# -----------------------------------------------------------------------
# Copyright: 2010-2021, imec Vision Lab, University of Antwerp
# 2013-2021, 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 .
#
# -----------------------------------------------------------------------
#
# distutils: language = c++
# distutils: libraries = astra
import six
cimport cython
from cython cimport view
cimport PyData2DManager
from .PyData2DManager cimport CData2DManager
cimport PyProjector2DManager
from .PyProjector2DManager cimport CProjector2DManager
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
from .pythonutils import geom_size
import operator
from six.moves import reduce
cdef CData2DManager * man2d = PyData2DManager.getSingletonPtr()
cdef CProjector2DManager * manProj = PyProjector2DManager.getSingletonPtr()
cdef extern from "CFloat32CustomPython.h":
cdef cppclass CFloat32CustomPython:
CFloat32CustomPython(arrIn)
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, link=False):
cdef Config *cfg
cdef CVolumeGeometry2D * pGeometry
cdef CProjectionGeometry2D * ppGeometry
cdef CFloat32Data2D * pDataObject2D
cdef CFloat32CustomMemory * pCustom
if link:
geom_shape = geom_size(geometry)
if data.shape != geom_shape:
raise ValueError("The dimensions of the data do not match those specified in the geometry: {} != {}".format(data.shape, geom_shape))
if datatype == '-vol':
cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry)
pGeometry = new CVolumeGeometry2D()
if not pGeometry.initialize(cfg[0]):
del cfg
del pGeometry
raise RuntimeError('Geometry class not initialized.')
if link:
pCustom = new CFloat32CustomPython(data)
pDataObject2D = new CFloat32VolumeData2D(pGeometry, pCustom)
else:
pDataObject2D = new CFloat32VolumeData2D(pGeometry)
del cfg
del pGeometry
elif datatype == '-sino':
cfg = utils.dictToConfig(six.b('ProjectionGeometry'), geometry)
tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type')))
if (tpe == 'sparse_matrix'):
ppGeometry = new CSparseMatrixProjectionGeometry2D()
elif (tpe == 'fanflat'):
ppGeometry = new CFanFlatProjectionGeometry2D()
elif (tpe == 'fanflat_vec'):
ppGeometry = new CFanFlatVecProjectionGeometry2D()
elif (tpe == 'parallel_vec'):
ppGeometry = new CParallelVecProjectionGeometry2D()
else:
ppGeometry = new CParallelProjectionGeometry2D()
if not ppGeometry.initialize(cfg[0]):
del cfg
del ppGeometry
raise RuntimeError('Geometry class not initialized.')
if link:
pCustom = new CFloat32CustomPython(data)
pDataObject2D = new CFloat32ProjectionData2D(ppGeometry, pCustom)
else:
pDataObject2D = new CFloat32ProjectionData2D(ppGeometry)
del ppGeometry
del cfg
else:
raise ValueError("Invalid datatype. Please specify '-vol' or '-sino'.")
if not pDataObject2D.isInitialized():
del pDataObject2D
raise RuntimeError("Couldn't initialize data object.")
if not link: 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):
obj_shape = (obj.getHeight(), obj.getWidth())
if data.shape != obj_shape:
raise ValueError(
"The dimensions of the data do not match those specified in the geometry: {} != {}".format(data.shape, obj_shape))
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):
cdef float [:,::1] cView = obj.getData2D()[0]
cView[:] = data
cdef CFloat32Data2D * getObject(i) except NULL:
cdef CFloat32Data2D * pDataObject = man2d.get(i)
if pDataObject == NULL:
raise ValueError("Data object not found")
if not pDataObject.isInitialized():
raise RuntimeError("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() == TWOPROJECTION:
pDataObject2 = pDataObject
geom = utils.configToDict(pDataObject2.getGeometry().getConfiguration())
elif pDataObject.getType() == TWOVOLUME:
pDataObject3 = pDataObject
geom = utils.configToDict(pDataObject3.getGeometry().getConfiguration())
else:
raise RuntimeError("Not a known data object")
return geom
cdef CProjector2D * getProjector(i) except NULL:
cdef CProjector2D * proj = manProj.get(i)
if proj == NULL:
raise RuntimeError("Projector not initialized.")
