Add examples

topasmc · Mar 3, 2016 · 53330f0 · 53330f0
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diff --git a/examples-docs/Basic/AllParameterForms.rst b/examples-docs/Basic/AllParameterForms.rst
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+AllParameterForms.txt
+---------------------
+
+.. literalinclude:: /examples/Basic/AllParameterForms.txt
diff --git a/examples-docs/Basic/DividedComponents.rst b/examples-docs/Basic/DividedComponents.rst
@@ -0,0 +1,4 @@
+DividedComponents.txt
+---------------------
+
+.. literalinclude:: /examples/Basic/DividedComponents.txt
diff --git a/examples-docs/Basic/Emittance_Gaussian.rst b/examples-docs/Basic/Emittance_Gaussian.rst
@@ -0,0 +1,4 @@
+Emittance_Gaussian.txt
+----------------------
+
+.. literalinclude:: /examples/Basic/Emittance_Gaussian.txt
diff --git a/examples-docs/Basic/Emittance_Twiss.rst b/examples-docs/Basic/Emittance_Twiss.rst
@@ -0,0 +1,4 @@
+Emittance_Twiss.txt
+-------------------
+
+.. literalinclude:: /examples/Basic/Emittance_Twiss.txt
diff --git a/examples-docs/Basic/Isotope.rst b/examples-docs/Basic/Isotope.rst
@@ -0,0 +1,4 @@
+Isotope.txt
+-----------
+
+.. literalinclude:: /examples/Basic/Isotope.txt
diff --git a/examples-docs/Basic/LayeredMassGeometry.rst b/examples-docs/Basic/LayeredMassGeometry.rst
@@ -0,0 +1,4 @@
+LayeredMassGeometry.txt
+-----------------------
+
+.. literalinclude:: /examples/Basic/LayeredMassGeometry.txt
diff --git a/examples-docs/Basic/OneBox.rst b/examples-docs/Basic/OneBox.rst
@@ -0,0 +1,4 @@
+OneBox.txt
+----------
+
+.. literalinclude:: /examples/Basic/OneBox.txt
diff --git a/examples-docs/Basic/OneBoxRotate.rst b/examples-docs/Basic/OneBoxRotate.rst
@@ -0,0 +1,4 @@
+OneBoxRotate.txt
+----------------
+
+.. literalinclude:: /examples/Basic/OneBoxRotate.txt
diff --git a/examples-docs/Basic/OneBoxTranslate.rst b/examples-docs/Basic/OneBoxTranslate.rst
@@ -0,0 +1,4 @@
+OneBoxTranslate.txt
+-------------------
+
+.. literalinclude:: /examples/Basic/OneBoxTranslate.txt
diff --git a/examples-docs/Basic/PhysicsSetting.rst b/examples-docs/Basic/PhysicsSetting.rst
@@ -0,0 +1,4 @@
+PhysicsSetting.txt
+------------------
+
+.. literalinclude:: /examples/Basic/PhysicsSetting.txt
diff --git a/examples-docs/Basic/ShapeTestWithAllParameters.rst b/examples-docs/Basic/ShapeTestWithAllParameters.rst
@@ -0,0 +1,4 @@
+ShapeTestWithAllParameters.txt
+------------------------------
+
+.. literalinclude:: /examples/Basic/ShapeTestWithAllParameters.txt
diff --git a/examples-docs/Basic/ShapeTestWithOnlyRequiredParameters.rst b/examples-docs/Basic/ShapeTestWithOnlyRequiredParameters.rst
@@ -0,0 +1,4 @@
+ShapeTestWithOnlyRequiredParameters.txt
+---------------------------------------
+
+.. literalinclude:: /examples/Basic/ShapeTestWithOnlyRequiredParameters.txt
diff --git a/examples-docs/Basic/Spectrum.rst b/examples-docs/Basic/Spectrum.rst
@@ -0,0 +1,4 @@
+Spectrum.txt
+------------
+
+.. literalinclude:: /examples/Basic/Spectrum.txt
diff --git a/examples-docs/Basic/TwissPrimary.rst b/examples-docs/Basic/TwissPrimary.rst
