Merge remote-tracking branch 'upstream/master' into parallel_vec

Conflicts:
	astra_vc11.vcxproj.filters
	python/astra/functions.py
	src/ParallelBeamBlobKernelProjector2D.cpp
	src/ProjectionGeometry2D.cpp

23 files changed, 1144 insertions, 278 deletions

diff --git a/python/astra/ASTRAProjector.py b/python/astra/ASTRAProjector.py
deleted file mode 100644
index 96acb10..0000000
--- a/python/astra/ASTRAProjector.py
+++ /dev/null
@@ -1,138 +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`
-    :param useCUDA: If ``True``, use CUDA for calculations, when possible.
-    :type useCUDA: :class:`bool`
-    """
-
-    def __init__(self, proj_geom, vol_geom, proj_type, useCUDA=False):
-        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.useCUDA = useCUDA
-        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, useCUDA=self.useCUDA, 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, useCUDA=self.useCUDA, 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 ea624fc..540aad4 100644
--- a/python/astra/PyIncludes.pxd
+++ b/python/astra/PyIncludes.pxd
@@ -27,6 +27,8 @@ from libcpp cimport bool
 from libcpp.string cimport string
 from .PyXMLDocument cimport XMLNode
 
+include "config.pxi"
+
 cdef extern from "astra/Globals.h" namespace "astra":
 	ctypedef float float32
 	ctypedef double float64
@@ -41,7 +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:
@@ -61,10 +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()
@@ -132,6 +138,7 @@ 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()
@@ -154,6 +161,20 @@ cdef extern from "astra/Projector2D.h" namespace "astra":
 		CVolumeGeometry2D* getVolumeGeometry()
 		CSparseMatrix* getMatrix()
 
+cdef extern from "astra/Projector3D.h" namespace "astra":
+	cdef cppclass CProjector3D:
+		bool isInitialized()
+		CProjectionGeometry3D* getProjectionGeometry()
+		CVolumeGeometry3D* getVolumeGeometry()
+
+IF HAVE_CUDA==True:
+	cdef extern from "astra/CudaProjector3D.h" namespace "astra":
+		cdef cppclass CCudaProjector3D
+
+	cdef extern from "astra/CudaProjector2D.h" namespace "astra":
+		cdef cppclass CCudaProjector2D
+
+
 cdef extern from "astra/SparseMatrix.h" namespace "astra":
 	cdef cppclass CSparseMatrix:
 		CSparseMatrix(unsigned int,unsigned int,unsigned long)
@@ -184,18 +205,30 @@ 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":
@@ -219,7 +252,13 @@ 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/PyProjector3DFactory.pxd b/python/astra/PyProjector3DFactory.pxd
new file mode 100644
index 0000000..bcbce94
--- /dev/null
+++ b/python/astra/PyProjector3DFactory.pxd
@@ -0,0 +1,35 @@
+#-----------------------------------------------------------------------
+#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 libcpp.string cimport string
+from libcpp cimport bool
+from .PyIncludes cimport *
+
+cdef extern from "astra/AstraObjectFactory.h" namespace "astra":
+    cdef cppclass CProjector3DFactory:
+        CProjector3D *create(Config)
+
+cdef extern from "astra/AstraObjectFactory.h" namespace "astra::CProjector3DFactory":
+    cdef CProjector3DFactory* getSingletonPtr()
diff --git a/python/astra/PyProjector3DManager.pxd b/python/astra/PyProjector3DManager.pxd
new file mode 100644
index 0000000..b1eac6b
--- /dev/null
+++ b/python/astra/PyProjector3DManager.pxd
@@ -0,0 +1,39 @@
+#-----------------------------------------------------------------------
+#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 libcpp.string cimport string
+
+from .PyIncludes cimport *
+
+cdef extern from "astra/AstraObjectManager.h" namespace "astra":
+    cdef cppclass CProjector3DManager:
+        string info()
+        void clear()
+        void remove(int i)
+        int store(CProjector3D *)
+        CProjector3D * get(int i)
+
+cdef extern from "astra/AstraObjectManager.h" namespace "astra::CProjector3DManager":
+    cdef CProjector3DManager* getSingletonPtr()
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 a61aafc..6c15d30 100644
--- a/python/astra/__init__.py
+++ b/python/astra/__init__.py
@@ -27,13 +27,15 @@ 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
 from . import algorithm
 from . import projector
+from . import projector3d
 from . import matrix
+from . import log
+from .optomo import OpTomo
 
