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-rw-r--r--python/astra/PyIndexManager.pxd40
-rw-r--r--python/astra/algorithm_c.pyx37
-rw-r--r--python/astra/astra.py20
-rw-r--r--python/astra/astra_c.pyx70
-rw-r--r--python/astra/data2d_c.pyx36
-rw-r--r--python/astra/data3d.py2
-rw-r--r--python/astra/data3d_c.pyx36
-rw-r--r--python/astra/experimental.pyx10
-rw-r--r--python/astra/extrautils.pyx35
-rw-r--r--python/astra/functions.py2
-rw-r--r--python/astra/log_c.pyx36
-rw-r--r--python/astra/matrix_c.pyx36
-rw-r--r--python/astra/optomo.py4
-rw-r--r--python/astra/plugin_c.pyx53
-rw-r--r--python/astra/projector3d_c.pyx36
-rw-r--r--python/astra/projector_c.pyx36
-rw-r--r--python/astra/src/PythonPluginAlgorithm.cpp372
-rw-r--r--python/astra/src/PythonPluginAlgorithm.h88
-rw-r--r--python/astra/utils.pyx48
19 files changed, 778 insertions, 219 deletions
diff --git a/python/astra/PyIndexManager.pxd b/python/astra/PyIndexManager.pxd
new file mode 100644
index 0000000..c1ad502
--- /dev/null
+++ b/python/astra/PyIndexManager.pxd
@@ -0,0 +1,40 @@
+# -----------------------------------------------------------------------
+# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
+# 2013-2016, CWI, Amsterdam
+#
+# Contact: astra@uantwerpen.be
+# Website: http://sf.net/projects/astra-toolbox
+#
+# This file is part of the ASTRA Toolbox.
+#
+#
+# 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 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 ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+#
+# -----------------------------------------------------------------------
+
+from libcpp.string cimport string
+
+from .PyIncludes cimport *
+
+cdef extern from "astra/AstraObjectManager.h" namespace "astra":
+ cdef cppclass CAstraObjectManagerBase:
+ string getInfo(int)
+ void remove(int)
+ string getType()
+ cdef cppclass CAstraIndexManager:
+ CAstraObjectManagerBase* get(int)
+
+cdef extern from "astra/AstraObjectManager.h" namespace "astra::CAstraIndexManager":
+ cdef CAstraIndexManager* getSingletonPtr()
+
diff --git a/python/astra/algorithm_c.pyx b/python/astra/algorithm_c.pyx
index 3231c1f..4e96578 100644
--- a/python/astra/algorithm_c.pyx
+++ b/python/astra/algorithm_c.pyx
@@ -1,29 +1,28 @@
-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
+# -----------------------------------------------------------------------
+# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
+# 2013-2016, CWI, Amsterdam
#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
+# Contact: astra@uantwerpen.be
+# Website: http://sf.net/projects/astra-toolbox
#
+# This file is part of the ASTRA Toolbox.
#
-#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 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.
+# 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/>.
+# You should have received a copy of the GNU General Public License
+# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+#
+# -----------------------------------------------------------------------
#
-#-----------------------------------------------------------------------
-
# distutils: language = c++
# distutils: libraries = astra
diff --git a/python/astra/astra.py b/python/astra/astra.py
index 9328b6b..61c26ee 100644
--- a/python/astra/astra.py
+++ b/python/astra/astra.py
@@ -56,3 +56,23 @@ def set_gpu_index(idx, memory=0):
:type idx: :class:`int`
"""
a.set_gpu_index(idx, memory)
+
+def delete(ids):
+ """Delete an astra object.
+
+ :param ids: ID or list of ID's to delete.
+ :type ids: :class:`int` or :class:`list`
+
+ """
+ return a.delete(ids)
+
+def info(ids):
+ """Print info about an astra object.
+
+ :param ids: ID or list of ID's to show.
+ :type ids: :class:`int` or :class:`list`
+
+ """
+ return a.info(ids)
+
+
diff --git a/python/astra/astra_c.pyx b/python/astra/astra_c.pyx
index 2a9c816..8e30e69 100644
--- a/python/astra/astra_c.pyx
+++ b/python/astra/astra_c.pyx
@@ -1,28 +1,28 @@
-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
+# -----------------------------------------------------------------------
+# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
+# 2013-2016, CWI, Amsterdam
#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
+# Contact: astra@uantwerpen.be
+# Website: http://sf.net/projects/astra-toolbox
#
+# This file is part of the ASTRA Toolbox.
#
-#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 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.
+# 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/>.
