diff options
| author | Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl> | 2016-03-01 14:47:43 +0100 | 
|---|---|---|
| committer | Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl> | 2016-03-01 14:47:43 +0100 | 
| commit | 0db21a84dd3cb0f6a78bd462a4a60a4b4a3c6fae (patch) | |
| tree | a833d4787504e8612282a82c60d3984be51bdffe | |
| parent | da11f9e7c7559eb01cc422ac55c9f7a1cd4bb803 (diff) | |
| parent | b74e64aef7845666d27cbf7e876a6a360eefed7f (diff) | |
Merge branch 'master' into indexmanager
25 files changed, 1097 insertions, 677 deletions
| diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 3018674..9535b4c 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -62,8 +62,6 @@ PYCPPFLAGS  := $(CPPFLAGS)  PYCPPFLAGS  += -I../include  PYLDFLAGS = $(LDFLAGS)  PYLDFLAGS   += -L$(abs_top_builddir)/.libs -LIBS		+= -l$(PYLIBVER) -LDFLAGS += -L$(PYLIBDIR)  endif  # This is below where PYCPPFLAGS copies CPPFLAGS.  The python code is built @@ -97,6 +95,11 @@ ifeq ($(cuda),yes)  MEXFLAGS += -DASTRA_CUDA  endif +ifeq ($(python),yes) +MEXPYLDFLAGS='$$LDFLAGS $(LDFLAGS) -L$(PYLIBDIR)' +MEXPYLIBS=$(MEXLIBS) -l$(PYLIBVER) +endif +  endif  LIBDIR=/usr/local/lib @@ -267,6 +270,11 @@ mex: $(MATLAB_MEX)  %.$(MEXSUFFIX): %.o $(MATLAB_CXX_OBJECTS) libastra.la  	$(MEX) LDFLAGS=$(MEXLDFLAGS) $(MEXFLAGS) $(LIBS) $(MEXLIBS) -lastra -output $* $*.o $(MATLAB_CXX_OBJECTS) + +ifeq ($(python),yes) +matlab/mex/astra_mex_plugin_c.$(MEXSUFFIX): matlab/mex/astra_mex_plugin_c.o $(MATLAB_CXX_OBJECTS) libastra.la +	$(MEX) LDFLAGS=$(MEXPYLDFLAGS) $(MEXFLAGS) $(LIBS) $(MEXPYLIBS) -lastra -output matlab/mex/astra_mex_plugin_c $< $(MATLAB_CXX_OBJECTS) +endif  endif  ifeq ($(python),yes) @@ -411,7 +419,7 @@ $(srcdir)/configure: $(srcdir)/configure.ac  	@echo "configure.ac has been changed. Regenerating configure script"  	cd $(srcdir) && $(SHELL) ./autogen.sh -.PHONY: all mex test clean distclean install install-libraries +.PHONY: all mex test clean distclean install install-libraries py python-root-install install-python  # don't remove intermediate files:  .SECONDARY: diff --git a/cuda/3d/mem3d.cu b/cuda/3d/mem3d.cu index 6d81dc0..0320117 100644 --- a/cuda/3d/mem3d.cu +++ b/cuda/3d/mem3d.cu @@ -62,6 +62,25 @@ size_t availableGPUMemory()  	return free;  } +int maxBlockDimension() +{ +	int dev; +	cudaError_t err = cudaGetDevice(&dev); +	if (err != cudaSuccess) { +		ASTRA_WARN("Error querying device"); +		return 0; +	} + +	cudaDeviceProp props; +	err = cudaGetDeviceProperties(&props, dev); +	if (err != cudaSuccess) { +		ASTRA_WARN("Error querying device %d properties", dev); +		return 0; +	} + +	return std::min(props.maxTexture3D[0], std::min(props.maxTexture3D[1], props.maxTexture3D[2])); +} +  MemHandle3D allocateGPUMemory(unsigned int x, unsigned int y, unsigned int z, Mem3DZeroMode zero)  {  	SMemHandle3D_internal hnd; diff --git a/cuda/3d/mem3d.h b/cuda/3d/mem3d.h index acb72cb..6fff80b 100644 --- a/cuda/3d/mem3d.h +++ b/cuda/3d/mem3d.h @@ -78,6 +78,7 @@ enum Mem3DZeroMode {  };  size_t availableGPUMemory(); +int maxBlockDimension();  MemHandle3D allocateGPUMemory(unsigned int x, unsigned int y, unsigned int z, Mem3DZeroMode zero); diff --git a/include/astra/AstraObjectFactory.h b/include/astra/AstraObjectFactory.h index 325989e..6af9cd8 100644 --- a/include/astra/AstraObjectFactory.h +++ b/include/astra/AstraObjectFactory.h @@ -155,8 +155,11 @@ class _AstraExport CAlgorithmFactory : public CAstraObjectFactory<CAlgorithm, Al  template <>  inline CAlgorithm* CAstraObjectFactory<CAlgorithm, AlgorithmTypeList>::findPlugin(std::string _sType)  	{ -		CPluginAlgorithmFactory *fac = CPluginAlgorithmFactory::getSingletonPtr(); -		return fac->getPlugin(_sType); +		CPluginAlgorithmFactory *fac = CPluginAlgorithmFactory::getFactory(); +		if (fac) +			return fac->getPlugin(_sType); +		else +			return 0;  	}  #endif diff --git a/include/astra/CompositeGeometryManager.h b/include/astra/CompositeGeometryManager.h index 4338994..18dd72f 100644 --- a/include/astra/CompositeGeometryManager.h +++ b/include/astra/CompositeGeometryManager.h @@ -79,7 +79,9 @@ public:  		bool uploadToGPU();  		bool downloadFromGPU(/*mode?*/); -		virtual TPartList split(size_t maxSize, int div) = 0; +		virtual void splitX(TPartList& out, size_t maxSize, size_t maxDim, int div) = 0; +		virtual void splitY(TPartList& out, size_t maxSize, size_t maxDim, int div) = 0; +		virtual void splitZ(TPartList& out, size_t maxSize, size_t maxDim, int div) = 0;  		virtual CPart* reduce(const CPart *other) = 0;  		virtual void getDims(size_t &x, size_t &y, size_t &z) = 0;  		size_t getSize(); @@ -93,7 +95,9 @@ public:  		CVolumeGeometry3D* pGeom; -		virtual TPartList split(size_t maxSize, int div); +		virtual void splitX(TPartList& out, size_t maxSize, size_t maxDim, int div); +		virtual void splitY(TPartList& out, size_t maxSize, size_t maxDim, int div); +		virtual void splitZ(TPartList& out, size_t maxSize, size_t maxDim, int div);  		virtual CPart* reduce(const CPart *other);  		virtual void getDims(size_t &x, size_t &y, size_t &z); @@ -107,7 +111,9 @@ public:  		CProjectionGeometry3D* pGeom; -		virtual TPartList split(size_t maxSize, int div); +		virtual void splitX(TPartList& out, size_t maxSize, size_t maxDim, int div); +		virtual void splitY(TPartList& out, size_t maxSize, size_t maxDim, int div); +		virtual void splitZ(TPartList& out, size_t maxSize, size_t maxDim, int div);  		virtual CPart* reduce(const CPart *other);  		virtual void getDims(size_t &x, size_t &y, size_t &z); diff --git a/include/astra/PluginAlgorithm.h b/include/astra/PluginAlgorithm.h index 667e813..cbd80fc 100644 --- a/include/astra/PluginAlgorithm.h +++ b/include/astra/PluginAlgorithm.h @@ -29,62 +29,37 @@ $Id$  #ifndef _INC_ASTRA_PLUGINALGORITHM  #define _INC_ASTRA_PLUGINALGORITHM -#ifdef ASTRA_PYTHON - -#include "astra/Algorithm.h" -#include "astra/Singleton.h" -#include "astra/XMLDocument.h" -#include "astra/XMLNode.h" - -// Slightly hackish forward declaration of PyObject -struct _object; -typedef _object PyObject; +#include "astra/Globals.h" +#include <map> +#include <string>  namespace astra { -class _AstraExport CPluginAlgorithm : public CAlgorithm { - -public: - -    CPluginAlgorithm(PyObject* pyclass); -    ~CPluginAlgorithm(); - -    bool initialize(const Config& _cfg); -    void run(int _iNrIterations); - -private: -    PyObject * instance; -}; +class CAlgorithm; -class _AstraExport CPluginAlgorithmFactory : public Singleton<CPluginAlgorithmFactory> { +class _AstraExport CPluginAlgorithmFactory {  public: +    CPluginAlgorithmFactory() { } +    virtual ~CPluginAlgorithmFactory() { } -    CPluginAlgorithmFactory(); -    ~CPluginAlgorithmFactory(); +    virtual CAlgorithm * getPlugin(const std::string &name) = 0; -    CPluginAlgorithm * getPlugin(std::string name); +    virtual bool registerPlugin(std::string name, std::string className) = 0; +    virtual bool registerPlugin(std::string className) = 0; -    bool registerPlugin(std::string name, std::string className); -    bool registerPlugin(std::string className); -    bool registerPluginClass(std::string name, PyObject * className); -    bool registerPluginClass(PyObject * className); +    virtual std::map<std::string, std::string> getRegisteredMap() = 0; -    PyObject * getRegistered(); -    std::map<std::string, std::string> getRegisteredMap(); -     -    std::string getHelp(std::string name); +    virtual std::string getHelp(const std::string &name) = 0; + +    static void registerFactory(CPluginAlgorithmFactory *factory) { m_factory = factory; } +	static CPluginAlgorithmFactory* getFactory() { return m_factory; }  private: -    PyObject * pluginDict; -    PyObject *inspect, *six; +    static CPluginAlgorithmFactory *m_factory;  }; -PyObject* XMLNode2dict(XMLNode node); -  }  #endif - -#endif diff --git a/matlab/mex/astra_mex_plugin_c.cpp b/matlab/mex/astra_mex_plugin_c.cpp index 177fcf4..4ed534e 100644 --- a/matlab/mex/astra_mex_plugin_c.cpp +++ b/matlab/mex/astra_mex_plugin_c.cpp @@ -37,9 +37,63 @@ $Id$  #include "astra/PluginAlgorithm.h" +#include <Python.h> +  using namespace std;  using namespace astra; +static 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); // RTLD_NOW|RTLD_DEEPBIND +            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); +    } +} + +//----------------------------------------------------------------------------------------- +/** astra_mex_plugin('init'); + * + * Initialize plugin support by initializing python and importing astra + */ +void astra_mex_plugin_init() +{ +    if(!Py_IsInitialized()){ +        Py_Initialize(); +        PyEval_InitThreads(); +    } + +#ifndef _MSC_VER +    fixLapackLoading(); +#endif + +    // Importing astra may be overkill, since we only need to initialize +    // PythonPluginAlgorithmFactory from astra.plugin_c. +    PyObject *mod = PyImport_ImportModule("astra"); +    Py_XDECREF(mod); +} +  //-----------------------------------------------------------------------------------------  /** astra_mex_plugin('get_registered'); @@ -48,7 +102,11 @@ using namespace astra;   */  void astra_mex_plugin_get_registered(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])  { -    astra::CPluginAlgorithmFactory *fact = astra::CPluginAlgorithmFactory::getSingletonPtr(); +    astra::CPluginAlgorithmFactory *fact = astra::CPluginAlgorithmFactory::getFactory(); +    if (!fact) { +        mexPrintf("Plugin support not initialized."); +        return; +    }      std::map<std::string, std::string> mp = fact->getRegisteredMap();      for(std::map<std::string,std::string>::iterator it=mp.begin();it!=mp.end();it++){          mexPrintf("%s: %s\n",it->first.c_str(), it->second.c_str()); @@ -62,9 +120,13 @@ void astra_mex_plugin_get_registered(int nlhs, mxArray* plhs[], int nrhs, const   */  void astra_mex_plugin_register(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])  { +    astra::CPluginAlgorithmFactory *fact = astra::CPluginAlgorithmFactory::getFactory(); +    if (!fact) { +        mexPrintf("Plugin support not initialized."); +        return; +    }      if (2 <= nrhs) {          string class_name = mexToString(prhs[1]); -        astra::CPluginAlgorithmFactory *fact = astra::CPluginAlgorithmFactory::getSingletonPtr();          fact->registerPlugin(class_name);      }else{          mexPrintf("astra_mex_plugin('register', class_name);\n"); @@ -78,9 +140,13 @@ void astra_mex_plugin_register(int nlhs, mxArray* plhs[], int nrhs, const mxArra   */  void astra_mex_plugin_get_help(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])  { +    astra::CPluginAlgorithmFactory *fact = astra::CPluginAlgorithmFactory::getFactory(); +    if (!fact) { +        mexPrintf("Plugin support not initialized."); +        return; +    }      if (2 <= nrhs) {          string name = mexToString(prhs[1]); -        astra::CPluginAlgorithmFactory *fact = astra::CPluginAlgorithmFactory::getSingletonPtr();          mexPrintf((fact->getHelp(name)+"\n").c_str());      }else{          mexPrintf("astra_mex_plugin('get_help', name);\n"); @@ -116,12 +182,14 @@ void mexFunction(int nlhs, mxArray* plhs[],  	initASTRAMex();  	// SWITCH (MODE) -	if (sMode ==  std::string("get_registered")) {  -		astra_mex_plugin_get_registered(nlhs, plhs, nrhs, prhs);  -    }else if (sMode ==  std::string("get_help")) {  -        astra_mex_plugin_get_help(nlhs, plhs, nrhs, prhs);  -    }else if (sMode ==  std::string("register")) {  -		astra_mex_plugin_register(nlhs, plhs, nrhs, prhs);  +	if (sMode == "init") { +		astra_mex_plugin_init(); +	} else if (sMode ==  std::string("get_registered")) { +		astra_mex_plugin_get_registered(nlhs, plhs, nrhs, prhs); +	}else if (sMode ==  std::string("get_help")) { +		astra_mex_plugin_get_help(nlhs, plhs, nrhs, prhs); +	}else if (sMode ==  std::string("register")) { +		astra_mex_plugin_register(nlhs, plhs, nrhs, prhs);  	} else {  		printHelp();  	} diff --git a/matlab/mex/mexInitFunctions.cpp b/matlab/mex/mexInitFunctions.cpp index bd3df2c..7245af2 100644 --- a/matlab/mex/mexInitFunctions.cpp +++ b/matlab/mex/mexInitFunctions.cpp @@ -23,5 +23,13 @@ void initASTRAMex(){      if(!astra::CLogger::setCallbackScreen(&logCallBack)){          mexErrMsgTxt("Error initializing mex functions.");      } +      mexIsInitialized=true; + + +    // If we have support for plugins, initialize them. +    // (NB: Call this after setting mexIsInitialized, to avoid recursively +    //      calling initASTRAMex) +    mexEvalString("if exist('astra_mex_plugin_c') == 3; astra_mex_plugin_c('init'); end"); +  } 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 c70bb8e..8e30e69 100644 --- a/python/astra/astra_c.pyx +++ b/python/astra/astra_c.pyx @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +#            2013-2016, CWI, Amsterdam  # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://sf.net/projects/astra-toolbox  # +# This file is part of the ASTRA Toolbox.  # -#This file is part of the Python interface to the -#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").  # -#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify -#it under the terms of the GNU General Public License as published by -#the Free Software Foundation, either version 3 of the License, or -#(at your option) any later version. +# The ASTRA Toolbox is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version.  # -#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, -#but WITHOUT ANY WARRANTY; without even the implied warranty of -#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -#GNU General Public License for more details. +# The ASTRA Toolbox is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details.  # -#You should have received a copy of the GNU General Public License -#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +# -----------------------------------------------------------------------  # -#-----------------------------------------------------------------------  # distutils: language = c++  # distutils: libraries = astra @@ -81,7 +81,8 @@ 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 collections      cdef SGPUParams params      if use_cuda()==True: @@ -93,6 +94,9 @@ def set_gpu_index(idx, memory=0):          ret = setGPUIndex(params.GPUIndices[0])          if not ret:              six.print_("Failed to set GPU " + str(params.GPUIndices[0])) +ELSE: +  def set_gpu_index(idx, memory=0): +    raise NotImplementedError("CUDA support is not enabled in ASTRA")  def delete(ids):      import collections @@ -114,5 +118,3 @@ def info(ids):          if ptr:              s = ptr.getType() + six.b("\t") + ptr.getInfo(i)              six.print_(wrap_from_bytes(s)) - - diff --git a/python/astra/data2d_c.pyx b/python/astra/data2d_c.pyx index 801fd8e..65e80ce 100644 --- a/python/astra/data2d_c.pyx +++ b/python/astra/data2d_c.pyx @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +#            2013-2016, CWI, Amsterdam  # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://sf.net/projects/astra-toolbox  # +# This file is part of the ASTRA Toolbox.  # -#This file is part of the Python interface to the -#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").  # -#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify -#it under the terms of the GNU General Public License as published by -#the Free Software Foundation, either version 3 of the License, or -#(at your option) any later version. +# The ASTRA Toolbox is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version.  # -#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, -#but WITHOUT ANY WARRANTY; without even the implied warranty of -#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -#GNU General Public License for more details. +# The ASTRA Toolbox is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details.  # -#You should have received a copy of the GNU General Public License -#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +# -----------------------------------------------------------------------  # -#-----------------------------------------------------------------------  # distutils: language = c++  # distutils: libraries = astra diff --git a/python/astra/data3d_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 8d6816b..ee04853 100644 --- a/python/astra/plugin_c.pyx +++ b/python/astra/plugin_c.pyx @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +#            2013-2016, CWI, Amsterdam  # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://sf.net/projects/astra-toolbox  # +# This file is part of the ASTRA Toolbox.  # -#This file is part of the Python interface to the -#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").  # -#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify -#it under the terms of the GNU General Public License as published by -#the Free Software Foundation, either version 3 of the License, or -#(at your option) any later version. +# The ASTRA Toolbox is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version.  # -#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, -#but WITHOUT ANY WARRANTY; without even the implied warranty of -#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -#GNU General Public License for more details. +# The ASTRA Toolbox is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details.  # -#You should have received a copy of the GNU General Public License -#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +# -----------------------------------------------------------------------  # -#-----------------------------------------------------------------------  # distutils: language = c++  # distutils: libraries = astra @@ -32,21 +32,25 @@ import inspect  from libcpp.string cimport string  from libcpp cimport bool -cdef CPluginAlgorithmFactory *fact = getSingletonPtr() +cdef CPythonPluginAlgorithmFactory *fact = getSingletonPtr()  from . import utils -cdef extern from "astra/PluginAlgorithm.h" namespace "astra": -    cdef cppclass CPluginAlgorithmFactory: +cdef extern from "src/PythonPluginAlgorithm.h" namespace "astra": +    cdef cppclass CPythonPluginAlgorithmFactory:          bool registerPlugin(string className)          bool registerPlugin(string name, string className)          bool registerPluginClass(object className)          bool registerPluginClass(string name, object className)          object getRegistered() -        string getHelp(string name) +        string getHelp(string &name) + +cdef extern from "src/PythonPluginAlgorithm.h" namespace "astra::CPythonPluginAlgorithmFactory": +    cdef CPythonPluginAlgorithmFactory* getSingletonPtr()  cdef extern from "astra/PluginAlgorithm.h" namespace "astra::CPluginAlgorithmFactory": -    cdef CPluginAlgorithmFactory* getSingletonPtr() +    # NB: Using wrong pointer type here for convenience +    cdef void registerFactory(CPythonPluginAlgorithmFactory *)  def register(className, name=None):      if inspect.isclass(className): @@ -65,3 +69,6 @@ def get_registered():  def get_help(name):      return utils.wrap_from_bytes(fact.getHelp(six.b(name))) + +# Register python plugin factory with astra +registerFactory(fact) diff --git a/python/astra/projector3d_c.pyx b/python/astra/projector3d_c.pyx index aec9cde..e355e38 100644 --- a/python/astra/projector3d_c.pyx +++ b/python/astra/projector3d_c.pyx @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +#            2013-2016, CWI, Amsterdam  # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://sf.net/projects/astra-toolbox  # +# This file is part of the ASTRA Toolbox.  # -#This file is part of the Python interface to the -#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").  # -#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify -#it under the terms of the GNU General Public License as published by -#the Free Software Foundation, either version 3 of the License, or -#(at your option) any later version. +# The ASTRA Toolbox is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version.  # -#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, -#but WITHOUT ANY WARRANTY; without even the implied warranty of -#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -#GNU General Public License for more details. +# The ASTRA Toolbox is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details.  # -#You should have received a copy of the GNU General Public License -#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +# -----------------------------------------------------------------------  # -#-----------------------------------------------------------------------  # distutils: language = c++  # distutils: libraries = astra diff --git a/python/astra/projector_c.pyx b/python/astra/projector_c.pyx index 77c64a4..53d38c3 100644 --- a/python/astra/projector_c.pyx +++ b/python/astra/projector_c.pyx @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +#            2013-2016, CWI, Amsterdam  # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://sf.net/projects/astra-toolbox  # +# This file is part of the ASTRA Toolbox.  # -#This file is part of the Python interface to the -#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").  # -#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify -#it under the terms of the GNU General Public License as published by -#the Free Software Foundation, either version 3 of the License, or -#(at your option) any later version. +# The ASTRA Toolbox is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version.  # -#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, -#but WITHOUT ANY WARRANTY; without even the implied warranty of -#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -#GNU General Public License for more details. +# The ASTRA Toolbox is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details.  # -#You should have received a copy of the GNU General Public License -#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +# -----------------------------------------------------------------------  # -#-----------------------------------------------------------------------  # distutils: language = c++  # distutils: libraries = astra diff --git a/python/astra/src/PythonPluginAlgorithm.cpp b/python/astra/src/PythonPluginAlgorithm.cpp new file mode 100644 index 0000000..617c0f4 --- /dev/null +++ b/python/astra/src/PythonPluginAlgorithm.cpp @@ -0,0 +1,372 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +           2014-2016, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the ASTRA Toolbox. + + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. + +----------------------------------------------------------------------- +*/ + +#ifdef ASTRA_PYTHON + +#include "PythonPluginAlgorithm.h" + +#include "astra/Logging.h" +#include "astra/Utilities.h" +#include <boost/algorithm/string.hpp> +#include <boost/algorithm/string/split.hpp> +#include <iostream> +#include <fstream> +#include <string> + +#include <Python.h> +#include "bytesobject.h" + +namespace astra { + + + +void logPythonError(){ +    if(PyErr_Occurred()){ +        PyObject *ptype, *pvalue, *ptraceback; +        PyErr_Fetch(&ptype, &pvalue, &ptraceback); +        PyErr_NormalizeException(&ptype, &pvalue, &ptraceback); +        PyObject *traceback = PyImport_ImportModule("traceback"); +        if(traceback!=NULL){ +            PyObject *exc; +            if(ptraceback==NULL){ +                exc = PyObject_CallMethod(traceback,"format_exception_only","OO",ptype, pvalue); +            }else{ +                exc = PyObject_CallMethod(traceback,"format_exception","OOO",ptype, pvalue, ptraceback); +            } +            if(exc!=NULL){ +                PyObject *six = PyImport_ImportModule("six"); +                if(six!=NULL){ +                    PyObject *iter = PyObject_GetIter(exc); +                    if(iter!=NULL){ +                        PyObject *line; +                        std::string errStr = ""; +                        while(line = PyIter_Next(iter)){ +                            PyObject *retb = PyObject_CallMethod(six,"b","O",line); +                            if(retb!=NULL){ +                                errStr += std::string(PyBytes_AsString(retb)); +                                Py_DECREF(retb); +                            } +                            Py_DECREF(line); +                        } +                        ASTRA_ERROR("%s",errStr.c_str()); +                        Py_DECREF(iter); +                    } +                    Py_DECREF(six); +                } +                Py_DECREF(exc); +            } +            Py_DECREF(traceback); +        } +        if(ptype!=NULL) Py_DECREF(ptype); +        if(pvalue!=NULL) Py_DECREF(pvalue); +        if(ptraceback!=NULL) Py_DECREF(ptraceback); +    } +} + + +CPluginAlgorithm::CPluginAlgorithm(PyObject* pyclass){ +    instance = PyObject_CallObject(pyclass, NULL); +    if(instance==NULL) logPythonError(); +} + +CPluginAlgorithm::~CPluginAlgorithm(){ +    if(instance!=NULL){ +        Py_DECREF(instance); +        instance = NULL; +    } +} + +bool CPluginAlgorithm::initialize(const Config& _cfg){ +    if(instance==NULL) return false; +    PyObject *cfgDict = XMLNode2dict(_cfg.self); +    PyObject *retVal = PyObject_CallMethod(instance, "astra_init", "O",cfgDict); +    Py_DECREF(cfgDict); +    if(retVal==NULL){ +        logPythonError(); +        return false; +    } +    m_bIsInitialized = true; +    Py_DECREF(retVal); +    return m_bIsInitialized; +} + +void CPluginAlgorithm::run(int _iNrIterations){ +    if(instance==NULL) return; +    PyGILState_STATE state = PyGILState_Ensure(); +    PyObject *retVal = PyObject_CallMethod(instance, "run", "i",_iNrIterations); +    if(retVal==NULL){ +        logPythonError(); +    }else{ +        Py_DECREF(retVal); +    } +    PyGILState_Release(state); +} + +CPythonPluginAlgorithmFactory::CPythonPluginAlgorithmFactory(){ +    if(!Py_IsInitialized()){ +        Py_Initialize(); +        PyEval_InitThreads(); +    } +    pluginDict = PyDict_New(); +    inspect = PyImport_ImportModule("inspect"); +    six = PyImport_ImportModule("six"); +} + +CPythonPluginAlgorithmFactory::~CPythonPluginAlgorithmFactory(){ +    if(pluginDict!=NULL){ +        Py_DECREF(pluginDict); +    } +    if(inspect!=NULL) Py_DECREF(inspect); +    if(six!=NULL) Py_DECREF(six); +} + +PyObject * getClassFromString(std::string str){ +    std::vector<std::string> items; +    boost::split(items, str, boost::is_any_of(".")); +    PyObject *pyclass = PyImport_ImportModule(items[0].c_str()); +    if(pyclass==NULL){ +        logPythonError(); +        return NULL; +    } +    PyObject *submod = pyclass; +    for(unsigned int i=1;i<items.size();i++){ +        submod = PyObject_GetAttrString(submod,items[i].c_str()); +        Py_DECREF(pyclass); +        pyclass = submod; +        if(pyclass==NULL){ +            logPythonError(); +            return NULL; +        } +    } +    return pyclass; +} + +bool CPythonPluginAlgorithmFactory::registerPlugin(std::string name, std::string className){ +    PyObject *str = PyBytes_FromString(className.c_str()); +    PyDict_SetItemString(pluginDict, name.c_str(), str); +    Py_DECREF(str); +    return true; +} + +bool CPythonPluginAlgorithmFactory::registerPlugin(std::string className){ +    PyObject *pyclass = getClassFromString(className); +    if(pyclass==NULL) return false; +    bool ret = registerPluginClass(pyclass); +    Py_DECREF(pyclass); +    return ret; +} + +bool CPythonPluginAlgorithmFactory::registerPluginClass(std::string name, PyObject * className){ +    PyDict_SetItemString(pluginDict, name.c_str(), className); +    return true; +} + +bool CPythonPluginAlgorithmFactory::registerPluginClass(PyObject * className){ +    PyObject *astra_name = PyObject_GetAttrString(className,"astra_name"); +    if(astra_name==NULL){ +        logPythonError(); +        return false; +    } +    PyObject *retb = PyObject_CallMethod(six,"b","O",astra_name); +    if(retb!=NULL){ +        PyDict_SetItemString(pluginDict,PyBytes_AsString(retb),className); +        Py_DECREF(retb); +    }else{ +        logPythonError(); +    } +    Py_DECREF(astra_name); +    return true; +} + +CAlgorithm * CPythonPluginAlgorithmFactory::getPlugin(const std::string &name){ +    PyObject *className = PyDict_GetItemString(pluginDict, name.c_str()); +    if(className==NULL) return NULL; +    CPluginAlgorithm *alg = NULL; +    if(PyBytes_Check(className)){ +        std::string str = std::string(PyBytes_AsString(className)); +        PyObject *pyclass = getClassFromString(str); +        if(pyclass!