matplotlib.pyplot as plt - import numpy as np - - from pyudv.read_mfprof import ( - amplitude_from_mfprof_reading, - read_mfprof, - velocity_from_mfprof_reading, - ) - - # - path_data = "src/data_sample.mfprof" - - # #### Loading data - Data, Parameters, Info, Units = read_mfprof(path_data) - Amplitude_data = amplitude_from_mfprof_reading(Data, Parameters) - Velocity_data = velocity_from_mfprof_reading(Data, Parameters) - time = Data["profileTime"] - z_coordinates = Data["DistanceAlongBeam"] * 1e2 - indmax_time = np.argwhere(Data["transducer"] == 0)[1][0] - 1 - indmax_z = -1 - ind_bottom = 572 - - # #### plotting velocity - divnorm = colors.TwoSlopeNorm(vcenter=0, vmin=-0.2, vmax=0.2) - fig, ax = plt.subplots(1, 1, constrained_layout=True) - c = ax.pcolormesh( - time[:indmax_time], - z_coordinates[:indmax_z], - Velocity_data[:indmax_z, :indmax_time], - cmap="PuOr", - norm=divnorm, - rasterized=True, - shading="auto", - ) - ax.axhline(y=z_coordinates[ind_bottom], color="k", lw="0.5", ls="--") - ax.invert_yaxis() - fig.colorbar(c, label="Velocity [m/s]") - ax.set_xlabel("Time [s]") - ax.set_ylabel("DistanceAlongBeam [cm]") - # fig.draw_without_rendering() - plt.savefig("plots/Spatio_temporal_velocity.pdf", dpi=600) - plt.show() - - # #### plotting amplitude - divnorm = colors.TwoSlopeNorm(vcenter=0, vmin=-0.1, vmax=0.1) - fig, ax = plt.subplots(1, 1, constrained_layout=True) - c = ax.pcolormesh( - time[:indmax_time], - z_coordinates[:indmax_z], - Amplitude_data[:indmax_z, :indmax_time], - rasterized=True, - shading="auto", - cmap="PuOr", - norm=divnorm, - ) - ax.axhline(y=z_coordinates[ind_bottom], color="k", lw="0.5", ls="--") - ax.invert_yaxis() - fig.colorbar(c, label="Amplitude [V]") - ax.set_xlabel("Time [s]") - ax.set_ylabel("DistanceAlongBeam [cm]") - plt.savefig("plots/Spatio_temporal_amplitude.pdf", dpi=600) - plt.show() - - -.. rst-class:: sphx-glr-timing - - **Total running time of the script:** ( 0 minutes 3.690 seconds) - - -.. _sphx_glr_download__examples_plot_read_plot_mfprof_data.py: - -.. only:: html - - .. container:: sphx-glr-footer sphx-glr-footer-example - - - - - .. container:: sphx-glr-download sphx-glr-download-python - - :download:`Download Python source code: plot_read_plot_mfprof_data.py ` - - .. container:: sphx-glr-download sphx-glr-download-jupyter - - :download:`Download Jupyter notebook: plot_read_plot_mfprof_data.ipynb ` - - -.. only:: html - - .. rst-class:: sphx-glr-signature - - `Gallery generated by Sphinx-Gallery `_ diff --git a/docs/_examples/plot_read_plot_mfprof_data_codeobj.pickle b/docs/_examples/plot_read_plot_mfprof_data_codeobj.pickle deleted file mode 100644 index d629d4c..0000000 Binary files a/docs/_examples/plot_read_plot_mfprof_data_codeobj.pickle and /dev/null differ diff --git a/docs/_examples/plot_reconstruct_velocity.ipynb b/docs/_examples/plot_reconstruct_velocity.ipynb deleted file mode 100644 index d494765..0000000 --- a/docs/_examples/plot_reconstruct_velocity.ipynb +++ /dev/null @@ -1,97 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "\n# Probes and velocity reconstruction\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "import matplotlib.pyplot as plt\nimport numpy as np\n\nfrom pyudv import reconstruct_velocity\nfrom pyudv.probes import Probe, sketch_probes\n\n\ndef U(z):\n u = 5 * (5 - z) ** 2\n v = u / 10\n U = np.array([u, v])\n return U" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Define probes and plot them\n\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "# define probes\nr = np.linspace(0, 5, 100)\nalpha1, alpha2 = -120, -70 # deg\nO1, O2 = np.array([1, 8]), np.array([-1, 7])\nprobe1_pars = [r, alpha1, [0, O1]]\nprobe2_pars = [r, alpha2, [0, O2]]\n#\nprobe1 = Probe(*probe1_pars)\nprobe2 = Probe(*probe2_pars)\n\nfig, ax = plt.subplots(1, 1, layout=\"constrained\")\nsketch_probes(\n [probe1, probe2],\n combinations=[[0, 1]],\n probe_colors=[None, None],\n combination_colors=[\"k\"],\n ax=ax,\n)\nax.set_xlabel(\"x\")\nax.set_ylabel(\"y\")\nplt.show()" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Create fake signal\n\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "u1 = U(probe1.z).T @ probe1.unit_vec\nu2 = U(probe2.z).T @ probe2.unit_vec\n#" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Velocity reconstruction\n\n" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "U_rec, z_interp, X, dx_1, dx_2 = reconstruct_velocity(u1, u2, probe1_pars, probe2_pars)\nU_th = U(z_interp)\n#\nfig, axarr = plt.subplots(1, 3, layout=\"constrained\", sharey=True)\nfor ax, u_th, u_rec in zip(axarr, U_th, U_rec):\n ax.plot(u_th, z_interp, \".\", label=\"base\")\n ax.plot(u_rec, z_interp, \".\", label=\"reconstructed\")\n ax.legend()\naxarr[0].set_xlabel(\"u\")\naxarr[1].set_xlabel(\"v\")\naxarr[0].set_ylabel(\"z\")\nplt.show()" - ] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.12" - } - }, - "nbformat": 4, - "nbformat_minor": 0 -} \ No newline at end of file diff --git a/docs/_examples/plot_reconstruct_velocity.py b/docs/_examples/plot_reconstruct_velocity.py deleted file mode 100644 index bc6545f..0000000 --- a/docs/_examples/plot_reconstruct_velocity.py +++ /dev/null @@ -1,70 +0,0 @@ -""" -================================== -Probes and velocity reconstruction -================================== -""" - -import matplotlib.pyplot as plt -import numpy as np - -from pyudv import reconstruct_velocity -from pyudv.probes import Probe, sketch_probes - - -def U(z): - u = 5 * (5 - z) ** 2 - v = u / 10 - U = np.array([u, v]) - return U - - -# %% -# Define probes and plot them -# =========================== - -# define probes -r = np.linspace(0, 5, 100) -alpha1, alpha2 = -120, -70 # deg -O1, O2 = np.array([1, 8]), np.array([-1, 7]) -probe1_pars = [r, alpha1, [0, O1]] -probe2_pars = [r, alpha2, [0, O2]] -# -probe1 = Probe(*probe1_pars) -probe2 = Probe(*probe2_pars) - -fig, ax = plt.subplots(1, 1, layout="constrained") -sketch_probes( - [probe1, probe2], - combinations=[[0, 1]], - probe_colors=[None, None], - combination_colors=["k"], - ax=ax, -) -ax.set_xlabel("x") -ax.set_ylabel("y") -plt.show() - -# %% -# Create fake signal -# ================== - -u1 = U(probe1.z).T @ probe1.unit_vec -u2 = U(probe2.z).T @ probe2.unit_vec -# - -# %% -# Velocity reconstruction -# ======================= - -U_rec, z_interp, X, dx_1, dx_2 = reconstruct_velocity(u1, u2, probe1_pars, probe2_pars) -U_th = U(z_interp) -# -fig, axarr = plt.subplots(1, 3, layout="constrained", sharey=True) -for ax, u_th, u_rec in zip(axarr, U_th, U_rec): - ax.plot(u_th, z_interp, ".", label="base") - ax.plot(u_rec, z_interp, ".", label="reconstructed") - ax.legend() -axarr[0].set_xlabel("u") -axarr[1].set_xlabel("v") -axarr[0].set_ylabel("z") -plt.show() diff --git a/docs/_examples/plot_reconstruct_velocity.py.md5 b/docs/_examples/plot_reconstruct_velocity.py.md5 deleted file mode 100644 index 917ac59..0000000 --- a/docs/_examples/plot_reconstruct_velocity.py.md5 +++ /dev/null @@ -1 +0,0 @@ -a2dfee472621fd03ecd0fadaaa24d645 \ No newline at end of file diff --git a/docs/_examples/plot_reconstruct_velocity.rst b/docs/_examples/plot_reconstruct_velocity.rst deleted file mode 100644 index 58527b4..0000000 --- a/docs/_examples/plot_reconstruct_velocity.rst +++ /dev/null @@ -1,178 +0,0 @@ - -.. DO NOT EDIT. -.