+# You should have received a copy of the GNU General Public License
+# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+#
+# -----------------------------------------------------------------------
#
-#-----------------------------------------------------------------------
# distutils: language = c++
# distutils: libraries = astra
@@ -33,6 +33,9 @@ from .utils import wrap_from_bytes
from libcpp.string cimport string
from libcpp.vector cimport vector
from libcpp cimport bool
+cimport PyIndexManager
+from .PyIndexManager cimport CAstraObjectManagerBase
+
cdef extern from "astra/Globals.h" namespace "astra":
int getVersion()
string getVersionString()
@@ -51,6 +54,7 @@ cdef extern from "astra/CompositeGeometryManager.h" namespace "astra":
cdef extern from "astra/CompositeGeometryManager.h" namespace "astra::CCompositeGeometryManager":
void setGlobalGPUParams(SGPUParams&)
+
def credits():
six.print_("""The ASTRA Toolbox has been developed at the University of Antwerp and CWI, Amsterdam by
* Prof. dr. Joost Batenburg
@@ -77,12 +81,12 @@ def version(printToScreen=False):
else:
return getVersion()
-def set_gpu_index(idx, memory=0):
- import types
+IF HAVE_CUDA==True:
+ def set_gpu_index(idx, memory=0):
import collections
cdef SGPUParams params
if use_cuda()==True:
- if not isinstance(idx, collections.Iterable) or isinstance(idx, types.StringTypes):
+ if not isinstance(idx, collections.Iterable) or isinstance(idx, six.string_types + (six.text_type,six.binary_type)):
idx = (idx,)
params.memory = memory
params.GPUIndices = idx
@@ -90,3 +94,27 @@ def set_gpu_index(idx, memory=0):
ret = setGPUIndex(params.GPUIndices[0])
if not ret:
six.print_("Failed to set GPU " + str(params.GPUIndices[0]))
+ELSE:
+ def set_gpu_index(idx, memory=0):
+ raise NotImplementedError("CUDA support is not enabled in ASTRA")
+
+def delete(ids):
+ import collections
+ cdef CAstraObjectManagerBase* ptr
+ if not isinstance(ids, collections.Iterable) or isinstance(ids, six.string_types + (six.text_type,six.binary_type)):
+ ids = (ids,)
+ for i in ids:
+ ptr = PyIndexManager.getSingletonPtr().get(i)
+ if ptr:
+ ptr.remove(i)
+
+def info(ids):
+ import collections
+ cdef CAstraObjectManagerBase* ptr
+ if not isinstance(ids, collections.Iterable) or isinstance(ids, six.string_types + (six.text_type,six.binary_type)):
+ ids = (ids,)
+ for i in ids:
+ ptr = PyIndexManager.getSingletonPtr().get(i)
+ if ptr:
+ s = ptr.getType() + six.b("\t") + ptr.getInfo(i)
+ six.print_(wrap_from_bytes(s))
diff --git a/python/astra/data2d_c.pyx b/python/astra/data2d_c.pyx
index 801fd8e..65e80ce 100644
--- a/python/astra/data2d_c.pyx
+++ b/python/astra/data2d_c.pyx
@@ -1,28 +1,28 @@
-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
+# -----------------------------------------------------------------------
+# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
+# 2013-2016, CWI, Amsterdam
#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
+# Contact: astra@uantwerpen.be
+# Website: http://sf.net/projects/astra-toolbox
#
+# This file is part of the ASTRA Toolbox.
#
-#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 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.
+# 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/>.
+# You should have received a copy of the GNU General Public License
+# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+#
+# -----------------------------------------------------------------------
#
-#-----------------------------------------------------------------------
# distutils: language = c++
# distutils: libraries = astra
diff --git a/python/astra/data3d.py b/python/astra/data3d.py
index e5ef6b0..f143659 100644
--- a/python/astra/data3d.py
+++ b/python/astra/data3d.py
@@ -89,7 +89,7 @@ def get_single(i):
:returns: :class:`numpy.ndarray` -- The object data.
"""
- return g.get_single(i)
+ return d.get_single(i)
def store(i,data):
"""Fill existing 3D object with data.
diff --git a/python/astra/data3d_c.pyx b/python/astra/data3d_c.pyx
index 3b27ab7..207d9a5 100644
--- a/python/astra/data3d_c.pyx
+++ b/python/astra/data3d_c.pyx
@@ -1,28 +1,28 @@
-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
+# -----------------------------------------------------------------------
+# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
+# 2013-2016, CWI, Amsterdam
#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
+# Contact: astra@uantwerpen.be
+# Website: http://sf.net/projects/astra-toolbox
#
+# This file is part of the ASTRA Toolbox.
#
-#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 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.
+# 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/>.
+# You should have received a copy of the GNU General Public License
+# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+#
+# -----------------------------------------------------------------------
#
-#-----------------------------------------------------------------------
# distutils: language = c++
# distutils: libraries = astra
diff --git a/python/astra/experimental.pyx b/python/astra/experimental.pyx
index aafc002..9bb73a2 100644
--- a/python/astra/experimental.pyx
+++ b/python/astra/experimental.pyx
@@ -1,6 +1,6 @@
-#-----------------------------------------------------------------------
-# Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp
-# 2014-2015, CWI, Amsterdam
+# -----------------------------------------------------------------------
+# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
+# 2013-2016, CWI, Amsterdam
#
# Contact: astra@uantwerpen.be
# Website: http://sf.net/projects/astra-toolbox
@@ -21,8 +21,8 @@
# You should have received a copy of the GNU General Public License
# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
#
-#-----------------------------------------------------------------------
-
+# -----------------------------------------------------------------------
+#
# distutils: language = c++
# distutils: libraries = astra
diff --git a/python/astra/extrautils.pyx b/python/astra/extrautils.pyx
index 998f5cb..5bc315f 100644
--- a/python/astra/extrautils.pyx
+++ b/python/astra/extrautils.pyx
@@ -1,28 +1,27 @@
-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
+# -----------------------------------------------------------------------
+# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
+# 2013-2016, CWI, Amsterdam
#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
+# Contact: astra@uantwerpen.be
+# Website: http://sf.net/projects/astra-toolbox
#
+# This file is part of the ASTRA Toolbox.
#
-#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 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.
+# 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/>.
+# You should have received a copy of the GNU General Public License
+# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
#
-#-----------------------------------------------------------------------
+# -----------------------------------------------------------------------
def clipCircle(img):
cdef int i,j
diff --git a/python/astra/functions.py b/python/astra/functions.py
index e38b5bc..3f4aa82 100644
--- a/python/astra/functions.py
+++ b/python/astra/functions.py
@@ -115,7 +115,7 @@ def add_noise_to_sino(sinogram_in, I0, seed=None):
sinogram_out = -max_sinogramRaw * np.log(sinogramCT_D)
if not isinstance(sinogram_in, np.ndarray):
- at.data2d.store(sinogram_in, sinogram_out)
+ data2d.store(sinogram_in, sinogram_out)
if not seed==None:
np.random.set_state(curstate)
diff --git a/python/astra/log_c.pyx b/python/astra/log_c.pyx
index 55c63e6..0d187e9 100644
--- a/python/astra/log_c.pyx
+++ b/python/astra/log_c.pyx
@@ -1,28 +1,28 @@
-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
+# -----------------------------------------------------------------------
+# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
+# 2013-2016, CWI, Amsterdam
#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
+# Contact: astra@uantwerpen.be
+# Website: http://sf.net/projects/astra-toolbox
#
+# This file is part of the ASTRA Toolbox.
#
-#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 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.
+# 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/>.
+# You should have received a copy of the GNU General Public License
+# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+#
+# -----------------------------------------------------------------------
#
-#-----------------------------------------------------------------------
# distutils: language = c++
# distutils: libraries = astra
diff --git a/python/astra/matrix_c.pyx b/python/astra/matrix_c.pyx
index d099a75..f5c0938 100644
--- a/python/astra/matrix_c.pyx
+++ b/python/astra/matrix_c.pyx
@@ -1,28 +1,28 @@
-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
+# -----------------------------------------------------------------------
+# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
+# 2013-2016, CWI, Amsterdam
#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
+# Contact: astra@uantwerpen.be
+# Website: http://sf.net/projects/astra-toolbox
#
+# This file is part of the ASTRA Toolbox.
#
-#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 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.
+# 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/>.
+# You should have received a copy of the GNU General Public License
+# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+#
+# -----------------------------------------------------------------------
#
-#-----------------------------------------------------------------------
# distutils: language = c++
# distutils: libraries = astra
diff --git a/python/astra/optomo.py b/python/astra/optomo.py
index 4a64150..dd10713 100644
--- a/python/astra/optomo.py
+++ b/python/astra/optomo.py
@@ -160,7 +160,7 @@ class OpTomo(scipy.sparse.linalg.LinearOperator):
return self._matvec(v)
return scipy.sparse.linalg.LinearOperator.__mul__(self, v)
- def reconstruct(self, method, s, iterations=1, extraOptions = {}):
+ def reconstruct(self, method, s, iterations=1, extraOptions = None):
"""Reconstruct an object.
