From 26198f7e1fbed9d294fc2856f796f408c85b66f3 Mon Sep 17 00:00:00 2001
From: Valerii Sokolov <valerii.sokolov@uantwerpen.be>
Date: Tue, 9 Jun 2015 11:26:42 +0200
Subject: Don't take address of temporary.
---
python/astra/utils.pyx | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
(limited to 'python/astra')
diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx
index ddb37aa..a8e9e4e 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:
--
cgit v1.2.3
From 63d78fbaafa7d247347f9052db86f575d89260b7 Mon Sep 17 00:00:00 2001
From: "Daniel M. Pelt" <D.M.Pelt@cwi.nl>
Date: Wed, 24 Jun 2015 20:28:46 +0200
Subject: Fix config to struct/dict translation for array options
---
python/astra/utils.pyx | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
(limited to 'python/astra')
diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx
index a8e9e4e..260c308 100644
--- a/python/astra/utils.pyx
+++ b/python/astra/utils.pyx
@@ -204,7 +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)
--
cgit v1.2.3
From 9e3472ea9041b8755050427d8bdb8a4701019c55 Mon Sep 17 00:00:00 2001
From: "Daniel M. Pelt" <D.M.Pelt@cwi.nl>
Date: Thu, 25 Jun 2015 21:52:07 +0200
Subject: Fix memory leak in configuration code
---
python/astra/projector3d_c.pyx | 10 ++++++++--
python/astra/projector_c.pyx | 10 ++++++++--
2 files changed, 16 insertions(+), 4 deletions(-)
(limited to 'python/astra')
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):
--
cgit v1.2.3
From 4d39c35d6c9124c26de64c9d227a25f612903a2a Mon Sep 17 00:00:00 2001
From: "Daniel M. Pelt" <D.M.Pelt@cwi.nl>
Date: Fri, 17 Jul 2015 13:44:59 +0200
Subject: Fix formatting when passing strings to log from high-level code
---
python/astra/log_c.pyx | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
(limited to 'python/astra')
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()
--
cgit v1.2.3
From 43155c03488ca98c24f8f369e5c8699efa20cca3 Mon Sep 17 00:00:00 2001
From: "Daniel M. Pelt" <D.M.Pelt@cwi.nl>
Date: Thu, 30 Jul 2015 15:28:16 +0200
Subject: Fix Python OpTomo for scipy 0.16
scipy 0.16 also uses .T to define a transpose, which conflicts
with the old OpTomo implementation. OpTomo now also defines the
_transpose() method, which .T will call in scipy 0.16.
---
python/astra/optomo.py | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
(limited to 'python/astra')
diff --git a/python/astra/optomo.py b/python/astra/optomo.py
index 0108674..19b07e3 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:
--
cgit v1.2.3
From b4bd441549ea71dd6c34a9f2158bbebc39ba4e9e Mon Sep 17 00:00:00 2001
From: "Daniel M. Pelt" <D.M.Pelt@cwi.nl>
Date: Thu, 30 Jul 2015 15:34:10 +0200
Subject: Define a transpose for the OpTomo transpose as well
Allows for chaining .T calls.
---
python/astra/optomo.py | 8 ++++++++
1 file changed, 8 insertions(+)
(limited to 'python/astra')
diff --git a/python/astra/optomo.py b/python/astra/optomo.py
index 19b07e3..4a64150 100644
--- a/python/astra/optomo.py
+++ b/python/astra/optomo.py
@@ -197,6 +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)
@@ -204,6 +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:
--
cgit v1.2.3
From ee790c305942675e94ee66bfd24896d1ef61335a Mon Sep 17 00:00:00 2001
From: "Daniel M. Pelt" <D.M.Pelt@cwi.nl>
Date: Mon, 10 Aug 2015 16:22:19 +0200
Subject: Release the gil in algorithm.run
---
python/astra/PyIncludes.pxd | 2 +-
python/astra/algorithm_c.pyx | 4 +++-
2 files changed, 4 insertions(+), 2 deletions(-)
(limited to 'python/astra')
diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd
index 909f58f..35dea5f 100644
--- a/python/astra/PyIncludes.pxd
+++ b/python/astra/PyIncludes.pxd
@@ -143,7 +143,7 @@ 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):
--
cgit v1.2.3