From 47fe3421585302f2101691a685ab99b0e1ad5cfc Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Fri, 1 May 2015 17:48:32 +0200 Subject: Change XMLNode* to XMLNode An XMLNode object is already simply a pointer, so no need to dynamically allocate XMLNodes. --- matlab/mex/astra_mex_algorithm_c.cpp | 2 +- matlab/mex/astra_mex_data2d_c.cpp | 4 +- matlab/mex/astra_mex_data3d_c.cpp | 2 +- matlab/mex/mexDataManagerHelpFunctions.cpp | 2 +- matlab/mex/mexHelpFunctions.cpp | 62 ++++++++++++++---------------- matlab/mex/mexHelpFunctions.h | 6 +-- 6 files changed, 36 insertions(+), 42 deletions(-) (limited to 'matlab') diff --git a/matlab/mex/astra_mex_algorithm_c.cpp b/matlab/mex/astra_mex_algorithm_c.cpp index e4afa63..ec7aa72 100644 --- a/matlab/mex/astra_mex_algorithm_c.cpp +++ b/matlab/mex/astra_mex_algorithm_c.cpp @@ -81,7 +81,7 @@ void astra_mex_algorithm_create(int nlhs, mxArray* plhs[], int nrhs, const mxArr // turn MATLAB struct to an XML-based Config object Config* cfg = structToConfig("Algorithm", prhs[1]); - CAlgorithm* pAlg = CAlgorithmFactory::getSingleton().create(cfg->self->getAttribute("type")); + CAlgorithm* pAlg = CAlgorithmFactory::getSingleton().create(cfg->self.getAttribute("type")); if (!pAlg) { delete cfg; mexErrMsgTxt("Unknown algorithm. \n"); diff --git a/matlab/mex/astra_mex_data2d_c.cpp b/matlab/mex/astra_mex_data2d_c.cpp index 9576896..909d229 100644 --- a/matlab/mex/astra_mex_data2d_c.cpp +++ b/matlab/mex/astra_mex_data2d_c.cpp @@ -149,7 +149,7 @@ void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra Config* cfg = structToConfig("ProjectionGeometry", prhs[2]); // FIXME: Change how the base class is created. (This is duplicated // in 'change_geometry' and Projector2D.cpp.) - std::string type = cfg->self->getAttribute("type"); + std::string type = cfg->self.getAttribute("type"); CProjectionGeometry2D* pGeometry; if (type == "sparse_matrix") { pGeometry = new CSparseMatrixProjectionGeometry2D(); @@ -438,7 +438,7 @@ void astra_mex_data2d_change_geometry(int nlhs, mxArray* plhs[], int nrhs, const Config* cfg = structToConfig("ProjectionGeometry2D", prhs[2]); // FIXME: Change how the base class is created. (This is duplicated // in 'create' and Projector2D.cpp.) - std::string type = cfg->self->getAttribute("type"); + std::string type = cfg->self.getAttribute("type"); CProjectionGeometry2D* pGeometry; if (type == "sparse_matrix") { pGeometry = new CSparseMatrixProjectionGeometry2D(); diff --git a/matlab/mex/astra_mex_data3d_c.cpp b/matlab/mex/astra_mex_data3d_c.cpp index 6096adc..fe4ce37 100644 --- a/matlab/mex/astra_mex_data3d_c.cpp +++ b/matlab/mex/astra_mex_data3d_c.cpp @@ -346,7 +346,7 @@ void astra_mex_data3d_change_geometry(int nlhs, mxArray* plhs[], int nrhs, const astra::Config* cfg = structToConfig("ProjectionGeometry3D", geometry); // FIXME: Change how the base class is created. (This is duplicated // in Projector3D.cpp.) - std::string type = cfg->self->getAttribute("type"); + std::string type = cfg->self.getAttribute("type"); astra::CProjectionGeometry3D* pGeometry = 0; if (type == "parallel3d") { pGeometry = new astra::CParallelProjectionGeometry3D(); diff --git a/matlab/mex/mexDataManagerHelpFunctions.cpp b/matlab/mex/mexDataManagerHelpFunctions.cpp index d482428..1794abb 100644 --- a/matlab/mex/mexDataManagerHelpFunctions.cpp +++ b/matlab/mex/mexDataManagerHelpFunctions.cpp @@ -285,7 +285,7 @@ allocateDataObject(const std::string & sDataType, astra::Config* cfg = structToConfig("ProjectionGeometry3D", geometry); // FIXME: Change how the base class is created. (This is duplicated // in Projector3D.cpp.) - std::string type = cfg->self->getAttribute("type"); + std::string type = cfg->self.getAttribute("type"); astra::CProjectionGeometry3D* pGeometry = 0; if (type == "parallel3d") { pGeometry = new astra::CParallelProjectionGeometry3D(); diff --git a/matlab/mex/mexHelpFunctions.cpp b/matlab/mex/mexHelpFunctions.cpp index c0ac711..00d766f 100644 --- a/matlab/mex/mexHelpFunctions.cpp +++ b/matlab/mex/mexHelpFunctions.cpp @@ -185,7 +185,7 @@ Config* structToConfig(string rootname, const mxArray* pStruct) } //----------------------------------------------------------------------------------------- -bool structToXMLNode(XMLNode* node, const mxArray* pStruct) +bool structToXMLNode(XMLNode node, const mxArray* pStruct) { // loop all fields int nfields = mxGetNumberOfFields(pStruct); @@ -199,16 +199,16 @@ bool structToXMLNode(XMLNode* node, const mxArray* pStruct) if (mxIsChar(pField)) { string sValue = mexToString(pField); if (sFieldName == "type") { - node->addAttribute("type", sValue); + node.addAttribute("type", sValue); } else { - delete node->addChildNode(sFieldName, sValue); + node.addChildNode(sFieldName, sValue); } } // scalar else if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) == 1) { string sValue = mexToString(pField); - delete node->addChildNode(sFieldName, sValue); + node.addChildNode(sFieldName, sValue); } // numerical array @@ -217,20 +217,18 @@ bool structToXMLNode(XMLNode* node, const mxArray* pStruct) mexErrMsgTxt("Numeric input must be double."); return false; } - XMLNode* listbase = node->addChildNode(sFieldName); - listbase->addAttribute("listsize", mxGetM(pField)*mxGetN(pField)); + XMLNode listbase = node.addChildNode(sFieldName); + listbase.addAttribute("listsize", mxGetM(pField)*mxGetN(pField)); double* pdValues = mxGetPr(pField); int index = 0; for (unsigned int row = 0; row < mxGetM(pField); row++) { for (unsigned int col = 0; col < mxGetN(pField); col++) { - XMLNode* item = listbase->addChildNode("ListItem"); - item->addAttribute("index", index); - item->addAttribute("value", pdValues[col*mxGetM(pField)+row]); + XMLNode item = listbase.addChildNode("ListItem"); + item.addAttribute("index", index); + item.addAttribute("value", pdValues[col*mxGetM(pField)+row]); index++; - delete item; } } - delete listbase; } // not castable to a single string @@ -240,9 +238,8 @@ bool structToXMLNode(XMLNode* node, const mxArray* pStruct) if (!ret) return false; } else { - XMLNode* newNode = node->addChildNode(sFieldName); + XMLNode newNode = node.addChildNode(sFieldName); bool ret = structToXMLNode(newNode, pField); - delete newNode; if (!ret) return false; } @@ -254,7 +251,7 @@ bool structToXMLNode(XMLNode* node, const mxArray* pStruct) } //----------------------------------------------------------------------------------------- // Options struct to xml node -bool optionsToXMLNode(XMLNode* node, const mxArray* pOptionStruct) +bool optionsToXMLNode(XMLNode node, const mxArray* pOptionStruct) { // loop all fields int nfields = mxGetNumberOfFields(pOptionStruct); @@ -262,7 +259,7 @@ bool optionsToXMLNode(XMLNode* node, const mxArray* pOptionStruct) std::string sFieldName = std::string(mxGetFieldNameByNumber(pOptionStruct, i)); const mxArray* pField = mxGetFieldByNumber(pOptionStruct, 0, i); - if (node->hasOption(sFieldName)) { + if (node.hasOption(sFieldName)) { mexErrMsgTxt("Duplicate option"); return false; } @@ -270,7 +267,7 @@ bool optionsToXMLNode(XMLNode* node, const mxArray* pOptionStruct) // string or scalar if (mxIsChar(pField) || mexIsScalar(pField)) { string sValue = mexToString(pField); - node->addOption(sFieldName, sValue); + node.addOption(sFieldName, sValue); } // numerical array else if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) > 1) { @@ -279,21 +276,19 @@ bool optionsToXMLNode(XMLNode* node, const mxArray* pOptionStruct) return false; } - XMLNode* listbase = node->addChildNode("Option"); - listbase->addAttribute("key", sFieldName); - listbase->addAttribute("listsize", mxGetM(pField)*mxGetN(pField)); + XMLNode listbase = node.addChildNode("Option"); + listbase.addAttribute("key", sFieldName); + listbase.addAttribute("listsize", mxGetM(pField)*mxGetN(pField)); double* pdValues = mxGetPr(pField); int index = 0; for (unsigned int row = 0; row < mxGetM(pField); row++) { for (unsigned int col = 0; col < mxGetN(pField); col++) { - XMLNode* item = listbase->addChildNode("ListItem"); - item->addAttribute("index", index); - item->addAttribute("value", pdValues[col*mxGetM(pField)+row]); + XMLNode item = listbase.addChildNode("ListItem"); + item.addAttribute("index", index); + item.addAttribute("value", pdValues[col*mxGetM(pField)+row]); index++; - delete item; } } - delete listbase; } else { mexErrMsgTxt("Unsupported option type"); return false; @@ -343,30 +338,29 @@ mxArray* configToStruct(astra::Config* cfg) } //----------------------------------------------------------------------------------------- -mxArray* XMLNodeToStruct(astra::XMLNode* node) +mxArray* XMLNodeToStruct(astra::XMLNode node) { std::map mList; std::map mOptions; // type_attribute - if (node->hasAttribute("type")) { - mList["type"] = mxCreateString(node->getAttribute("type").c_str()); + if (node.hasAttribute("type")) { + mList["type"] = mxCreateString(node.getAttribute("type").c_str()); } - list nodes = node->getNodes(); - for (list::iterator it = nodes.begin(); it != nodes.end(); it++) { - XMLNode* subnode = (*it); + list nodes = node.getNodes(); + for (list::iterator it = nodes.begin(); it != nodes.end(); it++) { + XMLNode subnode = (*it); // option - if (subnode->getName() == "Option") { - mOptions[subnode->getAttribute("key")] = stringToMxArray(subnode->getAttribute("value")); + if (subnode.getName() == "Option") { + mOptions[subnode.getAttribute("key")] = stringToMxArray(subnode.getAttribute("value")); } // regular content else { - mList[subnode->getName()] = stringToMxArray(subnode->getContent()); + mList[subnode.getName()] = stringToMxArray(subnode.getContent()); } - delete subnode; } if (mOptions.size() > 0) mList["options"] = buildStruct(mOptions); diff --git a/matlab/mex/mexHelpFunctions.h b/matlab/mex/mexHelpFunctions.h index f9ffcf2..3ac5bd8 100644 --- a/matlab/mex/mexHelpFunctions.h +++ b/matlab/mex/mexHelpFunctions.h @@ -58,13 +58,13 @@ mxArray* anyToMxArray(boost::any _any); // turn a MATLAB struct into a Config object astra::Config* structToConfig(string rootname, const mxArray* pStruct); -bool structToXMLNode(astra::XMLNode* node, const mxArray* pStruct); -bool optionsToXMLNode(astra::XMLNode* node, const mxArray* pOptionStruct); +bool structToXMLNode(astra::XMLNode node, const mxArray* pStruct); +bool optionsToXMLNode(astra::XMLNode node, const mxArray* pOptionStruct); std::map parseStruct(const mxArray* pInput); // turn a Config object into a MATLAB struct mxArray* configToStruct(astra::Config* cfg); -mxArray* XMLNodeToStruct(astra::XMLNode* xml); +mxArray* XMLNodeToStruct(astra::XMLNode xml); mxArray* stringToMxArray(std::string input); mxArray* buildStruct(std::map mInput); -- cgit v1.2.3 From fff7470f1d74b0085355130350fa834ea8d37069 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 6 May 2015 13:50:11 +0200 Subject: Make XML array handling consistent setContent and getContent were using different XML formats previously. --- include/astra/XMLNode.h | 35 +++++++--- matlab/mex/mexHelpFunctions.cpp | 22 +----- python/astra/PyXMLDocument.pxd | 2 + python/astra/utils.pyx | 35 +++------- src/XMLNode.cpp | 150 +++++++++++++++++++++++----------------- 5 files changed, 127 insertions(+), 117 deletions(-) (limited to 'matlab') diff --git a/include/astra/XMLNode.h b/include/astra/XMLNode.h index f79c1a8..4d29d5c 100644 --- a/include/astra/XMLNode.h +++ b/include/astra/XMLNode.h @@ -119,14 +119,8 @@ public: */ vector getContentArray() const; - /** Get the content of the XML node as a c-array of float32 data. - * - * @param _pfData data array, shouldn't be initialized already. - * @param _iSize number of elements stored in _pfData - */ - void getContentNumericalArray(float32*& _pfData, int& _iSize) const; - /** Get the content of the XML node as a stl container of float32 data. + * NB: A 2D matrix is returned as a linear list * * @return node content */ @@ -259,13 +253,38 @@ public: */ void setContent(float32 _fValue); - /** Add a list of numerical data to the node: <...>_sText</...> + /** Add a list of numerical data to the node * * @param _pfList data * @param _iSize number of elements in the list */ void setContent(float32* _pfList, int _iSize); + /** Add a list of numerical data to the node + * + * @param _pfList data + * @param _iSize number of elements in the list + */ + void setContent(double* _pfList, int _iSize); + + /** Add a (2D) matrix of numerical data to the node + * + * @param _pfMatrix data + * @param _iWidth width of the matrix + * @param _iHeight height of the matrix + * @param transposed true is C order, false is Fortran order + */ + void setContent(float32* _pfMatrix, int _iWidth, int _iHeight, bool transposed); + + /** Add a (2D) matrix of numerical data to the node + * + * @param _pfMatrix data + * @param _iWidth width of the matrix + * @param _iHeight height of the matrix + * @param transposed true is C order, false is Fortran order + */ + void setContent(double* _pfMatrix, int _iWidth, int _iHeight, bool transposed); + /** Add an attribute to this node: <... _sName="_sValue"> * * @param _sName name of the attribute diff --git a/matlab/mex/mexHelpFunctions.cpp b/matlab/mex/mexHelpFunctions.cpp index 00d766f..87a9672 100644 --- a/matlab/mex/mexHelpFunctions.cpp +++ b/matlab/mex/mexHelpFunctions.cpp @@ -218,17 +218,8 @@ bool structToXMLNode(XMLNode node, const mxArray* pStruct) return false; } XMLNode listbase = node.addChildNode(sFieldName); - listbase.addAttribute("listsize", mxGetM(pField)*mxGetN(pField)); double* pdValues = mxGetPr(pField); - int index = 0; - for (unsigned int row = 0; row < mxGetM(pField); row++) { - for (unsigned int col = 0; col < mxGetN(pField); col++) { - XMLNode item = listbase.addChildNode("ListItem"); - item.addAttribute("index", index); - item.addAttribute("value", pdValues[col*mxGetM(pField)+row]); - index++; - } - } + listbase.setContent(pdValues, mxGetN(pField), mxGetM(pField), true); } // not castable to a single string @@ -278,17 +269,8 @@ bool optionsToXMLNode(XMLNode node, const mxArray* pOptionStruct) XMLNode listbase = node.addChildNode("Option"); listbase.addAttribute("key", sFieldName); - listbase.addAttribute("listsize", mxGetM(pField)*mxGetN(pField)); double* pdValues = mxGetPr(pField); - int index = 0; - for (unsigned int row = 0; row < mxGetM(pField); row++) { - for (unsigned int col = 0; col < mxGetN(pField); col++) { - XMLNode item = listbase.addChildNode("ListItem"); - item.addAttribute("index", index); - item.addAttribute("value", pdValues[col*mxGetM(pField)+row]); - index++; - } - } + listbase.setContent(pdValues, mxGetN(pField), mxGetM(pField), true); } else { mexErrMsgTxt("Unsupported option type"); return false; diff --git a/python/astra/PyXMLDocument.pxd b/python/astra/PyXMLDocument.pxd index 57c447e..033b8ef 100644 --- a/python/astra/PyXMLDocument.pxd +++ b/python/astra/PyXMLDocument.pxd @@ -53,6 +53,8 @@ cdef extern from "astra/XMLNode.h" namespace "astra": string getAttribute(string) list[XMLNode] getNodes() vector[float32] getContentNumericalArray() + void setContent(double*, int, int, bool) + void setContent(double*, int) string getContent() bool hasAttribute(string) diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx index 8f1e0b7..ddb37aa 100644 --- a/python/astra/utils.pyx +++ b/python/astra/utils.pyx @@ -26,6 +26,7 @@ # distutils: language = c++ # distutils: libraries = astra +cimport numpy as np import numpy as np import six from libcpp.string cimport string @@ -85,6 +86,7 @@ cdef void readDict(XMLNode root, _dc): cdef XMLNode itm cdef int i cdef int j + cdef double* data dc = convert_item(_dc) for item in dc: @@ -93,21 +95,11 @@ cdef void readDict(XMLNode root, _dc): if val.size == 0: break listbase = root.addChildNode(item) - listbase.addAttribute(< string > six.b('listsize'), < float32 > val.size) - index = 0 + data = np.PyArray_DATA(np.ascontiguousarray(val,dtype=np.float64)) 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 + listbase.setContent(data, val.shape[1], val.shape[0], False) 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 + listbase.setContent(data, val.shape[0]) else: raise Exception("Only 1 or 2 dimensions are allowed") elif isinstance(val, dict): @@ -127,6 +119,7 @@ cdef void readOptions(XMLNode node, dc): cdef XMLNode itm cdef int i cdef int j + cdef double* data for item in dc: val = dc[item] if node.hasOption(item): @@ -136,21 +129,11 @@ cdef void readOptions(XMLNode node, dc): 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 + data = np.PyArray_DATA(np.ascontiguousarray(val,dtype=np.float64)) 