:param method: Method to use for reconstruction.
@@ -172,6 +172,8 @@ class OpTomo(scipy.sparse.linalg.LinearOperator):
:param extraOptions: Extra options to use during reconstruction (i.e. for cfg['option']).
:type extraOptions: :class:`dict`
"""
+ if extraOptions is None:
+ extraOptions={}
s = self.__checkArray(s, self.sshape)
sid = self.data_mod.link('-sino',self.pg,s)
v = np.zeros(self.vshape,dtype=np.float32)
diff --git a/python/astra/plugin_c.pyx b/python/astra/plugin_c.pyx
index 8d6816b..ee04853 100644
--- a/python/astra/plugin_c.pyx
+++ b/python/astra/plugin_c.pyx
@@ -1,28 +1,28 @@
-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
+# -----------------------------------------------------------------------
+# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
+# 2013-2016, CWI, Amsterdam
#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
+# Contact: astra@uantwerpen.be
+# Website: http://sf.net/projects/astra-toolbox
#
+# This file is part of the ASTRA Toolbox.
#
-#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 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.
+# 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/>.
+# You should have received a copy of the GNU General Public License
+# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+#
+# -----------------------------------------------------------------------
#
-#-----------------------------------------------------------------------
# distutils: language = c++
# distutils: libraries = astra
@@ -32,21 +32,25 @@ import inspect
from libcpp.string cimport string
from libcpp cimport bool
-cdef CPluginAlgorithmFactory *fact = getSingletonPtr()
+cdef CPythonPluginAlgorithmFactory *fact = getSingletonPtr()
from . import utils
-cdef extern from "astra/PluginAlgorithm.h" namespace "astra":
- cdef cppclass CPluginAlgorithmFactory:
+cdef extern from "src/PythonPluginAlgorithm.h" namespace "astra":
+ cdef cppclass CPythonPluginAlgorithmFactory:
bool registerPlugin(string className)
bool registerPlugin(string name, string className)
bool registerPluginClass(object className)
bool registerPluginClass(string name, object className)
object getRegistered()
- string getHelp(string name)
+ string getHelp(string &name)
+
+cdef extern from "src/PythonPluginAlgorithm.h" namespace "astra::CPythonPluginAlgorithmFactory":
+ cdef CPythonPluginAlgorithmFactory* getSingletonPtr()
cdef extern from "astra/PluginAlgorithm.h" namespace "astra::CPluginAlgorithmFactory":
- cdef CPluginAlgorithmFactory* getSingletonPtr()
+ # NB: Using wrong pointer type here for convenience
+ cdef void registerFactory(CPythonPluginAlgorithmFactory *)
def register(className, name=None):
if inspect.isclass(className):
@@ -65,3 +69,6 @@ def get_registered():
def get_help(name):
return utils.wrap_from_bytes(fact.getHelp(six.b(name)))
+
+# Register python plugin factory with astra
+registerFactory(fact)
diff --git a/python/astra/projector3d_c.pyx b/python/astra/projector3d_c.pyx
index aec9cde..e355e38 100644
--- a/python/astra/projector3d_c.pyx
+++ b/python/astra/projector3d_c.pyx
@@ -1,28 +1,28 @@
-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
+# -----------------------------------------------------------------------
+# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
+# 2013-2016, CWI, Amsterdam
#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
+# Contact: astra@uantwerpen.be
+# Website: http://sf.net/projects/astra-toolbox
#
+# This file is part of the ASTRA Toolbox.
#
-#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 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.
+# 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/>.
+# You should have received a copy of the GNU General Public License
+# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+#
+# -----------------------------------------------------------------------
#
-#-----------------------------------------------------------------------
# distutils: language = c++
# distutils: libraries = astra
diff --git a/python/astra/projector_c.pyx b/python/astra/projector_c.pyx
index 77c64a4..53d38c3 100644
--- a/python/astra/projector_c.pyx
+++ b/python/astra/projector_c.pyx
@@ -1,28 +1,28 @@
-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
+# -----------------------------------------------------------------------
+# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
+# 2013-2016, CWI, Amsterdam
#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
+# Contact: astra@uantwerpen.be
+# Website: http://sf.net/projects/astra-toolbox
#
+# This file is part of the ASTRA Toolbox.
#
-#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 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.
+# 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/>.
