From 169e912d2633cda7ffc234e78afba1b096e122ea Mon Sep 17 00:00:00 2001 From: Wim van Aarle Date: Thu, 26 Feb 2015 16:11:38 +0100 Subject: code cleanup --- matlab/mex/astra_mex_algorithm_c.cpp | 17 +- matlab/mex/astra_mex_c.cpp | 2 +- matlab/mex/astra_mex_data2d_c.cpp | 74 ++-- matlab/mex/astra_mex_data3d_c.cpp | 6 +- matlab/mex/astra_mex_matrix_c.cpp | 2 +- matlab/mex/astra_mex_projector3d_c.cpp | 10 +- matlab/mex/astra_mex_projector_c.cpp | 13 +- matlab/mex/mexCopyDataHelpFunctions.cpp | 2 +- matlab/mex/mexDataManagerHelpFunctions.cpp | 40 +- matlab/mex/mexHelpFunctions.cpp | 601 ++++++++++------------------- matlab/mex/mexHelpFunctions.h | 39 +- 11 files changed, 288 insertions(+), 518 deletions(-) (limited to 'matlab') diff --git a/matlab/mex/astra_mex_algorithm_c.cpp b/matlab/mex/astra_mex_algorithm_c.cpp index f719a6b..98cf8a4 100644 --- a/matlab/mex/astra_mex_algorithm_c.cpp +++ b/matlab/mex/astra_mex_algorithm_c.cpp @@ -78,26 +78,23 @@ void astra_mex_algorithm_create(int nlhs, mxArray* plhs[], int nrhs, const mxArr } // turn MATLAB struct to an XML-based Config object - XMLDocument* xml = struct2XML("Algorithm", prhs[1]); - Config cfg; - cfg.self = xml->getRootNode(); + 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 xml; + delete cfg; mexErrMsgTxt("Unknown algorithm. \n"); return; } // create algorithm - if (!pAlg->initialize(cfg)) { - delete xml; + if (!pAlg->initialize(*cfg)) { + delete cfg; delete pAlg; mexErrMsgTxt("Algorithm not initialized. \n"); return; } - - delete xml; + delete cfg; // store algorithm int iIndex = CAlgorithmManager::getSingleton().store(pAlg); @@ -322,7 +319,7 @@ void mexFunction(int nlhs, mxArray* plhs[], // INPUT: Mode string sMode = ""; if (1 <= nrhs) { - sMode = mex_util_get_string(prhs[0]); + sMode = mexToString(prhs[0]); } else { printHelp(); return; diff --git a/matlab/mex/astra_mex_c.cpp b/matlab/mex/astra_mex_c.cpp index 2989b7a..760bd51 100644 --- a/matlab/mex/astra_mex_c.cpp +++ b/matlab/mex/astra_mex_c.cpp @@ -122,7 +122,7 @@ void mexFunction(int nlhs, mxArray* plhs[], // INPUT0: Mode string sMode = ""; if (1 <= nrhs) { - sMode = mex_util_get_string(prhs[0]); + sMode = mexToString(prhs[0]); } else { printHelp(); return; diff --git a/matlab/mex/astra_mex_data2d_c.cpp b/matlab/mex/astra_mex_data2d_c.cpp index 03d3807..5f79e98 100644 --- a/matlab/mex/astra_mex_data2d_c.cpp +++ b/matlab/mex/astra_mex_data2d_c.cpp @@ -98,10 +98,10 @@ void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra return; } - string sDataType = mex_util_get_string(prhs[1]); + string sDataType = mexToString(prhs[1]); CFloat32Data2D* pDataObject2D = NULL; - if (nrhs >= 4 && !(mex_is_scalar(prhs[3])|| mxIsDouble(prhs[3]) || mxIsLogical(prhs[3]) || mxIsSingle(prhs[3]) )) { + if (nrhs >= 4 && !(mexIsScalar(prhs[3])|| mxIsDouble(prhs[3]) || mxIsLogical(prhs[3]) || mxIsSingle(prhs[3]) )) { mexErrMsgTxt("Data must be single, double or logical."); return; } @@ -116,23 +116,20 @@ void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra if (!mxIsStruct(prhs[2])) { mexErrMsgTxt("Argument 3 is not a valid MATLAB struct.\n"); } - XMLDocument* xml = struct2XML(string("VolumeGeometry"), prhs[2]); - if (!xml) - return; - Config cfg; - cfg.self = xml->getRootNode(); + + Config* cfg = structToConfig("VolumeGeometry", prhs[2]); CVolumeGeometry2D* pGeometry = new CVolumeGeometry2D(); - if (!pGeometry->initialize(cfg)) { + if (!pGeometry->initialize(*cfg)) { mexErrMsgTxt("Geometry class not initialized. \n"); - delete xml; + delete cfg; delete pGeometry; return; } // If data is specified, check dimensions - if (nrhs >= 4 && !mex_is_scalar(prhs[3])) { + if (nrhs >= 4 && !mexIsScalar(prhs[3])) { if (pGeometry->getGridColCount() != mxGetN(prhs[3]) || pGeometry->getGridRowCount() != mxGetM(prhs[3])) { mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n"); - delete xml; + delete cfg; delete pGeometry; return; } @@ -140,21 +137,18 @@ void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra // Initialize data object pDataObject2D = new CFloat32VolumeData2D(pGeometry); delete pGeometry; - delete xml; + delete cfg; } else if (sDataType == "-sino") { // Read geometry if (!mxIsStruct(prhs[2])) { mexErrMsgTxt("Argument 3 is not a valid MATLAB struct.