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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/>.
#
#-----------------------------------------------------------------------
# distutils: language = c++
# distutils: libraries = astra
import six
cimport cython
from cython cimport view
cimport PyData2DManager
from .PyData2DManager cimport CData2DManager
cimport PyXMLDocument
from .PyXMLDocument cimport XMLDocument
import numpy as np
cimport numpy as np
np.import_array()
from .PyIncludes cimport *
cimport utils
from .utils import wrap_from_bytes
cdef CData2DManager * man2d = <CData2DManager * >PyData2DManager.getSingletonPtr()
def clear():
man2d.clear()
def delete(ids):
try:
for i in ids:
man2d.remove(i)
except TypeError:
man2d.remove(ids)
def create(datatype, geometry, data=None):
cdef XMLDocument * xml
cdef Config cfg
cdef CVolumeGeometry2D * pGeometry
cdef CProjectionGeometry2D * ppGeometry
cdef CFloat32Data2D * pDataObject2D
if datatype == '-vol':
xml = utils.dict2XML(six.b('VolumeGeometry'), geometry)
cfg.self = xml.getRootNode()
pGeometry = new CVolumeGeometry2D()
if not pGeometry.initialize(cfg):
del xml
del pGeometry
raise Exception('Geometry class not initialized.')
pDataObject2D = <CFloat32Data2D * > new CFloat32VolumeData2D(pGeometry)
del xml
del pGeometry
elif datatype == '-sino':
xml = utils.dict2XML(six.b('ProjectionGeometry'), geometry)
cfg.self = xml.getRootNode()
tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type')))
if (tpe == 'sparse_matrix'):
ppGeometry = <CProjectionGeometry2D * >new CSparseMatrixProjectionGeometry2D()
elif (tpe == 'fanflat'):
ppGeometry = <CProjectionGeometry2D * >new CFanFlatProjectionGeometry2D()
elif (tpe == 'fanflat_vec'):
ppGeometry = <CProjectionGeometry2D * >new CFanFlatVecProjectionGeometry2D()
elif (tpe == 'parallel_vec'):
ppGeometry = <CProjectionGeometry2D * >new CParallelVecProjectionGeometry2D()
else:
ppGeometry = <CProjectionGeometry2D * >new CParallelProjectionGeometry2D()
if not ppGeometry.initialize(cfg):
del xml
del ppGeometry
raise Exception('Geometry class not initialized.')
pDataObject2D = <CFloat32Data2D * > new CFloat32ProjectionData2D(ppGeometry)
del ppGeometry
del xml
else:
raise Exception("Invalid datatype. Please specify '-vol' or '-sino'.")
if not pDataObject2D.isInitialized():
del pDataObject2D
raise Exception("Couldn't initialize data object.")
fillDataObject(pDataObject2D, data)
return man2d.store(pDataObject2D)
cdef fillDataObject(CFloat32Data2D * obj, data):
if data is None:
fillDataObjectScalar(obj, 0)
else:
if isinstance(data, np.ndarray):
fillDataObjectArray(obj, np.ascontiguousarray(data,dtype=np.float32))
else:
fillDataObjectScalar(obj, np.float32(data))
cdef fillDataObjectScalar(CFloat32Data2D * obj, float s):
cdef int i
for i in range(obj.getSize()):
obj.getData()[i] = s
@cython.boundscheck(False)
@cython.wraparound(False)
cdef fillDataObjectArray(CFloat32Data2D * obj, float [:,::1] data):
if (not data.shape[0] == obj.getHeight()) or (not data.shape[1] == obj.getWidth()):
raise Exception(
"The dimensions of the data do not match those specified in the geometry.")
cdef float [:,::1] cView = <float[:data.shape[0],:data.shape[1]]> obj.getData2D()[0]
cView[:] = data
cdef CFloat32Data2D * getObject(i) except NULL:
cdef CFloat32Data2D * pDataObject = man2d.get(i)
if pDataObject == NULL:
raise Exception("Data object not found")
if not pDataObject.isInitialized():
raise Exception("Data object not initialized properly.")