+# You should have received a copy of the GNU General Public License
+# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+#
+# -----------------------------------------------------------------------
#
-#-----------------------------------------------------------------------
# distutils: language = c++
# distutils: libraries = astra
diff --git a/python/astra/src/PythonPluginAlgorithm.cpp b/python/astra/src/PythonPluginAlgorithm.cpp
new file mode 100644
index 0000000..617c0f4
--- /dev/null
+++ b/python/astra/src/PythonPluginAlgorithm.cpp
@@ -0,0 +1,372 @@
+/*
+-----------------------------------------------------------------------
+Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
+ 2014-2016, CWI, Amsterdam
+
+Contact: astra@uantwerpen.be
+Website: http://sf.net/projects/astra-toolbox
+
+This file is part of the ASTRA Toolbox.
+
+
+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 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 ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+
+-----------------------------------------------------------------------
+*/
+
+#ifdef ASTRA_PYTHON
+
+#include "PythonPluginAlgorithm.h"
+
+#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>
+
+#include <Python.h>
+#include "bytesobject.h"
+
+namespace astra {
+
+
+
+void logPythonError(){
+ if(PyErr_Occurred()){
+ PyObject *ptype, *pvalue, *ptraceback;
+ PyErr_Fetch(&ptype, &pvalue, &ptraceback);
+ PyErr_NormalizeException(&ptype, &pvalue, &ptraceback);
+ PyObject *traceback = PyImport_ImportModule("traceback");
+ if(traceback!=NULL){
+ PyObject *exc;
+ if(ptraceback==NULL){
+ exc = PyObject_CallMethod(traceback,"format_exception_only","OO",ptype, pvalue);
+ }else{
+ exc = PyObject_CallMethod(traceback,"format_exception","OOO",ptype, pvalue, ptraceback);
+ }
+ if(exc!=NULL){
+ PyObject *six = PyImport_ImportModule("six");
+ if(six!=NULL){
+ PyObject *iter = PyObject_GetIter(exc);
+ if(iter!=NULL){
+ PyObject *line;
+ std::string errStr = "";
+ while(line = PyIter_Next(iter)){
+ PyObject *retb = PyObject_CallMethod(six,"b","O",line);
+ if(retb!=NULL){
+ errStr += std::string(PyBytes_AsString(retb));
+ Py_DECREF(retb);
+ }
+ Py_DECREF(line);
+ }
+ ASTRA_ERROR("%s",errStr.c_str());
+ Py_DECREF(iter);
+ }
+ Py_DECREF(six);
+ }
+ Py_DECREF(exc);
+ }
+ Py_DECREF(traceback);
+ }
+ if(ptype!=NULL) Py_DECREF(ptype);
+ if(pvalue!=NULL) Py_DECREF(pvalue);
+ if(ptraceback!=NULL) Py_DECREF(ptraceback);
+ }
+}
+
+
+CPluginAlgorithm::CPluginAlgorithm(PyObject* pyclass){
+ instance = PyObject_CallObject(pyclass, NULL);
+ if(instance==NULL) logPythonError();
+}
+
+CPluginAlgorithm::~CPluginAlgorithm(){
+ if(instance!=NULL){
+ Py_DECREF(instance);
+ instance = NULL;
+ }
+}
+
+bool CPluginAlgorithm::initialize(const Config& _cfg){
+ if(instance==NULL) return false;
+ PyObject *cfgDict = XMLNode2dict(_cfg.self);
+ PyObject *retVal = PyObject_CallMethod(instance, "astra_init", "O",cfgDict);
+ Py_DECREF(cfgDict);
+ if(retVal==NULL){
+ logPythonError();
+ return false;
+ }
+ m_bIsInitialized = true;
+ Py_DECREF(retVal);
+ return m_bIsInitialized;
+}
+
+void CPluginAlgorithm::run(int _iNrIterations){
+ if(instance==NULL) return;
+ PyGILState_STATE state = PyGILState_Ensure();
+ PyObject *retVal = PyObject_CallMethod(instance, "run", "i",_iNrIterations);
+ if(retVal==NULL){
+ logPythonError();
+ }else{
+ Py_DECREF(retVal);
+ }
+ PyGILState_Release(state);
+}
+
+CPythonPluginAlgorithmFactory::CPythonPluginAlgorithmFactory(){