\n"); } - XMLDocument* xml = struct2XML("ProjectionGeometry", prhs[2]); - if (!xml) - return; - Config cfg; - cfg.self = xml->getRootNode(); + + 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(); @@ -168,25 +162,25 @@ void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra } else { pGeometry = new CParallelProjectionGeometry2D(); } - if (!pGeometry->initialize(cfg)) { + if (!pGeometry->initialize(*cfg)) { mexErrMsgTxt("Geometry class not initialized. \n"); delete pGeometry; - delete xml; + delete cfg; return; } // If data is specified, check dimensions - if (nrhs >= 4 && !mex_is_scalar(prhs[3])) { + if (nrhs >= 4 && !mexIsScalar(prhs[3])) { if (pGeometry->getDetectorCount() != mxGetN(prhs[3]) || pGeometry->getProjectionAngleCount() != mxGetM(prhs[3])) { mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n"); delete pGeometry; - delete xml; + delete cfg; return; } } // Initialize data object pDataObject2D = new CFloat32ProjectionData2D(pGeometry); delete pGeometry; - delete xml; + delete cfg; } else { mexErrMsgTxt("Invalid datatype. Please specify '-vol' or '-sino'. \n"); @@ -210,7 +204,7 @@ void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra // Store data if (nrhs >= 4) { // fill with scalar value - if (mex_is_scalar(prhs[3])) { + if (mexIsScalar(prhs[3])) { float32 fValue = (float32)mxGetScalar(prhs[3]); for (int i = 0; i < pDataObject2D->getSize(); ++i) { pDataObject2D->getData()[i] = fValue; @@ -294,7 +288,7 @@ void astra_mex_data2d_store(int nlhs, mxArray* plhs[], int nrhs, const mxArray* } int iDataID = (int)(mxGetScalar(prhs[1])); - if (!(mex_is_scalar(prhs[2]) || mxIsDouble(prhs[2]) || mxIsLogical(prhs[2]) || mxIsSingle(prhs[2]))) { + if (!(mexIsScalar(prhs[2]) || mxIsDouble(prhs[2]) || mxIsLogical(prhs[2]) || mxIsSingle(prhs[2]))) { mexErrMsgTxt("Data must be single, double or logical."); return; } @@ -312,7 +306,7 @@ void astra_mex_data2d_store(int nlhs, mxArray* plhs[], int nrhs, const mxArray* // step3: insert data // fill with scalar value - if (mex_is_scalar(prhs[2])) { + if (mexIsScalar(prhs[2])) { float32 fValue = (float32)mxGetScalar(prhs[2]); for (int i = 0; i < pDataObject->getSize(); ++i) { pDataObject->getData()[i] = fValue; @@ -440,12 +434,10 @@ void astra_mex_data2d_change_geometry(int nlhs, mxArray* plhs[], int nrhs, const if (!mxIsStruct(prhs[2])) { mexErrMsgTxt("Argument 3 is not a valid MATLAB struct.\n"); } - XMLDocument* xml = struct2XML("ProjectionGeometry", prhs[2]); - Config cfg; - cfg.self = xml->getRootNode(); + 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(); @@ -459,24 +451,24 @@ void astra_mex_data2d_change_geometry(int nlhs, mxArray* plhs[], int nrhs, const } else { pGeometry = new CParallelProjectionGeometry2D(); } - if (!pGeometry->initialize(cfg)) { + if (!pGeometry->initialize(*cfg)) { mexErrMsgTxt("Geometry class not initialized. \n"); delete pGeometry; - delete xml; + delete cfg; return; } // If data is specified, check dimensions if (pGeometry->getDetectorCount() != pSinogram->getDetectorCount() || pGeometry->getProjectionAngleCount() != pSinogram->getAngleCount()) { mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n"); delete pGeometry; - delete xml; + delete cfg; return; } // If ok, change geometry pSinogram->changeGeometry(pGeometry); delete pGeometry; - delete xml; + delete cfg; return; } @@ -490,27 +482,25 @@ void astra_mex_data2d_change_geometry(int nlhs, mxArray* plhs[], int nrhs, const if (!mxIsStruct(prhs[2])) { mexErrMsgTxt("Argument 3 is not a valid MATLAB struct.\n"); } - XMLDocument* xml = struct2XML(string("VolumeGeometry"), prhs[2]); - Config cfg; - cfg.self = xml->getRootNode(); + Config* cfg = structToConfig("VolumeGeometry2D", prhs[2]); CVolumeGeometry2D* pGeometry = new CVolumeGeometry2D(); - if (!pGeometry->initialize(cfg)) { + if (!pGeometry->initialize(*cfg)) { mexErrMsgTxt("Geometry class not initialized. \n"); - delete xml; + delete cfg; delete pGeometry; return; } // If data is specified, check dimensions if (pGeometry->getGridColCount() != pVolume->getWidth() || pGeometry->getGridRowCount() != pVolume->getHeight()) { mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n"); - delete xml; + delete cfg; delete pGeometry; return; } // If ok, change geometry pVolume->changeGeometry(pGeometry); - delete xml; + delete cfg; delete pGeometry; } @@ -639,7 +629,7 @@ void mexFunction(int nlhs, mxArray* plhs[], // INPUT0: Mode string sMode = ""; if (1 <= nrhs) { - sMode = mex_util_get_string(prhs[0]); + sMode = mexToString(prhs[0]); } else { printHelp(); return; diff --git a/matlab/mex/astra_mex_data3d_c.cpp b/matlab/mex/astra_mex_data3d_c.cpp index 64c013d..0a3f85d 100644 --- a/matlab/mex/astra_mex_data3d_c.cpp +++ b/matlab/mex/astra_mex_data3d_c.cpp @@ -83,7 +83,7 @@ void astra_mex_data3d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra return; } - const string sDataType = mex_util_get_string(prhs[1]); + const string sDataType = mexToString(prhs[1]); // step2: Allocate data CFloat32Data3DMemory* pDataObject3D = @@ -152,7 +152,7 @@ void astra_mex_data3d_link(int& nlhs, mxArray* plhs[], int& nrhs, const mxArray* return; } - string