From db8587475efd44bc728caa79cd7ae7120eaf045b Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Tue, 21 Jul 2015 15:15:08 +0200 Subject: Add matlab plugin .m file --- matlab/tools/astra_mex_plugin.m | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 matlab/tools/astra_mex_plugin.m (limited to 'matlab/tools') diff --git a/matlab/tools/astra_mex_plugin.m b/matlab/tools/astra_mex_plugin.m new file mode 100644 index 0000000..4159365 --- /dev/null +++ b/matlab/tools/astra_mex_plugin.m @@ -0,0 +1,24 @@ +function [varargout] = astra_mex_plugin(varargin) +%------------------------------------------------------------------------ +% Reference page in Help browser +% astra_mex_plugin. +%------------------------------------------------------------------------ +%------------------------------------------------------------------------ +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +%------------------------------------------------------------------------ +% $Id$ +if nargout == 0 + astra_mex_plugin_c(varargin{:}); + if exist('ans','var') + varargout{1} = ans; + end +else + varargout = cell(1,nargout); + [varargout{:}] = astra_mex_plugin_c(varargin{:}); +end \ No newline at end of file -- cgit v1.2.3 From c39b12fc42a7254bad1e68cbdb948eee0421ad81 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 16 Sep 2015 16:44:10 +0200 Subject: Let astra_create_vol_geom also generate flexible volume geometries --- matlab/tools/astra_create_vol_geom.m | 15 +++++++++++++++ python/astra/creators.py | 15 +++++++++++++++ 2 files changed, 30 insertions(+) (limited to 'matlab/tools') diff --git a/matlab/tools/astra_create_vol_geom.m b/matlab/tools/astra_create_vol_geom.m index ea975e6..a3ba7de 100644 --- a/matlab/tools/astra_create_vol_geom.m +++ b/matlab/tools/astra_create_vol_geom.m @@ -15,6 +15,7 @@ function vol_geom = astra_create_vol_geom(varargin) % vol_geom: MATLAB struct containing all information of the geometry. %-------------------------------------------------------------------------- % vol_geom = astra_create_vol_geom(row_count, col_count, slice_count); +% vol_geom = astra_create_vol_geom(row_count, col_count, slice_count, min_x, max_x, min_y, max_y, min_z, max_z); % % Create a 3D volume geometry. See the API for more information. % row_count: number of rows. @@ -93,4 +94,18 @@ elseif numel(varargin) == 3 vol_geom.GridRowCount = varargin{1}; vol_geom.GridColCount = varargin{2}; vol_geom.GridSliceCount = varargin{3}; + +% astra_create_vol_geom(row_count, col_count, slice_count, min_x, max_x, min_y, max_y, min_z, max_z) +elseif numel(varargin) == 9 + vol_geom = struct(); + vol_geom.GridRowCount = varargin{1}; + vol_geom.GridColCount = varargin{2}; + vol_geom.GridSliceCount = varargin{3}; + vol_geom.option.WindowMinX = varargin{4}; + vol_geom.option.WindowMaxX = varargin{5}; + vol_geom.option.WindowMinY = varargin{6}; + vol_geom.option.WindowMaxY = varargin{7}; + vol_geom.option.WindowMinZ = varargin{8}; + vol_geom.option.WindowMaxZ = varargin{9}; + end diff --git a/python/astra/creators.py b/python/astra/creators.py index 68bc8a2..f3474d8 100644 --- a/python/astra/creators.py +++ b/python/astra/creators.py @@ -72,6 +72,10 @@ This method can be called in a number of ways: ``create_vol_geom(M, N, Z)``: :returns: A 3D volume geometry of size :math:`M \\times N \\times Z`. +``create_vol_geom(M, N, Z, minx, maxx, miny, maxy, minz, maxz)``: + :returns: A 3D volume geometry of size :math:`M \\times N \\times Z`, windowed as :math:`minx \\leq x \\leq maxx` and :math:`miny \\leq y \\leq maxy` and :math:`minz \\leq z \\leq maxz` . + + """ vol_geom = {'option': {}} # astra_create_vol_geom(row_count) @@ -122,6 +126,17 @@ This method can be called in a number of ways: vol_geom['GridRowCount'] = varargin[0] vol_geom['GridColCount'] = varargin[1] vol_geom['GridSliceCount'] = varargin[2] + # astra_create_vol_geom(row_count, col_count, slice_count, min_x, max_x, min_y, max_y, min_z, max_z) + elif len(varargin) == 9: + vol_geom['GridRowCount'] = varargin[0] + vol_geom['GridColCount'] = varargin[1] + vol_geom['GridSliceCount'] = varargin[2] + vol_geom['option']['WindowMinX'] = varargin[3] + vol_geom['option']['WindowMaxX'] = varargin[4] + vol_geom['option']['WindowMinY'] = varargin[5] + vol_geom['option']['WindowMaxY'] = varargin[6] + vol_geom['option']['WindowMinZ'] = varargin[7] + vol_geom['option']['WindowMaxZ'] = varargin[8] return vol_geom -- cgit v1.2.3 From 1cc67c1e4d9b6b24c096f52d6f086a3f224ece8a Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 7 Oct 2015 17:29:20 +0200 Subject: Add astra_mex_direct('FP3D'/'BP3D', ...) --- build/linux/Makefile.in | 3 +- matlab/mex/astra_mex_direct_c.cpp | 332 ++++++++++++++++++++++++++++++++++++++ matlab/tools/astra_mex_direct.m | 24 +++ 3 files changed, 358 insertions(+), 1 deletion(-) create mode 100755 matlab/mex/astra_mex_direct_c.cpp create mode 100644 matlab/tools/astra_mex_direct.m (limited to 'matlab/tools') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 2d862f2..abbebe2 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -232,7 +232,8 @@ MATLAB_MEX=\ matlab/mex/astra_mex_projector_c.$(MEXSUFFIX) \ matlab/mex/astra_mex_projector3d_c.$(MEXSUFFIX) \ matlab/mex/astra_mex_log_c.$(MEXSUFFIX) \ - matlab/mex/astra_mex_data3d_c.$(MEXSUFFIX) + matlab/mex/astra_mex_data3d_c.$(MEXSUFFIX) \ + matlab/mex/astra_mex_direct_c.$(MEXSUFFIX) OBJECT_DIRS = src/ tests/ cuda/2d/ cuda/3d/ matlab/mex/ ./ diff --git a/matlab/mex/astra_mex_direct_c.cpp b/matlab/mex/astra_mex_direct_c.cpp new file mode 100755 index 0000000..94eb1cd --- /dev/null +++ b/matlab/mex/astra_mex_direct_c.cpp @@ -0,0 +1,332 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the 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 . + +----------------------------------------------------------------------- +$Id$ +*/ + +/** \file astra_mex_direct_c.cpp + * + * \brief Utility functions for low-overhead FP and BP calls. + */ +#include +#include "mexHelpFunctions.h" +#include "mexCopyDataHelpFunctions.h" +#include "mexDataManagerHelpFunctions.h" + +#include + +#include "astra/Globals.h" + +#include "astra/AstraObjectManager.h" + +#include "astra/Float32ProjectionData2D.h" +#include "astra/Float32VolumeData2D.h" +#include "astra/CudaProjector3D.h" +#include "astra/Projector3D.h" +#include "astra/Float32ProjectionData3DMemory.h" +#include "astra/Float32VolumeData3DMemory.h" + +#include "astra/CudaForwardProjectionAlgorithm3D.h" + +#include "astra/CudaBackProjectionAlgorithm3D.h" + +using namespace std; +using namespace astra; + +#define USE_MATLAB_UNDOCUMENTED + + +class CFloat32CustomMemory_simple : public astra::CFloat32CustomMemory { +public: + CFloat32CustomMemory_simple(float *ptr) { m_fPtr = ptr; } + ~CFloat32CustomMemory_simple() { } +}; + +#ifdef ASTRA_CUDA + +//----------------------------------------------------------------------------------------- +/** + * projection = astra_mex_direct_c('FP3D', projector_id, volume); + * Both 'projection' and 'volume' are Matlab arrays. + */ +void astra_mex_direct_fp3d(int& nlhs, mxArray* plhs[], int& nrhs, const mxArray* prhs[]) +{ + // TODO: Add an optional way of specifying extra options + + if (nrhs < 3) { + mexErrMsgTxt("Not enough arguments. Syntax: astra_mex_direct_c('FP3D', projector_id, data)"); + return; + } + + int iPid = (int)(mxGetScalar(prhs[1])); + astra::CProjector3D* pProjector; + pProjector = astra::CProjector3DManager::getSingleton().get(iPid); + if (!pProjector) { + mexErrMsgTxt("Projector not found."); + return; + } + if (!pProjector->isInitialized()) { + mexErrMsgTxt("Projector not initialized."); + return; + } + bool isCuda = false; + if (dynamic_cast(pProjector)) + isCuda = true; + if (!isCuda) { + mexErrMsgTxt("Only CUDA projectors are currently supported."); + return; + } + + astra::CVolumeGeometry3D* pVolGeom = pProjector->getVolumeGeometry(); + astra::CProjectionGeometry3D* pProjGeom = pProjector->getProjectionGeometry(); + + const mxArray* const data = prhs[2]; + if (!checkDataType(data)) { + mexErrMsgTxt("Data must be single or double."); + return; + } + + if (!checkDataSize(data, pVolGeom)) { + mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry."); + return; + } + + + // Allocate input data + astra::CFloat32VolumeData3DMemory* pInput; + if (mxIsSingle(data)) { + astra::CFloat32CustomMemory* m = new CFloat32CustomMemory_simple((float *)mxGetData(data)); + pInput = new astra::CFloat32VolumeData3DMemory(pVolGeom, m); + } else { + pInput = new astra::CFloat32VolumeData3DMemory(pVolGeom); + copyMexToCFloat32Array(data, pInput->getData(), pInput->getSize()); + } + + + // Allocate output data + // If the input is single, we also allocate single output. + // Otherwise, double. + astra::CFloat32ProjectionData3DMemory* pOutput; + mxArray *pOutputMx; + if (mxIsSingle(data)) { + mwSize dims[3]; + dims[0] = pProjGeom->getDetectorColCount(); + dims[1] = pProjGeom->getProjectionCount(); + dims[2] = pProjGeom->getDetectorRowCount(); + pOutputMx = mxCreateNumericArray(3, dims, mxSINGLE_CLASS, mxREAL); + + astra::CFloat32CustomMemory* m = new CFloat32CustomMemory_simple((float *)mxGetData(pOutputMx)); + pOutput = new astra::CFloat32ProjectionData3DMemory(pProjGeom, m); + } else { + pOutput = new astra::CFloat32ProjectionData3DMemory(pProjGeom); + } + + // Perform FP + + astra::CCudaForwardProjectionAlgorithm3D* pAlg; + pAlg = new astra::CCudaForwardProjectionAlgorithm3D(); + pAlg->initialize(pProjector, pOutput, pInput); + + if (!pAlg->isInitialized()) { + mexErrMsgTxt("Error initializing algorithm."); + // TODO: Delete pOutputMx? + delete pAlg; + delete pInput; + delete pOutput; + return; + } + + pAlg->run(); + + delete pAlg; + + + if (mxIsSingle(data)) { + + } else { + pOutputMx = createEquivMexArray(pOutput); + copyCFloat32ArrayToMex(pOutput->getData(), pOutputMx); + } + plhs[0] = pOutputMx; + + delete pOutput; + delete pInput; +} +//----------------------------------------------------------------------------------------- +/** + * projection = astra_mex_direct_c('BP3D', projector_id, volume); + * Both 'projection' and 'volume' are