From 56809b0359af7e9108adeb1fd21823a225edf6fa Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Wed, 20 Jan 2016 18:08:59 +0100
Subject: Remove dependency of libastra on libpython by refactoring
 PluginAlgorithm

---
 python/astra/plugin_c.pyx                  |  17 +-
 python/astra/src/PythonPluginAlgorithm.cpp | 402 +++++++++++++++++++++++++++++
 python/astra/src/PythonPluginAlgorithm.h   |  89 +++++++
 3 files changed, 503 insertions(+), 5 deletions(-)
 create mode 100644 python/astra/src/PythonPluginAlgorithm.cpp
 create mode 100644 python/astra/src/PythonPluginAlgorithm.h

(limited to 'python/astra')

diff --git a/python/astra/plugin_c.pyx b/python/astra/plugin_c.pyx
index 8d6816b..775ccd4 100644
--- a/python/astra/plugin_c.pyx
+++ b/python/astra/plugin_c.pyx
@@ -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/src/PythonPluginAlgorithm.cpp b/python/astra/src/PythonPluginAlgorithm.cpp
new file mode 100644
index 0000000..1ea858d
--- /dev/null
+++ b/python/astra/src/PythonPluginAlgorithm.cpp
@@ -0,0 +1,402 @@
+/*
+-----------------------------------------------------------------------
+Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp
+           2014-2015, 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/>.
+
+-----------------------------------------------------------------------
+$Id$
+*/
+
+#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);
+}
+
+void fixLapackLoading(){
+    // When running in Matlab, we need to force numpy
+    // to use its internal lapack library instead of
+    // Matlab's MKL library to avoid errors. To do this,
+    // we set Python's dlopen flags to RTLD_NOW|RTLD_DEEPBIND
+    // and import 'numpy.linalg.lapack_lite' here. We reset
+    // Python's dlopen flags afterwards.
+    PyObject *sys = PyImport_ImportModule("sys");
+    if(sys!=NULL){
+        PyObject *curFlags = PyObject_CallMethod(sys,"getdlopenflags",NULL);
+        if(curFlags!=NULL){
+            PyObject *retVal = PyObject_CallMethod(sys, "setdlopenflags", "i",10);
+            if(retVal!=NULL){
+                PyObject *lapack = PyImport_ImportModule("numpy.linalg.lapack_lite");
+                if(lapack!=NULL){
+                    Py_DECREF(lapack);
+                }
+                PyObject_CallMethod(sys, "setdlopenflags", "O",curFlags);
+                Py_DECREF(retVal);
+            }
+            Py_DECREF(curFlags);
+        }
+        Py_DECREF(sys);
+    }
+}
+
+CPythonPluginAlgorithmFactory::CPythonPluginAlgorithmFactory(){
+    if(!Py_IsInitialized()){
+        Py_Initialize();
+        PyEval_InitThreads();
+    }
+#ifndef _MSC_VER
+    if(astra::running_in_matlab) fixLapackLoading();
+#endif
+    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..0b1309e
--- /dev/null
+++ b/python/astra/src/PythonPluginAlgorithm.h
@@ -0,0 +1,89 @@
+/*
+-----------------------------------------------------------------------
+Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp
+           2014-2015, 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/>.
+
+-----------------------------------------------------------------------
+$Id$
+*/
+
+#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
-- 
cgit v1.2.3


From 7f11ed333cdc93e9e93d4677f857d97ffbbfec87 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Thu, 21 Jan 2016 12:14:44 +0100
Subject: Fix whitespace

---
 python/astra/src/PythonPluginAlgorithm.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'python/astra')

diff --git a/python/astra/src/PythonPluginAlgorithm.cpp b/python/astra/src/PythonPluginAlgorithm.cpp
index 1ea858d..0100bed 100644
--- a/python/astra/src/PythonPluginAlgorithm.cpp
+++ b/python/astra/src/PythonPluginAlgorithm.cpp
@@ -238,7 +238,7 @@ CAlgorithm * CPythonPluginAlgorithmFactory::getPlugin(const std::string &name){
     CPluginAlgorithm *alg = NULL;
     if(PyBytes_Check(className)){
         std::string str = std::string(PyBytes_AsString(className));
-    	PyObject *pyclass = getClassFromString(str);
+        PyObject *pyclass = getClassFromString(str);
         if(pyclass!=NULL){
             alg = new CPluginAlgorithm(pyclass);
             Py_DECREF(pyclass);
-- 
cgit v1.2.3


From cf0eff7075d21ccfa985676eb3a5e30f8694fc4c Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Wed, 27 Jan 2016 09:48:25 +0100
Subject: Decrement refcount of CallMethod return value

---
 python/astra/src/PythonPluginAlgorithm.cpp | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

