Merge branch 'master'

13 files changed, 498 insertions, 218 deletions

diff --git a/python/astra/ASTRAProjector.py b/python/astra/ASTRAProjector.py
deleted file mode 100644
index f282618..0000000
--- a/python/astra/ASTRAProjector.py
+++ /dev/null
@@ -1,135 +0,0 @@
-#-----------------------------------------------------------------------
-#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/>.
-#
-#-----------------------------------------------------------------------
-
-import math
-from . import creators as ac
-from . import data2d
-
-
-class ASTRAProjector2DTranspose():
-    """Implements the ``proj.T`` functionality.
-
-    Do not use directly, since it can be accessed as member ``.T`` of
-    an :class:`ASTRAProjector2D` object.
-
-    """
-    def __init__(self, parentProj):
-        self.parentProj = parentProj
-
-    def __mul__(self, data):
-        return self.parentProj.backProject(data)
-
-
-class ASTRAProjector2D(object):
-    """Helps with various common ASTRA Toolbox 2D operations.
-
-    This class can perform several often used toolbox operations, such as:
-
-    * Forward projecting
-    * Back projecting
-    * Reconstructing
-
-    Note that this class has a some computational overhead, because it
-    copies a lot of data. If you use many repeated operations, directly
-    using the PyAstraToolbox methods directly is faster.
-
-    You can use this class as an abstracted weight matrix :math:`W`: multiplying an instance
-    ``proj`` of this class by an image results in a forward projection of the image, and multiplying
-    ``proj.T`` by a sinogram results in a backprojection of the sinogram::
-
-        proj = ASTRAProjector2D(...)
-        fp = proj*image
-        bp = proj.T*sinogram
-
-    :param proj_geom: The projection geometry.
-    :type proj_geom: :class:`dict`
-    :param vol_geom: The volume geometry.
-    :type vol_geom: :class:`dict`
-    :param proj_type: Projector type, such as ``'line'``, ``'linear'``, ...
-    :type proj_type: :class:`string`
-    """
-
-    def __init__(self, proj_geom, vol_geom, proj_type):
-        self.vol_geom = vol_geom
-        self.recSize = vol_geom['GridColCount']
-        self.angles = proj_geom['ProjectionAngles']
-        self.nDet = proj_geom['DetectorCount']
-        nexpow = int(pow(2, math.ceil(math.log(2 * self.nDet, 2))))
-        self.filterSize = nexpow / 2 + 1
-        self.nProj = self.angles.shape[0]
-        self.proj_geom = proj_geom
-        self.proj_id = ac.create_projector(proj_type, proj_geom, vol_geom)
-        self.T = ASTRAProjector2DTranspose(self)
-
-    def backProject(self, data):
-        """Backproject a sinogram.
-
-        :param data: The sinogram data or ID.
-        :type data: :class:`numpy.ndarray` or :class:`int`
-        :returns: :class:`numpy.ndarray` -- The backprojection.
-
-        """
-        vol_id, vol = ac.create_backprojection(
-            data, self.proj_id, returnData=True)
-        data2d.delete(vol_id)
-        return vol
-
-    def forwardProject(self, data):
-        """Forward project an image.
-
-        :param data: The image data or ID.
-        :type data: :class:`numpy.ndarray` or :class:`int`
-        :returns: :class:`numpy.ndarray` -- The forward projection.
-
-        """
-        sin_id, sino = ac.create_sino(data, self.proj_id, returnData=True)
-        data2d.delete(sin_id)
-        return sino
-
-    def reconstruct(self, data, method, **kwargs):
-        """Reconstruct an image from a sinogram.
-
-        :param data: The sinogram data or ID.
-        :type data: :class:`numpy.ndarray` or :class:`int`
-        :param method: Name of the reconstruction algorithm.
-        :type method: :class:`string`
-        :param kwargs: Additional named parameters to pass to :func:`astra.creators.create_reconstruction`.
-        :returns: :class:`numpy.ndarray` -- The reconstruction.
-
-        Example of a SIRT reconstruction using CUDA::
-
-            proj = ASTRAProjector2D(...)
-            rec = proj.reconstruct(sinogram,'SIRT_CUDA',iterations=1000)
-
-        """
-        kwargs['returnData'] = True
-        rec_id, rec = ac.create_reconstruction(
-            method, self.proj_id, data, **kwargs)
-        data2d.delete(rec_id)
-        return rec
-
-    def __mul__(self, data):
-        return self.forwardProject(data)
diff --git a/python/astra/CFloat32CustomPython.h b/python/astra/CFloat32CustomPython.h
new file mode 100644
index 0000000..d8593fc
--- /dev/null
+++ b/python/astra/CFloat32CustomPython.h
@@ -0,0 +1,17 @@
+class CFloat32CustomPython : public astra::CFloat32CustomMemory {
+public:
+    CFloat32CustomPython(PyObject * arrIn)
+    {
+        arr = arrIn;
+        // Set pointer to numpy data pointer
+        m_fPtr = (float *)PyArray_DATA(arr);
+        // Increase reference count since ASTRA has a reference
+        Py_INCREF(arr);
+    }
+    virtual ~CFloat32CustomPython() {
+        // Decrease reference count since ASTRA object is destroyed
+        Py_DECREF(arr);
+    }
+private:
+    PyObject* arr;
+};
\ No newline at end of file
diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd
index 7df02c5..909f58f 100644
--- a/python/astra/PyIncludes.pxd
+++ b/python/astra/PyIncludes.pxd
@@ -43,7 +43,7 @@ cdef extern from "astra/Config.h" namespace "astra":
 	cdef cppclass Config:
 		Config()
 		void initialize(string rootname)
-		XMLNode *self
+		XMLNode self
 
