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|
/*
-----------------------------------------------------------------------
Copyright: 2010-2021, imec Vision Lab, University of Antwerp
2014-2021, CWI, Amsterdam
Contact: astra@astra-toolbox.com
Website: http://www.astra-toolbox.com/
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 <http://www.gnu.org/licenses/>.
-----------------------------------------------------------------------
*/
/** \file astra_mex_data2d_c.cpp
*
* \brief Creates, manages and manipulates 2D volume and projection data objects.
*/
#include <mex.h>
#include "mexHelpFunctions.h"
#include "mexInitFunctions.h"
#include <list>
#include "astra/Globals.h"
#include "astra/AstraObjectManager.h"
#include "astra/Float32ProjectionData2D.h"
#include "astra/Float32VolumeData2D.h"
#include "astra/SparseMatrixProjectionGeometry2D.h"
#include "astra/FanFlatProjectionGeometry2D.h"
#include "astra/FanFlatVecProjectionGeometry2D.h"
#include "astra/ParallelVecProjectionGeometry2D.h"
using namespace std;
using namespace astra;
//-----------------------------------------------------------------------------------------
/** astra_mex_data2d('delete', id1, id2, ...);
*
* Delete one or more data objects currently stored in the astra-library.
* id1, id2, ... : identifiers of the 2d data objects as stored in the astra-library.
*/
void astra_mex_data2d_delete(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
{
// step1: read input
if (nrhs < 2) {
mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n");
return;
}
// step2: delete all specified data objects
for (int i = 1; i < nrhs; i++) {
int iDataID = (int)(mxGetScalar(prhs[i]));
CData2DManager::getSingleton().remove(iDataID);
}
}
//-----------------------------------------------------------------------------------------
/** astra_mex_data2d('clear');
*
* Delete all data objects currently stored in the astra-library.
*/
void astra_mex_data2d_clear(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
{
CData2DManager::getSingleton().clear();
}
//-----------------------------------------------------------------------------------------
/** id = astra_mex_data2d('create', datatype, geometry, data);
*
* Create a new data 2d object in the astra-library.
* type: '-vol' for volume data, '-sino' for projection data
* geom: MATLAB struct with the geometry for the data
* data: Optional. Can be either a MATLAB matrix containing the data. In that case the dimensions
* should match that of the geometry of the object. It can also be a single value, in which case
* the entire data will be set to that value. If this isn't specified all values are set to 0.
* id: identifier of the 2d data object as it is now stored in the astra-library.
*/
void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArray* prhs[])
{
// step1: get datatype
if (nrhs < 3) {
mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n");
return;
}
string sDataType = mexToString(prhs[1]);
CFloat32Data2D* pDataObject2D = NULL;
if (nrhs >= 4 && !(mexIsScalar(prhs[3])|| mxIsDouble(prhs[3]) || mxIsLogical(prhs[3]) || mxIsSingle(prhs[3]) )) {
mexErrMsgTxt("Data must be single, double or logical.");
return;
}
if (mxIsSparse(prhs[2])) {
mexErrMsgTxt("Data may not be sparse.");
return;
}
// SWITCH DataType
if (sDataType == "-vol") {
// Read geometry
if (!mxIsStruct(prhs[2])) {
mexErrMsgTxt("Argument 3 is not a valid MATLAB struct.\n");
}
Config* cfg = structToConfig("VolumeGeometry", prhs[2]);
CVolumeGeometry2D* pGeometry = new CVolumeGeometry2D();
if (!pGeometry->initialize(*cfg)) {
mexErrMsgTxt("Geometry class not initialized. \n");
delete cfg;
delete pGeometry;
return;
}
// If data is specified, check dimensions
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 cfg;
