From c58929ca7d0201335b5036773b26f82361793f25 Mon Sep 17 00:00:00 2001
From: "Daniel M. Pelt" <D.M.Pelt@cwi.nl>
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 <http://www.gnu.org/licenses/>.
#
# -----------------------------------------------------------------------
+# 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" <D.M.Pelt@cwi.nl>
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 <Willem.Jan.Palenstijn@cwi.nl>
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 <Willem.Jan.Palenstijn@cwi.nl>
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 <Willem.Jan.Palenstijn@cwi.nl>
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 <http://www.gnu.org/licenses/>.
#include "astra/Logging.h"
#include "astra/Utilities.h"
-#include <boost/algorithm/string.hpp>
-#include <boost/algorithm/string/split.hpp>
#include <iostream>
#include <fstream>
#include <string>
@@ -146,7 +144,7 @@ CPythonPluginAlgorithmFactory::~CPythonPluginAlgorithmFactory(){
PyObject * getClassFromString(std::string str){
std::vector<std::string> 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<std::string> 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<rows.size(); i++){
- boost::split(row, rows[i], boost::is_any_of(","));
+ StringUtil::splitString(row, rows[i], ",");
PyObject *rowlist = PyList_New(row.size());
for(unsigned int j=0;j<row.size();j++){
PyList_SetItem(rowlist, j, PyFloat_FromDouble(StringUtil::stringToDouble(row[j])));
@@ -317,7 +315,7 @@ PyObject* stringToPythonValue(std::string str){
}
if(str.find(",")!=std::string::npos){
std::vector<std::string> 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<vec.size();i++){
PyList_SetItem(veclist, i, PyFloat_FromDouble(StringUtil::stringToDouble(vec[i])));
--
cgit v1.2.3