Merge pull request #46 from dmpelt/spot-like-python

Add SPOT-like object for Python (overrides `__mul__` and works with scipy.sparse.linalg)

5 files changed, 201 insertions, 139 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/__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/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/docSRC/index.rst b/python/docSRC/index.rst
index 8d17a4a..b7cc6d6 100644
--- a/python/docSRC/index.rst
+++ b/python/docSRC/index.rst
@@ -18,7 +18,7 @@ Contents:
    matrix
    creators
    functions
-   ASTRAProjector
+   operator
    matlab
    astra
 .. astra
diff --git a/python/docSRC/ASTRAProjector.rst b/python/docSRC/operator.rst
index 1c267e3..f5369fa 100644
--- a/python/docSRC/ASTRAProjector.rst
+++ b/python/docSRC/operator.rst
@@ -1,7 +1,7 @@
-Helper class: the :mod:`ASTRAProjector` module
+OpTomo class: the :mod:`operator` module
 ==============================================
 
-.. automodule:: astra.ASTRAProjector
+.. automodule:: astra.operator
     :members:
     :undoc-members:
     :show-inheritance: