diff options
87 files changed, 1389 insertions, 934 deletions
@@ -64,9 +64,14 @@ Install by copying AstraCuda32.dll or AstraCuda64.dll from bin/ and ## References -If you use parallel beam GPU code for your research, we would appreciate it if you would refer to the following paper: +If you use the ASTRA Toolbox for your research, we would appreciate it if you would refer to the following paper: + +W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K J. Batenburg, and J. Sijbers, "The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography", Ultramicroscopy (2015), http://dx.doi.org/10.1016/j.ultramic.2015.05.002 + +Additionally, if you use parallel beam GPU code, we would appreciate it if you would refer to the following paper: + +W. J. Palenstijn, K J. Batenburg, and J. Sijbers, "Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)", Journal of Structural Biology, vol. 176, issue 2, pp. 250-253, 2011, http://dx.doi.org/10.1016/j.jsb.2011.07.017 -W. J. Palenstijn, K J. Batenburg, and J. Sijbers, "Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)", Journal of Structural Biology, vol. 176, issue 2, pp. 250-253, 2011. ## License @@ -79,4 +84,4 @@ website: http://sf.net/projects/astra-toolbox Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp 2014-2015, CWI, Amsterdam - http://visielab.uantwerpen.be/ and http://www.cwi.nl/
\ No newline at end of file + http://visielab.uantwerpen.be/ and http://www.cwi.nl/ @@ -90,11 +90,14 @@ Install by copying AstraCuda32.dll or AstraCuda64.dll from bin/ and References: ------------ -If you use parallel beam GPU code for your research, we would appreciate it if -you would refer to the following paper: +If you use the ASTRA Toolbox for your research, we would appreciate it if you would refer to the following paper: + +W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K J. Batenburg, and J. Sijbers, "The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography", Ultramicroscopy (2015), http://dx.doi.org/10.1016/j.ultramic.2015.05.002 + +Additionally, if you use parallel beam GPU code, we would appreciate it if you would refer to the following paper: W. J. Palenstijn, K J. Batenburg, and J. Sijbers, "Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)", Journal of Structural Biology, vol. 176, issue 2, pp. 250-253, -2011 +2011, http://dx.doi.org/10.1016/j.jsb.2011.07.017 diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 0dfa15a..2d862f2 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -28,7 +28,7 @@ CXXFLAGS=@SAVED_CXXFLAGS@ LDFLAGS=@SAVED_LDFLAGS@ LIBS=@SAVED_LIBS@ -CPPFLAGS+=-I../.. -I../../include -I../../lib/include/rapidxml +CPPFLAGS+=-I../.. -I../../include -I../../lib/include CXXFLAGS+=-g -O3 -Wall -Wshadow LIBS+=-lpthread LDFLAGS+=-g diff --git a/build/linux/configure.ac b/build/linux/configure.ac index d9e1f1a..58a3f4c 100644 --- a/build/linux/configure.ac +++ b/build/linux/configure.ac @@ -190,7 +190,7 @@ if test x"$with_python" != x -a x"$with_python" != xno; then AC_MSG_CHECKING(for python) ASTRA_RUN_LOGOUTPUT(echo 'import sys' | $PYTHON -) if test $? -ne 0; then - AC_MSG_ERROR(Python binary not found)] + AC_MSG_ERROR(Python binary not found) fi AC_MSG_RESULT([$PYTHON]) HAVEPYTHON=yes diff --git a/cuda/2d/darthelper.cu b/cuda/2d/darthelper.cu index 28ca557..1d10d49 100644 --- a/cuda/2d/darthelper.cu +++ b/cuda/2d/darthelper.cu @@ -57,7 +57,7 @@ void roiSelect(float* out, float radius, unsigned int width, unsigned int height // We abuse dims here... SDimensions dims; dims.iVolWidth = width; - dims.iVolHeight = width; + dims.iVolHeight = height; allocateVolumeData(D_data, pitch, dims); copyVolumeToDevice(out, width, dims, D_data, pitch); @@ -245,7 +245,7 @@ void dartMask(float* mask, const float* segmentation, unsigned int conn, unsigne // We abuse dims here... SDimensions dims; dims.iVolWidth = width; - dims.iVolHeight = width; + dims.iVolHeight = height; allocateVolumeData(D_segmentationData, pitch, dims); copyVolumeToDevice(segmentation, width, dims, D_segmentationData, pitch); @@ -278,7 +278,7 @@ __global__ void devDartSmoothingRadius(float* out, const float* in, float b, uns unsigned int x = threadIdx.x + 16*blockIdx.x; unsigned int y = threadIdx.y + 16*blockIdx.y; - // Sacrifice the border pixels to simplify the implementation. + // Sacrifice the border pixels to simplify the implementation. if (x > radius-1 && x < width - radius && y > radius-1 && y < height - radius) { float* d = (float*)in; @@ -286,9 +286,10 @@ __global__ void devDartSmoothingRadius(float* out, const float* in, float b, uns unsigned int o2 = y*pitch+x; int r = radius; + float count = 4*r*(r+1); float res = -d[o2]; - for (int row = -r; row < r; row++) + for (int row = -r; row <= r; row++) { unsigned int o1 = (y+row)*pitch+x; for (int col = -r; col <= r; col++) @@ -297,7 +298,7 @@ __global__ void devDartSmoothingRadius(float* out, const float* in, float b, uns } } - res *= b / 4*r*(r+1); + res *= b / count; res += (1.0f-b) * d[o2]; m[o2] = res; @@ -333,7 +334,7 @@ void dartSmoothing(float* out, const float* in, float b, unsigned int radius, un // We abuse dims here... SDimensions dims; dims.iVolWidth = width; - dims.iVolHeight = width; + dims.iVolHeight = height; allocateVolumeData(D_inData, pitch, dims); copyVolumeToDevice(in, width, dims, D_inData, pitch); diff --git a/cuda/2d/par_fp.cu b/cuda/2d/par_fp.cu index d0ca7ff..bb8b909 100644 --- a/cuda/2d/par_fp.cu +++ b/cuda/2d/par_fp.cu @@ -487,7 +487,7 @@ bool FP_simple_internal(float* D_volumeData, unsigned int volumePitch, unsigned int blockEnd = 0; bool blockVertical = false; for (unsigned int a = 0; a <= dims.iProjAngles; ++a) { - bool vertical; + bool vertical = false; // TODO: Having <= instead of < below causes a 5% speedup. // Maybe we should detect corner cases and put them in the optimal // group of angles. diff --git a/cuda/3d/cone_fp.cu b/cuda/3d/cone_fp.cu index bda71ba..b36d2bc 100644 --- a/cuda/3d/cone_fp.cu +++ b/cuda/3d/cone_fp.cu @@ -340,7 +340,7 @@ bool ConeFP_Array_internal(cudaPitchedPtr D_projData, // tic(t); for (unsigned int a = 0; a <= angleCount; ++a) { - int dir; + int dir = -1; if (a != angleCount) { float dX = fabsf(angles[a].fSrcX - (angles[a].fDetSX + dims.iProjU*angles[a].fDetUX*0.5f + dims.iProjV*angles[a].fDetVX*0.5f)); float dY = fabsf(angles[a].fSrcY - (angles[a].fDetSY + dims.iProjU*angles[a].fDetUY*0.5f + dims.iProjV*angles[a].fDetVY*0.5f)); diff --git a/cuda/3d/par3d_fp.cu b/cuda/3d/par3d_fp.cu index 8d44540..b14c494 100644 --- a/cuda/3d/par3d_fp.cu +++ b/cuda/3d/par3d_fp.cu @@ -440,7 +440,7 @@ bool Par3DFP_Array_internal(cudaPitchedPtr D_projData, // tic(t); for (unsigned int a = 0; a <= angleCount; ++a) { - int dir; + int dir = -1; if (a != dims.iProjAngles) { float dX = fabsf(angles[a].fRayX); float dY = fabsf(angles[a].fRayY); diff --git a/include/astra/AstraObjectFactory.h b/include/astra/AstraObjectFactory.h index ba4ec11..1ed4955 100644 --- a/include/astra/AstraObjectFactory.h +++ b/include/astra/AstraObjectFactory.h @@ -110,7 +110,7 @@ template <typename T, typename TypeList> T* CAstraObjectFactory<T, TypeList>::create(const Config& _cfg) { functor_find<T> finder = functor_find<T>(); - finder.tofind = _cfg.self->getAttribute("type"); + finder.tofind = _cfg.self.getAttribute("type"); CreateObject<TypeList>::find(finder); if (finder.res == NULL) return NULL; if (finder.res->initialize(_cfg)) diff --git a/include/astra/Config.h b/include/astra/Config.h index 9893c90..c10a16e 100644 --- a/include/astra/Config.h +++ b/include/astra/Config.h @@ -44,13 +44,14 @@ namespace astra { struct _AstraExport Config { Config(); - Config(XMLNode* _self); + Config(XMLNode _self); ~Config(); void initialize(std::string rootname); - XMLNode* self; - XMLNode* global; + XMLNode self; + + XMLDocument *_doc; }; struct ConfigCheckData { diff --git a/include/astra/Float32ProjectionData2D.h b/include/astra/Float32ProjectionData2D.h index 7461491..bb99f4b 100644 --- a/include/astra/Float32ProjectionData2D.h +++ b/include/astra/Float32ProjectionData2D.h @@ -101,6 +101,19 @@ public: * Copy constructor */ CFloat32ProjectionData2D(const CFloat32ProjectionData2D& _other); + + /** Constructor. Create an instance of the CFloat32ProjectionData2D class with pre-allocated memory. + * + * Creates an instance of the CFloat32ProjectionData2D class. Memory + * is pre-allocated and passed via the abstract CFloat32CustomMemory handle + * class. The handle will be deleted when the memory can be freed. + * You should override the destructor to provide custom behaviour on free. + * + * @param _pGeometry Projection Geometry object. This object will be HARDCOPIED into this class. + * @param _pCustomMemory custom memory handle + * + */ + CFloat32ProjectionData2D(CProjectionGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory); /** * Assignment operator @@ -148,6 +161,18 @@ public: * @param _fScalar scalar value to be put at each index. */ bool initialize(CProjectionGeometry2D* _pGeometry, float32 _fScalar); + + /** Initialization. Initializes an instance of the CFloat32ProjectionData2D class with pre-allocated memory. + * + * Memory is pre-allocated and passed via the abstract CFloat32CustomMemory handle + * class. The handle will be deleted when the memory can be freed. + * You should override the destructor to provide custom behaviour on free. + * + * @param _pGeometry Projection Geometry object. This object will be HARDCOPIED into this class. + * @param _pCustomMemory custom memory handle + * + */ + bool initialize(CProjectionGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory); /** Get the number of detectors. * diff --git a/include/astra/Float32ProjectionData3D.h b/include/astra/Float32ProjectionData3D.h index 79b762e..329c9a4 100644 --- a/include/astra/Float32ProjectionData3D.h +++ b/include/astra/Float32ProjectionData3D.h @@ -196,6 +196,11 @@ public: * @return pointer to projection geometry. */ virtual CProjectionGeometry3D* getGeometry() const; + + /** Change the projection geometry. + * Note that this can't change the dimensions of the data. + */ + virtual void changeGeometry(CProjectionGeometry3D* pGeometry); }; diff --git a/include/astra/Float32VolumeData2D.h b/include/astra/Float32VolumeData2D.h index 4f44a8c..abecebf 100644 --- a/include/astra/Float32VolumeData2D.h +++ b/include/astra/Float32VolumeData2D.h @@ -92,6 +92,19 @@ public: * Copy constructor */ CFloat32VolumeData2D(const CFloat32VolumeData2D& _other); + + /** Constructor. Create an instance of the CFloat32VolumeData2D class with pre-allocated memory. + * + * Creates an instance of the CFloat32VolumeData2D class. Memory + * is pre-allocated and passed via the abstract CFloat32CustomMemory handle + * class. The handle will be deleted when the memory can be freed. + * You should override the destructor to provide custom behaviour on free. + * + * @param _pGeometry Volume Geometry object. This object will be HARDCOPIED into this class. + * @param _pCustomMemory custom memory handle + * + */ + CFloat32VolumeData2D(CVolumeGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory); /** * Assignment operator @@ -132,6 +145,18 @@ public: * @param _fScalar scalar value to be put at each index. */ bool initialize(CVolumeGeometry2D* _pGeometry, float32 _fScalar); + + /** Initialization. Initializes an instance of the CFloat32VolumeData2D class with pre-allocated memory. + * + * Memory is pre-allocated and passed via the abstract CFloat32CustomMemory handle + * class. The handle will be deleted when the memory can be freed. + * You should override the destructor to provide custom behaviour on free. + * + * @param _pGeometry Volume Geometry object. This object will be HARDCOPIED into this class. + * @param _pCustomMemory custom memory handle + * + */ + bool initialize(CVolumeGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory); /** Destructor. */ diff --git a/include/astra/Float32VolumeData3D.h b/include/astra/Float32VolumeData3D.h index d8f0ae9..07df78f 100644 --- a/include/astra/Float32VolumeData3D.h +++ b/include/astra/Float32VolumeData3D.h @@ -214,6 +214,11 @@ public: * @return The geometry describing the data stored in this volume */ virtual CVolumeGeometry3D* getGeometry() const; + + /** Change the projection geometry. + * Note that this can't change the dimensions of the data. + */ + virtual void changeGeometry(CVolumeGeometry3D* pGeometry); }; //---------------------------------------------------------------------------------------- diff --git a/include/astra/XMLDocument.h b/include/astra/XMLDocument.h index 869e1a3..eddd908 100644 --- a/include/astra/XMLDocument.h +++ b/include/astra/XMLDocument.h @@ -78,7 +78,7 @@ public: * * @return first XML node of the document */ - XMLNode* getRootNode(); + XMLNode getRootNode(); /** Save an XML DOM tree to an XML file * diff --git a/include/astra/XMLNode.h b/include/astra/XMLNode.h index eceffe1..4d29d5c 100644 --- a/include/astra/XMLNode.h +++ b/include/astra/XMLNode.h @@ -64,71 +64,68 @@ public: /** Deconstructor */ ~XMLNode(); - + + /** Check validity + */ + operator bool() const { return fDOMElement != 0; } /** Get a single child XML node. If there are more, the first one is returned * * @param _sName tagname of the requested child node * @return first child node with the correct tagname, null pointer if it doesn't exist */ - XMLNode* getSingleNode(string _sName); + XMLNode getSingleNode(string _sName) const; /** Get all child XML nodes that have the tagname name * * @param _sName tagname of the requested child nodes * @return list with all child nodes with the correct tagname */ - std::list<XMLNode*> getNodes(string _sName); + std::list<XMLNode> getNodes(string _sName) const; /** Get all child XML nodes * * @return list with all child nodes */ - std::list<XMLNode*> getNodes(); + std::list<XMLNode> getNodes() const; /** Get the name of this node * * @return name of node */ - std::string getName(); + std::string getName() const; /** Get the content of the XML node as a single string. * * @return node content */ - string getContent(); + string getContent() const; /** Get the content of the XML node as a numerical. * * @return node content */ - float32 getContentNumerical(); + float32 getContentNumerical() const; /** Get the content of the XML node as a boolean. * * @return node content */ - bool getContentBool(); + bool getContentBool() const; /** Get the content of the XML node as a vector of strings. * * @return node content */ - vector<string> getContentArray(); - - /** Get the content of the XML node as a c-array of float32 data. - * - * @param _pfData data array, shouldn't be initialized already. - * @param _iSize number of elements stored in _pfData - */ - void getContentNumericalArray(float32*& _pfData, int& _iSize); + vector<string> getContentArray() const; /** Get the content of the XML node as a stl container of float32 data. + * NB: A 2D matrix is returned as a linear list * * @return node content */ - vector<float32> getContentNumericalArray(); - vector<double> getContentNumericalArrayDouble(); + vector<float32> getContentNumericalArray() const; + vector<double> getContentNumericalArrayDouble() const; @@ -137,7 +134,7 @@ public: * @param _sName of the attribute. * @return attribute value, empty string if it doesn't exist. */ - bool hasAttribute(string _sName); + bool hasAttribute(string _sName) const; /** Get the value of an attribute. * @@ -145,7 +142,7 @@ public: * @param _sDefaultValue value to return if the attribute isn't found * @return attribute value, _sDefaultValue if it doesn't exist. */ - string getAttribute(string _sName, string _sDefaultValue = ""); + string getAttribute(string _sName, string _sDefaultValue = "") const; /** Get the value of a numerical attribute. * @@ -153,8 +150,8 @@ public: * @param _fDefaultValue value to return if the attribute isn't found * @return attribute value, _fDefaultValue if it doesn't exist. */ - float32 getAttributeNumerical(string _sName, float32 _fDefaultValue = 0); - double getAttributeNumericalDouble(string _sName, double _fDefaultValue = 0); + float32 getAttributeNumerical(string _sName, float32 _fDefaultValue = 0) const; + double getAttributeNumericalDouble(string _sName, double _fDefaultValue = 0) const; /** Get the value of a boolean attribute. * @@ -162,7 +159,7 @@ public: * @param _bDefaultValue value to return if the attribute isn't found * @return attribute value, _bDefaultValue if it doesn't exist. */ - bool getAttributeBool(string _sName, bool _bDefaultValue = false); + bool getAttributeBool(string _sName, bool _bDefaultValue = false) const; @@ -172,7 +169,7 @@ public: * @param _sKey option key * @return true if option does exist */ - bool hasOption(string _sKey); + bool hasOption(string _sKey) const; /** Get the value of an option within this XML Node * @@ -180,7 +177,7 @@ public: * @param _sDefaultValue value to return if key isn't found * @return option value, _sDefaultValue if the option doesn't exist */ - string getOption(string _sKey, string _sDefaultValue = ""); + string getOption(string _sKey, string _sDefaultValue = "") const; /** Get the value of an option within this XML Node * @@ -188,7 +185,7 @@ public: * @param _fDefaultValue value to return if key isn't found * @return option value, _fDefaultValue if the option doesn't exist */ - float32 getOptionNumerical(string _sKey, float32 _fDefaultValue = 0); + float32 getOptionNumerical(string _sKey, float32 _fDefaultValue = 0) const; /** Get the value of an option within this XML Node * @@ -196,14 +193,14 @@ public: * @param _bDefaultValue value to return if key isn't found * @return option value, _bDefaultValue if the option doesn't exist */ - bool getOptionBool(string _sKey, bool _bDefaultValue = false); + bool getOptionBool(string _sKey, bool _bDefaultValue = false) const; /** Get the value of an option within this XML Node * * @param _sKey option key * @return numerical array */ - vector<float32> getOptionNumericalArray(string _sKey); + vector<float32> getOptionNumericalArray(string _sKey) const; @@ -214,7 +211,7 @@ public: * @param _sNodeName the name of the new childnode * @return new child node */ - XMLNode* addChildNode(string _sNodeName); + XMLNode addChildNode(string _sNodeName); /** Create a new XML node as a child to this one, also add some content: * <...><_sNodeName>_sValue</_sNodeName></...> @@ -223,7 +220,7 @@ public: * @param _sValue some node content * @return new child node */ - XMLNode* addChildNode(string _sNodeName, string _sValue); + XMLNode addChildNode(string _sNodeName, string _sValue); /** Create a new XML node as a child to this one, also add some numerical content: * <...><_sNodeName>_sValue</_sNodeName></...> @@ -232,7 +229,7 @@ public: * @param _fValue some node content * @return new child node */ - XMLNode* addChildNode(string _sNodeName, float32 _fValue); + XMLNode addChildNode(string _sNodeName, float32 _fValue); /** Create a new XML node as a child to this one, also add a list of numerical content: * <...><_sNodeName>_sValue</_sNodeName></...> @@ -242,7 +239,7 @@ public: * @param _iSize number of elements in _pfList * @return new child node */ - XMLNode* addChildNode(string _sNodeName, float32* _pfList, int _iSize); + XMLNode addChildNode(string _sNodeName, float32* _pfList, int _iSize); /** Add some text to the node: <...>_sText</...> * @@ -256,13 +253,38 @@ public: */ void setContent(float32 _fValue); - /** Add a list of numerical data to the node: <...>_sText</...> + /** Add a list of numerical data to the node * * @param _pfList data * @param _iSize number of elements in the list */ void setContent(float32* _pfList, int _iSize); + /** Add a list of numerical data to the node + * + * @param _pfList data + * @param _iSize number of elements in the list + */ + void setContent(double* _pfList, int _iSize); + + /** Add a (2D) matrix of numerical data to the node + * + * @param _pfMatrix data + * @param _iWidth width of the matrix + * @param _iHeight height of the matrix + * @param transposed true is C order, false is Fortran order + */ + void setContent(float32* _pfMatrix, int _iWidth, int _iHeight, bool transposed); + + /** Add a (2D) matrix of numerical data to the node + * + * @param _pfMatrix data + * @param _iWidth width of the matrix + * @param _iHeight height of the matrix + * @param transposed true is C order, false is Fortran order + */ + void setContent(double* _pfMatrix, int _iWidth, int _iHeight, bool transposed); + /** Add an attribute to this node: <... _sName="_sValue"> * * @param _sName name of the attribute @@ -294,11 +316,11 @@ public: /** Print to String */ - std::string toString(); + std::string toString() const; /** Print the node */ - void print(); + void print() const; protected: diff --git a/matlab/mex/astra_mex_algorithm_c.cpp b/matlab/mex/astra_mex_algorithm_c.cpp index e4afa63..ec7aa72 100644 --- a/matlab/mex/astra_mex_algorithm_c.cpp +++ b/matlab/mex/astra_mex_algorithm_c.cpp @@ -81,7 +81,7 @@ void astra_mex_algorithm_create(int nlhs, mxArray* plhs[], int nrhs, const mxArr // turn MATLAB struct to an XML-based Config object 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 cfg; mexErrMsgTxt("Unknown algorithm. \n"); diff --git a/matlab/mex/astra_mex_data2d_c.cpp b/matlab/mex/astra_mex_data2d_c.cpp index 9576896..909d229 100644 --- a/matlab/mex/astra_mex_data2d_c.cpp +++ b/matlab/mex/astra_mex_data2d_c.cpp @@ -149,7 +149,7 @@ void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra 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(); @@ -438,7 +438,7 @@ void astra_mex_data2d_change_geometry(int nlhs, mxArray* plhs[], int nrhs, const 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(); diff --git a/matlab/mex/astra_mex_data3d_c.cpp b/matlab/mex/astra_mex_data3d_c.cpp index 32b0ba7..fe4ce37 100644 --- a/matlab/mex/astra_mex_data3d_c.cpp +++ b/matlab/mex/astra_mex_data3d_c.cpp @@ -148,8 +148,8 @@ void astra_mex_data3d_link(int& nlhs, mxArray* plhs[], int& nrhs, const mxArray* return; } - if (data && !checkDataType(data)) { - mexErrMsgTxt("Data must be single or double."); + if (data && !mxIsSingle(data)) { + mexErrMsgTxt("Data must be single."); return; } @@ -310,6 +310,112 @@ void astra_mex_data3d_get_geometry(int nlhs, mxArray* plhs[], int nrhs, const mx } //----------------------------------------------------------------------------------------- +/** astra_mex_data3d('change_geometry', id, geom); + * + * Change the geometry of a 3d data object. + * id: identifier of the 3d data object as stored in the astra-library. + * geom: the new geometry struct, as created by astra_create_vol/proj_geom + */ +void astra_mex_data3d_change_geometry(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) +{ + // parse input + if (nrhs < 3) { + mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n"); + return; + } + + // get data object + CFloat32Data3DMemory* pDataObject = NULL; + if (!checkID(mxGetScalar(prhs[1]), pDataObject)) { + mexErrMsgTxt("Data object not found or not initialized properly.