diff options
| -rw-r--r-- | docs/source/astra.rst | 32 | ||||
| -rwxr-xr-x | docs/source/conf.py | 4 | ||||
| -rw-r--r-- | docs/source/contrib.rst | 14 | ||||
| -rw-r--r-- | docs/source/framework.rst | 37 | ||||
| -rwxr-xr-x | docs/source/index.rst | 4 | ||||
| -rw-r--r-- | docs/source/io.rst | 20 | ||||
| -rw-r--r-- | docs/source/optimisation.rst | 43 | ||||
| -rw-r--r-- | docs/source/plugins.rst | 34 |
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>` |