 cdef extern from "astra/VolumeGeometry2D.h" namespace "astra":
 	cdef cppclass CVolumeGeometry2D:
@@ -63,10 +63,14 @@ cdef extern from "astra/VolumeGeometry2D.h" namespace "astra":
 		float32 getWindowMaxY()
 		Config* getConfiguration()
 
+cdef extern from "astra/Float32Data2D.h" namespace "astra":
+	cdef cppclass CFloat32CustomMemory:
+		pass
 
 cdef extern from "astra/Float32VolumeData2D.h" namespace "astra":
 	cdef cppclass CFloat32VolumeData2D:
 		CFloat32VolumeData2D(CVolumeGeometry2D*)
+		CFloat32VolumeData2D(CVolumeGeometry2D*, CFloat32CustomMemory*)
 		CVolumeGeometry2D * getGeometry()
 		int getWidth()
 		int getHeight()
@@ -130,6 +134,7 @@ cdef extern from "astra/ParallelProjectionGeometry2D.h" namespace "astra":
 cdef extern from "astra/Float32ProjectionData2D.h" namespace "astra":
 	cdef cppclass CFloat32ProjectionData2D:
 		CFloat32ProjectionData2D(CProjectionGeometry2D*)
+		CFloat32ProjectionData2D(CProjectionGeometry2D*, CFloat32CustomMemory*)
 		CProjectionGeometry2D * getGeometry()
 		void changeGeometry(CProjectionGeometry2D*)
 		int getDetectorCount()
@@ -196,18 +201,30 @@ cdef extern from "astra/VolumeGeometry3D.h" namespace "astra":
 		CVolumeGeometry3D()
 		bool initialize(Config)
 		Config * getConfiguration()
+		int getGridColCount()
+		int getGridRowCount()
+		int getGridSliceCount()
 
 cdef extern from "astra/ProjectionGeometry3D.h" namespace "astra":
 	cdef cppclass CProjectionGeometry3D:
 		CProjectionGeometry3D()
 		bool initialize(Config)
 		Config * getConfiguration()
+		int getProjectionCount()
+		int getDetectorColCount()
+		int getDetectorRowCount()
 
 
 cdef extern from "astra/Float32VolumeData3DMemory.h" namespace "astra":
 	cdef cppclass CFloat32VolumeData3DMemory:
 		CFloat32VolumeData3DMemory(CVolumeGeometry3D*)
+		CFloat32VolumeData3DMemory(CVolumeGeometry3D*, CFloat32CustomMemory*)
 		CVolumeGeometry3D* getGeometry()
+		void changeGeometry(CVolumeGeometry3D*)
+		int getRowCount()
+		int getColCount()
+		int getSliceCount()
+
 
 
 cdef extern from "astra/ParallelProjectionGeometry3D.h" namespace "astra":
@@ -231,7 +248,13 @@ cdef extern from "astra/Float32ProjectionData3DMemory.h" namespace "astra":
 	cdef cppclass CFloat32ProjectionData3DMemory:
 		CFloat32ProjectionData3DMemory(CProjectionGeometry3D*)
 		CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*)
+		CFloat32ProjectionData3DMemory(CProjectionGeometry3D*, CFloat32CustomMemory*)
+		CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*, CFloat32CustomMemory*)
 		CProjectionGeometry3D* getGeometry()
+		void changeGeometry(CProjectionGeometry3D*)
+		int getDetectorColCount()
+		int getDetectorRowCount()
+		int getAngleCount()
 
 cdef extern from "astra/Float32Data3D.h" namespace "astra":
 	cdef cppclass CFloat32Data3D:
diff --git a/python/astra/PyXMLDocument.pxd b/python/astra/PyXMLDocument.pxd
index 69781f1..033b8ef 100644
--- a/python/astra/PyXMLDocument.pxd
+++ b/python/astra/PyXMLDocument.pxd
@@ -44,22 +44,24 @@ cdef extern from "astra/Globals.h" namespace "astra":
 cdef extern from "astra/XMLNode.h" namespace "astra":
     cdef cppclass XMLNode:
         string getName()
-        XMLNode *addChildNode(string name)
-        XMLNode *addChildNode(string, string)
+        XMLNode addChildNode(string name)
+        XMLNode addChildNode(string, string)
         void addAttribute(string, string)
         void addAttribute(string, float32)
         void addOption(string, string)
         bool hasOption(string)
         string getAttribute(string)
-        list[XMLNode *] getNodes()
+        list[XMLNode] getNodes()
         vector[float32] getContentNumericalArray()
+        void setContent(double*, int, int, bool)
+        void setContent(double*, int)
         string getContent()
         bool hasAttribute(string)
 
