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/astra') 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 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'python/astra') 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 *. -- 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/astra') 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/astra') 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 --- python/astra/src/PythonPluginAlgorithm.cpp | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) (limited to 'python/astra') 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