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. -.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: -.. "_examples/plot_reconstruct_velocity.py" -.. LINE NUMBERS ARE GIVEN BELOW. - -.. only:: html - - .. note:: - :class: sphx-glr-download-link-note - - :ref:`Go to the end ` - to download the full example code - -.. rst-class:: sphx-glr-example-title - -.. _sphx_glr__examples_plot_reconstruct_velocity.py: - - -================================== -Probes and velocity reconstruction -================================== - -.. GENERATED FROM PYTHON SOURCE LINES 6-21 - -.. code-block:: default - - - import matplotlib.pyplot as plt - import numpy as np - - from pyudv import reconstruct_velocity - from pyudv.probes import Probe, sketch_probes - - - def U(z): - u = 5 * (5 - z) ** 2 - v = u / 10 - U = np.array([u, v]) - return U - - - - - - - - - -.. GENERATED FROM PYTHON SOURCE LINES 22-24 - -Define probes and plot them -=========================== - -.. GENERATED FROM PYTHON SOURCE LINES 24-47 - -.. code-block:: default - - - # define probes - r = np.linspace(0, 5, 100) - alpha1, alpha2 = -120, -70 # deg - O1, O2 = np.array([1, 8]), np.array([-1, 7]) - probe1_pars = [r, alpha1, [0, O1]] - probe2_pars = [r, alpha2, [0, O2]] - # - probe1 = Probe(*probe1_pars) - probe2 = Probe(*probe2_pars) - - fig, ax = plt.subplots(1, 1, layout="constrained") - sketch_probes( - [probe1, probe2], - combinations=[[0, 1]], - probe_colors=[None, None], - combination_colors=["k"], - ax=ax, - ) - ax.set_xlabel("x") - ax.set_ylabel("y") - plt.show() - - - - -.. image-sg:: /_examples/images/sphx_glr_plot_reconstruct_velocity_001.png - :alt: plot reconstruct velocity - :srcset: /_examples/images/sphx_glr_plot_reconstruct_velocity_001.png - :class: sphx-glr-single-img - - - - - -.. GENERATED FROM PYTHON SOURCE LINES 48-50 - -Create fake signal -================== - -.. GENERATED FROM PYTHON SOURCE LINES 50-55 - -.. code-block:: default - - - u1 = U(probe1.z).T @ probe1.unit_vec - u2 = U(probe2.z).T @ probe2.unit_vec - # - - - - - - - - -.. GENERATED FROM PYTHON SOURCE LINES 56-58 - -Velocity reconstruction -======================= - -.. GENERATED FROM PYTHON SOURCE LINES 58-71 - -.. code-block:: default - - - U_rec, z_interp, X, dx_1, dx_2 = reconstruct_velocity(u1, u2, probe1_pars, probe2_pars) - U_th = U(z_interp) - # - fig, axarr = plt.subplots(1, 3, layout="constrained", sharey=True) - for ax, u_th, u_rec in zip(axarr, U_th, U_rec): - ax.plot(u_th, z_interp, ".", label="base") - ax.plot(u_rec, z_interp, ".", label="reconstructed") - ax.legend() - axarr[0].set_xlabel("u") - axarr[1].set_xlabel("v") - axarr[0].set_ylabel("z") - plt.show() - - - -.. image-sg:: /_examples/images/sphx_glr_plot_reconstruct_velocity_002.png - :alt: plot reconstruct velocity - :srcset: /_examples/images/sphx_glr_plot_reconstruct_velocity_002.png - :class: sphx-glr-single-img - - - - - - -.. rst-class:: sphx-glr-timing - - **Total running time of the script:** ( 0 minutes 0.408 seconds) - - -.. _sphx_glr_download__examples_plot_reconstruct_velocity.py: - -.. only:: html - - .. container:: sphx-glr-footer sphx-glr-footer-example - - - - - .. container:: sphx-glr-download sphx-glr-download-python - - :download:`Download Python source code: plot_reconstruct_velocity.py ` - - .. container:: sphx-glr-download sphx-glr-download-jupyter - - :download:`Download Jupyter notebook: plot_reconstruct_velocity.ipynb ` - - -.. only:: html - - .. rst-class:: sphx-glr-signature - - `Gallery generated by Sphinx-Gallery `_ diff --git a/docs/_examples/plot_reconstruct_velocity_codeobj.pickle b/docs/_examples/plot_reconstruct_velocity_codeobj.pickle deleted file mode 100644 index 2d0e62a..0000000 Binary files a/docs/_examples/plot_reconstruct_velocity_codeobj.pickle and /dev/null differ diff --git a/docs/_examples/searchindex b/docs/_examples/searchindex deleted file mode 100644 index 0b91f34..0000000 Binary files a/docs/_examples/searchindex and /dev/null differ diff --git a/docs/_examples/sg_execution_times.rst b/docs/_examples/sg_execution_times.rst deleted file mode 100644 index 414e511..0000000 --- a/docs/_examples/sg_execution_times.rst +++ /dev/null @@ -1,17 +0,0 @@ - -:orphan: - -.. _sphx_glr__examples_sg_execution_times: - - -Computation times -================= -**00:04.069** total execution time for **_examples** files: - -+---------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr__examples_plot_direct_inversion.py` (``plot_direct_inversion.py``) | 00:03.661 | 0.0 MB | -+---------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr__examples_plot_reconstruct_velocity.py` (``plot_reconstruct_velocity.py``) | 00:00.408 | 0.0 MB | -+---------------------------------------------------------------------------------------------+-----------+--------+ -| :ref:`sphx_glr__examples_plot_read_plot_mfprof_data.py` (``plot_read_plot_mfprof_data.py``) | 00:00.000 | 0.0 MB | -+---------------------------------------------------------------------------------------------+-----------+--------+ diff --git a/docs/_gen_modules/backreferences/datetime.date.examples b/docs/_gen_modules/backreferences/datetime.date.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/datetime.time.examples b/docs/_gen_modules/backreferences/datetime.time.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.Probe.examples b/docs/_gen_modules/backreferences/pyudv.Probe.examples deleted file mode 100644 index a1b5fbe..0000000 --- a/docs/_gen_modules/backreferences/pyudv.Probe.examples +++ /dev/null @@ -1,39 +0,0 @@ - - -Examples using ``pyudv.Probe`` -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - - -.. start-sphx-glr-thumbnails - - -.. raw:: html - -
- - -.. raw:: html - -
- -.. only:: html - - .. image:: /_examples/images/thumb/sphx_glr_plot_reconstruct_velocity_thumb.png - :alt: - - :ref:`sphx_glr__examples_plot_reconstruct_velocity.py` - -.. raw:: html - -
Probes and velocity reconstruction
-
- - -.. only:: not html - - * :ref:`sphx_glr__examples_plot_reconstruct_velocity.py` - -.. raw:: html - -
- diff --git a/docs/_gen_modules/backreferences/pyudv.amplitude.direct_models.alpha_w.examples b/docs/_gen_modules/backreferences/pyudv.amplitude.direct_models.alpha_w.examples deleted file mode 100644 index abe9b2d..0000000 --- a/docs/_gen_modules/backreferences/pyudv.amplitude.direct_models.alpha_w.examples +++ /dev/null @@ -1,39 +0,0 @@ - - -Examples using ``pyudv.amplitude.direct_models.alpha_w`` -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - - -.. start-sphx-glr-thumbnails - - -.. raw:: html - -
- - -.. raw:: html - -
- -.. only:: html - - .. image:: /_examples/images/thumb/sphx_glr_plot_direct_inversion_thumb.png - :alt: - - :ref:`sphx_glr__examples_plot_direct_inversion.py` - -.. raw:: html - -