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 + listbase.setContent(data, val.shape[1], val.shape[0], False) 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 + listbase.setContent(data, val.shape[0]) else: raise Exception("Only 1 or 2 dimensions are allowed") else: diff --git a/src/XMLNode.cpp b/src/XMLNode.cpp index 75985cc..0ec701f 100644 --- a/src/XMLNode.cpp +++ b/src/XMLNode.cpp @@ -32,6 +32,11 @@ $Id$ #include "rapidxml/rapidxml_print.hpp" #include +#include +#include +#include + + using namespace rapidxml; using namespace astra; @@ -167,77 +172,43 @@ vector XMLNode::getContentArray() const //----------------------------------------------------------------------------- // Get node content - NUMERICAL LIST +// NB: A 2D matrix is returned as a linear list vector XMLNode::getContentNumericalArray() const { - // is scalar - if (!hasAttribute("listsize")) { - vector res(1); - res[0] = getContentNumerical(); - return res; - } + string input = getContent(); - int iSize = boost::lexical_cast(getAttribute("listsize")); - // create result array - vector res(iSize); - // loop all list item nodes - list nodes = getNodes("ListItem"); - for (list::iterator it = nodes.begin(); it != nodes.end(); it++) { - int iIndex = it->getAttributeNumerical("index"); - float32 fValue = it->getAttributeNumerical("value"); - ASTRA_ASSERT(iIndex < iSize); - res[iIndex] = fValue; + // split + std::vector items; + boost::split(items, input, boost::is_any_of(",;")); + + // init list + vector out; + out.resize(items.size()); + + // loop elements + for (unsigned int i = 0; i < items.size(); i++) { + out[i] = boost::lexical_cast(items[i]); } - // return - return res; + return out; } vector XMLNode::getContentNumericalArrayDouble() const { - // is scalar - if (!hasAttribute("listsize")) { - vector res(1); - res[0] = getContentNumerical(); - return res; - } + string input = getContent(); - int iSize = boost::lexical_cast(getAttribute("listsize")); - // create result array - vector res(iSize); - // loop all list item nodes - list nodes = getNodes("ListItem"); - for (list::iterator it = nodes.begin(); it != nodes.end(); it++) { - int iIndex = it->getAttributeNumerical("index"); - double fValue = it->getAttributeNumericalDouble("value"); - ASTRA_ASSERT(iIndex < iSize); - res[iIndex] = fValue; - } - // return - return res; -} + // split + std::vector items; + boost::split(items, input, boost::is_any_of(",;")); -//----------------------------------------------------------------------------- -// Get node content - NUMERICAL LIST 2 -void XMLNode::getContentNumericalArray(float32*& _pfData, int& _iSize) const -{ - // is scalar - if (!hasAttribute("listsize")) { - _iSize = 1; - _pfData = new float32[_iSize]; - _pfData[0] = getContentNumerical(); - return; - } - // get listsize - _iSize = boost::lexical_cast(getAttribute("listsize")); - // create result array - _pfData = new float32[_iSize]; - // loop all list item nodes - list nodes = getNodes("ListItem"); - for (list::iterator it = nodes.begin(); it != nodes.end(); it++) { - int iIndex = it->getAttributeNumerical("index"); - float32 fValue = it->getAttributeNumerical("value"); - ASTRA_ASSERT(iIndex < _iSize); - _pfData[iIndex] = fValue; + // init list + vector out; + out.resize(items.size()); + + // loop elements + for (unsigned int i = 0; i < items.size(); i++) { + out[i] = boost::lexical_cast(items[i]); } + return out; } //----------------------------------------------------------------------------- @@ -420,15 +391,68 @@ void XMLNode::setContent(float32 _fValue) //----------------------------------------------------------------------------- // Set content - LIST -void XMLNode::setContent(float32* pfList, int _iSize) -{ + +template +static std::string setContentList_internal(T* pfList, int _iSize) { std::string str = (_iSize > 0) ? boost::lexical_cast(pfList[0]) : ""; for (int i = 1; i < _iSize; i++) { str += "," + boost::lexical_cast(pfList[i]); } - setContent(str); + return str; +} + +void XMLNode::setContent(float32* pfList, int _iSize) +{ + setContent(setContentList_internal(pfList, _iSize)); +} + +void XMLNode::setContent(double* pfList, int _iSize) +{ + setContent(setContentList_internal(pfList, _iSize)); } +//----------------------------------------------------------------------------- +// Set content - MATRIX + +template +static std::string setContentMatrix_internal(T* _pfMatrix, int _iWidth, int _iHeight, bool transposed) +{ + std::string str = ""; + + int s1,s2; + + if (!transposed) { + s1 = 1; + s2 = _iWidth; + } else { + s1 = _iHeight; + s2 = 1; + } + + for (int y = 0; y < _iHeight; ++y) { + if (_iWidth > 0) + str += boost::lexical_cast(_pfMatrix[0*s1 + y*s2]); + for (int x = 1; x < _iWidth; x++) + str += "," + boost::lexical_cast(_pfMatrix[x*s1 + y*s2]); + + if (y != _iHeight-1) + str += ";"; + } + + return str; +} + +void XMLNode::setContent(float32* _pfMatrix, int _iWidth, int _iHeight, bool transposed) +{ + setContent(setContentMatrix_internal(_pfMatrix, _iWidth, _iHeight, transposed)); +} + +void XMLNode::setContent(double* _pfMatrix, int _iWidth, int _iHeight, bool transposed) +{ + setContent(setContentMatrix_internal(_pfMatrix, _iWidth, _iHeight, transposed)); +} + + //----------------------------------------------------------------------------- // Add attribute - STRING void XMLNode::addAttribute(string _sName, string _sText) -- cgit v1.2.3 From dc31a371a7f5c66e32226698999f345e350f3049 Mon Sep 17 00:00:00 2001 From: Folkert Bleichrodt Date: Wed, 8 Apr 2015 16:03:41 +0200 Subject: Added ASTRA-Spot operator opTomo A Spot operator for the ASTRA projectors. Wraps the forward and backprojection operation into a Spot operator, which can be used with matrix-vector syntax in Matlab. --- matlab/tools/opTomo.m | 280 ++++++++++++++++++++++++++++++++++++ matlab/tools/opTomo_helper_handle.m | 29 ++++ samples/matlab/s017_opTomo.m | 44 ++++++ 3 files changed, 353 insertions(+) create mode 100644 matlab/tools/opTomo.m create mode 100644 matlab/tools/opTomo_helper_handle.m create mode 100644 samples/matlab/s017_opTomo.m (limited to 'matlab') diff --git a/matlab/tools/opTomo.m b/matlab/tools/opTomo.m new file mode 100644 index 0000000..14128d2 --- /dev/null +++ b/matlab/tools/opTomo.m @@ -0,0 +1,280 @@ +%OPTOMO Wrapper for ASTRA tomography projector +% +% OP = OPTOMO(TYPE, PROJ_GEOM, VOL_GEOM) generates a Spot operator OP for +% the ASTRA forward and backprojection operations. The string TYPE +% determines the model used for the projections. Possible choices are: +% TYPE: * using the CPU +% 'line' - use a line kernel +% 'linear' - use a Joseph kernel +% 'strip' - use the strip kernel +% * using the GPU +% 'cuda' - use a Joseph kernel, on the GPU, currently using +% 'cuda' is the only option in 3D. +% The PROJ_GEOM and VOL_GEOM structures are projection and volume +% geometries as used in the ASTRA toolbox. +% +% OP = OPTOMO(TYPE, PROJ_GEOM, VOL_GEOM, GPU_INDEX) also specify the +% index of the GPU that should be used, if multiple GPUs are present in +% the host system. By default GPU_INDEX is 0. +% +% Note: this code depends on the Matlab toolbox +% "Spot - A Linear-Operator Toolbox" which can be downloaded from +% http://www.cs.ubc.ca/labs/scl/spot/ +%-------------------------------------------------------------------------- +% This file is part of the ASTRA Toolbox +% +% Copyright: 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Author: Folkert Bleichrodt +% Contact: F.Bleichrodt@cwi.nl +% Website: http://sf.net/projects/astra-toolbox +%-------------------------------------------------------------------------- +% $Id$ + +classdef opTomo < opSpot + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + % Properties + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + properties ( Access = private ) + % multiplication function + funHandle + % ASTRA identifiers + sino_id + vol_id + fp_alg_id + bp_alg_id + % ASTRA IDs handle + astra_handle + % geometries + proj_geom; + vol_geom; + end % properties + + properties ( SetAccess = private, GetAccess = public ) + proj_size + vol_size + end % properties + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + % Methods - public + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + methods + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + % opTomo - constructor + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + function op = opTomo(type, proj_geom, vol_geom, gpu_index) + + if nargin < 4 || isempty(gpu_index), gpu_index = 0; end + + proj_size = astra_geom_size(proj_geom); + vol_size = astra_geom_size(vol_geom); + + % construct operator + op = op@opSpot('opTomo', prod(proj_size), prod(vol_size)); + + % determine the dimension + is2D = ~isfield(vol_geom, 'GridSliceCount'); + gpuEnabled = strcmpi(type, 'cuda'); + + if is2D + % create a projector + proj_id = astra_create_projector(type, proj_geom, vol_geom); + + % create a function handle + op.funHandle = @opTomo_intrnl2D; + + % Initialize ASTRA data objects. + % projection data + sino_id = astra_mex_data2d('create', '-sino', proj_geom, 0); + % image data + vol_id = astra_mex_data2d('create', '-vol', vol_geom, 0); + + % Setup forward and back projection algorithms. + if gpuEnabled + fp_alg = 'FP_CUDA'; + bp_alg = 'BP_CUDA'; + proj_id = []; + else + fp_alg = 'FP'; + bp_alg = 'BP'; + proj_id = astra_create_projector(type, proj_geom, vol_geom); + end + + % configuration for ASTRA fp algorithm + cfg_fp = astra_struct(fp_alg); + cfg_fp.ProjectorId = proj_id; + cfg_fp.ProjectionDataId = sino_id; + cfg_fp.VolumeDataId = vol_id; + + % configuration for ASTRA bp algorithm + cfg_bp = astra_struct(bp_alg); + cfg_bp.ProjectionDataId = sino_id; + cfg_bp.ProjectorId = proj_id; + cfg_bp.ReconstructionDataId = vol_id; + + % set GPU index + if gpuEnabled + cfg_fp.option.GPUindex = gpu_index; + cfg_bp.option.GPUindex = gpu_index; + end + + fp_alg_id = astra_mex_algorithm('create', cfg_fp); + bp_alg_id = astra_mex_algorithm('create', cfg_bp); + + % Create handle to ASTRA objects, so they will be deleted + % if opTomo is deleted. + op.astra_handle = opTomo_helper_handle([sino_id, ... + vol_id, proj_id, fp_alg_id, bp_alg_id]); + + op.fp_alg_id = fp_alg_id; + op.bp_alg_id = bp_alg_id; + op.sino_id = sino_id; + op.vol_id = vol_id; + else + % 3D + % only gpu/cuda code for 3D + if ~gpuEnabled + error(['Only type ' 39 'cuda' 39 ' is supported ' ... + 'for 3D geometries.']) + end + + % create a function handle + op.funHandle = @opTomo_intrnl3D; + end + + + % pass object properties + op.proj_size = proj_size; + op.vol_size = vol_size; + op.proj_geom = proj_geom; + op.vol_geom = vol_geom; + op.cflag = false; + op.sweepflag = false; + + end % opTomo - constructor + + end % methods - public + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + % Methods - protected + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + methods( Access = protected ) + + % multiplication + function y = multiply(op,x,mode) + + % ASTRA cannot handle sparse vectors + if issparse(x) + x = full(x); + end + + % convert input to single + if isa(x, 'single') == false + x = single(x); + end + + % the multiplication + y = op.funHandle(op, x, mode); + + % make sure output is column vector + y = y(:); + + end % multiply + + end % methods - protected + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + % Methods - private + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + methods( Access = private ) + + % 2D projection code + function y = opTomo_intrnl2D(op,x,mode) + + if mode == 1 + % X is passed as a vector, reshape it into an image. + x = reshape(x, op.vol_size); + + % Matlab data copied to ASTRA data + astra_mex_data2d('store', op.vol_id, x); + + % forward projection + astra_mex_algorithm('iterate', op.fp_alg_id); + + % retrieve Matlab array + y = astra_mex_data2d('get_single', op.sino_id); + else + % X is passed as a vector, reshape it into a sinogram. + x = reshape(x, op.proj_size); + + % Matlab data copied to ASTRA data + astra_mex_data2d('store', op.sino_id, x); + + % backprojection + astra_mex_algorithm('iterate', op.bp_alg_id); + + % retrieve Matlab array + y = astra_mex_data2d('get_single', op.vol_id); + end + end % opTomo_intrnl2D + + + % 3D projection code + function y = opTomo_intrnl3D(op,x,mode) + + if mode == 1 + % X is passed as a vector, reshape it into an image + x = reshape(x, op.vol_size); + + % initialize output + y = zeros(op.proj_size, 'single'); + + % link matlab array to ASTRA + vol_id = astra_mex_data3d_c('link', '-vol', op.vol_geom, x, 0); + sino_id = astra_mex_data3d_c('link', '-sino', op.proj_geom, y, 1); + + % initialize fp algorithm + cfg = astra_struct('FP3D_CUDA'); + cfg.ProjectionDataId = sino_id; + cfg.VolumeDataId = vol_id; + + alg_id = astra_mex_algorithm('create', cfg); + + % forward projection + astra_mex_algorithm('iterate', alg_id); + + % cleanup + astra_mex_data3d('delete', vol_id); + astra_mex_data3d('delete', sino_id); + else + % X is passed as a vector, reshape it into projection data + x = reshape(x, op.proj_size); + + % initialize output + y = zeros(op.vol_size,'single'); + + % link matlab array to ASTRA + vol_id = astra_mex_data3d_c('link', '-vol', op.vol_geom, y, 1); + sino_id = astra_mex_data3d_c('link', '-sino', op.proj_geom, x, 0); + + % initialize bp algorithm + cfg = astra_struct('BP3D_CUDA'); + cfg.ProjectionDataId = sino_id; + cfg.ReconstructionDataId = vol_id; + + alg_id = astra_mex_algorithm('create', cfg); + + % backprojection + astra_mex_algorithm('iterate', alg_id); + + % cleanup + astra_mex_data3d('delete', vol_id); + astra_mex_data3d('delete', sino_id); + end + end % opTomo_intrnl3D + + end % methods - private + +end % classdef diff --git a/matlab/tools/opTomo_helper_handle.m b/matlab/tools/opTomo_helper_handle.m new file mode 100644 index 0000000..d9be51f --- /dev/null +++ b/matlab/tools/opTomo_helper_handle.m @@ -0,0 +1,29 @@ +classdef opTomo_helper_handle < handle + %ASTRA.OPTOMO_HELPER_HANDLE Handle class around an astra identifier + % Automatically deletes the data when object is deleted. + % Multiple id's can be passed as an array as input to + % the constructor. + + properties + id + end + + methods + function obj = opTomo_helper_handle(id) + obj.id = id; + end + function delete(obj) + for i = 1:numel(obj.id) + % delete any kind of object + astra_mex_data2d('delete', obj.id(i)); + astra_mex_data3d('delete', obj.id(i)); + astra_mex_algorithm('delete', obj.id(i)); + astra_mex_matrix('delete', obj.id(i)); + astra_mex_projector('delete', obj.id(i)); + astra_mex_projector3d('delete', obj.id(i)) + end + end + end + +end + diff --git a/samples/matlab/s017_opTomo.m b/samples/matlab/s017_opTomo.m new file mode 100644 index 0000000..4886cc5 --- /dev/null +++ b/samples/matlab/s017_opTomo.m @@ -0,0 +1,44 @@ +% load a phantom image +im = phantom(256); +% and flatten it to a vector +x = im(:); + +%% Setting up the geometry +% projection geometry +proj_geom = astra_create_proj_geom('parallel', 1, 256, linspace2(0,pi,180)); +% object dimensions +vol_geom = astra_create_vol_geom(256,256); + +%% Generate projection data +% Create the Spot operator for ASTRA using the GPU. +W = opTomo('cuda', proj_geom, vol_geom); + +p = W*x; + +% reshape the vector into a sinogram +sinogram = reshape(p, W.proj_size); +imshow(sinogram, []); + + +%% Reconstruction +% We use a least squares solver lsqr from Matlab to solve the +% equation W*x = p. +% Max number of iterations is 100, convergence tolerance of 1e-6. +y = lsqr(W, p, 1e-6, 100); + +% the output is a vector, so we reshape it into an image +reconstruction = reshape(y, W.vol_size); + +subplot(1,3,1); +imshow(reconstruction, []); +title('Reconstruction'); + +subplot(1,3,2); +imshow(im, []); +title('Ground truth'); + +% The transpose of the operator corresponds to the backprojection. +backProjection = W'*p; +subplot(1,3,3); +imshow(reshape(backProjection, W.vol_size), []); +title('Backprojection'); -- cgit v1.2.3 From ba3629c6c1bc1d03ccdc6ef2aeae6872ea59559f Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Sat, 20 Jun 2015 00:33:23 +0200 Subject: Fix matlab compilation without CUDA --- matlab/mex/astra_mex_c.