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Diffstat (limited to 'python/astra/optomo.py')
| -rw-r--r-- | python/astra/optomo.py | 203 |
1 files changed, 203 insertions, 0 deletions
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) |