Concentration inference from amplitude signals
-
- - -.. only:: not html - - * :ref:`sphx_glr__examples_plot_direct_inversion.py` - -.. raw:: html - -
- diff --git a/docs/_gen_modules/backreferences/pyudv.amplitude.direct_models.correction_factor.examples b/docs/_gen_modules/backreferences/pyudv.amplitude.direct_models.correction_factor.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.amplitude.direct_models.create_MSvoltage.examples b/docs/_gen_modules/backreferences/pyudv.amplitude.direct_models.create_MSvoltage.examples deleted file mode 100644 index d175816..0000000 --- a/docs/_gen_modules/backreferences/pyudv.amplitude.direct_models.create_MSvoltage.examples +++ /dev/null @@ -1,39 +0,0 @@ - - -Examples using ``pyudv.amplitude.direct_models.create_MSvoltage`` -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - - -.. start-sphx-glr-thumbnails - - -.. raw:: html - -
- - -.. raw:: html - -
- -.. only:: html - - .. image:: /_examples/images/thumb/sphx_glr_plot_direct_inversion_thumb.png - :alt: - - :ref:`sphx_glr__examples_plot_direct_inversion.py` - -.. raw:: html - -
Concentration inference from amplitude signals
-
- - -.. only:: not html - - * :ref:`sphx_glr__examples_plot_direct_inversion.py` - -.. raw:: html - -
- diff --git a/docs/_gen_modules/backreferences/pyudv.amplitude.direct_models.cumulative_trapezoid.examples b/docs/_gen_modules/backreferences/pyudv.amplitude.direct_models.cumulative_trapezoid.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.amplitude.direct_models.examples b/docs/_gen_modules/backreferences/pyudv.amplitude.direct_models.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.amplitude.direct_models.near_field_theoretical.examples b/docs/_gen_modules/backreferences/pyudv.amplitude.direct_models.near_field_theoretical.examples deleted file mode 100644 index 063bb93..0000000 --- a/docs/_gen_modules/backreferences/pyudv.amplitude.direct_models.near_field_theoretical.examples +++ /dev/null @@ -1,39 +0,0 @@ - - -Examples using ``pyudv.amplitude.direct_models.near_field_theoretical`` -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - - -.. start-sphx-glr-thumbnails - - -.. raw:: html - -
- - -.. raw:: html - -
- -.. only:: html - - .. image:: /_examples/images/thumb/sphx_glr_plot_direct_inversion_thumb.png - :alt: - - :ref:`sphx_glr__examples_plot_direct_inversion.py` - -.. raw:: html - -
Concentration inference from amplitude signals
-
- - -.. only:: not html - - * :ref:`sphx_glr__examples_plot_direct_inversion.py` - -.. raw:: html - -
- diff --git a/docs/_gen_modules/backreferences/pyudv.amplitude.direct_models.sound_velocity.examples b/docs/_gen_modules/backreferences/pyudv.amplitude.direct_models.sound_velocity.examples deleted file mode 100644 index 8ddf2a6..0000000 --- a/docs/_gen_modules/backreferences/pyudv.amplitude.direct_models.sound_velocity.examples +++ /dev/null @@ -1,39 +0,0 @@ - - -Examples using ``pyudv.amplitude.direct_models.sound_velocity`` -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - - -.. start-sphx-glr-thumbnails - - -.. raw:: html - -
- - -.. raw:: html - -
- -.. only:: html - - .. image:: /_examples/images/thumb/sphx_glr_plot_direct_inversion_thumb.png - :alt: - - :ref:`sphx_glr__examples_plot_direct_inversion.py` - -.. raw:: html - -
Concentration inference from amplitude signals
-
- - -.. only:: not html - - * :ref:`sphx_glr__examples_plot_direct_inversion.py` - -.. raw:: html - -
- diff --git a/docs/_gen_modules/backreferences/pyudv.amplitude.examples b/docs/_gen_modules/backreferences/pyudv.amplitude.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.amplitude.inversion.correction_factor.examples b/docs/_gen_modules/backreferences/pyudv.amplitude.inversion.correction_factor.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.amplitude.inversion.cumulative_trapezoid.examples b/docs/_gen_modules/backreferences/pyudv.amplitude.inversion.cumulative_trapezoid.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.amplitude.inversion.examples b/docs/_gen_modules/backreferences/pyudv.amplitude.inversion.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.amplitude.inversion.explicit_inversion.examples b/docs/_gen_modules/backreferences/pyudv.amplitude.inversion.explicit_inversion.examples deleted file mode 100644 index 9a9b03d..0000000 --- a/docs/_gen_modules/backreferences/pyudv.amplitude.inversion.explicit_inversion.examples +++ /dev/null @@ -1,39 +0,0 @@ - - -Examples using ``pyudv.amplitude.inversion.explicit_inversion`` -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - - -.. start-sphx-glr-thumbnails - - -.. raw:: html - -
- - -.. raw:: html - -
- -.. only:: html - - .. image:: /_examples/images/thumb/sphx_glr_plot_direct_inversion_thumb.png - :alt: - - :ref:`sphx_glr__examples_plot_direct_inversion.py` - -.. raw:: html - -
Concentration inference from amplitude signals
-
- - -.. only:: not html - - * :ref:`sphx_glr__examples_plot_direct_inversion.py` - -.. raw:: html - -
- diff --git a/docs/_gen_modules/backreferences/pyudv.amplitude.inversion.trapezoid.examples b/docs/_gen_modules/backreferences/pyudv.amplitude.inversion.trapezoid.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.amplitude.sediment_acoustic_models.quartz_sand.Xi.examples b/docs/_gen_modules/backreferences/pyudv.amplitude.sediment_acoustic_models.quartz_sand.Xi.examples deleted file mode 100644 index eb82645..0000000 --- a/docs/_gen_modules/backreferences/pyudv.amplitude.sediment_acoustic_models.quartz_sand.Xi.examples +++ /dev/null @@ -1,39 +0,0 @@ - - -Examples using ``pyudv.amplitude.sediment_acoustic_models.quartz_sand.Xi`` -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - - -.. start-sphx-glr-thumbnails - - -.. raw:: html - -
- - -.. raw:: html - -
- -.. only:: html - - .. image:: /_examples/images/thumb/sphx_glr_plot_direct_inversion_thumb.png - :alt: - - :ref:`sphx_glr__examples_plot_direct_inversion.py` - -.. raw:: html - -
Concentration inference from amplitude signals
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- - -.. only:: not html - - * :ref:`sphx_glr__examples_plot_direct_inversion.py` - -.. raw:: html - -
- diff --git a/docs/_gen_modules/backreferences/pyudv.examples b/docs/_gen_modules/backreferences/pyudv.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.helpers.create_arboresence.examples b/docs/_gen_modules/backreferences/pyudv.helpers.create_arboresence.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.helpers.examples b/docs/_gen_modules/backreferences/pyudv.helpers.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.helpers.moving_std.examples b/docs/_gen_modules/backreferences/pyudv.helpers.moving_std.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.helpers.moving_std1d.examples b/docs/_gen_modules/backreferences/pyudv.helpers.moving_std1d.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.helpers.uniform_filter.examples b/docs/_gen_modules/backreferences/pyudv.helpers.uniform_filter.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.helpers.uniform_filter1d.examples b/docs/_gen_modules/backreferences/pyudv.helpers.uniform_filter1d.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.probes.Dummy.examples b/docs/_gen_modules/backreferences/pyudv.probes.Dummy.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.probes.Probe.examples b/docs/_gen_modules/backreferences/pyudv.probes.Probe.examples deleted file mode 100644 index f711c62..0000000 --- a/docs/_gen_modules/backreferences/pyudv.probes.Probe.examples +++ /dev/null @@ -1,39 +0,0 @@ - - -Examples using ``pyudv.probes.Probe`` -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - - -.. start-sphx-glr-thumbnails - - -.. raw:: html - -