 import os
 try:
diff --git a/python/astra/creators.py b/python/astra/creators.py
index b5ecd5a..4cd7f2d 100644
--- a/python/astra/creators.py
+++ b/python/astra/creators.py
@@ -30,15 +30,16 @@ import math
 from . import data2d
 from . import data3d
 from . import projector
+from . import projector3d
 from . import algorithm
 
 def astra_dict(intype):
     """Creates a dict to use with the ASTRA Toolbox.
-    
+
     :param intype: Type of the ASTRA object.
     :type intype: :class:`string`
     :returns: :class:`dict` -- An ASTRA dict of type ``intype``.
-    
+
     """
     if intype == 'SIRT_CUDA2':
         intype = 'SIRT_CUDA'
@@ -268,25 +269,23 @@ This method can be called in a number of ways:
             raise Exception('not enough variables: astra_create_proj_geom(parallel3d_vec, det_row_count, det_col_count, V)')
         if not args[2].shape[1] == 12:
             raise Exception('V should be a Nx12 matrix, with N the number of projections')
-        return {'type': 'parallel3d_vec','DetectorRowCount':args[0],'DetectorColCount':args[1],'Vectors':args[2]}    
+        return {'type': 'parallel3d_vec','DetectorRowCount':args[0],'DetectorColCount':args[1],'Vectors':args[2]}
     elif intype == 'sparse_matrix':
         if len(args) < 4:
             raise Exception(
                 'not enough variables: astra_create_proj_geom(sparse_matrix, det_width, det_count, angles, matrix_id)')
         return {'type': 'sparse_matrix', 'DetectorWidth': args[0], 'DetectorCount': args[1], 'ProjectionAngles': args[2], 'MatrixID': args[3]}
     else:
-        raise Exception('Error: unknown type ' + intype) 
+        raise Exception('Error: unknown type ' + intype)
 
 
-def create_backprojection(data, proj_id, useCUDA=False, returnData=True):
+def create_backprojection(data, proj_id, returnData=True):
     """Create a backprojection of a sinogram (2D).
 
 :param data: Sinogram data or ID.
 :type data: :class:`numpy.ndarray` or :class:`int`
 :param proj_id: ID of the projector to use.
 :type proj_id: :class:`int`
-:param useCUDA: If ``True``, use CUDA for the calculation.
-:type useCUDA: :class:`bool`
 :param returnData: If False, only return the ID of the backprojection.
 :type returnData: :class:`bool`
 :returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order.
@@ -300,13 +299,13 @@ def create_backprojection(data, proj_id, useCUDA=False, returnData=True):
         sino_id = data
     vol_id = data2d.create('-vol', vol_geom, 0)
 
-    algString = 'BP'
-    if useCUDA:
-        algString = algString + '_CUDA'
+    if projector.is_cuda(proj_id):
+        algString = 'BP_CUDA'
+    else:
+        algString = 'BP'
 
     cfg = astra_dict(algString)
-    if not useCUDA:
-        cfg['ProjectorId'] = proj_id
+    cfg['ProjectorId'] = proj_id
     cfg['ProjectionDataId'] = sino_id
     cfg['ReconstructionDataId'] = vol_id
     alg_id = algorithm.create(cfg)
@@ -358,20 +357,13 @@ def create_backprojection3d_gpu(data, proj_geom, vol_geom, returnData=True):
         return vol_id
 
 
-def create_sino(data, proj_id=None, proj_geom=None, vol_geom=None,
-                useCUDA=False, returnData=True, gpuIndex=None):
+def create_sino(data, proj_id, returnData=True, gpuIndex=None):
     """Create a forward projection of an image (2D).
 