if not proj.isInitialized():
raise RuntimeError("Projector not initialized.")
return proj
def check_compatible(i, proj_id):
cdef CProjector2D * proj = getProjector(proj_id)
cdef CFloat32Data2D * pDataObject = getObject(i)
cdef CFloat32ProjectionData2D * pDataObject2
cdef CFloat32VolumeData2D * pDataObject3
if pDataObject.getType() == TWOPROJECTION:
pDataObject2 = pDataObject
return pDataObject2.getGeometry().isEqual(proj.getProjectionGeometry())
elif pDataObject.getType() == TWOVOLUME:
pDataObject3 = pDataObject
return pDataObject3.getGeometry().isEqual(proj.getVolumeGeometry())
else:
raise RuntimeError("Not a known data object")
def change_geometry(i, geom):
cdef Config *cfg
cdef CVolumeGeometry2D * pGeometry
cdef CProjectionGeometry2D * ppGeometry
cdef CFloat32Data2D * pDataObject = getObject(i)
cdef CFloat32ProjectionData2D * pDataObject2
cdef CFloat32VolumeData2D * pDataObject3
if pDataObject.getType() == TWOPROJECTION:
pDataObject2 = pDataObject
cfg = utils.dictToConfig(six.b('ProjectionGeometry'), geom)
tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type')))
if (tpe == 'sparse_matrix'):
ppGeometry = new CSparseMatrixProjectionGeometry2D()
elif (tpe == 'fanflat'):
ppGeometry = new CFanFlatProjectionGeometry2D()
elif (tpe == 'fanflat_vec'):
ppGeometry = new CFanFlatVecProjectionGeometry2D()
elif (tpe == 'parallel_vec'):
ppGeometry = new CParallelVecProjectionGeometry2D()
else:
ppGeometry = new CParallelProjectionGeometry2D()
if not ppGeometry.initialize(cfg[0]):
del cfg
del ppGeometry
raise RuntimeError('Geometry class not initialized.')
geom_shape = (ppGeometry.getProjectionAngleCount(), ppGeometry.getDetectorCount())
obj_shape = (pDataObject2.getAngleCount(), pDataObject2.getDetectorCount())
if geom_shape != obj_shape:
del ppGeometry
del cfg
raise ValueError(
"The dimensions of the data do not match those specified in the geometry: {} != {}", obj_shape, geom_shape)
pDataObject2.changeGeometry(ppGeometry)
del ppGeometry
del cfg
elif pDataObject.getType() == TWOVOLUME:
pDataObject3 = pDataObject
cfg = utils.dictToConfig(six.b('VolumeGeometry'), geom)
pGeometry = new CVolumeGeometry2D()
if not pGeometry.initialize(cfg[0]):
del cfg
del pGeometry
raise RuntimeError('Geometry class not initialized.')
geom_shape = (pGeometry.getGridRowCount(), pGeometry.getGridColCount())
obj_shape = (pDataObject3.getHeight(), pDataObject3.getWidth())
if geom_shape != obj_shape:
del cfg
del pGeometry
raise ValueError(
"The dimensions of the data do not match those specified in the geometry: {} != {}", obj_shape, geom_shape)
pDataObject3.changeGeometry(pGeometry)
del cfg
del pGeometry
else:
raise RuntimeError("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 = pDataObject.getData2D()[0]
mView[:] = cView
return outArr
def get_shared(i):
cdef CFloat32Data2D * pDataObject = getObject(i)
cdef np.npy_intp shape[2]
shape[0] = pDataObject.getHeight()
shape[1] = pDataObject.getWidth()
return np.PyArray_SimpleNewFromData(2,shape,np.NPY_FLOAT32,pDataObject.getData2D()[0])
def get_single(i):
raise NotImplementedError("Not yet implemented")
def info():
six.print_(wrap_from_bytes(man2d.info()))