+ if(!Py_IsInitialized()){
+ Py_Initialize();
+ PyEval_InitThreads();
+ }
+ pluginDict = PyDict_New();
+ inspect = PyImport_ImportModule("inspect");
+ six = PyImport_ImportModule("six");
+}
+
+CPythonPluginAlgorithmFactory::~CPythonPluginAlgorithmFactory(){
+ if(pluginDict!=NULL){
+ Py_DECREF(pluginDict);
+ }
+ if(inspect!=NULL) Py_DECREF(inspect);
+ if(six!=NULL) Py_DECREF(six);
+}
+
+PyObject * getClassFromString(std::string str){
+ std::vector<std::string> items;
+ boost::split(items, str, boost::is_any_of("."));
+ PyObject *pyclass = PyImport_ImportModule(items[0].c_str());
+ if(pyclass==NULL){
+ logPythonError();
+ return NULL;
+ }
+ PyObject *submod = pyclass;
+ for(unsigned int i=1;i<items.size();i++){
+ submod = PyObject_GetAttrString(submod,items[i].c_str());
+ Py_DECREF(pyclass);
+ pyclass = submod;
+ if(pyclass==NULL){
+ logPythonError();
+ return NULL;
+ }
+ }
+ return pyclass;
+}
+
+bool CPythonPluginAlgorithmFactory::registerPlugin(std::string name, std::string className){
+ PyObject *str = PyBytes_FromString(className.c_str());
+ PyDict_SetItemString(pluginDict, name.c_str(), str);
+ Py_DECREF(str);
+ return true;
+}
+
+bool CPythonPluginAlgorithmFactory::registerPlugin(std::string className){
+ PyObject *pyclass = getClassFromString(className);
+ if(pyclass==NULL) return false;
+ bool ret = registerPluginClass(pyclass);
+ Py_DECREF(pyclass);
+ return ret;
+}
+
+bool CPythonPluginAlgorithmFactory::registerPluginClass(std::string name, PyObject * className){
+ PyDict_SetItemString(pluginDict, name.c_str(), className);
+ return true;
+}
+
+bool CPythonPluginAlgorithmFactory::registerPluginClass(PyObject * className){
+ PyObject *astra_name = PyObject_GetAttrString(className,"astra_name");
+ if(astra_name==NULL){
+ logPythonError();
+ return false;
+ }
+ PyObject *retb = PyObject_CallMethod(six,"b","O",astra_name);
+ if(retb!=NULL){
+ PyDict_SetItemString(pluginDict,PyBytes_AsString(retb),className);
+ Py_DECREF(retb);
+ }else{
+ logPythonError();
+ }
+ Py_DECREF(astra_name);
+ return true;
+}
+
+CAlgorithm * CPythonPluginAlgorithmFactory::getPlugin(const std::string &name){
+ PyObject *className = PyDict_GetItemString(pluginDict, name.c_str());
+ if(className==NULL) return NULL;
+ CPluginAlgorithm *alg = NULL;
+ if(PyBytes_Check(className)){
+ std::string str = std::string(PyBytes_AsString(className));
+ PyObject *pyclass = getClassFromString(str);
+ if(pyclass!=NULL){
+ alg = new CPluginAlgorithm(pyclass);
+ Py_DECREF(pyclass);
+ }
+ }else{
+ alg = new CPluginAlgorithm(className);
+ }
+ return alg;
+}
+
+PyObject * CPythonPluginAlgorithmFactory::getRegistered(){
+ Py_INCREF(pluginDict);
+ return pluginDict;
+}
+
+std::map<std::string, std::string> CPythonPluginAlgorithmFactory::getRegisteredMap(){
+ std::map<std::string, std::string> ret;
+ PyObject *key, *value;
+ Py_ssize_t pos = 0;
+ while (PyDict_Next(pluginDict, &pos, &key, &value)) {
+ PyObject *keystr = PyObject_Str(key);
+ if(keystr!=NULL){
+ PyObject *valstr = PyObject_Str(value);
+ if(valstr!=NULL){
+ PyObject * keyb = PyObject_CallMethod(six,"b","O",keystr);
+ if(keyb!=NULL){
+ PyObject * valb = PyObject_CallMethod(six,"b","O",valstr);
+ if(valb!=NULL){
+ ret[PyBytes_AsString(keyb)] = PyBytes_AsString(valb);
+ Py_DECREF(valb);
+ }
+ Py_DECREF(keyb);
+ }
+ Py_DECREF(valstr);
+ }
+ Py_DECREF(keystr);
+ }
+ logPythonError();
+ }
+ return ret;
+}
+
+std::string CPythonPluginAlgorithmFactory::getHelp(const std::string &name){