     :param data: Image data or ID.
     :type data: :class:`numpy.ndarray` or :class:`int`
     :param proj_id: ID of the projector to use.
     :type proj_id: :class:`int`
-    :param proj_geom: Projection geometry.
-    :type proj_geom: :class:`dict`
-    :param vol_geom: Volume geometry.
-    :type vol_geom: :class:`dict`
-    :param useCUDA: If ``True``, use CUDA for the calculation.
-    :type useCUDA: :class:`bool`
     :param returnData: If False, only return the ID of the forward projection.
     :type returnData: :class:`bool`
     :param gpuIndex: Optional GPU index.
@@ -382,36 +374,21 @@ def create_sino(data, proj_id=None, proj_geom=None, vol_geom=None,
     projection. Otherwise, returns a tuple containing the ID of the
     forward projection and the forward projection itself, in that
     order.
-
-    The geometry of setup is defined by ``proj_id`` or with
-    ``proj_geom`` and ``vol_geom``. If ``proj_id`` is given, then
-    ``proj_geom`` and ``vol_geom`` must be None and vice versa.
 """
-    if proj_id is not None:
-        proj_geom = projector.projection_geometry(proj_id)
-        vol_geom = projector.volume_geometry(proj_id)
-    elif proj_geom is not None and vol_geom is not None:
-        if not useCUDA:
-            # We need more parameters to create projector.
-            raise ValueError(
-                """A ``proj_id`` is needed when CUDA is not used.""")
-    else:
-        raise Exception("""The geometry setup is not defined.
-        The geometry of setup is defined by ``proj_id`` or with
-        ``proj_geom`` and ``vol_geom``. If ``proj_id`` is given, then
-        ``proj_geom`` and ``vol_geom`` must be None and vice versa.""")
+    proj_geom = projector.projection_geometry(proj_id)
+    vol_geom = projector.volume_geometry(proj_id)
 
     if isinstance(data, np.ndarray):
         volume_id = data2d.create('-vol', vol_geom, data)
     else:
         volume_id = data
     sino_id = data2d.create('-sino', proj_geom, 0)
-    algString = 'FP'
-    if useCUDA:
-        algString = algString + '_CUDA'
+    if projector.is_cuda(proj_id):
+        algString = 'FP_CUDA'
+    else:
+        algString = 'FP'
     cfg = astra_dict(algString)
-    if not useCUDA:
-        cfg['ProjectorId'] = proj_id
+    cfg['ProjectorId'] = proj_id
     if gpuIndex is not None:
         cfg['option'] = {'GPUindex': gpuIndex}
     cfg['ProjectionDataId'] = sino_id
@@ -509,8 +486,7 @@ def create_reconstruction(rec_type, proj_id, sinogram, iterations=1, use_mask='n
     vol_geom = projector.volume_geometry(proj_id)
     recon_id = data2d.create('-vol', vol_geom, 0)
     cfg = astra_dict(rec_type)
-    if not 'CUDA' in rec_type:
-        cfg['ProjectorId'] = proj_id
+    cfg['ProjectorId'] = proj_id
     cfg['ProjectionDataId'] = sino_id
     cfg['ReconstructionDataId'] = recon_id
     cfg['options'] = {}
@@ -573,4 +549,8 @@ def create_projector(proj_type, proj_geom, vol_geom):
     cfg = astra_dict(proj_type)
     cfg['ProjectionGeometry'] = proj_geom
     cfg['VolumeGeometry'] = vol_geom
-    return projector.create(cfg)
+    types3d = ['linear3d', 'linearcone', 'cuda3d']
+    if proj_type in types3d:
+        return projector3d.create(cfg)
+    else:
+        return projector.create(cfg)
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 882051c..42854b3 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':
@@ -93,7 +112,11 @@ 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:
@@ -103,7 +126,7 @@ 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 bbbb355..13ca911 100644
--- a/python/astra/functions.py
+++ b/python/astra/functions.py
@@ -32,12 +32,17 @@
 
 from . import creators as ac
 import numpy as np
-from six.moves import range
+try:
+    from six.moves import range
+except ImportError:
+    # six 1.3.0
+    from six.moves import xrange as range
 
 from . import data2d
 from . import data3d
 from . import projector
 from . import algorithm
+from . import pythonutils
 
