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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 numpy as np
import six
from libcpp.string cimport string
from libcpp.list cimport list
from libcpp.vector cimport vector
from cython.operator cimport dereference as deref
from cpython.version cimport PY_MAJOR_VERSION
cimport PyXMLDocument
from .PyXMLDocument cimport XMLDocument
from .PyXMLDocument cimport XMLNode
from .PyIncludes cimport *
cdef XMLDocument * dict2XML(string rootname, dc):
cdef XMLDocument * doc = PyXMLDocument.createDocument(rootname)
cdef XMLNode * node = doc.getRootNode()
try:
readDict(node, dc)
except:
six.print_('Error reading XML')
del doc
doc = NULL
finally:
del node
return doc
def convert_item(item):
if isinstance(item, six.string_types):
return item.encode('ascii')
if type(item) is not dict:
return item
out_dict = {}
for k in item:
out_dict[convert_item(k)] = convert_item(item[k])
return out_dict
def wrap_to_bytes(value):
if isinstance(value, six.binary_type):
return value
s = str(value)
if PY_MAJOR_VERSION == 3:
s = s.encode('ascii')
return s
def wrap_from_bytes(value):
s = value
if PY_MAJOR_VERSION == 3:
s = s.decode('ascii')
return s
cdef void readDict(XMLNode * root, _dc):
cdef XMLNode * listbase
cdef XMLNode * itm
cdef int i
cdef int j
dc = convert_item(_dc)
for item in dc:
val = dc[item]
if isinstance(val, np.ndarray):
if val.size == 0:
break
listbase = root.addChildNode(item)
listbase.addAttribute(< string > six.b('listsize'), < float32 > val.size)
index = 0
if val.ndim == 2:
for i in range(val.shape[0]):
for j in range(val.shape[1]):
itm = listbase.addChildNode(six.b('ListItem'))
itm.addAttribute(< string > six.b('index'), < float32 > index)
itm.addAttribute( < string > six.b('value'), < float32 > val[i, j])
index += 1
del itm
elif val.ndim == 1:
for i in range(val.shape[0]):
itm = listbase.addChildNode(six.b('ListItem'))
itm.addAttribute(< string > six.b('index'), < float32 > index)
itm.addAttribute(< string > six.b('value'), < float32 > val[i])
index += 1
del itm
else:
raise Exception("Only 1 or 2 dimensions are allowed")
del listbase
elif isinstance(val, dict):
if item == six.b('option') or item == six.b('options') or item == six.b('Option') or item == six.b('Options'):
readOptions(root, val)
else:
itm = root.addChildNode(item)
readDict(itm, val)
del itm
else:
if item == six.b('type'):
root.addAttribute(< string > six.b('type'), <string> wrap_to_bytes(val))
else:
itm = root.addChildNode(item, wrap_to_bytes(val))
del itm
cdef void readOptions(XMLNode * node, dc):
cdef XMLNode * listbase
cdef XMLNode * itm
cdef int i
cdef int j
for item in dc:
val = dc[item]
if node.hasOption(item):
raise Exception('Duplicate Option: %s' % item)
if isinstance(val, np.ndarray):
if val.size == 0:
break
listbase = node.addChildNode(six.b('Option'))
listbase.addAttribute(< string > six.b('key'), < string > item)
listbase.addAttribute(< string > six.b('listsize'), < float32 > val.size)
index = 0
if val.ndim == 2:
for i in range(val.shape[0]):
for j in range(val.shape[1]):
itm = listbase.addChildNode(six.b('ListItem'))
itm.addAttribute(< string > six.b('index'), < float32 > index)
itm.addAttribute( < string > six.b('value'), < float32 > val[i, j])
index += 1
del itm
elif val.ndim == 1:
for i in range(val.shape[0]):
itm = listbase.addChildNode(six.b('ListItem'))
itm.addAttribute(< string > six.b('index'), < float32 > index)
itm.addAttribute(< string > six.b('value'), < float32 > val[i])
