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-rw-r--r--.gitignore31
-rw-r--r--matlab/mex/astra_mex_c.cpp4
-rw-r--r--matlab/mex/astra_mex_projector3d_c.cpp8
-rw-r--r--matlab/mex/astra_mex_projector_c.cpp9
-rw-r--r--matlab/mex/mexHelpFunctions.cpp6
-rw-r--r--matlab/tools/astra_create_reconstruction_cuda.m2
-rw-r--r--python/astra/projector3d_c.pyx10
-rw-r--r--python/astra/projector_c.pyx10
-rw-r--r--python/astra/utils.pyx11
-rw-r--r--python/docSRC/operator.rst4
-rw-r--r--src/ParallelProjectionGeometry2D.cpp5
11 files changed, 82 insertions, 18 deletions
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..ec0eafb
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,31 @@
+.*.swp
+.*.swo
+*~
+*.orig
+*.rej
+.nfs*
+
+/python/build/*
+/python/finalbuild/*
+/python/dist/*
+/python/astra/*.pyc
+/python/astra/*.cpp
+/python/astra/*.c
+/python/astra/config.pxi
+
+/build/linux/.libs/*
+/build/linux/Makefile
+/build/linux/aclocal.m4
+/build/linux/autom4te.cache/*
+/build/linux/config.guess
+/build/linux/config.log
+/build/linux/config.status
+/build/linux/config.sub
+/build/linux/configure
+/build/linux/cuda/*
+/build/linux/install-sh
+/build/linux/libastra.la
+/build/linux/libtool
+/build/linux/ltmain.sh
+/build/linux/src/*
+/build/linux/matlab/*
diff --git a/matlab/mex/astra_mex_c.cpp b/matlab/mex/astra_mex_c.cpp
index 4a331f5..a9b9654 100644
--- a/matlab/mex/astra_mex_c.cpp
+++ b/matlab/mex/astra_mex_c.cpp
@@ -36,9 +36,9 @@ $Id$
#include "mexInitFunctions.h"
#include "astra/Globals.h"
-
+#ifdef ASTRA_CUDA
#include "../cuda/2d/darthelper.h"
-
+#endif
using namespace std;
using namespace astra;
diff --git a/matlab/mex/astra_mex_projector3d_c.cpp b/matlab/mex/astra_mex_projector3d_c.cpp
index c3b547f..e25802c 100644
--- a/matlab/mex/astra_mex_projector3d_c.cpp
+++ b/matlab/mex/astra_mex_projector3d_c.cpp
@@ -137,7 +137,9 @@ void astra_mex_projector3d_get_projection_geometry(int nlhs, mxArray* plhs[], in
// step3: get projection_geometry and turn it into a MATLAB struct
if (1 <= nlhs) {
- plhs[0] = configToStruct(pProjector->getProjectionGeometry()->getConfiguration());
+ Config *cfg = pProjector->getProjectionGeometry()->getConfiguration();
+ plhs[0] = configToStruct(cfg);
+ delete cfg;
}
}
@@ -163,7 +165,9 @@ void astra_mex_projector3d_get_volume_geometry(int nlhs, mxArray* plhs[], int nr
// step3: get projection_geometry and turn it into a MATLAB struct
if (1 <= nlhs) {
- plhs[0] = configToStruct(pProjector->getVolumeGeometry()->getConfiguration());
+ Config *cfg = pProjector->getVolumeGeometry()->getConfiguration();
+ plhs[0] = configToStruct(cfg);
+ delete cfg;
}
}
diff --git a/matlab/mex/astra_mex_projector_c.cpp b/matlab/mex/astra_mex_projector_c.cpp
index 204ba8e..bf701af 100644
--- a/matlab/mex/astra_mex_projector_c.cpp
+++ b/matlab/mex/astra_mex_projector_c.cpp
@@ -160,7 +160,9 @@ void astra_mex_projector_projection_geometry(int nlhs, mxArray* plhs[], int nrhs
// step3: get projection_geometry and turn it into a MATLAB struct
if (1 <= nlhs) {
- plhs[0] = configToStruct(pProjector->getProjectionGeometry()->getConfiguration());
+ Config *cfg = pProjector->getProjectionGeometry()->getConfiguration();
+ plhs[0] = configToStruct(cfg);
+ delete cfg;
}
}
@@ -189,8 +191,9 @@ void astra_mex_projector_volume_geometry(int nlhs, mxArray* plhs[], int nrhs, co
// step3: get projection_geometry and turn it into a MATLAB struct
if (1 <= nlhs) {
- plhs[0] = configToStruct(pProjector->getVolumeGeometry()->getConfiguration());
-
+ Config *cfg = pProjector->getVolumeGeometry()->getConfiguration();
+ plhs[0] = configToStruct(cfg);
+ delete cfg;
}
}
diff --git a/matlab/mex/mexHelpFunctions.cpp b/matlab/mex/mexHelpFunctions.cpp
index 87a9672..58e84d2 100644
--- a/matlab/mex/mexHelpFunctions.cpp
+++ b/matlab/mex/mexHelpFunctions.cpp
@@ -336,7 +336,11 @@ mxArray* XMLNodeToStruct(astra::XMLNode node)
// option
if (subnode.getName() == "Option") {
- mOptions[subnode.getAttribute("key")] = stringToMxArray(subnode.getAttribute("value"));
+ if(subnode.hasAttribute("value")){
+ mOptions[subnode.getAttribute("key")] = stringToMxArray(subnode.getAttribute("value"));
+ }else{
+ mOptions[subnode.getAttribute("key")] = stringToMxArray(subnode.getContent());
+ }
}
// regular content
diff --git a/matlab/tools/astra_create_reconstruction_cuda.m b/matlab/tools/astra_create_reconstruction_cuda.m
index 7d9e1dd..7d0421c 100644
--- a/matlab/tools/astra_create_reconstruction_cuda.m
+++ b/matlab/tools/astra_create_reconstruction_cuda.m
@@ -45,7 +45,7 @@ if strcmp(rec_type,'')
end
% configure
-cfg = astra_struct('SIRT_CUDA');
+cfg = astra_struct(rec_type);
cfg.ProjectionGeometry = proj_geom;
cfg.ReconstructionGeometry = vol_geom;
cfg.ProjectionDataId = sinogram_id;
diff --git a/python/astra/projector3d_c.pyx b/python/astra/projector3d_c.pyx
index 8b978d7..aec9cde 100644
--- a/python/astra/projector3d_c.pyx
+++ b/python/astra/projector3d_c.pyx
@@ -87,12 +87,18 @@ cdef CProjector3D * getObject(i) except NULL:
def projection_geometry(i):
cdef CProjector3D * proj = getObject(i)
- return utils.configToDict(proj.getProjectionGeometry().getConfiguration())
+ cdef Config * cfg = proj.getProjectionGeometry().getConfiguration()
+ dct = utils.configToDict(cfg)
+ del cfg
+ return dct
def volume_geometry(i):
cdef CProjector3D * proj = getObject(i)
- return utils.configToDict(proj.getVolumeGeometry().getConfiguration())
+ cdef Config * cfg = proj.getVolumeGeometry().getConfiguration()
+ dct = utils.configToDict(cfg)
+ del cfg
+ return dct
def weights_single_ray(i, projection_index, detector_index):
diff --git a/python/astra/projector_c.pyx b/python/astra/projector_c.pyx
index 9aa868e..77c64a4 100644
--- a/python/astra/projector_c.pyx
+++ b/python/astra/projector_c.pyx
@@ -91,12 +91,18 @@ cdef CProjector2D * getObject(i) except NULL:
def projection_geometry(i):
cdef CProjector2D * proj = getObject(i)
- return utils.configToDict(proj.getProjectionGeometry().getConfiguration())
+ cdef Config * cfg = proj.getProjectionGeometry().getConfiguration()
+ dct = utils.configToDict(cfg)
+ del cfg
+ return dct
def volume_geometry(i):
cdef CProjector2D * proj = getObject(i)
- return utils.configToDict(proj.getVolumeGeometry().getConfiguration())
+ cdef Config * cfg = proj.getVolumeGeometry().getConfiguration()
+ dct = utils.configToDict(cfg)
+ del cfg
+ return dct
def weights_single_ray(i, projection_index, detector_index):
diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx
index ddb37aa..260c308 100644
--- a/python/astra/utils.pyx
+++ b/python/astra/utils.pyx
@@ -95,7 +95,8 @@ cdef void readDict(XMLNode root, _dc):
if val.size == 0:
break
listbase = root.addChildNode(item)
- data = <double*>np.PyArray_DATA(np.ascontiguousarray(val,dtype=np.float64))
+ contig_data = np.ascontiguousarray(val,dtype=np.float64)
+ data = <double*>np.PyArray_DATA(contig_data)
if val.ndim == 2:
listbase.setContent(data, val.shape[1], val.shape[0], False)
elif val.ndim == 1:
@@ -129,7 +130,8 @@ cdef void readOptions(XMLNode node, dc):
break
listbase = node.addChildNode(six.b('Option'))
listbase.addAttribute(< string > six.b('key'), < string > item)
- data = <double*>np.PyArray_DATA(np.ascontiguousarray(val,dtype=np.float64))
+ contig_data = np.ascontiguousarray(val,dtype=np.float64)
+ data = <double*>np.PyArray_DATA(contig_data)
if val.ndim == 2:
listbase.setContent(data, val.shape[1], val.shape[0], False)
elif val.ndim == 1:
@@ -202,7 +204,10 @@ cdef XMLNode2dict(XMLNode node):
while it != nodes.end():
subnode = deref(it)
if castString(subnode.getName())=="Option":
- opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getAttribute('value'))
+ if subnode.hasAttribute('value'):
+ opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getAttribute('value'))
+ else:
+ opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getContent())
else:
dct[castString(subnode.getName())] = stringToPythonValue(subnode.getContent())
inc(it)
diff --git a/python/docSRC/operator.rst b/python/docSRC/operator.rst
index f5369fa..fe500ba 100644
--- a/python/docSRC/operator.rst
+++ b/python/docSRC/operator.rst
@@ -1,7 +1,7 @@
-OpTomo class: the :mod:`operator` module
+OpTomo class: the :mod:`optomo` module
==============================================
-.. automodule:: astra.operator
+.. automodule:: astra.optomo
:members:
:undoc-members:
:show-inheritance:
diff --git a/src/ParallelProjectionGeometry2D.cpp b/src/ParallelProjectionGeometry2D.cpp
index 699e141..7260b83 100644
--- a/src/ParallelProjectionGeometry2D.cpp
+++ b/src/ParallelProjectionGeometry2D.cpp
@@ -180,6 +180,11 @@ Config* CParallelProjectionGeometry2D::getConfiguration() const
cfg->self.addChildNode("DetectorCount", getDetectorCount());
cfg->self.addChildNode("DetectorWidth", getDetectorWidth());
cfg->self.addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount);
+ if(m_pfExtraDetectorOffset!=NULL){
+ XMLNode opt = cfg->self.addChildNode("Option");
+ opt.addAttribute("key","ExtraDetectorOffset");
+ opt.setContent(m_pfExtraDetectorOffset, m_iProjectionAngleCount);
+ }
return cfg;
}
//----------------------------------------------------------------------------------------
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-06 21:28:37 +0000