sDataType = mex_util_get_string(prhs[1]); + string sDataType = mexToString(prhs[1]); // step2: Allocate data CFloat32Data3DMemory* pDataObject3D = @@ -365,7 +365,7 @@ void mexFunction(int nlhs, mxArray* plhs[], // INPUT: Mode string sMode = ""; if (1 <= nrhs) { - sMode = mex_util_get_string(prhs[0]); + sMode = mexToString(prhs[0]); } else { printHelp(); return; diff --git a/matlab/mex/astra_mex_matrix_c.cpp b/matlab/mex/astra_mex_matrix_c.cpp index 016566a..01ad08b 100644 --- a/matlab/mex/astra_mex_matrix_c.cpp +++ b/matlab/mex/astra_mex_matrix_c.cpp @@ -406,7 +406,7 @@ void mexFunction(int nlhs, mxArray* plhs[], // INPUT0: Mode string sMode = ""; if (1 <= nrhs) { - sMode = mex_util_get_string(prhs[0]); + sMode = mexToString(prhs[0]); } else { printHelp(); return; diff --git a/matlab/mex/astra_mex_projector3d_c.cpp b/matlab/mex/astra_mex_projector3d_c.cpp index b2f6b02..5381cf6 100644 --- a/matlab/mex/astra_mex_projector3d_c.cpp +++ b/matlab/mex/astra_mex_projector3d_c.cpp @@ -65,16 +65,16 @@ void astra_mex_projector3d_create(int nlhs, mxArray* plhs[], int nrhs, const mxA } // turn MATLAB struct to an XML-based Config object - XMLDocument* xml = struct2XML("Projector3D", prhs[1]); - Config cfg; - cfg.self = xml->getRootNode(); + Config* cfg = structToConfig("Projector3D", prhs[1]); // create algorithm - CProjector3D* pProj = CProjector3DFactory::getSingleton().create(cfg); + CProjector3D* pProj = CProjector3DFactory::getSingleton().create(*cfg); if (pProj == NULL) { + delete cfg; mexErrMsgTxt("Error creating Projector3D. \n"); return; } + delete cfg; // store projector int iIndex = CProjector3DManager::getSingleton().store(pProj); @@ -397,7 +397,7 @@ void mexFunction(int nlhs, mxArray* plhs[], // INPUT: Mode string sMode = ""; if (1 <= nrhs) { - sMode = mex_util_get_string(prhs[0]); + sMode = mexToString(prhs[0]); } else { printHelp(); return; diff --git a/matlab/mex/astra_mex_projector_c.cpp b/matlab/mex/astra_mex_projector_c.cpp index 4793020..58cd953 100644 --- a/matlab/mex/astra_mex_projector_c.cpp +++ b/matlab/mex/astra_mex_projector_c.cpp @@ -74,19 +74,16 @@ void astra_mex_projector_create(int nlhs, mxArray* plhs[], int nrhs, const mxArr // turn MATLAB struct to an XML-based Config object - XMLDocument* xml = struct2XML("Projector2D", prhs[1]); - Config cfg; - cfg.self = xml->getRootNode(); + Config* cfg = structToConfig("Projector2D", prhs[1]); // create algorithm - CProjector2D* pProj = CProjector2DFactory::getSingleton().create(cfg); + CProjector2D* pProj = CProjector2DFactory::getSingleton().create(*cfg); if (pProj == NULL) { - delete xml; + delete cfg; mexErrMsgTxt("Error creating projector. \n"); return; } - - delete xml; + delete cfg; // store projector iIndex = CProjector2DManager::getSingleton().store(pProj); @@ -473,7 +470,7 @@ void mexFunction(int nlhs, mxArray* plhs[], // INPUT: Mode string sMode = ""; if (1 <= nrhs) { - sMode = mex_util_get_string(prhs[0]); + sMode = mexToString(prhs[0]); } else { printHelp(); return; diff --git a/matlab/mex/mexCopyDataHelpFunctions.cpp b/matlab/mex/mexCopyDataHelpFunctions.cpp index 6dfd4a6..80fb834 100644 --- a/matlab/mex/mexCopyDataHelpFunctions.cpp +++ b/matlab/mex/mexCopyDataHelpFunctions.cpp @@ -263,7 +263,7 @@ copyMexToCFloat32Array(const mxArray * const in, #pragma omp parallel { // fill with scalar value - if (mex_is_scalar(in)) { + if (mexIsScalar(in)) { astra::float32 fValue = 0.f; if (!mxIsEmpty(in)) { fValue = (astra::float32)mxGetScalar(in); diff --git a/matlab/mex/mexDataManagerHelpFunctions.cpp b/matlab/mex/mexDataManagerHelpFunctions.cpp index f9d971c..d482428 100644 --- a/matlab/mex/mexDataManagerHelpFunctions.cpp +++ b/matlab/mex/mexDataManagerHelpFunctions.cpp @@ -105,7 +105,7 @@ checkID(const astra::int32 & id, astra::CFloat32Data3DMemory *& pDataObj) bool checkDataType(const mxArray * const in) { - return (mex_is_scalar(in) || mxIsDouble(in) || mxIsSingle(in) || mxIsLogical(in)); + return (mexIsScalar(in) || mxIsDouble(in) || mxIsSingle(in) || mxIsLogical(in)); } //----------------------------------------------------------------------------------------- @@ -213,7 +213,7 @@ allocateDataObject(const std::string & sDataType, bool bUnshare = true; if (unshare) { - if (!mex_is_scalar(unshare)) + if (!mexIsScalar(unshare)) { mexErrMsgTxt("Argument 5 (read-only) must be scalar"); return NULL; @@ -225,7 +225,7 @@ allocateDataObject(const std::string & sDataType, mwIndex iZ = 0; if (zIndex) { - if (!mex_is_scalar(zIndex)) + if (!mexIsScalar(zIndex)) { mexErrMsgTxt("Argument 6 (Z) must be scalar"); return NULL; @@ -237,25 +237,19 @@ allocateDataObject(const std::string & sDataType, if (sDataType == "-vol") { // Read