- - -.. raw:: html - -
- -.. only:: html - - .. image:: /_examples/images/thumb/sphx_glr_plot_reconstruct_velocity_thumb.png - :alt: - - :ref:`sphx_glr__examples_plot_reconstruct_velocity.py` - -.. raw:: html - -
Probes and velocity reconstruction
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- - -.. only:: not html - - * :ref:`sphx_glr__examples_plot_reconstruct_velocity.py` - -.. raw:: html - -
- diff --git a/docs/_gen_modules/backreferences/pyudv.probes.Probe.plot_probe.examples b/docs/_gen_modules/backreferences/pyudv.probes.Probe.plot_probe.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.probes.compute_vertical_axis.examples b/docs/_gen_modules/backreferences/pyudv.probes.compute_vertical_axis.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.probes.examples b/docs/_gen_modules/backreferences/pyudv.probes.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.probes.probe_crossing_point.examples b/docs/_gen_modules/backreferences/pyudv.probes.probe_crossing_point.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.probes.sketch_probes.examples b/docs/_gen_modules/backreferences/pyudv.probes.sketch_probes.examples deleted file mode 100644 index 9af625d..0000000 --- a/docs/_gen_modules/backreferences/pyudv.probes.sketch_probes.examples +++ /dev/null @@ -1,39 +0,0 @@ - - -Examples using ``pyudv.probes.sketch_probes`` -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - - -.. start-sphx-glr-thumbnails - - -.. raw:: html - -
- - -.. raw:: html - -
- -.. only:: html - - .. image:: /_examples/images/thumb/sphx_glr_plot_reconstruct_velocity_thumb.png - :alt: - - :ref:`sphx_glr__examples_plot_reconstruct_velocity.py` - -.. raw:: html - -
Probes and velocity reconstruction
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- diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.close.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.close.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.cmptypes.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.cmptypes.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.createCompoundType.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.createCompoundType.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.createDimension.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.createDimension.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.createEnumType.examples 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html - -
- - -.. raw:: html - -
- -.. only:: html - - .. image:: /_examples/images/thumb/sphx_glr_plot_read_plot_mfprof_data_thumb.png - :alt: - - :ref:`sphx_glr__examples_plot_read_plot_mfprof_data.py` - -.. raw:: html - -
Read and plot .mfprof data
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- diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.create_variable.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.create_variable.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.__add__.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.__add__.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.astimezone.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.astimezone.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.combine.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.combine.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.ctime.examples 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b/docs/_gen_modules/backreferences/pyudv.read_mfprof.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.filetime_to_dt.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.filetime_to_dt.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.mfprof_to_netcdf.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.mfprof_to_netcdf.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.read_mfprof.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.read_mfprof.examples deleted file mode 100644 index e96e5e6..0000000 --- a/docs/_gen_modules/backreferences/pyudv.read_mfprof.read_mfprof.examples +++ /dev/null @@ -1,39 +0,0 @@ - - -Examples using ``pyudv.read_mfprof.read_mfprof`` -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - - -.. start-sphx-glr-thumbnails - - -.. raw:: html - -
- - -.. raw:: html - -
- -.. only:: html - - .. image:: /_examples/images/thumb/sphx_glr_plot_read_plot_mfprof_data_thumb.png - :alt: - - :ref:`sphx_glr__examples_plot_read_plot_mfprof_data.py` - -.. raw:: html - -
Read and plot .mfprof data
-
- - -.. only:: not html - - * :ref:`sphx_glr__examples_plot_read_plot_mfprof_data.py` - -.. raw:: html - -
- diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.timedelta.__add__.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.timedelta.__add__.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.timedelta.__mul__.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.timedelta.__mul__.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.timedelta.days.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.timedelta.days.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.timedelta.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.timedelta.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.timedelta.microseconds.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.timedelta.microseconds.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.timedelta.seconds.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.timedelta.seconds.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.timedelta.total_seconds.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.timedelta.total_seconds.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.velocity_from_UVPdata.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.velocity_from_UVPdata.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.velocity_from_mfprof_reading.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.velocity_from_mfprof_reading.examples deleted file mode 100644 index c5e38aa..0000000 --- a/docs/_gen_modules/backreferences/pyudv.read_mfprof.velocity_from_mfprof_reading.examples +++ /dev/null @@ -1,39 +0,0 @@ - - -Examples using ``pyudv.read_mfprof.velocity_from_mfprof_reading`` -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - - -.. start-sphx-glr-thumbnails - - -.. raw:: html - -
