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-rw-r--r--matlab/mex/astra_mex_data3d_c.cpp231
1 files changed, 230 insertions, 1 deletions
diff --git a/matlab/mex/astra_mex_data3d_c.cpp b/matlab/mex/astra_mex_data3d_c.cpp
index 1af8844..dfb3003 100644
--- a/matlab/mex/astra_mex_data3d_c.cpp
+++ b/matlab/mex/astra_mex_data3d_c.cpp
@@ -53,7 +53,7 @@ $Id$
using namespace std;
using namespace astra;
-
+#define USE_MATLAB_UNDOCUMENTED
//-----------------------------------------------------------------------------------------
/**
@@ -261,6 +261,231 @@ void astra_mex_data3d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra
}
//-----------------------------------------------------------------------------------------
+
+/** id = astra_mex_data3d('link', datatype, geometry, data);
+ *
+ * Create a new data 3d object in the astra-library.
+ * type:
+ * geom: MATLAB struct with the geometry for the data
+ * data: A MATLAB matrix containing the data.
+ * This matrix will be edited _in-place_!
+ * id: identifier of the 3d data object as it is now stored in the astra-library.
+ */
+
+#ifdef USE_MATLAB_UNDOCUMENTED
+extern "C" {
+mxArray *mxCreateSharedDataCopy(const mxArray *pr);
+bool mxUnshareArray(const mxArray *pr, const bool noDeepCopy);
+mxArray *mxUnreference(const mxArray *pr);
+}
+
+class CFloat32CustomMemoryMatlab3D : public 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) {
+ //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) {
+ 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;
+};
+
+void astra_mex_data3d_link(int& nlhs, mxArray* plhs[], int& nrhs, const mxArray* prhs[])
+{
+ // TODO: Reduce code duplication with _create!
+ // TODO: Also allow empty argument to let this function create its own mxArray
+ // step1: get datatype
+ if (nrhs < 4) {
+ mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n");
+ return;
+ }
+
+ if (!mxIsStruct(prhs[2])) {
+ mexErrMsgTxt("Argument 3 is not a valid MATLAB struct.\n");
+ }
+
+ const mxArray* _pArray = prhs[3];
+
+ string sDataType = mex_util_get_string(prhs[1]);
+ CFloat32Data3DMemory* pDataObject3D = NULL;
+
+ if (mex_is_scalar(_pArray) || !mxIsSingle(_pArray)) {
+ mexErrMsgTxt("Data must be a single array.");
+ return;
+ }
+
+ unsigned int iZ = 0;
+ bool bUnshare = true;
+ if (nrhs > 4) {
+ if (!mex_is_scalar(prhs[4])) {
+ mexErrMsgTxt("Argument 5 (read-only) must be scalar");
+ return;
+ }
+ // unshare the array if we're not linking read-only
+ bUnshare = !(bool)mxGetScalar(prhs[4]);
+ }
+ if (nrhs > 5) {
+ if (!mex_is_scalar(prhs[5])) {
+ mexErrMsgTxt("Argument 6 (Z) must be scalar");
+ return;
+ }
+ iZ = (unsigned int)mxGetScalar(prhs[5]);
+ }
+
+ mwSize dims[3];
+
+ // SWITCH DataType
+ if (sDataType == "-vol") {
+ // Read geometry
+ Config cfg;
+ XMLDocument* xml = struct2XML("VolumeGeometry", prhs[2]);
+ if (!xml)
+ return;
+ cfg.self = xml->getRootNode();
+ CVolumeGeometry3D* pGeometry = new CVolumeGeometry3D();
+ if (!pGeometry->initialize(cfg)) {
+ mexErrMsgTxt("Geometry class not initialized. \n");
+ delete pGeometry;
+ delete xml;
+ return;
+ }
+ delete xml;
+
+ // If data is specified, check dimensions
+ if (nrhs >= 4) {
+ get3DMatrixDims(prhs[3], dims);
+ bool ok = pGeometry->getGridColCount() == dims[0] && pGeometry->getGridRowCount() == dims[1];
+ if (nrhs == 4) {
+ ok &= pGeometry->getGridSliceCount() == dims[2];
+ } else if (nrhs > 4) {
+ // sub-volume in Z direction
+ ok &= iZ + pGeometry->getGridSliceCount() <= dims[2];
+ }
+ if (!ok) {
+ mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n");
+ delete pGeometry;
+ return;
+ }
+ }
+
+ size_t iOffset = iZ;
+ iOffset *= dims[0];
+ iOffset *= dims[1];
+ CFloat32CustomMemoryMatlab3D* pHandle = new CFloat32CustomMemoryMatlab3D(_pArray, bUnshare, iOffset);
+
+ // Initialize data object
+ pDataObject3D = new CFloat32VolumeData3DMemory(pGeometry, pHandle);
+
+ //delete pGeometry; // ??