geometry - astra::XMLDocument* xml = struct2XML("VolumeGeometry", geometry); - if (!xml) { - return NULL; - } - astra::Config cfg; - cfg.self = xml->getRootNode(); - + astra::Config* cfg = structToConfig("VolumeGeometry3D", geometry); astra::CVolumeGeometry3D* pGeometry = new astra::CVolumeGeometry3D(); - if (!pGeometry->initialize(cfg)) + if (!pGeometry->initialize(*cfg)) { mexErrMsgTxt("Geometry class not initialized. \n"); delete pGeometry; - delete xml; + delete cfg; return NULL; } - delete xml; + delete cfg; // If data is specified, check dimensions - if (data && !mex_is_scalar(data)) + if (data && !mexIsScalar(data)) { if (! (zIndex ? checkDataSize(data, pGeometry, iZ) @@ -288,16 +282,10 @@ allocateDataObject(const std::string & sDataType, else if (sDataType == "-sino" || sDataType == "-proj3d" || sDataType == "-sinocone") { // Read geometry - astra::XMLDocument* xml = struct2XML("ProjectionGeometry", geometry); - if (!xml) { - return NULL; - } - astra::Config cfg; - cfg.self = xml->getRootNode(); - + 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(); @@ -312,16 +300,16 @@ allocateDataObject(const std::string & sDataType, return NULL; } - if (!pGeometry->initialize(cfg)) { + if (!pGeometry->initialize(*cfg)) { mexErrMsgTxt("Geometry class not initialized. \n"); delete pGeometry; - delete xml; + delete cfg; return NULL; } - delete xml; + delete cfg; // If data is specified, check dimensions - if (data && !mex_is_scalar(data)) + if (data && !mexIsScalar(data)) { if (! (zIndex ? checkDataSize(data, pGeometry, iZ) diff --git a/matlab/mex/mexHelpFunctions.cpp b/matlab/mex/mexHelpFunctions.cpp index c25123a..c0ac711 100644 --- a/matlab/mex/mexHelpFunctions.cpp +++ b/matlab/mex/mexHelpFunctions.cpp @@ -38,307 +38,154 @@ $Id$ #include #include -#include "astra/SparseMatrixProjectionGeometry2D.h" -#include "astra/FanFlatVecProjectionGeometry2D.h" -#include "astra/AstraObjectManager.h" - using namespace std; using namespace astra; //----------------------------------------------------------------------------------------- // get string from matlab -std::string mex_util_get_string(const mxArray* pInput) +string mexToString(const mxArray* pInput) { - if (!mxIsChar(pInput)) { - return ""; + // is string? + if (mxIsChar(pInput)) { + mwSize iLength = mxGetNumberOfElements(pInput) + 1; + char* buf = new char[iLength]; + mxGetString(pInput, buf, iLength); + std::string res = std::string(buf); + delete[] buf; + return res; } - mwSize iLength = mxGetNumberOfElements(pInput) + 1; - char* buf = new char[iLength]; - mxGetString(pInput, buf, iLength); - std::string res = std::string(buf); - delete[] buf; - return res; + + // is scalar? + if (mxIsNumeric(pInput) && mxGetM(pInput)*mxGetN(pInput) == 1) { + return boost::lexical_cast(mxGetScalar(pInput)); + } + + return ""; } //----------------------------------------------------------------------------------------- -// is option -bool isOption(std::list lOptions, std::string sOption) +// return true if the argument is a scalar +bool mexIsScalar(const mxArray* pInput) { - return std::find(lOptions.begin(), lOptions.end(), sOption) != lOptions.end(); + return (mxIsNumeric(pInput) && mxGetM(pInput)*mxGetN(pInput) == 1); } //----------------------------------------------------------------------------------------- -// turn a matlab struct into a c++ map -std::map parseStruct(const mxArray* pInput) +void get3DMatrixDims(const mxArray* x, mwSize *dims) { - std::map res; - - // check type - if (!mxIsStruct(pInput)) { - mexErrMsgTxt("Input must be a struct."); - return res; + const mwSize* mdims = mxGetDimensions(x); + mwSize dimCount = mxGetNumberOfDimensions(x); + if (dimCount == 1) { + dims[0] = mdims[0]; + dims[1] = 1; + dims[2] = 1; + } else if (dimCount == 2) { + dims[0] = mdims[0]; + dims[1] = mdims[1]; + dims[2] = 1; + } else if (dimCount == 3) { + dims[0] = mdims[0]; + dims[1] = mdims[1]; + dims[2] = mdims[2]; + } else { + dims[0] = 0; + dims[1] = 0; + dims[2] = 0; } +} + + + + - // get field names - int nfields = mxGetNumberOfFields(pInput); - for (int i = 0; i < nfields; i++) { - std::string sFieldName = std::string(mxGetFieldNameByNumber(pInput, i)); - res[sFieldName] = mxGetFieldByNumber(pInput,0,i); - } - return res; -} //----------------------------------------------------------------------------------------- -// turn a c++ map into a matlab struct -mxArray* buildStruct(std::map mInput) +// turn an std vector object to an mxArray +mxArray* vectorToMxArray(std::vector mInput) { - mwSize dims[2] = {1, 1}; - mxArray* res = mxCreateStructArray(2,dims,0,0); - - for (std::map::iterator it = mInput.begin(); it != mInput.end(); it++) { - mxAddField(res, (*it).first.c_str()); - mxSetField(res, 0, (*it).first.c_str(), (*it).second); + mxArray* res = mxCreateDoubleMatrix(1, mInput.size(), mxREAL); + double* pdData = mxGetPr(res); + for (unsigned int i = 0; i < mInput.size(); i++) { + pdData[i] = mInput[i]; } return res; } //----------------------------------------------------------------------------------------- -// parse projection geometry data -astra::CProjectionGeometry2D* parseProjectionGeometryStruct(const mxArray* prhs) +// turn a vector> object to an mxArray +mxArray* vector2DToMxArray(std::vector > mInput) { - // parse struct - std::map mStruct = parseStruct(prhs); - - // create projection geometry object - string type = mex_util_get_string(mStruct["type"]); - if (type == "parallel") { - - // detector_width - float32 fDetWidth = 1.0f; - mxArray* tmp = mStruct["detector_width"]; - if (tmp != NULL) { - fDetWidth = (float32)(mxGetScalar(tmp)); - } - - // detector_count - int iDetCount = 100; - tmp = mStruct["detector_count"]; - if (tmp != NULL) { - iDetCount = (int)(mxGetScalar(tmp)); - } - - // angles - float32* pfAngles; - int iAngleCount; - tmp = mStruct["projection_angles"]; - if (tmp != NULL) { - double* angleValues = mxGetPr(tmp); - iAngleCount = mxGetN(tmp) * mxGetM(tmp); - pfAngles = new float32[iAngleCount]; - for (int i = 0; i < iAngleCount; i++) { - pfAngles[i] = angleValues[i]; - } - } else { - mexErrMsgTxt("'angles' not specified, error."); - return NULL; - } - - // create projection geometry - return new astra::CParallelProjectionGeometry2D(iAngleCount, // number of projections - iDetCount, // number of detectors - fDetWidth, // width of the detectors - pfAngles); // angles array - } - - else if (type == "fanflat") { - - // detector_width - float32 fDetWidth = 1.0f; - mxArray* tmp = mStruct["detector_width"]; - if (tmp != NULL) { - fDetWidth = (float32)(mxGetScalar(tmp)); - } - - // detector_count - int iDetCount = 100; - tmp = mStruct["detector_count"]; - if (tmp != NULL) { - iDetCount = (int)(mxGetScalar(tmp)); - } - - // angles - float32* pfAngles; - int iAngleCount; - tmp = mStruct["projection_angles"]; - if (tmp != NULL) { - double* angleValues = mxGetPr(tmp); - iAngleCount = mxGetN(tmp) * mxGetM(tmp); - pfAngles = new float32[iAngleCount]; - for (int i = 0; i < iAngleCount; i++) { - pfAngles[i] = angleValues[i]; - } - } else { - mexErrMsgTxt("'angles' not specified, error."); - return NULL; - } - - // origin_source_dist - int iDistOriginSource = 100; - tmp = mStruct["origin_source_dist"]; - if (tmp != NULL) { - iDistOriginSource = (int)(mxGetScalar(tmp)); - } + unsigned int sizex = mInput.size(); + if (sizex == 0) return mxCreateString("empty"); + unsigned int sizey = mInput[0].size(); - // origin_det_dist - int iDistOriginDet = 100; - tmp = mStruct["origin_det_dist"]; - if (tmp != NULL) { - iDistOriginDet = (int)(mxGetScalar(tmp)); + mxArray* res = mxCreateDoubleMatrix(sizex, sizey, mxREAL); + double* pdData = mxGetPr(res); + for (unsigned int i = 0; i < sizex; i++) { + for (unsigned int j = 0; j < sizey && j < mInput[i].size(); j++) { + pdData[j*sizex+i] = mInput[i][j]; } - - // create projection geometry - return new astra::CFanFlatProjectionGeometry2D(iAngleCount, // number of projections - iDetCount, // number of detectors - fDetWidth, // width of the detectors - pfAngles, // angles array - iDistOriginSource, // distance origin source - iDistOriginDet); // distance origin detector - } - - else { - mexPrintf("Only parallel and fanflat projection geometry implemented."); - return NULL; } + return res; } //----------------------------------------------------------------------------------------- -// parse reconstruction geometry data -astra::CVolumeGeometry2D* parseVolumeGeometryStruct(const mxArray* prhs) +// turn a boost::any object to an mxArray +mxArray* anyToMxArray(boost::any _any) { - // parse struct - std::map mStruct = parseStruct(prhs); - - std::map mOptions = parseStruct(mStruct["option"]); - - // GridColCount - int iWindowColCount = 128; - mxArray* tmp = mStruct["GridColCount"]; - if (tmp != NULL) { - iWindowColCount = (int)(mxGetScalar(tmp)); - } - - // GridRowCount - int iWindowRowCount = 128; - tmp = mStruct["GridRowCount"]; - if (tmp != NULL) { - iWindowRowCount = (int)(mxGetScalar(tmp)); + if (_any.type() == typeid(std::string)) { + std::string str = boost::any_cast(_any); + return mxCreateString(str.c_str()); } - - // WindowMinX - float32 fWindowMinX = - iWindowColCount / 2; - tmp = mOptions["WindowMinX"]; - if (tmp != NULL) { - fWindowMinX = (float32)(mxGetScalar(tmp)); - } - - // WindowMaxX - float32 fWindowMaxX = iWindowColCount / 2; - tmp = mOptions["WindowMaxX"]; - if (tmp != NULL) { - fWindowMaxX = (float32)(mxGetScalar(tmp)); - } - - // WindowMinY - float32 fWindowMinY = - iWindowRowCount / 2; - tmp = mOptions["WindowMinY"]; - if (tmp != NULL) { - fWindowMinY = (float32)(mxGetScalar(tmp)); - } - - // WindowMaxX - float32 fWindowMaxY = iWindowRowCount / 2; - tmp = mOptions["WindowMaxY"]; - if (tmp != NULL) { - fWindowMaxY = (float32)(mxGetScalar(tmp)); - } - - // create and return reconstruction geometry - return new astra::CVolumeGeometry2D(iWindowColCount, iWindowRowCount, - fWindowMinX, fWindowMinY, - fWindowMaxX, fWindowMaxY); + if (_any.type() == typeid(int)) { + return mxCreateDoubleScalar(boost::any_cast(_any)); + } + if (_any.type() == typeid(float32)) { + return mxCreateDoubleScalar(boost::any_cast(_any)); + } + if (_any.type() == typeid(std::vector)) { + return vectorToMxArray(boost::any_cast >(_any)); + } + if (_any.type() == typeid(std::vector >)) { + return vector2DToMxArray(boost::any_cast > >(_any)); + } + return NULL; } -//----------------------------------------------------------------------------------------- -string matlab2string(const mxArray* pField) -{ - // is string? - if (mxIsChar(pField)) { - return mex_util_get_string(pField); - } - // is scalar? - if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) == 1) { - return boost::lexical_cast(mxGetScalar(pField)); - } - return ""; -} + + + + //----------------------------------------------------------------------------------------- -// Options struct to xml node -bool readOptions(XMLNode* node, const mxArray* pOptionStruct) +// turn a MATLAB struct into a Config object +Config* structToConfig(string rootname, const mxArray* pStruct) { - // loop all fields - int nfields = mxGetNumberOfFields(pOptionStruct); - for (int i = 0; i < nfields; i++) { - std::string sFieldName = std::string(mxGetFieldNameByNumber(pOptionStruct, i)); - const mxArray* pField = mxGetFieldByNumber(pOptionStruct, 0, i); + if (!mxIsStruct(pStruct)) { + mexErrMsgTxt("Input must be a struct."); + return NULL; + } - if (node->hasOption(sFieldName)) { - mexErrMsgTxt("Duplicate option"); - return false; - } - - // string or scalar - if (mxIsChar(pField) || mex_is_scalar(pField)) { - string sValue = matlab2string(pField); - node->addOption(sFieldName, sValue); - } else - // numerical array - if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) > 1) { - if (!mxIsDouble(pField)) { - mexErrMsgTxt("Numeric input must be double."); - return false; - } + // create the document + Config* cfg = new Config(); + cfg->initialize(rootname); - 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++; - delete item; - } - } - delete listbase; - } else { - mexErrMsgTxt("Unsupported option type"); - return false; - } + // read the struct + bool ret = structToXMLNode(cfg->self, pStruct); + if (!ret) { + delete cfg; + mexErrMsgTxt("Error parsing struct."); + return NULL; } - return true; + return cfg; } //----------------------------------------------------------------------------------------- -// struct to xml node -bool readStruct(XMLNode* root, const mxArray* pStruct) +bool structToXMLNode(XMLNode* node, const mxArray* pStruct) { // loop all fields int nfields = mxGetNumberOfFields(pStruct); @@ -350,27 +197,27 @@ bool readStruct(XMLNode* root, const mxArray* pStruct) // string if (mxIsChar(pField)) { - string sValue = matlab2string(pField); + string sValue = mexToString(pField); if (sFieldName == "type") { - root->addAttribute("type", sValue); + node->addAttribute("type", sValue); } else { - delete root->addChildNode(sFieldName, sValue); + delete node->addChildNode(sFieldName, sValue); } } // scalar - if (mex_is_scalar(pField)) { - string sValue = matlab2string(pField); - delete root->addChildNode(sFieldName, sValue); + else if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) == 1) { + string sValue = mexToString(pField); + delete node->addChildNode(sFieldName, sValue); } // numerical array - if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) > 1) { + else if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) > 1) { if (!mxIsDouble(pField)) { mexErrMsgTxt("Numeric input must be double."); return false; } - XMLNode* listbase = root->addChildNode(sFieldName); + XMLNode* listbase = node->addChildNode(sFieldName); listbase->addAttribute("listsize", mxGetM(pField)*mxGetN(pField)); double* pdValues = mxGetPr(pField); int index = 0; @@ -386,16 +233,15 @@ bool readStruct(XMLNode* root, const mxArray* pStruct) delete listbase; } - // not castable to a single string - if (mxIsStruct(pField)) { + else if (mxIsStruct(pField)) { if (sFieldName == "options" || sFieldName == "option" || sFieldName == "Options" || sFieldName == "Option") { - bool ret = readOptions(root, pField); + bool ret = optionsToXMLNode(node, pField); if (!ret) return false; } else { - XMLNode* newNode = root->addChildNode(sFieldName); - bool ret = readStruct(newNode, pField); + XMLNode* newNode = node->addChildNode(sFieldName); + bool ret = structToXMLNode(newNode, pField); delete newNode; if (!ret) return false; @@ -406,93 +252,74 @@ bool readStruct(XMLNode* root, const mxArray* pStruct) return true; } - //----------------------------------------------------------------------------------------- -// turn a MATLAB struct into an XML Document -XMLDocument* struct2XML(string rootname, const mxArray* pStruct) +// Options struct to xml node +bool optionsToXMLNode(XMLNode* node, const mxArray* pOptionStruct) { - if (!mxIsStruct(pStruct)) { - mexErrMsgTxt("Input must be a struct."); - return NULL; - } - - // create the document - XMLDocument* doc = XMLDocument::createDocument(rootname); - XMLNode* rootnode = doc->getRootNode(); - - // read the struct - bool ret = readStruct(rootnode, pStruct); - delete rootnode; - - if (!ret) { - delete doc; - doc = 0; - } - - return doc; -} - - - + // loop all fields + int nfields = mxGetNumberOfFields(pOptionStruct); + for (int i = 0; i < nfields; i++) { + std::string sFieldName = std::string(mxGetFieldNameByNumber(pOptionStruct, i)); + const mxArray* pField = mxGetFieldByNumber(pOptionStruct, 0, i); + if (node->hasOption(sFieldName)) { + mexErrMsgTxt("Duplicate option"); + return false; + } + + // string or scalar + if (mxIsChar(pField) || mexIsScalar(pField)) { + string sValue = mexToString(pField); + node->addOption(sFieldName, sValue); + } + // numerical array + else if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) > 1) { + if (!mxIsDouble(pField)) { + mexErrMsgTxt("Numeric input must be double."); + return false; + } -//----------------------------------------------------------------------------------------- -// turn an std vector object to an mxArray -mxArray* vectorToMxArray(std::vector mInput) -{ - mxArray* res = mxCreateDoubleMatrix(1, mInput.size(), mxREAL); - double* pdData = mxGetPr(res); - for (unsigned int i = 0; i < mInput.size(); i++) { - pdData[i] = mInput[i]; + 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++; + delete item; + } + } + delete listbase; + } else { + mexErrMsgTxt("Unsupported option type"); + return false; + } } - return res; + return true; } - //----------------------------------------------------------------------------------------- -// turn a vector> object to an mxArray -mxArray* vector2DToMxArray(std::vector > mInput) +// turn a matlab struct into a c++ map +std::map parseStruct(const mxArray* pInput) { - unsigned int sizex = mInput.size(); - if (sizex == 0) return mxCreateString("empty"); - unsigned int sizey = mInput[0].size(); + std::map res; - mxArray* res = mxCreateDoubleMatrix(sizex, sizey, mxREAL); - double* pdData = mxGetPr(res); - for (unsigned int i = 0; i < sizex; i++) { - for (unsigned int j = 0; j < sizey && j < mInput[i].size(); j++) { - pdData[j*sizex+i] = mInput[i][j]; - } + // check type + if (!mxIsStruct(pInput)) { + mexErrMsgTxt("Input must be a struct."); + return res; } - return res; -} -//----------------------------------------------------------------------------------------- -// turn a boost::any object to an mxArray -mxArray* anyToMxArray(boost::any _any) -{ - if (_any.type() == typeid(std::string)) { - std::string str = boost::any_cast(_any); - return mxCreateString(str.c_str()); - } - if (_any.type() == typeid(int)) { - return mxCreateDoubleScalar(boost::any_cast(_any)); - } - if (_any.type() == typeid(float32)) { - return mxCreateDoubleScalar(boost::any_cast(_any)); - } - if (_any.type() == typeid(std::vector)) { - return vectorToMxArray(boost::any_cast >(_any)); - } - if (_any.type() == typeid(std::vector >)) { - return vector2DToMxArray(boost::any_cast > >(_any)); + // get field names + int nfields = mxGetNumberOfFields(pInput); + for (int i = 0; i < nfields; i++) { + std::string sFieldName = std::string(mxGetFieldNameByNumber(pInput, i)); + res[sFieldName] = mxGetFieldByNumber(pInput,0,i); } - return NULL; -} -//----------------------------------------------------------------------------------------- -// return true ig the argument is a scalar -bool mex_is_scalar(const mxArray* pInput) -{ - return (mxIsNumeric(pInput) && mxGetM(pInput)*mxGetN(pInput) == 1); + return res; } @@ -509,18 +336,41 @@ bool mex_is_scalar(const mxArray* pInput) //----------------------------------------------------------------------------------------- +// turn a Config object into a MATLAB struct mxArray* configToStruct(astra::Config* cfg) { - return