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# -----------------------------------------------------------------------
# Copyright: 2010-2022, imec Vision Lab, University of Antwerp
# 2013-2022, CWI, Amsterdam
#
# Contact: astra@astra-toolbox.com
# Website: http://www.astra-toolbox.com/
#
# This file is part of the ASTRA Toolbox.
#
#
# 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 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 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 functools import 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.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
# real operator
_adjoint = _transpose
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`
"""
return self.FP(v, out=None).ravel()
def rmatvec(self,s):
"""Implements the transpose operator.
:param s: The projection data.
:type s: :class:`numpy.ndarray`
"""
return self.BP(s, out=None).ravel()
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 = None):
"""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`
"""
if extraOptions is None:
extraOptions={}
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
def FP(self,v,out=None):
"""Perform forward projection.
Output must have the right 2D/3D shape. Input may also be flattened.
Output must also be contiguous and float32. This isn't required for the
input, but it is more efficient if it is.
:param v: Volume to forward project.
:type v: :class:`numpy.ndarray`
:param out: Array to store result in.
:type out: :class:`numpy.ndarray`
"""
v = self.__checkArray(v, self.vshape)
vid = self.data_mod.link('-vol',self.vg,v)
if out is None:
out = np.zeros(self.sshape,dtype=np.float32)
sid = self.data_mod.link('-sino',self.pg,out)
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 out
def BP(self,s,out=None):
"""Perform backprojection.
Output must have the right 2D/3D shape. Input may also be flattened.
Output must also be contiguous and float32. This isn't required for the
input, but it is more efficient if it is.
:param : The projection data.
:type s: :class:`numpy.ndarray`
:param out: Array to store result in.
:type out: :class:`numpy.ndarray`
"""
s = self.__checkArray(s, self.sshape)
sid = self.data_mod.link('-sino',self.pg,s)
if out is None:
out = np.zeros(self.vshape,dtype=np.float32)
vid = self.data_mod.link('-vol',self.vg,out)
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 out
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
# real operator
_adjoint = _transpose
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)
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