\n"); + return; + } + + const mxArray * const geometry = prhs[2]; + + if (!checkStructs(geometry)) { + mexErrMsgTxt("Argument 3 is not a valid MATLAB struct.\n"); + return; + } + + CFloat32ProjectionData3D* pProjData = dynamic_cast<CFloat32ProjectionData3D*>(pDataObject); + if (pProjData) { + // Projection data + + // Read geometry + 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"); + 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; + } + + if (!pGeometry->initialize(*cfg)) { + mexErrMsgTxt("Geometry class not initialized. \n"); + delete pGeometry; + delete cfg; + return; + } + delete cfg; + + // Check dimensions + if (pGeometry->getDetectorColCount() != pProjData->getDetectorColCount() || + pGeometry->getProjectionCount() != pProjData->getAngleCount() || + pGeometry->getDetectorRowCount() != pProjData->getDetectorRowCount()) + { + mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n"); + delete pGeometry; + return; + } + + // If ok, change geometry + pProjData->changeGeometry(pGeometry); + delete pGeometry; + } else { + // Volume data + CFloat32VolumeData3D* pVolData = dynamic_cast<CFloat32VolumeData3D*>(pDataObject); + assert(pVolData); + + // Read geometry + astra::Config* cfg = structToConfig("VolumeGeometry3D", geometry); + astra::CVolumeGeometry3D* pGeometry = new astra::CVolumeGeometry3D(); + if (!pGeometry->initialize(*cfg)) + { + mexErrMsgTxt("Geometry class not initialized. \n"); + delete pGeometry; + delete cfg; + return; + } + delete cfg; + + // Check dimensions + if (pGeometry->getGridColCount() != pVolData->getColCount() || + pGeometry->getGridRowCount() != pVolData->getRowCount() || + pGeometry->getGridSliceCount() != pVolData->getSliceCount()) + { + mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n"); + delete pGeometry; + return; + } + + // If ok, change geometry + pVolData->changeGeometry(pGeometry); + delete pGeometry; + } +} + +//----------------------------------------------------------------------------------------- /** * astra_mex_data3d('delete', did1, did2, ...); */ @@ -351,7 +457,7 @@ static void printHelp() { mexPrintf("Please specify a mode of operation.\n"); mexPrintf("Valid modes: create, get, get_single, delete, clear, info\n"); - mexPrintf(" dimensions\n"); + mexPrintf(" dimensions, get_geometry, change_geometry\n"); } @@ -398,6 +504,8 @@ void mexFunction(int nlhs, mxArray* plhs[], astra_mex_data3d_dimensions(nlhs, plhs, nrhs, prhs); } else if (sMode == std::string("get_geometry")) { astra_mex_data3d_get_geometry(nlhs, plhs, nrhs, prhs); + } else if (sMode == std::string("change_geometry")) { + astra_mex_data3d_change_geometry(nlhs, plhs, nrhs, prhs); } else { printHelp(); } diff --git a/matlab/mex/mexCopyDataHelpFunctions.cpp b/matlab/mex/mexCopyDataHelpFunctions.cpp index 80fb834..4db6abd 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 (mexIsScalar(in)) { + if (mexIsScalar(in) || mxIsEmpty(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 d482428..1794abb 100644 --- a/matlab/mex/mexDataManagerHelpFunctions.cpp +++ b/matlab/mex/mexDataManagerHelpFunctions.cpp @@ -285,7 +285,7 @@ allocateDataObject(const std::string & sDataType, 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(); diff --git a/matlab/mex/mexHelpFunctions.cpp b/matlab/mex/mexHelpFunctions.cpp index c0ac711..87a9672 100644 --- a/matlab/mex/mexHelpFunctions.cpp +++ b/matlab/mex/mexHelpFunctions.cpp @@ -185,7 +185,7 @@ Config* structToConfig(string rootname, const mxArray* pStruct) } //----------------------------------------------------------------------------------------- -bool structToXMLNode(XMLNode* node, const mxArray* pStruct) +bool structToXMLNode(XMLNode node, const mxArray* pStruct) { // loop all fields int nfields = mxGetNumberOfFields(pStruct); @@ -199,16 +199,16 @@ bool structToXMLNode(XMLNode* node, const mxArray* pStruct) if (mxIsChar(pField)) { string sValue = mexToString(pField); if (sFieldName == "type") { - node->addAttribute("type", sValue); + node.addAttribute("type", sValue); } else { - delete node->addChildNode(sFieldName, sValue); + node.addChildNode(sFieldName, sValue); } } // scalar else if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) == 1) { string sValue = mexToString(pField); - delete node->addChildNode(sFieldName, sValue); + node.addChildNode(sFieldName, sValue); } // numerical array @@ -217,20 +217,9 @@ bool structToXMLNode(XMLNode* node, const mxArray* pStruct) mexErrMsgTxt("Numeric input must be double."); return false; } - XMLNode* listbase = node->addChildNode(sFieldName); - listbase->addAttribute("listsize", mxGetM(pField)*mxGetN(pField)); + XMLNode listbase = node.addChildNode(sFieldName); 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; + listbase.setContent(pdValues, mxGetN(pField), mxGetM(pField), true); } // not castable to a single string @@ -240,9 +229,8 @@ bool structToXMLNode(XMLNode* node, const mxArray* pStruct) if (!ret) return false; } else { - XMLNode* newNode = node->addChildNode(sFieldName); + XMLNode newNode = node.addChildNode(sFieldName); bool ret = structToXMLNode(newNode, pField); - delete newNode; if (!ret) return false; } @@ -254,7 +242,7 @@ bool structToXMLNode(XMLNode* node, const mxArray* pStruct) } //----------------------------------------------------------------------------------------- // Options struct to xml node -bool optionsToXMLNode(XMLNode* node, const mxArray* pOptionStruct) +bool optionsToXMLNode(XMLNode node, const mxArray* pOptionStruct) { // loop all fields int nfields = mxGetNumberOfFields(pOptionStruct); @@ -262,7 +250,7 @@ bool optionsToXMLNode(XMLNode* node, const mxArray* pOptionStruct) std::string sFieldName = std::string(mxGetFieldNameByNumber(pOptionStruct, i)); const mxArray* pField = mxGetFieldByNumber(pOptionStruct, 0, i); - if (node->hasOption(sFieldName)) { + if (node.hasOption(sFieldName)) { mexErrMsgTxt("Duplicate option"); return false; } @@ -270,7 +258,7 @@ bool optionsToXMLNode(XMLNode* node, const mxArray* pOptionStruct) // string or scalar if (mxIsChar(pField) || mexIsScalar(pField)) { string sValue = mexToString(pField); - node->addOption(sFieldName, sValue); + node.addOption(sFieldName, sValue); } // numerical array else if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) > 1) { @@ -279,21 +267,10 @@ bool optionsToXMLNode(XMLNode* node, const mxArray* pOptionStruct) return false; } - XMLNode* listbase = node->addChildNode("Option"); - listbase->addAttribute("key", sFieldName); - listbase->addAttribute("listsize", mxGetM(pField)*mxGetN(pField)); + XMLNode listbase = node.addChildNode("Option"); + listbase.addAttribute("key", sFieldName); 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; + listbase.setContent(pdValues, mxGetN(pField), mxGetM(pField), true); } else { mexErrMsgTxt("Unsupported option type"); return false; @@ -343,30 +320,29 @@ mxArray* configToStruct(astra::Config* cfg) } //----------------------------------------------------------------------------------------- -mxArray* XMLNodeToStruct(astra::XMLNode* node) +mxArray* XMLNodeToStruct(astra::XMLNode node) { std::map<std::string, mxArray*> mList; std::map<std::string, mxArray*> mOptions; // type_attribute - if (node->hasAttribute("type")) { - mList["type"] = mxCreateString(node->getAttribute("type").c_str()); + if (node.hasAttribute("type")) { + mList["type"] = mxCreateString(node.getAttribute("type").c_str()); } - list<XMLNode*> nodes = node->getNodes(); - for (list<XMLNode*>::iterator it = nodes.begin(); it != nodes.end(); it++) { - XMLNode* subnode = (*it); + list<XMLNode> nodes = node.getNodes(); + for (list<XMLNode>::iterator it = nodes.begin(); it != nodes.end(); it++) { + XMLNode subnode = (*it); // option - if (subnode->getName() == "Option") { - mOptions[subnode->getAttribute("key")] = stringToMxArray(subnode->getAttribute("value")); + if (subnode.getName() == "Option") { + mOptions[subnode.getAttribute("key")] = stringToMxArray(subnode.getAttribute("value")); } // regular content else { - mList[subnode->getName()] = stringToMxArray(subnode->getContent()); + mList[subnode.getName()] = stringToMxArray(subnode.getContent()); } - delete subnode; } if (mOptions.size() > 0) mList["options"] = buildStruct(mOptions); diff --git a/matlab/mex/mexHelpFunctions.h b/matlab/mex/mexHelpFunctions.h index f9ffcf2..3ac5bd8 100644 --- a/matlab/mex/mexHelpFunctions.h +++ b/matlab/mex/mexHelpFunctions.h @@ -58,13 +58,13 @@ mxArray* anyToMxArray(boost::any _any); // 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); +bool structToXMLNode(astra::XMLNode node, const mxArray* pStruct); +bool optionsToXMLNode(astra::XMLNode node, const mxArray* pOptionStruct); std::map<std::string, mxArray*> parseStruct(const mxArray* pInput); // turn a Config object into a MATLAB struct mxArray* configToStruct(astra::Config* cfg); -mxArray* XMLNodeToStruct(astra::XMLNode* xml); +mxArray* XMLNodeToStruct(astra::XMLNode xml); mxArray* stringToMxArray(std::string input); mxArray* buildStruct(std::map<std::string, mxArray*> mInput); diff --git a/python/astra/ASTRAProjector.py b/python/astra/ASTRAProjector.py deleted file mode 100644 index f282618..0000000 --- a/python/astra/ASTRAProjector.py +++ /dev/null @@ -1,135 +0,0 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam -# -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ -# -# -#This file is part of the Python interface to the -#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). -# -#The Python interface to 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 Python interface to 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 Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. -# -#----------------------------------------------------------------------- - -import math -from . import creators as ac -from . import data2d - - -class ASTRAProjector2DTranspose(): - """Implements the ``proj.T`` functionality. - - Do not use directly, since it can be accessed as member ``.T`` of - an :class:`ASTRAProjector2D` object. - - """ - def __init__(self, parentProj): - self.parentProj = parentProj - - def __mul__(self, data): - return self.parentProj.backProject(data) - - -class ASTRAProjector2D(object): - """Helps with various common ASTRA Toolbox 2D operations. - - This class can perform several often used toolbox operations, such as: - - * Forward projecting - * Back projecting - * Reconstructing - - Note that this class has a some computational overhead, because it - copies a lot of data. If you use many repeated operations, directly - using the PyAstraToolbox methods directly is faster. - - You can use this class as an abstracted weight matrix :math:`W`: multiplying an instance - ``proj`` of this class by an image results in a forward projection of the image, and multiplying - ``proj.T`` by a sinogram results in a backprojection of the sinogram:: - - proj = ASTRAProjector2D(...) - fp = proj*image - bp = proj.T*sinogram - - :param proj_geom: The projection geometry. - :type proj_geom: :class:`dict` - :param vol_geom: The volume geometry. - :type vol_geom: :class:`dict` - :param proj_type: Projector type, such as ``'line'``, ``'linear'``, ... - :type proj_type: :class:`string` - """ - - def __init__(self, proj_geom, vol_geom, proj_type): - self.vol_geom = vol_geom - self.recSize = vol_geom['GridColCount'] - self.angles = proj_geom['ProjectionAngles'] - self.nDet = proj_geom['DetectorCount'] - nexpow = int(pow(2, math.ceil(math.log(2 * self.nDet, 2)))) - self.filterSize = nexpow / 2 + 1 - self.nProj = self.angles.shape[0] - self.proj_geom = proj_geom - self.proj_id = ac.create_projector(proj_type, proj_geom, vol_geom) - self.T = ASTRAProjector2DTranspose(self) - - def backProject(self, data): - """Backproject a sinogram. - - :param data: The sinogram data or ID. - :type data: :class:`numpy.ndarray` or :class:`int` - :returns: :class:`numpy.ndarray` -- The backprojection. - - """ - vol_id, vol = ac.create_backprojection( - data, self.proj_id, returnData=True) - data2d.delete(vol_id) - return vol - - def forwardProject(self, data): - """Forward project an image. - - :param data: The image data or ID. - :type data: :class:`numpy.ndarray` or :class:`int` - :returns: :class:`numpy.ndarray` -- The forward projection. - - """ - sin_id, sino = ac.create_sino(data, self.proj_id, returnData=True) - data2d.delete(sin_id) - return sino - - def reconstruct(self, data, method, **kwargs): - """Reconstruct an image from a sinogram. - - :param data: The sinogram data or ID. - :type data: :class:`numpy.ndarray` or :class:`int` - :param method: Name of the reconstruction algorithm. - :type method: :class:`string` - :param kwargs: Additional named parameters to pass to :func:`astra.creators.create_reconstruction`. - :returns: :class:`numpy.ndarray` -- The reconstruction. - - Example of a SIRT reconstruction using CUDA:: - - proj = ASTRAProjector2D(...) - rec = proj.reconstruct(sinogram,'SIRT_CUDA',iterations=1000) - - """ - kwargs['returnData'] = True - rec_id, rec = ac.create_reconstruction( - method, self.proj_id, data, **kwargs) - data2d.delete(rec_id) - return rec - - def __mul__(self, data): - return self.forwardProject(data) diff --git a/python/astra/CFloat32CustomPython.h b/python/astra/CFloat32CustomPython.h new file mode 100644 index 0000000..d8593fc --- /dev/null +++ b/python/astra/CFloat32CustomPython.h @@ -0,0 +1,17 @@ +class CFloat32CustomPython : public astra::CFloat32CustomMemory { +public: + CFloat32CustomPython(PyObject * arrIn) + { + arr = arrIn; + // Set pointer to numpy data pointer + m_fPtr = (float *)PyArray_DATA(arr); + // Increase reference count since ASTRA has a reference + Py_INCREF(arr); + } + virtual ~CFloat32CustomPython() { + // Decrease reference count since ASTRA object is destroyed + Py_DECREF(arr); + } +private: + PyObject* arr; +};
\ No newline at end of file diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd index 7df02c5..909f58f 100644 --- a/python/astra/PyIncludes.pxd +++ b/python/astra/PyIncludes.pxd @@ -43,7 +43,7 @@ cdef extern from "astra/Config.h" namespace "astra": cdef cppclass Config: Config() void initialize(string rootname) - XMLNode *self + XMLNode self cdef extern from "astra/VolumeGeometry2D.h" namespace "astra": cdef cppclass CVolumeGeometry2D: @@ -63,10 +63,14 @@ cdef extern from "astra/VolumeGeometry2D.h" namespace "astra": float32 getWindowMaxY() Config* getConfiguration() +cdef extern from "astra/Float32Data2D.h" namespace "astra": + cdef cppclass CFloat32CustomMemory: + pass cdef extern from "astra/Float32VolumeData2D.h" namespace "astra": cdef cppclass CFloat32VolumeData2D: CFloat32VolumeData2D(CVolumeGeometry2D*) + CFloat32VolumeData2D(CVolumeGeometry2D*, CFloat32CustomMemory*) CVolumeGeometry2D * getGeometry() int getWidth() int getHeight() @@ -130,6 +134,7 @@ cdef extern from "astra/ParallelProjectionGeometry2D.h" namespace "astra": cdef extern from "astra/Float32ProjectionData2D.h" namespace "astra": cdef cppclass CFloat32ProjectionData2D: CFloat32ProjectionData2D(CProjectionGeometry2D*) + CFloat32ProjectionData2D(CProjectionGeometry2D*, CFloat32CustomMemory*) CProjectionGeometry2D * getGeometry() void changeGeometry(CProjectionGeometry2D*) int getDetectorCount() @@ -196,18 +201,30 @@ cdef extern from "astra/VolumeGeometry3D.h" namespace "astra": CVolumeGeometry3D() bool initialize(Config) Config * getConfiguration() + int getGridColCount() + int getGridRowCount() + int getGridSliceCount() cdef extern from "astra/ProjectionGeometry3D.h" namespace "astra": cdef cppclass CProjectionGeometry3D: CProjectionGeometry3D() bool initialize(Config) Config * getConfiguration() + int getProjectionCount() + int getDetectorColCount() + int getDetectorRowCount() cdef extern from "astra/Float32VolumeData3DMemory.h" namespace "astra": cdef cppclass CFloat32VolumeData3DMemory: CFloat32VolumeData3DMemory(CVolumeGeometry3D*) + CFloat32VolumeData3DMemory(CVolumeGeometry3D*, CFloat32CustomMemory*) CVolumeGeometry3D* getGeometry() + void changeGeometry(CVolumeGeometry3D*) + int getRowCount() + int getColCount() + int getSliceCount() + cdef extern from "astra/ParallelProjectionGeometry3D.h" namespace "astra": @@ -231,7 +248,13 @@ cdef extern from "astra/Float32ProjectionData3DMemory.h" namespace "astra": cdef cppclass CFloat32ProjectionData3DMemory: CFloat32ProjectionData3DMemory(CProjectionGeometry3D*) CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*) + CFloat32ProjectionData3DMemory(CProjectionGeometry3D*, CFloat32CustomMemory*) + CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*, CFloat32CustomMemory*) CProjectionGeometry3D* getGeometry() + void changeGeometry(CProjectionGeometry3D*) + int getDetectorColCount() + int getDetectorRowCount() + int getAngleCount() cdef extern from "astra/Float32Data3D.h" namespace "astra": cdef cppclass CFloat32Data3D: diff --git a/python/astra/PyXMLDocument.pxd b/python/astra/PyXMLDocument.pxd index 69781f1..033b8ef 100644 --- a/python/astra/PyXMLDocument.pxd +++ b/python/astra/PyXMLDocument.pxd @@ -44,22 +44,24 @@ cdef extern from "astra/Globals.h" namespace "astra": cdef extern from "astra/XMLNode.h" namespace "astra": cdef cppclass XMLNode: string getName() - XMLNode *addChildNode(string name) - XMLNode *addChildNode(string, string) + XMLNode addChildNode(string name) + XMLNode addChildNode(string, string) void addAttribute(string, string) void addAttribute(string, float32) void addOption(string, string) bool hasOption(string) string getAttribute(string) - list[XMLNode *] getNodes() + list[XMLNode] getNodes() vector[float32] getContentNumericalArray() + void setContent(double*, int, int, bool) + void setContent(double*, int) string getContent() bool hasAttribute(string) cdef extern from "astra/XMLDocument.h" namespace "astra": cdef cppclass XMLDocument: void saveToFile(string sFilename) - XMLNode *getRootNode() + XMLNode getRootNode() cdef extern from "astra/XMLDocument.h" namespace "astra::XMLDocument": cdef XMLDocument *createDocument(string rootname) diff --git a/python/astra/__init__.py b/python/astra/__init__.py index 063dc16..6c15d30 100644 --- a/python/astra/__init__.py +++ b/python/astra/__init__.py @@ -27,7 +27,6 @@ from . import matlab as m from .creators import astra_dict,create_vol_geom, create_proj_geom, create_backprojection, create_sino, create_reconstruction, create_projector,create_sino3d_gpu, create_backprojection3d_gpu from .functions import data_op, add_noise_to_sino, clear, move_vol_geom from .extrautils import clipCircle -from .ASTRAProjector import ASTRAProjector2D from . import data2d from . import astra from . import data3d @@ -36,6 +35,7 @@ from . import projector from . import projector3d from . import matrix from . import log +from .optomo import OpTomo import os try: diff --git a/python/astra/data2d.py b/python/astra/data2d.py index 8c4be03..f119f05 100644 --- a/python/astra/data2d.py +++ b/python/astra/data2d.py @@ -24,6 +24,7 @@ # #----------------------------------------------------------------------- from . import data2d_c as d +import numpy as np def clear(): """Clear all 2D data objects.""" @@ -52,6 +53,26 @@ def create(datatype, geometry, data=None): """ return d.create(datatype,geometry,data) +def link(datatype, geometry, data): + """Link a 2D numpy array with the toolbox. + + :param datatype: Data object type, '-vol' or '-sino'. + :type datatype: :class:`string` + :param geometry: Volume or projection geometry. + :type geometry: :class:`dict` + :param data: Numpy array to link + :type data: :class:`numpy.ndarray` + :returns: :class:`int` -- the ID of the constructed object. + + """ + if not isinstance(data,np.ndarray): + raise ValueError("Input should be a numpy array") + if not data.dtype==np.float32: + raise ValueError("Numpy array should be float32") + if not (data.flags['C_CONTIGUOUS'] and data.flags['ALIGNED']): + raise ValueError("Numpy array should be C_CONTIGUOUS and ALIGNED") + return d.create(datatype,geometry,data,True) + def store(i, data): """Fill existing 2D object with data. diff --git a/python/astra/data2d_c.pyx b/python/astra/data2d_c.pyx index b9c105e..4919bf2 100644 --- a/python/astra/data2d_c.pyx +++ b/python/astra/data2d_c.pyx @@ -47,8 +47,18 @@ from .PyIncludes cimport * cimport utils from .utils import wrap_from_bytes +from .pythonutils import geom_size + +import operator + +from six.moves import reduce + cdef CData2DManager * man2d = <CData2DManager * >PyData2DManager.getSingletonPtr() +cdef extern from "CFloat32CustomPython.h": + cdef cppclass CFloat32CustomPython: + CFloat32CustomPython(arrIn) + def clear(): man2d.clear() @@ -61,11 +71,16 @@ def delete(ids): man2d.remove(ids) -def create(datatype, geometry, data=None): +def create(datatype, geometry, data=None, link=False): cdef Config *cfg cdef CVolumeGeometry2D * pGeometry cdef CProjectionGeometry2D * ppGeometry cdef CFloat32Data2D * pDataObject2D + cdef CFloat32CustomMemory * pCustom + + if link and data.shape!