 
 
@@ -158,29 +163,7 @@ 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'] == 'parallel_vec' or 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/log.py b/python/astra/log.py
new file mode 100644
index 0000000..3ec0df5
--- /dev/null
+++ b/python/astra/log.py
@@ -0,0 +1,153 @@
+#-----------------------------------------------------------------------
+#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 log_c as l
+
+import inspect
+
+def debug(message):
+    """Log a debug message.
+    
+    :param message: Message to log.
+    :type message: :class:`string`
+    """
+    prev_f = inspect.getframeinfo(inspect.currentframe().f_back)
+    l.log_debug(prev_f.filename,prev_f.lineno,message)
+
+def info(message):
+    """Log an info message.
+    
+    :param message: Message to log.
+    :type message: :class:`string`
+    """
+    prev_f = inspect.getframeinfo(inspect.currentframe().f_back)
+    l.log_info(prev_f.filename,prev_f.lineno,message)
+
+def warn(message):
+    """Log a warning message.
+    
+    :param message: Message to log.
+    :type message: :class:`string`
+    """
+    prev_f = inspect.getframeinfo(inspect.currentframe().f_back)
+    l.log_warn(prev_f.filename,prev_f.lineno,message)
+
+def error(message):
+    """Log an error message.
+    
+    :param message: Message to log.
+    :type message: :class:`string`
+    """
+    prev_f = inspect.getframeinfo(inspect.currentframe().f_back)
+    l.log_error(prev_f.filename,prev_f.lineno,message)
+
+def enable():
+    """Enable logging to screen and file."""
+    l.log_enable()
+
+def enableScreen():
+    """Enable logging to screen."""
+    l.log_enableScreen()
+
+def enableFile():
+    """Enable logging to file (note that a file has to be set)."""
+    l.log_enableFile()
+
+def disable():
+    """Disable all logging."""
+    l.log_disable()
+
+def disableScreen():
+    """Disable logging to screen."""
+    l.log_disableScreen()
+
+def disableFile():
+    """Disable logging to file."""
+    l.log_disableFile()
+
+def setFormatFile(fmt):
+    """Set the format string for log messages.  Here are the substitutions you may use:
+    
+    %f: Source file name generating the log call.
+    %n: Source line number where the log call was made.
+    %m: The message text sent to the logger (after printf formatting).
+    %d: The current date, formatted using the logger's date format.
+    %t: The current time, formatted using the logger's time format.
+    %l: The log level (one of "DEBUG", "INFO", "WARN", or "ERROR").
+    %%: A literal percent sign.
+    
+    The default format string is "%d %t %f(%n): %l: %m\n".
+    
+    :param fmt: Format to use, end with "\n".
+    :type fmt: :class:`string`
+    """
+    l.log_setFormatFile(fmt)
+
+def setFormatScreen(fmt):
+    """Set the format string for log messages.  Here are the substitutions you may use:
+    
+    %f: Source file name generating the log call.
+    %n: Source line number where the log call was made.
+    %m: The message text sent to the logger (after printf formatting).
+    %d: The current date, formatted using the logger's date format.
+    %t: The current time, formatted using the logger's time format.
+    %l: The log level (one of "DEBUG", "INFO", "WARN", or "ERROR").
+    %%: A literal percent sign.
+    
+    The default format string is "%d %t %f(%n): %l: %m\n".
+    
+    :param fmt: Format to use, end with "\n".
+    :type fmt: :class:`string`
+    """
+    l.log_setFormatScreen(fmt)
+
+STDOUT=1
+STDERR=2
+
+DEBUG=0
+INFO=1
+WARN=2
+ERROR=3
+
+def setOutputScreen(fd, level):
+    """Set which screen to output to, and which level to use.
+    
+    :param fd: File descriptor of output screen (STDOUT or STDERR).
+    :type fd: :class:`int`
+    :param level: Logging level to use (DEBUG, INFO, WARN, or ERROR).
+    :type level: :class:`int`
+    """
+    l.log_setOutputScreen(fd, level)
+
+def setOutputFile(filename, level):
+    """Set which file to output to, and which level to use.
+    
+    :param filename: File name of output file.
+    :type filename: :class:`string`
+    :param level: Logging level to use (DEBUG, INFO, WARN, or ERROR).
+    :type level: :class:`int`
+    """
+    l.log_setOutputFile(filename, level)
\ No newline at end of file
diff --git a/python/astra/log_c.pyx b/python/astra/log_c.pyx
new file mode 100644
index 0000000..f16329f
--- /dev/null
+++ b/python/astra/log_c.pyx
@@ -0,0 +1,103 @@
+#-----------------------------------------------------------------------
+#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
+
+cdef extern from "astra/Logging.h" namespace "astra":
+    cdef enum log_level:
+        LOG_DEBUG
+        LOG_INFO
+        LOG_WARN
+        LOG_ERROR
+
+cdef extern from "astra/Logging.h" namespace "astra::CLogger":
+    void debug(const char *sfile, int sline, const char *fmt, ...)
+    void info(const char *sfile, int sline, const char *fmt, ...)
+    void warn(const char *sfile, int sline, const char *fmt, ...)
+    void error(const char *sfile, int sline, const char *fmt, ...)
+    void setOutputScreen(int fd, log_level m_eLevel)
+    void setOutputFile(const char *filename, log_level m_eLevel)
+    void enable()
+    void enableScreen()
+    void enableFile()
+    void disable()
+    void disableScreen()
+    void disableFile()
+    void setFormatFile(const char *fmt)
+    void setFormatScreen(const char *fmt)
+
+def log_debug(sfile, sline, message):
+    cstr = list(map(six.b,(sfile,message)))
+    debug(cstr[0],sline,cstr[1])
+
+def log_info(sfile, sline, message):
+    cstr = list(map(six.b,(sfile,message)))
+    info(cstr[0],sline,cstr[1])
+
+def log_warn(sfile, sline, message):
+    cstr = list(map(six.b,(sfile,message)))
+    warn(cstr[0],sline,cstr[1])
+
+def log_error(sfile, sline, message):
+    cstr = list(map(six.b,(sfile,message)))
+    error(cstr[0],sline,cstr[1])
+
+def log_enable():
+    enable()
+
+def log_enableScreen():
+    enableScreen()
+
+def log_enableFile():
+    enableFile()
+
+def log_disable():
+    disable()
+
+def log_disableScreen():
+    disableScreen()
+
+def log_disableFile():
+    disableFile()
+
+def log_setFormatFile(fmt):
+    cstr = six.b(fmt)
+    setFormatFile(cstr)
+
+def log_setFormatScreen(fmt):
+    cstr = six.b(fmt)
+    setFormatScreen(cstr)
+
+enumList = [LOG_DEBUG,LOG_INFO,LOG_WARN,LOG_ERROR]
+
+def log_setOutputScreen(fd, level):
+    setOutputScreen(fd, enumList[level])
+
+def log_setOutputFile(filename, level):
+    cstr = six.b(filename)
+    setOutputFile(cstr, enumList[level])
diff --git a/python/astra/matrix_c.pyx b/python/astra/matrix_c.pyx
index b0d8bc4..d099a75 100644
--- a/python/astra/matrix_c.pyx
+++ b/python/astra/matrix_c.pyx
@@ -27,7 +27,12 @@
 # distutils: libraries = astra
 
