Easier Output Saving for Proton Radiography (PlasmaPy#1134)

Tlord18 · Oct 6, 2021 · 20741c5 · 20741c5
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diff --git a/changelog/1134.breaking.1.rst b/changelog/1134.breaking.1.rst
@@ -0,0 +1,4 @@
+Renamed subpacakge ``plasmapy.diagnostics.proton_radiography`` to
+`plasmapy.diagnostics.charged_particle_radiography`, and renamed the
+``SyntheticProtonRadiograph`` class within that module to
+`~plasmapy.diagnostics.charged_particle_radiography.Tracker`.
diff --git a/changelog/1134.breaking.2.rst b/changelog/1134.breaking.2.rst
@@ -0,0 +1,6 @@
+`~plasmapy.diagnostics.charged_particle_radiography.Tracker` no longer
+supports making changes to an instantiated object and
+re-running the simulation.  Subsequent simulations should be performed
+by instantiating a new
+`~plasmapy.diagnostics.charged_particle_radiography.Tracker` object and
+running.
diff --git a/changelog/1134.breaking.3.rst b/changelog/1134.breaking.3.rst
@@ -0,0 +1,7 @@
+Removed the ``Tracker.synthetic_radiograph()`` method and created the
+standalone function
+:func:`~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiograph`
+in its place.  This new function takes either a
+`~plasmapy.diagnostics.charged_particle_radiography.Tracker` object or
+a dictionary equivalent to
+`~plasmapy.diagnostics.charged_particle_radiography.Tracker.results_dict`.
diff --git a/changelog/1134.bugfix.rst b/changelog/1134.bugfix.rst
@@ -0,0 +1,5 @@
+Running `~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiograph`
+with the ``optical_density=True`` keyword will now return `numpy.inf`
+where the source profile intensity is zero. Previously, an incorrect value
+was returned since zero entries were replaced with values of ``1`` before
+taking the logarithm.
diff --git a/changelog/1134.feature.rst b/changelog/1134.feature.rst
@@ -0,0 +1,5 @@
+Added the
+:meth:`~plasmapy.diagnostics.charged_particle_radiography.Tracker.save_results`
+method to `~plasmapy.diagnostics.charged_particle_radiography.Tracker`
+for saving results to a ``.npz`` file format (see `numpy.lib.format` for
+details on the file format).
diff --git a/changelog/1134.trivial.rst b/changelog/1134.trivial.rst
@@ -0,0 +1,3 @@
+`~plasmapy.diagnostics.charged_particle_radiography.synthetic_radiograph`
+now determines the default detector size to be the smallest detector
+plane centered on the origin that includes all particles.
diff --git a/docs/ad/diagnostics/charged_particle_radiography.rst b/docs/ad/diagnostics/charged_particle_radiography.rst
@@ -0,0 +1,16 @@
+.. _charged_particle_radiography:
+
+*************************************
+Charged particle radiography analysis
+*************************************
+
+.. currentmodule:: plasmapy.diagnostics.charged_particle_radiography
+
+.. automodapi:: plasmapy.diagnostics.charged_particle_radiography
+
+.. nbgallery::
+    :caption: Examples
+
+    /notebooks/diagnostics/charged_particle_radiography_particle_tracing
+    /notebooks/diagnostics/charged_particle_radiography_particle_tracing_custom_source
+    /notebooks/diagnostics/charged_particle_radiography_particle_tracing_wire_mesh
diff --git a/docs/ad/diagnostics/index.rst b/docs/ad/diagnostics/index.rst
@@ -10,7 +10,7 @@
    :maxdepth: 1
    :caption: Sub-Packages & Modules
 
-   proton_radiography
+   charged_particle_radiography
    Swept Langmuir (will be deprecated) <langmuir>
    thomson
 

diff --git a/docs/ad/diagnostics/proton_radiography.rst b/docs/ad/diagnostics/proton_radiography.rst
diff --git a/docs/index.rst b/docs/index.rst
@@ -20,7 +20,7 @@ Example highlights
 .. nbgallery::
    :hidden:
 
-   notebooks/diagnostics/proton_radiography_particle_tracing
+   notebooks/diagnostics/charged_particle_radiography_particle_tracing
    notebooks/dispersion/two_fluid_dispersion
    notebooks/diagnostics/thomson
    notebooks/analysis/swept_langmuir/find_floating_potential

diff --git a/docs/notebooks/diagnostics/charged_particle_radiography_particle_tracing.ipynb b/docs/notebooks/diagnostics/charged_particle_radiography_particle_tracing.ipynb
diff --git a/docs/notebooks/diagnostics/charged_particle_radiography_particle_tracing_custom_source.ipynb b/docs/notebooks/diagnostics/charged_particle_radiography_particle_tracing_custom_source.ipynb
diff --git a/docs/notebooks/diagnostics/charged_particle_radiography_particle_tracing_wire_mesh.ipynb b/docs/notebooks/diagnostics/charged_particle_radiography_particle_tracing_wire_mesh.ipynb