 cdef extern from "astra/XMLDocument.h" namespace "astra":
     cdef cppclass XMLDocument:
         void saveToFile(string sFilename)
-        XMLNode *getRootNode()
+        XMLNode getRootNode()
         
 cdef extern from "astra/XMLDocument.h" namespace "astra::XMLDocument":
     cdef XMLDocument *createDocument(string rootname)
diff --git a/python/astra/__init__.py b/python/astra/__init__.py
index 063dc16..6c15d30 100644
--- a/python/astra/__init__.py
+++ b/python/astra/__init__.py
@@ -27,7 +27,6 @@ from . import matlab as m
 from .creators import astra_dict,create_vol_geom, create_proj_geom, create_backprojection, create_sino, create_reconstruction, create_projector,create_sino3d_gpu, create_backprojection3d_gpu
 from .functions import data_op, add_noise_to_sino, clear, move_vol_geom
 from .extrautils import clipCircle
-from .ASTRAProjector import ASTRAProjector2D
 from . import data2d
 from . import astra
 from . import data3d
@@ -36,6 +35,7 @@ from . import projector
 from . import projector3d
 from . import matrix
 from . import log
+from .optomo import OpTomo
 
 import os
 try:
diff --git a/python/astra/data2d.py b/python/astra/data2d.py
index 8c4be03..f119f05 100644
--- a/python/astra/data2d.py
+++ b/python/astra/data2d.py
@@ -24,6 +24,7 @@
 #
 #-----------------------------------------------------------------------
 from . import data2d_c as d
+import numpy as np
 
 def clear():
     """Clear all 2D data objects."""
@@ -52,6 +53,26 @@ def create(datatype, geometry, data=None):
     """
     return d.create(datatype,geometry,data)
 
+def link(datatype, geometry, data):
+    """Link a 2D numpy array with the toolbox.
+        
+    :param datatype: Data object type, '-vol' or '-sino'.
+    :type datatype: :class:`string`
+    :param geometry: Volume or projection geometry.
+    :type geometry: :class:`dict`
+    :param data: Numpy array to link
+    :type data: :class:`numpy.ndarray`
+    :returns: :class:`int` -- the ID of the constructed object.
+    
+    """
+    if not isinstance(data,np.ndarray):
+        raise ValueError("Input should be a numpy array")
+    if not data.dtype==np.float32:
+        raise ValueError("Numpy array should be float32")
+    if not (data.flags['C_CONTIGUOUS'] and data.flags['ALIGNED']):
+        raise ValueError("Numpy array should be C_CONTIGUOUS and ALIGNED")
+    return d.create(datatype,geometry,data,True)
+
 def store(i, data):
     """Fill existing 2D object with data.
     
diff --git a/python/astra/data2d_c.pyx b/python/astra/data2d_c.pyx
index b9c105e..4919bf2 100644
--- a/python/astra/data2d_c.pyx
+++ b/python/astra/data2d_c.pyx
@@ -47,8 +47,18 @@ from .PyIncludes cimport *
 cimport utils
 from .utils import wrap_from_bytes
 
+from .pythonutils import geom_size
+
+import operator
+
+from six.moves import reduce
+
 cdef CData2DManager * man2d = <CData2DManager * >PyData2DManager.getSingletonPtr()
 
+cdef extern from "CFloat32CustomPython.h":
+    cdef cppclass CFloat32CustomPython:
+        CFloat32CustomPython(arrIn)
+
 def clear():
     man2d.clear()
 
@@ -61,11 +71,16 @@ def delete(ids):
         man2d.remove(ids)
 
 
-def create(datatype, geometry, data=None):
+def create(datatype, geometry, data=None, link=False):
     cdef Config *cfg
     cdef CVolumeGeometry2D * pGeometry
     cdef CProjectionGeometry2D * ppGeometry
     cdef CFloat32Data2D * pDataObject2D
+    cdef CFloat32CustomMemory * pCustom
+
+    if link and data.shape!=geom_size(geometry):
+        raise Exception("The dimensions of the data do not match those specified in the geometry.")
+
     if datatype == '-vol':
         cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry)
         pGeometry = new CVolumeGeometry2D()
@@ -73,7 +88,11 @@ def create(datatype, geometry, data=None):
             del cfg
             del pGeometry
             raise Exception('Geometry class not initialized.')
-        pDataObject2D = <CFloat32Data2D * > new CFloat32VolumeData2D(pGeometry)
+        if link:
+            pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+            pDataObject2D = <CFloat32Data2D * > new CFloat32VolumeData2D(pGeometry, pCustom)
+        else:
+            pDataObject2D = <CFloat32Data2D * > new CFloat32VolumeData2D(pGeometry)
         del cfg
         del pGeometry
     elif datatype == '-sino':
@@ -91,7 +110,11 @@ def create(datatype, geometry, data=None):
             del cfg
             del ppGeometry
             raise Exception('Geometry class not initialized.')
-        pDataObject2D = <CFloat32Data2D * > new CFloat32ProjectionData2D(ppGeometry)
+        if link:
+            pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+            pDataObject2D = <CFloat32Data2D * > new CFloat32ProjectionData2D(ppGeometry, pCustom)
+        else:
+            pDataObject2D = <CFloat32Data2D * > new CFloat32ProjectionData2D(ppGeometry)
         del ppGeometry
         del cfg
     else:
@@ -101,7 +124,7 @@ def create(datatype, geometry, data=None):
         del pDataObject2D
         raise Exception("Couldn't initialize data object.")
 
