updated docs & added submodule API docs. Docstring tweaks. Dropped na…

…poleon from requirements & bumped pydicom
jrkerns · Jan 29, 2015 · 8a51582 · 8a51582
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diff --git a/docs/source/cbct_docs.rst b/docs/source/cbct_docs.rst
@@ -7,6 +7,7 @@ Overview
 --------
 
 .. automodule:: pylinac.cbct
+    :no-members:
 
 Running the Demo
 ----------------
@@ -87,13 +88,12 @@ The CBCT module is based on the tests and values given in the CatPhan 504 Manual
 
 **Restrictions**
 
-    .. warning:: Analysis can catastrophically fail or give unreliable results if any Restriction is violated.
+    .. warning:: Analysis can fail or give unreliable results if any Restriction is violated.
 
 * The phantom used must be an unmodified CatPhan 504, as endorsed and supplied by Varian.
 * The phantom must have <0.5cm offset in the z (In-Out) direction (work to remove this is in the plans).
 
 
-
 **Pre-Analysis**
 
 * **Determine image properties** -- Upon load, the image set is analyzed for its DICOM properties to determine mm/pixel
@@ -148,54 +148,43 @@ The CBCT class uses several other classes. There are several Slices of Interest
 SoIs have a base class as well as specialized classes for each specific slice.
 
 .. autoclass:: pylinac.cbct.CBCT
-    :members:
-    :inherited-members:
+    :no-show-inheritance:
 
 Supporting Data Structure
 
 .. autoclass:: pylinac.cbct.Algo_Data
-    :members:
+    :no-show-inheritance:
 
 Slice Objects
 
 .. autoclass:: pylinac.cbct.HU_Slice
-    :members:
 
 .. autoclass:: pylinac.cbct.Base_HU_Slice
-    :members:
 
 .. autoclass:: pylinac.cbct.UNIF_Slice
-    :members:
 
 .. autoclass:: pylinac.cbct.GEO_Slice
-    :members:
 
 .. autoclass:: pylinac.cbct.SR_Slice
-    :members:
 
 .. autoclass:: pylinac.cbct.Locon_Slice
-    :members:
 
 .. autoclass:: pylinac.cbct.Slice
-    :members:
+    :no-show-inheritance:
 
 ROI Objects
 
 .. autoclass:: pylinac.cbct.HU_ROI
-    :members:
 
 .. autoclass:: pylinac.cbct.GEO_ROI
-    :members:
 
 .. autoclass:: pylinac.cbct.SR_Circle_ROI
-    :members:
 
 .. autoclass:: pylinac.cbct.ROI_Disk
-    :members:
 
 .. autoclass:: pylinac.cbct.ROI
-    :members:
+    :no-show-inheritance:
 
 .. autoclass:: pylinac.cbct.GEO_Line
-    :members:
+
 
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -35,6 +35,8 @@
 for mod_name in MOCK_MODULES:
     sys.modules[mod_name] = mock.Mock()
 
+# TODO: replace above with: autodoc_mock_imports when RTD upgrades to v1.3; http://sphinx-doc.org/latest/ext/autodoc.html#confval-autodoc_mock_imports
+
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -66,6 +68,7 @@
 copyright = '2015, James Kerns'
 # Document both class docstring and __init__ docstring. See: http://sphinx-doc.org/ext/autodoc.html#confval-autoclass_content
 autoclass_content = 'both'
+autodoc_default_flags = ['members', 'show-inheritance']  # See: http://sphinx-doc.org/latest/ext/autodoc.html#confval-autodoc_default_flags
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

diff --git a/docs/source/core_modules.rst b/docs/source/core_modules.rst
@@ -0,0 +1,31 @@
+==========================
+Core Modules Documentation
+==========================
+
+The following is the API documentation for the core modules of pylinac. These can be used
+directly, or as the base for mixin classes or methods.
+
+Analysis Module
+---------------
+.. automodule:: pylinac.core.analysis
+    :no-show-inheritance:
+Image Module
+------------
+.. automodule:: pylinac.core.image
+
+Geometry Module
+---------------
+.. automodule:: pylinac.core.geometry
+
+IO Module
+---------
+.. automodule:: pylinac.core.io
+
+Utilities Module
+----------------
+.. automodule:: pylinac.core.utilities
+
+Decorators Module
+-----------------
+.. automodule:: pylinac.core.decorators
+
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -33,6 +33,7 @@ or jump right in by doing :ref:`installation` and then :ref:`getting_started`!
    starshot_docs
    vmat_docs
    cbct_docs
+   core_modules
 