@@ -0,0 +1,4 @@
+TwissPrimary.txt
+----------------
+
+.. literalinclude:: /examples/Basic/TwissPrimary.txt
diff --git a/examples-docs/Basic/TwoBeams.rst b/examples-docs/Basic/TwoBeams.rst
@@ -0,0 +1,4 @@
+TwoBeams.txt
+------------
+
+.. literalinclude:: /examples/Basic/TwoBeams.txt
diff --git a/examples-docs/Basic/index.rst b/examples-docs/Basic/index.rst
@@ -0,0 +1,21 @@
+Basic
+=====
+
+.. toctree::
+	:maxdepth: 1
+
+	AllParameterForms
+	DividedComponents
+	Emittance_Gaussian
+	Emittance_Twiss
+	Isotope
+	LayeredMassGeometry
+	OneBox
+	OneBoxRotate
+	OneBoxTranslate
+	PhysicsSetting
+	ShapeTestWithAllParameters
+	ShapeTestWithOnlyRequiredParameters
+	Spectrum
+	TwissPrimary
+	TwoBeams
diff --git a/examples-docs/DICOM/DoseTo4DCT.rst b/examples-docs/DICOM/DoseTo4DCT.rst
@@ -0,0 +1,4 @@
+DoseTo4DCT.txt
+--------------
+
+.. literalinclude:: /examples/DICOM/DoseTo4DCT.txt
diff --git a/examples-docs/DICOM/DoseToCT.rst b/examples-docs/DICOM/DoseToCT.rst
@@ -0,0 +1,4 @@
+DoseToCT.txt
+------------
+
+.. literalinclude:: /examples/DICOM/DoseToCT.txt
diff --git a/examples-docs/DICOM/Implant.rst b/examples-docs/DICOM/Implant.rst
@@ -0,0 +1,4 @@
+Implant.txt
+-----------
+
+.. literalinclude:: /examples/DICOM/Implant.txt
diff --git a/examples-docs/DICOM/ViewAbdomen.rst b/examples-docs/DICOM/ViewAbdomen.rst
@@ -0,0 +1,4 @@
+ViewAbdomen.txt
+---------------
+
+.. literalinclude:: /examples/DICOM/ViewAbdomen.txt
diff --git a/examples-docs/DICOM/index.rst b/examples-docs/DICOM/index.rst
@@ -0,0 +1,10 @@
+DICOM
+=====
+
+.. toctree::
+	:maxdepth: 1
+
+	DoseTo4DCT
+	DoseToCT
+	Implant
+	ViewAbdomen
diff --git a/examples-docs/Graphics/ColorByOriginComponent.rst b/examples-docs/Graphics/ColorByOriginComponent.rst
@@ -0,0 +1,4 @@
+ColorByOriginComponent.txt
+--------------------------
+
+.. literalinclude:: /examples/Graphics/ColorByOriginComponent.txt
diff --git a/examples-docs/Graphics/SolidSphere.rst b/examples-docs/Graphics/SolidSphere.rst
@@ -0,0 +1,4 @@
+SolidSphere.txt
+---------------
+
+.. literalinclude:: /examples/Graphics/SolidSphere.txt
diff --git a/examples-docs/Graphics/TestGraphics.rst b/examples-docs/Graphics/TestGraphics.rst
@@ -0,0 +1,4 @@
+TestGraphics.txt
+----------------
+
+.. literalinclude:: /examples/Graphics/TestGraphics.txt
diff --git a/examples-docs/Graphics/TwoProjections.rst b/examples-docs/Graphics/TwoProjections.rst
@@ -0,0 +1,4 @@
+TwoProjections.txt
+------------------
+
+.. literalinclude:: /examples/Graphics/TwoProjections.txt
diff --git a/examples-docs/Graphics/index.rst b/examples-docs/Graphics/index.rst
@@ -0,0 +1,10 @@
+Graphics
+========
+
+.. toctree::
+	:maxdepth: 1
+
+	ColorByOriginComponent
+	SolidSphere
+	TestGraphics
+	TwoProjections
diff --git a/examples-docs/Nozzle/RasterScanningPattern.rst b/examples-docs/Nozzle/RasterScanningPattern.rst
@@ -0,0 +1,4 @@
+RasterScanningPattern.txt
+-------------------------
+
+.. literalinclude:: /examples/Nozzle/RasterScanningPattern.txt