=NULL){ +            alg = new CPluginAlgorithm(pyclass); +            Py_DECREF(pyclass); +        } +    }else{ +        alg = new CPluginAlgorithm(className); +    } +    return alg; +} + +PyObject * CPythonPluginAlgorithmFactory::getRegistered(){ +    Py_INCREF(pluginDict); +    return pluginDict; +} + +std::map<std::string, std::string> CPythonPluginAlgorithmFactory::getRegisteredMap(){ +    std::map<std::string, std::string> ret; +    PyObject *key, *value; +    Py_ssize_t pos = 0; +    while (PyDict_Next(pluginDict, &pos, &key, &value)) { +        PyObject *keystr = PyObject_Str(key); +        if(keystr!=NULL){ +            PyObject *valstr = PyObject_Str(value); +            if(valstr!=NULL){ +                PyObject * keyb = PyObject_CallMethod(six,"b","O",keystr); +                if(keyb!=NULL){ +                    PyObject * valb = PyObject_CallMethod(six,"b","O",valstr); +                    if(valb!=NULL){ +                        ret[PyBytes_AsString(keyb)] = PyBytes_AsString(valb); +                        Py_DECREF(valb); +                    } +                    Py_DECREF(keyb); +                } +                Py_DECREF(valstr); +            } +            Py_DECREF(keystr); +        } +        logPythonError(); +    } +    return ret; +} + +std::string CPythonPluginAlgorithmFactory::getHelp(const std::string &name){ +    PyObject *className = PyDict_GetItemString(pluginDict, name.c_str()); +    if(className==NULL){ +        ASTRA_ERROR("Plugin %s not found!",name.c_str()); +        PyErr_Clear(); +        return ""; +    } +    std::string ret = ""; +    PyObject *pyclass; +    if(PyBytes_Check(className)){ +        std::string str = std::string(PyBytes_AsString(className)); +        pyclass = getClassFromString(str); +    }else{ +        pyclass = className; +    } +    if(pyclass==NULL) return ""; +    if(inspect!=NULL && six!=NULL){ +        PyObject *retVal = PyObject_CallMethod(inspect,"getdoc","O",pyclass); +        if(retVal!=NULL){ +            if(retVal!=Py_None){ +                PyObject *retb = PyObject_CallMethod(six,"b","O",retVal); +                if(retb!=NULL){ +                    ret = std::string(PyBytes_AsString(retb)); +                    Py_DECREF(retb); +                } +            } +            Py_DECREF(retVal); +        }else{ +            logPythonError(); +        } +    } +    if(PyBytes_Check(className)){ +        Py_DECREF(pyclass); +    } +    return ret; +} + +DEFINE_SINGLETON(CPythonPluginAlgorithmFactory); + +#if PY_MAJOR_VERSION >= 3 +PyObject * pyStringFromString(std::string str){ +    return PyUnicode_FromString(str.c_str()); +} +#else +PyObject * pyStringFromString(std::string str){ +    return PyBytes_FromString(str.c_str()); +} +#endif + +PyObject* stringToPythonValue(std::string str){ +    if(str.find(";")!=std::string::npos){ +        std::vector<std::string> rows, row; +        boost::split(rows, str, boost::is_any_of(";")); +        PyObject *mat = PyList_New(rows.size()); +        for(unsigned int i=0; i<rows.size(); i++){ +            boost::split(row, rows[i], boost::is_any_of(",")); +            PyObject *rowlist = PyList_New(row.size()); +            for(unsigned int j=0;j<row.size();j++){ +                PyList_SetItem(rowlist, j, PyFloat_FromDouble(StringUtil::stringToDouble(row[j]))); +            } +            PyList_SetItem(mat, i, rowlist); +        } +        return mat; +    } +    if(str.find(",")!=std::string::npos){ +        std::vector<std::string> vec; +        boost::split(vec, str, boost::is_any_of(",")); +        PyObject *veclist = PyList_New(vec.size()); +        for(unsigned int i=0;i<vec.size();i++){ +            PyList_SetItem(veclist, i, PyFloat_FromDouble(StringUtil::stringToDouble(vec[i]))); +        } +        return veclist; +    } +    try{ +        return PyLong_FromLong(StringUtil::stringToInt(str)); +    }catch(const StringUtil::bad_cast &){ +        try{ +            return PyFloat_FromDouble(StringUtil::stringToDouble(str)); +        }catch(const StringUtil::bad_cast &){ +            return pyStringFromString(str); +        } +    } +} + +PyObject* XMLNode2dict(XMLNode node){ +    PyObject *dct = PyDict_New(); +    PyObject *opts = PyDict_New(); +    if(node.hasAttribute("type")){ +        PyObject *obj = pyStringFromString(node.getAttribute("type").c_str()); +        PyDict_SetItemString(dct, "type", obj); +        Py_DECREF(obj); +    } +    std::list<XMLNode> nodes = node.getNodes(); +    std::list<XMLNode>::iterator it = nodes.begin(); +    while(it!=nodes.end()){ +        XMLNode subnode = *it; +        if(subnode.getName()=="Option"){ +            PyObject *obj; +            if(subnode.hasAttribute("value")){ +                obj = stringToPythonValue(subnode.getAttribute("value")); +            }else{ +                obj = stringToPythonValue(subnode.getContent()); +            } +            PyDict_SetItemString(opts, subnode.getAttribute("key").c_str(), obj); +            Py_DECREF(obj); +        }else{ +            PyObject *obj = stringToPythonValue(subnode.getContent()); +            PyDict_SetItemString(dct, subnode.getName().c_str(), obj); +            Py_DECREF(obj); +        } +        ++it; +    } +    PyDict_SetItemString(dct, "options", opts); +    Py_DECREF(opts); +    return dct; +} + +} +#endif diff --git a/python/astra/src/PythonPluginAlgorithm.h b/python/astra/src/PythonPluginAlgorithm.h new file mode 100644 index 0000000..ea4c6fb --- /dev/null +++ b/python/astra/src/PythonPluginAlgorithm.h @@ -0,0 +1,88 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +           2014-2016, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the