delete pGeometry;
return;
}
}
// Initialize data object
pDataObject2D = new CFloat32VolumeData2D(pGeometry);
delete pGeometry;
delete cfg;
}
else if (sDataType == "-sino") {
// Read geometry
if (!mxIsStruct(prhs[2])) {
mexErrMsgTxt("Argument 3 is not a valid MATLAB struct.\n");
}
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");
CProjectionGeometry2D* pGeometry;
if (type == "sparse_matrix") {
pGeometry = new CSparseMatrixProjectionGeometry2D();
} else if (type == "fanflat") {
//CFanFlatProjectionGeometry2D* pFanFlatProjectionGeometry = new CFanFlatProjectionGeometry2D();
//pFanFlatProjectionGeometry->initialize(Config(node));
//m_pProjectionGeometry = pFanFlatProjectionGeometry;
pGeometry = new CFanFlatProjectionGeometry2D();
} else if (type == "fanflat_vec") {
pGeometry = new CFanFlatVecProjectionGeometry2D();
} else if (type == "parallel_vec") {
pGeometry = new CParallelVecProjectionGeometry2D();
} else {
pGeometry = new CParallelProjectionGeometry2D();
}
if (!pGeometry->initialize(*cfg)) {
mexErrMsgTxt("Geometry class not initialized. \n");
delete pGeometry;
delete cfg;
return;
}
// If data is specified, check dimensions
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 cfg;
return;
}
}
// Initialize data object
pDataObject2D = new CFloat32ProjectionData2D(pGeometry);
delete pGeometry;
delete cfg;
}
else {
mexErrMsgTxt("Invalid datatype. Please specify '-vol' or '-sino'. \n");
return;
}
// Check initialization
if (!pDataObject2D->isInitialized()) {
mexErrMsgTxt("Couldn't initialize data object.\n");
delete pDataObject2D;
return;
}
// Store data
if (nrhs == 3) {
for (int i = 0; i < pDataObject2D->getSize(); ++i) {
pDataObject2D->getData()[i] = 0.0f;
}
}
// Store data
if (nrhs >= 4) {
// fill with scalar value
if (mexIsScalar(prhs[3])) {
float32 fValue = (float32)mxGetScalar(prhs[3]);
for (int i = 0; i < pDataObject2D->getSize(); ++i) {
pDataObject2D->getData()[i] = fValue;
}
}
// fill with array value
else {
const mwSize* dims = mxGetDimensions(prhs[3]);
// Check Data dimensions
if (pDataObject2D->getWidth() != mxGetN(prhs[3]) || pDataObject2D->getHeight() != mxGetM(prhs[3])) {
mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n");
return;
}
// logical data
if (mxIsLogical(prhs[3])) {
mxLogical* pbMatlabData = mxGetLogicals(prhs[3]);
int i = 0;
int col, row;
for (col = 0; col < dims[1]; ++col) {
for (row = 0; row < dims[0]; ++row) {
pDataObject2D->getData2D()[row][col] = (float32)pbMatlabData[i];
++i;
}
}
// double data
} else if (mxIsDouble(prhs[3])) {
double* pdMatlabData = mxGetPr(prhs[3]);
int i = 0;
int col, row;
for (col = 0; col < dims[1]; ++col) {
for (row = 0; row < dims[0]; ++row) {
pDataObject2D->getData2D()[row][col] = pdMatlabData[i];
++i;
}
}
// single data
} else if (mxIsSingle(prhs[3])) {
const float* pfMatlabData = (const float *)mxGetData(prhs[3]);
int i = 0;
int col, row;
for (col = 0; col < dims[1]; ++col) {
for (row = 0; row < dims[0]; ++row) {
pDataObject2D->getData2D()[row][col] = pfMatlabData[i];
++i;
}
}
} else {
ASTRA_ASSERT(false);
}
}
}
// step4: store data object
int iIndex = CData2DManager::getSingleton().store(pDataObject2D);
// step5: return data id
if (1 <= nlhs) {
plhs[0] = mxCreateDoubleScalar(iIndex);
}
}
//-----------------------------------------------------------------------------------------
/** astra_mex_data2d('store', id, data);
*
* Store data in an existing astra 2d dataobject with a MATLAB matrix or with a scalar value.
* id: identifier of the 2d data object as stored in the astra-library.
* data: can be either a MATLAB matrix containing the data. In that case the dimensions should match that of the geometry of the object. It can also be a single value, in which case the entire data will be set to that value.