=geom_size(geometry): + raise Exception("The dimensions of the data do not match those specified in the geometry.") + if datatype == '-vol': cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry) pGeometry = new CVolumeGeometry2D() @@ -73,7 +88,11 @@ def create(datatype, geometry, data=None): del cfg del pGeometry raise Exception('Geometry class not initialized.') - pDataObject2D = <CFloat32Data2D * > new CFloat32VolumeData2D(pGeometry) + if link: + pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data) + pDataObject2D = <CFloat32Data2D * > new CFloat32VolumeData2D(pGeometry, pCustom) + else: + pDataObject2D = <CFloat32Data2D * > new CFloat32VolumeData2D(pGeometry) del cfg del pGeometry elif datatype == '-sino': @@ -91,7 +110,11 @@ def create(datatype, geometry, data=None): del cfg del ppGeometry raise Exception('Geometry class not initialized.') - pDataObject2D = <CFloat32Data2D * > new CFloat32ProjectionData2D(ppGeometry) + if link: + pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data) + pDataObject2D = <CFloat32Data2D * > new CFloat32ProjectionData2D(ppGeometry, pCustom) + else: + pDataObject2D = <CFloat32Data2D * > new CFloat32ProjectionData2D(ppGeometry) del ppGeometry del cfg else: @@ -101,7 +124,7 @@ def create(datatype, geometry, data=None): del pDataObject2D raise Exception("Couldn't initialize data object.") - fillDataObject(pDataObject2D, data) + if not link: fillDataObject(pDataObject2D, data) return man2d.store(pDataObject2D) diff --git a/python/astra/data3d.py b/python/astra/data3d.py index a2e9201..e5ef6b0 100644 --- a/python/astra/data3d.py +++ b/python/astra/data3d.py @@ -24,6 +24,7 @@ # #----------------------------------------------------------------------- from . import data3d_c as d +import numpy as np def create(datatype,geometry,data=None): """Create a 3D object. @@ -39,6 +40,27 @@ def create(datatype,geometry,data=None): """ return d.create(datatype,geometry,data) +def link(datatype, geometry, data): + """Link a 3D numpy array with the toolbox. + + :param datatype: Data object type, '-vol' or '-sino'. + :type datatype: :class:`string` + :param geometry: Volume or projection geometry. + :type geometry: :class:`dict` + :param data: Numpy array to link + :type data: :class:`numpy.ndarray` + :returns: :class:`int` -- the ID of the constructed object. + + """ + if not isinstance(data,np.ndarray): + raise ValueError("Input should be a numpy array") + if not data.dtype==np.float32: + raise ValueError("Numpy array should be float32") + if not (data.flags['C_CONTIGUOUS'] and data.flags['ALIGNED']): + raise ValueError("Numpy array should be C_CONTIGUOUS and ALIGNED") + return d.create(datatype,geometry,data,True) + + def get(i): """Get a 3D object. @@ -90,6 +112,17 @@ def get_geometry(i): """ return d.get_geometry(i) +def change_geometry(i, geometry): + """Change the geometry of a 3D object. + + :param i: ID of object. + :type i: :class:`int` + :param geometry: Volume or projection geometry. + :type geometry: :class:`dict` + + """ + return d.change_geometry(i, geometry) + def dimensions(i): """Get dimensions of a 3D object. diff --git a/python/astra/data3d_c.pyx b/python/astra/data3d_c.pyx index 4b069f7..3b27ab7 100644 --- a/python/astra/data3d_c.pyx +++ b/python/astra/data3d_c.pyx @@ -45,17 +45,33 @@ from .PyXMLDocument cimport XMLDocument cimport utils from .utils import wrap_from_bytes +from .pythonutils import geom_size + +import operator + +from six.moves import reduce + + cdef CData3DManager * man3d = <CData3DManager * >PyData3DManager.getSingletonPtr() cdef extern from *: CFloat32Data3DMemory * dynamic_cast_mem "dynamic_cast<astra::CFloat32Data3DMemory*>" (CFloat32Data3D * ) except NULL -def create(datatype,geometry,data=None): +cdef extern from "CFloat32CustomPython.h": + cdef cppclass CFloat32CustomPython: + CFloat32CustomPython(arrIn) + +def create(datatype,geometry,data=None, link=False): cdef Config *cfg cdef CVolumeGeometry3D * pGeometry cdef CProjectionGeometry3D * ppGeometry cdef CFloat32Data3DMemory * pDataObject3D cdef CConeProjectionGeometry3D* pppGeometry + cdef CFloat32CustomMemory * pCustom + + if link and data.shape!=geom_size(geometry): + raise Exception("The dimensions of the data do not match those specified in the geometry.") + if datatype == '-vol': cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry) pGeometry = new CVolumeGeometry3D() @@ -63,7 +79,11 @@ def create(datatype,geometry,data=None): del cfg del pGeometry raise Exception('Geometry class not initialized.') - pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry) + if link: + pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data) + pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry, pCustom) + else: + pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry) del cfg del pGeometry elif datatype == '-sino' or datatype == '-proj3d': @@ -84,7 +104,11 @@ def create(datatype,geometry,data=None): del cfg del ppGeometry raise Exception('Geometry class not initialized.') - pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry) + if link: + pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data) + pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry, pCustom) + else: + pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry) del ppGeometry del cfg elif datatype == "-sinocone": @@ -94,7 +118,11 @@ def create(datatype,geometry,data=None): del cfg del pppGeometry raise Exception('Geometry class not initialized.') - pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(pppGeometry) + if link: + pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data) + pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(pppGeometry, pCustom) + else: + pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(pppGeometry) else: raise Exception("Invalid datatype. Please specify '-vol' or '-proj3d'.") @@ -102,7 +130,7 @@ def create(datatype,geometry,data=None): del pDataObject3D raise Exception("Couldn't initialize data object.") - fillDataObject(pDataObject3D, data) + if not link: fillDataObject(pDataObject3D, data) pDataObject3D.updateStatistics() @@ -122,6 +150,61 @@ def get_geometry(i): raise Exception("Not a known data object") return geom +def change_geometry(i, geom): + cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem(getObject(i)) + cdef CFloat32ProjectionData3DMemory * pDataObject2 + cdef CFloat32VolumeData3DMemory * pDataObject3 + if pDataObject.getType() == THREEPROJECTION: + pDataObject2 = <CFloat32ProjectionData3DMemory * >pDataObject + # TODO: Reduce code duplication here + cfg = utils.dictToConfig(six.b('ProjectionGeometry'), geom) + tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type'))) + if (tpe == "parallel3d"): + ppGeometry = <CProjectionGeometry3D*> new CParallelProjectionGeometry3D(); + elif (tpe == "parallel3d_vec"): + ppGeometry = <CProjectionGeometry3D*> new CParallelVecProjectionGeometry3D(); + elif (tpe == "cone"): + ppGeometry = <CProjectionGeometry3D*> new CConeProjectionGeometry3D(); + elif (tpe == "cone_vec"): + ppGeometry = <CProjectionGeometry3D*> new CConeVecProjectionGeometry3D(); + else: + raise Exception("Invalid geometry type.") + if not ppGeometry.initialize(cfg[0]): + del cfg + del ppGeometry + raise Exception('Geometry class not initialized.') + del cfg + if (ppGeometry.getDetectorColCount() != pDataObject2.getDetectorColCount() or \ + ppGeometry.getProjectionCount() != pDataObject2.getAngleCount() or \ + ppGeometry.getDetectorRowCount() != pDataObject2.getDetectorRowCount()): + del ppGeometry + raise Exception( + "The dimensions of the data do not match those specified in the geometry.") + pDataObject2.changeGeometry(ppGeometry) + del ppGeometry + + elif pDataObject.getType() == THREEVOLUME: + pDataObject3 = <CFloat32VolumeData3DMemory * >pDataObject + cfg = utils.dictToConfig(six.b('VolumeGeometry'), geom) + pGeometry = new CVolumeGeometry3D() + if not pGeometry.initialize(cfg[0]): + del cfg + del pGeometry + raise Exception('Geometry class not initialized.') + del cfg + if (pGeometry.getGridColCount() != pDataObject3.getColCount() or \ + pGeometry.getGridRowCount() != pDataObject3.getRowCount() or \ + pGeometry.getGridSliceCount() != pDataObject3.getSliceCount()): + del pGeometry + raise Exception( + "The dimensions of the data do not match those specified in the geometry.") + pDataObject3.changeGeometry(pGeometry) + del pGeometry + + else: + raise Exception("Not a known data object") + + cdef fillDataObject(CFloat32Data3DMemory * obj, data): if data is None: fillDataObjectScalar(obj, 0) diff --git a/python/astra/functions.py b/python/astra/functions.py index 4025468..b826b86 100644 --- a/python/astra/functions.py +++ b/python/astra/functions.py @@ -38,6 +38,7 @@ from . import data2d from . import data3d from . import projector from . import algorithm +from . import pythonutils @@ -158,29 +159,7 @@ def geom_size(geom, dim=None): :param dim: Optional axis index to return :type dim: :class:`int` """ - - if 'GridSliceCount' in geom: - # 3D Volume geometry? - s = (geom['GridSliceCount'], geom[ - 'GridRowCount'], geom['GridColCount']) - elif 'GridColCount' in geom: - # 2D Volume geometry? - s = (geom['GridRowCount'], geom['GridColCount']) - elif geom['type'] == 'parallel' or geom['type'] == 'fanflat': - s = (len(geom['ProjectionAngles']), geom['DetectorCount']) - elif geom['type'] == 'parallel3d' or geom['type'] == 'cone': - s = (geom['DetectorRowCount'], len( - geom['ProjectionAngles']), geom['DetectorColCount']) - elif geom['type'] == 'fanflat_vec': - s = (geom['Vectors'].shape[0], geom['DetectorCount']) - elif geom['type'] == 'parallel3d_vec' or geom['type'] == 'cone_vec': - s = (geom['DetectorRowCount'], geom[ - 'Vectors'].shape[0], geom['DetectorColCount']) - - if dim != None: - s = s[dim] - - return s + return pythonutils.geom_size(geom,dim) def geom_2vec(proj_geom): diff --git a/python/astra/optomo.py b/python/astra/optomo.py new file mode 100644 index 0000000..0c37353 --- /dev/null +++ b/python/astra/optomo.py @@ -0,0 +1,197 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to 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 Python interface to 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 Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +from . import data2d +from . import data3d +from . import projector +from . import projector3d +from . import creators +from . import algorithm +from . import functions +import numpy as np +from six.moves import range, reduce +import operator +import scipy.sparse.linalg + +class OpTomo(scipy.sparse.linalg.LinearOperator): + """Object that imitates a projection matrix with a given projector. + + This object can do forward projection by using the ``*`` operator:: + + W = astra.OpTomo(proj_id) + fp = W*image + bp = W.T*sinogram + + It can also be used in minimization methods of the :mod:`scipy.sparse.linalg` module:: + + W = astra.OpTomo(proj_id) + output = scipy.sparse.linalg.lsqr(W,sinogram) + + :param proj_id: ID to a projector. + :type proj_id: :class:`int` + """ + + def __init__(self,proj_id): + self.dtype = np.float32 + try: + self.vg = projector.volume_geometry(proj_id) + self.pg = projector.projection_geometry(proj_id) + self.data_mod = data2d + self.appendString = "" + if projector.is_cuda(proj_id): + self.appendString += "_CUDA" + except Exception: + self.vg = projector3d.volume_geometry(proj_id) + self.pg = projector3d.projection_geometry(proj_id) + self.data_mod = data3d + self.appendString = "3D" + if projector3d.is_cuda(proj_id): + self.appendString += "_CUDA" + + self.vshape = functions.geom_size(self.vg) + self.vsize = reduce(operator.mul,self.vshape) + self.sshape = functions.geom_size(self.pg) + self.ssize = reduce(operator.mul,self.sshape) + + self.shape = (self.ssize, self.vsize) + + self.proj_id = proj_id + + self.T = OpTomoTranspose(self) + + def __checkArray(self, arr, shp): + if len(arr.shape)==1: + arr = arr.reshape(shp) + if arr.dtype != np.float32: + arr = arr.astype(np.float32) + if arr.flags['C_CONTIGUOUS']==False: + arr = np.ascontiguousarray(arr) + return arr + + def _matvec(self,v): + """Implements the forward operator. + + :param v: Volume to forward project. + :type v: :class:`numpy.ndarray` + """ + v = self.__checkArray(v, self.vshape) + vid = self.data_mod.link('-vol',self.vg,v) + s = np.zeros(self.sshape,dtype=np.float32) + sid = self.data_mod.link('-sino',self.pg,s) + + cfg = creators.astra_dict('FP'+self.appendString) + cfg['ProjectionDataId'] = sid + cfg['VolumeDataId'] = vid + cfg['ProjectorId'] = self.proj_id + fp_id = algorithm.create(cfg) + algorithm.run(fp_id) + + algorithm.delete(fp_id) + self.data_mod.delete([vid,sid]) + return s.flatten() + + def rmatvec(self,s): + """Implements the transpose operator. + + :param s: The projection data. + :type s: :class:`numpy.ndarray` + """ + s = self.__checkArray(s, self.sshape) + sid = self.data_mod.link('-sino',self.pg,s) + v = np.zeros(self.vshape,dtype=np.float32) + vid = self.data_mod.link('-vol',self.vg,v) + + cfg = creators.astra_dict('BP'+self.appendString) + cfg['ProjectionDataId'] = sid + cfg['ReconstructionDataId'] = vid + cfg['ProjectorId'] = self.proj_id + bp_id = algorithm.create(cfg) + algorithm.run(bp_id) + + algorithm.delete(bp_id) + self.data_mod.delete([vid,sid]) + return v.flatten() + + def __mul__(self,v): + """Provides easy forward operator by *. + + :param v: Volume to forward project. + :type v: :class:`numpy.ndarray` + """ + # Catch the case of a forward projection of a 2D/3D image + if isinstance(v, np.ndarray) and v.shape==self.vshape: + return self._matvec(v) + return scipy.sparse.linalg.LinearOperator.__mul__(self, v) + + def reconstruct(self, method, s, iterations=1, extraOptions = {}): + """Reconstruct an object. + + :param method: Method to use for reconstruction. + :type method: :class:`string` + :param s: The projection data. + :type s: :class:`numpy.ndarray` + :param iterations: Number of iterations to use. + :type iterations: :class:`int` + :param extraOptions: Extra options to use during reconstruction (i.e. for cfg['option']). + :type extraOptions: :class:`dict` + """ + self.__checkArray(s, self.sshape) + sid = self.data_mod.link('-sino',self.pg,s) + v = np.zeros(self.vshape,dtype=np.float32) + vid = self.data_mod.link('-vol',self.vg,v) + cfg = creators.astra_dict(method) + cfg['ProjectionDataId'] = sid + cfg['ReconstructionDataId'] = vid + cfg['ProjectorId'] = self.proj_id + cfg['option'] = extraOptions + alg_id = algorithm.create(cfg) + algorithm.run(alg_id,iterations) + algorithm.delete(alg_id) + self.data_mod.delete([vid,sid]) + return v + +class OpTomoTranspose(scipy.sparse.linalg.LinearOperator): + """This object provides the transpose operation (``.T``) of the OpTomo object. + + Do not use directly, since it can be accessed as member ``.T`` of + an :class:`OpTomo` object. + """ + def __init__(self,parent): + self.parent = parent + self.dtype = np.float32 + self.shape = (parent.shape[1], parent.shape[0]) + + def _matvec(self, s): + return self.parent.rmatvec(s) + + def rmatvec(self, v): + return self.parent.matvec(v) + + def __mul__(self,s): + # Catch the case of a backprojection of 2D/3D data + if isinstance(s, np.ndarray) and s.shape==self.parent.sshape: + return self._matvec(s) + return scipy.sparse.linalg.LinearOperator.__mul__(self, s) diff --git a/python/astra/pythonutils.py b/python/astra/pythonutils.py new file mode 100644 index 0000000..8ea4af5 --- /dev/null +++ b/python/astra/pythonutils.py @@ -0,0 +1,63 @@ +#----------------------------------------------------------------------- +# Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +# Author: Daniel M. Pelt +# Contact: D.M.Pelt@cwi.nl +# Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +# This file is part of the Python interface to the +# All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +# The Python interface to 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 Python interface to 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 Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +"""Additional purely Python functions for PyAstraToolbox. + +.. moduleauthor:: Daniel M. Pelt <D.M.Pelt@cwi.nl> + + +""" + +def geom_size(geom, dim=None): + """Returns the size of a volume or sinogram, based on the projection or volume geometry. + + :param geom: Geometry to calculate size from + :type geometry: :class:`dict` + :param dim: Optional axis index to return + :type dim: :class:`int` + """ + + if 'GridSliceCount' in geom: + # 3D Volume geometry? + s = (geom['GridSliceCount'], geom[ + 'GridRowCount'], geom['GridColCount']) + elif 'GridColCount' in geom: + # 2D Volume geometry? + s = (geom['GridRowCount'], geom['GridColCount']) + elif geom['type'] == 'parallel' or geom['type'] == 'fanflat': + s = (len(geom['ProjectionAngles']), geom['DetectorCount']) + elif geom['type'] == 'parallel3d' or geom['type'] == 'cone': + s = (geom['DetectorRowCount'], len( + geom['ProjectionAngles']), geom['DetectorColCount']) + elif geom['type'] == 'fanflat_vec': + s = (geom['Vectors'].shape[0], geom['DetectorCount']) + elif geom['type'] == 'parallel3d_vec' or geom['type'] == 'cone_vec': + s = (geom['DetectorRowCount'], geom[ + 'Vectors'].shape[0], geom['DetectorColCount']) + + if dim != None: + s = s[dim] + + return s diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx index 0439f1b..ddb37aa 100644 --- a/python/astra/utils.pyx +++ b/python/astra/utils.pyx @@ -26,6 +26,7 @@ # distutils: language = c++ # distutils: libraries = astra +cimport numpy as np import numpy as np import six from libcpp.string cimport string @@ -80,11 +81,12 @@ def wrap_from_bytes(value): return s -cdef void readDict(XMLNode * root, _dc): - cdef XMLNode * listbase - cdef XMLNode * itm +cdef void readDict(XMLNode root, _dc): + cdef XMLNode listbase + cdef XMLNode itm cdef int i cdef int j + cdef double* data dc = convert_item(_dc) for item in dc: @@ -93,45 +95,31 @@ cdef void readDict(XMLNode * root, _dc): if val.size == 0: break listbase = root.addChildNode(item) - listbase.addAttribute(< string > six.b('listsize'), < float32 > val.size) - index = 0 + data = <double*>np.PyArray_DATA(np.ascontiguousarray(val,dtype=np.float64)) if val.ndim == 2: - for i in range(val.shape[0]): - for j in range(val.shape[1]): - itm = listbase.addChildNode(six.b('ListItem')) - itm.addAttribute(< string > six.b('index'), < float32 > index) - itm.addAttribute( < string > six.b('value'), < float32 > val[i, j]) - index += 1 - del itm + listbase.setContent(data, val.shape[1], val.shape[0], False) elif val.ndim == 1: - for i in range(val.shape[0]): - itm = listbase.addChildNode(six.b('ListItem')) - itm.addAttribute(< string > six.b('index'), < float32 > index) - itm.addAttribute(< string > six.b('value'), < float32 > val[i]) - index += 1 - del itm + listbase.setContent(data, val.shape[0]) else: raise Exception("Only 1 or 2 dimensions are allowed") - del listbase elif isinstance(val, dict): if item == six.b('option') or item == six.b('options') or item == six.b('Option') or item == six.b('Options'): readOptions(root, val) else: itm = root.addChildNode(item) readDict(itm, val) - del itm else: if item == six.b('type'): root.addAttribute(< string > six.b('type'), <string> wrap_to_bytes(val)) else: itm = root.addChildNode(item, wrap_to_bytes(val)) - del itm -cdef void readOptions(XMLNode * node, dc): - cdef XMLNode * listbase - cdef XMLNode * itm +cdef void readOptions(XMLNode node, dc): + cdef XMLNode listbase + cdef XMLNode itm cdef int i cdef int j + cdef double* data for item in dc: val = dc[item] if node.hasOption(item): @@ -141,26 +129,13 @@ cdef void readOptions(XMLNode * node, dc): break listbase = node.addChildNode(six.b('Option')) listbase.addAttribute(< string > six.b('key'), < string > item) - listbase.addAttribute(< string > six.b('listsize'), < float32 > val.size) - index = 0 + data = <double*>np.PyArray_DATA(np.ascontiguousarray(val,dtype=np.float64)) if val.ndim == 2: - for i in range(val.shape[0]): - for j in range(val.shape[1]): - itm = listbase.addChildNode(six.b('ListItem')) - itm.addAttribute(< string > six.b('index'), < float32 > index) - itm.addAttribute( < string > six.b('value'), < float32 > val[i, j]) - index += 1 - del itm + listbase.setContent(data, val.shape[1], val.shape[0], False) elif val.ndim == 1: - for i in range(val.shape[0]): - itm = listbase.addChildNode(six.b('ListItem')) - itm.addAttribute(< string > six.b('index'), < float32 > index) - itm.addAttribute(< string > six.b('value'), < float32 > val[i]) - index += 1 - del itm + listbase.setContent(data, val.shape[0]) else: raise Exception("Only 1 or 2 dimensions are allowed") - del listbase else: node.addOption(item, wrap_to_bytes(val)) @@ -214,10 +189,10 @@ def stringToPythonValue(inputIn): return str(input) -cdef XMLNode2dict(XMLNode * node): - cdef XMLNode * subnode - cdef list[XMLNode * ] nodes - cdef list[XMLNode * ].iterator it +cdef XMLNode2dict(XMLNode node): + cdef XMLNode subnode + cdef list[XMLNode] nodes + cdef list[XMLNode].iterator it dct = {} opts = {} if node.hasAttribute(six.b('type')): @@ -230,7 +205,6 @@ cdef XMLNode2dict(XMLNode * node): opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getAttribute('value')) else: dct[castString(subnode.getName())] = stringToPythonValue(subnode.getContent()) - del subnode inc(it) if len(opts)>0: dct['options'] = opts return dct diff --git a/python/docSRC/index.rst b/python/docSRC/index.rst index 8d17a4a..b7cc6d6 100644 --- a/python/docSRC/index.rst +++ b/python/docSRC/index.rst @@ -18,7 +18,7 @@ Contents: matrix creators functions - ASTRAProjector + operator matlab astra .. astra diff --git a/python/docSRC/ASTRAProjector.rst b/python/docSRC/operator.rst index 1c267e3..f5369fa 100644 --- a/python/docSRC/ASTRAProjector.rst +++ b/python/docSRC/operator.rst @@ -1,7 +1,7 @@ -Helper class: the :mod:`ASTRAProjector` module +OpTomo class: the :mod:`operator` module ============================================== -.. automodule:: astra.ASTRAProjector +.. automodule:: astra.operator :members: :undoc-members: :show-inheritance: diff --git a/src/ArtAlgorithm.cpp b/src/ArtAlgorithm.cpp index 8f058a3..6a699ec 100644 --- a/src/ArtAlgorithm.cpp +++ b/src/ArtAlgorithm.cpp @@ -132,7 +132,7 @@ bool CArtAlgorithm::initialize(const Config& _cfg) } // ray order - string projOrder = _cfg.self->getOption("RayOrder", "sequential"); + string projOrder = _cfg.self.getOption("RayOrder", "sequential"); CC.markOptionParsed("RayOrder"); m_iCurrentRay = 0; m_iRayCount = m_pProjector->getProjectionGeometry()->getProjectionAngleCount() * @@ -145,7 +145,7 @@ bool CArtAlgorithm::initialize(const Config& _cfg) m_piDetectorOrder[i] = i % m_pProjector->getProjectionGeometry()->getDetectorCount(); } } else if (projOrder == "custom") { - vector<float32> rayOrderList = _cfg.self->getOptionNumericalArray("RayOrderList"); + vector<float32> rayOrderList = _cfg.self.getOptionNumericalArray("RayOrderList"); m_iRayCount = rayOrderList.size() / 2; m_piProjectionOrder = new int[m_iRayCount]; m_piDetectorOrder = new int[m_iRayCount]; @@ -158,7 +158,7 @@ bool CArtAlgorithm::initialize(const Config& _cfg) return false; } - m_fLambda = _cfg.self->getOptionNumerical("Lambda", 1.0f); + m_fLambda = _cfg.self.getOptionNumerical("Lambda", 1.0f); CC.markOptionParsed("Lambda"); // success diff --git a/src/ConeProjectionGeometry3D.cpp b/src/ConeProjectionGeometry3D.cpp index 1976901..dd22eba 100644 --- a/src/ConeProjectionGeometry3D.cpp +++ b/src/ConeProjectionGeometry3D.cpp @@ -87,17 +87,15 @@ bool CConeProjectionGeometry3D::initialize(const Config& _cfg) CProjectionGeometry3D::initialize(_cfg); // Required: DistanceOriginDetector - XMLNode* node = _cfg.self->getSingleNode("DistanceOriginDetector"); + XMLNode node = _cfg.self.getSingleNode("DistanceOriginDetector"); ASTRA_CONFIG_CHECK(node, "ConeProjectionGeometry3D", "No DistanceOriginDetector tag specified."); - m_fOriginDetectorDistance = boost::lexical_cast<float32>(node->getContent()); - ASTRA_DELETE(node); + m_fOriginDetectorDistance = boost::lexical_cast<float32>(node.getContent()); CC.markNodeParsed("DistanceOriginDetector"); // Required: DetectorOriginSource - node = _cfg.self->getSingleNode("DistanceOriginSource"); + node = _cfg.self.getSingleNode("DistanceOriginSource"); ASTRA_CONFIG_CHECK(node, "ConeProjectionGeometry3D", "No DistanceOriginSource tag specified."); - m_fOriginSourceDistance = boost::lexical_cast<float32>(node->getContent()); - ASTRA_DELETE(node); + m_fOriginSourceDistance = boost::lexical_cast<float32>(node.getContent()); CC.markNodeParsed("DistanceOriginSource"); // success @@ -193,14 +191,14 @@ Config* CConeProjectionGeometry3D::getConfiguration() const { Config* cfg = new Config(); cfg->initialize("ProjectionGeometry3D"); - cfg->self->addAttribute("type", "cone"); - cfg->self->addChildNode("DetectorSpacingX", m_fDetectorSpacingX); - cfg->self->addChildNode("DetectorSpacingY", m_fDetectorSpacingY); - cfg->self->addChildNode("DetectorRowCount", m_iDetectorRowCount); - cfg->self->addChildNode("DetectorColCount", m_iDetectorColCount); - cfg->self->addChildNode("DistanceOriginDetector", m_fOriginDetectorDistance); - cfg->self->addChildNode("DistanceOriginSource", m_fOriginSourceDistance); - cfg->self->addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); + cfg->self.addAttribute("type", "cone"); + cfg->self.addChildNode("DetectorSpacingX", m_fDetectorSpacingX); + cfg->self.addChildNode("DetectorSpacingY", m_fDetectorSpacingY); + cfg->self.addChildNode("DetectorRowCount", m_iDetectorRowCount); + cfg->self.addChildNode("DetectorColCount", m_iDetectorColCount); + cfg->self.addChildNode("DistanceOriginDetector", m_fOriginDetectorDistance); + cfg->self.addChildNode("DistanceOriginSource", m_fOriginSourceDistance); + cfg->self.addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); return cfg; } diff --git a/src/ConeVecProjectionGeometry3D.cpp b/src/ConeVecProjectionGeometry3D.cpp index 9dc273d..47ed630 100644 --- a/src/ConeVecProjectionGeometry3D.cpp +++ b/src/ConeVecProjectionGeometry3D.cpp @@ -73,33 +73,30 @@ bool CConeVecProjectionGeometry3D::initialize(const Config& _cfg) ASTRA_ASSERT(_cfg.self); ConfigStackCheck<CProjectionGeometry3D> CC("ConeVecProjectionGeometry3D", this, _cfg); - XMLNode* node; + XMLNode node; // TODO: Fix up class hierarchy... this class doesn't fit very well. // initialization of parent class //CProjectionGeometry3D::initialize(_cfg); // Required: DetectorRowCount - node = _cfg.self->getSingleNode("DetectorRowCount"); + node = _cfg.self.getSingleNode("DetectorRowCount"); ASTRA_CONFIG_CHECK(node, "ConeVecProjectionGeometry3D", "No DetectorRowCount tag specified."); - m_iDetectorRowCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iDetectorRowCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("DetectorRowCount"); // Required: DetectorColCount - node = _cfg.self->getSingleNode("DetectorColCount"); + node = _cfg.self.getSingleNode("DetectorColCount"); ASTRA_CONFIG_CHECK(node, "ConeVecProjectionGeometry3D", "No DetectorColCount tag specified."); - m_iDetectorColCount = boost::lexical_cast<int>(node->getContent()); + m_iDetectorColCount = boost::lexical_cast<int>(node.getContent()); m_iDetectorTotCount = m_iDetectorRowCount * m_iDetectorColCount; - ASTRA_DELETE(node); CC.markNodeParsed("DetectorColCount"); // Required: Vectors - node = _cfg.self->getSingleNode("Vectors"); + node = _cfg.self.getSingleNode("Vectors"); ASTRA_CONFIG_CHECK(node, "ConeVecProjectionGeometry3D", "No Vectors tag specified."); - vector<double> data = node->getContentNumericalArrayDouble(); + vector<double> data = node.getContentNumericalArrayDouble(); CC.markNodeParsed("Vectors"); - ASTRA_DELETE(node); ASTRA_CONFIG_CHECK(data.size() % 12 == 0, "ConeVecProjectionGeometry3D", "Vectors doesn't consist of 12-tuples."); m_iProjectionAngleCount = data.size() / 12; m_pProjectionAngles = new SConeProjection[m_iProjectionAngleCount]; @@ -208,9 +205,9 @@ Config* CConeVecProjectionGeometry3D::getConfiguration() const Config* cfg = new Config(); cfg->initialize("ProjectionGeometry3D"); - cfg->self->addAttribute("type", "cone_vec"); - cfg->self->addChildNode("DetectorRowCount", m_iDetectorRowCount); - cfg->self->addChildNode("DetectorColCount", m_iDetectorColCount); + cfg->self.addAttribute("type", "cone_vec"); + cfg->self.addChildNode("DetectorRowCount", m_iDetectorRowCount); + cfg->self.addChildNode("DetectorColCount", m_iDetectorColCount); std::string vectors = ""; for (int i = 0; i < m_iProjectionAngleCount; ++i) { @@ -229,7 +226,7 @@ Config* CConeVecProjectionGeometry3D::getConfiguration() const vectors += boost::lexical_cast<string>(p.fDetVZ); if (i < m_iProjectionAngleCount-1) vectors += ';'; } - cfg->self->addChildNode("Vectors", vectors); + cfg->self.addChildNode("Vectors", vectors); return cfg; } diff --git a/src/Config.cpp b/src/Config.cpp index d860638..395080b 100644 --- a/src/Config.cpp +++ b/src/Config.cpp @@ -45,31 +45,33 @@ using namespace std; //----------------------------------------------------------------------------- // default constructor -Config::Config() +Config::Config() : self() { - self = 0; + _doc = 0; } //----------------------------------------------------------------------------- // not so default constructor -Config::Config(XMLNode* _self) +Config::Config(XMLNode _self) { self = _self; + _doc = 0; } //----------------------------------------------------------------------------- Config::~Config() { - delete self; - self = 0; + delete _doc; + _doc = 0; } //----------------------------------------------------------------------------- void Config::initialize(std::string rootname) { - if (self == 0) { + if (!self) { XMLDocument* doc = XMLDocument::createDocument(rootname); self = doc->getRootNode(); + _doc = doc; } } @@ -124,13 +126,13 @@ bool ConfigStackCheck<T>::stopParsing() std::string errors; - std::list<XMLNode*> nodes = cfg->self->getNodes(); - for (std::list<XMLNode*>::iterator i = nodes.begin(); i != nodes.end(); ++i) + std::list<XMLNode> nodes = cfg->self.getNodes(); + for (std::list<XMLNode>::iterator i = nodes.begin(); i != nodes.end(); ++i) { - std::string nodeName = (*i)->getName(); + std::string nodeName = i->getName(); if (nodeName == "Option") { - nodeName = (*i)->getAttribute("key", ""); + nodeName = i->getAttribute("key", ""); if (object->configCheckData->parsedOptions.find(nodeName) == object->configCheckData->parsedOptions.end()) { if (!errors.empty()) errors += ", "; errors += nodeName; @@ -142,8 +144,6 @@ bool ConfigStackCheck<T>::stopParsing() } } } - for (std::list<XMLNode*>::iterator i = nodes.begin(); i != nodes.end(); ++i) - delete (*i); nodes.clear(); if (!errors.empty()) { diff --git a/src/CudaBackProjectionAlgorithm3D.cpp b/src/CudaBackProjectionAlgorithm3D.cpp index abcf096..fbb8f28 100644 --- a/src/CudaBackProjectionAlgorithm3D.cpp +++ b/src/CudaBackProjectionAlgorithm3D.cpp @@ -102,9 +102,9 @@ bool CCudaBackProjectionAlgorithm3D::initialize(const Config& _cfg) return false; } - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); CC.markOptionParsed("GPUindex"); - m_iVoxelSuperSampling = (int)_cfg.self->getOptionNumerical("VoxelSuperSampling", 1); + m_iVoxelSuperSampling = (int)_cfg.self.getOptionNumerical("VoxelSuperSampling", 1); CC.markOptionParsed("VoxelSuperSampling"); CFloat32ProjectionData3DMemory* pSinoMem = dynamic_cast<CFloat32ProjectionData3DMemory*>(m_pSinogram); @@ -114,7 +114,7 @@ const CParallelProjectionGeometry3D* par3dgeom = dynamic_cast<const CParallelPro const CParallelVecProjectionGeometry3D* parvec3dgeom = dynamic_cast<const CParallelVecProjectionGeometry3D*>(projgeom); if (parvec3dgeom || par3dgeom) { // This option is only supported for Par3D currently - m_bSIRTWeighting = _cfg.self->getOptionBool("SIRTWeighting", false); + m_bSIRTWeighting = _cfg.self.getOptionBool("SIRTWeighting", false); CC.markOptionParsed("SIRTWeighting"); } diff --git a/src/CudaCglsAlgorithm3D.cpp b/src/CudaCglsAlgorithm3D.cpp index a5500d6..3457b81 100644 --- a/src/CudaCglsAlgorithm3D.cpp +++ b/src/CudaCglsAlgorithm3D.cpp @@ -106,11 +106,11 @@ bool CCudaCglsAlgorithm3D::initialize(const Config& _cfg) return false; } - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); CC.markOptionParsed("GPUindex"); - m_iDetectorSuperSampling = (int)_cfg.self->getOptionNumerical("DetectorSuperSampling", 1); + m_iDetectorSuperSampling = (int)_cfg.self.getOptionNumerical("DetectorSuperSampling", 1); CC.markOptionParsed("DetectorSuperSampling"); - m_iVoxelSuperSampling = (int)_cfg.self->getOptionNumerical("VoxelSuperSampling", 1); + m_iVoxelSuperSampling = (int)_cfg.self.getOptionNumerical("VoxelSuperSampling", 1); CC.markOptionParsed("VoxelSuperSampling"); m_pCgls = new AstraCGLS3d(); diff --git a/src/CudaDartMaskAlgorithm.cpp b/src/CudaDartMaskAlgorithm.cpp index dcdefcc..950b428 100644 --- a/src/CudaDartMaskAlgorithm.cpp +++ b/src/CudaDartMaskAlgorithm.cpp @@ -65,38 +65,36 @@ bool CCudaDartMaskAlgorithm::initialize(const Config& _cfg) ConfigStackCheck<CAlgorithm> CC("CudaDartMaskAlgorithm", this, _cfg); // reconstruction data - XMLNode* node = _cfg.self->getSingleNode("SegmentationDataId"); + XMLNode node = _cfg.self.getSingleNode("SegmentationDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No SegmentationDataId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pSegmentation = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("SegmentationDataId"); // reconstruction data - node = _cfg.self->getSingleNode("MaskDataId"); + node = _cfg.self.getSingleNode("MaskDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No MaskDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pMask = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("MaskDataId"); // Option: GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUIndex", m_iGPUIndex); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUIndex", m_iGPUIndex); CC.markOptionParsed("GPUindex"); - if (!_cfg.self->hasOption("GPUindex")) + if (!_cfg.self.hasOption("GPUindex")) CC.markOptionParsed("GPUIndex"); // Option: Connectivity - m_iConn = (unsigned int)_cfg.self->getOptionNumerical("Connectivity", 8); + m_iConn = (unsigned int)_cfg.self.getOptionNumerical("Connectivity", 8); CC.markOptionParsed("Connectivity"); // Option: Threshold - m_iThreshold = (unsigned int)_cfg.self->getOptionNumerical("Threshold", 1); + m_iThreshold = (unsigned int)_cfg.self.getOptionNumerical("Threshold", 1); CC.markOptionParsed("Threshold"); // Option: Radius - m_iRadius = (unsigned int)_cfg.self->getOptionNumerical("Radius", 1); + m_iRadius = (unsigned int)_cfg.self.getOptionNumerical("Radius", 1); CC.markOptionParsed("Radius"); _check(); diff --git a/src/CudaDartMaskAlgorithm3D.cpp b/src/CudaDartMaskAlgorithm3D.cpp index f3500b9..b0dfc5b 100644 --- a/src/CudaDartMaskAlgorithm3D.cpp +++ b/src/CudaDartMaskAlgorithm3D.cpp @@ -65,38 +65,36 @@ bool CCudaDartMaskAlgorithm3D::initialize(const Config& _cfg) ConfigStackCheck<CAlgorithm> CC("CudaDartMaskAlgorithm", this, _cfg); // reconstruction data - XMLNode* node = _cfg.self->getSingleNode("SegmentationDataId"); + XMLNode node = _cfg.self.getSingleNode("SegmentationDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No SegmentationDataId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pSegmentation = dynamic_cast<CFloat32VolumeData3DMemory*>(CData3DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("SegmentationDataId"); // reconstruction data - node = _cfg.self->getSingleNode("MaskDataId"); + node = _cfg.self.getSingleNode("MaskDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No MaskDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pMask = dynamic_cast<CFloat32VolumeData3DMemory*>(CData3DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("MaskDataId"); // Option: GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUIndex", m_iGPUIndex); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUIndex", m_iGPUIndex); CC.markOptionParsed("GPUindex"); - if (!_cfg.self->hasOption("GPUindex")) + if (!_cfg.self.hasOption("GPUindex")) CC.markOptionParsed("GPUIndex"); // Option: Connectivity - m_iConn = (unsigned int)_cfg.self->getOptionNumerical("Connectivity", 8); + m_iConn = (unsigned int)_cfg.self.getOptionNumerical("Connectivity", 8); CC.markOptionParsed("Connectivity"); // Option: Threshold - m_iThreshold = (unsigned int)_cfg.self->getOptionNumerical("Threshold", 1); + m_iThreshold = (unsigned int)_cfg.self.getOptionNumerical("Threshold", 1); CC.markOptionParsed("Threshold"); // Option: Radius - m_iRadius = (unsigned int)_cfg.self->getOptionNumerical("Radius", 1); + m_iRadius = (unsigned int)_cfg.self.getOptionNumerical("Radius", 1); CC.markOptionParsed("Radius"); _check(); diff --git a/src/CudaDartSmoothingAlgorithm.cpp b/src/CudaDartSmoothingAlgorithm.cpp index 2f2103f..7e22809 100644 --- a/src/CudaDartSmoothingAlgorithm.cpp +++ b/src/CudaDartSmoothingAlgorithm.cpp @@ -65,34 +65,32 @@ bool CCudaDartSmoothingAlgorithm::initialize(const Config& _cfg) ConfigStackCheck<CAlgorithm> CC("CudaDartSmoothingAlgorithm", this, _cfg); // reconstruction data - XMLNode* node = _cfg.self->getSingleNode("InDataId"); + XMLNode node = _cfg.self.getSingleNode("InDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No InDataId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pIn = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("InDataId"); // reconstruction data - node = _cfg.self->getSingleNode("OutDataId"); + node = _cfg.self.getSingleNode("OutDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No OutDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pOut = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("OutDataId"); // Option: GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUIndex", m_iGPUIndex); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUIndex", m_iGPUIndex); CC.markOptionParsed("GPUindex"); - if (!_cfg.self->hasOption("GPUindex")) + if (!_cfg.self.hasOption("GPUindex")) CC.markOptionParsed("GPUIndex"); // Option: Radius - m_fB = (float)_cfg.self->getOptionNumerical("Intensity", 0.3f); + m_fB = (float)_cfg.self.getOptionNumerical("Intensity", 0.3f); CC.markOptionParsed("Intensity"); // Option: Radius - m_iRadius = (unsigned int)_cfg.self->getOptionNumerical("Radius", 1); + m_iRadius = (unsigned int)_cfg.self.getOptionNumerical("Radius", 1); CC.markOptionParsed("Radius"); diff --git a/src/CudaDartSmoothingAlgorithm3D.cpp b/src/CudaDartSmoothingAlgorithm3D.cpp index f3cf015..9c4437a 100644 --- a/src/CudaDartSmoothingAlgorithm3D.cpp +++ b/src/CudaDartSmoothingAlgorithm3D.cpp @@ -65,34 +65,32 @@ bool CCudaDartSmoothingAlgorithm3D::initialize(const Config& _cfg) ConfigStackCheck<CAlgorithm> CC("CudaDartSmoothingAlgorithm", this, _cfg); // reconstruction data - XMLNode* node = _cfg.self->getSingleNode("InDataId"); + XMLNode node = _cfg.self.getSingleNode("InDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No InDataId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pIn = dynamic_cast<CFloat32VolumeData3DMemory*>(CData3DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("InDataId"); // reconstruction data - node = _cfg.self->getSingleNode("OutDataId"); + node = _cfg.self.getSingleNode("OutDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No OutDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pOut = dynamic_cast<CFloat32VolumeData3DMemory*>(CData3DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("OutDataId"); // Option: GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUIndex", m_iGPUIndex); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUIndex", m_iGPUIndex); CC.markOptionParsed("GPUindex"); - if (!_cfg.self->hasOption("GPUindex")) + if (!_cfg.self.hasOption("GPUindex")) CC.markOptionParsed("GPUIndex"); // Option: Intensity - m_fB = (float)_cfg.self->getOptionNumerical("Intensity", 0.3f); + m_fB = (float)_cfg.self.getOptionNumerical("Intensity", 0.3f); CC.markOptionParsed("Intensity"); // Option: Radius - m_iRadius = (unsigned int)_cfg.self->getOptionNumerical("Radius", 1); + m_iRadius = (unsigned int)_cfg.self.getOptionNumerical("Radius", 1); CC.markOptionParsed("Radius"); _check(); diff --git a/src/CudaDataOperationAlgorithm.cpp b/src/CudaDataOperationAlgorithm.cpp index 79a9d7f..ae133c2 100644 --- a/src/CudaDataOperationAlgorithm.cpp +++ b/src/CudaDataOperationAlgorithm.cpp @@ -67,40 +67,37 @@ bool CCudaDataOperationAlgorithm::initialize(const Config& _cfg) ConfigStackCheck<CAlgorithm> CC("CCudaDataOperationAlgorithm", this, _cfg); // operation - XMLNode* node = _cfg.self->getSingleNode("Operation"); + XMLNode node = _cfg.self.getSingleNode("Operation"); ASTRA_CONFIG_CHECK(node, "CCudaDataOperationAlgorithm", "No Operation tag specified."); - m_sOperation = node->getContent(); + m_sOperation = node.getContent(); m_sOperation.erase(std::remove(m_sOperation.begin(), m_sOperation.end(), ' '), m_sOperation.end()); - ASTRA_DELETE(node); CC.markNodeParsed("Operation"); // data - node = _cfg.self->getSingleNode("DataId"); + node = _cfg.self.getSingleNode("DataId"); ASTRA_CONFIG_CHECK(node, "CCudaDataOperationAlgorithm", "No DataId tag specified."); - vector<string> data = node->getContentArray(); + vector<string> data = node.getContentArray(); for (vector<string>::iterator it = data.begin(); it != data.end(); it++){ int id = boost::lexical_cast<int>(*it); m_pData.push_back(dynamic_cast<CFloat32Data2D*>(CData2DManager::getSingleton().get(id))); } - ASTRA_DELETE(node); CC.markNodeParsed("DataId"); // scalar - node = _cfg.self->getSingleNode("Scalar"); + node = _cfg.self.getSingleNode("Scalar"); ASTRA_CONFIG_CHECK(node, "CCudaDataOperationAlgorithm", "No Scalar tag specified."); - m_fScalar = node->getContentNumericalArray(); - ASTRA_DELETE(node); + m_fScalar = node.getContentNumericalArray(); CC.markNodeParsed("Scalar"); // Option: GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUIndex", m_iGPUIndex); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUIndex", m_iGPUIndex); CC.markOptionParsed("GPUindex"); - if (!_cfg.self->hasOption("GPUindex")) + if (!