diff --git a/examples-docs/Nozzle/ScanningNozzle.rst b/examples-docs/Nozzle/ScanningNozzle.rst
@@ -0,0 +1,4 @@
+ScanningNozzle.txt
+------------------
+
+.. literalinclude:: /examples/Nozzle/ScanningNozzle.txt
diff --git a/examples-docs/Nozzle/ScanningStationaryTarget.rst b/examples-docs/Nozzle/ScanningStationaryTarget.rst
@@ -0,0 +1,4 @@
+ScanningStationaryTarget.txt
+----------------------------
+
+.. literalinclude:: /examples/Nozzle/ScanningStationaryTarget.txt
diff --git a/examples-docs/Nozzle/ScanningTargetMovingHorizontal.rst b/examples-docs/Nozzle/ScanningTargetMovingHorizontal.rst
@@ -0,0 +1,4 @@
+ScanningTargetMovingHorizontal.txt
+----------------------------------
+
+.. literalinclude:: /examples/Nozzle/ScanningTargetMovingHorizontal.txt
diff --git a/examples-docs/Nozzle/ScanningTargetMovingInDepth.rst b/examples-docs/Nozzle/ScanningTargetMovingInDepth.rst
@@ -0,0 +1,4 @@
+ScanningTargetMovingInDepth.txt
+-------------------------------
+
+.. literalinclude:: /examples/Nozzle/ScanningTargetMovingInDepth.txt
diff --git a/examples-docs/Nozzle/ScatteringNozzle_run.rst b/examples-docs/Nozzle/ScatteringNozzle_run.rst
@@ -0,0 +1,4 @@
+ScatteringNozzle_run.txt
+------------------------
+
+.. literalinclude:: /examples/Nozzle/ScatteringNozzle_run.txt
diff --git a/examples-docs/Nozzle/index.rst b/examples-docs/Nozzle/index.rst
@@ -0,0 +1,12 @@
+Nozzle
+======
+
+.. toctree::
+	:maxdepth: 1
+
+	RasterScanningPattern
+	ScanningNozzle
+	ScanningStationaryTarget
+	ScanningTargetMovingHorizontal
+	ScanningTargetMovingInDepth
+	ScatteringNozzle_run
diff --git a/examples-docs/Optical/PlasticScintillator.rst b/examples-docs/Optical/PlasticScintillator.rst
@@ -0,0 +1,4 @@
+PlasticScintillator.txt
+-----------------------
+
+.. literalinclude:: /examples/Optical/PlasticScintillator.txt
diff --git a/examples-docs/Optical/Rotating_Surfaces.rst b/examples-docs/Optical/Rotating_Surfaces.rst
@@ -0,0 +1,4 @@
+Rotating_Surfaces.txt
+---------------------
+
+.. literalinclude:: /examples/Optical/Rotating_Surfaces.txt
diff --git a/examples-docs/Optical/Surfaces.rst b/examples-docs/Optical/Surfaces.rst
@@ -0,0 +1,4 @@
+Surfaces.txt
+------------
+
+.. literalinclude:: /examples/Optical/Surfaces.txt
diff --git a/examples-docs/Optical/WavelengthShifter.rst b/examples-docs/Optical/WavelengthShifter.rst
@@ -0,0 +1,4 @@
+WavelengthShifter.txt
+---------------------
+
+.. literalinclude:: /examples/Optical/WavelengthShifter.txt
diff --git a/examples-docs/Optical/index.rst b/examples-docs/Optical/index.rst
@@ -0,0 +1,10 @@
+Optical
+=======
+
+.. toctree::
+	:maxdepth: 1
+
+	PlasticScintillator
+	Rotating_Surfaces
+	Surfaces
+	WavelengthShifter
diff --git a/examples-docs/PhaseSpace/MultiRun_Write_ASCII.rst b/examples-docs/PhaseSpace/MultiRun_Write_ASCII.rst
@@ -0,0 +1,4 @@
+MultiRun_Write_ASCII.txt
+------------------------
+
+.. literalinclude:: /examples/PhaseSpace/MultiRun_Write_ASCII.txt
diff --git a/examples-docs/PhaseSpace/ReadASCII.rst b/examples-docs/PhaseSpace/ReadASCII.rst
@@ -0,0 +1,4 @@
+ReadASCII.txt
+-------------
+