*/
void astra_mex_data2d_store(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
{
// step1: input
if (nrhs < 3) {
mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n");
return;
}
if (!mxIsDouble(prhs[1])) {
mexErrMsgTxt("Identifier should be a scalar value. \n");
return;
}
int iDataID = (int)(mxGetScalar(prhs[1]));
if (!(mexIsScalar(prhs[2]) || mxIsDouble(prhs[2]) || mxIsLogical(prhs[2]) || mxIsSingle(prhs[2]))) {
mexErrMsgTxt("Data must be single, double or logical.");
return;
}
if (mxIsSparse(prhs[2])) {
mexErrMsgTxt("Data may not be sparse.");
return;
}
// step2: get data object
CFloat32Data2D* pDataObject = astra::CData2DManager::getSingleton().get(iDataID);
if (!pDataObject || !pDataObject->isInitialized()) {
mexErrMsgTxt("Data object not found or not initialized properly.\n");
return;
}
// step3: insert data
// fill with scalar value
if (mexIsScalar(prhs[2])) {
float32 fValue = (float32)mxGetScalar(prhs[2]);
for (int i = 0; i < pDataObject->getSize(); ++i) {
pDataObject->getData()[i] = fValue;
}
} else {
// Check Data dimensions
if (pDataObject->getWidth() != mxGetN(prhs[2]) || pDataObject->getHeight() != mxGetM(prhs[2])) {
mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n");
return;
}
const mwSize* dims = mxGetDimensions(prhs[2]);
// logical data
if (mxIsLogical(prhs[2])) {
mxLogical* pbMatlabData = mxGetLogicals(prhs[2]);
int i = 0;
int col, row;
for (col = 0; col < dims[1]; ++col) {
for (row = 0; row < dims[0]; ++row) {
pDataObject->getData2D()[row][col] = (float32)pbMatlabData[i];
++i;
}
}
// double data
} else if (mxIsDouble(prhs[2])) {
double* pdMatlabData = mxGetPr(prhs[2]);
int i = 0;
int col, row;
for (col = 0; col < dims[1]; ++col) {
for (row = 0; row < dims[0]; ++row) {
pDataObject->getData2D()[row][col] = pdMatlabData[i];
++i;
}
}
// single data
} else if (mxIsSingle(prhs[2])) {
const float* pfMatlabData = (const float *)mxGetData(prhs[2]);
int i = 0;
int col, row;
for (col = 0; col < dims[1]; ++col) {
for (row = 0; row < dims[0]; ++row) {
pDataObject->getData2D()[row][col] = pfMatlabData[i];
++i;
}
}
} else {
ASTRA_ASSERT(false);
}
}
}
//-----------------------------------------------------------------------------------------
/** geom = astra_mex_data2d('get_geometry', id);
*
* Fetch the geometry of a 2d data object stored in the astra-library.
* id: identifier of the 2d data object as stored in the astra-library.
* geom: MATLAB-struct containing information about the used geometry.
*/
void astra_mex_data2d_get_geometry(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
{
// parse input
if (nrhs < 2) {
mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n");
return;
}
if (!mxIsDouble(prhs[1])) {
mexErrMsgTxt("Identifier should be a scalar value. \n");
return;
}
int iDataID = (int)(mxGetScalar(prhs[1]));
// fetch data object
CFloat32Data2D* pDataObject = astra::CData2DManager::getSingleton().get(iDataID);
if (!pDataObject || !pDataObject->isInitialized()) {
mexErrMsgTxt("Data object not found or not initialized properly.\n");
return;
}
// create output
if (1 <= nlhs) {
if (pDataObject->getType() == CFloat32Data2D::PROJECTION) {
CFloat32ProjectionData2D* pDataObject2 = dynamic_cast<CFloat32ProjectionData2D*>(pDataObject);
plhs[0] = configToStruct(pDataObject2->getGeometry()->getConfiguration());
}
else if (pDataObject->getType() == CFloat32Data2D::VOLUME) {
CFloat32VolumeData2D* pDataObject2 = dynamic_cast<CFloat32VolumeData2D*>(pDataObject);
plhs[0] = configToStruct(pDataObject2->getGeometry()->getConfiguration());
}
}
}
//-----------------------------------------------------------------------------------------
/** astra_mex_data2d('change_geometry', id, geom);
*
* Change the associated geometry of a 2d data object (volume or sinogram)
* id: identifier of the 2d data object as stored in the astra-library.