ASTRA Toolbox. + + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. + +----------------------------------------------------------------------- +*/ + +#ifndef _INC_PYTHONPLUGINALGORITHM +#define _INC_PYTHONPLUGINALGORITHM + +#ifdef ASTRA_PYTHON + +#include "astra/Algorithm.h" +#include "astra/Singleton.h" +#include "astra/XMLDocument.h" +#include "astra/XMLNode.h" +#include "astra/PluginAlgorithm.h" + +#include <Python.h> + +namespace astra { +class CPluginAlgorithm : public CAlgorithm { + +public: + +    CPluginAlgorithm(PyObject* pyclass); +    ~CPluginAlgorithm(); + +    bool initialize(const Config& _cfg); +    void run(int _iNrIterations); + +private: +    PyObject * instance; + +}; + +class CPythonPluginAlgorithmFactory : public CPluginAlgorithmFactory, public Singleton<CPythonPluginAlgorithmFactory> { + +public: + +    CPythonPluginAlgorithmFactory(); +    virtual ~CPythonPluginAlgorithmFactory(); + +    virtual CAlgorithm * getPlugin(const std::string &name); + +    virtual bool registerPlugin(std::string name, std::string className); +    virtual bool registerPlugin(std::string className); +    bool registerPluginClass(std::string name, PyObject * className); +    bool registerPluginClass(PyObject * className); + +    PyObject * getRegistered(); +    virtual std::map<std::string, std::string> getRegisteredMap(); + +    virtual std::string getHelp(const std::string &name); + +private: +    PyObject * pluginDict; +    PyObject *inspect, *six; +}; + +PyObject* XMLNode2dict(XMLNode node); + +} + + +#endif + +#endif diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx index 07727ce..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 diff --git a/python/builder.py b/python/builder.py index 018b26b..dcd62d8 100644 --- a/python/builder.py +++ b/python/builder.py @@ -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/>.  #  #----------------------------------------------------------------------- +  import sys  import os  import numpy as np @@ -70,12 +70,16 @@ 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',         author='D.M. Pelt',         author_email='D.M.Pelt@cwi.nl', -       url='http://dmpelt.github.io/pyastratoolbox/', +       url='http://sf.net/projects/astra-toolbox',         #ext_package='astra',         #ext_modules = cythonize(Extension("astra/*.pyx",extra_compile_args=extra_compile_args,extra_linker_args=extra_compile_args)),         license='GPLv3', diff --git a/src/CompositeGeometryManager.cpp b/src/CompositeGeometryManager.cpp index 96b28e9..c9cbaaa 100644 --- a/src/CompositeGeometryManager.cpp +++ b/src/CompositeGeometryManager.cpp @@ -45,14 +45,15 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.  #include <cstring>  #include <sstream> +#include <stdint.h>  #ifndef USE_PTHREADS  #include <boost/thread/mutex.hpp>  #include <boost/thread.hpp>  #endif -namespace astra { +namespace astra {  SGPUParams* CCompositeGeometryManager::s_params = 0; @@ -98,6 +99,9 @@ CCompositeGeometryManager::CCompositeGeometryManager()  bool CCompositeGeometryManager::splitJobs(TJobSet &jobs, size_t maxSize, int div, TJobSet &split)  { +	int maxBlockDim = astraCUDA3d::maxBlockDimension(); +	ASTRA_DEBUG("Found max block dim %d", maxBlockDim); +  	split.clear();  	for (TJobSet::const_iterator i = jobs.begin(); i != jobs.end(); ++i) @@ -111,7 +115,22 @@ bool CCompositeGeometryManager::splitJobs(TJobSet &jobs, size_t maxSize, int div  		//    b. split input part  		//    c. create jobs for new (input,output) subparts -		TPartList splitOutput = pOutput->split(maxSize/3, div); +		TPartList splitOutput; +		pOutput->splitZ(splitOutput, maxSize/3, SIZE_MAX, div); +#if 0 +		TPartList splitOutput2; +		for (TPartList::iterator i_out = splitOutput.begin(); i_out != splitOutput.end(); ++i_out) { +			boost::shared_ptr<CPart> outputPart = *i_out; +			outputPart.get()->splitX(splitOutput2, SIZE_MAX, SIZE_MAX, 1); +		} +		splitOutput.clear(); +		for (TPartList::iterator i_out = splitOutput2.begin(); i_out != splitOutput2.end(); ++i_out) { +			boost::shared_ptr<CPart> outputPart = *i_out; +					outputPart.get()->splitY(splitOutput, SIZE_MAX, SIZE_MAX, 1); +		} +		splitOutput2.clear(); +#endif +  		for (TJobList::const_iterator j = L.begin(); j != L.end(); ++j)  		{ @@ -139,8 +158,21 @@ bool CCompositeGeometryManager::splitJobs(TJobSet &jobs, size_t maxSize, int div  				size_t remainingSize = ( maxSize - outputPart->getSize() ) / 2; -				TPartList splitInput = input->split(remainingSize, 1); +				TPartList splitInput; +				input->splitZ(splitInput, remainingSize, maxBlockDim, 1);  				delete input; +				TPartList splitInput2; +				for (TPartList::iterator i_in = splitInput.begin(); i_in != splitInput.end(); ++i_in) { +					boost::shared_ptr<CPart> inputPart = *i_in; +					inputPart.get()->splitX(splitInput2, SIZE_MAX, maxBlockDim, 1); +				} +				splitInput.clear(); +				for (TPartList::iterator i_in = splitInput2.begin(); i_in != splitInput2.end(); ++i_in) { +					boost::shared_ptr<CPart> inputPart = *i_in; +					inputPart.get()->splitY(splitInput, SIZE_MAX, maxBlockDim, 1); +				} +				splitInput2.clear(); +  				ASTRA_DEBUG("Input split into %d parts", splitInput.size());  				for (TPartList::iterator i_in = splitInput.begin(); @@ -327,10 +359,14 @@ static size_t ceildiv(size_t a, size_t b) {  	return (a + b - 1) / b;  } -static size_t computeVerticalSplit(size_t maxBlock, int div, size_t sliceCount) +static size_t computeLinearSplit(size_t maxBlock, int div, size_t sliceCount)  {  	size_t blockSize = maxBlock; -	size_t blockCount = ceildiv(sliceCount, blockSize); +	size_t blockCount; +	if (sliceCount <= blockSize) +		blockCount = 1; +	else +		blockCount = ceildiv(sliceCount, blockSize);  	