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'matlab') diff --git a/matlab/mex/astra_mex_c.cpp b/matlab/mex/astra_mex_c.cpp index 4a331f5..a9b9654 100644 --- a/matlab/mex/astra_mex_c.cpp +++ b/matlab/mex/astra_mex_c.cpp @@ -36,9 +36,9 @@ $Id$ #include "mexInitFunctions.h" #include "astra/Globals.h" - +#ifdef ASTRA_CUDA #include "../cuda/2d/darthelper.h" - +#endif using namespace std; using namespace astra; -- cgit v1.2.3 From f6b6a2f84806a89fe6bacc583e13cb14629fb5dc Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Sat, 20 Jun 2015 00:35:16 +0200 Subject: Actually use the rec_type argument in astra_create_reconstruction_cuda --- matlab/tools/astra_create_reconstruction_cuda.m | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'matlab') diff --git a/matlab/tools/astra_create_reconstruction_cuda.m b/matlab/tools/astra_create_reconstruction_cuda.m index 7d9e1dd..7d0421c 100644 --- a/matlab/tools/astra_create_reconstruction_cuda.m +++ b/matlab/tools/astra_create_reconstruction_cuda.m @@ -45,7 +45,7 @@ if strcmp(rec_type,'') end % configure -cfg = astra_struct('SIRT_CUDA'); +cfg = astra_struct(rec_type); cfg.ProjectionGeometry = proj_geom; cfg.ReconstructionGeometry = vol_geom; cfg.ProjectionDataId = sinogram_id; -- cgit v1.2.3 From 63d78fbaafa7d247347f9052db86f575d89260b7 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Wed, 24 Jun 2015 20:28:46 +0200 Subject: Fix config to struct/dict translation for array options --- matlab/mex/mexHelpFunctions.cpp | 6 +++++- python/astra/utils.pyx | 5 ++++- 2 files changed, 9 insertions(+), 2 deletions(-) (limited to 'matlab') diff --git a/matlab/mex/mexHelpFunctions.cpp b/matlab/mex/mexHelpFunctions.cpp index 87a9672..58e84d2 100644 --- a/matlab/mex/mexHelpFunctions.cpp +++ b/matlab/mex/mexHelpFunctions.cpp @@ -336,7 +336,11 @@ mxArray* XMLNodeToStruct(astra::XMLNode node) // option if (subnode.getName() == "Option") { - mOptions[subnode.getAttribute("key")] = stringToMxArray(subnode.getAttribute("value")); + if(subnode.hasAttribute("value")){ + mOptions[subnode.getAttribute("key")] = stringToMxArray(subnode.getAttribute("value")); + }else{ + mOptions[subnode.getAttribute("key")] = stringToMxArray(subnode.getContent()); + } } // regular content diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx index a8e9e4e..260c308 100644 --- a/python/astra/utils.pyx +++ b/python/astra/utils.pyx @@ -204,7 +204,10 @@ cdef XMLNode2dict(XMLNode node): while it != nodes.end(): subnode = deref(it) if castString(subnode.getName())=="Option": - opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getAttribute('value')) + if subnode.hasAttribute('value'): + opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getAttribute('value')) + else: + opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getContent()) else: dct[castString(subnode.getName())] = stringToPythonValue(subnode.getContent()) inc(it) -- cgit v1.2.3 From 9e3472ea9041b8755050427d8bdb8a4701019c55 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Thu, 25 Jun 2015 21:52:07 +0200 Subject: Fix memory leak in configuration code --- matlab/mex/astra_mex_projector3d_c.cpp | 8 ++++++-- matlab/mex/astra_mex_projector_c.cpp | 9 ++++++--- python/astra/projector3d_c.pyx | 10 ++++++++-- python/astra/projector_c.pyx | 10 ++++++++-- 4 files changed, 28 insertions(+), 9 deletions(-) (limited to 'matlab') diff --git a/matlab/mex/astra_mex_projector3d_c.cpp b/matlab/mex/astra_mex_projector3d_c.cpp index c3b547f..e25802c 100644 --- a/matlab/mex/astra_mex_projector3d_c.cpp +++ b/matlab/mex/astra_mex_projector3d_c.cpp @@ -137,7 +137,9 @@ void astra_mex_projector3d_get_projection_geometry(int nlhs, mxArray* plhs[], in // step3: get projection_geometry and turn it into a MATLAB struct if (1 <= nlhs) { - plhs[0] = configToStruct(pProjector->getProjectionGeometry()->getConfiguration()); + Config *cfg = pProjector->getProjectionGeometry()->getConfiguration(); + plhs[0] = configToStruct(cfg); + delete cfg; } } @@ -163,7 +165,9 @@ void astra_mex_projector3d_get_volume_geometry(int nlhs, mxArray* plhs[], int nr // step3: get projection_geometry and turn it into a MATLAB struct if (1 <= nlhs) { - plhs[0] = configToStruct(pProjector->getVolumeGeometry()->getConfiguration()); + Config *cfg = pProjector->getVolumeGeometry()->getConfiguration(); + plhs[0] = configToStruct(cfg); + delete cfg; } } diff --git a/matlab/mex/astra_mex_projector_c.cpp b/matlab/mex/astra_mex_projector_c.cpp index 204ba8e..bf701af 100644 --- a/matlab/mex/astra_mex_projector_c.cpp +++ b/matlab/mex/astra_mex_projector_c.cpp @@ -160,7 +160,9 @@ void astra_mex_projector_projection_geometry(int nlhs, mxArray* plhs[], int nrhs // step3: get projection_geometry and turn it into a MATLAB struct if (1 <= nlhs) { - plhs[0] = configToStruct(pProjector->getProjectionGeometry()->getConfiguration()); + Config *cfg = pProjector->getProjectionGeometry()->getConfiguration(); + plhs[0] = configToStruct(cfg); + delete cfg; } } @@ -189,8 +191,9 @@ void astra_mex_projector_volume_geometry(int nlhs, mxArray* plhs[], int nrhs, co // step3: get projection_geometry and turn it into a MATLAB struct if (1 <= nlhs) { - plhs[0] = configToStruct(pProjector->getVolumeGeometry()->getConfiguration()); - + Config *cfg = pProjector->getVolumeGeometry()->getConfiguration(); + plhs[0] = configToStruct(cfg); + delete cfg; } } diff --git a/python/astra/projector3d_c.pyx b/python/astra/projector3d_c.pyx index 8b978d7..aec9cde 100644 --- a/python/astra/projector3d_c.pyx +++ b/python/astra/projector3d_c.pyx @@ -87,12 +87,18 @@ cdef CProjector3D * getObject(i) except NULL: def projection_geometry(i): cdef CProjector3D * proj = getObject(i) - return utils.configToDict(proj.getProjectionGeometry().getConfiguration()) + cdef Config * cfg = proj.getProjectionGeometry().getConfiguration() + dct = utils.configToDict(cfg) + del cfg + return dct def volume_geometry(i): cdef CProjector3D * proj = getObject(i) - return