* geom: the new geometry struct, as created by astra_create_vol/proj_geom
*/
void astra_mex_data2d_change_geometry(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
{
// step1: check input
if (nrhs < 3) {
mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n");
return;
}
if (!mxIsDouble(prhs[1])) {
mexErrMsgTxt("Identifier should be a scalar value. \n");
return;
}
// step2: get data object
int iDataID = (int)(mxGetScalar(prhs[1]));
CFloat32Data2D* pDataObject = astra::CData2DManager::getSingleton().get(iDataID);
if (!pDataObject || !pDataObject->isInitialized()) {
mexErrMsgTxt("Data object not found or not initialized properly.\n");
return;
}
CFloat32ProjectionData2D* pSinogram = dynamic_cast<CFloat32ProjectionData2D*>(pDataObject);
if (pSinogram) {
// Projection data
// Read geometry
if (!mxIsStruct(prhs[2])) {
mexErrMsgTxt("Argument 3 is not a valid MATLAB struct.\n");
}
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");
CProjectionGeometry2D* pGeometry;
if (type == "sparse_matrix") {
pGeometry = new CSparseMatrixProjectionGeometry2D();
} else if (type == "fanflat") {
//CFanFlatProjectionGeometry2D* pFanFlatProjectionGeometry = new CFanFlatProjectionGeometry2D();
//pFanFlatProjectionGeometry->initialize(Config(node));
//m_pProjectionGeometry = pFanFlatProjectionGeometry;
pGeometry = new CFanFlatProjectionGeometry2D();
} else if (type == "fanflat_vec") {
pGeometry = new CFanFlatVecProjectionGeometry2D();
} else if (type == "parallel_vec") {
pGeometry = new CParallelVecProjectionGeometry2D();
} else {
pGeometry = new CParallelProjectionGeometry2D();
}
if (!pGeometry->initialize(*cfg)) {
mexErrMsgTxt("Geometry class not initialized. \n");
delete pGeometry;
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 cfg;
return;
}
// If ok, change geometry
pSinogram->changeGeometry(pGeometry);
delete pGeometry;
delete cfg;
return;
}
CFloat32VolumeData2D* pVolume = dynamic_cast<CFloat32VolumeData2D*>(pDataObject);
if (pVolume) {
// Volume data
// Read geometry
if (!mxIsStruct(prhs[2])) {
mexErrMsgTxt("Argument 3 is not a valid MATLAB struct.\n");
}
Config* cfg = structToConfig("VolumeGeometry2D", prhs[2]);
CVolumeGeometry2D* pGeometry = new CVolumeGeometry2D();
if (!pGeometry->initialize(*cfg)) {
mexErrMsgTxt("Geometry class not initialized. \n");
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 cfg;
delete pGeometry;
return;
}
// If ok, change geometry
pVolume->changeGeometry(pGeometry);
delete cfg;
delete pGeometry;
}
mexErrMsgTxt("Data object not found or not initialized properly.\n");
return;
}
//-----------------------------------------------------------------------------------------
/** data = astra_mex_data2d('get', id);
*
* Fetch data from the astra-library to a MATLAB matrix.
* id: identifier of the 2d data object as stored in the astra-library.
