From c58929ca7d0201335b5036773b26f82361793f25 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Tue, 19 Apr 2016 16:40:14 +0200 Subject: Use CXX for Python compilation as well --- python/astra/extrautils.pyx | 2 ++ 1 file changed, 2 insertions(+) (limited to 'python') diff --git a/python/astra/extrautils.pyx b/python/astra/extrautils.pyx index 5bc315f..2c7771e 100644 --- a/python/astra/extrautils.pyx +++ b/python/astra/extrautils.pyx @@ -22,6 +22,8 @@ # along with the ASTRA Toolbox. If not, see . # # ----------------------------------------------------------------------- +# distutils: language = c++ + def clipCircle(img): cdef int i,j -- cgit v1.2.3 From 1e26f7602b6685c584fd4d857353f390622e3a34 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Mon, 25 Apr 2016 10:47:59 +0200 Subject: Change flatten to ravel in Python code --- python/astra/optomo.py | 4 ++-- samples/python/s009_projection_matrix.py | 2 +- samples/python/s015_fp_bp.py | 6 +++--- samples/python/s017_OpTomo.py | 2 +- 4 files changed, 7 insertions(+), 7 deletions(-) (limited to 'python') diff --git a/python/astra/optomo.py b/python/astra/optomo.py index dd10713..5a92998 100644 --- a/python/astra/optomo.py +++ b/python/astra/optomo.py @@ -125,7 +125,7 @@ class OpTomo(scipy.sparse.linalg.LinearOperator): algorithm.delete(fp_id) self.data_mod.delete([vid,sid]) - return s.flatten() + return s.ravel() def rmatvec(self,s): """Implements the transpose operator. @@ -147,7 +147,7 @@ class OpTomo(scipy.sparse.linalg.LinearOperator): algorithm.delete(bp_id) self.data_mod.delete([vid,sid]) - return v.flatten() + return v.ravel() def __mul__(self,v): """Provides easy forward operator by *. diff --git a/samples/python/s009_projection_matrix.py b/samples/python/s009_projection_matrix.py index c4c4557..e20d58c 100644 --- a/samples/python/s009_projection_matrix.py +++ b/samples/python/s009_projection_matrix.py @@ -46,7 +46,7 @@ W = astra.matrix.get(matrix_id) # Manually use this projection matrix to do a projection: import scipy.io P = scipy.io.loadmat('phantom.mat')['phantom256'] -s = W.dot(P.flatten()) +s = W.dot(P.ravel()) s = np.reshape(s, (len(proj_geom['ProjectionAngles']),proj_geom['DetectorCount'])) import pylab diff --git a/samples/python/s015_fp_bp.py b/samples/python/s015_fp_bp.py index fa0bf86..ff0b30a 100644 --- a/samples/python/s015_fp_bp.py +++ b/samples/python/s015_fp_bp.py @@ -46,12 +46,12 @@ class astra_wrap(object): def matvec(self,v): sid, s = astra.create_sino(np.reshape(v,(vol_geom['GridRowCount'],vol_geom['GridColCount'])),self.proj_id) astra.data2d.delete(sid) - return s.flatten() + return s.ravel() def rmatvec(self,v): bid, b = astra.create_backprojection(np.reshape(v,(len(proj_geom['ProjectionAngles']),proj_geom['DetectorCount'],)),self.proj_id) astra.data2d.delete(bid) - return b.flatten() + return b.ravel() vol_geom = astra.create_vol_geom(256, 256) proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) @@ -65,7 +65,7 @@ proj_id = astra.create_projector('cuda',proj_geom,vol_geom) sinogram_id, sinogram = astra.create_sino(P, proj_id) # Reshape the sinogram into a vector -b = sinogram.flatten() +b = sinogram.ravel() # Call lsqr with ASTRA FP and BP import scipy.sparse.linalg diff --git a/samples/python/s017_OpTomo.py b/samples/python/s017_OpTomo.py index 967fa64..214e9a7 100644 --- a/samples/python/s017_OpTomo.py +++ b/samples/python/s017_OpTomo.py @@ -50,7 +50,7 @@ pylab.figure(2) pylab.imshow(sinogram) # Run the lsqr linear solver -output = scipy.sparse.linalg.lsqr(W, sinogram.flatten(), iter_lim=150) +output = scipy.sparse.linalg.lsqr(W, sinogram.ravel(), iter_lim=150) rec = output[0].reshape([256, 256]) pylab.figure(3) -- cgit v1.2.3 From a33b2a0e4e0663145fb0d4d67a9145948f90341a Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Mon, 25 Apr 2016 11:03:18 +0200 Subject: Reverse output of astra.data3d.dimensions This makes the output directly usable in numpy commands like zeros, reshape. We were not using data3d.dimensions ourselves, as far as I can tell. --- python/astra/data3d_c.pyx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'python') diff --git a/python/astra/data3d_c.pyx b/python/astra/data3d_c.pyx index 207d9a5..811d1e4 100644 --- a/python/astra/data3d_c.pyx +++ b/python/astra/data3d_c.pyx @@ -264,7 +264,7 @@ def store(i,data): def dimensions(i): cdef CFloat32Data3D * pDataObject = getObject(i) - return (pDataObject.getWidth(),pDataObject.getHeight(),pDataObject.getDepth()) + return (pDataObject.getDepth(),pDataObject.getHeight(),pDataObject.getWidth()) def delete(ids): try: -- cgit v1.2.3 From 63e22423350089a37b188a53164867eedab781ac Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Thu, 21 Apr 2016 11:39:51 +0200 Subject: Give OpTomo FP/BP functions with optional out argument This allows more efficient use of allocated arrays. --- python/astra/optomo.py | 96 ++++++++++++++++++++++++++++++++++---------------- 1 file changed, 66 insertions(+), 30 deletions(-) (limited to 'python') diff --git a/python/astra/optomo.py b/python/astra/optomo.py index 5a92998..dde719e 100644 --- a/python/astra/optomo.py +++ b/python/astra/optomo.py @@ -111,21 +111,7 @@ class OpTomo(scipy.sparse.linalg.LinearOperator): :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.ravel() + return self.FP(v, out=None).ravel() def rmatvec(self,s): """Implements the transpose operator. @@ -133,21 +119,7 @@ class OpTomo(scipy.sparse.linalg.LinearOperator): :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.ravel() + return self.BP(s, out=None).ravel() def __mul__(self,v): """Provides easy forward operator by *. @@ -189,6 +161,70 @@ class OpTomo(scipy.sparse.linalg.LinearOperator): self.data_mod.delete([vid,sid]) return v + def FP(self,v,out=None): + """Perform forward projection. + + Output must have the right 2D/3D shape. Input may also be flattened. + + Output must also be contiguous and float32. This isn't required for the + input, but it is more efficient if it is. + + :param v: Volume to forward project. + :type v: :class:`numpy.ndarray` + :param out: Array to store result in. + :type out: :class:`numpy.ndarray` + """ + + v = self.__checkArray(v, self.vshape) + vid = self.data_mod.link('-vol',self.vg,v) + if out is None: + out = np.zeros(self.sshape,dtype=np.float32) + sid = self.data_mod.link('-sino',self.pg,out) + + 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 out + + def BP(self,s,out=None): + """Perform backprojection. + + Output must have the right 2D/3D shape. Input may also be flattened. + + Output must also be contiguous and float32. This isn't required for the + input, but it is more efficient if it is. + + :param : The projection data. + :type s: :class:`numpy.ndarray` + :param out: Array to store result in. + :type out: :class:`numpy.ndarray` + """ + s = self.__checkArray(s, self.sshape) + sid = self.data_mod.link('-sino',self.pg,s) + if out is None: + out = np.zeros(self.vshape,dtype=np.float32) + vid = self.data_mod.link('-vol',self.vg,out) + + 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 out + + + + class OpTomoTranspose(scipy.sparse.linalg.LinearOperator): """This object provides the transpose operation (``.T``) of the OpTomo object. -- cgit v1.2.3 From 584fb584816aefca42518c9a6075ac2df814dac6 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Thu, 28 Jul 2016 15:32:50 +0200 Subject: Replace use of boost::split by own function --- include/astra/Utilities.h | 3 +++ matlab/mex/mexHelpFunctions.cpp | 13 ++++-------- python/astra/src/PythonPluginAlgorithm.cpp | 10 ++++----- src/Utilities.cpp | 34 ++++++++++++++++++------------ 4 files changed, 31 insertions(+), 29 deletions(-) (limited to 'python') diff --git a/include/astra/Utilities.h b/include/astra/Utilities.h index 8d7c44d..22adfe2 100644 --- a/include/astra/Utilities.h +++ b/include/astra/Utilities.h @@ -85,6 +85,9 @@ _AstraExport std::string doubleToString(double f); template _AstraExport std::string toString(T f); + +_AstraExport