Matlab arrays. + */ +void astra_mex_direct_bp3d(int& nlhs, mxArray* plhs[], int& nrhs, const mxArray* prhs[]) +{ + // TODO: Add an optional way of specifying extra options + + if (nrhs < 3) { + mexErrMsgTxt("Not enough arguments. Syntax: astra_mex_direct_c('BP3D', projector_id, data)"); + return; + } + + int iPid = (int)(mxGetScalar(prhs[1])); + astra::CProjector3D* pProjector; + pProjector = astra::CProjector3DManager::getSingleton().get(iPid); + if (!pProjector) { + mexErrMsgTxt("Projector not found."); + return; + } + if (!pProjector->isInitialized()) { + mexErrMsgTxt("Projector not initialized."); + return; + } + bool isCuda = false; + if (dynamic_cast(pProjector)) + isCuda = true; + if (!isCuda) { + mexErrMsgTxt("Only CUDA projectors are currently supported."); + return; + } + + astra::CVolumeGeometry3D* pVolGeom = pProjector->getVolumeGeometry(); + astra::CProjectionGeometry3D* pProjGeom = pProjector->getProjectionGeometry(); + + const mxArray* const data = prhs[2]; + if (!checkDataType(data)) { + mexErrMsgTxt("Data must be single or double."); + return; + } + + if (!checkDataSize(data, pProjGeom)) { + mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry."); + return; + } + + + // Allocate input data + astra::CFloat32ProjectionData3DMemory* pInput; + if (mxIsSingle(data)) { + astra::CFloat32CustomMemory* m = new CFloat32CustomMemory_simple((float *)mxGetData(data)); + pInput = new astra::CFloat32ProjectionData3DMemory(pProjGeom, m); + } else { + pInput = new astra::CFloat32ProjectionData3DMemory(pProjGeom); + copyMexToCFloat32Array(data, pInput->getData(), pInput->getSize()); + } + + + // Allocate output data + // If the input is single, we also allocate single output. + // Otherwise, double. + astra::CFloat32VolumeData3DMemory* pOutput; + mxArray *pOutputMx; + if (mxIsSingle(data)) { + mwSize dims[3]; + dims[0] = pVolGeom->getGridColCount(); + dims[1] = pVolGeom->getGridRowCount(); + dims[2] = pVolGeom->getGridSliceCount(); + pOutputMx = mxCreateNumericArray(3, dims, mxSINGLE_CLASS, mxREAL); + + astra::CFloat32CustomMemory* m = new CFloat32CustomMemory_simple((float *)mxGetData(pOutputMx)); + pOutput = new astra::CFloat32VolumeData3DMemory(pVolGeom, m); + } else { + pOutput = new astra::CFloat32VolumeData3DMemory(pVolGeom); + } + + // Perform BP + + astra::CCudaBackProjectionAlgorithm3D* pAlg; + pAlg = new astra::CCudaBackProjectionAlgorithm3D(); + pAlg->initialize(pProjector, pInput, pOutput); + + if (!pAlg->isInitialized()) { + mexErrMsgTxt("Error initializing algorithm."); + // TODO: Delete pOutputMx? + delete pAlg; + delete pInput; + delete pOutput; + return; + } + + pAlg->run(); + + delete pAlg; + + + if (mxIsSingle(data)) { + + } else { + pOutputMx = createEquivMexArray(pOutput); + copyCFloat32ArrayToMex(pOutput->getData(), pOutputMx); + } + plhs[0] = pOutputMx; + + delete pOutput; + delete pInput; +} + +#endif + +//----------------------------------------------------------------------------------------- + +static void printHelp() +{ + mexPrintf("Please specify a mode of operation.