utils.configToDict(proj.getVolumeGeometry().getConfiguration()) + cdef Config * cfg = proj.getVolumeGeometry().getConfiguration() + dct = utils.configToDict(cfg) + del cfg + return dct def weights_single_ray(i, projection_index, detector_index): diff --git a/python/astra/projector_c.pyx b/python/astra/projector_c.pyx index 9aa868e..77c64a4 100644 --- a/python/astra/projector_c.pyx +++ b/python/astra/projector_c.pyx @@ -91,12 +91,18 @@ cdef CProjector2D * getObject(i) except NULL: def projection_geometry(i): cdef CProjector2D * proj = getObject(i) - return utils.configToDict(proj.getProjectionGeometry().getConfiguration()) + cdef Config * cfg = proj.getProjectionGeometry().getConfiguration() + dct = utils.configToDict(cfg) + del cfg + return dct def volume_geometry(i): cdef CProjector2D * proj = getObject(i) - return utils.configToDict(proj.getVolumeGeometry().getConfiguration()) + cdef Config * cfg = proj.getVolumeGeometry().getConfiguration() + dct = utils.configToDict(cfg) + del cfg + return dct def weights_single_ray(i, projection_index, detector_index): -- cgit v1.2.3 From 4d39c35d6c9124c26de64c9d227a25f612903a2a Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Fri, 17 Jul 2015 13:44:59 +0200 Subject: Fix formatting when passing strings to log from high-level code --- matlab/mex/astra_mex_log_c.cpp | 8 ++++---- matlab/mex/mexInitFunctions.cpp | 2 +- python/astra/log_c.pyx | 8 ++++---- 3 files changed, 9 insertions(+), 9 deletions(-) (limited to 'matlab') diff --git a/matlab/mex/astra_mex_log_c.cpp b/matlab/mex/astra_mex_log_c.cpp index ea4621e..905612c 100644 --- a/matlab/mex/astra_mex_log_c.cpp +++ b/matlab/mex/astra_mex_log_c.cpp @@ -55,7 +55,7 @@ void astra_mex_log_debug(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prh string filename = mexToString(prhs[1]); int linenumber = (int)mxGetScalar(prhs[2]); string message = mexToString(prhs[3]); - astra::CLogger::debug(filename.c_str(),linenumber,message.c_str()); + astra::CLogger::debug(filename.c_str(),linenumber,"%s",message.c_str()); } //----------------------------------------------------------------------------------------- @@ -75,7 +75,7 @@ void astra_mex_log_info(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs string filename = mexToString(prhs[1]); int linenumber = (int)mxGetScalar(prhs[2]); string message = mexToString(prhs[3]); - astra::CLogger::info(filename.c_str(),linenumber,message.c_str()); + astra::CLogger::info(filename.c_str(),linenumber,"%s",message.c_str()); } //----------------------------------------------------------------------------------------- @@ -95,7 +95,7 @@ void astra_mex_log_warn(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs string filename = mexToString(prhs[1]); int linenumber = (int)mxGetScalar(prhs[2]); string message = mexToString(prhs[3]); - astra::CLogger::warn(filename.c_str(),linenumber,message.c_str()); + astra::CLogger::warn(filename.c_str(),linenumber,"%s",message.c_str()); } //----------------------------------------------------------------------------------------- @@ -115,7 +115,7 @@ void astra_mex_log_error(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prh string filename = mexToString(prhs[1]); int linenumber = (int)mxGetScalar(prhs[2]); string message = mexToString(prhs[3]); - astra::CLogger::error(filename.c_str(),linenumber,message.c_str()); + astra::CLogger::error(filename.c_str(),linenumber,"%s",message.c_str()); } //----------------------------------------------------------------------------------------- diff --git a/matlab/mex/mexInitFunctions.cpp b/matlab/mex/mexInitFunctions.cpp index d8a50d7..89a31a1 100644 --- a/matlab/mex/mexInitFunctions.cpp +++ b/matlab/mex/mexInitFunctions.cpp @@ -8,7 +8,7 @@ bool mexIsInitialized=false; * */ void logCallBack(const char *msg, size_t len){ - mexPrintf(msg); + mexPrintf("%s",msg); } /** diff --git a/python/astra/log_c.pyx b/python/astra/log_c.pyx index f16329f..55c63e6 100644 --- a/python/astra/log_c.pyx +++ b/python/astra/log_c.pyx @@ -53,19 +53,19 @@ cdef extern from "astra/Logging.h" namespace "astra::CLogger": def log_debug(sfile, sline, message): cstr = list(map(six.b,(sfile,message))) - debug(cstr[0],sline,cstr[1]) + debug(cstr[0],sline,"%s",cstr[1]) def log_info(sfile, sline, message): cstr = list(map(six.b,(sfile,message))) - info(cstr[0],sline,cstr[1]) + info(cstr[0],sline,"%s",cstr[1]) def log_warn(sfile, sline, message): cstr = list(map(six.b,(sfile,message))) - warn(cstr[0],sline,cstr[1]) + warn(cstr[0],sline,"%s",cstr[1]) def log_error(sfile, sline, message): cstr = list(map(six.b,(sfile,message))) - error(cstr[0],sline,cstr[1]) + error(cstr[0],sline,"%s",cstr[1]) def log_enable(): enable() -- cgit v1.2.3 From 026aa46c5db24ddd687cec0fa6e056a2ee3790c5 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 12 Aug 2015 15:45:12 +0200 Subject: Fix algorithm object leak in astra_create_fbp_reconstruction.m --- matlab/tools/astra_create_fbp_reconstruction.m | 1 + 1 file changed, 1 insertion(+) (limited to 'matlab') diff --git a/matlab/tools/astra_create_fbp_reconstruction.m b/matlab/tools/astra_create_fbp_reconstruction.m index 5540f27..a2561b7 100644 --- a/matlab/tools/astra_create_fbp_reconstruction.m +++ b/matlab/tools/astra_create_fbp_reconstruction.m @@ -19,6 +19,7 @@ cfg.ProjectorId = proj_id; cfg.Options.GPUindex = 0; alg_id = astra_mex_algorithm('create', cfg); astra_mex_algorithm('run', alg_id); +astra_mex_algorithm('delete', alg_id); if numel(sinogram) ~= 1 astra_mex_data2d('delete', sinogram_id); -- cgit v1.2.3