updated documentation with all classes

8 files changed, 182 insertions, 6 deletions

diff --git a/docs/source/astra.rst b/docs/source/astra.rst
new file mode 100644
index 0000000..602ce31
--- /dev/null
+++ b/docs/source/astra.rst
@@ -0,0 +1,32 @@
+Astra plugin
+************
+
+Processors
+=====
+
+.. autoclass:: ccpi.astra.processors.AstraBackProjector
+   :members:
+.. autoclass:: ccpi.astra.processors.AstraBackProjector3D
+   :members:
+.. autoclass:: ccpi.astra.processors.AstraBackProjectorMC
+   :members:
+.. autoclass:: ccpi.astra.processors.AstraForwardProjector
+   :members:
+.. autoclass:: ccpi.astra.processors.AstraForwardProjector3D
+   :members:
+.. autoclass:: ccpi.astra.processors.AstraForwardProjectorMC
+   :members:
+|
+
+Operators
+=========
+.. autoclass:: ccpi.astra.operators.AstraProjectorSimple
+   :members:
+.. autoclass:: ccpi.astra.operators.AstraProjector3DSimple
+   :members:
+.. autoclass:: ccpi.astra.operators.AstraProjectorMC
+   :members:
+|
+
+
+:ref:`Return Home <mastertoc>`
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 406877b..62790cc 100755
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -24,9 +24,9 @@ copyright = '2019, Edoardo Pasca'
 author = 'Edoardo Pasca'

 

 # The short X.Y version

-version = ''

+version = '19.07'

 # The full version, including alpha/beta/rc tags

-release = '19.02'

+release = '19.07'

 

 

 # -- General configuration ---------------------------------------------------

diff --git a/docs/source/contrib.rst b/docs/source/contrib.rst
new file mode 100644
index 0000000..bc07fa1
--- /dev/null
+++ b/docs/source/contrib.rst
@@ -0,0 +1,14 @@
+Contributed code
+****************
+
+
+Stochastic PDHG 
+===============
+Contributed by Dr. Matthias Ehrhardt.
+
+.. autoclass:: ccpi.contrib.optimisation.algorithms.spdhg.spdhg
+   :members:
+|
+
+
+:ref:`Return Home <mastertoc>`
diff --git a/docs/source/framework.rst b/docs/source/framework.rst
index 4da0d6a..2b8ebf0 100644
--- a/docs/source/framework.rst
+++ b/docs/source/framework.rst
@@ -1,20 +1,51 @@
-DataContainers and Geometry
-========================================
+Framework 
+*********
 |
 
+DataContainer and subclasses
+============================
 .. autoclass:: ccpi.framework.DataContainer
    :members:
+   :private-members:
+   :special-members:
 .. autoclass:: ccpi.framework.ImageData
    :members:
 .. autoclass:: ccpi.framework.AcquisitionData
    :members:
-.. autoclass:: ccpi.framework.AcquisitionGeometry
+.. autoclass:: ccpi.framework.VectorData
    :members:
+
 .. autoclass:: ccpi.framework.ImageGeometry
    :members:
+.. autoclass:: ccpi.framework.AcquisitionGeometry
+   :members:
+.. autoclass:: ccpi.framework.VectorGeometry
+   :members:
+|
+
+Block Framework 
+===============
+.. autoclass:: ccpi.framework.BlockDataContainer
+   :members:
+   :private-members:
+   :special-members:
+.. autoclass:: ccpi.framework.BlockGeometry
+   :members:
+   :private-members:
+   :special-members:
+
+|
+DataProcessor
+=============
 .. autoclass:: ccpi.framework.DataProcessor
    :members:
 
+.. autoclass:: ccpi.processors.CenterOfRotationFinder
+   :members:
+.. autoclass:: ccpi.processors.Normalizer
+   :members:
+.. autoclass:: ccpi.processors.Resizer
+   :members:
 |
 
 :ref:`Return Home <mastertoc>`
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 4342bec..654a083 100755
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -14,6 +14,10 @@ Welcome to CCPi-Framework's documentation!
 

    framework

    optimisation

+   io

+   plugins

+   astra

+   contrib

 

 Indices and tables

 ==================

diff --git a/docs/source/io.rst b/docs/source/io.rst
new file mode 100644
index 0000000..91ddcae
--- /dev/null
+++ b/docs/source/io.rst
@@ -0,0 +1,20 @@
+Input/Output
+************
+
+NeXus
+=====
+
+.. autoclass:: ccpi.io.NEXUSDataReader
+   :members:
+.. autoclass:: ccpi.io.NEXUSDataWriter
+   :members:
+|
+
+Nikon
+=====
+.. autoclass:: ccpi.io.NikonDataReader
+   :members:
+|
+
+
+:ref:`Return Home <mastertoc>`
diff --git a/docs/source/optimisation.rst b/docs/source/optimisation.rst
index 7c1eda6..51b6cc3 100644
--- a/docs/source/optimisation.rst
+++ b/docs/source/optimisation.rst
@@ -16,7 +16,11 @@ Algorithm
 =========
 
 A number of generic algorithm implementations are provided including 
-Gradient Descent CGLS and FISTA. An algorithm is designed for a 
+Gradient Descent (GD), Conjugate Gradient Least Squares (CGLS), 
+Simultaneous Iterative Reconstruction Technique (SIRT), Primal Dual Hybrid 
+Gradient (PDHG) and Fast Iterative Shrinkage Thresholding Algorithm (FISTA).
+
+An algorithm is designed for a 
 particular generic optimisation problem accepts and number of 
 Functions and/or Operators as input to define a specific instance of 
 the generic optimisation problem to be solved.
@@ -67,6 +71,25 @@ forward and backprojection operations.
    :members:
 .. autoclass:: ccpi.optimisation.operators.ScaledOperator
    :members:
+.. autoclass:: ccpi.optimisation.operators.GradientOperator
+   :members:
+.. autoclass:: ccpi.optimisation.operators.Identity
+   :members:
+.. autoclass:: ccpi.optimisation.operators.LinearOperatorMatrix
+   :members:
+.. autoclass:: ccpi.optimisation.operators.ShrinkageOperator
+   :members:
+.. autoclass:: ccpi.optimisation.operators.SparseFiniteDiff
+   :members:
+.. autoclass:: ccpi.optimisation.operators.SymmetrizedGradientOperator
+   :members:
+.. autoclass:: ccpi.optimisation.operators.ZeroOperator
+   :members:
+.. autoclass:: ccpi.optimisation.operators.BlockOperator
+   :members:
+.. autoclass:: ccpi.optimisation.operators.BlockScaledOperator
+   :members:
+
 
 Function
 ========
@@ -87,6 +110,24 @@ e.g. :code:`f(x)` for a :code:`Function f` and input point :code:`x`.
 
 .. autoclass:: ccpi.optimisation.functions.Function
    :members:
+.. autoclass:: ccpi.optimisation.functions.FunctionOperatorComposition
+   :members:
+.. autoclass:: ccpi.optimisation.functions.IndicatorBox
+   :members:
+.. autoclass:: ccpi.optimisation.functions.KullbackLeibler
+   :members:
+.. autoclass:: ccpi.optimisation.functions.L1Norm
+   :members:
+.. autoclass:: ccpi.optimisation.functions.L2NormSquared
+   :members:
+.. autoclass:: ccpi.optimisation.functions.MixedL21Norm
+   :members:
+.. autoclass:: ccpi.optimisation.functions.Norm2Sq
+   :members:
+.. autoclass:: ccpi.optimisation.functions.ScaledFunction
+   :members:
+.. autoclass:: ccpi.optimisation.functions.ZeroFunction
+   :members:
 
 
 :ref:`Return Home <mastertoc>`
diff --git a/docs/source/plugins.rst b/docs/source/plugins.rst
new file mode 100644
index 0000000..8788db8
--- /dev/null
+++ b/docs/source/plugins.rst
@@ -0,0 +1,34 @@
+CCPi Plugins
+************
+
+Operators
+=========
+
+.. autoclass:: ccpi.plugins.operators.CCPiProjectorSimple
+   :members:
+|
+
+Processors
+==========
+.. autoclass:: ccpi.plugins.processors.AcquisitionDataPadder
+   :members:
+.. autoclass:: ccpi.plugins.processors.CCPiForwardProjector
+   :members:
+.. autoclass:: ccpi.plugins.processors.CCPiBackwardProjector
+   :members:
+.. autoclass:: ccpi.plugins.processors.setupCCPiGeometries
+   :members:
+|
+
+Regularisers
+============
+
+.. autoclass:: ccpi.plugins.regularisers.ROF_TV
+   :members:
+.. autoclass:: ccpi.plugins.regularisers.FGP_TV
+   :members:
+.. autoclass:: ccpi.plugins.regularisers.SB_TV
+   :members:
+
+
+:ref:`Return Home <mastertoc>`