\n"); + mexPrintf("Valid modes: FP3D, BP3D\n"); +} + + +//----------------------------------------------------------------------------------------- +/** + * ... = astra_mex_direct_c(mode,...); + */ +void mexFunction(int nlhs, mxArray* plhs[], + int nrhs, const mxArray* prhs[]) +{ + + // INPUT: Mode + string sMode; + if (1 <= nrhs) { + sMode = mexToString(prhs[0]); + } else { + printHelp(); + return; + } + +#ifndef ASTRA_CUDA + mexErrMsgTxt("Only CUDA projectors are currently supported."); + return; +#else + + // 3D data + if (sMode == "FP3D") { + astra_mex_direct_fp3d(nlhs, plhs, nrhs, prhs); + } else if (sMode == "BP3D") { + astra_mex_direct_bp3d(nlhs, plhs, nrhs, prhs); + } else { + printHelp(); + } +#endif + + return; +} + + diff --git a/matlab/tools/astra_mex_direct.m b/matlab/tools/astra_mex_direct.m new file mode 100644 index 0000000..58c4fd2 --- /dev/null +++ b/matlab/tools/astra_mex_direct.m @@ -0,0 +1,24 @@ +function [varargout] = astra_mex_direct(varargin) +%------------------------------------------------------------------------ +% Reference page in Help browser +% astra_mex_data3d. +%------------------------------------------------------------------------ +%------------------------------------------------------------------------ +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +%------------------------------------------------------------------------ +% $Id$ +if nargout == 0 + astra_mex_direct_c(varargin{:}); + if exist('ans','var') + varargout{1} = ans; + end +else + varargout = cell(1,nargout); + [varargout{:}] = astra_mex_direct_c(varargin{:}); +end -- cgit v1.2.3 From 0ebd8dfe60cc0d1f05d65d3840278defce0da091 Mon Sep 17 00:00:00 2001 From: Nicola Vigano Date: Wed, 7 Oct 2015 17:25:06 +0200 Subject: Add options passing to projectors from matlab Signed-off-by: Nicola Vigano --- matlab/tools/astra_create_projector.m | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) (limited to 'matlab/tools') diff --git a/matlab/tools/astra_create_projector.m b/matlab/tools/astra_create_projector.m index da9c083..9bbef9e 100644 --- a/matlab/tools/astra_create_projector.m +++ b/matlab/tools/astra_create_projector.m @@ -1,7 +1,7 @@ -function proj_id = astra_create_projector(type, proj_geom, vol_geom) +function proj_id = astra_create_projector(type, proj_geom, vol_geom, options) %-------------------------------------------------------------------------- -% proj_id = astra_create_projector(type, proj_geom, vol_geom) +% proj_id = astra_create_projector(type, proj_geom, vol_geom, options) % % Create a new projector object based on projection and volume geometry. % Used when the default values of each projector are sufficient. @@ -9,6 +9,7 @@ function proj_id = astra_create_projector(type, proj_geom, vol_geom) % type: type of the projector. 'blob', 'line', 'linear' 'strip', ... See API for more information. % proj_geom: MATLAB struct containing the projection geometry. % vol_geom: MATLAB struct containing the volume geometry. +% options: Optional MATLAB struct containing projector options (like: 'GPUindex', 'DetectorSuperSampling', and 'VoxelSuperSampling') % proj_id: identifier of the projector as it is now stored in the astra-library. %-------------------------------------------------------------------------- %-------------------------------------------------------------------------- @@ -38,6 +39,10 @@ if strcmp(type,'blob') cfg_proj.Kernel.KernelValues = blob_values; end +if exist('options', 'var') + cfg_proj.options = options; +end + if strcmp(type,'linear3d') || strcmp(type,'linearcone') || strcmp(type,'cuda3d') proj_id = astra_mex_projector3d('create', cfg_proj); else -- cgit v1.2.3