* data: MATLAB data
*/
void astra_mex_data2d_get(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
{
// step1: check input
if (nrhs < 2) {
mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n");
return;
}
if (!mxIsDouble(prhs[1])) {
mexErrMsgTxt("Identifier should be a scalar value. \n");
return;
}
// step2: get data object
int iDataID = (int)(mxGetScalar(prhs[1]));
CFloat32Data2D* pDataObject = astra::CData2DManager::getSingleton().get(iDataID);
if (!pDataObject || !pDataObject->isInitialized()) {
mexErrMsgTxt("Data object not found or not initialized properly.\n");
return;
}
// create output
if (1 <= nlhs) {
plhs[0] = mxCreateDoubleMatrix(pDataObject->getHeight(), // # rows
pDataObject->getWidth(), // # cols
mxREAL); // datatype 64-bits
double* out = mxGetPr(plhs[0]);
int i = 0;
int row, col;
for (col = 0; col < pDataObject->getWidth(); ++col) {
for (row = 0; row < pDataObject->getHeight(); ++row) {
out[i] = pDataObject->getData2D()[row][col];
++i;
}
}
}
}
//-----------------------------------------------------------------------------------------
/** data = astra_mex_data2d('get_single', id);
*
* Fetch data from the astra-library to a MATLAB matrix.
* id: identifier of the 2d data object as stored in the astra-library.
* data: MATLAB data
*/
void astra_mex_data2d_get_single(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
{
// step1: check input
if (nrhs < 2) {
mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n");
return;
}
if (!mxIsDouble(prhs[1])) {
mexErrMsgTxt("Identifier should be a scalar value. \n");
return;
}
// step2: get data object
int iDataID = (int)(mxGetScalar(prhs[1]));
CFloat32Data2D* pDataObject = astra::CData2DManager::getSingleton().get(iDataID);
if (!pDataObject || !pDataObject->isInitialized()) {
mexErrMsgTxt("Data object not found or not initialized properly.\n");
return;
}
// create output
if (1 <= nlhs) {
mwSize dims[2];
dims[0] = pDataObject->getHeight();
dims[1] = pDataObject->getWidth();
plhs[0] = mxCreateNumericArray(2, dims, mxSINGLE_CLASS, mxREAL);
float* out = (float *)mxGetData(plhs[0]);
int i = 0;
int row, col;
for (col = 0; col < pDataObject->getWidth(); ++col) {
for (row = 0; row < pDataObject->getHeight(); ++row) {
out[i] = pDataObject->getData2D()[row][col];
++i;
}
}
}
}
//-----------------------------------------------------------------------------------------
/** astra_mex_data2d('info');
*
* Print information about all the 2d data objects currently stored in the astra-library.
*/
void astra_mex_data2d_info(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
{
mexPrintf("%s", astra::CData2DManager::getSingleton().info().c_str());
}
//-----------------------------------------------------------------------------------------
static void printHelp()
{
mexPrintf("Please specify a mode of operation.\n");
mexPrintf("Valid modes: get, get_single, delete, clear, set/store, create, get_geometry, change_geometry, info\n");
}
//-----------------------------------------------------------------------------------------
/**
* ... = astra_mex_data2d(type,...);
*/
void mexFunction(int nlhs, mxArray* plhs[],
int nrhs, const mxArray* prhs[])
{
// INPUT0: Mode
string sMode = "";
if (1 <= nrhs) {
sMode = mexToString(prhs[0]);
} else {
printHelp();
return;
}
initASTRAMex();
// SWITCH (MODE)
if (sMode == std::string("get")) {
astra_mex_data2d_get(nlhs, plhs, nrhs, prhs);
} else if (sMode == std::string("get_single")) {
astra_mex_data2d_get_single(nlhs, plhs, nrhs, prhs);
} else if (sMode == std::string("delete")) {
astra_mex_data2d_delete(nlhs, plhs, nrhs, prhs);
} else if (sMode == "clear") {
astra_mex_data2d_clear(nlhs, plhs, nrhs, prhs);
} else if (sMode == std::string("store") ||
sMode == std::string("set")) {
astra_mex_data2d_store(nlhs, plhs, nrhs, prhs);
} else if (sMode == std::string("create")) {
astra_mex_data2d_create(nlhs, plhs, nrhs, prhs);
} else if (sMode == std::string("get_geometry")) {
astra_mex_data2d_get_geometry(nlhs, plhs, nrhs, prhs);
} else if (sMode == std::string("change_geometry")) {
astra_mex_data2d_change_geometry(nlhs, plhs, nrhs, prhs);
} else if (sMode == std::string("info")) {
astra_mex_data2d_info(nlhs, plhs, nrhs, prhs);
} else {
printHelp();
}
return;
}
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