-    fillDataObject(pDataObject2D, data)
+    if not link: fillDataObject(pDataObject2D, data)
 
     return man2d.store(pDataObject2D)
 
diff --git a/python/astra/data3d.py b/python/astra/data3d.py
index a2e9201..e5ef6b0 100644
--- a/python/astra/data3d.py
+++ b/python/astra/data3d.py
@@ -24,6 +24,7 @@
 #
 #-----------------------------------------------------------------------
 from . import data3d_c as d
+import numpy as np
 
 def create(datatype,geometry,data=None):
     """Create a 3D object.
@@ -39,6 +40,27 @@ def create(datatype,geometry,data=None):
     """
     return d.create(datatype,geometry,data)
 
+def link(datatype, geometry, data):
+    """Link a 3D numpy array with the toolbox.
+        
+    :param datatype: Data object type, '-vol' or '-sino'.
+    :type datatype: :class:`string`
+    :param geometry: Volume or projection geometry.
+    :type geometry: :class:`dict`
+    :param data: Numpy array to link
+    :type data: :class:`numpy.ndarray`
+    :returns: :class:`int` -- the ID of the constructed object.
+    
+    """
+    if not isinstance(data,np.ndarray):
+        raise ValueError("Input should be a numpy array")
+    if not data.dtype==np.float32:
+        raise ValueError("Numpy array should be float32")
+    if not (data.flags['C_CONTIGUOUS'] and data.flags['ALIGNED']):
+        raise ValueError("Numpy array should be C_CONTIGUOUS and ALIGNED")
+    return d.create(datatype,geometry,data,True)
+
+
 def get(i):
     """Get a 3D object.
 
@@ -90,6 +112,17 @@ def get_geometry(i):
     """
     return d.get_geometry(i)
 
+def change_geometry(i, geometry):
+    """Change the geometry of a 3D object.
+
+    :param i: ID of object.
+    :type i: :class:`int`
+    :param geometry: Volume or projection geometry.
+    :type geometry: :class:`dict`
+
+    """
+    return d.change_geometry(i, geometry)
+
 def dimensions(i):
     """Get dimensions of a 3D object.
 
diff --git a/python/astra/data3d_c.pyx b/python/astra/data3d_c.pyx
index 4b069f7..3b27ab7 100644
--- a/python/astra/data3d_c.pyx
+++ b/python/astra/data3d_c.pyx
@@ -45,17 +45,33 @@ from .PyXMLDocument cimport XMLDocument
 cimport utils
 from .utils import wrap_from_bytes
 
+from .pythonutils import geom_size
+
+import operator
+
+from six.moves import reduce
+
+
 cdef CData3DManager * man3d = <CData3DManager * >PyData3DManager.getSingletonPtr()
 
 cdef extern from *:
     CFloat32Data3DMemory * dynamic_cast_mem "dynamic_cast<astra::CFloat32Data3DMemory*>" (CFloat32Data3D * ) except NULL
 
-def create(datatype,geometry,data=None):
+cdef extern from "CFloat32CustomPython.h":
+    cdef cppclass CFloat32CustomPython:
+        CFloat32CustomPython(arrIn)
+
+def create(datatype,geometry,data=None, link=False):
     cdef Config *cfg
     cdef CVolumeGeometry3D * pGeometry
     cdef CProjectionGeometry3D * ppGeometry
     cdef CFloat32Data3DMemory * pDataObject3D
     cdef CConeProjectionGeometry3D* pppGeometry
+    cdef CFloat32CustomMemory * pCustom
+
+    if link and data.shape!=geom_size(geometry):
+        raise Exception("The dimensions of the data do not match those specified in the geometry.")
+
     if datatype == '-vol':
         cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry)
         pGeometry = new CVolumeGeometry3D()
@@ -63,7 +79,11 @@ def create(datatype,geometry,data=None):
             del cfg
             del pGeometry
             raise Exception('Geometry class not initialized.')
-        pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry)
+        if link:
+            pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+            pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry, pCustom)
+        else:
+            pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry)
         del cfg
         del pGeometry
     elif datatype == '-sino' or datatype == '-proj3d':
@@ -84,7 +104,11 @@ def create(datatype,geometry,data=None):
             del cfg
             del ppGeometry
             raise Exception('Geometry class not initialized.')
-        pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry)
+        if link:
+            pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+            pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry, pCustom)
+        else:
+            pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry)
         del ppGeometry
         del cfg
     elif datatype == "-sinocone":
@@ -94,7 +118,11 @@ def create(datatype,geometry,data=None):
             del cfg
             del pppGeometry
             raise Exception('Geometry class not initialized.')
-        pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(pppGeometry)
+        if link:
+            pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+            pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(pppGeometry, pCustom)
+        else:
+            pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(pppGeometry)
     else:
         raise Exception("Invalid datatype.  Please specify '-vol' or '-proj3d'.")
 
@@ -102,7 +130,7 @@ def create(datatype,geometry,data=None):
         del pDataObject3D
         raise Exception("Couldn't initialize data object.")
 
-    fillDataObject(pDataObject3D, data)
+    if not link: fillDataObject(pDataObject3D, data)
 
     pDataObject3D.updateStatistics()
 
@@ -122,6 +150,61 @@ def get_geometry(i):
         raise Exception("Not a known data object")
     return geom
 
+def change_geometry(i, geom):
+    cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem(getObject(i))
+    cdef CFloat32ProjectionData3DMemory * pDataObject2
+    cdef CFloat32VolumeData3DMemory * pDataObject3
+    if pDataObject.getType() == THREEPROJECTION:
+        pDataObject2 = <CFloat32ProjectionData3DMemory * >pDataObject
+        # TODO: Reduce code duplication here
+        cfg = utils.dictToConfig(six.b('ProjectionGeometry'), geom)
+        tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type')))
+        if (tpe == "parallel3d"):
+            ppGeometry = <CProjectionGeometry3D*> new CParallelProjectionGeometry3D();
+        elif (tpe == "parallel3d_vec"):
+            ppGeometry = <CProjectionGeometry3D*> new CParallelVecProjectionGeometry3D();
+        elif (tpe == "cone"):
+            ppGeometry = <CProjectionGeometry3D*> new CConeProjectionGeometry3D();
+        elif (tpe == "cone_vec"):
+            ppGeometry = <CProjectionGeometry3D*> new CConeVecProjectionGeometry3D();
+        else:
+            raise Exception("Invalid geometry type.")
+        if not ppGeometry.initialize(cfg[0]):
+            del cfg
+            del ppGeometry
+            raise Exception('Geometry class not initialized.')
+        del cfg
+        if (ppGeometry.getDetectorColCount() != pDataObject2.getDetectorColCount() or \
+            ppGeometry.getProjectionCount() != pDataObject2.getAngleCount() or \
+            ppGeometry.getDetectorRowCount() != pDataObject2.getDetectorRowCount()):
+            del ppGeometry
+            raise Exception(
+                "The dimensions of the data do not match those specified in the geometry.")
+        pDataObject2.changeGeometry(ppGeometry)
+        del ppGeometry
+
+    elif pDataObject.getType() == THREEVOLUME:
+        pDataObject3 = <CFloat32VolumeData3DMemory * >pDataObject
+        cfg = utils.dictToConfig(six.b('VolumeGeometry'), geom)
+        pGeometry = new CVolumeGeometry3D()
+        if not pGeometry.initialize(cfg[0]):
+            del cfg
+            del pGeometry
+            raise Exception('Geometry class not initialized.')
+        del cfg
+        if (pGeometry.getGridColCount() != pDataObject3.getColCount() or \
+            pGeometry.getGridRowCount() != pDataObject3.getRowCount() or \
+            pGeometry.getGridSliceCount() != pDataObject3.getSliceCount()):
+            del pGeometry
+            raise Exception(
+                "The dimensions of the data do not match those specified in the geometry.")
+        pDataObject3.changeGeometry(pGeometry)
+        del pGeometry
+
+    else:
+        raise Exception("Not a known data object")
+
+
 cdef fillDataObject(CFloat32Data3DMemory * obj, data):
     if data is None:
         fillDataObjectScalar(obj, 0)
diff --git a/python/astra/functions.py b/python/astra/functions.py
index 4025468..b826b86 100644
--- a/python/astra/functions.py
+++ b/python/astra/functions.py
@@ -38,6 +38,7 @@ from . import data2d
 from . import data3d
 from . import projector
 from . import algorithm
+from . import pythonutils
 
 
 
@@ -158,29 +159,7 @@ def geom_size(geom, dim=None):
     :param dim: Optional axis index to return
     :type dim: :class:`int`
     """
-
-    if 'GridSliceCount' in geom:
-        # 3D Volume geometry?
-        s = (geom['GridSliceCount'], geom[
-             'GridRowCount'], geom['GridColCount'])
-    elif 'GridColCount' in geom:
-        # 2D Volume geometry?
-        s = (geom['GridRowCount'], geom['GridColCount'])
-    elif geom['type'] == 'parallel' or geom['type'] == 'fanflat':
-        s = (len(geom['ProjectionAngles']), geom['DetectorCount'])
-    elif geom['type'] == 'parallel3d' or geom['type'] == 'cone':
-        s = (geom['DetectorRowCount'], len(
-            geom['ProjectionAngles']), geom['DetectorColCount'])
-    elif geom['type'] == 'fanflat_vec':
-        s = (geom['Vectors'].shape[0], geom['DetectorCount'])
-    elif geom['type'] == 'parallel3d_vec' or geom['type'] == 'cone_vec':
-        s = (geom['DetectorRowCount'], geom[
-             'Vectors'].shape[0], geom['DetectorColCount'])
-
-    if dim != None:
-        s = s[dim]
-
-    return s
+    return pythonutils.geom_size(geom,dim)
 
 
 def geom_2vec(proj_geom):
diff --git a/python/astra/optomo.py b/python/astra/optomo.py
new file mode 100644
index 0000000..0c37353
--- /dev/null
+++ b/python/astra/optomo.py
@@ -0,0 +1,197 @@
+#-----------------------------------------------------------------------
+#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 data2d
+from . import data3d
+from . import projector
+from . import projector3d
+from . import creators
+from . import algorithm
+from . import functions
+import numpy as np
+from six.moves import range, reduce
+import operator
+import scipy.sparse.linalg
+
+class OpTomo(scipy.sparse.linalg.LinearOperator):
+    """Object that imitates a projection matrix with a given projector.
+
+    This object can do forward projection by using the ``*`` operator::
+
+        W = astra.OpTomo(proj_id)
+        fp = W*image
+        bp = W.T*sinogram
+
+    It can also be used in minimization methods of the :mod:`scipy.sparse.linalg` module::
+
+        W = astra.OpTomo(proj_id)
+        output = scipy.sparse.linalg.lsqr(W,sinogram)
+
+    :param proj_id: ID to a projector.
+    :type proj_id: :class:`int`
+    """
+
+    def __init__(self,proj_id):
+        self.dtype = np.float32
+        try:
+            self.vg = projector.volume_geometry(proj_id)
+            self.pg = projector.projection_geometry(proj_id)
+            self.data_mod = data2d
+            self.appendString = ""
+            if projector.is_cuda(proj_id):
+                self.appendString += "_CUDA"
+        except Exception:
+            self.vg = projector3d.volume_geometry(proj_id)
+            self.pg = projector3d.projection_geometry(proj_id)
+            self.data_mod = data3d
+            self.appendString = "3D"
+            if projector3d.is_cuda(proj_id):
+                self.appendString += "_CUDA"
+
+        self.vshape = functions.geom_size(self.vg)
+        self.vsize = reduce(operator.mul,self.vshape)
+        self.sshape = functions.geom_size(self.pg)
+        self.ssize = reduce(operator.mul,self.sshape)
+
+        self.shape = (self.ssize, self.vsize)
+
+        self.proj_id = proj_id
+
+        self.T = OpTomoTranspose(self)
+
+    def __checkArray(self, arr, shp):
+        if len(arr.shape)==1:
+            arr = arr.reshape(shp)
+        if arr.dtype != np.float32:
+            arr = arr.astype(np.float32)
+        if arr.flags['C_CONTIGUOUS']==False:
+            arr = np.ascontiguousarray(arr)
+        return arr
+
+    def _matvec(self,v):
+        """Implements the forward operator.
+
+        :param v: Volume to forward project.
+        :type v: :class:`numpy.ndarray`
+        """
+        v = self.__checkArray(v, self.vshape)
+        vid = self.data_mod.link('-vol',self.vg,v)
+        s = np.zeros(self.sshape,dtype=np.float32)
+        sid = self.data_mod.link('-sino',self.pg,s)
+
+        cfg = creators.astra_dict('FP'+self.appendString)
+        cfg['ProjectionDataId'] = sid
+        cfg['VolumeDataId'] = vid
+        cfg['ProjectorId'] = self.proj_id
+        fp_id = algorithm.create(cfg)
+        algorithm.run(fp_id)
+
+        algorithm.delete(fp_id)
+        self.data_mod.delete([vid,sid])
+        return s.flatten()
+
+    def rmatvec(self,s):
+        """Implements the transpose operator.
+
+        :param s: The projection data.
+        :type s: :class:`numpy.ndarray`
+        """
+        s = self.__checkArray(s, self.sshape)
+        sid = self.data_mod.link('-sino',self.pg,s)
+        v = np.zeros(self.vshape,dtype=np.float32)
+        vid = self.data_mod.link('-vol',self.vg,v)
+
+        cfg = creators.astra_dict('BP'+self.appendString)
+        cfg['ProjectionDataId'] = sid
+        cfg['ReconstructionDataId'] = vid
+        cfg['ProjectorId'] = self.proj_id
+        bp_id = algorithm.create(cfg)
+        algorithm.run(bp_id)
+
+        algorithm.delete(bp_id)
+        self.data_mod.delete([vid,sid])
+        return v.flatten()
+
+    def __mul__(self,v):
+        """Provides easy forward operator by *.
+
+        :param v: Volume to forward project.
+        :type v: :class:`numpy.ndarray`
+        """
+        # Catch the case of a forward projection of a 2D/3D image
+        if isinstance(v, np.ndarray) and v.shape==self.vshape:
+            return self._matvec(v)
+        return scipy.sparse.linalg.LinearOperator.__mul__(self, v)
+
+    def reconstruct(self, method, s, iterations=1, extraOptions = {}):
+        """Reconstruct an object.
+
+        :param method: Method to use for reconstruction.
+        :type method: :class:`string`
+        :param s: The projection data.
+        :type s: :class:`numpy.ndarray`
+        :param iterations: Number of iterations to use.
+        :type iterations: :class:`int`
+        :param extraOptions: Extra options to use during reconstruction (i.e. for cfg['option']).
+        :type extraOptions: :class:`dict`
+        """
+        self.__checkArray(s, self.sshape)
+        sid = self.data_mod.link('-sino',self.pg,s)
+        v = np.zeros(self.vshape,dtype=np.float32)
+        vid = self.data_mod.link('-vol',self.vg,v)
+        cfg = creators.astra_dict(method)
+        cfg['ProjectionDataId'] = sid
+        cfg['ReconstructionDataId'] = vid
+        cfg['ProjectorId'] = self.proj_id
+        cfg['option'] = extraOptions
+        alg_id = algorithm.create(cfg)
+        algorithm.run(alg_id,iterations)
+        algorithm.delete(alg_id)
+        self.data_mod.delete([vid,sid])
+        return v
+
+class OpTomoTranspose(scipy.sparse.linalg.LinearOperator):
+    """This object provides the transpose operation (``.T``) of the OpTomo object.
+
+    Do not use directly, since it can be accessed as member ``.T`` of
+    an :class:`OpTomo` object.
+    """
+    def __init__(self,parent):
+        self.parent = parent
+        self.dtype = np.float32
+        self.shape = (parent.shape[1], parent.shape[0])
+
+    def _matvec(self, s):
+        return self.parent.rmatvec(s)
+
+    def rmatvec(self, v):
+        return self.parent.matvec(v)
+
+    def __mul__(self,s):
+        # Catch the case of a backprojection of 2D/3D data
+        if isinstance(s, np.ndarray) and s.shape==self.parent.sshape:
+            return self._matvec(s)
+        return scipy.sparse.linalg.LinearOperator.__mul__(self, s)
diff --git a/python/astra/pythonutils.py b/python/astra/pythonutils.py
new file mode 100644
index 0000000..8ea4af5
--- /dev/null
+++ b/python/astra/pythonutils.py
@@ -0,0 +1,63 @@
+#-----------------------------------------------------------------------
+# 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/>.
+#
+#-----------------------------------------------------------------------
+"""Additional purely Python functions for PyAstraToolbox.
+
+.. moduleauthor:: Daniel M. Pelt <D.M.Pelt@cwi.nl>
+
+
+"""
+
+def geom_size(geom, dim=None):
+    """Returns the size of a volume or sinogram, based on the projection or volume geometry.
+
+    :param geom: Geometry to calculate size from
+    :type geometry: :class:`dict`
+    :param dim: Optional axis index to return
+    :type dim: :class:`int`
+    """
+
+    if 'GridSliceCount' in geom:
+        # 3D Volume geometry?
+        s = (geom['GridSliceCount'], geom[
+             'GridRowCount'], geom['GridColCount'])
+    elif 'GridColCount' in geom:
+        # 2D Volume geometry?
+        s = (geom['GridRowCount'], geom['GridColCount'])
+    elif geom['type'] == 'parallel' or geom['type'] == 'fanflat':
+        s = (len(geom['ProjectionAngles']), geom['DetectorCount'])
+    elif geom['type'] == 'parallel3d' or geom['type'] == 'cone':
+        s = (geom['DetectorRowCount'], len(
+            geom['ProjectionAngles']), geom['DetectorColCount'])
+    elif geom['type'] == 'fanflat_vec':
+        s = (geom['Vectors'].shape[0], geom['DetectorCount'])
+    elif geom['type'] == 'parallel3d_vec' or geom['type'] == 'cone_vec':
+        s = (geom['DetectorRowCount'], geom[
+             'Vectors'].shape[0], geom['DetectorColCount'])
+
+    if dim != None:
+        s = s[dim]
+
+    return s
diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx
index 0439f1b..ddb37aa 100644
--- a/python/astra/utils.pyx
+++ b/python/astra/utils.pyx
@@ -26,6 +26,7 @@
 # distutils: language = c++
 # distutils: libraries = astra
 
+cimport numpy as np
 import numpy as np
 import six
 from libcpp.string cimport string
@@ -80,11 +81,12 @@ def wrap_from_bytes(value):
     return s
 
 
-cdef void readDict(XMLNode * root, _dc):
-    cdef XMLNode * listbase
-    cdef XMLNode * itm
+cdef void readDict(XMLNode root, _dc):
+    cdef XMLNode listbase
+    cdef XMLNode itm
     cdef int i
     cdef int j
+    cdef double* data
 
     dc = convert_item(_dc)
     for item in dc:
@@ -93,45 +95,31 @@ cdef void readDict(XMLNode * root, _dc):
             if val.size == 0:
                 break
             listbase = root.addChildNode(item)
-            listbase.addAttribute(< string > six.b('listsize'), < float32 > val.size)
-            index = 0
+            data = <double*>np.PyArray_DATA(np.ascontiguousarray(val,dtype=np.float64)) 
             if val.ndim == 2:
-                for i in range(val.shape[0]):
-                    for j in range(val.shape[1]):
-                        itm = listbase.addChildNode(six.b('ListItem'))
-                        itm.addAttribute(< string > six.b('index'), < float32 > index)
-                        itm.addAttribute( < string > six.b('value'), < float32 > val[i, j])
-                        index += 1
-                        del itm
+                listbase.setContent(data, val.shape[1], val.shape[0], False)
             elif val.ndim == 1:
-                for i in range(val.shape[0]):
-                    itm = listbase.addChildNode(six.b('ListItem'))
-                    itm.addAttribute(< string > six.b('index'), < float32 > index)
-                    itm.addAttribute(< string > six.b('value'), < float32 > val[i])
-                    index += 1
-                    del itm
+                listbase.setContent(data, val.shape[0])
             else:
                 raise Exception("Only 1 or 2 dimensions are allowed")
-            del listbase
         elif isinstance(val, dict):
             if item == six.b('option') or item == six.b('options') or item == six.b('Option') or item == six.b('Options'):
                 readOptions(root, val)
             else:
                 itm = root.addChildNode(item)
                 readDict(itm, val)
-                del itm
         else:
             if item == six.b('type'):
                 root.addAttribute(< string > six.b('type'), <string> wrap_to_bytes(val))
             else:
                 itm = root.addChildNode(item, wrap_to_bytes(val))
-                del itm
 
-cdef void readOptions(XMLNode * node, dc):
-    cdef XMLNode * listbase
-    cdef XMLNode * itm
+cdef void readOptions(XMLNode node, dc):
+    cdef XMLNode listbase
+    cdef XMLNode itm
     cdef int i
     cdef int j
+    cdef double* data
     for item in dc:
         val = dc[item]
         if node.hasOption(item):
@@ -141,26 +129,13 @@ cdef void readOptions(XMLNode * node, dc):
                 break
             listbase = node.addChildNode(six.b('Option'))
             listbase.addAttribute(< string > six.b('key'), < string > item)
-            listbase.addAttribute(< string > six.b('listsize'), < float32 > val.size)
-            index = 0
+            data = <double*>np.PyArray_DATA(np.ascontiguousarray(val,dtype=np.float64)) 
             if val.ndim == 2:
-                for i in range(val.shape[0]):
-                    for j in range(val.shape[1]):
-                        itm = listbase.addChildNode(six.b('ListItem'))
-                        itm.addAttribute(< string > six.b('index'), < float32 > index)
-                        itm.addAttribute( < string > six.b('value'), < float32 > val[i, j])
-                        index += 1
-                        del itm
+                listbase.setContent(data, val.shape[1], val.shape[0], False)
             elif val.ndim == 1:
-                for i in range(val.shape[0]):
-                    itm = listbase.addChildNode(six.b('ListItem'))
-                    itm.addAttribute(< string > six.b('index'), < float32 > index)
-                    itm.addAttribute(< string > six.b('value'), < float32 > val[i])
-                    index += 1
-                    del itm
+                listbase.setContent(data, val.shape[0])
             else:
                 raise Exception("Only 1 or 2 dimensions are allowed")
-            del listbase
         else:
             node.addOption(item, wrap_to_bytes(val))
 
@@ -214,10 +189,10 @@ def stringToPythonValue(inputIn):
             return str(input)
 
 
-cdef XMLNode2dict(XMLNode * node):
-    cdef XMLNode * subnode
-    cdef list[XMLNode * ] nodes
-    cdef list[XMLNode * ].iterator it
+cdef XMLNode2dict(XMLNode node):
+    cdef XMLNode subnode
+    cdef list[XMLNode] nodes
+    cdef list[XMLNode].iterator it
     dct = {}
     opts = {}
     if node.hasAttribute(six.b('type')):
@@ -230,7 +205,6 @@ cdef XMLNode2dict(XMLNode * node):
             opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getAttribute('value'))
         else:
             dct[castString(subnode.getName())] = stringToPythonValue(subnode.getContent())
-        del subnode
         inc(it)
     if len(opts)>0: dct['options'] = opts
     return dct