return pDataObject
def store(i, data):
cdef CFloat32Data2D * pDataObject = getObject(i)
fillDataObject(pDataObject, data)
def get_geometry(i):
cdef CFloat32Data2D * pDataObject = getObject(i)
cdef CFloat32ProjectionData2D * pDataObject2
cdef CFloat32VolumeData2D * pDataObject3
if pDataObject.getType() == PROJECTION:
pDataObject2 = <CFloat32ProjectionData2D * >pDataObject
geom = utils.createProjectionGeometryStruct(pDataObject2.getGeometry())
elif pDataObject.getType() == VOLUME:
pDataObject3 = <CFloat32VolumeData2D * >pDataObject
geom = utils.createVolumeGeometryStruct(pDataObject3.getGeometry())
else:
raise Exception("Not a known data object")
return geom
def change_geometry(i, geom):
cdef XMLDocument * xml
cdef Config cfg
cdef CVolumeGeometry2D * pGeometry
cdef CProjectionGeometry2D * ppGeometry
cdef CFloat32Data2D * pDataObject = getObject(i)
cdef CFloat32ProjectionData2D * pDataObject2
cdef CFloat32VolumeData2D * pDataObject3
if pDataObject.getType() == PROJECTION:
pDataObject2 = <CFloat32ProjectionData2D * >pDataObject
xml = utils.dict2XML(six.b('ProjectionGeometry'), geom)
cfg.self = xml.getRootNode()
tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type')))
if (tpe == 'sparse_matrix'):
ppGeometry = <CProjectionGeometry2D * >new CSparseMatrixProjectionGeometry2D()
elif (tpe == 'fanflat'):
ppGeometry = <CProjectionGeometry2D * >new CFanFlatProjectionGeometry2D()
elif (tpe == 'fanflat_vec'):
ppGeometry = <CProjectionGeometry2D * >new CFanFlatVecProjectionGeometry2D()
elif (tpe == 'parallel_vec'):
ppGeometry = <CProjectionGeometry2D * >new CParallelVecProjectionGeometry2D()
else:
ppGeometry = <CProjectionGeometry2D * >new CParallelProjectionGeometry2D()
if not ppGeometry.initialize(cfg):
del xml
del ppGeometry
raise Exception('Geometry class not initialized.')
if (ppGeometry.getDetectorCount() != pDataObject2.getDetectorCount() or ppGeometry.getProjectionAngleCount() != pDataObject2.getAngleCount()):
del ppGeometry
del xml
raise Exception(
"The dimensions of the data do not match those specified in the geometry.")
pDataObject2.changeGeometry(ppGeometry)
del ppGeometry
del xml
elif pDataObject.getType() == VOLUME:
pDataObject3 = <CFloat32VolumeData2D * >pDataObject
xml = utils.dict2XML(six.b('VolumeGeometry'), geom)
cfg.self = xml.getRootNode()
pGeometry = new CVolumeGeometry2D()
if not pGeometry.initialize(cfg):
del xml
del pGeometry
raise Exception('Geometry class not initialized.')
if (pGeometry.getGridColCount() != pDataObject3.getWidth() or pGeometry.getGridRowCount() != pDataObject3.getHeight()):
del xml
del pGeometry
raise Exception(
'The dimensions of the data do not match those specified in the geometry.')
pDataObject3.changeGeometry(pGeometry)
del xml
del pGeometry
else:
raise Exception("Not a known data object")
@cython.boundscheck(False)
@cython.wraparound(False)
def get(i):
cdef CFloat32Data2D * pDataObject = getObject(i)
outArr = np.empty((pDataObject.getHeight(), pDataObject.getWidth()),dtype=np.float32,order='C')
cdef float [:,::1] mView = outArr
cdef float [:,::1] cView = <float[:outArr.shape[0],:outArr.shape[1]]> pDataObject.getData2D()[0]
mView[:] = cView
return outArr
def get_shared(i):
cdef CFloat32Data2D * pDataObject = getObject(i)
cdef np.npy_intp shape[2]
shape[0] = <np.npy_intp> pDataObject.getHeight()
shape[1] = <np.npy_intp> pDataObject.getWidth()
return np.PyArray_SimpleNewFromData(2,shape,np.NPY_FLOAT32,<void *>pDataObject.getData2D()[0])
def get_single(i):
raise Exception("Not yet implemented")
def info():
six.print_(wrap_from_bytes(man2d.info()))
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