+.. literalinclude:: /examples/PhaseSpace/ReadASCII.txt
diff --git a/examples-docs/PhaseSpace/ReadBinary.rst b/examples-docs/PhaseSpace/ReadBinary.rst
@@ -0,0 +1,4 @@
+ReadBinary.txt
+--------------
+
+.. literalinclude:: /examples/PhaseSpace/ReadBinary.txt
diff --git a/examples-docs/PhaseSpace/ReadLimited.rst b/examples-docs/PhaseSpace/ReadLimited.rst
@@ -0,0 +1,4 @@
+ReadLimited.txt
+---------------
+
+.. literalinclude:: /examples/PhaseSpace/ReadLimited.txt
diff --git a/examples-docs/PhaseSpace/WriteASCII.rst b/examples-docs/PhaseSpace/WriteASCII.rst
@@ -0,0 +1,4 @@
+WriteASCII.txt
+--------------
+
+.. literalinclude:: /examples/PhaseSpace/WriteASCII.txt
diff --git a/examples-docs/PhaseSpace/WriteBinary.rst b/examples-docs/PhaseSpace/WriteBinary.rst
@@ -0,0 +1,4 @@
+WriteBinary.txt
+---------------
+
+.. literalinclude:: /examples/PhaseSpace/WriteBinary.txt
diff --git a/examples-docs/PhaseSpace/WriteIonsASCII.rst b/examples-docs/PhaseSpace/WriteIonsASCII.rst
@@ -0,0 +1,4 @@
+WriteIonsASCII.txt
+------------------
+
+.. literalinclude:: /examples/PhaseSpace/WriteIonsASCII.txt
diff --git a/examples-docs/PhaseSpace/WriteLimited.rst b/examples-docs/PhaseSpace/WriteLimited.rst
@@ -0,0 +1,4 @@
+WriteLimited.txt
+----------------
+
+.. literalinclude:: /examples/PhaseSpace/WriteLimited.txt
diff --git a/examples-docs/PhaseSpace/index.rst b/examples-docs/PhaseSpace/index.rst
@@ -0,0 +1,14 @@
+PhaseSpace
+==========
+
+.. toctree::
+	:maxdepth: 1
+
+	MultiRun_Write_ASCII
+	ReadASCII
+	ReadBinary
+	ReadLimited
+	WriteASCII
+	WriteBinary
+	WriteIonsASCII
+	WriteLimited
diff --git a/examples-docs/Scoring/ChargeInSphere.rst b/examples-docs/Scoring/ChargeInSphere.rst
@@ -0,0 +1,4 @@
+ChargeInSphere.txt
+------------------
+
+.. literalinclude:: /examples/Scoring/ChargeInSphere.txt
diff --git a/examples-docs/Scoring/Complex.rst b/examples-docs/Scoring/Complex.rst
@@ -0,0 +1,4 @@
+Complex.txt
+-----------
+
+.. literalinclude:: /examples/Scoring/Complex.txt
diff --git a/examples-docs/Scoring/Dose.rst b/examples-docs/Scoring/Dose.rst
@@ -0,0 +1,4 @@
+Dose.txt
+--------
+
+.. literalinclude:: /examples/Scoring/Dose.txt
diff --git a/examples-docs/Scoring/DoseInVoxelMaterials.rst b/examples-docs/Scoring/DoseInVoxelMaterials.rst
@@ -0,0 +1,4 @@
+DoseInVoxelMaterials.txt
+------------------------
+
+.. literalinclude:: /examples/Scoring/DoseInVoxelMaterials.txt
diff --git a/examples-docs/Scoring/DoseToMediumVsWater.rst b/examples-docs/Scoring/DoseToMediumVsWater.rst
@@ -0,0 +1,4 @@
+DoseToMediumVsWater.txt
+-----------------------
+
+.. literalinclude:: /examples/Scoring/DoseToMediumVsWater.txt
diff --git a/examples-docs/Scoring/DoseVolumeHistogram.rst b/examples-docs/Scoring/DoseVolumeHistogram.rst
@@ -0,0 +1,4 @@
+DoseVolumeHistogram.txt
+-----------------------
+
+.. literalinclude:: /examples/Scoring/DoseVolumeHistogram.txt
diff --git a/examples-docs/Scoring/EnergyAndDose.rst b/examples-docs/Scoring/EnergyAndDose.rst
@@ -0,0 +1,4 @@
+EnergyAndDose.txt
+-----------------
+
+.. literalinclude:: /examples/Scoring/EnergyAndDose.txt
