Merge branch 'master' into python-plugins

Conflicts:
	python/astra/utils.pyx

8 files changed, 47 insertions, 16 deletions

diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd
index a099c31..77346b0 100644
--- a/python/astra/PyIncludes.pxd
+++ b/python/astra/PyIncludes.pxd
@@ -145,7 +145,7 @@ cdef extern from "astra/Float32ProjectionData2D.h" namespace "astra":
 cdef extern from "astra/Algorithm.h" namespace "astra":
 	cdef cppclass CAlgorithm:
 		bool initialize(Config)
-		void run(int)
+		void run(int) nogil
 		bool isInitialized()
 
 cdef extern from "astra/ReconstructionAlgorithm2D.h" namespace "astra":
diff --git a/python/astra/algorithm_c.pyx b/python/astra/algorithm_c.pyx
index 966d3d7..3231c1f 100644
--- a/python/astra/algorithm_c.pyx
+++ b/python/astra/algorithm_c.pyx
@@ -73,7 +73,9 @@ cdef CAlgorithm * getAlg(i) except NULL:
 
 def run(i, iterations=0):
     cdef CAlgorithm * alg = getAlg(i)
-    alg.run(iterations)
+    cdef int its = iterations
+    with nogil:
+        alg.run(its)
 
 
 def get_res_norm(i):
diff --git a/python/astra/log_c.pyx b/python/astra/log_c.pyx
index f16329f..55c63e6 100644
--- a/python/astra/log_c.pyx
+++ b/python/astra/log_c.pyx
@@ -53,19 +53,19 @@ cdef extern from "astra/Logging.h" namespace "astra::CLogger":
 
 def log_debug(sfile, sline, message):
     cstr = list(map(six.b,(sfile,message)))
-    debug(cstr[0],sline,cstr[1])
+    debug(cstr[0],sline,"%s",<char*>cstr[1])
 
 def log_info(sfile, sline, message):
     cstr = list(map(six.b,(sfile,message)))
-    info(cstr[0],sline,cstr[1])
+    info(cstr[0],sline,"%s",<char*>cstr[1])
 
 def log_warn(sfile, sline, message):
     cstr = list(map(six.b,(sfile,message)))
-    warn(cstr[0],sline,cstr[1])
+    warn(cstr[0],sline,"%s",<char*>cstr[1])
 
 def log_error(sfile, sline, message):
     cstr = list(map(six.b,(sfile,message)))
-    error(cstr[0],sline,cstr[1])
+    error(cstr[0],sline,"%s",<char*>cstr[1])
 
 def log_enable():
     enable()
diff --git a/python/astra/optomo.py b/python/astra/optomo.py
index 0108674..4a64150 100644
--- a/python/astra/optomo.py
+++ b/python/astra/optomo.py
@@ -86,7 +86,15 @@ class OpTomo(scipy.sparse.linalg.LinearOperator):
 
         self.proj_id = proj_id
 
-        self.T = OpTomoTranspose(self)
+        self.transposeOpTomo = OpTomoTranspose(self)
+        try:
+            self.T = self.transposeOpTomo
+        except AttributeError:
+            # Scipy >= 0.16 defines self.T using self._transpose()
+            pass
+
+    def _transpose(self):
+        return self.transposeOpTomo
 
     def __checkArray(self, arr, shp):
         if len(arr.shape)==1:
@@ -189,6 +197,11 @@ class OpTomoTranspose(scipy.sparse.linalg.LinearOperator):
         self.parent = parent
         self.dtype = np.float32
         self.shape = (parent.shape[1], parent.shape[0])
+        try:
+            self.T = self.parent
+        except AttributeError:
+            # Scipy >= 0.16 defines self.T using self._transpose()
+            pass
 
     def _matvec(self, s):
         return self.parent.rmatvec(s)
@@ -196,6 +209,9 @@ class OpTomoTranspose(scipy.sparse.linalg.LinearOperator):
     def rmatvec(self, v):
         return self.parent.matvec(v)
 
+    def _transpose(self):
+        return self.parent
+
     def __mul__(self,s):
         # Catch the case of a backprojection of 2D/3D data
         if isinstance(s, np.ndarray) and s.shape==self.parent.sshape:
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 9d2e9ab..9871ac6 100644
--- a/python/astra/utils.pyx
+++ b/python/astra/utils.pyx
@@ -99,7 +99,8 @@ 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:
@@ -135,7 +136,8 @@ 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:
@@ -147,4 +149,3 @@ cdef void readOptions(XMLNode node, dc):
 
 cdef configToDict(Config *cfg):
     return XMLNode2dict(cfg.self)
-
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: