Merge pull request #73 from dmpelt/python-plugins

Add support for Python algorithm plugins

8 files changed, 235 insertions, 2 deletions

diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd
index 35dea5f..77346b0 100644
--- a/python/astra/PyIncludes.pxd
+++ b/python/astra/PyIncludes.pxd
@@ -62,6 +62,7 @@ cdef extern from "astra/VolumeGeometry2D.h" namespace "astra":
 		float32 getWindowMaxX()
 		float32 getWindowMaxY()
 		Config* getConfiguration()
+		bool isEqual(CVolumeGeometry2D*)
 
 cdef extern from "astra/Float32Data2D.h" namespace "astra":
 	cdef cppclass CFloat32CustomMemory:
@@ -89,6 +90,7 @@ cdef extern from "astra/ProjectionGeometry2D.h" namespace "astra":
 		float32 getProjectionAngle(int)
 		float32 getDetectorWidth()
 		Config* getConfiguration()
+		bool isEqual(CProjectionGeometry2D*)
 
 cdef extern from "astra/Float32Data2D.h" namespace "astra::CFloat32Data2D":
 	cdef enum TWOEDataType "astra::CFloat32Data2D::EDataType":
diff --git a/python/astra/__init__.py b/python/astra/__init__.py
index 6c15d30..10ed74d 100644
--- a/python/astra/__init__.py
+++ b/python/astra/__init__.py
@@ -34,6 +34,7 @@ from . import algorithm
 from . import projector
 from . import projector3d
 from . import matrix
+from . import plugin
 from . import log
 from .optomo import OpTomo
 
diff --git a/python/astra/data2d_c.pyx b/python/astra/data2d_c.pyx
index 4919bf2..801fd8e 100644
--- a/python/astra/data2d_c.pyx
+++ b/python/astra/data2d_c.pyx
@@ -34,6 +34,9 @@ from cython cimport view
 cimport PyData2DManager
 from .PyData2DManager cimport CData2DManager
 
+cimport PyProjector2DManager
+from .PyProjector2DManager cimport CProjector2DManager
+
 cimport PyXMLDocument
 from .PyXMLDocument cimport XMLDocument
 
@@ -54,6 +57,8 @@ import operator
 from six.moves import reduce
 
 cdef CData2DManager * man2d = <CData2DManager * >PyData2DManager.getSingletonPtr()
+cdef CProjector2DManager * manProj = <CProjector2DManager * >PyProjector2DManager.getSingletonPtr()
+
 
 cdef extern from "CFloat32CustomPython.h":
     cdef cppclass CFloat32CustomPython:
@@ -164,7 +169,6 @@ def store(i, data):
     cdef CFloat32Data2D * pDataObject = getObject(i)
     fillDataObject(pDataObject, data)
 
-
 def get_geometry(i):
     cdef CFloat32Data2D * pDataObject = getObject(i)
     cdef CFloat32ProjectionData2D * pDataObject2
@@ -179,6 +183,27 @@ def get_geometry(i):
         raise Exception("Not a known data object")
     return geom
 
+cdef CProjector2D * getProjector(i) except NULL:
+    cdef CProjector2D * proj = manProj.get(i)
+    if proj == NULL:
+        raise Exception("Projector not initialized.")
+    if not proj.isInitialized():
+        raise Exception("Projector not initialized.")
+    return proj
+
+def check_compatible(i, proj_id):
+    cdef CProjector2D * proj = getProjector(proj_id)
+    cdef CFloat32Data2D * pDataObject = getObject(i)
+    cdef CFloat32ProjectionData2D * pDataObject2
+    cdef CFloat32VolumeData2D * pDataObject3
+    if pDataObject.getType() == TWOPROJECTION:
+        pDataObject2 = <CFloat32ProjectionData2D * >pDataObject
+        return pDataObject2.getGeometry().isEqual(proj.getProjectionGeometry())
+    elif pDataObject.getType() == TWOVOLUME:
+        pDataObject3 = <CFloat32VolumeData2D * >pDataObject
+        return pDataObject3.getGeometry().isEqual(proj.getVolumeGeometry())
+    else:
+        raise Exception("Not a known data object")
 
