From 50598bfd0c4959da66780fe695755e2be1a28b87 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Thu, 30 Oct 2014 17:41:58 +0100 Subject: Refactor astra_mex_data3d MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit (Modified) patch by Nicola Viganò --- matlab/mex/mexDataManagerHelpFunctions.cpp | 371 +++++++++++++++++++++++++++++ 1 file changed, 371 insertions(+) create mode 100644 matlab/mex/mexDataManagerHelpFunctions.cpp (limited to 'matlab/mex/mexDataManagerHelpFunctions.cpp') diff --git a/matlab/mex/mexDataManagerHelpFunctions.cpp b/matlab/mex/mexDataManagerHelpFunctions.cpp new file mode 100644 index 0000000..2985a9d --- /dev/null +++ b/matlab/mex/mexDataManagerHelpFunctions.cpp @@ -0,0 +1,371 @@ +/* +----------------------------------------------------------------------- +Copyright 2013 iMinds-Vision Lab, University of Antwerp + +Contact: astra@ua.ac.be +Website: http://astra.ua.ac.be + + +This file is part of the +All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see . + +----------------------------------------------------------------------- +$Id$ +*/ + +#include "mexDataManagerHelpFunctions.h" + +#include "mexHelpFunctions.h" + +#include "astra/ParallelProjectionGeometry3D.h" +#include "astra/ParallelVecProjectionGeometry3D.h" +#include "astra/ConeProjectionGeometry3D.h" +#include "astra/ConeVecProjectionGeometry3D.h" +#include "astra/Float32VolumeData3DMemory.h" +#include "astra/Float32ProjectionData3DMemory.h" + +#define USE_MATLAB_UNDOCUMENTED + +#ifdef USE_MATLAB_UNDOCUMENTED +extern "C" { +mxArray *mxCreateSharedDataCopy(const mxArray *pr); +bool mxUnshareArray(const mxArray *pr, const bool noDeepCopy); +mxArray *mxUnreference(const mxArray *pr); +#if 0 +// Unsupported in Matlab R2014b +bool mxIsSharedArray(const mxArray *pr); +#endif +} + +class CFloat32CustomMemoryMatlab3D : public astra::CFloat32CustomMemory { +public: + // offset allows linking the data object to a sub-volume (in the z direction) + // offset is measured in floats. + CFloat32CustomMemoryMatlab3D(const mxArray* _pArray, bool bUnshare, size_t iOffset) + { + // Convert from slice to offset + mwSize dims[3]; + get3DMatrixDims(_pArray, dims); + iOffset *= dims[0]; + iOffset *= dims[1]; + + //fprintf(stderr, "Passed:\narray: %p\tdata: %p\n", (void*)_pArray, (void*)mxGetData(_pArray)); + // First unshare the input array, so that we may modify it. + if (bUnshare) { +#if 0 + // Unsupported in Matlab R2014b + if (mxIsSharedArray(_pArray)) { + fprintf(stderr, "Performance note: unsharing shared array in link\n"); + } +#endif + mxUnshareArray(_pArray, false); + //fprintf(stderr, "Unshared:\narray: %p\tdata: %p\n", (void*)_pArray, (void*)mxGetData(_pArray)); + } + // Then create a (persistent) copy so the data won't be deleted + // or changed. + m_pLink = mxCreateSharedDataCopy(_pArray); + //fprintf(stderr, "SharedDataCopy:\narray: %p\tdata: %p\n", (void*)m_pLink, (void*)mxGetData(m_pLink)); + mexMakeArrayPersistent(m_pLink); + m_fPtr = (float *)mxGetData(m_pLink); + m_fPtr += iOffset; + } + virtual ~CFloat32CustomMemoryMatlab3D() { + // destroy the shared array + //fprintf(stderr, "Destroy:\narray: %p\tdata: %p\n", (void*)m_pLink, (void*)mxGetData(m_pLink)); + mxDestroyArray(m_pLink); + } +private: + mxArray* m_pLink; +}; +#endif + +//----------------------------------------------------------------------------------------- +bool +checkID(const astra::int32 & id, astra::CFloat32Data3DMemory *& pDataObj) +{ + pDataObj = dynamic_cast( + astra::CData3DManager::getSingleton().get(id) ); + return (pDataObj && pDataObj->isInitialized()); +} + +//----------------------------------------------------------------------------------------- +bool +checkDataType(const mxArray * const in) +{ + return (mex_is_scalar(in) || mxIsDouble(in) || mxIsSingle(in)); +} + +//----------------------------------------------------------------------------------------- +bool +checkStructs(const mxArray * const in) +{ + return mxIsStruct(in); +} + +//----------------------------------------------------------------------------------------- +bool +checkDataSize(const mxArray * const mArray, + const astra::CProjectionGeometry3D * const geom) +{ + mwSize dims[3]; + get3DMatrixDims(mArray, dims); + return (geom->getDetectorColCount() == dims[0] + && geom->getProjectionCount() == dims[1] + && geom->getDetectorRowCount() == dims[2]); +} + +//----------------------------------------------------------------------------------------- +bool +checkDataSize(const mxArray * const mArray, + const astra::CVolumeGeometry3D * const geom) +{ + mwSize dims[3]; + get3DMatrixDims(mArray, dims); + return (geom->getGridColCount() == dims[0] + && geom->getGridRowCount() == dims[1] + && geom->getGridSliceCount() == dims[2]); +} + +//----------------------------------------------------------------------------------------- +bool +checkDataSize(const mxArray * const mArray, + const astra::CProjectionGeometry3D * const geom, + const mwIndex & zOffset) +{ + mwSize dims[3]; + get3DMatrixDims(mArray, dims); + return (geom->getDetectorColCount() == dims[0] + && geom->getProjectionCount() == dims[1] + && (zOffset + geom->getDetectorRowCount()) <= dims[2]); +} + +//----------------------------------------------------------------------------------------- +bool +checkDataSize(const mxArray * const mArray, + const astra::CVolumeGeometry3D * const geom, + const mwIndex & zOffset) +{ + mwSize dims[3]; + get3DMatrixDims(mArray, dims); + return (geom->getGridColCount() == dims[0] + && geom->getGridRowCount() == dims[1] + && (zOffset + geom->getGridSliceCount()) <= dims[2]); +} + +//----------------------------------------------------------------------------------------- +void +updateStatistics(const std::vector & vecIn) +{ + const size_t tot_size = vecIn.size(); + for (size_t count = 0; count < tot_size; count++) + { + vecIn[count]->updateStatistics(); + } +} + +//----------------------------------------------------------------------------------------- +void +getDataPointers(const std::vector & vecIn, + std::vector & vecOut) +{ + const size_t tot_size = vecIn.size(); + vecOut.resize(tot_size); + for (size_t count = 0; count < tot_size; count++) + { + vecOut[count] = vecIn[count]->getData(); + } +} + +//----------------------------------------------------------------------------------------- +void +getDataSizes(const std::vector & vecIn, + std::vector & vecOut) +{ + const size_t tot_size = vecIn.size(); + vecOut.resize(tot_size); + for (size_t count = 0; count < tot_size; count++) + { + vecOut[count] = vecIn[count]->getSize(); + } +} + +//----------------------------------------------------------------------------------------- +astra::CFloat32Data3DMemory * +allocateDataObject(const std::string & sDataType, + const mxArray * const geometry, const mxArray * const data, + const mxArray * const unshare, const mxArray * const zIndex) +{ + astra::CFloat32Data3DMemory* pDataObject3D = NULL; + + bool bUnshare = true; + if (unshare) + { + if (!mex_is_scalar(unshare)) + { + mexErrMsgTxt("Argument 5 (read-only) must be scalar"); + return NULL; + } + // unshare the array if we're not linking read-only + bUnshare = !