+ PyObject *className = PyDict_GetItemString(pluginDict, name.c_str());
+ if(className==NULL){
+ ASTRA_ERROR("Plugin %s not found!",name.c_str());
+ PyErr_Clear();
+ return "";
+ }
+ std::string ret = "";
+ PyObject *pyclass;
+ if(PyBytes_Check(className)){
+ std::string str = std::string(PyBytes_AsString(className));
+ pyclass = getClassFromString(str);
+ }else{
+ pyclass = className;
+ }
+ if(pyclass==NULL) return "";
+ if(inspect!=NULL && six!=NULL){
+ PyObject *retVal = PyObject_CallMethod(inspect,"getdoc","O",pyclass);
+ if(retVal!=NULL){
+ if(retVal!=Py_None){
+ PyObject *retb = PyObject_CallMethod(six,"b","O",retVal);
+ if(retb!=NULL){
+ ret = std::string(PyBytes_AsString(retb));
+ Py_DECREF(retb);
+ }
+ }
+ Py_DECREF(retVal);
+ }else{
+ logPythonError();
+ }
+ }
+ if(PyBytes_Check(className)){
+ Py_DECREF(pyclass);
+ }
+ return ret;
+}
+
+DEFINE_SINGLETON(CPythonPluginAlgorithmFactory);
+
+#if PY_MAJOR_VERSION >= 3
+PyObject * pyStringFromString(std::string str){
+ return PyUnicode_FromString(str.c_str());
+}
+#else
+PyObject * pyStringFromString(std::string str){
+ return PyBytes_FromString(str.c_str());
+}
+#endif
+
+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(";"));
+ PyObject *mat = PyList_New(rows.size());
+ for(unsigned int i=0; i<rows.size(); i++){
+ boost::split(row, rows[i], boost::is_any_of(","));
+ 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])));
+ }
+ PyList_SetItem(mat, i, rowlist);
+ }
+ return mat;
+ }
+ if(str.find(",")!=std::string::npos){
+ std::vector<std::string> vec;
+ boost::split(vec, str, boost::is_any_of(","));
+ 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])));
+ }
+ return veclist;
+ }
+ try{
+ return PyLong_FromLong(StringUtil::stringToInt(str));
+ }catch(const StringUtil::bad_cast &){
+ try{
+ return PyFloat_FromDouble(StringUtil::stringToDouble(str));
+ }catch(const StringUtil::bad_cast &){
+ return pyStringFromString(str);
+ }
+ }
+}
+
+PyObject* XMLNode2dict(XMLNode node){
+ PyObject *dct = PyDict_New();
+ PyObject *opts = PyDict_New();
+ if(node.hasAttribute("type")){
+ PyObject *obj = pyStringFromString(node.getAttribute("type").c_str());
+ PyDict_SetItemString(dct, "type", obj);
+ Py_DECREF(obj);
+ }
+ std::list<XMLNode> nodes = node.getNodes();
+ std::list<XMLNode>::iterator it = nodes.begin();
+ while(it!=nodes.end()){
+ XMLNode subnode = *it;
+ if(subnode.getName()=="Option"){
+ PyObject *obj;
+ if(subnode.hasAttribute("value")){
+ obj = stringToPythonValue(subnode.getAttribute("value"));
+ }else{
+ obj = stringToPythonValue(subnode.getContent());
+ }
+ PyDict_SetItemString(opts, subnode.getAttribute("key").c_str(), obj);
+ Py_DECREF(obj);
+ }else{
+ PyObject *obj = stringToPythonValue(subnode.getContent());
+ PyDict_SetItemString(dct, subnode.getName().c_str(), obj);
+ Py_DECREF(obj);
+ }
+ ++it;
+ }
+ PyDict_SetItemString(dct, "options", opts);
+ Py_DECREF(opts);
+ return dct;
+}
+
+}
+#endif
diff --git a/python/astra/src/PythonPluginAlgorithm.h b/python/astra/src/PythonPluginAlgorithm.h
new file mode 100644
index 0000000..ea4c6fb
--- /dev/null
+++ b/python/astra/src/PythonPluginAlgorithm.h
@@ -0,0 +1,88 @@
+/*
+-----------------------------------------------------------------------
+Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
+ 2014-2016, CWI, Amsterdam
+
+Contact: astra@uantwerpen.be
+Website: http://sf.net/projects/astra-toolbox
+
+This file is part of the ASTRA Toolbox.