- - -.. raw:: html - -
- -.. only:: html - - .. image:: /_examples/images/thumb/sphx_glr_plot_read_plot_mfprof_data_thumb.png - :alt: - - :ref:`sphx_glr__examples_plot_read_plot_mfprof_data.py` - -.. raw:: html - -
Read and plot .mfprof data
-
- - -.. only:: not html - - * :ref:`sphx_glr__examples_plot_read_plot_mfprof_data.py` - -.. raw:: html - -
- diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.write_dictionnary.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.write_dictionnary.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.reconstruct_velocity.examples b/docs/_gen_modules/backreferences/pyudv.reconstruct_velocity.examples deleted file mode 100644 index a15351d..0000000 --- a/docs/_gen_modules/backreferences/pyudv.reconstruct_velocity.examples +++ /dev/null @@ -1,39 +0,0 @@ - - -Examples using ``pyudv.reconstruct_velocity`` -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - - -.. start-sphx-glr-thumbnails - - -.. raw:: html - -
- - -.. raw:: html - -
- -.. only:: html - - .. image:: /_examples/images/thumb/sphx_glr_plot_reconstruct_velocity_thumb.png - :alt: - - :ref:`sphx_glr__examples_plot_reconstruct_velocity.py` - -.. raw:: html - -
Probes and velocity reconstruction
-
- - -.. only:: not html - - * :ref:`sphx_glr__examples_plot_reconstruct_velocity.py` - -.. raw:: html - -
- diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.all.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.all.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.any.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.any.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.argmax.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.argmax.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.argmin.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.argmin.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.argpartition.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.argpartition.examples deleted 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b/docs/_gen_modules/backreferences/pyudv.velocity.reconstruct_velocity.examples deleted file mode 100644 index e69de29..0000000 diff --git a/docs/_static/pydata-custom.css b/docs/_static/pydata-custom.css index 4bba9cd..02bf321 100644 --- a/docs/_static/pydata-custom.css +++ b/docs/_static/pydata-custom.css @@ -15,3 +15,42 @@ p.rubric { border-bottom: 0px; } flex-grow: 1; max-width: 100%; } + + +/* from sphinx gallery*/ + +.wy-nav-top { + background-color: #FF8C38 !important; +} +.wy-side-nav-search { + background-color: #FF8C38 !important; +} + + +div[class^="highlight"] a { + background-color: #E6E6E6; +} + +div[class^="highlight"] a:hover { + background-color: #ABECFC; +} + +.rst-versions { + position: relative; +} +.rst-versions.shift-up { + overflow-y: visible; +} + +a[class^="sphx-glr-backref-module-"] { + text-decoration: none; + background-color: rgba(0, 0, 0, 0) !important; +} +a.sphx-glr-backref-module-sphinx_gallery { + text-decoration: underline; + background-color: #E6E6E6; +} + +.anim-state label { + display: inline-block; +} \ No newline at end of file diff --git a/docs/_templates/autosummary/attribute.rst b/docs/_templates/autosummary/attribute.rst new file mode 100644 index 0000000..1ea2a51 --- /dev/null +++ b/docs/_templates/autosummary/attribute.rst @@ -0,0 +1,7 @@ +:orphan: + +{{ fullname | escape | underline}} + +.. currentmodule:: {{ module }} + +attribute \ No newline at end of file diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst new file mode 100644 index 0000000..c9a046a --- /dev/null +++ b/docs/_templates/autosummary/class.rst @@ -0,0 +1,44 @@ +{{ fullname }} +{{ underline }} + +.. currentmodule:: {{ module }} + +.. autoclass:: {{ objname }} + + {% block methods %} + .. HACK -- the point here is that we don't want this to appear in the output, but the autosummary should still generate the pages. + .. autosummary:: + :toctree: + {% for item in all_methods %} + {%- if not item.startswith('_') or item in ['__call__', '__mul__', '__getitem__', '__len__'] %} + {{ name }}.{{ item }} + {%- endif -%} + {%- endfor %} + {% for item in inherited_members %} + {%- if item in ['__call__', '__mul__', '__getitem__', '__len__'] %} + {{ name }}.{{ item }} + {%- endif -%} + {%- endfor %} + {% endblock %} + + {% block attributes %} + {% if attributes %} + .. rubric:: {{ _('Attributes') }} + + .. autosummary:: + :toctree: + {% for item in all_attributes %} + {%- if not item.startswith('_') %} + {{ name }}.{{ item }} + {%- endif -%} + {%- endfor %} + {% endif %} + {% endblock %} + + + +.. _sphx_glr_backref_{{fullname}}: + +.. minigallery:: {{fullname}} + :add-heading: + diff --git a/docs/_templates/custom-function-template.rst b/docs/_templates/autosummary/function.rst similarity index 90% rename from docs/_templates/custom-function-template.rst rename to docs/_templates/autosummary/function.rst index 934304e..5b2a51c 100644 --- a/docs/_templates/custom-function-template.rst +++ b/docs/_templates/autosummary/function.rst @@ -7,4 +7,4 @@ .. _sphx_glr_backreferences_{{ fullname }}: .. minigallery:: {{ fullname }} - :add-heading: + :add-heading: \ No newline at end of file diff --git a/docs/_templates/autosummary/method.rst b/docs/_templates/autosummary/method.rst new file mode 100644 index 0000000..3cd8cbc --- /dev/null +++ b/docs/_templates/autosummary/method.rst @@ -0,0 +1,10 @@ +{{ fullname | escape | underline}} + +.. currentmodule:: {{ module }} + +.. automethod:: {{ objname }} + +.. _sphx_glr_backref_{{fullname}}: + +.. minigallery:: {{fullname}} + :add-heading: \ No newline at end of file diff --git a/docs/_templates/custom-module-template.rst b/docs/_templates/autosummary/module.rst similarity index 90% rename from docs/_templates/custom-module-template.rst rename to docs/_templates/autosummary/module.rst index f8df867..64c51fa 100644 --- a/docs/_templates/custom-module-template.rst +++ b/docs/_templates/autosummary/module.rst @@ -8,7 +8,6 @@ .. autosummary:: :toctree: - :template: custom-module-template.rst :recursive: {% for item in modules %} {{ item }} @@ -34,7 +33,6 @@ .. autosummary:: :toctree: - :template: custom-function-template.rst :nosignatures: {% for item in functions %} {{ item }} @@ -48,7 +46,6 @@ .. autosummary:: :toctree: - :template: custom-class-template.rst :nosignatures: {% for item in classes %} {{ item }} diff --git a/docs/_templates/custom-class-template.rst b/docs/_templates/custom-class-template.rst deleted file mode 100644 index 91b5996..0000000 --- a/docs/_templates/custom-class-template.rst +++ /dev/null @@ -1,33 +0,0 @@ -{{ fullname | escape | underline}} - -.. currentmodule:: {{ module }} - -.. autoclass:: {{ objname }} - :show-inheritance: - :inherited-members: - :special-members: __call__, __add__, __mul__ - - {% block methods %} - {% if methods %} - .. rubric:: {{ _('Methods') }} - - .. autosummary:: - :toctree: - {% for item in methods %} - {%- if not item.startswith('_') %} - ~{{ name }}.