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
-
-
-
-.. 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
-
-
-
-.. 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
-
-
-
-.. only:: not html
-
- * :ref:`sphx_glr__examples_plot_reconstruct_velocity.py`
-
-.. raw:: html
-
-
-
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 b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.createEnumType.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.createGroup.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.createGroup.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.createVLType.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.createVLType.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.createVariable.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.createVariable.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.data_model.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.data_model.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.delncattr.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.delncattr.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.dimensions.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.dimensions.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.disk_format.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.disk_format.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.enumtypes.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.enumtypes.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.file_format.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.file_format.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.filepath.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.filepath.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.fromcdl.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.fromcdl.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.get_variables_by_attributes.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.get_variables_by_attributes.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.getncattr.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.getncattr.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.groups.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.groups.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.has_blosc_filter.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.has_blosc_filter.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.has_bzip2_filter.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.has_bzip2_filter.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.has_szip_filter.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.has_szip_filter.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.has_zstd_filter.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.has_zstd_filter.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.isopen.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.isopen.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.keepweakref.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.keepweakref.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.name.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.name.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.ncattrs.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.ncattrs.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.parent.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.parent.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.path.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.path.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.renameAttribute.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.renameAttribute.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.renameDimension.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.renameDimension.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.renameGroup.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.renameGroup.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.renameVariable.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.renameVariable.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.set_always_mask.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.set_always_mask.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.set_auto_chartostring.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.set_auto_chartostring.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.set_auto_mask.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.set_auto_mask.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.set_auto_maskandscale.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.set_auto_maskandscale.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.set_auto_scale.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.set_auto_scale.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.set_fill_off.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.set_fill_off.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.set_fill_on.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.set_fill_on.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.set_ncstring_attrs.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.set_ncstring_attrs.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.setncattr.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.setncattr.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.setncattr_string.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.setncattr_string.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.setncatts.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.setncatts.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.sync.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.sync.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.tocdl.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.tocdl.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.variables.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.variables.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.vltypes.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.Dataset.vltypes.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.amplitude_from_UVPdata.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.amplitude_from_UVPdata.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.amplitude_from_mfprof_reading.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.amplitude_from_mfprof_reading.examples
deleted file mode 100644
index ccee0dd..0000000
--- a/docs/_gen_modules/backreferences/pyudv.read_mfprof.amplitude_from_mfprof_reading.examples
+++ /dev/null
@@ -1,39 +0,0 @@
-
-
-Examples using ``pyudv.read_mfprof.amplitude_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.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 b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.ctime.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.date.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.date.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.day.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.day.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.dst.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.dst.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.fold.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.fold.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.fromisocalendar.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.fromisocalendar.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.fromisoformat.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.fromisoformat.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.fromordinal.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.fromordinal.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.fromtimestamp.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.fromtimestamp.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.hour.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.hour.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.isocalendar.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.isocalendar.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.isoformat.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.isoformat.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.isoweekday.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.isoweekday.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.microsecond.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.microsecond.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.minute.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.minute.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.month.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.month.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.now.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.now.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.replace.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.replace.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.second.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.second.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.strftime.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.strftime.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.strptime.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.strptime.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.time.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.time.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.timestamp.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.timestamp.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.timetuple.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.timetuple.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.timetz.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.timetz.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.today.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.today.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.toordinal.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.toordinal.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.tzinfo.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.tzinfo.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.tzname.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.tzname.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.utcfromtimestamp.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.utcfromtimestamp.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.utcnow.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.utcnow.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.utcoffset.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.utcoffset.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.utctimetuple.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.utctimetuple.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.weekday.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.weekday.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.year.examples b/docs/_gen_modules/backreferences/pyudv.read_mfprof.datetime.year.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.read_mfprof.examples 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 file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.argsort.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.argsort.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.astype.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.astype.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.byteswap.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.byteswap.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.choose.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.choose.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.clip.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.clip.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.compress.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.compress.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.conj.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.conj.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.conjugate.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.conjugate.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.copy.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.copy.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.cumprod.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.cumprod.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.cumsum.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.cumsum.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.diagonal.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.diagonal.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.dot.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.dot.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.dump.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.dump.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.dumps.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.dumps.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.fill.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.fill.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.flatten.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.flatten.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.getfield.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.getfield.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.item.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.item.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.itemset.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.itemset.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.max.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.max.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.mean.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.mean.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.min.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.min.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.newbyteorder.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.newbyteorder.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.nonzero.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.nonzero.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.partition.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.partition.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.prod.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.prod.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.ptp.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.ptp.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.put.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.put.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.ravel.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.ravel.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.repeat.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.repeat.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.reshape.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.reshape.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.resize.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.resize.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.round.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.round.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.searchsorted.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.searchsorted.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.setfield.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.setfield.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.setflags.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.setflags.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.sort.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.sort.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.squeeze.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.squeeze.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.std.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.std.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.sum.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.sum.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.swapaxes.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.swapaxes.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.take.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.take.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.tobytes.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.tobytes.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.tofile.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.tofile.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.tolist.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.tolist.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.tostring.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.tostring.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.trace.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.trace.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.transpose.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.transpose.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.var.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.var.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.view.examples b/docs/_gen_modules/backreferences/pyudv.velocity.NDArray.view.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.Probe.examples b/docs/_gen_modules/backreferences/pyudv.velocity.Probe.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.Probe.plot_probe.examples b/docs/_gen_modules/backreferences/pyudv.velocity.Probe.plot_probe.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.compute_vertical_axis.examples b/docs/_gen_modules/backreferences/pyudv.velocity.compute_vertical_axis.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.examples b/docs/_gen_modules/backreferences/pyudv.velocity.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.interp1d.__call__.examples b/docs/_gen_modules/backreferences/pyudv.velocity.interp1d.__call__.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.interp1d.dtype.examples b/docs/_gen_modules/backreferences/pyudv.velocity.interp1d.dtype.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.interp1d.examples b/docs/_gen_modules/backreferences/pyudv.velocity.interp1d.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.interp1d.fill_value.examples b/docs/_gen_modules/backreferences/pyudv.velocity.interp1d.fill_value.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.probe_crossing_point.examples b/docs/_gen_modules/backreferences/pyudv.velocity.probe_crossing_point.examples
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/_gen_modules/backreferences/pyudv.velocity.reconstruct_velocity.examples 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