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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
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-01 21:28:29 +0000