{{ item }} - {%- endif -%} - {%- endfor %} - {% endif %} - {% endblock %} - - {% block attributes %} - {% if attributes %} - .. rubric:: {{ _('Attributes') }} - - .. autosummary:: - {% for item in attributes %} - ~{{ name }}.{{ item }} - {%- endfor %} - {% endif %} - {% endblock %} diff --git a/docs/api.rst b/docs/api.rst index 7e7eee1..81386f8 100644 --- a/docs/api.rst +++ b/docs/api.rst @@ -1,6 +1,5 @@ .. autosummary:: :toctree: _autosummary - :template: custom-module-template.rst :recursive: pyudv diff --git a/docs/conf.py b/docs/conf.py index 83f27d7..dae2ac8 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -47,7 +47,6 @@ autosummary_generate = True # Turn on sphinx.ext.autosummary autosummary_imported_members = True # Also dosuments imports in __init__.py -autoclass_content = "both" # Add __init__ doc (ie. params) to class summaries # Remove 'view source code' from top of page (for html, not python) html_show_sourcelink = False autodoc_inherit_docstrings = True # If no docstring, inherit from base class @@ -57,6 +56,9 @@ # autodoc_typehints = "description" # Sphinx-native method. Not as good as sphinx_autodoc_typehints add_module_names = False # Remove namespaces from class/method signatures +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = "sphinx" +highlight_language = "python3" templates_path = ["_templates"] exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] @@ -67,7 +69,7 @@ "python": ("https://docs.python.org/{.major}".format(sys.version_info), None), "numpy": ("https://numpy.org/doc/stable/", None), "matplotlib": ("https://matplotlib.org/stable", None), - "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None), + "scipy": ("https://docs.scipy.org/doc/scipy/", None), } examples_dirs = ["../examples"] @@ -83,7 +85,7 @@ "reference_url": { "pyudv": None, # The module you locally document uses None "numpy": "https://docs.scipy.org/doc/numpy/", - "scipy": "https://docs.scipy.org/doc/scipy/reference/", + "scipy": "https://docs.scipy.org/doc/scipy/", "matplotlib": "https://matplotlib.org/stable", }, "matplotlib_animations": True, @@ -102,6 +104,7 @@ "logo": { "text": "pyudv", }, + "github_url": "https://github.com/cgadal-pythonpackages/pyudv", } html_static_path = ["_static"] diff --git a/examples/plot_reconstruct_velocity.py b/examples/plot_reconstruct_velocity.py index 357ee24..d7da3e1 100644 --- a/examples/plot_reconstruct_velocity.py +++ b/examples/plot_reconstruct_velocity.py @@ -7,7 +7,7 @@ import matplotlib.pyplot as plt import numpy as np -from pyudv import reconstruct_velocity +from pyudv.velocity import reconstruct_velocity from pyudv.probes import Probe, sketch_probes @@ -36,7 +36,6 @@ def U(z): sketch_probes( [probe1, probe2], combinations=[[0, 1]], - probe_colors=[None, None], combination_colors=["k"], ax=ax, ) @@ -58,7 +57,7 @@ def U(z): U_rec, z_interp, X, dx_1, dx_2 = reconstruct_velocity(u1, u2, probe1_pars, probe2_pars) U_th = U(z_interp) # -fig, axarr = plt.subplots(1, 3, layout="constrained", sharey=True) +fig, axarr = plt.subplots(1, 2, layout="constrained", sharey=True) for ax, u_th, u_rec in zip(axarr, U_th, U_rec): ax.plot(u_th, z_interp, ".", label="base") ax.plot(u_rec, z_interp, ".", label="reconstructed") diff --git a/examples/plot_sketch_multiple_probes.py b/examples/plot_sketch_multiple_probes.py new file mode 100644 index 0000000..84ddd19 --- /dev/null +++ b/examples/plot_sketch_multiple_probes.py @@ -0,0 +1,50 @@ +""" +====================== +Sketch multiple probes +====================== +""" + +import matplotlib.pyplot as plt +import numpy as np + +from pyudv.probes import Probe, sketch_probes + +# ## define probes +r = np.linspace(0, 5, 100) # beam radial coordiantes, same for all probes +alpha1, alpha2, alpha3, alpha4 = -120, -70, 70, -80 # probe inclinations in degree +# probe origin points +O1, O2, O3, O4 = ( + np.array([1, 8]), + np.array([-1, 7]), + np.array([2, 2]), + np.array([3, 8.5]), +) +# probe parameters +PROBE_PARS = [ + [r, alpha1, [0, O1]], # probe1 + [r, alpha2, [0, O2]], # probe2 + [r, alpha3, [0, O3]], # probe3 + [r, alpha4, [0, O4]], # probe4 +] +# +probes = [Probe(*probe_pars) for probe_pars in PROBE_PARS] +probe_colors = ["tab:blue", "tab:green", "tab:orange", "tab:red"] +combinations = [(0, 1), (2, 3)] +combination_colors = ["k", "grey"] + +fig, ax = plt.subplots(1, 1, layout="constrained") +sketch_probes( + probes, + combinations=combinations, + probe_colors=probe_colors, + combination_colors=combination_colors, + ax=ax, +) + +# adding another probe afterwards +probe_add = Probe(r, 70, [0, np.array([4, 2])]) +probe_add.plot_probe(ax, color="tab:pink") + +ax.set_xlabel("x") +ax.set_ylabel("y") +plt.show() diff --git a/examples/plots/Spatio_temporal_amplitude.pdf b/examples/plots/Spatio_temporal_amplitude.pdf index 3911bac..48a3496 100644 Binary files a/examples/plots/Spatio_temporal_amplitude.pdf and b/examples/plots/Spatio_temporal_amplitude.pdf differ diff --git a/examples/plots/Spatio_temporal_velocity.pdf b/examples/plots/Spatio_temporal_velocity.pdf index 0cf2d9e..069f417 100644 Binary files a/examples/plots/Spatio_temporal_velocity.pdf and b/examples/plots/Spatio_temporal_velocity.pdf differ diff --git a/pyudv/__init__.py b/pyudv/__init__.py index 0fdf6bc..e69de29 100644 --- a/pyudv/__init__.py +++ b/pyudv/__init__.py @@ -1 +0,0 @@ -from .velocity import reconstruct_velocity diff --git a/pyudv/amplitude/__init__.py b/pyudv/amplitude/__init__.py index e69de29..31b1706 100644 --- a/pyudv/amplitude/__init__.py +++ b/pyudv/amplitude/__init__.py @@ -0,0 +1,3 @@ +""" +The amplitude model is currently under development, and yet undocumented. +""" diff --git a/pyudv/probes.py b/pyudv/probes.py index 905d24f..471b01e 100644 --- a/pyudv/probes.py +++ b/pyudv/probes.py @@ -1,3 +1,7 @@ +""" +This module helps you deal with probe geometries. +""" + import matplotlib.pyplot as plt import numpy as np import numpy.typing as npt @@ -5,31 +9,73 @@ class Probe: + """ + A class used to represent a single probe. + + Parameters + ---------- + r : ndarray, (N,) + a numpy array containing the radial coordinates of the beam. + alpha : float + orientation of the probe, in degree in the trigonometric referential. + Pref : list[float, ndarray] + A list a size 2 defining a reference point by containing its radial coordinate, and a numpy array containing its coordinate in the "real" reference space. + """ + + a = 1 #: test + def __init__( self, - r: npt.ArrayLike, + r: npt.NDArray, alpha: float, - Pref: list[float, npt.ArrayLike], + Pref: list[float, npt.NDArray], ): - self.r = r # vector along beam axis - self.alpha = alpha # beam axis inclination, trigo referential - self.Pref = Pref # refernce point [r_ref, (x_ref, y_ref)] + """ + Parameters + ---------- + r : ndarray + a numpy array containing the radial coordinates of the beam. + alpha : float + orientation of the probe, in degree in the trigonometric referential. + Pref : list[float, ndarray] + A list a size 2 defining a reference point by containing