 
 Indices and tables

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -40,7 +40,7 @@ Pylinac, as a scientific package, has fairly standard scientific dependencies (>
 * numpy >= 1.8
 * scipy >= 0.13
 * matplotlib >= 1.3.1; Image plotting
-* pydicom >= 0.9.8; For reading DICOM files
+* pydicom >= 0.9.9; For reading DICOM files
 * Pillow >= 2.5; For reading image files
 
 .. note::

diff --git a/docs/source/starshot_docs.rst b/docs/source/starshot_docs.rst
@@ -11,6 +11,7 @@ Overview
 --------
 
 .. automodule:: pylinac.starshot
+    :no-members:
 
 Running the Demo
 ----------------
@@ -84,7 +85,7 @@ Algorithm
 
 **Restrictions**
 
-    .. warning:: Analysis can catastrophically fail or give unreliable results if any Restriction is violated.
+    .. warning:: Analysis can fail or give unreliable results if any Restriction is violated.
 
 * The center of the "star" must be in the central 1/3 of the image.
 * The radiation spokes must extend to both sides of the center. I.e. the spokes must not end at the center of the circle.
@@ -123,14 +124,9 @@ API Documentation
 -----------------
 
 .. autoclass:: pylinac.starshot.Starshot
-    :members:
-    :inherited-members:
 
 .. autoclass:: pylinac.starshot.StarProfile
-    :members:
-    :inherited-members:
 
 .. autoclass:: pylinac.starshot.Wobble
-    :members:
-    :inherited-members:
+
 
diff --git a/docs/source/vmat_docs.rst b/docs/source/vmat_docs.rst
@@ -7,6 +7,7 @@ Overview
 --------
 
 .. automodule:: pylinac.vmat
+    :no-members:
 
 Running the Demo
 ----------------
@@ -90,7 +91,7 @@ The minimum needed to get going is to:
       dmlc_img = "C:/QA Folder/VMAT/dmlc_field.dcm"
       # load the images from the file path
       myvmat.load_image(open_img, im_type='open')
-      myvmat.load_image(mlc_img, im_type='mlc')
+      myvmat.load_image(dmlc_img, im_type='mlc')
 
       # *OR*
 
@@ -131,7 +132,7 @@ The algorithm works like such:
 
 **Restrictions**
 
-    .. warning:: Analysis can catastrophically fail or give unreliable results if any Restriction is violated.
+    .. warning:: Analysis can fail or give unreliable results if any Restriction is violated.
 
 * The tests must be delivered using the DICOM RT plan files provided by Varian which follow the test layout of Jorgensen et al.
 * The images must be acquired with the EPID.
@@ -145,6 +146,10 @@ The algorithm works like such:
 
 **Analysis**
 
+.. note::
+    Calculations tend to be lazy, computed only on demand. This represents a nominal analysis
+    where all calculations are performed.
+
 * **Calculate sample boundaries & extract** -- Because the Jorgensen tests are always the
   same in terms of where the radiation gets delivered, these values are hardcoded as offsets from the center pixel.
   These values are then scaled with the image scaling factor determined above. The mean of the pixel values within
@@ -166,14 +171,11 @@ API Documentation
 -----------------
 
 .. autoclass:: pylinac.vmat.VMAT
-    :members:
-    :inherited-members:
+    :no-show-inheritance:
 
 .. autoclass:: pylinac.vmat.Segment
-    :members:
-    :inherited-members:
+    :no-show-inheritance:
 
 .. autoclass:: pylinac.vmat.Sample
-    :members:
-    :inherited-members:
+