+
+
+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 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 ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+
+-----------------------------------------------------------------------
+*/
+
+#ifndef _INC_PYTHONPLUGINALGORITHM
+#define _INC_PYTHONPLUGINALGORITHM
+
+#ifdef ASTRA_PYTHON
+
+#include "astra/Algorithm.h"
+#include "astra/Singleton.h"
+#include "astra/XMLDocument.h"
+#include "astra/XMLNode.h"
+#include "astra/PluginAlgorithm.h"
+
+#include <Python.h>
+
+namespace astra {
+class CPluginAlgorithm : public CAlgorithm {
+
+public:
+
+ CPluginAlgorithm(PyObject* pyclass);
+ ~CPluginAlgorithm();
+
+ bool initialize(const Config& _cfg);
+ void run(int _iNrIterations);
+
+private:
+ PyObject * instance;
+
+};
+
+class CPythonPluginAlgorithmFactory : public CPluginAlgorithmFactory, public Singleton<CPythonPluginAlgorithmFactory> {
+
+public:
+
+ CPythonPluginAlgorithmFactory();
+ virtual ~CPythonPluginAlgorithmFactory();
+
+ virtual CAlgorithm * getPlugin(const std::string &name);
+
+ virtual bool registerPlugin(std::string name, std::string className);
+ virtual bool registerPlugin(std::string className);
+ bool registerPluginClass(std::string name, PyObject * className);
+ bool registerPluginClass(PyObject * className);
+
+ PyObject * getRegistered();
+ virtual std::map<std::string, std::string> getRegisteredMap();
+
+ virtual std::string getHelp(const std::string &name);
+
+private:
+ PyObject * pluginDict;
+ PyObject *inspect, *six;
+};
+
+PyObject* XMLNode2dict(XMLNode node);
+
+}
+
+
+#endif
+
+#endif
diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx
index 07727ce..34d1902 100644
--- a/python/astra/utils.pyx
+++ b/python/astra/utils.pyx
@@ -1,28 +1,28 @@
-#-----------------------------------------------------------------------
-#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
+# -----------------------------------------------------------------------
+# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
+# 2013-2016, CWI, Amsterdam
#
-#Author: Daniel M. Pelt
-#Contact: D.M.Pelt@cwi.nl
-#Website: http://dmpelt.github.io/pyastratoolbox/
+# Contact: astra@uantwerpen.be
+# Website: http://sf.net/projects/astra-toolbox
#
+# This file is part of the ASTRA Toolbox.
#
-#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 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.
+# 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/>.
+# You should have received a copy of the GNU General Public License
+# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+#
+# -----------------------------------------------------------------------
#
-#-----------------------------------------------------------------------
# distutils: language = c++
# distutils: libraries = astra
@@ -32,7 +32,7 @@ import six
if six.PY3:
import builtins
else:
- import __builtin__
+ import __builtin__ as builtins
from libcpp.string cimport string
from libcpp.vector cimport vector
from libcpp.list cimport list
@@ -95,14 +95,14 @@ cdef void readDict(XMLNode root, _dc):
dc = convert_item(_dc)
for item in dc:
val = dc[item]
- if isinstance(val, __builtins__.list) or isinstance(val, tuple):
+ if isinstance(val, builtins.list) or isinstance(val, tuple):
val = np.array(val,dtype=np.float64)
if isinstance(val, np.ndarray):
if val.size == 0:
break
listbase = root.addChildNode(item)
contig_data = np.ascontiguousarray(val,dtype=np.float64)
- data = <double*>np.PyArray_DATA(contig_data)
+ 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:
@@ -119,6 +119,8 @@ cdef void readDict(XMLNode root, _dc):
if item == six.b('type'):
root.addAttribute(< string > six.b('type'), <string> wrap_to_bytes(val))
else:
+ if isinstance(val, builtins.bool):
+ val = int(val)
itm = root.addChildNode(item, wrap_to_bytes(val))
cdef void readOptions(XMLNode node, dc):
@@ -131,7 +133,7 @@ cdef void readOptions(XMLNode node, dc):
val = dc[item]
if node.hasOption(item):
raise Exception('Duplicate Option: %s' % item)
- if isinstance(val, __builtins__.list) or isinstance(val, tuple):
+ if isinstance(val, builtins.list) or isinstance(val, tuple):
val = np.array(val,dtype=np.float64)
if isinstance(val, np.ndarray):
if val.size == 0:
@@ -147,6 +149,8 @@ cdef void readOptions(XMLNode node, dc):
else:
raise Exception("Only 1 or 2 dimensions are allowed")
else:
+ if isinstance(val, builtins.bool):
+ val = int(val)
node.addOption(item, wrap_to_bytes(val))
cdef configToDict(Config *cfg):