Remove dependency of libastra on libpython by refactoring PluginAlgorithm

4 files changed, 507 insertions, 5 deletions

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
diff --git a/python/builder.py b/python/builder.py
index 018b26b..9a77ecc 100644
--- a/python/builder.py
+++ b/python/builder.py
@@ -70,6 +70,10 @@ ext_modules = [ ]
 ext_modules = cythonize("astra/*.pyx", language_level=2)
 cmdclass = { 'build_ext': build_ext }
 
+for m in ext_modules:
+  if m.name == 'astra.plugin_c':
+    m.sources.append('astra/src/PythonPluginAlgorithm.cpp')
+
 setup (name = 'PyASTRAToolbox',
        version = '1.7.1',
        description = 'Python interface to the ASTRA-Toolbox',