 import six
-from six.moves import range
+try:
+    from six.moves import range
+except ImportError:
+    # six 1.3.0
+    from six.moves import xrange as range
+
 import numpy as np
 import scipy.sparse as ss
 
diff --git a/python/astra/optomo.py b/python/astra/optomo.py
new file mode 100644
index 0000000..2937d9c
--- /dev/null
+++ b/python/astra/optomo.py
@@ -0,0 +1,203 @@
+#-----------------------------------------------------------------------
+#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 reduce
+try:
+    from six.moves import range
+except ImportError:
+    # six 1.3.0
+    from six.moves import xrange as range
+
+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/projector.py b/python/astra/projector.py
index c916c52..e370e5a 100644
--- a/python/astra/projector.py
+++ b/python/astra/projector.py
@@ -27,21 +27,21 @@ from . import projector_c as p
 
 def create(config):
     """Create projector object.
-    
+
     :param config: Projector options.
     :type config: :class:`dict`
     :returns: :class:`int` -- the ID of the constructed object.
-    
+
     """
     return p.create(config)
 
 
 def delete(ids):
     """Delete a projector object.
-    
+
     :param ids: ID or list of ID's to delete.
     :type ids: :class:`int` or :class:`list`
-    
+
     """
     return p.delete(ids)
 
