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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/>.
#
# -----------------------------------------------------------------------
#
# distutils: language = c++
# distutils: libraries = astra
from __future__ import print_function
cimport cython
from libcpp.utility cimport move
from . cimport PyData3DManager
from .PyData3DManager cimport CData3DManager
from .PyIncludes cimport *
import numpy as np
cimport numpy as np
np.import_array()
from . cimport PyXMLDocument
from .PyXMLDocument cimport XMLDocument
from . cimport utils
from .utils import wrap_from_bytes
from .utils cimport linkVolFromGeometry, linkProjFromGeometry, createProjectionGeometry3D, createVolumeGeometry3D
from .log import AstraError
from .pythonutils import geom_size, GPULink
import operator
include "config.pxi"
cdef extern from "astra/SheppLogan.h" namespace "astra":
cdef void generateSheppLogan3D(CFloat32VolumeData3D*, bool)
cdef CData3DManager * man3d = <CData3DManager * >PyData3DManager.getSingletonPtr()
def create(datatype,geometry,data=None, link=False):
cdef unique_ptr[CVolumeGeometry3D] pGeometry
cdef unique_ptr[CProjectionGeometry3D] ppGeometry
cdef CData3D * pDataObject3D
if datatype == '-vol':
pGeometry = createVolumeGeometry3D(geometry)
if link:
pDataObject3D = linkVolFromGeometry(cython.operator.dereference(pGeometry), data)
else:
pDataObject3D = createCFloat32VolumeData3DMemory(move(pGeometry))
elif datatype == '-sino' or datatype == '-proj3d' or datatype == '-sinocone':
ppGeometry = createProjectionGeometry3D(geometry)
if link:
pDataObject3D = linkProjFromGeometry(cython.operator.dereference(ppGeometry), data)
else:
pDataObject3D = createCFloat32ProjectionData3DMemory(move(ppGeometry))
else:
raise ValueError("Invalid datatype. Please specify '-vol' or '-proj3d'")
if not pDataObject3D.isInitialized():
del pDataObject3D
raise AstraError("Couldn't initialize data object", append_log=True)
if not link:
fillDataObject(pDataObject3D, data)
return man3d.store(pDataObject3D)
def get_geometry(i):
cdef CData3D * pDataObject = getObject(i)
cdef CFloat32ProjectionData3D * pDataObject2
cdef CFloat32VolumeData3D * pDataObject3
if pDataObject.getType() == THREEPROJECTION:
pDataObject2 = <CFloat32ProjectionData3D * >pDataObject
geom = utils.configToDict(pDataObject2.getGeometry().getConfiguration())
elif pDataObject.getType() == THREEVOLUME:
pDataObject3 = <CFloat32VolumeData3D * >pDataObject
geom = utils.configToDict(pDataObject3.getGeometry().getConfiguration())
else:
raise AstraError("Not a known data object")
return geom
def change_geometry(i, geom):
cdef CData3D * pDataObject = getObject(i)
cdef CFloat32ProjectionData3D * pDataObject2
cdef CFloat32VolumeData3D * pDataObject3
if pDataObject.getType() == THREEPROJECTION:
pDataObject2 = <CFloat32ProjectionData3D * >pDataObject
ppGeometry = createProjectionGeometry3D(geom)
geom_shape = (ppGeometry.get().getDetectorRowCount(), ppGeometry.get().getProjectionCount(), ppGeometry.get().getDetectorColCount())
obj_shape = (pDataObject2.getDetectorRowCount(), pDataObject2.getAngleCount(), pDataObject2.getDetectorColCount())
if geom_shape != obj_shape:
raise ValueError("The dimensions of the data {} do not match those "
"specified in the geometry {}".format(obj_shape, geom_shape))
pDataObject2.changeGeometry(move(ppGeometry))
elif pDataObject.getType() == THREEVOLUME:
pDataObject3 = <CFloat32VolumeData3D * >pDataObject
pGeometry = createVolumeGeometry3D(geom)
geom_shape = (pGeometry.get().getGridSliceCount(), pGeometry.get().getGridRowCount(), pGeometry.get().getGridColCount())
obj_shape = (pDataObject3.getSliceCount(), pDataObject3.getRowCount(), pDataObject3.getColCount())
if geom_shape != obj_shape:
raise ValueError("The dimensions of the data {} do not match those "
"specified in the geometry {}".format(obj_shape, geom_shape))
pDataObject3.changeGeometry(move(pGeometry))
else:
raise AstraError("Not a known data object")
cdef fillDataObject(CData3D * obj, data):
if not obj.isFloat32Memory():
raise ValueError("Data object is not float32/memory")
if data is None:
fillDataObjectScalar(obj, 0)
else:
if isinstance(data, np.ndarray):
obj_shape = (obj.getDepth(), 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(CData3D * obj, float s):
cdef size_t i
for i in range(obj.getSize()):
obj.getFloat32Memory()[i] = s
@cython.boundscheck(False)
@cython.wraparound(False)
cdef fillDataObjectArray(CData3D* obj, const float [:,:,::1] data):
cdef const float [:,:,::1] cView = <const float[:data.shape[0],:data.shape[1],:data.shape[2]]> obj.getFloat32Memory()
cView[:] = data
cdef CData3D * getObject(i) except NULL:
cdef CData3D * pDataObject = man3d.get(i)
if pDataObject == NULL:
raise AstraError("Data object not found")
if not pDataObject.isInitialized():
raise AstraError("Data object not initialized properly")
return pDataObject
@cython.boundscheck(False)
@cython.wraparound(False)
def get(i):
cdef CData3D * pDataObject = getObject(i)
if not pDataObject.isFloat32Memory():
raise ValueError("Data object is not float32/memory")
outArr = np.empty((pDataObject.getDepth(),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],:outArr.shape[2]]> pDataObject.getFloat32Memory()
mView[:] = cView
return outArr
def get_shared(i):
cdef CData3D * pDataObject = getObject(i)
if not pDataObject.isFloat32Memory():
raise ValueError("Data object is not float32/memory")
cdef np.npy_intp shape[3]
shape[0] = <np.npy_intp> pDataObject.getDepth()
shape[1] = <np.npy_intp> pDataObject.getHeight()
shape[2] = <np.npy_intp> pDataObject.getWidth()
return np.PyArray_SimpleNewFromData(3,shape,np.NPY_FLOAT32,<void *>pDataObject.getFloat32Memory())
def get_single(i):
raise NotImplementedError("Not yet implemented")
def store(i,data):
cdef CData3D * pDataObject = getObject(i)
fillDataObject(pDataObject, data)
def dimensions(i):
cdef CData3D * pDataObject = getObject(i)
return (pDataObject.getDepth(),pDataObject.getHeight(),pDataObject.getWidth())
def shepp_logan(i, modified=True):
cdef CData3D * pDataObject = getObject(i)
cdef CFloat32VolumeData3D * pVolumeDataObject = <CFloat32VolumeData3D * >pDataObject
generateSheppLogan3D(pVolumeDataObject, modified);
def delete(ids):
try:
for i in ids:
man3d.remove(i)
except TypeError:
man3d.remove(ids)
def clear():
man3d.clear()
def info():
print(wrap_from_bytes(man3d.info()))
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