its radial coordinate, and a numpy array containing its coordinate in the "real" reference space. + """ + + self.r = r #: vector along beam axis + self.alpha = alpha #: beam axis inclination, trigo referential + self.Pref = Pref #: refernce point [r_ref, (x_ref, y_ref)] # - self.r_ref = self.Pref[0] - self.X_ref = self.Pref[1] + self.r_ref = self.Pref[0] #: reference point radial coordinats + self.X_ref = self.Pref[1] #: reference point real coordinates self.unit_vec = np.array( [np.cos(np.radians(alpha)), np.sin(np.radians(alpha))] - ) # beam unit vector in real coordinates - self.O = Pref[1] - Pref[0] * self.unit_vec # Beam origin in real coordinates + ) #: unit vector defining the beam direction in real coordinates + self.O = ( + Pref[1] - Pref[0] * self.unit_vec + ) #: coordinates of the origin of the beam self.E = ( self.X_ref + (r.max() - self.r_ref) * self.unit_vec - ) # Beam end in real coordinates + ) #: coordinates of the end of the beam # Beam coordinates - self.x = self.O[0] + self.r * self.unit_vec[0] - self.z = self.O[1] + self.r * self.unit_vec[1] + self.x = ( + self.O[0] + self.r * self.unit_vec[0] + ) #: horizontal coordinates of the points along the beam + self.z = ( + self.O[1] + self.r * self.unit_vec[1] + ) #: vertical coordinates of the points along the beam + + def plot_probe(self, ax: mplaxes.Axes, color: str = None): + """ + Sketch the probe and its beam on a given matplotlib axe. - def plot_probe(self, ax: mplaxes.Axes, color=None): + Parameters + ---------- + ax : mplaxes.Axes + matplotlib axe on which the probe is sketched. + color : str, optional + probe color, by default None + """ ax.scatter(self.O[0], self.O[1], color=color) (a,) = ax.plot( [self.O[0], self.E[0]], @@ -48,11 +94,27 @@ def plot_probe(self, ax: mplaxes.Axes, color=None): def sketch_probes( probes: list[Probe], - combinations: list[tuple] = None, - ax=None, + combinations: list[tuple[int, int]] = None, + ax: mplaxes.Axes = None, probe_colors: list[str] = None, combination_colors: list[str] = None, ): + """ + Sketch multiple probes, and optionaly their intersections, etc ... + + Parameters + ---------- + probes : list[Probe] + list of :class:`Probe ` object to be sketched. + combinations : list[tuple[int, int]], optional + list of tuple of size 2 containing indexes of `probes` whose intersection should be sketched. + ax : mplaxes.Axes, optional + matplotlib axe on which the sketch is drawn. If None, a new figure is created (default is None). + probe_colors : list[str], optional + list of colors for the probes, by default None. It should be the same size as `probes`. + combination_colors : list[str], optional + list of colors for the intersetctions, by default None. It should be the same size as `combinations`. + """ if ax is None: fig, ax = plt.subplots(1, 1, layout="constrained") ax.set_aspect("equal") @@ -75,7 +137,22 @@ def sketch_probes( ax.plot([X[0], X[0]], [z_min, z_max], color=combination_color) -def probe_crossing_point(probe1: Probe, probe2: Probe): +def probe_crossing_point(probe1: Probe, probe2: Probe) -> npt.NDArray: + """ + calculate the crossing point of two probe beams. + + Parameters + ---------- + probe1 : Probe + First :class:`Probe ` object. + probe2 : Probe + Second :class:`Probe ` object. + + Returns + ------- + ndarray, (2. ) + coordinates of the crossing point. + """ M = np.array([-probe1.unit_vec, probe2.unit_vec]).T S = probe1.O - probe2.O T = np.linalg.inv(M) @ S @@ -84,6 +161,25 @@ def probe_crossing_point(probe1: Probe, probe2: Probe): def compute_vertical_axis(probe1: Probe, probe2: Probe): + """ + compute the common vertical axis between two probe beams. + + Parameters + ---------- + probe1 : Probe + First :class:`Probe ` object. + probe2 : Probe + Second :class:`Probe ` object. + + Returns + ------- + z_interp : ndarray + numpy array containg the vertical coordinates of the common axis. + z_min : float + minimal vertical coordinate + z_max : float + maximal vertical coordinate + """ z_min = max(probe1.z.min(), probe2.z.min()) z_max = min(probe1.z.max(), probe2.z.max()) n_pts = ( diff --git a/pyudv/read_mfprof.py b/pyudv/read_mfprof.py index 9c482d3..0b3fe3d 100644 --- a/pyudv/read_mfprof.py +++ b/pyudv/read_mfprof.py @@ -1,3 +1,8 @@ +""" +This module allows you to read `.mfprof` files from Met-Flow UDVs, and extract the contained data. + +""" + import datetime as dt import numpy as np @@ -110,7 +115,7 @@ } -def read_mfprof(fileName, SI_units=True, convert_time=True): +def read_mfprof(fileName: str, SI_units: bool = True, convert_time: bool = True): """Read .mfprof binary files of the Met-Flow UDV. This is mostly a direct python translation of the matlab script given by Met-Flow. Parameters @@ -128,9 +133,9 @@ def read_mfprof(fileName, SI_units=True, convert_time=True): Dictionnary with the data stored in the mprof files. Available keys are: 'transducer', 'profileTime', 'DopplerData', 'AmplitudeData', 'DistanceAlongBeam' Parameters : dict Dictionnary with the parameters used in the UVP software when sampling the data. See UVP documentation for detail. Keys are: 'Frequency', 'StartChannel', 'ChannelDistance', 'ChannelWidth', 'MaximumDepth', 'SoundSpeed', 'Angle', 'GainStart', 'GainEnd', 'Voltage', 'Iterations', 'NoiseLevel', 'CyclesPerPulse', 'TriggerMode', 'TriggerModeName', 'ProfileLength', 'ProfilesPerBlock', 'Blocks', 'AmplitudeStored', 'DoNotStoreDoppler', 'RawDataMin', 'RawDataMax', 'RawDataRange', 'AmplDataMin', 'AmplDataMax', 'VelocityInterpretingMode', 'UserSampleTime', 'SampleTime', 'UseMultiplexer', 'FlowMapping', 'FirstValidChannel', 'LastValidChannel', 'FlowRateType', 'PeriodEnhOffset', 'PeriodEnhPeriod', 'PeriodEnhNCycles', 'Comment', 'MeasurementProtocol', 'NumberOfCycles', 'CycleDelay', 'Version', 'Table' - Infos + Infos: dict Dictionnary with some informations stored during sampling of the data. Keys are 'Signum', 'measParamsOffset', 'nProfiles', 'reserved1', 'flags', 'recordSize', 'nChannels', 'reserved2', 'startTime'. - Units1 + Units: dict Dictionnary with the units of the variables stored in the other dictionnaries. Keys are the name of the variables. """ @@ -254,13 +259,13 @@ def read_mfprof(fileName, SI_units=True, convert_time=True): return Data, Parameters, Infos, Units -def filetime_to_dt(ft): - us = int(ft) // 10 - return dt.datetime(1601, 1, 1) + dt.timedelta(microseconds=us) +# def filetime_to_dt(ft): +# us = int(ft) // 10 +# return dt.datetime(1601, 1, 1) + dt.timedelta(microseconds=us) def velocity_from_UVPdata( - raw_data, SoundSpeed, MaximumDepth, Angle, Frequency, Nbytes=8 + raw_data, SoundSpeed, MaximumDepth, Angle: float, Frequency: float, Nbytes: int = 8 ): """Calculate velocity from UDV raw data. Units must be checked outside of this function - no conversion is done here. @@ -296,16 +301,16 @@ def velocity_from_UVPdata( return Fd * SoundSpeed * Angle_correction / (2 * Frequency) -def velocity_from_mfprof_reading(Data, Parameters, Nbytes=8): - """Calculate velocity from `Data` and `Parameters` dictionnaries as output of :func:`read_mfprof `, - using the function :func:`velocity_from_UVPdata `. +def velocity_from_mfprof_reading(Data: dict, Parameters: dict, Nbytes: int = 8): + """Calculate velocity from `Data` and `Parameters` dictionnaries as output of :func:`read_mfprof `, + using the function :func:`velocity_from_UVPdata `. Parameters ---------- Data : dict - Data dictionnary coming from :func:`read_mfprof `. + Data dictionnary coming from :func:`read_mfprof `. Parameters : dict - Parameters dictionnary coming from :func:`read_mfprof `. + Parameters dictionnary coming from :func:`read_mfprof `. Nbytes : int Number of bytes over which the raw data are coded (the default is 8). @@ -328,7 +333,14 @@ def velocity_from_mfprof_reading(Data, Parameters, Nbytes=8): def amplitude_from_UVPdata( - raw_data, z, GainStart, GainEnd, zend, zstart=0.37 * 1e-3, Nbytes=14, deltaV=5 + raw_data, + z, + GainStart, + GainEnd, + zend: float, + zstart: float = 0.37 * 1e-3, + Nbytes: int = 14, + deltaV: float = 5, ): """Correct the raw amplitude data as outut of the UVP-DUO. @@ -342,9 +354,9 @@ def amplitude_from_UVPdata( start absolute gain. GainEnd : scalar end absolute gain. - zend : type + zend : float Maximum measurable distance by the UVP. - zstart : type + zstart : float minimum measurable distance by the UVP (the default is 0.00037)). Nbytes : int Number of bytes over which the raw data are coded (the default is 14). @@ -366,16 +378,18 @@ def amplitude_from_UVPdata( ) -def amplitude_from_mfprof_reading(Data, Parameters, Nbytes=14, deltaV=5): - """Calculate the unamplified/corrected echo signal from `Data` and `Parameters` dictionnaries as output of :func:`read_mfprof `, - using the function :func:`amplitude_from_UVPdata `. +def amplitude_from_mfprof_reading( + Data: dict, Parameters: dict, Nbytes: int = 14, deltaV: float = 5 +): + """Calculate the unamplified/corrected echo signal from `Data` and `Parameters` dictionnaries as output of :func:`read_mfprof `, + using the function :func:`amplitude_from_UVPdata `. Parameters ---------- Data : dict - Data dictionnary coming from :func:`read_mfprof `. + Data dictionnary coming from :func:`read_mfprof `. Parameters : dict - Parameters dictionnary coming from :func:`read_mfprof `. + Parameters dictionnary coming from :func:`read_mfprof `. Nbytes : int Number of bytes over which the raw data are coded (the default is 14). deltaV : int @@ -402,9 +416,9 @@ def amplitude_from_mfprof_reading(Data, Parameters, Nbytes=14, deltaV=5): # #### Writing functions -def write_dictionnary(dico, file): +def write_dictionnary(dico: dict, file: str): """Write parameter dictionnary to a .txt file. - Each line of this file is a dictionnary key, followed by the corresponding entry, directly converted using `str()`. + Each line of this file is a dictionnary key, followed by the corresponding entry, directly converted using :func:`str `. Parameters ---------- @@ -425,7 +439,7 @@ def write_dictionnary(dico, file): f.write(line) -def create_variable( +def _create_variable( netcdf_group, name, data, @@ -448,10 +462,30 @@ def create_variable( var.comments = comments -def mfprof_to_netcdf(input, output, add_attr=None, cut_zeros=True): - newfile = netCDF4.Dataset(output, "w", format="NETCDF4") +def mfprof_to_netcdf( + input_mfprof: str, output_netcdf: str, add_attr: dict = None, cut_zeros: bool = True +): + """ + Convert a .mfprof file to a netCDF file. + + Parameters + ---------- + input_mfprof : str + input .mfprof file path + output_netcdf : str + output netCDF file path + add_attr : dict, optional + dictionnary containing attributes to be added to the netCDF file, by default None. For example, `add_attr = {name: 'John Smith', team: 'the best'}` + cut_zeros : bool, optional + If True, cut the measurements data and remove all the trailing 0 added when the measurements are stopped bedore the attributed time, by default True + + Example + ------- + >>> mfprof_to_netcdf('input.mfprof', 'output.nc', add_attr = {name: 'John Smith', team: 'the best'}, cut_zeros=True) + """ + newfile = netCDF4.Dataset(output_netcdf, "w", format="NETCDF4") # - Data, Parameters, Info, Units = read_mfprof(input) + Data, Parameters, Info, Units = read_mfprof(input_mfprof) amplitude_data = amplitude_from_mfprof_reading(Data, Parameters) velocity_data = velocity_from_mfprof_reading(Data, Parameters) # @@ -472,21 +506,21 @@ def mfprof_to_netcdf(input, output, add_attr=None, cut_zeros=True): else: dims = ("z", "time") # - create_variable( + _create_variable( newfile, key, var[..., :tmax] if key != "DistanceAlongBeam" else var, dimensions=dims, unit=Units[key] if key in Units.keys() else None, ) - create_variable( + _create_variable( newfile, "amplitude_data", amplitude_data[..., :tmax], dimensions=("z", "time"), unit="V", ) - create_variable( + _create_variable( newfile, "velocity_data", velocity_data[..., :tmax], diff --git a/pyudv/velocity.py b/pyudv/velocity.py index 389ac5b..8ed6137 100644 --- a/pyudv/velocity.py +++ b/pyudv/velocity.py @@ -2,7 +2,7 @@ import numpy.typing as npt import scipy.interpolate as scipyinterp -from pyudv.probes import Probe, compute_vertical_axis, probe_crossing_point +import pyudv.probes as pb def reconstruct_velocity( @@ -29,24 +29,24 @@ def reconstruct_velocity( Returns ------- - U : NDArray + U : ndarray reconstructed velocity components in the coordinate system corresponding to the one of the refernce points of the probes. - z_interp : NDArray + z_interp : ndarray coordinate vector corresponding to `U` - X : NDArray + X : ndarray crossing point of the probes - dx_1 : NDArray + dx_1 : ndarray horizontal distance between the first probe beam, and the vertical axis passing by the crossing point `X` - dx_2 : NDArray + dx_2 : ndarray horizontal distance between the second probe beam, and the vertical axis passing by the crossing point `X` """ # # init probes - probe1 = Probe(*probe1_pars) - probe2 = Probe(*probe2_pars) + probe1 = pb.Probe(*probe1_pars) + probe2 = pb.Probe(*probe2_pars) # # # Build common vertical axis - z_interp, _, _ = compute_vertical_axis(probe1, probe2) + z_interp, _, _ = pb.compute_vertical_axis(probe1, probe2) # # interpolating velocity interp1 = scipyinterp.interp1d(probe1.z, u1) interp2 = scipyinterp.interp1d(probe2.z, u2) @@ -60,7 +60,7 @@ def reconstruct_velocity( # # # other quantities # crossing point - X = probe_crossing_point(probe1, probe2) + X = pb.probe_crossing_point(probe1, probe2) # horizontal distances to the vertical axis passing by the crossing point dx_1 = np.tan(np.radians(probe1.alpha)) * (z_interp - X[1]) dx_2 = np.tan(np.radians(probe2.alpha)) * (z_interp - X[1]) @@ -83,8 +83,8 @@ def U(z): probe1_pars = [r, alpha1, [0, O1]] probe2_pars = [r, alpha2, [0, O2]] # - probe1 = Probe(*probe1_pars) - probe2 = Probe(*probe2_pars) + probe1 = pb.Probe(*probe1_pars) + probe2 = pb.Probe(*probe2_pars) # make fake signals u1 = U(probe1.z).T @ probe1.unit_vec u2 = U(probe2.z).T @ probe2.unit_vec