diff --git a/examples-docs/Scoring/EnergyDivisions.rst b/examples-docs/Scoring/EnergyDivisions.rst
@@ -0,0 +1,4 @@
+EnergyDivisions.txt
+-------------------
+
+.. literalinclude:: /examples/Scoring/EnergyDivisions.txt
diff --git a/examples-docs/Scoring/EnergyInBinnedCylinder.rst b/examples-docs/Scoring/EnergyInBinnedCylinder.rst
@@ -0,0 +1,4 @@
+EnergyInBinnedCylinder.txt
+--------------------------
+
+.. literalinclude:: /examples/Scoring/EnergyInBinnedCylinder.txt
diff --git a/examples-docs/Scoring/Filters.rst b/examples-docs/Scoring/Filters.rst
@@ -0,0 +1,4 @@
+Filters.txt
+-----------
+
+.. literalinclude:: /examples/Scoring/Filters.txt
diff --git a/examples-docs/Scoring/FoilToBox.rst b/examples-docs/Scoring/FoilToBox.rst
@@ -0,0 +1,4 @@
+FoilToBox.txt
+-------------
+
+.. literalinclude:: /examples/Scoring/FoilToBox.txt
diff --git a/examples-docs/Scoring/FoilToCylinder.rst b/examples-docs/Scoring/FoilToCylinder.rst
@@ -0,0 +1,4 @@
+FoilToCylinder.txt
+------------------
+
+.. literalinclude:: /examples/Scoring/FoilToCylinder.txt
diff --git a/examples-docs/Scoring/FoilToSphere.rst b/examples-docs/Scoring/FoilToSphere.rst
@@ -0,0 +1,4 @@
+FoilToSphere.txt
+----------------
+
+.. literalinclude:: /examples/Scoring/FoilToSphere.txt
diff --git a/examples-docs/Scoring/Gated.rst b/examples-docs/Scoring/Gated.rst
@@ -0,0 +1,4 @@
+Gated.txt
+---------
+
+.. literalinclude:: /examples/Scoring/Gated.txt
diff --git a/examples-docs/Scoring/GeometryDivisions.rst b/examples-docs/Scoring/GeometryDivisions.rst
@@ -0,0 +1,4 @@
+GeometryDivisions.txt
+---------------------
+
+.. literalinclude:: /examples/Scoring/GeometryDivisions.txt
diff --git a/examples-docs/Scoring/Histograms.rst b/examples-docs/Scoring/Histograms.rst
@@ -0,0 +1,4 @@
+Histograms.txt
+--------------
+
+.. literalinclude:: /examples/Scoring/Histograms.txt
diff --git a/examples-docs/Scoring/Inactive.rst b/examples-docs/Scoring/Inactive.rst
@@ -0,0 +1,4 @@
+Inactive.txt
+------------
+
+.. literalinclude:: /examples/Scoring/Inactive.txt
diff --git a/examples-docs/Scoring/Ion.rst b/examples-docs/Scoring/Ion.rst
@@ -0,0 +1,4 @@
+Ion.txt
+-------
+
+.. literalinclude:: /examples/Scoring/Ion.txt
diff --git a/examples-docs/Scoring/Origin.rst b/examples-docs/Scoring/Origin.rst
@@ -0,0 +1,4 @@
+Origin.txt
+----------
+
+.. literalinclude:: /examples/Scoring/Origin.txt
diff --git a/examples-docs/Scoring/ParallelBoxRebinned.rst b/examples-docs/Scoring/ParallelBoxRebinned.rst
@@ -0,0 +1,4 @@
+ParallelBoxRebinned.txt
+-----------------------
+
+.. literalinclude:: /examples/Scoring/ParallelBoxRebinned.txt
diff --git a/examples-docs/Scoring/SplitByTimeFeature.rst b/examples-docs/Scoring/SplitByTimeFeature.rst
@@ -0,0 +1,4 @@
+SplitByTimeFeature.txt
+----------------------
+
+.. literalinclude:: /examples/Scoring/SplitByTimeFeature.txt
diff --git a/examples-docs/Scoring/Surfaces.rst b/examples-docs/Scoring/Surfaces.rst
@@ -0,0 +1,4 @@
+Surfaces.txt
+------------
+
+.. literalinclude:: /examples/Scoring/Surfaces.txt