(bool)mxGetScalar(unshare); + } + + mwIndex iZ = 0; + if (zIndex) + { + if (!mex_is_scalar(zIndex)) + { + mexErrMsgTxt("Argument 6 (Z) must be scalar"); + return NULL; + } + iZ = (mwSignedIndex)mxGetScalar(zIndex); + } + + // SWITCH DataType + if (sDataType == "-vol") + { + // Read geometry + astra::XMLDocument* xml = struct2XML("VolumeGeometry", geometry); + if (!xml) { + return NULL; + } + astra::Config cfg; + cfg.self = xml->getRootNode(); + + astra::CVolumeGeometry3D* pGeometry = new astra::CVolumeGeometry3D(); + if (!pGeometry->initialize(cfg)) + { + mexErrMsgTxt("Geometry class not initialized. \n"); + delete pGeometry; + delete xml; + return NULL; + } + delete xml; + + // If data is specified, check dimensions + if (data && !mex_is_scalar(data)) + { + if (! (zIndex + ? checkDataSize(data, pGeometry, iZ) + : checkDataSize(data, pGeometry)) ) + { + mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n"); + delete pGeometry; + return NULL; + } + } + + // Initialize data object +#ifdef USE_MATLAB_UNDOCUMENTED + if (unshare) { + CFloat32CustomMemoryMatlab3D* pHandle = + new CFloat32CustomMemoryMatlab3D(data, bUnshare, iZ); + + // Initialize data object + pDataObject3D = new astra::CFloat32VolumeData3DMemory(pGeometry, pHandle); + } + else + { + pDataObject3D = new astra::CFloat32VolumeData3DMemory(pGeometry); + } +#else + pDataObject3D = new astra::CFloat32VolumeData3DMemory(pGeometry); +#endif + delete pGeometry; + } + 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(); + + // FIXME: Change how the base class is created. (This is duplicated + // in Projector2D.cpp.) + std::string type = cfg.self->getAttribute("type"); + astra::CProjectionGeometry3D* pGeometry = 0; + if (type == "parallel3d") { + pGeometry = new astra::CParallelProjectionGeometry3D(); + } else if (type == "parallel3d_vec") { + pGeometry = new astra::CParallelVecProjectionGeometry3D(); + } else if (type == "cone") { + pGeometry = new astra::CConeProjectionGeometry3D(); + } else if (type == "cone_vec") { + pGeometry = new astra::CConeVecProjectionGeometry3D(); + } else { + mexErrMsgTxt("Invalid geometry type.\n"); + return NULL; + } + + if (!pGeometry->initialize(cfg)) { + mexErrMsgTxt("Geometry class not initialized. \n"); + delete pGeometry; + delete xml; + return NULL; + } + delete xml; + + // If data is specified, check dimensions + if (data && !mex_is_scalar(data)) + { + if (! (zIndex + ? checkDataSize(data, pGeometry, iZ) + : checkDataSize(data, pGeometry)) ) + { + mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n"); + delete pGeometry; + return NULL; + } + } + + // Initialize data object +#ifdef USE_MATLAB_UNDOCUMENTED + if (unshare) + { + CFloat32CustomMemoryMatlab3D* pHandle = + new CFloat32CustomMemoryMatlab3D(data, bUnshare, iZ); + + // Initialize data object + pDataObject3D = new astra::CFloat32ProjectionData3DMemory(pGeometry, pHandle); + } + else + { + pDataObject3D = new astra::CFloat32ProjectionData3DMemory(pGeometry); + } +#else + pDataObject3D = new astra::CFloat32ProjectionData3DMemory(pGeometry); +#endif + delete pGeometry; + } + else + { + mexErrMsgTxt("Invalid datatype. Please specify '-vol' or '-proj3d'. \n"); + return NULL; + } + + // Check initialization + if (!pDataObject3D->isInitialized()) + { + mexErrMsgTxt("Couldn't initialize data object.\n"); + delete pDataObject3D; + return NULL; + } + + return pDataObject3D; +} + -- cgit v1.2.3