@@ -57,22 +57,22 @@ def info():
 
 def projection_geometry(i):
     """Get projection geometry of a projector.
-    
+
     :param i: ID of projector.
     :type i: :class:`int`
     :returns: :class:`dict` -- projection geometry
-    
+
     """
     return p.projection_geometry(i)
 
 
 def volume_geometry(i):
     """Get volume geometry of a projector.
-    
+
     :param i: ID of projector.
     :type i: :class:`int`
     :returns: :class:`dict` -- volume geometry
-    
+
     """
     return p.volume_geometry(i)
 
@@ -88,13 +88,23 @@ def weights_projection(i, projection_index):
 def splat(i, row, col):
     return p.splat(i, row, col)
 
+def is_cuda(i):
+    """Check whether a projector is a CUDA projector.
+
+    :param i: ID of projector.
+    :type i: :class:`int`
+    :returns: :class:`bool` -- True if the projector is a CUDA projector.
+
+    """
+    return p.is_cuda(i)
+
 
 def matrix(i):
     """Get sparse matrix of a projector.
-    
+
     :param i: ID of projector.
     :type i: :class:`int`
     :returns: :class:`int` -- ID of sparse matrix.
-    
+
     """
     return p.matrix(i)
diff --git a/python/astra/projector3d.py b/python/astra/projector3d.py
new file mode 100644
index 0000000..d1086b9
--- /dev/null
+++ b/python/astra/projector3d.py
@@ -0,0 +1,100 @@
+#-----------------------------------------------------------------------
+#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 projector3d_c as p
+
+def create(config):
+    """Create projector object.
+
+    :param config: Projector options.
+    :type config: :class:`dict`
+    :returns: :class:`int` -- the ID of the constructed object.
+
+    """
+    return p.create(config)
+
+
+def delete(ids):
+    """Delete a projector object.
+
+    :param ids: ID or list of ID's to delete.
+    :type ids: :class:`int` or :class:`list`
+
+    """
+    return p.delete(ids)
+
+
+def clear():
+    """Clear all projector objects."""
+    return p.clear()
+
+
+def info():
+    """Print info on projector objects in memory."""
+    return p.info()
+
+def projection_geometry(i):
+    """Get projection geometry of a projector.
+
+    :param i: ID of projector.
+    :type i: :class:`int`
+    :returns: :class:`dict` -- projection geometry
+
+    """
+    return p.projection_geometry(i)
+
+
+def volume_geometry(i):
+    """Get volume geometry of a projector.
+
+    :param i: ID of projector.
+    :type i: :class:`int`
+    :returns: :class:`dict` -- volume geometry
+
+    """
+    return p.volume_geometry(i)
+
+
+def weights_single_ray(i, projection_index, detector_index):
+    return p.weights_single_ray(i, projection_index, detector_index)
+
+
+def weights_projection(i, projection_index):
+    return p.weights_projection(i, projection_index)
+
+
+def splat(i, row, col):
+    return p.splat(i, row, col)
+
+
+def is_cuda(i):
+    """Check whether a projector is a CUDA projector.
+
+    :param i: ID of projector.
+    :type i: :class:`int`
+    :returns: :class:`bool` -- True if the projector is a CUDA projector.
+
+    """
+    return p.is_cuda(i)
diff --git a/python/astra/projector3d_c.pyx b/python/astra/projector3d_c.pyx
new file mode 100644
index 0000000..8b978d7
--- /dev/null
+++ b/python/astra/projector3d_c.pyx
@@ -0,0 +1,119 @@
+#-----------------------------------------------------------------------
+#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
+from .PyIncludes cimport *
+
+cimport utils
+from .utils import wrap_from_bytes
+
+cimport PyProjector3DFactory