(limited to 'python/astra')

diff --git a/python/astra/src/PythonPluginAlgorithm.cpp b/python/astra/src/PythonPluginAlgorithm.cpp
index 0100bed..61a56ea 100644
--- a/python/astra/src/PythonPluginAlgorithm.cpp
+++ b/python/astra/src/PythonPluginAlgorithm.cpp
@@ -144,7 +144,10 @@ void fixLapackLoading(){
                 if(lapack!=NULL){
                     Py_DECREF(lapack);
                 }
-                PyObject_CallMethod(sys, "setdlopenflags", "O",curFlags);
+                PyObject *retVal2 = PyObject_CallMethod(sys, "setdlopenflags", "O",curFlags);
+                if(retVal2!=NULL){
+                    Py_DECREF(retVal2);
+                }
                 Py_DECREF(retVal);
             }
             Py_DECREF(curFlags);
-- 
cgit v1.2.3


From 4a75ab09962015d90acaa3e2be8357a1c917d5eb Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Wed, 27 Jan 2016 10:05:57 +0100
Subject: Move fixLapackLoading to astra_mex_plugin

---
 python/astra/src/PythonPluginAlgorithm.cpp | 32 ------------------------------
 1 file changed, 32 deletions(-)

(limited to 'python/astra')

diff --git a/python/astra/src/PythonPluginAlgorithm.cpp b/python/astra/src/PythonPluginAlgorithm.cpp
index 61a56ea..e34861a 100644
--- a/python/astra/src/PythonPluginAlgorithm.cpp
+++ b/python/astra/src/PythonPluginAlgorithm.cpp
@@ -127,43 +127,11 @@ void CPluginAlgorithm::run(int _iNrIterations){
     PyGILState_Release(state);
 }
 
-void fixLapackLoading(){
-    // When running in Matlab, we need to force numpy
-    // to use its internal lapack library instead of
-    // Matlab's MKL library to avoid errors. To do this,
-    // we set Python's dlopen flags to RTLD_NOW|RTLD_DEEPBIND
-    // and import 'numpy.linalg.lapack_lite' here. We reset
-    // Python's dlopen flags afterwards.
-    PyObject *sys = PyImport_ImportModule("sys");
-    if(sys!=NULL){
-        PyObject *curFlags = PyObject_CallMethod(sys,"getdlopenflags",NULL);
-        if(curFlags!=NULL){
-            PyObject *retVal = PyObject_CallMethod(sys, "setdlopenflags", "i",10);
-            if(retVal!=NULL){
-                PyObject *lapack = PyImport_ImportModule("numpy.linalg.lapack_lite");
-                if(lapack!=NULL){
-                    Py_DECREF(lapack);
-                }
-                PyObject *retVal2 = PyObject_CallMethod(sys, "setdlopenflags", "O",curFlags);
-                if(retVal2!=NULL){
-                    Py_DECREF(retVal2);
-                }
-                Py_DECREF(retVal);
-            }
-            Py_DECREF(curFlags);
-        }
-        Py_DECREF(sys);
-    }
-}
-
 CPythonPluginAlgorithmFactory::CPythonPluginAlgorithmFactory(){
     if(!Py_IsInitialized()){
         Py_Initialize();
         PyEval_InitThreads();
     }
-#ifndef _MSC_VER
-    if(astra::running_in_matlab) fixLapackLoading();
-#endif
     pluginDict = PyDict_New();
     inspect = PyImport_ImportModule("inspect");
     six = PyImport_ImportModule("six");
-- 
cgit v1.2.3


From d2705f52766716b4d4627a62de92e7a2480b6b86 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Tue, 2 Feb 2016 14:12:41 +0100
Subject: Make copyright/license headers consistent with rest of astra

---
 python/astra/algorithm_c.pyx               | 37 +++++++++++++++---------------
 python/astra/astra_c.pyx                   | 36 ++++++++++++++---------------
 python/astra/data2d_c.pyx                  | 36 ++++++++++++++---------------
 python/astra/data3d_c.pyx                  | 36 ++++++++++++++---------------
 python/astra/experimental.pyx              | 10 ++++----
 python/astra/extrautils.pyx                | 35 ++++++++++++++--------------
 python/astra/log_c.pyx                     | 36 ++++++++++++++---------------
 python/astra/matrix_c.pyx                  | 36 ++++++++++++++---------------
 python/astra/plugin_c.pyx                  | 36 ++++++++++++++---------------
 python/astra/projector3d_c.pyx             | 36 ++++++++++++++---------------
 python/astra/projector_c.pyx               | 36 ++++++++++++++---------------
 python/astra/src/PythonPluginAlgorithm.cpp |  5 ++--
 python/astra/src/PythonPluginAlgorithm.h   |  5 ++--
 python/astra/utils.pyx                     | 36 ++++++++++++++---------------
 14 files changed, 206 insertions(+), 210 deletions(-)

(limited to 'python/astra')