 def change_geometry(i, geom):
     cdef Config *cfg
diff --git a/python/astra/plugin.py b/python/astra/plugin.py
new file mode 100644
index 0000000..3e3528d
--- /dev/null
+++ b/python/astra/plugin.py
@@ -0,0 +1,121 @@
+#-----------------------------------------------------------------------
+#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
+#
+#Author: Daniel M. Pelt
+#Contact: D.M.Pelt@cwi.nl
+#Website: http://dmpelt.github.io/pyastratoolbox/
+#
+#
+#This file is part of the Python interface to the
+#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
+#
+#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify
+#it under the terms of the GNU General Public License as published by
+#the Free Software Foundation, either version 3 of the License, or
+#(at your option) any later version.
+#
+#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,
+#but WITHOUT ANY WARRANTY; without even the implied warranty of
+#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+#GNU General Public License for more details.
+#
+#You should have received a copy of the GNU General Public License
+#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+#
+#-----------------------------------------------------------------------
+
+from . import plugin_c as p
+from . import log
+from . import data2d
+from . import data2d_c
+from . import data3d
+from . import projector
+import inspect
+import traceback
+
+class base(object):
+
+    def astra_init(self, cfg):
+        args, varargs, varkw, defaults = inspect.getargspec(self.initialize)
+        if not defaults is None:
+            nopt = len(defaults)
+        else:
+            nopt = 0
+        if nopt>0:
+            req = args[2:-nopt]
+            opt = args[-nopt:]
+        else:
+            req = args[2:]
+            opt = []
+
+        try:
+            optDict = cfg['options']
+        except KeyError:
+            optDict = {}
+
+        cfgKeys = set(optDict.keys())
+        reqKeys = set(req)
+        optKeys = set(opt)
+
+        if not reqKeys.issubset(cfgKeys):
+            for key in reqKeys.difference(cfgKeys):
+                log.error("Required option '" + key + "' for plugin '" + self.__class__.__name__ + "' not specified")
+            raise ValueError("Missing required options")
+
+        if not cfgKeys.issubset(reqKeys | optKeys):
+            log.warn(self.__class__.__name__ + ": unused configuration option: " + str(list(cfgKeys.difference(reqKeys | optKeys))))
+
+        args = [optDict[k] for k in req]
+        kwargs = dict((k,optDict[k]) for k in opt if k in optDict)
+        self.initialize(cfg, *args, **kwargs)
+
+class ReconstructionAlgorithm2D(base):
+
+    def astra_init(self, cfg):
+        self.pid = cfg['ProjectorId']
+        self.s = data2d.get_shared(cfg['ProjectionDataId'])
+        self.v = data2d.get_shared(cfg['ReconstructionDataId'])
+        self.vg = projector.volume_geometry(self.pid)
+        self.pg = projector.projection_geometry(self.pid)
+        if not data2d_c.check_compatible(cfg['ProjectionDataId'], self.pid):
+            raise ValueError("Projection data and projector not compatible")
+        if not data2d_c.check_compatible(cfg['ReconstructionDataId'], self.pid):
+            raise ValueError("Reconstruction data and projector not compatible")
+        super(ReconstructionAlgorithm2D,self).astra_init(cfg)
+
+class ReconstructionAlgorithm3D(base):
+
+    def astra_init(self, cfg):
+        self.pid = cfg['ProjectorId']
+        self.s = data3d.get_shared(cfg['ProjectionDataId'])
+        self.v = data3d.get_shared(cfg['ReconstructionDataId'])
+        self.vg = data3d.get_geometry(cfg['ReconstructionDataId'])
+        self.pg = data3d.get_geometry(cfg['ProjectionDataId'])
+        super(ReconstructionAlgorithm3D,self).astra_init(cfg)
+
+def register(className):
+    """Register plugin with ASTRA.
+    
+    :param className: Class name or class object to register
+    :type className: :class:`str` or :class:`class`
+    
+    """
+    p.register(className)
+
+def get_registered():
+    """Get dictionary of registered plugins.
+    
+    :returns: :class:`dict` -- Registered plugins.
+    
+    """
+    return p.get_registered()
+
+def get_help(name):
+    """Get help for registered plugin.
+    
+    :param name: Plugin name to get help for
+    :type name: :class:`str`
+    :returns: :class:`str` -- Help string (docstring).
+    
+    """
+    return p.get_help(name)
\ No newline at end of file
diff --git a/python/astra/plugin_c.pyx b/python/astra/plugin_c.pyx
new file mode 100644
index 0000000..8d6816b
--- /dev/null
+++ b/python/astra/plugin_c.pyx
@@ -0,0 +1,67 @@
+#-----------------------------------------------------------------------
+#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
+#
+#Author: Daniel M. Pelt
+#Contact: D.M.Pelt@cwi.nl
+#Website: http://dmpelt.github.io/pyastratoolbox/
+#
+#
+#This file is part of the Python interface to the
+#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
+#
+#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify
+#it under the terms of the GNU General Public License as published by
+#the Free Software Foundation, either version 3 of the License, or
+#(at your option) any later version.
+#
+#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,
+#but WITHOUT ANY WARRANTY; without even the implied warranty of
+#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+#GNU General Public License for more details.
+#
+#You should have received a copy of the GNU General Public License
+#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+#
+#-----------------------------------------------------------------------
+# distutils: language = c++
+# distutils: libraries = astra
+
+import six
+import inspect
+
+from libcpp.string cimport string
+from libcpp cimport bool
+
+cdef CPluginAlgorithmFactory *fact = getSingletonPtr()
+
+from . import utils
+
+cdef extern from "astra/PluginAlgorithm.h" namespace "astra":
+    cdef cppclass CPluginAlgorithmFactory:
+        bool registerPlugin(string className)
+        bool registerPlugin(string name, string className)
+        bool registerPluginClass(object className)
+        bool registerPluginClass(string name, object className)
+        object getRegistered()
+        string getHelp(string name)
+
+cdef extern from "astra/PluginAlgorithm.h" namespace "astra::CPluginAlgorithmFactory":
+    cdef CPluginAlgorithmFactory* getSingletonPtr()
+
+def register(className, name=None):
+    if inspect.isclass(className):
+        if name==None:
+            fact.registerPluginClass(className)
+        else:
+            fact.registerPluginClass(six.b(name), className)
+    else:
+        if name==None:
+            fact.registerPlugin(six.b(className))
+        else:
+            fact.registerPlugin(six.b(name), six.b(className))
+
+def get_registered():
+    return fact.getRegistered()
+
+def get_help(name):
+    return utils.wrap_from_bytes(fact.getHelp(six.b(name)))
diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx
index 260c308..07727ce 100644
--- a/python/astra/utils.pyx
+++ b/python/astra/utils.pyx
@@ -29,9 +29,13 @@
 cimport numpy as np
 import numpy as np
 import six
+if six.PY3:
+    import builtins
+else:
+    import __builtin__
 from libcpp.string cimport string
-from libcpp.list cimport list
 from libcpp.vector cimport vector
+from libcpp.list cimport list
 from cython.operator cimport dereference as deref, preincrement as inc
 from cpython.version cimport PY_MAJOR_VERSION
 
@@ -91,6 +95,8 @@ cdef void readDict(XMLNode root, _dc):
     dc = convert_item(_dc)
     for item in dc:
         val = dc[item]
+        if isinstance(val, __builtins__.list) or isinstance(val, tuple):
+            val = np.array(val,dtype=np.float64)
         if isinstance(val, np.ndarray):
             if val.size == 0:
                 break
@@ -125,6 +131,8 @@ cdef void readOptions(XMLNode node, dc):
         val = dc[item]
         if node.hasOption(item):
             raise Exception('Duplicate Option: %s' % item)
+        if isinstance(val, __builtins__.list) or isinstance(val, tuple):
+            val = np.array(val,dtype=np.float64)
         if isinstance(val, np.ndarray):
             if val.size == 0:
                 break
diff --git a/python/docSRC/index.rst b/python/docSRC/index.rst
index b7cc6d6..dcc6590 100644
--- a/python/docSRC/index.rst
+++ b/python/docSRC/index.rst
@@ -19,6 +19,7 @@ Contents:
    creators
    functions
    operator
+   plugins
    matlab
    astra
 .. astra
diff --git a/python/docSRC/plugins.rst b/python/docSRC/plugins.rst
new file mode 100644
index 0000000..dc7c607
--- /dev/null
+++ b/python/docSRC/plugins.rst
@@ -0,0 +1,8 @@
+Plugins: the :mod:`plugin` module
+=========================================
+
+.. automodule:: astra.plugin
+    :members:
+    :undoc-members:
+    :show-inheritance:
+