_cfg.self.hasOption("GPUindex")) CC.markOptionParsed("GPUIndex"); - if (_cfg.self->hasOption("MaskId")) { - int id = boost::lexical_cast<int>(_cfg.self->getOption("MaskId")); + if (_cfg.self.hasOption("MaskId")) { + int id = boost::lexical_cast<int>(_cfg.self.getOption("MaskId")); m_pMask = dynamic_cast<CFloat32Data2D*>(CData2DManager::getSingleton().get(id)); } CC.markOptionParsed("MaskId"); diff --git a/src/CudaFDKAlgorithm3D.cpp b/src/CudaFDKAlgorithm3D.cpp index 7638696..467e641 100644 --- a/src/CudaFDKAlgorithm3D.cpp +++ b/src/CudaFDKAlgorithm3D.cpp @@ -100,12 +100,12 @@ bool CCudaFDKAlgorithm3D::initialize(const Config& _cfg) return false; } - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); CC.markOptionParsed("GPUindex"); - m_iVoxelSuperSampling = (int)_cfg.self->getOptionNumerical("VoxelSuperSampling", 1); + m_iVoxelSuperSampling = (int)_cfg.self.getOptionNumerical("VoxelSuperSampling", 1); CC.markOptionParsed("VoxelSuperSampling"); - m_bShortScan = _cfg.self->getOptionBool("ShortScan", false); + m_bShortScan = _cfg.self.getOptionBool("ShortScan", false); CC.markOptionParsed("ShortScan"); // success diff --git a/src/CudaFilteredBackProjectionAlgorithm.cpp b/src/CudaFilteredBackProjectionAlgorithm.cpp index 0badc20..5d6c166 100644 --- a/src/CudaFilteredBackProjectionAlgorithm.cpp +++ b/src/CudaFilteredBackProjectionAlgorithm.cpp @@ -78,39 +78,36 @@ bool CCudaFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) } // sinogram data - XMLNode* node = _cfg.self->getSingleNode("ProjectionDataId"); + XMLNode node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "CudaFBP", "No ProjectionDataId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pSinogram = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ProjectionDataId"); // reconstruction data - node = _cfg.self->getSingleNode("ReconstructionDataId"); + node = _cfg.self.getSingleNode("ReconstructionDataId"); ASTRA_CONFIG_CHECK(node, "CudaFBP", "No ReconstructionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pReconstruction = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ReconstructionDataId"); // filter type - node = _cfg.self->getSingleNode("FilterType"); - if(node != NULL) + node = _cfg.self.getSingleNode("FilterType"); + if (node) { - m_eFilter = _convertStringToFilter(node->getContent().c_str()); + m_eFilter = _convertStringToFilter(node.getContent().c_str()); } else { m_eFilter = FILTER_RAMLAK; } CC.markNodeParsed("FilterType"); - ASTRA_DELETE(node); // filter - node = _cfg.self->getSingleNode("FilterSinogramId"); - if(node != NULL) + node = _cfg.self.getSingleNode("FilterSinogramId"); + if (node) { - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); const CFloat32ProjectionData2D * pFilterData = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); m_iFilterWidth = pFilterData->getGeometry()->getDetectorCount(); int iFilterProjectionCount = pFilterData->getGeometry()->getProjectionAngleCount(); @@ -124,13 +121,12 @@ bool CCudaFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) m_pfFilter = NULL; } CC.markNodeParsed("FilterSinogramId"); // TODO: Only for some types! - ASTRA_DELETE(node); // filter parameter - node = _cfg.self->getSingleNode("FilterParameter"); - if(node != NULL) + node = _cfg.self.getSingleNode("FilterParameter"); + if (node) { - float fParameter = boost::lexical_cast<float>(node->getContent()); + float fParameter = boost::lexical_cast<float>(node.getContent()); m_fFilterParameter = fParameter; } else @@ -138,13 +134,12 @@ bool CCudaFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) m_fFilterParameter = -1.0f; } CC.markNodeParsed("FilterParameter"); // TODO: Only for some types! - ASTRA_DELETE(node); // D value - node = _cfg.self->getSingleNode("FilterD"); - if(node != NULL) + node = _cfg.self.getSingleNode("FilterD"); + if (node) { - float fD = boost::lexical_cast<float>(node->getContent()); + float fD = boost::lexical_cast<float>(node.getContent()); m_fFilterD = fD; } else @@ -152,19 +147,18 @@ bool CCudaFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) m_fFilterD = 1.0f; } CC.markNodeParsed("FilterD"); // TODO: Only for some types! - ASTRA_DELETE(node); // GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); CC.markOptionParsed("GPUindex"); // Pixel supersampling factor - m_iPixelSuperSampling = (int)_cfg.self->getOptionNumerical("PixelSuperSampling", 1); + m_iPixelSuperSampling = (int)_cfg.self.getOptionNumerical("PixelSuperSampling", 1); CC.markOptionParsed("PixelSuperSampling"); // Fan beam short scan mode if (m_pSinogram && dynamic_cast<CFanFlatProjectionGeometry2D*>(m_pSinogram->getGeometry())) { - m_bShortScan = (int)_cfg.self->getOptionBool("ShortScan", false); + m_bShortScan = (int)_cfg.self.getOptionBool("ShortScan", false); CC.markOptionParsed("ShortScan"); } diff --git a/src/CudaForwardProjectionAlgorithm.cpp b/src/CudaForwardProjectionAlgorithm.cpp index 95abb62..0f97d59 100644 --- a/src/CudaForwardProjectionAlgorithm.cpp +++ b/src/CudaForwardProjectionAlgorithm.cpp @@ -73,42 +73,39 @@ bool CCudaForwardProjectionAlgorithm::initialize(const Config& _cfg) ConfigStackCheck<CAlgorithm> CC("CudaForwardProjectionAlgorithm", this, _cfg); // sinogram data - XMLNode* node = _cfg.self->getSingleNode("ProjectionDataId"); + XMLNode node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "FP_CUDA", "No ProjectionDataId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pSinogram = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ProjectionDataId"); // volume data - node = _cfg.self->getSingleNode("VolumeDataId"); + node = _cfg.self.getSingleNode("VolumeDataId"); ASTRA_CONFIG_CHECK(node, "FP_CUDA", "No VolumeDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pVolume = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("VolumeDataId"); // GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUIndex", m_iGPUIndex); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUIndex", m_iGPUIndex); CC.markOptionParsed("GPUindex"); - if (!_cfg.self->hasOption("GPUindex")) + if (!_cfg.self.hasOption("GPUindex")) CC.markOptionParsed("GPUIndex"); // Detector supersampling factor - m_iDetectorSuperSampling = (int)_cfg.self->getOptionNumerical("DetectorSuperSampling", 1); + m_iDetectorSuperSampling = (int)_cfg.self.getOptionNumerical("DetectorSuperSampling", 1); CC.markOptionParsed("DetectorSuperSampling"); // This isn't used yet, but passing it is not something to warn about - node = _cfg.self->getSingleNode("ProjectorId"); + node = _cfg.self.getSingleNode("ProjectorId"); if (node) { - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); CProjector2D *projector = CProjector2DManager::getSingleton().get(id); if (!dynamic_cast<CCudaProjector2D*>(projector)) { ASTRA_WARN("non-CUDA Projector2D passed to FP_CUDA"); } - delete node; } CC.markNodeParsed("ProjectorId"); diff --git a/src/CudaForwardProjectionAlgorithm3D.cpp b/src/CudaForwardProjectionAlgorithm3D.cpp index 8e6bab5..e29b5a9 100644 --- a/src/CudaForwardProjectionAlgorithm3D.cpp +++ b/src/CudaForwardProjectionAlgorithm3D.cpp @@ -78,40 +78,37 @@ bool CCudaForwardProjectionAlgorithm3D::initialize(const Config& _cfg) ASTRA_ASSERT(_cfg.self); ConfigStackCheck<CAlgorithm> CC("CudaForwardProjectionAlgorithm3D", this, _cfg); - XMLNode* node; + XMLNode node; int id; // sinogram data - node = _cfg.self->getSingleNode("ProjectionDataId"); + node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "CudaForwardProjection3D", "No ProjectionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pProjections = dynamic_cast<CFloat32ProjectionData3DMemory*>(CData3DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ProjectionDataId"); // reconstruction data - node = _cfg.self->getSingleNode("VolumeDataId"); + node = _cfg.self.getSingleNode("VolumeDataId"); ASTRA_CONFIG_CHECK(node, "CudaForwardProjection3D", "No VolumeDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pVolume = dynamic_cast<CFloat32VolumeData3DMemory*>(CData3DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("VolumeDataId"); // optional: projector - node = _cfg.self->getSingleNode("ProjectorId"); + node = _cfg.self.getSingleNode("ProjectorId"); if (node) { - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pProjector = CProjector3DManager::getSingleton().get(id); - ASTRA_DELETE(node); } else { m_pProjector = 0; // TODO: or manually construct default projector? } CC.markNodeParsed("ProjectorId"); // GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); CC.markOptionParsed("GPUindex"); - m_iDetectorSuperSampling = (int)_cfg.self->getOptionNumerical("DetectorSuperSampling", 1); + m_iDetectorSuperSampling = (int)_cfg.self.getOptionNumerical("DetectorSuperSampling", 1); CC.markOptionParsed("DetectorSuperSampling"); // success diff --git a/src/CudaProjector2D.cpp b/src/CudaProjector2D.cpp index 056ea3b..fa024c8 100644 --- a/src/CudaProjector2D.cpp +++ b/src/CudaProjector2D.cpp @@ -104,10 +104,10 @@ bool CCudaProjector2D::initialize(const Config& _cfg) // TODO: Check the projection geometry is a supported type - XMLNode* node = _cfg.self->getSingleNode("ProjectionKernel"); + XMLNode node = _cfg.self.getSingleNode("ProjectionKernel"); m_projectionKernel = ker2d_default; if (node) { - std::string sProjKernel = node->getContent(); + std::string sProjKernel = node.getContent(); if (sProjKernel == "default") { @@ -115,7 +115,6 @@ bool CCudaProjector2D::initialize(const Config& _cfg) return false; } } - ASTRA_DELETE(node); CC.markNodeParsed("ProjectionKernel"); m_bIsInitialized = _check(); diff --git a/src/CudaProjector3D.cpp b/src/CudaProjector3D.cpp index 2f4c799..41529a5 100644 --- a/src/CudaProjector3D.cpp +++ b/src/CudaProjector3D.cpp @@ -105,10 +105,10 @@ bool CCudaProjector3D::initialize(const Config& _cfg) return false; } - XMLNode* node = _cfg.self->getSingleNode("ProjectionKernel"); + XMLNode node = _cfg.self.getSingleNode("ProjectionKernel"); m_projectionKernel = ker3d_default; if (node) { - std::string sProjKernel = node->getContent(); + std::string sProjKernel = node.getContent(); if (sProjKernel == "default") { @@ -118,7 +118,6 @@ bool CCudaProjector3D::initialize(const Config& _cfg) return false; } } - ASTRA_DELETE(node); CC.markNodeParsed("ProjectionKernel"); m_bIsInitialized = _check(); diff --git a/src/CudaReconstructionAlgorithm2D.cpp b/src/CudaReconstructionAlgorithm2D.cpp index 1c6b763..db99d42 100644 --- a/src/CudaReconstructionAlgorithm2D.cpp +++ b/src/CudaReconstructionAlgorithm2D.cpp @@ -96,91 +96,88 @@ bool CCudaReconstructionAlgorithm2D::initialize(const Config& _cfg) } // sinogram data - XMLNode* node = _cfg.self->getSingleNode("ProjectionDataId"); + XMLNode node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "CudaSirt2", "No ProjectionDataId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pSinogram = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ProjectionDataId"); // reconstruction data - node = _cfg.self->getSingleNode("ReconstructionDataId"); + node = _cfg.self.getSingleNode("ReconstructionDataId"); ASTRA_CONFIG_CHECK(node, "CudaSirt2", "No ReconstructionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pReconstruction = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ReconstructionDataId"); // fixed mask - if (_cfg.self->hasOption("ReconstructionMaskId")) { + if (_cfg.self.hasOption("ReconstructionMaskId")) { m_bUseReconstructionMask = true; - id = boost::lexical_cast<int>(_cfg.self->getOption("ReconstructionMaskId")); + id = boost::lexical_cast<int>(_cfg.self.getOption("ReconstructionMaskId")); m_pReconstructionMask = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); ASTRA_CONFIG_CHECK(m_pReconstructionMask, "CudaReconstruction2D", "Invalid ReconstructionMaskId."); } CC.markOptionParsed("ReconstructionMaskId"); // fixed mask - if (_cfg.self->hasOption("SinogramMaskId")) { + if (_cfg.self.hasOption("SinogramMaskId")) { m_bUseSinogramMask = true; - id = boost::lexical_cast<int>(_cfg.self->getOption("SinogramMaskId")); + id = boost::lexical_cast<int>(_cfg.self.getOption("SinogramMaskId")); m_pSinogramMask = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); ASTRA_CONFIG_CHECK(m_pSinogramMask, "CudaReconstruction2D", "Invalid SinogramMaskId."); } CC.markOptionParsed("SinogramMaskId"); // Constraints - NEW - if (_cfg.self->hasOption("MinConstraint")) { + if (_cfg.self.hasOption("MinConstraint")) { m_bUseMinConstraint = true; - m_fMinValue = _cfg.self->getOptionNumerical("MinConstraint", 0.0f); + m_fMinValue = _cfg.self.getOptionNumerical("MinConstraint", 0.0f); CC.markOptionParsed("MinConstraint"); } else { // Constraint - OLD - m_bUseMinConstraint = _cfg.self->getOptionBool("UseMinConstraint", false); + m_bUseMinConstraint = _cfg.self.getOptionBool("UseMinConstraint", false); CC.markOptionParsed("UseMinConstraint"); if (m_bUseMinConstraint) { - m_fMinValue = _cfg.self->getOptionNumerical("MinConstraintValue", 0.0f); + m_fMinValue = _cfg.self.getOptionNumerical("MinConstraintValue", 0.0f); CC.markOptionParsed("MinConstraintValue"); } } - if (_cfg.self->hasOption("MaxConstraint")) { + if (_cfg.self.hasOption("MaxConstraint")) { m_bUseMaxConstraint = true; - m_fMaxValue = _cfg.self->getOptionNumerical("MaxConstraint", 255.0f); + m_fMaxValue = _cfg.self.getOptionNumerical("MaxConstraint", 255.0f); CC.markOptionParsed("MaxConstraint"); } else { // Constraint - OLD - m_bUseMaxConstraint = _cfg.self->getOptionBool("UseMaxConstraint", false); + m_bUseMaxConstraint = _cfg.self.getOptionBool("UseMaxConstraint", false); CC.markOptionParsed("UseMaxConstraint"); if (m_bUseMaxConstraint) { - m_fMaxValue = _cfg.self->getOptionNumerical("MaxConstraintValue", 0.0f); + m_fMaxValue = _cfg.self.getOptionNumerical("MaxConstraintValue", 0.0f); CC.markOptionParsed("MaxConstraintValue"); } } // GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUIndex", m_iGPUIndex); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUIndex", m_iGPUIndex); CC.markOptionParsed("GPUindex"); - if (!_cfg.self->hasOption("GPUindex")) + if (!_cfg.self.hasOption("GPUindex")) CC.markOptionParsed("GPUIndex"); // Detector supersampling factor - m_iDetectorSuperSampling = (int)_cfg.self->getOptionNumerical("DetectorSuperSampling", 1); + m_iDetectorSuperSampling = (int)_cfg.self.getOptionNumerical("DetectorSuperSampling", 1); CC.markOptionParsed("DetectorSuperSampling"); // Pixel supersampling factor - m_iPixelSuperSampling = (int)_cfg.self->getOptionNumerical("PixelSuperSampling", 1); + m_iPixelSuperSampling = (int)_cfg.self.getOptionNumerical("PixelSuperSampling", 1); CC.markOptionParsed("PixelSuperSampling"); // This isn't used yet, but passing it is not something to warn about - node = _cfg.self->getSingleNode("ProjectorId"); + node = _cfg.self.getSingleNode("ProjectorId"); if (node) { - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); CProjector2D *projector = CProjector2DManager::getSingleton().get(id); if (!dynamic_cast<CCudaProjector2D*>(projector)) { ASTRA_WARN("non-CUDA Projector2D passed"); } - delete node; } CC.markNodeParsed("ProjectorId"); diff --git a/src/CudaRoiSelectAlgorithm.cpp b/src/CudaRoiSelectAlgorithm.cpp index bfccb3a..7635c69 100644 --- a/src/CudaRoiSelectAlgorithm.cpp +++ b/src/CudaRoiSelectAlgorithm.cpp @@ -66,22 +66,21 @@ bool CCudaRoiSelectAlgorithm::initialize(const Config& _cfg) ConfigStackCheck<CAlgorithm> CC("CudaDartMaskAlgorithm", this, _cfg); // reconstruction data - XMLNode* node = _cfg.self->getSingleNode("DataId"); + XMLNode node = _cfg.self.getSingleNode("DataId"); ASTRA_CONFIG_CHECK(node, "CudaRoiSelect", "No DataId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pData = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("DataId"); // Option: GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUIndex", m_iGPUIndex); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUIndex", m_iGPUIndex); CC.markOptionParsed("GPUindex"); - if (!_cfg.self->hasOption("GPUindex")) + if (!_cfg.self.hasOption("GPUindex")) CC.markOptionParsed("GPUIndex"); // Option: Radius - m_fRadius = (unsigned int)_cfg.self->getOptionNumerical("Radius", 0.0f); + m_fRadius = (unsigned int)_cfg.self.getOptionNumerical("Radius", 0.0f); CC.markOptionParsed("Radius"); _check(); diff --git a/src/CudaSartAlgorithm.cpp b/src/CudaSartAlgorithm.cpp index 8e22c59..8c0c6d7 100644 --- a/src/CudaSartAlgorithm.cpp +++ b/src/CudaSartAlgorithm.cpp @@ -74,7 +74,7 @@ bool CCudaSartAlgorithm::initialize(const Config& _cfg) // projection order int projectionCount = m_pSinogram->getGeometry()->getProjectionAngleCount(); int* projectionOrder = NULL; - string projOrder = _cfg.self->getOption("ProjectionOrder", "random"); + string projOrder = _cfg.self.getOption("ProjectionOrder", "random"); CC.markOptionParsed("ProjectionOrder"); if (projOrder == "sequential") { projectionOrder = new int[projectionCount]; @@ -97,7 +97,7 @@ bool CCudaSartAlgorithm::initialize(const Config& _cfg) sart->setProjectionOrder(projectionOrder, projectionCount); delete[] projectionOrder; } else if (projOrder == "custom") { - vector<float32> projOrderList = _cfg.self->getOptionNumericalArray("ProjectionOrderList"); + vector<float32> projOrderList = _cfg.self.getOptionNumericalArray("ProjectionOrderList"); projectionOrder = new int[projOrderList.size()]; for (int i = 0; i < projOrderList.size(); i++) { projectionOrder[i] = static_cast<int>(projOrderList[i]); diff --git a/src/CudaSirtAlgorithm.cpp b/src/CudaSirtAlgorithm.cpp index f6eb79a..d424915 100644 --- a/src/CudaSirtAlgorithm.cpp +++ b/src/CudaSirtAlgorithm.cpp @@ -76,13 +76,13 @@ bool CCudaSirtAlgorithm::initialize(const Config& _cfg) return false; // min/max masks - if (_cfg.self->hasOption("MinMaskId")) { - int id = boost::lexical_cast<int>(_cfg.self->getOption("MinMaskId")); + if (_cfg.self.hasOption("MinMaskId")) { + int id = boost::lexical_cast<int>(_cfg.self.getOption("MinMaskId")); m_pMinMask = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); } CC.markOptionParsed("MinMaskId"); - if (_cfg.self->hasOption("MaxMaskId")) { - int id = boost::lexical_cast<int>(_cfg.self->getOption("MaxMaskId")); + if (_cfg.self.hasOption("MaxMaskId")) { + int id = boost::lexical_cast<int>(_cfg.self.getOption("MaxMaskId")); m_pMaxMask = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); } CC.markOptionParsed("MaxMaskId"); diff --git a/src/CudaSirtAlgorithm3D.cpp b/src/CudaSirtAlgorithm3D.cpp index da83c7e..5ad131b 100644 --- a/src/CudaSirtAlgorithm3D.cpp +++ b/src/CudaSirtAlgorithm3D.cpp @@ -107,11 +107,11 @@ bool CCudaSirtAlgorithm3D::initialize(const Config& _cfg) return false; } - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); CC.markOptionParsed("GPUindex"); - m_iDetectorSuperSampling = (int)_cfg.self->getOptionNumerical("DetectorSuperSampling", 1); + m_iDetectorSuperSampling = (int)_cfg.self.getOptionNumerical("DetectorSuperSampling", 1); CC.markOptionParsed("DetectorSuperSampling"); - m_iVoxelSuperSampling = (int)_cfg.self->getOptionNumerical("VoxelSuperSampling", 1); + m_iVoxelSuperSampling = (int)_cfg.self.getOptionNumerical("VoxelSuperSampling", 1); CC.markOptionParsed("VoxelSuperSampling"); m_pSirt = new AstraSIRT3d(); diff --git a/src/FanFlatProjectionGeometry2D.cpp b/src/FanFlatProjectionGeometry2D.cpp index d757f18..32a19bc 100644 --- a/src/FanFlatProjectionGeometry2D.cpp +++ b/src/FanFlatProjectionGeometry2D.cpp @@ -134,17 +134,15 @@ bool CFanFlatProjectionGeometry2D::initialize(const Config& _cfg) CProjectionGeometry2D::initialize(_cfg); // Required: DistanceOriginDetector - XMLNode* node = _cfg.self->getSingleNode("DistanceOriginDetector"); + XMLNode node = _cfg.self.getSingleNode("DistanceOriginDetector"); ASTRA_CONFIG_CHECK(node, "FanFlatProjectionGeometry2D", "No DistanceOriginDetector tag specified."); - m_fOriginDetectorDistance = boost::lexical_cast<float32>(node->getContent()); - ASTRA_DELETE(node); + m_fOriginDetectorDistance = boost::lexical_cast<float32>(node.getContent()); CC.markNodeParsed("DistanceOriginDetector"); // Required: DetectorOriginSource - node = _cfg.self->getSingleNode("DistanceOriginSource"); + node = _cfg.self.getSingleNode("DistanceOriginSource"); ASTRA_CONFIG_CHECK(node, "FanFlatProjectionGeometry2D", "No DistanceOriginSource tag specified."); - m_fOriginSourceDistance = boost::lexical_cast<float32>(node->getContent()); - ASTRA_DELETE(node); + m_fOriginSourceDistance = boost::lexical_cast<float32>(node.getContent()); CC.markNodeParsed("DistanceOriginSource"); // success @@ -209,12 +207,12 @@ Config* CFanFlatProjectionGeometry2D::getConfiguration() const { Config* cfg = new Config(); cfg->initialize("ProjectionGeometry2D"); - cfg->self->addAttribute("type", "fanflat"); - cfg->self->addChildNode("DetectorCount", getDetectorCount()); - cfg->self->addChildNode("DetectorWidth", getDetectorWidth()); - cfg->self->addChildNode("DistanceOriginSource", getOriginSourceDistance()); - cfg->self->addChildNode("DistanceOriginDetector", getOriginDetectorDistance()); - cfg->self->addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); + cfg->self.addAttribute("type", "fanflat"); + cfg->self.addChildNode("DetectorCount", getDetectorCount()); + cfg->self.addChildNode("DetectorWidth", getDetectorWidth()); + cfg->self.addChildNode("DistanceOriginSource", getOriginSourceDistance()); + cfg->self.addChildNode("DistanceOriginDetector", getOriginDetectorDistance()); + cfg->self.addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); return cfg; } //---------------------------------------------------------------------------------------- diff --git a/src/FanFlatVecProjectionGeometry2D.cpp b/src/FanFlatVecProjectionGeometry2D.cpp index 9c7b596..4104379 100644 --- a/src/FanFlatVecProjectionGeometry2D.cpp +++ b/src/FanFlatVecProjectionGeometry2D.cpp @@ -116,25 +116,23 @@ bool CFanFlatVecProjectionGeometry2D::initialize(const Config& _cfg) ASTRA_ASSERT(_cfg.self); ConfigStackCheck<CProjectionGeometry2D> CC("FanFlatVecProjectionGeometry2D", this, _cfg); - XMLNode* node; + XMLNode node; // TODO: Fix up class hierarchy... this class doesn't fit very well. // initialization of parent class //CProjectionGeometry2D::initialize(_cfg); // Required: DetectorCount - node = _cfg.self->getSingleNode("DetectorCount"); + node = _cfg.self.getSingleNode("DetectorCount"); ASTRA_CONFIG_CHECK(node, "FanFlatVecProjectionGeometry3D", "No DetectorRowCount tag specified."); - m_iDetectorCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iDetectorCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("DetectorCount"); // Required: Vectors - node = _cfg.self->getSingleNode("Vectors"); + node = _cfg.self.getSingleNode("Vectors"); ASTRA_CONFIG_CHECK(node, "FanFlatVecProjectionGeometry3D", "No Vectors tag specified."); - vector<float32> data = node->getContentNumericalArray(); + vector<float32> data = node.getContentNumericalArray(); CC.markNodeParsed("Vectors"); - ASTRA_DELETE(node); ASTRA_CONFIG_CHECK(data.size() % 6 == 0, "FanFlatVecProjectionGeometry3D", "Vectors doesn't consist of 6-tuples."); m_iProjectionAngleCount = data.size() / 6; m_pProjectionAngles = new SFanProjection[m_iProjectionAngleCount]; @@ -232,8 +230,8 @@ Config* CFanFlatVecProjectionGeometry2D::getConfiguration() const { Config* cfg = new Config(); cfg->initialize("ProjectionGeometry2D"); - cfg->self->addAttribute("type", "fanflat_vec"); - cfg->self->addChildNode("DetectorCount", getDetectorCount()); + cfg->self.addAttribute("type", "fanflat_vec"); + cfg->self.addChildNode("DetectorCount", getDetectorCount()); std::string vectors = ""; for (int i = 0; i < m_iProjectionAngleCount; ++i) { SFanProjection& p = m_pProjectionAngles[i]; @@ -245,7 +243,7 @@ Config* CFanFlatVecProjectionGeometry2D::getConfiguration() const vectors += boost::lexical_cast<string>(p.fDetUY); if (i < m_iProjectionAngleCount-1) vectors += ';'; } - cfg->self->addChildNode("Vectors", vectors); + cfg->self.addChildNode("Vectors", vectors); return cfg; } //---------------------------------------------------------------------------------------- diff --git a/src/FilteredBackProjectionAlgorithm.cpp b/src/FilteredBackProjectionAlgorithm.cpp index 4a8e5ac..f494d22 100644 --- a/src/FilteredBackProjectionAlgorithm.cpp +++ b/src/FilteredBackProjectionAlgorithm.cpp @@ -94,30 +94,27 @@ bool CFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) ASTRA_ASSERT(_cfg.self); // projector - XMLNode* node = _cfg.self->getSingleNode("ProjectorId"); + XMLNode node = _cfg.self.getSingleNode("ProjectorId"); ASTRA_CONFIG_CHECK(node, "FilteredBackProjection", "No ProjectorId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pProjector = CProjector2DManager::getSingleton().get(id); - ASTRA_DELETE(node); // sinogram data - node = _cfg.self->getSingleNode("ProjectionDataId"); + node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "FilteredBackProjection", "No ProjectionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pSinogram = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); // volume data - node = _cfg.self->getSingleNode("ReconstructionDataId"); + node = _cfg.self.getSingleNode("ReconstructionDataId"); ASTRA_CONFIG_CHECK(node, "FilteredBackProjection", "No ReconstructionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pReconstruction = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); - node = _cfg.self->getSingleNode("ProjectionIndex"); + node = _cfg.self.getSingleNode("ProjectionIndex"); if (node) { - vector<float32> projectionIndex = node->getContentNumericalArray(); + vector<float32> projectionIndex = node.getContentNumericalArray(); int angleCount = projectionIndex.size(); int detectorCount = m_pProjector->getProjectionGeometry()->getDetectorCount(); @@ -154,7 +151,6 @@ bool CFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) m_pProjector = new CParallelBeamLineKernelProjector2D(pg,m_pReconstruction->getGeometry()); m_pSinogram = new CFloat32ProjectionData2D(pg, sinogramData2D); } - ASTRA_DELETE(node); // TODO: check that the angles are linearly spaced between 0 and pi diff --git a/src/Float32ProjectionData2D.cpp b/src/Float32ProjectionData2D.cpp index 85e0cdd..f7f83e3 100644 --- a/src/Float32ProjectionData2D.cpp +++ b/src/Float32ProjectionData2D.cpp @@ -75,6 +75,16 @@ CFloat32ProjectionData2D::CFloat32ProjectionData2D(const CFloat32ProjectionData2 m_bInitialized = true; } +//---------------------------------------------------------------------------------------- +// Create an instance of the CFloat32ProjectionData2D class with pre-allocated data +CFloat32ProjectionData2D::CFloat32ProjectionData2D(CProjectionGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory) +{ + m_bInitialized = false; + m_bInitialized = initialize(_pGeometry, _pCustomMemory); +} + + + // Assignment operator CFloat32ProjectionData2D& CFloat32ProjectionData2D::operator=(const CFloat32ProjectionData2D& _other) @@ -119,6 +129,15 @@ bool CFloat32ProjectionData2D::initialize(CProjectionGeometry2D* _pGeometry, flo } //---------------------------------------------------------------------------------------- +// Initialization +bool CFloat32ProjectionData2D::initialize(CProjectionGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory) +{ + m_pGeometry = _pGeometry->clone(); + m_bInitialized = _initialize(m_pGeometry->getDetectorCount(), m_pGeometry->getProjectionAngleCount(), _pCustomMemory); + return m_bInitialized; +} + +//---------------------------------------------------------------------------------------- // Destructor CFloat32ProjectionData2D::~CFloat32ProjectionData2D() { diff --git a/src/Float32ProjectionData3D.cpp b/src/Float32ProjectionData3D.cpp index d039c83..2bd0447 100644 --- a/src/Float32ProjectionData3D.cpp +++ b/src/Float32ProjectionData3D.cpp @@ -270,4 +270,13 @@ CFloat32ProjectionData3D& CFloat32ProjectionData3D::operator-=(const float32& _f return *this; } +void CFloat32ProjectionData3D::changeGeometry(CProjectionGeometry3D* _pGeometry) +{ + if (!m_bInitialized) return; + + delete m_pGeometry; + m_pGeometry = _pGeometry->clone(); +} + + } // end namespace astra diff --git a/src/Float32VolumeData2D.cpp b/src/Float32VolumeData2D.cpp index e11c4e4..c903c66 100644 --- a/src/Float32VolumeData2D.cpp +++ b/src/Float32VolumeData2D.cpp @@ -72,6 +72,15 @@ CFloat32VolumeData2D::CFloat32VolumeData2D(const CFloat32VolumeData2D& _other) : m_bInitialized = true; } +//---------------------------------------------------------------------------------------- +// Create an instance of the CFloat32VolumeData2D class with pre-allocated data +CFloat32VolumeData2D::CFloat32VolumeData2D(CVolumeGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory) +{ + m_bInitialized = false; + m_bInitialized = initialize(_pGeometry, _pCustomMemory); +} + + // Assignment operator CFloat32VolumeData2D& CFloat32VolumeData2D::operator=(const CFloat32VolumeData2D& _other) @@ -122,6 +131,17 @@ bool CFloat32VolumeData2D::initialize(CVolumeGeometry2D* _pGeometry, float32 _fS m_bInitialized = _initialize(m_pGeometry->getGridColCount(), m_pGeometry->getGridRowCount(), _fScalar); return m_bInitialized; } + +//---------------------------------------------------------------------------------------- +// Initialization +bool CFloat32VolumeData2D::initialize(CVolumeGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory) +{ + m_pGeometry = _pGeometry->clone(); + m_bInitialized = _initialize(m_pGeometry->getGridColCount(), m_pGeometry->getGridRowCount(), _pCustomMemory); + return m_bInitialized; +} + + //---------------------------------------------------------------------------------------- void CFloat32VolumeData2D::changeGeometry(CVolumeGeometry2D* _pGeometry) { diff --git a/src/Float32VolumeData3D.cpp b/src/Float32VolumeData3D.cpp index ce00a10..bd78001 100644 --- a/src/Float32VolumeData3D.cpp +++ b/src/Float32VolumeData3D.cpp @@ -266,4 +266,13 @@ CFloat32VolumeData3D& CFloat32VolumeData3D::operator-=(const float32& _fScalar) return *this; } +void CFloat32VolumeData3D::changeGeometry(CVolumeGeometry3D* _pGeometry) +{ + if (!m_bInitialized) return; + + delete m_pGeometry; + m_pGeometry = _pGeometry->clone(); +} + + } // end namespace astra diff --git a/src/ForwardProjectionAlgorithm.cpp b/src/ForwardProjectionAlgorithm.cpp index b530491..f356824 100644 --- a/src/ForwardProjectionAlgorithm.cpp +++ b/src/ForwardProjectionAlgorithm.cpp @@ -126,37 +126,34 @@ bool CForwardProjectionAlgorithm::initialize(const Config& _cfg) } // projector - XMLNode* node = _cfg.self->getSingleNode("ProjectorId"); + XMLNode node = _cfg.self.getSingleNode("ProjectorId"); ASTRA_CONFIG_CHECK(node, "ForwardProjection", "No ProjectorId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pProjector = CProjector2DManager::getSingleton().get(id); - ASTRA_DELETE(node); // sinogram data - node = _cfg.self->getSingleNode("ProjectionDataId"); + node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "ForwardProjection", "No ProjectionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pSinogram = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); // volume data - node = _cfg.self->getSingleNode("VolumeDataId"); + node = _cfg.self.getSingleNode("VolumeDataId"); ASTRA_CONFIG_CHECK(node, "ForwardProjection", "No VolumeDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pVolume = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); // volume mask - if (_cfg.self->hasOption("VolumeMaskId")) { + if (_cfg.self.hasOption("VolumeMaskId")) { m_bUseVolumeMask = true; - id = boost::lexical_cast<int>(_cfg.self->getOption("VolumeMaskId")); + id = boost::lexical_cast<int>(_cfg.self.getOption("VolumeMaskId")); m_pVolumeMask = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); } // sino mask - if (_cfg.self->hasOption("SinogramMaskId")) { + if (_cfg.self.hasOption("SinogramMaskId")) { m_bUseSinogramMask = true; - id = boost::lexical_cast<int>(_cfg.self->getOption("SinogramMaskId")); + id = boost::lexical_cast<int>(_cfg.self.getOption("SinogramMaskId")); m_pSinogramMask = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); } diff --git a/src/ParallelBeamBlobKernelProjector2D.cpp b/src/ParallelBeamBlobKernelProjector2D.cpp index 3253f88..4559a48 100644 --- a/src/ParallelBeamBlobKernelProjector2D.cpp +++ b/src/ParallelBeamBlobKernelProjector2D.cpp @@ -128,28 +128,28 @@ bool CParallelBeamBlobKernelProjector2D::initialize(const Config& _cfg) } // required: Kernel - XMLNode* node = _cfg.self->getSingleNode("Kernel"); + XMLNode node = _cfg.self.getSingleNode("Kernel"); ASTRA_CONFIG_CHECK(node, "BlobProjector", "No Kernel tag specified."); { // Required: KernelSize - XMLNode* node2 = node->getSingleNode("KernelSize"); + XMLNode node2 = node.getSingleNode("KernelSize"); ASTRA_CONFIG_CHECK(node2, "BlobProjector", "No Kernel/KernelSize tag specified."); - m_fBlobSize = boost::lexical_cast<float32>(node2->getContent()); + m_fBlobSize = boost::lexical_cast<float32>(node2.getContent()); // Required: SampleRate - node2 = node->getSingleNode("SampleRate"); + node2 = node.getSingleNode("SampleRate"); ASTRA_CONFIG_CHECK(node2, "BlobProjector", "No Kernel/SampleRate tag specified."); - m_fBlobSampleRate = boost::lexical_cast<float32>(node2->getContent()); + m_fBlobSampleRate = boost::lexical_cast<float32>(node2.getContent()); // Required: SampleCount - node2 = node->getSingleNode("SampleCount"); + node2 = node.getSingleNode("SampleCount"); ASTRA_CONFIG_CHECK(node2, "BlobProjector", "No Kernel/SampleCount tag specified."); - m_iBlobSampleCount = boost::lexical_cast<int>(node2->getContent()); + m_iBlobSampleCount = boost::lexical_cast<int>(node2.getContent()); // Required: KernelValues - node2 = node->getSingleNode("KernelValues"); + node2 = node.getSingleNode("KernelValues"); ASTRA_CONFIG_CHECK(node2, "BlobProjector", "No Kernel/KernelValues tag specified."); - vector<float32> values = node2->getContentNumericalArray(); + vector<float32> values = node2.getContentNumericalArray(); ASTRA_CONFIG_CHECK(values.size() == (unsigned int)m_iBlobSampleCount, "BlobProjector", "Number of specified values doesn't match SampleCount."); m_pfBlobValues = new float32[m_iBlobSampleCount]; for (int i = 0; i < m_iBlobSampleCount; i++) { @@ -157,9 +157,9 @@ bool CParallelBeamBlobKernelProjector2D::initialize(const Config& _cfg) } // Required: KernelValues - node2 = node->getSingleNode("KernelValuesNeg"); + node2 = node.getSingleNode("KernelValuesNeg"); ASTRA_CONFIG_CHECK(node2, "BlobProjector", "No Kernel/KernelValuesNeg tag specified."); - vector<float32> values2 = node2->getContentNumericalArray(); + vector<float32> values2 = node2.getContentNumericalArray(); ASTRA_CONFIG_CHECK(values2.size() == (unsigned int)m_iBlobSampleCount, "BlobProjector", "Number of specified values doesn't match SampleCount."); m_pfBlobValuesNeg = new float32[m_iBlobSampleCount]; for (int i = 0; i < m_iBlobSampleCount; i++) { diff --git a/src/ParallelProjectionGeometry2D.cpp b/src/ParallelProjectionGeometry2D.cpp index cac8f30..699e141 100644 --- a/src/ParallelProjectionGeometry2D.cpp +++ b/src/ParallelProjectionGeometry2D.cpp @@ -176,10 +176,10 @@ Config* CParallelProjectionGeometry2D::getConfiguration() const { Config* cfg = new Config(); cfg->initialize("ProjectionGeometry2D"); - cfg->self->addAttribute("type", "parallel"); - cfg->self->addChildNode("DetectorCount", getDetectorCount()); - cfg->self->addChildNode("DetectorWidth", getDetectorWidth()); - cfg->self->addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); + cfg->self.addAttribute("type", "parallel"); + cfg->self.addChildNode("DetectorCount", getDetectorCount()); + cfg->self.addChildNode("DetectorWidth", getDetectorWidth()); + cfg->self.addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); return cfg; } //---------------------------------------------------------------------------------------- diff --git a/src/ParallelProjectionGeometry3D.cpp b/src/ParallelProjectionGeometry3D.cpp index eb200f9..1c87157 100644 --- a/src/ParallelProjectionGeometry3D.cpp +++ b/src/ParallelProjectionGeometry3D.cpp @@ -164,12 +164,12 @@ Config* CParallelProjectionGeometry3D::getConfiguration() const { Config* cfg = new Config(); cfg->initialize("ProjectionGeometry3D"); - cfg->self->addAttribute("type", "parallel3d"); - cfg->self->addChildNode("DetectorRowCount", m_iDetectorRowCount); - cfg->self->addChildNode("DetectorColCount", m_iDetectorColCount); - cfg->self->addChildNode("DetectorSpacingX", m_fDetectorSpacingX); - cfg->self->addChildNode("DetectorSpacingY", m_fDetectorSpacingY); - cfg->self->addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); + cfg->self.addAttribute("type", "parallel3d"); + cfg->self.addChildNode("DetectorRowCount", m_iDetectorRowCount); + cfg->self.addChildNode("DetectorColCount", m_iDetectorColCount); + cfg->self.addChildNode("DetectorSpacingX", m_fDetectorSpacingX); + cfg->self.addChildNode("DetectorSpacingY", m_fDetectorSpacingY); + cfg->self.addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); return cfg; } //---------------------------------------------------------------------------------------- diff --git a/src/ParallelVecProjectionGeometry3D.cpp b/src/ParallelVecProjectionGeometry3D.cpp index dc325e9..ffad6d0 100644 --- a/src/ParallelVecProjectionGeometry3D.cpp +++ b/src/ParallelVecProjectionGeometry3D.cpp @@ -73,33 +73,30 @@ bool CParallelVecProjectionGeometry3D::initialize(const Config& _cfg) ASTRA_ASSERT(_cfg.self); ConfigStackCheck<CProjectionGeometry3D> CC("ParallelVecProjectionGeometry3D", this, _cfg); - XMLNode* node; + XMLNode node; // TODO: Fix up class hierarchy... this class doesn't fit very well. // initialization of parent class //CProjectionGeometry3D::initialize(_cfg); // Required: DetectorRowCount - node = _cfg.self->getSingleNode("DetectorRowCount"); + node = _cfg.self.getSingleNode("DetectorRowCount"); ASTRA_CONFIG_CHECK(node, "ParallelVecProjectionGeometry3D", "No DetectorRowCount tag specified."); - m_iDetectorRowCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iDetectorRowCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("DetectorRowCount"); // Required: DetectorCount - node = _cfg.self->getSingleNode("DetectorColCount"); + node = _cfg.self.getSingleNode("DetectorColCount"); ASTRA_CONFIG_CHECK(node, "", "No DetectorColCount tag specified."); - m_iDetectorColCount = boost::lexical_cast<int>(node->getContent()); + m_iDetectorColCount = boost::lexical_cast<int>(node.getContent()); m_iDetectorTotCount = m_iDetectorRowCount * m_iDetectorColCount; - ASTRA_DELETE(node); CC.markNodeParsed("DetectorColCount"); // Required: Vectors - node = _cfg.self->getSingleNode("Vectors"); + node = _cfg.self.getSingleNode("Vectors"); ASTRA_CONFIG_CHECK(node, "ParallelVecProjectionGeometry3D", "No Vectors tag specified."); - vector<double> data = node->getContentNumericalArrayDouble(); + vector<double> data = node.getContentNumericalArrayDouble(); CC.markNodeParsed("Vectors"); - ASTRA_DELETE(node); ASTRA_CONFIG_CHECK(data.size() % 12 == 0, "ParallelVecProjectionGeometry3D", "Vectors doesn't consist of 12-tuples."); m_iProjectionAngleCount = data.size() / 12; m_pProjectionAngles = new SPar3DProjection[m_iProjectionAngleCount]; @@ -208,9 +205,9 @@ Config* CParallelVecProjectionGeometry3D::getConfiguration() const Config* cfg = new Config(); cfg->initialize("ProjectionGeometry3D"); - cfg->self->addAttribute("type", "parallel3d_vec"); - cfg->self->addChildNode("DetectorRowCount", m_iDetectorRowCount); - cfg->self->addChildNode("DetectorColCount", m_iDetectorColCount); + cfg->self.addAttribute("type", "parallel3d_vec"); + cfg->self.addChildNode("DetectorRowCount", m_iDetectorRowCount); + cfg->self.addChildNode("DetectorColCount", m_iDetectorColCount); std::string vectors = ""; for (int i = 0; i < m_iProjectionAngleCount; ++i) { @@ -229,7 +226,7 @@ Config* CParallelVecProjectionGeometry3D::getConfiguration() const vectors += boost::lexical_cast<string>(p.fDetVZ); if (i < m_iProjectionAngleCount-1) vectors += ';'; } - cfg->self->addChildNode("Vectors", vectors); + cfg->self.addChildNode("Vectors", vectors); return cfg; } diff --git a/src/ProjectionGeometry2D.cpp b/src/ProjectionGeometry2D.cpp index 89b5fe0..b89605b 100644 --- a/src/ProjectionGeometry2D.cpp +++ b/src/ProjectionGeometry2D.cpp @@ -124,24 +124,21 @@ bool CProjectionGeometry2D::initialize(const Config& _cfg) } // Required: DetectorWidth - XMLNode* node = _cfg.self->getSingleNode("DetectorWidth"); + XMLNode node = _cfg.self.getSingleNode("DetectorWidth"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry2D", "No DetectorWidth tag specified."); - m_fDetectorWidth = boost::lexical_cast<float32>(node->getContent()); - ASTRA_DELETE(node); + m_fDetectorWidth = boost::lexical_cast<float32>(node.getContent()); CC.markNodeParsed("DetectorWidth"); // Required: DetectorCount - node = _cfg.self->getSingleNode("DetectorCount"); + node = _cfg.self.getSingleNode("DetectorCount"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry2D", "No DetectorCount tag specified."); - m_iDetectorCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iDetectorCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("DetectorCount"); // Required: ProjectionAngles - node = _cfg.self->getSingleNode("ProjectionAngles"); + node = _cfg.self.getSingleNode("ProjectionAngles"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry2D", "No ProjectionAngles tag specified."); - vector<float32> angles = node->getContentNumericalArray(); - delete node; + vector<float32> angles = node.getContentNumericalArray(); m_iProjectionAngleCount = angles.size(); ASTRA_CONFIG_CHECK(m_iProjectionAngleCount > 0, "ProjectionGeometry2D", "Not enough ProjectionAngles specified."); m_pfProjectionAngles = new float32[m_iProjectionAngleCount]; @@ -150,7 +147,7 @@ bool CProjectionGeometry2D::initialize(const Config& _cfg) } CC.markNodeParsed("ProjectionAngles"); - vector<float32> offset = _cfg.self->getOptionNumericalArray("ExtraDetectorOffset"); + vector<float32> offset = _cfg.self.getOptionNumericalArray("ExtraDetectorOffset"); m_pfExtraDetectorOffset = new float32[m_iProjectionAngleCount]; if (offset.size() == (size_t)m_iProjectionAngleCount) { for (int i = 0; i < m_iProjectionAngleCount; i++) { diff --git a/src/ProjectionGeometry3D.cpp b/src/ProjectionGeometry3D.cpp index 5b77767..ef0246c 100644 --- a/src/ProjectionGeometry3D.cpp +++ b/src/ProjectionGeometry3D.cpp @@ -149,38 +149,34 @@ bool CProjectionGeometry3D::initialize(const Config& _cfg) ASTRA_ASSERT(_cfg.self); // Required: DetectorWidth - XMLNode* node = _cfg.self->getSingleNode("DetectorSpacingX"); + XMLNode node = _cfg.self.getSingleNode("DetectorSpacingX"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry3D", "No DetectorSpacingX tag specified."); - m_fDetectorSpacingX = boost::lexical_cast<float32>(node->getContent()); - ASTRA_DELETE(node); + m_fDetectorSpacingX = boost::lexical_cast<float32>(node.getContent()); CC.markNodeParsed("DetectorSpacingX"); // Required: DetectorHeight - node = _cfg.self->getSingleNode("DetectorSpacingY"); + node = _cfg.self.getSingleNode("DetectorSpacingY"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry3D", "No DetectorSpacingY tag specified."); - m_fDetectorSpacingY = boost::lexical_cast<float32>(node->getContent()); - ASTRA_DELETE(node); + m_fDetectorSpacingY = boost::lexical_cast<float32>(node.getContent()); CC.markNodeParsed("DetectorSpacingY"); // Required: DetectorRowCount - node = _cfg.self->getSingleNode("DetectorRowCount"); + node = _cfg.self.getSingleNode("DetectorRowCount"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry3D", "No DetectorRowCount tag specified."); - m_iDetectorRowCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iDetectorRowCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("DetectorRowCount"); // Required: DetectorCount - node = _cfg.self->getSingleNode("DetectorColCount"); + node = _cfg.self.getSingleNode("DetectorColCount"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry3D", "No DetectorColCount tag specified."); - m_iDetectorColCount = boost::lexical_cast<int>(node->getContent()); + m_iDetectorColCount = boost::lexical_cast<int>(node.getContent()); m_iDetectorTotCount = m_iDetectorRowCount * m_iDetectorColCount; - ASTRA_DELETE(node); CC.markNodeParsed("DetectorColCount"); // Required: ProjectionAngles - node = _cfg.self->getSingleNode("ProjectionAngles"); + node = _cfg.self.getSingleNode("ProjectionAngles"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry3D", "No ProjectionAngles tag specified."); - vector<float32> angles = node->getContentNumericalArray(); + vector<float32> angles = node.getContentNumericalArray(); m_iProjectionAngleCount = angles.size(); ASTRA_CONFIG_CHECK(m_iProjectionAngleCount > 0, "ProjectionGeometry3D", "Not enough ProjectionAngles specified."); m_pfProjectionAngles = new float32[m_iProjectionAngleCount]; @@ -188,7 +184,6 @@ bool CProjectionGeometry3D::initialize(const Config& _cfg) m_pfProjectionAngles[i] = angles[i]; } CC.markNodeParsed("ProjectionAngles"); - ASTRA_DELETE(node); // Interface class, so don't return true return false; diff --git a/src/Projector2D.cpp b/src/Projector2D.cpp index 32a2956..cf233a0 100644 --- a/src/Projector2D.cpp +++ b/src/Projector2D.cpp @@ -114,12 +114,12 @@ bool CProjector2D::initialize(const Config& _cfg) } // required: ProjectionGeometry - XMLNode* node = _cfg.self->getSingleNode("ProjectionGeometry"); + XMLNode node = _cfg.self.getSingleNode("ProjectionGeometry"); ASTRA_CONFIG_CHECK(node, "Projector2D", "No ProjectionGeometry tag specified."); // FIXME: Change how the base class is created. (This is duplicated // in astra_mex_data2d.cpp.) - std::string type = node->getAttribute("type"); + std::string type = node.getAttribute("type"); if (type == "sparse_matrix") { m_pProjectionGeometry = new CSparseMatrixProjectionGeometry2D(); m_pProjectionGeometry->initialize(Config(node)); @@ -141,7 +141,7 @@ bool CProjector2D::initialize(const Config& _cfg) // required: VolumeGeometry - node = _cfg.self->getSingleNode("VolumeGeometry"); + node = _cfg.self.getSingleNode("VolumeGeometry"); ASTRA_CONFIG_CHECK(node, "Projector2D", "No VolumeGeometry tag specified."); m_pVolumeGeometry = new CVolumeGeometry2D(); m_pVolumeGeometry->initialize(Config(node)); diff --git a/src/Projector3D.cpp b/src/Projector3D.cpp index b546ee9..5e22105 100644 --- a/src/Projector3D.cpp +++ b/src/Projector3D.cpp @@ -92,11 +92,11 @@ bool CProjector3D::initialize(const Config& _cfg) assert(_cfg.self); ConfigStackCheck<CProjector3D> CC("Projector3D", this, _cfg); - XMLNode* node; + XMLNode node; - node = _cfg.self->getSingleNode("ProjectionGeometry"); + node = _cfg.self.getSingleNode("ProjectionGeometry"); ASTRA_CONFIG_CHECK(node, "Projector3D", "No ProjectionGeometry tag specified."); - std::string type = node->getAttribute("type"); + std::string type = node.getAttribute("type"); CProjectionGeometry3D* pProjGeometry = 0; if (type == "parallel3d") { pProjGeometry = new CParallelProjectionGeometry3D(); @@ -108,18 +108,19 @@ bool CProjector3D::initialize(const Config& _cfg) pProjGeometry = new CConeVecProjectionGeometry3D(); } else { // Invalid geometry type + ASTRA_CONFIG_CHECK(false, "Projector3D", "Invalid projection geometry type specified."); } pProjGeometry->initialize(Config(node)); // this deletes node m_pProjectionGeometry = pProjGeometry; ASTRA_CONFIG_CHECK(m_pProjectionGeometry->isInitialized(), "Projector3D", "ProjectionGeometry not initialized."); CC.markNodeParsed("ProjectionGeometry"); - node = _cfg.self->getSingleNode("VolumeGeometry"); + node = _cfg.self.getSingleNode("VolumeGeometry"); ASTRA_CONFIG_CHECK(node, "Projector3D", "No VolumeGeometry tag specified."); CVolumeGeometry3D* pVolGeometry = new CVolumeGeometry3D(); pVolGeometry->initialize(Config(node)); // this deletes node m_pVolumeGeometry = pVolGeometry; - ASTRA_CONFIG_CHECK(m_pVolumeGeometry->isInitialized(), "Projector2D", "VolumeGeometry not initialized."); + ASTRA_CONFIG_CHECK(m_pVolumeGeometry->isInitialized(), "Projector3D", "VolumeGeometry not initialized."); CC.markNodeParsed("VolumeGeometry"); return true; diff --git a/src/ReconstructionAlgorithm2D.cpp b/src/ReconstructionAlgorithm2D.cpp index e089fac..767efe6 100644 --- a/src/ReconstructionAlgorithm2D.cpp +++ b/src/ReconstructionAlgorithm2D.cpp @@ -84,71 +84,68 @@ bool CReconstructionAlgorithm2D::initialize(const Config& _cfg) ConfigStackCheck<CAlgorithm> CC("ReconstructionAlgorithm2D", this, _cfg); // projector - XMLNode* node = _cfg.self->getSingleNode("ProjectorId"); + XMLNode node = _cfg.self.getSingleNode("ProjectorId"); ASTRA_CONFIG_CHECK(node, "Reconstruction2D", "No ProjectorId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pProjector = CProjector2DManager::getSingleton().get(id); - ASTRA_DELETE(node); CC.markNodeParsed("ProjectorId"); // sinogram data - node = _cfg.self->getSingleNode("ProjectionDataId"); + node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "Reconstruction2D", "No ProjectionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pSinogram = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ProjectionDataId"); // reconstruction data - node = _cfg.self->getSingleNode("ReconstructionDataId"); + node = _cfg.self.getSingleNode("ReconstructionDataId"); ASTRA_CONFIG_CHECK(node, "Reconstruction2D", "No ReconstructionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pReconstruction = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ReconstructionDataId"); // fixed mask - if (_cfg.self->hasOption("ReconstructionMaskId")) { + if (_cfg.self.hasOption("ReconstructionMaskId")) { m_bUseReconstructionMask = true; - id = boost::lexical_cast<int>(_cfg.self->getOption("ReconstructionMaskId")); + id = boost::lexical_cast<int>(_cfg.self.getOption("ReconstructionMaskId")); m_pReconstructionMask = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); ASTRA_CONFIG_CHECK(m_pReconstructionMask, "Reconstruction2D", "Invalid ReconstructionMaskId."); } CC.markOptionParsed("ReconstructionMaskId"); // fixed mask - if (_cfg.self->hasOption("SinogramMaskId")) { + if (_cfg.self.hasOption("SinogramMaskId")) { m_bUseSinogramMask = true; - id = boost::lexical_cast<int>(_cfg.self->getOption("SinogramMaskId")); + id = boost::lexical_cast<int>(_cfg.self.getOption("SinogramMaskId")); m_pSinogramMask = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); ASTRA_CONFIG_CHECK(m_pSinogramMask, "Reconstruction2D", "Invalid SinogramMaskId."); } CC.markOptionParsed("SinogramMaskId"); // Constraints - NEW - if (_cfg.self->hasOption("MinConstraint")) { + if (_cfg.self.hasOption("MinConstraint")) { m_bUseMinConstraint = true; - m_fMinValue = _cfg.self->getOptionNumerical("MinConstraint", 0.0f); + m_fMinValue = _cfg.self.getOptionNumerical("MinConstraint", 0.0f); CC.markOptionParsed("MinConstraint"); } else { // Constraint - OLD - m_bUseMinConstraint = _cfg.self->getOptionBool("UseMinConstraint", false); + m_bUseMinConstraint = _cfg.self.getOptionBool("UseMinConstraint", false); CC.markOptionParsed("UseMinConstraint"); if (m_bUseMinConstraint) { - m_fMinValue = _cfg.self->getOptionNumerical("MinConstraintValue", 0.0f); + m_fMinValue = _cfg.self.getOptionNumerical("MinConstraintValue", 0.0f); CC.markOptionParsed("MinConstraintValue"); } } - if (_cfg.self->hasOption("MaxConstraint")) { + if (_cfg.self.hasOption("MaxConstraint")) { m_bUseMaxConstraint = true; - m_fMaxValue = _cfg.self->getOptionNumerical("MaxConstraint", 255.0f); + m_fMaxValue = _cfg.self.getOptionNumerical("MaxConstraint", 255.0f); CC.markOptionParsed("MaxConstraint"); } else { // Constraint - OLD - m_bUseMaxConstraint = _cfg.self->getOptionBool("UseMaxConstraint", false); + m_bUseMaxConstraint = _cfg.self.getOptionBool("UseMaxConstraint", false); CC.markOptionParsed("UseMaxConstraint"); if (m_bUseMaxConstraint) { - m_fMaxValue = _cfg.self->getOptionNumerical("MaxConstraintValue", 0.0f); + m_fMaxValue = _cfg.self.getOptionNumerical("MaxConstraintValue", 0.0f); CC.markOptionParsed("MaxConstraintValue"); } } diff --git a/src/ReconstructionAlgorithm3D.cpp b/src/ReconstructionAlgorithm3D.cpp index 13d069d..86b8ab2 100644 --- a/src/ReconstructionAlgorithm3D.cpp +++ b/src/ReconstructionAlgorithm3D.cpp @@ -104,7 +104,7 @@ bool CReconstructionAlgorithm3D::initialize(const Config& _cfg) ASTRA_ASSERT(_cfg.self); ConfigStackCheck<CAlgorithm> CC("ReconstructionAlgorithm3D", this, _cfg); - XMLNode* node; + XMLNode node; int id; #if 0 // projector @@ -116,60 +116,58 @@ bool CReconstructionAlgorithm3D::initialize(const Config& _cfg) #endif // sinogram data - node = _cfg.self->getSingleNode("ProjectionDataId"); + node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "Reconstruction3D", "No ProjectionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pSinogram = dynamic_cast<CFloat32ProjectionData3D*>(CData3DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ProjectionDataId"); // reconstruction data - node = _cfg.self->getSingleNode("ReconstructionDataId"); + node = _cfg.self.getSingleNode("ReconstructionDataId"); ASTRA_CONFIG_CHECK(node, "Reconstruction3D", "No ReconstructionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pReconstruction = dynamic_cast<CFloat32VolumeData3D*>(CData3DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ReconstructionDataId"); // fixed mask - if (_cfg.self->hasOption("ReconstructionMaskId")) { + if (_cfg.self.hasOption("ReconstructionMaskId")) { m_bUseReconstructionMask = true; - id = boost::lexical_cast<int>(_cfg.self->getOption("ReconstructionMaskId")); + id = boost::lexical_cast<int>(_cfg.self.getOption("ReconstructionMaskId")); m_pReconstructionMask = dynamic_cast<CFloat32VolumeData3D*>(CData3DManager::getSingleton().get(id)); } CC.markOptionParsed("ReconstructionMaskId"); // fixed mask - if (_cfg.self->hasOption("SinogramMaskId")) { + if (_cfg.self.hasOption("SinogramMaskId")) { m_bUseSinogramMask = true; - id = boost::lexical_cast<int>(_cfg.self->getOption("SinogramMaskId")); + id = boost::lexical_cast<int>(_cfg.self.getOption("SinogramMaskId")); m_pSinogramMask = dynamic_cast<CFloat32ProjectionData3D*>(CData3DManager::getSingleton().get(id)); } // Constraints - NEW - if (_cfg.self->hasOption("MinConstraint")) { + if (_cfg.self.hasOption("MinConstraint")) { m_bUseMinConstraint = true; - m_fMinValue = _cfg.self->getOptionNumerical("MinConstraint", 0.0f); + m_fMinValue = _cfg.self.getOptionNumerical("MinConstraint", 0.0f); CC.markOptionParsed("MinConstraint"); } else { // Constraint - OLD - m_bUseMinConstraint = _cfg.self->getOptionBool("UseMinConstraint", false); + m_bUseMinConstraint = _cfg.self.getOptionBool("UseMinConstraint", false); CC.markOptionParsed("UseMinConstraint"); if (m_bUseMinConstraint) { - m_fMinValue = _cfg.self->getOptionNumerical("MinConstraintValue", 0.0f); + m_fMinValue = _cfg.self.getOptionNumerical("MinConstraintValue", 0.0f); CC.markOptionParsed("MinConstraintValue"); } } - if (_cfg.self->hasOption("MaxConstraint")) { + if (_cfg.self.hasOption("MaxConstraint")) { m_bUseMaxConstraint = true; - m_fMaxValue = _cfg.self->getOptionNumerical("MaxConstraint", 255.0f); + m_fMaxValue = _cfg.self.getOptionNumerical("MaxConstraint", 255.0f); CC.markOptionParsed("MaxConstraint"); } else { // Constraint - OLD - m_bUseMaxConstraint = _cfg.self->getOptionBool("UseMaxConstraint", false); + m_bUseMaxConstraint = _cfg.self.getOptionBool("UseMaxConstraint", false); CC.markOptionParsed("UseMaxConstraint"); if (m_bUseMaxConstraint) { - m_fMaxValue = _cfg.self->getOptionNumerical("MaxConstraintValue", 0.0f); + m_fMaxValue = _cfg.self.getOptionNumerical("MaxConstraintValue", 0.0f); CC.markOptionParsed("MaxConstraintValue"); } } diff --git a/src/SartAlgorithm.cpp b/src/SartAlgorithm.cpp index f7a1677..e4dc5c7 100644 --- a/src/SartAlgorithm.cpp +++ b/src/SartAlgorithm.cpp @@ -126,7 +126,7 @@ bool CSartAlgorithm::initialize(const Config& _cfg) // projection order m_iCurrentProjection = 0; m_iProjectionCount = m_pProjector->getProjectionGeometry()->getProjectionAngleCount(); - string projOrder = _cfg.self->getOption("ProjectionOrder", "sequential"); + string projOrder = _cfg.self.getOption("ProjectionOrder", "sequential"); CC.markOptionParsed("ProjectionOrder"); if (projOrder == "sequential") { m_piProjectionOrder = new int[m_iProjectionCount]; @@ -145,7 +145,7 @@ bool CSartAlgorithm::initialize(const Config& _cfg) m_piProjectionOrder[i + k] = t; } } else if (projOrder == "custom") { - vector<float32> projOrderList = _cfg.self->getOptionNumericalArray("ProjectionOrderList"); + vector<float32> projOrderList = _cfg.self.getOptionNumericalArray("ProjectionOrderList"); m_piProjectionOrder = new int[projOrderList.size()]; for (int i = 0; i < m_iProjectionCount; i++) { m_piProjectionOrder[i] = static_cast<int>(projOrderList[i]); diff --git a/src/SparseMatrixProjectionGeometry2D.cpp b/src/SparseMatrixProjectionGeometry2D.cpp index 86357d2..073720f 100644 --- a/src/SparseMatrixProjectionGeometry2D.cpp +++ b/src/SparseMatrixProjectionGeometry2D.cpp @@ -98,11 +98,10 @@ bool CSparseMatrixProjectionGeometry2D::initialize(const Config& _cfg) CProjectionGeometry2D::initialize(_cfg); // get matrix - XMLNode* node = _cfg.self->getSingleNode("MatrixID"); + XMLNode node = _cfg.self.getSingleNode("MatrixID"); ASTRA_CONFIG_CHECK(node, "SparseMatrixProjectionGeometry2D", "No MatrixID tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pMatrix = CMatrixManager::getSingleton().get(id); - ASTRA_DELETE(node); CC.markNodeParsed("MatrixID"); // success @@ -194,11 +193,11 @@ Config* CSparseMatrixProjectionGeometry2D::getConfiguration() const { Config* cfg = new Config(); cfg->initialize("ProjectionGeometry2D"); - cfg->self->addAttribute("type", "sparse matrix"); - cfg->self->addChildNode("DetectorCount", getDetectorCount()); - cfg->self->addChildNode("DetectorWidth", getDetectorWidth()); - cfg->self->addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); - cfg->self->addChildNode("MatrixID", CMatrixManager::getSingleton().getIndex(m_pMatrix)); + cfg->self.addAttribute("type", "sparse matrix"); + cfg->self.addChildNode("DetectorCount", getDetectorCount()); + cfg->self.addChildNode("DetectorWidth", getDetectorWidth()); + cfg->self.addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); + cfg->self.addChildNode("MatrixID", CMatrixManager::getSingleton().getIndex(m_pMatrix)); return cfg; } diff --git a/src/VolumeGeometry2D.cpp b/src/VolumeGeometry2D.cpp index d412914..6eea1b2 100644 --- a/src/VolumeGeometry2D.cpp +++ b/src/VolumeGeometry2D.cpp @@ -164,24 +164,22 @@ bool CVolumeGeometry2D::initialize(const Config& _cfg) } // Required: GridColCount - XMLNode* node = _cfg.self->getSingleNode("GridColCount"); + XMLNode node = _cfg.self.getSingleNode("GridColCount"); ASTRA_CONFIG_CHECK(node, "ReconstructionGeometry2D", "No GridColCount tag specified."); - m_iGridColCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iGridColCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("GridColCount"); // Required: GridRowCount - node = _cfg.self->getSingleNode("GridRowCount"); + node = _cfg.self.getSingleNode("GridRowCount"); ASTRA_CONFIG_CHECK(node, "ReconstructionGeometry2D", "No GridRowCount tag specified."); - m_iGridRowCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iGridRowCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("GridRowCount"); // Optional: Window minima and maxima - m_fWindowMinX = _cfg.self->getOptionNumerical("WindowMinX", -m_iGridColCount/2.0f); - m_fWindowMaxX = _cfg.self->getOptionNumerical("WindowMaxX", m_iGridColCount/2.0f); - m_fWindowMinY = _cfg.self->getOptionNumerical("WindowMinY", -m_iGridRowCount/2.0f); - m_fWindowMaxY = _cfg.self->getOptionNumerical("WindowMaxY", m_iGridRowCount/2.0f); + m_fWindowMinX = _cfg.self.getOptionNumerical("WindowMinX", -m_iGridColCount/2.0f); + m_fWindowMaxX = _cfg.self.getOptionNumerical("WindowMaxX", m_iGridColCount/2.0f); + m_fWindowMinY = _cfg.self.getOptionNumerical("WindowMinY", -m_iGridRowCount/2.0f); + m_fWindowMaxY = _cfg.self.getOptionNumerical("WindowMaxY", m_iGridRowCount/2.0f); CC.markOptionParsed("WindowMinX"); CC.markOptionParsed("WindowMaxX"); CC.markOptionParsed("WindowMinY"); @@ -285,13 +283,13 @@ Config* CVolumeGeometry2D::getConfiguration() const Config* cfg = new Config(); cfg->initialize("VolumeGeometry2D"); - cfg->self->addChildNode("GridColCount", m_iGridColCount); - cfg->self->addChildNode("GridRowCount", m_iGridRowCount); + cfg->self.addChildNode("GridColCount", m_iGridColCount); + cfg->self.addChildNode("GridRowCount", m_iGridRowCount); - cfg->self->addOption("WindowMinX", m_fWindowMinX); - cfg->self->addOption("WindowMaxX", m_fWindowMaxX); - cfg->self->addOption("WindowMinY", m_fWindowMinY); - cfg->self->addOption("WindowMaxY", m_fWindowMaxY); + cfg->self.addOption("WindowMinX", m_fWindowMinX); + cfg->self.addOption("WindowMaxX", m_fWindowMaxX); + cfg->self.addOption("WindowMinY", m_fWindowMinY); + cfg->self.addOption("WindowMaxY", m_fWindowMaxY); return cfg; } diff --git a/src/VolumeGeometry3D.cpp b/src/VolumeGeometry3D.cpp index 66e6f0c..a1cf424 100644 --- a/src/VolumeGeometry3D.cpp +++ b/src/VolumeGeometry3D.cpp @@ -192,33 +192,30 @@ bool CVolumeGeometry3D::initialize(const Config& _cfg) } // Required: GridColCount - XMLNode* node = _cfg.self->getSingleNode("GridColCount"); + XMLNode node = _cfg.self.getSingleNode("GridColCount"); ASTRA_CONFIG_CHECK(node, "ReconstructionGeometry2D", "No GridColCount tag specified."); - m_iGridColCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iGridColCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("GridColCount"); // Required: GridRowCount - node = _cfg.self->getSingleNode("GridRowCount"); + node = _cfg.self.getSingleNode("GridRowCount"); ASTRA_CONFIG_CHECK(node, "ReconstructionGeometry2D", "No GridRowCount tag specified."); - m_iGridRowCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iGridRowCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("GridRowCount"); // Required: GridRowCount - node = _cfg.self->getSingleNode("GridSliceCount"); + node = _cfg.self.getSingleNode("GridSliceCount"); ASTRA_CONFIG_CHECK(node, "ReconstructionGeometry2D", "No GridSliceCount tag specified."); - m_iGridSliceCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iGridSliceCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("GridSliceCount"); // Optional: Window minima and maxima - m_fWindowMinX = _cfg.self->getOptionNumerical("WindowMinX", -m_iGridColCount/2.0f); - m_fWindowMaxX = _cfg.self->getOptionNumerical("WindowMaxX", m_iGridColCount/2.0f); - m_fWindowMinY = _cfg.self->getOptionNumerical("WindowMinY", -m_iGridRowCount/2.0f); - m_fWindowMaxY = _cfg.self->getOptionNumerical("WindowMaxY", m_iGridRowCount/2.0f); - m_fWindowMinZ = _cfg.self->getOptionNumerical("WindowMinZ", -m_iGridSliceCount/2.0f); - m_fWindowMaxZ = _cfg.self->getOptionNumerical("WindowMaxZ", m_iGridSliceCount/2.0f); + m_fWindowMinX = _cfg.self.getOptionNumerical("WindowMinX", -m_iGridColCount/2.0f); + m_fWindowMaxX = _cfg.self.getOptionNumerical("WindowMaxX", m_iGridColCount/2.0f); + m_fWindowMinY = _cfg.self.getOptionNumerical("WindowMinY", -m_iGridRowCount/2.0f); + m_fWindowMaxY = _cfg.self.getOptionNumerical("WindowMaxY", m_iGridRowCount/2.0f); + m_fWindowMinZ = _cfg.self.getOptionNumerical("WindowMinZ", -m_iGridSliceCount/2.0f); + m_fWindowMaxZ = _cfg.self.getOptionNumerical("WindowMaxZ", m_iGridSliceCount/2.0f); CC.markOptionParsed("WindowMinX"); CC.markOptionParsed("WindowMaxX"); CC.markOptionParsed("WindowMinY"); @@ -386,16 +383,16 @@ Config* CVolumeGeometry3D::getConfiguration() const Config* cfg = new Config(); cfg->initialize("VolumeGeometry3D"); - cfg->self->addChildNode("GridColCount", m_iGridColCount); - cfg->self->addChildNode("GridRowCount", m_iGridRowCount); - cfg->self->addChildNode("GridSliceCount", m_iGridSliceCount); + cfg->self.addChildNode("GridColCount", m_iGridColCount); + cfg->self.addChildNode("GridRowCount", m_iGridRowCount); + cfg->self.addChildNode("GridSliceCount", m_iGridSliceCount); - cfg->self->addOption("WindowMinX", m_fWindowMinX); - cfg->self->addOption("WindowMaxX", m_fWindowMaxX); - cfg->self->addOption("WindowMinY", m_fWindowMinY); - cfg->self->addOption("WindowMaxY", m_fWindowMaxY); - cfg->self->addOption("WindowMinZ", m_fWindowMinZ); - cfg->self->addOption("WindowMaxZ", m_fWindowMaxZ); + cfg->self.addOption("WindowMinX", m_fWindowMinX); + cfg->self.addOption("WindowMaxX", m_fWindowMaxX); + cfg->self.addOption("WindowMinY", m_fWindowMinY); + cfg->self.addOption("WindowMaxY", m_fWindowMaxY); + cfg->self.addOption("WindowMinZ", m_fWindowMinZ); + cfg->self.addOption("WindowMaxZ", m_fWindowMaxZ); return cfg; } diff --git a/src/XMLDocument.cpp b/src/XMLDocument.cpp index 406564f..716ed9e 100644 --- a/src/XMLDocument.cpp +++ b/src/XMLDocument.cpp @@ -32,13 +32,8 @@ $Id$ #include <iostream> #include <sstream> -#ifdef _MSC_VER #include "rapidxml/rapidxml.hpp" #include "rapidxml/rapidxml_print.hpp" -#else -#include "rapidxml.hpp" -#include "rapidxml_print.hpp" -#endif using namespace rapidxml; using namespace astra; @@ -94,10 +89,9 @@ XMLDocument* XMLDocument::createDocument(string sRootName) } //----------------------------------------------------------------------------- -XMLNode* XMLDocument::getRootNode() +XMLNode XMLDocument::getRootNode() { - // TODO: clean up: this 'new' requires callers to do memory management - return new XMLNode(fDOMDocument->first_node()); + return XMLNode(fDOMDocument->first_node()); } //----------------------------------------------------------------------------- diff --git a/src/XMLNode.cpp b/src/XMLNode.cpp index 4b2bdf4..0ec701f 100644 --- a/src/XMLNode.cpp +++ b/src/XMLNode.cpp @@ -28,15 +28,15 @@ $Id$ #include "astra/XMLNode.h" -#ifdef _MSC_VER #include "rapidxml/rapidxml.hpp" #include "rapidxml/rapidxml_print.hpp" -#else -#include "rapidxml.hpp" -#include "rapidxml_print.hpp" -#endif #include <boost/lexical_cast.hpp> +#include <boost/algorithm/string.hpp> +#include <boost/algorithm/string/split.hpp> +#include <boost/algorithm/string/classification.hpp> + + using namespace rapidxml; using namespace astra; @@ -44,21 +44,10 @@ using namespace std; //----------------------------------------------------------------------------- -// Utility function to delete a list of nodes -static void deleteNodes(list<XMLNode*>& nodes) -{ - for (list<XMLNode*>::iterator i = nodes.begin(); i != nodes.end(); ++i) - delete (*i); - - nodes.clear(); -} - - -//----------------------------------------------------------------------------- // default constructor XMLNode::XMLNode() { - + fDOMElement = 0; } //----------------------------------------------------------------------------- @@ -84,14 +73,14 @@ void XMLNode::setDOMNode(xml_node<>* n) //----------------------------------------------------------------------------- // print XML Node -void XMLNode::print() +void XMLNode::print() const { std::cout << fDOMElement; } //----------------------------------------------------------------------------- // print XML Node -std::string XMLNode::toString() +std::string XMLNode::toString() const { std::string s; ::print(std::back_inserter(s), *fDOMElement, 0); @@ -100,64 +89,61 @@ std::string XMLNode::toString() //----------------------------------------------------------------------------- // Get single node -XMLNode* XMLNode::getSingleNode(string name) +XMLNode XMLNode::getSingleNode(string name) const { xml_node<> *node = fDOMElement->first_node(name.c_str()); - if (node) - return new XMLNode(node); - else - return 0; + return XMLNode(node); } //----------------------------------------------------------------------------- // Get list of nodes -list<XMLNode*> XMLNode::getNodes(string name) +list<XMLNode> XMLNode::getNodes(string name) const { - list<XMLNode*> result; + list<XMLNode> result; xml_node<> *iter; for (iter = fDOMElement->first_node(name.c_str()); iter; iter = iter->next_sibling(name.c_str())) { - result.push_back(new XMLNode(iter)); + result.push_back(XMLNode(iter)); } return result; } //----------------------------------------------------------------------------- // Get list of nodes -list<XMLNode*> XMLNode::getNodes() +list<XMLNode> XMLNode::getNodes() const { - list<XMLNode*> result; + list<XMLNode> result; xml_node<> *iter; for (iter = fDOMElement->first_node(); iter; iter = iter->next_sibling()) { - result.push_back(new XMLNode(iter)); + result.push_back(XMLNode(iter)); } return result; } //----------------------------------------------------------------------------- // Get name of this node -std::string XMLNode::getName() +std::string XMLNode::getName() const { return fDOMElement->name(); } //----------------------------------------------------------------------------- // Get node content - STRING -string XMLNode::getContent() +string XMLNode::getContent() const { return fDOMElement->value(); } //----------------------------------------------------------------------------- // Get node content - NUMERICAL -float32 XMLNode::getContentNumerical() +float32 XMLNode::getContentNumerical() const { return boost::lexical_cast<float32>(getContent()); } //----------------------------------------------------------------------------- // Get node content - BOOLEAN -bool XMLNode::getContentBool() +bool XMLNode::getContentBool() const { string res = getContent(); return ((res == "1") || (res == "yes") || (res == "true") || (res == "on")); @@ -165,21 +151,20 @@ bool XMLNode::getContentBool() //----------------------------------------------------------------------------- // Get node content - STRING LIST -vector<string> XMLNode::getContentArray() +vector<string> XMLNode::getContentArray() const { // get listsize int iSize = boost::lexical_cast<int>(getAttribute("listsize")); // create result array vector<string> res(iSize); // loop all list item nodes - list<XMLNode*> nodes = getNodes("ListItem"); - for (list<XMLNode*>::iterator it = nodes.begin(); it != nodes.end(); it++) { - int iIndex = (*it)->getAttributeNumerical("index"); - string sValue = (*it)->getAttribute("value"); + list<XMLNode> nodes = getNodes("ListItem"); + for (list<XMLNode>::iterator it = nodes.begin(); it != nodes.end(); it++) { + int iIndex = it->getAttributeNumerical("index"); + string sValue = it->getAttribute("value"); ASTRA_ASSERT(iIndex < iSize); res[iIndex] = sValue; } - deleteNodes(nodes); // return return res; @@ -187,85 +172,48 @@ vector<string> XMLNode::getContentArray() //----------------------------------------------------------------------------- // Get node content - NUMERICAL LIST -vector<float32> XMLNode::getContentNumericalArray() +// NB: A 2D matrix is returned as a linear list +vector<float32> XMLNode::getContentNumericalArray() const { - // is scalar - if (!hasAttribute("listsize")) { - vector<float32> res(1); - res[0] = getContentNumerical(); - return res; - } + string input = getContent(); - int iSize = boost::lexical_cast<int>(getAttribute("listsize")); - // create result array - vector<float32> res(iSize); - // loop all list item nodes - list<XMLNode*> nodes = getNodes("ListItem"); - for (list<XMLNode*>::iterator it = nodes.begin(); it != nodes.end(); it++) { - int iIndex = (*it)->getAttributeNumerical("index"); - float32 fValue = (*it)->getAttributeNumerical("value"); - ASTRA_ASSERT(iIndex < iSize); - res[iIndex] = fValue; - } - deleteNodes(nodes); - // return - return res; -} + // split + std::vector<std::string> items; + boost::split(items, input, boost::is_any_of(",;")); -vector<double> XMLNode::getContentNumericalArrayDouble() -{ - // is scalar - if (!hasAttribute("listsize")) { - vector<double> res(1); - res[0] = getContentNumerical(); - return res; - } + // init list + vector<float32> out; + out.resize(items.size()); - int iSize = boost::lexical_cast<int>(getAttribute("listsize")); - // create result array - vector<double> res(iSize); - // loop all list item nodes - list<XMLNode*> nodes = getNodes("ListItem"); - for (list<XMLNode*>::iterator it = nodes.begin(); it != nodes.end(); it++) { - int iIndex = (*it)->getAttributeNumerical("index"); - double fValue = (*it)->getAttributeNumericalDouble("value"); - ASTRA_ASSERT(iIndex < iSize); - res[iIndex] = fValue; + // loop elements + for (unsigned int i = 0; i < items.size(); i++) { + out[i] = boost::lexical_cast<float32>(items[i]); } - deleteNodes(nodes); - // return - return res; + return out; } -//----------------------------------------------------------------------------- -// Get node content - NUMERICAL LIST 2 -void XMLNode::getContentNumericalArray(float32*& _pfData, int& _iSize) +vector<double> XMLNode::getContentNumericalArrayDouble() const { - // is scalar - if (!hasAttribute("listsize")) { - _iSize = 1; - _pfData = new float32[_iSize]; - _pfData[0] = getContentNumerical(); - return; - } - // get listsize - _iSize = boost::lexical_cast<int>(getAttribute("listsize")); - // create result array - _pfData = new float32[_iSize]; - // loop all list item nodes - list<XMLNode*> nodes = getNodes("ListItem"); - for (list<XMLNode*>::iterator it = nodes.begin(); it != nodes.end(); it++) { - int iIndex = (*it)->getAttributeNumerical("index"); - float32 fValue = (*it)->getAttributeNumerical("value"); - ASTRA_ASSERT(iIndex < _iSize); - _pfData[iIndex] = fValue; + string input = getContent(); + + // split + std::vector<std::string> items; + boost::split(items, input, boost::is_any_of(",;")); + + // init list + vector<double> out; + out.resize(items.size()); + + // loop elements + for (unsigned int i = 0; i < items.size(); i++) { + out[i] = boost::lexical_cast<double>(items[i]); } - deleteNodes(nodes); + return out; } //----------------------------------------------------------------------------- // Is attribute? -bool XMLNode::hasAttribute(string _sName) +bool XMLNode::hasAttribute(string _sName) const { xml_attribute<> *attr = fDOMElement->first_attribute(_sName.c_str()); return (attr != 0); @@ -273,7 +221,7 @@ bool XMLNode::hasAttribute(string _sName) //----------------------------------------------------------------------------- // Get attribute - STRING -string XMLNode::getAttribute(string _sName, string _sDefaultValue) +string XMLNode::getAttribute(string _sName, string _sDefaultValue) const { xml_attribute<> *attr = fDOMElement->first_attribute(_sName.c_str()); @@ -284,12 +232,12 @@ string XMLNode::getAttribute(string _sName, string _sDefaultValue) //----------------------------------------------------------------------------- // Get attribute - NUMERICAL -float32 XMLNode::getAttributeNumerical(string _sName, float32 _fDefaultValue) +float32 XMLNode::getAttributeNumerical(string _sName, float32 _fDefaultValue) const { if (!hasAttribute(_sName)) return _fDefaultValue; return boost::lexical_cast<float32>(getAttribute(_sName)); } -double XMLNode::getAttributeNumericalDouble(string _sName, double _fDefaultValue) +double XMLNode::getAttributeNumericalDouble(string _sName, double _fDefaultValue) const { if (!hasAttribute(_sName)) return _fDefaultValue; return boost::lexical_cast<double>(getAttribute(_sName)); @@ -297,7 +245,7 @@ double XMLNode::getAttributeNumericalDouble(string _sName, double _fDefaultValue //----------------------------------------------------------------------------- // Get attribute - BOOLEAN -bool XMLNode::getAttributeBool(string _sName, bool _bDefaultValue) +bool XMLNode::getAttributeBool(string _sName, bool _bDefaultValue) const { if (!hasAttribute(_sName)) return _bDefaultValue; string res = getAttribute(_sName); @@ -306,7 +254,7 @@ bool XMLNode::getAttributeBool(string _sName, bool _bDefaultValue) //----------------------------------------------------------------------------- // Has option? -bool XMLNode::hasOption(string _sKey) +bool XMLNode::hasOption(string _sKey) const { xml_node<> *iter; for (iter = fDOMElement->first_node("Option"); iter; iter = iter->next_sibling("Option")) { @@ -319,7 +267,7 @@ bool XMLNode::hasOption(string _sKey) //----------------------------------------------------------------------------- // Get option - STRING -string XMLNode::getOption(string _sKey, string _sDefaultValue) +string XMLNode::getOption(string _sKey, string _sDefaultValue) const { xml_node<> *iter; for (iter = fDOMElement->first_node("Option"); iter; iter = iter->next_sibling("Option")) { @@ -336,7 +284,7 @@ string XMLNode::getOption(string _sKey, string _sDefaultValue) //----------------------------------------------------------------------------- // Get option - NUMERICAL -float32 XMLNode::getOptionNumerical(string _sKey, float32 _fDefaultValue) +float32 XMLNode::getOptionNumerical(string _sKey, float32 _fDefaultValue) const { if (!hasOption(_sKey)) return _fDefaultValue; return boost::lexical_cast<float32>(getOption(_sKey)); @@ -344,7 +292,7 @@ float32 XMLNode::getOptionNumerical(string _sKey, float32 _fDefaultValue) //----------------------------------------------------------------------------- // Get option - BOOL -bool XMLNode::getOptionBool(string _sKey, bool _bDefaultValue) +bool XMLNode::getOptionBool(string _sKey, bool _bDefaultValue) const { bool bHasOption = hasOption(_sKey); if (!bHasOption) return _bDefaultValue; @@ -354,20 +302,18 @@ bool XMLNode::getOptionBool(string _sKey, bool _bDefaultValue) //----------------------------------------------------------------------------- // Get option - NUMERICAL ARRAY -vector<float32> XMLNode::getOptionNumericalArray(string _sKey) +vector<float32> XMLNode::getOptionNumericalArray(string _sKey) const { if (!hasOption(_sKey)) return vector<float32>(); - list<XMLNode*> nodes = getNodes("Option"); - for (list<XMLNode*>::iterator it = nodes.begin(); it != nodes.end(); it++) { - if ((*it)->getAttribute("key") == _sKey) { - vector<float32> vals = (*it)->getContentNumericalArray(); - deleteNodes(nodes); + list<XMLNode> nodes = getNodes("Option"); + for (list<XMLNode>::iterator it = nodes.begin(); it != nodes.end(); it++) { + if (it->getAttribute("key") == _sKey) { + vector<float32> vals = it->getContentNumericalArray(); return vals; } } - deleteNodes(nodes); return vector<float32>(); } @@ -390,41 +336,40 @@ vector<float32> XMLNode::getOptionNumericalArray(string _sKey) //----------------------------------------------------------------------------- // Add child node - EMPTY -XMLNode* XMLNode::addChildNode(string _sNodeName) +XMLNode XMLNode::addChildNode(string _sNodeName) { xml_document<> *doc = fDOMElement->document(); char *node_name = doc->allocate_string(_sNodeName.c_str()); xml_node<> *node = doc->allocate_node(node_element, node_name); fDOMElement->append_node(node); - // TODO: clean up: this 'new' requires callers to do memory management - return new XMLNode(node); + return XMLNode(node); } //----------------------------------------------------------------------------- // Add child node - STRING -XMLNode* XMLNode::addChildNode(string _sNodeName, string _sText) +XMLNode XMLNode::addChildNode(string _sNodeName, string _sText) { - XMLNode* res = addChildNode(_sNodeName); - res->setContent(_sText); + XMLNode res = addChildNode(_sNodeName); + res.setContent(_sText); return res; } //----------------------------------------------------------------------------- // Add child node - FLOAT -XMLNode* XMLNode::addChildNode(string _sNodeName, float32 _fValue) +XMLNode XMLNode::addChildNode(string _sNodeName, float32 _fValue) { - XMLNode* res = addChildNode(_sNodeName); - res->setContent(_fValue); + XMLNode res = addChildNode(_sNodeName); + res.setContent(_fValue); return res; } //----------------------------------------------------------------------------- // Add child node - LIST -XMLNode* XMLNode::addChildNode(string _sNodeName, float32* _pfList, int _iSize) +XMLNode XMLNode::addChildNode(string _sNodeName, float32* _pfList, int _iSize) { - XMLNode* res = addChildNode(_sNodeName); - res->setContent(_pfList, _iSize); + XMLNode res = addChildNode(_sNodeName); + res.setContent(_pfList, _iSize); return res; } @@ -446,15 +391,68 @@ void XMLNode::setContent(float32 _fValue) //----------------------------------------------------------------------------- // Set content - LIST -void XMLNode::setContent(float32* pfList, int _iSize) -{ + +template<typename T> +static std::string setContentList_internal(T* pfList, int _iSize) { std::string str = (_iSize > 0) ? boost::lexical_cast<std::string>(pfList[0]) : ""; for (int i = 1; i < _iSize; i++) { str += "," + boost::lexical_cast<std::string>(pfList[i]); } - setContent(str); + return str; +} + +void XMLNode::setContent(float32* pfList, int _iSize) +{ + setContent(setContentList_internal<float32>(pfList, _iSize)); +} + +void XMLNode::setContent(double* pfList, int _iSize) +{ + setContent(setContentList_internal<double>(pfList, _iSize)); +} + +//----------------------------------------------------------------------------- +// Set content - MATRIX + +template<typename T> +static std::string setContentMatrix_internal(T* _pfMatrix, int _iWidth, int _iHeight, bool transposed) +{ + std::string str = ""; + + int s1,s2; + + if (!transposed) { + s1 = 1; + s2 = _iWidth; + } else { + s1 = _iHeight; + s2 = 1; + } + + for (int y = 0; y < _iHeight; ++y) { + if (_iWidth > 0) + str += boost::lexical_cast<std::string>(_pfMatrix[0*s1 + y*s2]); + for (int x = 1; x < _iWidth; x++) + str += "," + boost::lexical_cast<std::string>(_pfMatrix[x*s1 + y*s2]); + + if (y != _iHeight-1) + str += ";"; + } + + return str; } +void XMLNode::setContent(float32* _pfMatrix, int _iWidth, int _iHeight, bool transposed) +{ + setContent(setContentMatrix_internal<float32>(_pfMatrix, _iWidth, _iHeight, transposed)); +} + +void XMLNode::setContent(double* _pfMatrix, int _iWidth, int _iHeight, bool transposed) +{ + setContent(setContentMatrix_internal<double>(_pfMatrix, _iWidth, _iHeight, transposed)); +} + + //----------------------------------------------------------------------------- // Add attribute - STRING void XMLNode::addAttribute(string _sName, string _sText) @@ -477,20 +475,18 @@ void XMLNode::addAttribute(string _sName, float32 _fValue) // Add option - STRING void XMLNode::addOption(string _sName, string _sText) { - XMLNode* node = addChildNode("Option"); - node->addAttribute("key", _sName); - node->addAttribute("value", _sText); - delete node; + XMLNode node = addChildNode("Option"); + node.addAttribute("key", _sName); + node.addAttribute("value", _sText); } //----------------------------------------------------------------------------- // Add option - FLOAT void XMLNode::addOption(string _sName, float32 _sText) { - XMLNode* node = addChildNode("Option"); - node->addAttribute("key", _sName); - node->addAttribute("value", _sText); - delete node; + XMLNode node = addChildNode("Option"); + node.addAttribute("key", _sName); + node.addAttribute("value", _sText); } //----------------------------------------------------------------------------- diff --git a/tests/test_Fourier.cpp b/tests/test_Fourier.cpp index 2602edb..ef12747 100644 --- a/tests/test_Fourier.cpp +++ b/tests/test_Fourier.cpp @@ -105,8 +105,8 @@ BOOST_AUTO_TEST_CASE( testFourier_FFT_1D_1 ) { astra::float32 inR[8] = { 1.0f, 1.0f, 1.0f, 0.0f, 0.0f, 0.0f, 1.0f, 1.0f }; astra::float32 inI[8] = { 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f }; - astra::float32 outR[5]; - astra::float32 outI[5]; + astra::float32 outR[8]; + astra::float32 outI[8]; astra::fastTwoPowerFourierTransform1D(8, inR, inI, outR, outI, 1, 1, false); diff --git a/tests/test_ParallelBeamLineKernelProjector2D.cpp b/tests/test_ParallelBeamLineKernelProjector2D.cpp index 86bc54f..c56ff37 100644 --- a/tests/test_ParallelBeamLineKernelProjector2D.cpp +++ b/tests/test_ParallelBeamLineKernelProjector2D.cpp @@ -77,6 +77,8 @@ BOOST_FIXTURE_TEST_CASE( testParallelBeamLineKernelProjector2D_Rectangle, TestPa fWeight += pPix[i].m_fWeight; BOOST_CHECK_SMALL(fWeight - 7.13037f, 0.00001f); + + delete[] pPix; } diff --git a/tests/test_XMLDocument.cpp b/tests/test_XMLDocument.cpp index adabdd6..95429cb 100644 --- a/tests/test_XMLDocument.cpp +++ b/tests/test_XMLDocument.cpp @@ -32,18 +32,22 @@ $Id$ #include <boost/test/auto_unit_test.hpp> #include "astra/XMLDocument.h" +#include "astra/Config.h" BOOST_AUTO_TEST_CASE( testXMLDocument_Constructor1 ) { astra::XMLDocument *doc = astra::XMLDocument::createDocument("test"); BOOST_REQUIRE(doc); - astra::XMLNode *root = doc->getRootNode(); + astra::XMLNode root = doc->getRootNode(); BOOST_REQUIRE(root); - BOOST_CHECK(root->getName() == "test"); - BOOST_CHECK(root->getContent().empty()); + BOOST_CHECK(root.getName() == "test"); + BOOST_CHECK(root.getContent().empty()); + + delete doc; + } BOOST_AUTO_TEST_CASE( testXMLDocument_FileIO ) @@ -53,12 +57,15 @@ BOOST_AUTO_TEST_CASE( testXMLDocument_FileIO ) doc->saveToFile("test.xml"); astra::XMLDocument *doc2 = astra::XMLDocument::readFromFile("test.xml"); - astra::XMLNode *root = doc2->getRootNode(); + astra::XMLNode root = doc2->getRootNode(); BOOST_REQUIRE(root); - BOOST_CHECK(root->getName() == "test"); - BOOST_CHECK(root->getContent().empty()); + BOOST_CHECK(root.getName() == "test"); + BOOST_CHECK(root.getContent().empty()); + + delete doc2; + delete doc; } @@ -67,32 +74,28 @@ BOOST_AUTO_TEST_CASE( testXMLDocument_CreateNodes ) astra::XMLDocument *doc = astra::XMLDocument::createDocument("test"); BOOST_REQUIRE(doc); - astra::XMLNode *root = doc->getRootNode(); + astra::XMLNode root = doc->getRootNode(); BOOST_REQUIRE(root); - astra::XMLNode *node = root->addChildNode("child"); + astra::XMLNode node = root.addChildNode("child"); BOOST_REQUIRE(node); - node->addAttribute("attr", "val"); + node.addAttribute("attr", "val"); doc->saveToFile("test2.xml"); - delete node; - delete root; delete doc; doc = astra::XMLDocument::readFromFile("test2.xml"); BOOST_REQUIRE(doc); root = doc->getRootNode(); BOOST_REQUIRE(node); - node = root->getSingleNode("child"); + node = root.getSingleNode("child"); BOOST_REQUIRE(node); - BOOST_CHECK(node->hasAttribute("attr")); - BOOST_CHECK(node->getAttribute("attr") == "val"); + BOOST_CHECK(node.hasAttribute("attr")); + BOOST_CHECK(node.getAttribute("attr") == "val"); - delete node; - delete root; delete doc; } @@ -101,16 +104,18 @@ BOOST_AUTO_TEST_CASE( testXMLDocument_Options ) astra::XMLDocument *doc = astra::XMLDocument::createDocument("test"); BOOST_REQUIRE(doc); - astra::XMLNode *root = doc->getRootNode(); + astra::XMLNode root = doc->getRootNode(); BOOST_REQUIRE(root); - BOOST_CHECK(!root->hasOption("opt")); + BOOST_CHECK(!root.hasOption("opt")); + + root.addOption("opt", "val"); - root->addOption("opt", "val"); + BOOST_CHECK(root.hasOption("opt")); - BOOST_CHECK(root->hasOption("opt")); + BOOST_CHECK(root.getOption("opt") == "val"); - BOOST_CHECK(root->getOption("opt") == "val"); + delete doc; } @@ -119,40 +124,51 @@ BOOST_AUTO_TEST_CASE( testXMLDocument_List ) astra::XMLDocument *doc = astra::XMLDocument::createDocument("test"); BOOST_REQUIRE(doc); - astra::XMLNode *root = doc->getRootNode(); + astra::XMLNode root = doc->getRootNode(); BOOST_REQUIRE(root); - astra::XMLNode *node = root->addChildNode("child"); + astra::XMLNode node = root.addChildNode("child"); BOOST_REQUIRE(node); float fl[] = { 1.0, 3.5, 2.0, 4.75 }; - node->setContent(fl, sizeof(fl)/sizeof(fl[0])); + node.setContent(fl, sizeof(fl)/sizeof(fl[0])); doc->saveToFile("test3.xml"); - delete node; - delete root; delete doc; doc = astra::XMLDocument::readFromFile("test3.xml"); BOOST_REQUIRE(doc); root = doc->getRootNode(); BOOST_REQUIRE(root); - node = root->getSingleNode("child"); + node = root.getSingleNode("child"); BOOST_REQUIRE(node); - std::vector<astra::float32> f = node->getContentNumericalArray(); + std::vector<astra::float32> f = node.getContentNumericalArray(); BOOST_CHECK(f[0] == fl[0]); BOOST_CHECK(f[1] == fl[1]); BOOST_CHECK(f[2] == fl[2]); BOOST_CHECK(f[3] == fl[3]); - delete node; - delete root; delete doc; } +BOOST_AUTO_TEST_CASE( testXMLDocument_Config ) +{ + astra::Config* cfg = new astra::Config(); + cfg->initialize("VolumeGeometry2D"); + + cfg->self.addChildNode("GridColCount", 1); + cfg->self.addChildNode("GridRowCount", 2); + + cfg->self.addOption("WindowMinX", 3); + cfg->self.addOption("WindowMaxX", 4); + cfg->self.addOption("WindowMinY", 5); + cfg->self.addOption("WindowMaxY", 6); + + delete cfg; +} |