XMLNode2struct(cfg->self); + return XMLNodeToStruct(cfg->self); } //----------------------------------------------------------------------------------------- -mxArray* XML2struct(astra::XMLDocument* xml) +mxArray* XMLNodeToStruct(astra::XMLNode* node) { - XMLNode* node = xml->getRootNode(); - mxArray* str = XMLNode2struct(xml->getRootNode()); - delete node; - return str; + std::map mList; + std::map mOptions; + + // type_attribute + 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); + + // option + if (subnode->getName() == "Option") { + mOptions[subnode->getAttribute("key")] = stringToMxArray(subnode->getAttribute("value")); + } + + // regular content + else { + mList[subnode->getName()] = stringToMxArray(subnode->getContent()); + } + delete subnode; + } + + if (mOptions.size() > 0) mList["options"] = buildStruct(mOptions); + return buildStruct(mList); } //----------------------------------------------------------------------------------------- @@ -583,36 +433,18 @@ mxArray* stringToMxArray(std::string input) // string return mxCreateString(input.c_str()); } - //----------------------------------------------------------------------------------------- -mxArray* XMLNode2struct(astra::XMLNode* node) +// turn a c++ map into a matlab struct +mxArray* buildStruct(std::map mInput) { - std::map mList; - std::map mOptions; - - // type_attribute - 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); - - // option - if (subnode->getName() == "Option") { - mOptions[subnode->getAttribute("key")] = stringToMxArray(subnode->getAttribute("value")); - } - - // regular content - else { - mList[subnode->getName()] = stringToMxArray(subnode->getContent()); - } - delete subnode; + mwSize dims[2] = {1, 1}; + mxArray* res = mxCreateStructArray(2,dims,0,0); + + for (std::map::iterator it = mInput.begin(); it != mInput.end(); it++) { + mxAddField(res, (*it).first.c_str()); + mxSetField(res, 0, (*it).first.c_str(), (*it).second); } - - if (mOptions.size() > 0) mList["options"] = buildStruct(mOptions); - return buildStruct(mList); + return res; } @@ -624,26 +456,3 @@ mxArray* XMLNode2struct(astra::XMLNode* node) -//----------------------------------------------------------------------------------------- -void get3DMatrixDims(const mxArray* x, mwSize *dims) -{ - const mwSize* mdims = mxGetDimensions(x); - mwSize dimCount = mxGetNumberOfDimensions(x); - if (dimCount == 1) { - dims[0] = mdims[0]; - dims[1] = 1; - dims[2] = 1; - } else if (dimCount == 2) { - dims[0] = mdims[0]; - dims[1] = mdims[1]; - dims[2] = 1; - } else if (dimCount == 3) { - dims[0] = mdims[0]; - dims[1] = mdims[1]; - dims[2] = mdims[2]; - } else { - dims[0] = 0; - dims[1] = 0; - dims[2] = 0; - } -} diff --git a/matlab/mex/mexHelpFunctions.h b/matlab/mex/mexHelpFunctions.h index 6c80f8c..f9ffcf2 100644 --- a/matlab/mex/mexHelpFunctions.h +++ b/matlab/mex/mexHelpFunctions.h @@ -43,42 +43,31 @@ $Id$ #include "astra/Globals.h" #include "astra/Utilities.h" -#include "astra/ParallelProjectionGeometry2D.h" -#include "astra/FanFlatProjectionGeometry2D.h" -#include "astra/ParallelProjectionGeometry3D.h" -#include "astra/ParallelVecProjectionGeometry3D.h" -#include "astra/ConeProjectionGeometry3D.h" -#include "astra/ConeVecProjectionGeometry3D.h" - -#include "astra/VolumeGeometry2D.h" -#include "astra/VolumeGeometry3D.h" - - +#include "astra/Config.h" #include "astra/XMLDocument.h" #include "astra/XMLNode.h" -std::string mex_util_get_string(const mxArray* pInput); -bool isOption(std::list lOptions, std::string sOption); - -bool mex_is_scalar(const mxArray* pInput); +// utility functions +string mexToString(const mxArray* pInput); +bool mexIsScalar(const mxArray* pInput); +void get3DMatrixDims(const mxArray* x, mwSize *dims); -std::map parseStruct(const mxArray* pInput); -mxArray* buildStruct(std::map mInput); +// convert boost::any into a MALTAB object mxArray* vectorToMxArray(std::vector mInput); - mxArray* anyToMxArray(boost::any _any); -astra::CProjectionGeometry2D* parseProjectionGeometryStruct(const mxArray*); -astra::CVolumeGeometry2D* parseVolumeGeometryStruct(const mxArray*); - -astra::XMLDocument* struct2XML(string rootname, const mxArray* pStruct); +// 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); +std::map parseStruct(const mxArray* pInput); +// turn a Config object into a MATLAB struct mxArray* configToStruct(astra::Config* cfg); -mxArray* XML2struct(astra::XMLDocument* xml); -mxArray* XMLNode2struct(astra::XMLNode* xml); +mxArray* XMLNodeToStruct(astra::XMLNode* xml); mxArray* stringToMxArray(std::string input); +mxArray* buildStruct(std::map mInput); -void get3DMatrixDims(const mxArray* x, mwSize *dims); #endif -- cgit v1.2.3