Merge branch 'master' into volgeom3d

Conflicts:
	src/CudaBackProjectionAlgorithm3D.cpp

1 files changed, 219 insertions, 0 deletions

diff --git a/python/astra/optomo.py b/python/astra/optomo.py
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+++ b/python/astra/optomo.py
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+#-----------------------------------------------------------------------
+#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.transposeOpTomo = OpTomoTranspose(self)
+        try:
+            self.T = self.transposeOpTomo
+        except AttributeError:
+            # Scipy >= 0.16 defines self.T using self._transpose()
+            pass
+
+    def _transpose(self):
+        return self.transposeOpTomo
+
+    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`
+        """
+        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(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])
+        try:
+            self.T = self.parent
+        except AttributeError:
+            # Scipy >= 0.16 defines self.T using self._transpose()
+            pass
+
+    def _matvec(self, s):
+        return self.parent.rmatvec(s)
+
+    def rmatvec(self, v):
+        return self.parent.matvec(v)
+
+    def _transpose(self):
+        return self.parent
+
+    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)