+from .PyProjector3DFactory cimport CProjector3DFactory
+
+cimport PyProjector3DManager
+from .PyProjector3DManager cimport CProjector3DManager
+
+cimport PyXMLDocument
+from .PyXMLDocument cimport XMLDocument
+
+cdef CProjector3DManager * manProj = <CProjector3DManager * >PyProjector3DManager.getSingletonPtr()
+
+include "config.pxi"
+
+IF HAVE_CUDA:
+  cdef extern from *:
+      CCudaProjector3D* dynamic_cast_cuda_projector "dynamic_cast<astra::CCudaProjector3D*>" (CProjector3D*)
+
+
+def create(config):
+    cdef Config * cfg = utils.dictToConfig(six.b('Projector3D'), config)
+    cdef CProjector3D * proj
+    proj = PyProjector3DFactory.getSingletonPtr().create(cfg[0])
+    if proj == NULL:
+        del cfg
+        raise Exception("Error creating Projector3D.")
+    del cfg
+    return manProj.store(proj)
+
+
+def delete(ids):
+    try:
+        for i in ids:
+            manProj.remove(i)
+    except TypeError:
+        manProj.remove(ids)
+
+
+def clear():
+    manProj.clear()
+
+
+def info():
+    six.print_(wrap_from_bytes(manProj.info()))
+
+cdef CProjector3D * getObject(i) except NULL:
+    cdef CProjector3D * proj = manProj.get(i)
+    if proj == NULL:
+        raise Exception("Projector not initialized.")
+    if not proj.isInitialized():
+        raise Exception("Projector not initialized.")
+    return proj
+
+
+def projection_geometry(i):
+    cdef CProjector3D * proj = getObject(i)
+    return utils.configToDict(proj.getProjectionGeometry().getConfiguration())
+
+
+def volume_geometry(i):
+    cdef CProjector3D * proj = getObject(i)
+    return utils.configToDict(proj.getVolumeGeometry().getConfiguration())
+
+
+def weights_single_ray(i, projection_index, detector_index):
+    raise Exception("Not yet implemented")
+
+
+def weights_projection(i, projection_index):
+    raise Exception("Not yet implemented")
+
+
+def splat(i, row, col):
+    raise Exception("Not yet implemented")
+
+def is_cuda(i):
+    cdef CProjector3D * proj = getObject(i)
+    IF HAVE_CUDA==True:
+      cdef CCudaProjector3D * cudaproj = NULL
+      cudaproj = dynamic_cast_cuda_projector(proj)
+      if cudaproj==NULL:
+          return False
+      else:
+          return True
+    ELSE:
+        return False
diff --git a/python/astra/projector_c.pyx b/python/astra/projector_c.pyx
index f91a8dd..9aa868e 100644
--- a/python/astra/projector_c.pyx
+++ b/python/astra/projector_c.pyx
@@ -47,6 +47,12 @@ from .PyMatrixManager cimport CMatrixManager
 cdef CProjector2DManager * manProj = <CProjector2DManager * >PyProjector2DManager.getSingletonPtr()
 cdef CMatrixManager * manM = <CMatrixManager * >PyMatrixManager.getSingletonPtr()
 
+include "config.pxi"
+
+IF HAVE_CUDA:
+  cdef extern from *:
+      CCudaProjector2D* dynamic_cast_cuda_projector "dynamic_cast<astra::CCudaProjector2D*>" (CProjector2D*)
+
 
 def create(config):
     cdef Config * cfg = utils.dictToConfig(six.b('Projector2D'), config)
@@ -104,6 +110,17 @@ def weights_projection(i, projection_index):
 def splat(i, row, col):
     raise Exception("Not yet implemented")
 
+def is_cuda(i):
+    cdef CProjector2D * proj = getObject(i)
+    IF HAVE_CUDA==True:
+      cdef CCudaProjector2D * cudaproj = NULL
+      cudaproj = dynamic_cast_cuda_projector(proj)
+      if cudaproj==NULL:
+          return False
+      else:
+          return True
+    ELSE:
+        return False
 
 def matrix(i):
     cdef CProjector2D * proj = getObject(i)
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