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_c.pyx b/python/astra/astra_c.pyx
index 6b246b6..5075fed 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
 
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_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/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/plugin_c.pyx b/python/astra/plugin_c.pyx
index 775ccd4..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
 
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
index e34861a..617c0f4 100644
--- a/python/astra/src/PythonPluginAlgorithm.cpp
+++ b/python/astra/src/PythonPluginAlgorithm.cpp
@@ -1,7 +1,7 @@
 /*
 -----------------------------------------------------------------------
-Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp
-           2014-2015, CWI, Amsterdam
+Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
+           2014-2016, CWI, Amsterdam
 
 Contact: astra@uantwerpen.be
 Website: http://sf.net/projects/astra-toolbox
@@ -23,7 +23,6 @@ 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/>.
 
 -----------------------------------------------------------------------
-$Id$
 */
 
 #ifdef ASTRA_PYTHON
diff --git a/python/astra/src/PythonPluginAlgorithm.h b/python/astra/src/PythonPluginAlgorithm.h
index 0b1309e..ea4c6fb 100644
--- a/python/astra/src/PythonPluginAlgorithm.h
+++ b/python/astra/src/PythonPluginAlgorithm.h
@@ -1,7 +1,7 @@
 /*
 -----------------------------------------------------------------------
-Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp
-           2014-2015, CWI, Amsterdam
+Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
+           2014-2016, CWI, Amsterdam
 
 Contact: astra@uantwerpen.be
 Website: http://sf.net/projects/astra-toolbox
@@ -23,7 +23,6 @@ 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/>.
 
 -----------------------------------------------------------------------
-$Id$
 */
 
 #ifndef _INC_PYTHONPLUGINALGORITHM
diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx
index 07727ce..52c2a8d 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
 
-- 
cgit v1.2.3


From 0884a3928395dd368aea61eeef768677018f9095 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Wed, 17 Feb 2016 16:18:23 +0100
Subject: Add python astra.astra delete/info based on index manager

---
 python/astra/PyIndexManager.pxd | 40 ++++++++++++++++++++++++++++++++++++++++
 python/astra/astra.py           | 20 ++++++++++++++++++++
 python/astra/astra_c.pyx        | 30 ++++++++++++++++++++++++++++--
 3 files changed, 88 insertions(+), 2 deletions(-)
 create mode 100644 python/astra/PyIndexManager.pxd

(limited to 'python/astra')

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/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..c70bb8e 100644
--- a/python/astra/astra_c.pyx
+++ b/python/astra/astra_c.pyx
@@ -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
@@ -78,11 +82,10 @@ def version(printToScreen=False):
         return getVersion()
 
 def set_gpu_index(idx, memory=0):
-    import types
     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 +93,26 @@ 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]))
+
+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))
+
+
-- 
cgit v1.2.3


From b74e64aef7845666d27cbf7e876a6a360eefed7f Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Mon, 29 Feb 2016 11:01:21 +0100
Subject: Disable astra.set_gpu_index when building without CUDA

---
 python/astra/astra_c.pyx | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

(limited to 'python/astra')

diff --git a/python/astra/astra_c.pyx b/python/astra/astra_c.pyx
index 65192b5..baad853 100644
--- a/python/astra/astra_c.pyx
+++ b/python/astra/astra_c.pyx
@@ -77,7 +77,8 @@ def version(printToScreen=False):
     else:
         return getVersion()
 
-def set_gpu_index(idx, memory=0):
+IF HAVE_CUDA==True:
+  def set_gpu_index(idx, memory=0):
     import types
     import collections
     cdef SGPUParams params
@@ -90,3 +91,6 @@ 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")
-- 
cgit v1.2.3


From 0fb04ca6fb4fca23b9d1b885b9f075a90542997b Mon Sep 17 00:00:00 2001
From: "Daniel M. Pelt" <D.M.Pelt@cwi.nl>
Date: Wed, 2 Mar 2016 13:49:40 +0100
Subject: Fix small Python errors

---
 python/astra/data3d.py    | 2 +-
 python/astra/functions.py | 2 +-
 python/astra/optomo.py    | 4 +++-
 3 files changed, 5 insertions(+), 3 deletions(-)

(limited to 'python/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/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/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)
-- 
cgit v1.2.3


From a3b742fd2dc8ea253addd7342388c73a40f6fd59 Mon Sep 17 00:00:00 2001
From: "Daniel M. Pelt" <D.M.Pelt@cwi.nl>
Date: Fri, 4 Mar 2016 18:09:06 +0100
Subject: Encode Python bool as int in XML instead of str

---
 python/astra/utils.pyx | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

(limited to 'python/astra')

diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx
index 52c2a8d..34d1902 100644
--- a/python/astra/utils.pyx
+++ b/python/astra/utils.pyx
@@ -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):
-- 
cgit v1.2.3