Merge branch 'master'

8 files changed, 327 insertions, 2 deletions

diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd
index 35dea5f..4a4ce43 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":
@@ -224,6 +226,7 @@ cdef extern from "astra/Float32VolumeData3DMemory.h" namespace "astra":
 		int getRowCount()
 		int getColCount()
 		int getSliceCount()
+		bool isInitialized()
 
 
 
@@ -255,6 +258,7 @@ cdef extern from "astra/Float32ProjectionData3DMemory.h" namespace "astra":
 		int getDetectorColCount()
 		int getDetectorRowCount()
 		int getAngleCount()
+		bool isInitialized()
 
 cdef extern from "astra/Float32Data3D.h" namespace "astra":
 	cdef cppclass CFloat32Data3D:
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/creators.py b/python/astra/creators.py
index 68bc8a2..f3474d8 100644
--- a/python/astra/creators.py
+++ b/python/astra/creators.py
@@ -72,6 +72,10 @@ This method can be called in a number of ways:
 ``create_vol_geom(M, N, Z)``:
     :returns: A 3D volume geometry of size :math:`M \\times N \\times Z`.
 
+``create_vol_geom(M, N, Z, minx, maxx, miny, maxy, minz, maxz)``:
+    :returns: A 3D volume geometry of size :math:`M \\times N \\times Z`, windowed as :math:`minx \\leq x \\leq maxx` and :math:`miny \\leq y \\leq maxy` and :math:`minz \\leq z \\leq maxz` .
+
+
 """
     vol_geom = {'option': {}}
     # astra_create_vol_geom(row_count)
@@ -122,6 +126,17 @@ This method can be called in a number of ways:
         vol_geom['GridRowCount'] = varargin[0]
         vol_geom['GridColCount'] = varargin[1]
         vol_geom['GridSliceCount'] = varargin[2]
+    # astra_create_vol_geom(row_count, col_count, slice_count, min_x, max_x, min_y, max_y, min_z, max_z)
+    elif len(varargin) == 9:
+        vol_geom['GridRowCount'] = varargin[0]
+        vol_geom['GridColCount'] = varargin[1]
+        vol_geom['GridSliceCount'] = varargin[2]
+        vol_geom['option']['WindowMinX'] = varargin[3]
+        vol_geom['option']['WindowMaxX'] = varargin[4]
+        vol_geom['option']['WindowMinY'] = varargin[5]
+        vol_geom['option']['WindowMaxY'] = varargin[6]
+        vol_geom['option']['WindowMinZ'] = varargin[7]
+        vol_geom['option']['WindowMaxZ'] = varargin[8]
     return vol_geom
 
 
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/experimental.pyx b/python/astra/experimental.pyx
new file mode 100644
index 0000000..da27504
--- /dev/null
+++ b/python/astra/experimental.pyx
@@ -0,0 +1,84 @@
+#-----------------------------------------------------------------------
+# Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp
+#            2014-2015, CWI, Amsterdam
+#
+# Contact: astra@uantwerpen.be
+# Website: http://sf.net/projects/astra-toolbox
+#
+# This file is part of the ASTRA Toolbox.
+#
+#
+# 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 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 ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+#
+#-----------------------------------------------------------------------
+
+# distutils: language = c++
+# distutils: libraries = astra
+
+include "config.pxi"
+
+import six
+from .PyIncludes cimport *
+from libcpp.vector cimport vector
+
+cdef extern from "astra/CompositeGeometryManager.h" namespace "astra":
+    cdef cppclass CCompositeGeometryManager:
+        bool doFP(CProjector3D *, vector[CFloat32VolumeData3DMemory *], vector[CFloat32ProjectionData3DMemory *])
+        bool doBP(CProjector3D *, vector[CFloat32VolumeData3DMemory *], vector[CFloat32ProjectionData3DMemory *])
+
+cdef extern from *:
+    CFloat32VolumeData3DMemory * dynamic_cast_vol_mem "dynamic_cast<astra::CFloat32VolumeData3DMemory*>" (CFloat32Data3D * ) except NULL
+    CFloat32ProjectionData3DMemory * dynamic_cast_proj_mem "dynamic_cast<astra::CFloat32ProjectionData3DMemory*>" (CFloat32Data3D * ) except NULL
+
+cimport PyProjector3DManager
+from .PyProjector3DManager cimport CProjector3DManager
+cimport PyData3DManager
+from .PyData3DManager cimport CData3DManager
+
+cdef CProjector3DManager * manProj = <CProjector3DManager * >PyProjector3DManager.getSingletonPtr()
+cdef CData3DManager * man3d = <CData3DManager * >PyData3DManager.getSingletonPtr()
+
+def do_composite(projector_id, vol_ids, proj_ids, t):
+    cdef vector[CFloat32VolumeData3DMemory *] vol
+    cdef CFloat32VolumeData3DMemory * pVolObject
+    cdef CFloat32ProjectionData3DMemory * pProjObject
+    for v in vol_ids:
+        pVolObject = dynamic_cast_vol_mem(man3d.get(v))
+        if pVolObject == NULL:
+            raise Exception("Data object not found")
+        if not pVolObject.isInitialized():
+            raise Exception("Data object not initialized properly")
+        vol.push_back(pVolObject)
+    cdef vector[CFloat32ProjectionData3DMemory *] proj
+    for v in proj_ids:
+        pProjObject = dynamic_cast_proj_mem(man3d.get(v))
+        if pProjObject == NULL:
+            raise Exception("Data object not found")
+        if not pProjObject.isInitialized():
+            raise Exception("Data object not initialized properly")
+        proj.push_back(pProjObject)
+    cdef CCompositeGeometryManager m
+    cdef CProjector3D * projector = manProj.get(projector_id) # may be NULL
+    if t == "FP":
+        if not m.doFP(projector, vol, proj):
+            raise Exception("Failed to perform FP")
+    else:
+        if not m.doBP(projector, vol, proj):
+            raise Exception("Failed to perform BP")
+
+def do_composite_FP(projector_id, vol_ids, proj_ids):
+    do_composite(projector_id, vol_ids, proj_ids, "FP")
+
+def do_composite_BP(projector_id, vol_ids, proj_ids):
+    do_composite(projector_id, vol_ids, proj_ids, "BP")
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