+ }
+ else if (sDataType == "-sino" || sDataType == "-proj3d" || sDataType == "-sinocone") {
+
+ // 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();
+
+ // FIXME: Change how the base class is created. (This is duplicated
+ // in Projector2D.cpp.)
+ std::string type = cfg.self->getAttribute("type");
+ CProjectionGeometry3D* pGeometry = 0;
+ if (type == "parallel3d") {
+ pGeometry = new CParallelProjectionGeometry3D();
+ } else if (type == "parallel3d_vec") {
+ pGeometry = new CParallelVecProjectionGeometry3D();
+ } else if (type == "cone") {
+ pGeometry = new CConeProjectionGeometry3D();
+ } else if (type == "cone_vec") {
+ pGeometry = new CConeVecProjectionGeometry3D();
+ } else {
+ mexErrMsgTxt("Invalid geometry type.\n");
+ return;
+ }
+
+ if (!pGeometry->initialize(cfg)) {
+ mexErrMsgTxt("Geometry class not initialized. \n");
+ delete pGeometry;
+ delete xml;
+ return;
+ }
+ delete xml;
+
+ // If data is specified, check dimensions
+ if (nrhs >= 4) {
+ get3DMatrixDims(prhs[3], dims);
+ bool ok = pGeometry->getDetectorColCount() == dims[0] && pGeometry->getProjectionCount() == dims[1];
+ if (nrhs == 4) {
+ ok &= pGeometry->getDetectorRowCount() == dims[2];
+ } else if (nrhs > 4) {
+ // sub-volume in Z direction
+ ok &= iZ + pGeometry->getDetectorRowCount() <= dims[2];
+ }
+ if (!ok) {
+ mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n");
+ delete pGeometry;
+ return;
+ }
+ }
+
+ size_t iOffset = iZ;
+ iOffset *= dims[0];
+ iOffset *= dims[1];
+ CFloat32CustomMemoryMatlab3D* pHandle = new CFloat32CustomMemoryMatlab3D(_pArray, bUnshare, iOffset);
+
+ // Initialize data object
+ pDataObject3D = new CFloat32ProjectionData3DMemory(pGeometry, pHandle);
+ }
+ else {
+ mexErrMsgTxt("Invalid datatype. Please specify '-vol' or '-proj3d'. \n");
+ return;
+ }
+
+ // Check initialization
+ if (!pDataObject3D->isInitialized()) {
+ mexErrMsgTxt("Couldn't initialize data object.\n");
+ delete pDataObject3D;
+ return;
+ }
+
+ //pDataObject3D->updateStatistics();
+
+ // step4: store data object
+ int iIndex = CData3DManager::getSingleton().store(pDataObject3D);
+
+ // step5: return data id
+ if (1 <= nlhs) {
+ plhs[0] = mxCreateDoubleScalar(iIndex);
+ }
+
+}
+
+
+#endif
+
+
+//-----------------------------------------------------------------------------------------
/**
* [id] = astra_mex_io_data('create_cache', config);
*/
@@ -989,6 +1214,10 @@ void mexFunction(int nlhs, mxArray* plhs[],
// 3D data
if (sMode == std::string("create")) {
astra_mex_data3d_create(nlhs, plhs, nrhs, prhs);
+#ifdef USE_MATLAB_UNDOCUMENTED
+ } else if (sMode == "link") {
+ astra_mex_data3d_link(nlhs, plhs, nrhs, prhs);
+#endif
} else if (sMode == std::string("create_cache")) {
astra_mex_data3d_create_cache(nlhs, plhs, nrhs, prhs);
} else if (sMode == std::string("get")) {
generated by cgit v1.2.3 (git 2.25.1) at 2024-09-20 13:22:08 +0000