index += 1
del itm
else:
raise Exception("Only 1 or 2 dimensions are allowed")
del listbase
else:
node.addOption(item, wrap_to_bytes(val))
cdef vectorToNumpy(vector[float32] inp):
cdef int i
cdef int sz = inp.size()
ret = np.empty(sz)
for i in range(sz):
ret[i] = inp[i]
return ret
cdef XMLNode2dict(XMLNode * node):
cdef XMLNode * subnode
cdef list[XMLNode * ] nodes
cdef list[XMLNode * ].iterator it
dct = {}
if node.hasAttribute(six.b('type')):
dct['type'] = node.getAttribute(six.b('type'))
nodes = node.getNodes()
it = nodes.begin()
while it != nodes.end():
subnode = deref(it)
if subnode.hasAttribute(six.b('listsize')):
dct[subnode.getName(
)] = vectorToNumpy(subnode.getContentNumericalArray())
else:
dct[subnode.getName()] = subnode.getContent()
del subnode
return dct
cdef XML2dict(XMLDocument * xml):
cdef XMLNode * node = xml.getRootNode()
dct = XMLNode2dict(node)
del node;
return dct;
cdef createProjectionGeometryStruct(CProjectionGeometry2D * geom):
cdef int i
cdef CFanFlatVecProjectionGeometry2D * fanvecGeom
# cdef SFanProjection* p
dct = {}
dct['DetectorCount'] = geom.getDetectorCount()
if not geom.isOfType(< string > six.b('fanflat_vec')):
dct['DetectorWidth'] = geom.getDetectorWidth()
angles = np.empty(geom.getProjectionAngleCount())
for i in range(geom.getProjectionAngleCount()):
angles[i] = geom.getProjectionAngle(i)
dct['ProjectionAngles'] = angles
else:
raise Exception("Not yet implemented")
# fanvecGeom = <CFanFlatVecProjectionGeometry2D*> geom
# vecs = np.empty(fanvecGeom.getProjectionAngleCount()*6)
# iDetCount = pVecGeom.getDetectorCount()
# for i in range(fanvecGeom.getProjectionAngleCount()):
# p = &fanvecGeom.getProjectionVectors()[i];
# out[6*i + 0] = p.fSrcX
# out[6*i + 1] = p.fSrcY
# out[6*i + 2] = p.fDetSX + 0.5f*iDetCount*p.fDetUX
# out[6*i + 3] = p.fDetSY + 0.5f*iDetCount*p.fDetUY
# out[6*i + 4] = p.fDetUX
# out[6*i + 5] = p.fDetUY
# dct['Vectors'] = vecs
if (geom.isOfType(< string > six.b('parallel'))):
dct["type"] = "parallel"
elif (geom.isOfType(< string > six.b('fanflat'))):
raise Exception("Not yet implemented")
# astra::CFanFlatProjectionGeometry2D* pFanFlatGeom = dynamic_cast<astra::CFanFlatProjectionGeometry2D*>(_pProjGeom)
# mGeometryInfo["DistanceOriginSource"] = mxCreateDoubleScalar(pFanFlatGeom->getOriginSourceDistance())
# mGeometryInfo["DistanceOriginDetector"] =
# mxCreateDoubleScalar(pFanFlatGeom->getOriginDetectorDistance())
dct["type"] = "fanflat"
elif (geom.isOfType(< string > six.b('sparse_matrix'))):
raise Exception("Not yet implemented")
# astra::CSparseMatrixProjectionGeometry2D* pSparseMatrixGeom =
# dynamic_cast<astra::CSparseMatrixProjectionGeometry2D*>(_pProjGeom);
dct["type"] = "sparse_matrix"
# dct["MatrixID"] =
# mxCreateDoubleScalar(CMatrixManager::getSingleton().getIndex(pSparseMatrixGeom->getMatrix()))
elif(geom.isOfType(< string > six.b('fanflat_vec'))):
dct["type"] = "fanflat_vec"
return dct
cdef createVolumeGeometryStruct(CVolumeGeometry2D * geom):
mGeometryInfo = {}
mGeometryInfo["GridColCount"] = geom.getGridColCount()
mGeometryInfo["GridRowCount"] = geom.getGridRowCount()
mGeometryOptions = {}
mGeometryOptions["WindowMinX"] = geom.getWindowMinX()
mGeometryOptions["WindowMaxX"] = geom.getWindowMaxX()
mGeometryOptions["WindowMinY"] = geom.getWindowMinY()
mGeometryOptions["WindowMaxY"] = geom.getWindowMaxY()
mGeometryInfo["option"] = mGeometryOptions
return mGeometryInfo
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