void splitString(std::vector &items, const std::string& s, const char *delim); + } diff --git a/matlab/mex/mexHelpFunctions.cpp b/matlab/mex/mexHelpFunctions.cpp index b13dde3..d957aea 100644 --- a/matlab/mex/mexHelpFunctions.cpp +++ b/matlab/mex/mexHelpFunctions.cpp @@ -33,11 +33,6 @@ $Id$ #include "mexHelpFunctions.h" #include "astra/Utilities.h" -#include -#include -#include -#include - using namespace std; using namespace astra; @@ -362,8 +357,8 @@ mxArray* stringToMxArray(std::string input) // split rows std::vector row_strings; std::vector col_strings; - boost::split(row_strings, input, boost::is_any_of(";")); - boost::split(col_strings, row_strings[0], boost::is_any_of(",")); + StringUtil::splitString(row_strings, input, ";"); + StringUtil::splitString(col_strings, row_strings[0], ","); // get dimensions int rows = row_strings.size(); @@ -375,7 +370,7 @@ mxArray* stringToMxArray(std::string input) // loop elements for (unsigned int row = 0; row < rows; row++) { - boost::split(col_strings, row_strings[row], boost::is_any_of(",")); + StringUtil::splitString(col_strings, row_strings[row], ","); // check size for (unsigned int col = 0; col < col_strings.size(); col++) { out[col*rows + row] = StringUtil::stringToFloat(col_strings[col]); @@ -389,7 +384,7 @@ mxArray* stringToMxArray(std::string input) // split std::vector items; - boost::split(items, input, boost::is_any_of(",")); + StringUtil::splitString(items, input, ","); // init matrix mxArray* pVector = mxCreateDoubleMatrix(1, items.size(), mxREAL); diff --git a/python/astra/src/PythonPluginAlgorithm.cpp b/python/astra/src/PythonPluginAlgorithm.cpp index 617c0f4..893db94 100644 --- a/python/astra/src/PythonPluginAlgorithm.cpp +++ b/python/astra/src/PythonPluginAlgorithm.cpp @@ -31,8 +31,6 @@ along with the ASTRA Toolbox. If not, see . #include "astra/Logging.h" #include "astra/Utilities.h" -#include -#include #include #include #include @@ -146,7 +144,7 @@ CPythonPluginAlgorithmFactory::~CPythonPluginAlgorithmFactory(){ PyObject * getClassFromString(std::string str){ std::vector items; - boost::split(items, str, boost::is_any_of(".")); + StringUtil::splitString(items, str, "."); PyObject *pyclass = PyImport_ImportModule(items[0].c_str()); if(pyclass==NULL){ logPythonError(); @@ -303,10 +301,10 @@ PyObject * pyStringFromString(std::string str){ PyObject* stringToPythonValue(std::string str){ if(str.find(";")!=std::string::npos){ std::vector rows, row; - boost::split(rows, str, boost::is_any_of(";")); + StringUtil::splitString(rows, str, ";"); PyObject *mat = PyList_New(rows.size()); for(unsigned int i=0; i vec; - boost::split(vec, str, boost::is_any_of(",")); + StringUtil::splitString(vec, str, ","); PyObject *veclist = PyList_New(vec.size()); for(unsigned int i=0;i -#include -#include - #include #include #include @@ -84,18 +80,16 @@ std::vector stringToDoubleVector(const std::string &s) template std::vector stringToVector(const std::string& s) { - // split - std::vector items; - boost::split(items, s, boost::is_any_of(",;")); - - // init list std::vector out; - out.resize(items.size()); + size_t current = 0; + size_t next; + do { + next = s.find_first_of(",;", current); + std::string t = s.substr(current, next - current); + out.push_back(stringTo(t)); + current = next + 1; + } while (next != std::string::npos); - // loop elements - for (unsigned int i = 0; i < items.size(); i++) { - out[i] = stringTo(items[i]); - } return out; } @@ -120,6 +114,18 @@ std::string doubleToString(double f) template<> std::string toString(float f) { return floatToString(f); } template<> std::string toString(double f) { return doubleToString(f); } +void splitString(std::vector &items, const std::string& s, + const char *delim) +{ + items.clear(); + size_t current = 0; + size_t next; + do { + next = s.find_first_of(",;", current); + items.push_back(s.substr(current, next - current)); + current = next + 1; + } while (next != std::string::npos); +} } -- cgit v1.2.3