// Increase number of blocks to be divisible by div  	size_t divCount = div * ceildiv(blockCount, div); @@ -410,7 +446,17 @@ SPar3DProjection* getProjectionVectors(const CParallelVecProjectionGeometry3D* p  template<class V> -static void translateProjectionVectors(V* pProjs, int count, double dv) +static void translateProjectionVectorsU(V* pProjs, int count, double du) +{ +	for (int i = 0; i < count; ++i) { +		pProjs[i].fDetSX += du * pProjs[i].fDetUX; +		pProjs[i].fDetSY += du * pProjs[i].fDetUY; +		pProjs[i].fDetSZ += du * pProjs[i].fDetUZ; +	} +} + +template<class V> +static void translateProjectionVectorsV(V* pProjs, int count, double dv)  {  	for (int i = 0; i < count; ++i) {  		pProjs[i].fDetSX += dv * pProjs[i].fDetVX; @@ -420,8 +466,58 @@ static void translateProjectionVectors(V* pProjs, int count, double dv)  } +static CProjectionGeometry3D* getSubProjectionGeometryU(const CProjectionGeometry3D* pProjGeom, int u, int size) +{ +	// First convert to vectors, then translate, then convert into new object -static CProjectionGeometry3D* getSubProjectionGeometry(const CProjectionGeometry3D* pProjGeom, int v, int size) +	const CConeProjectionGeometry3D* conegeom = dynamic_cast<const CConeProjectionGeometry3D*>(pProjGeom); +	const CParallelProjectionGeometry3D* par3dgeom = dynamic_cast<const CParallelProjectionGeometry3D*>(pProjGeom); +	const CParallelVecProjectionGeometry3D* parvec3dgeom = dynamic_cast<const CParallelVecProjectionGeometry3D*>(pProjGeom); +	const CConeVecProjectionGeometry3D* conevec3dgeom = dynamic_cast<const CConeVecProjectionGeometry3D*>(pProjGeom); + +	if (conegeom || conevec3dgeom) { +		SConeProjection* pConeProjs; +		if (conegeom) { +			pConeProjs = getProjectionVectors<SConeProjection>(conegeom); +		} else { +			pConeProjs = getProjectionVectors<SConeProjection>(conevec3dgeom); +		} + +		translateProjectionVectorsU(pConeProjs, pProjGeom->getProjectionCount(), u); + +		CProjectionGeometry3D* ret = new CConeVecProjectionGeometry3D(pProjGeom->getProjectionCount(), +		                                                              pProjGeom->getDetectorRowCount(), +		                                                              size, +		                                                              pConeProjs); + + +		delete[] pConeProjs; +		return ret; +	} else { +		assert(par3dgeom || parvec3dgeom); +		SPar3DProjection* pParProjs; +		if (par3dgeom) { +			pParProjs = getProjectionVectors<SPar3DProjection>(par3dgeom); +		} else { +			pParProjs = getProjectionVectors<SPar3DProjection>(parvec3dgeom); +		} + +		translateProjectionVectorsU(pParProjs, pProjGeom->getProjectionCount(), u); + +		CProjectionGeometry3D* ret = new CParallelVecProjectionGeometry3D(pProjGeom->getProjectionCount(), +		                                                                  pProjGeom->getDetectorRowCount(), +		                                                                  size, +		                                                                  pParProjs); + +		delete[] pParProjs; +		return ret; +	} + +} + + + +static CProjectionGeometry3D* getSubProjectionGeometryV(const CProjectionGeometry3D* pProjGeom, int v, int size)  {  	// First convert to vectors, then translate, then convert into new object @@ -438,7 +534,7 @@ static CProjectionGeometry3D* getSubProjectionGeometry(const CProjectionGeometry  			pConeProjs = getProjectionVectors<SConeProjection>(conevec3dgeom);  		} -		translateProjectionVectors(pConeProjs, pProjGeom->getProjectionCount(), v); +		translateProjectionVectorsV(pConeProjs, pProjGeom->getProjectionCount(), v);  		CProjectionGeometry3D* ret = new CConeVecProjectionGeometry3D(pProjGeom->getProjectionCount(),  		                                                              size, @@ -457,7 +553,7 @@ static CProjectionGeometry3D* getSubProjectionGeometry(const CProjectionGeometry  			pParProjs = getProjectionVectors<SPar3DProjection>(parvec3dgeom);  		} -		translateProjectionVectors(pParProjs, pProjGeom->getProjectionCount(), v); +		translateProjectionVectorsV(pParProjs, pProjGeom->getProjectionCount(), v);  		CProjectionGeometry3D* ret = new CParallelVecProjectionGeometry3D(pProjGeom->getProjectionCount(),  		                                                                  size, @@ -476,17 +572,110 @@ static CProjectionGeometry3D* getSubProjectionGeometry(const CProjectionGeometry  // - each no bigger than maxSize  // - number of sub-parts is divisible by div  // - maybe all approximately the same size? -CCompositeGeometryManager::TPartList CCompositeGeometryManager::CVolumePart::split(size_t maxSize, int div) +void CCompositeGeometryManager::CVolumePart::splitX(CCompositeGeometryManager::TPartList& out, size_t maxSize, size_t maxDim, int div) +{ +	if (true) { +		// Split in vertical direction only at first, until we figure out +		// a model for splitting in other directions + +		size_t sliceSize = ((size_t) pGeom->getGridSliceCount()) * pGeom->getGridRowCount(); +		int sliceCount = pGeom->getGridColCount(); +		size_t m = std::min(maxSize / sliceSize, maxDim); +		size_t blockSize = computeLinearSplit(m, div, sliceCount); + +		int rem = sliceCount % blockSize; + +		ASTRA_DEBUG("From %d to %d step %d", -(rem / 2), sliceCount, blockSize); + +		for (int x = -(rem / 2); x < sliceCount; x += blockSize) { +			int newsubX = x; +			if (newsubX < 0) newsubX = 0; +			int endX = x + blockSize; +			if (endX > sliceCount) endX = sliceCount; +			int size = endX - newsubX; + +			CVolumePart *sub = new CVolumePart(); +			sub->subX = this->subX + newsubX; +			sub->subY = this->subY; +			sub->subZ = this->subZ; + +			ASTRA_DEBUG("VolumePart split %d %d %d -> %p", sub->subX, sub->subY, sub->subZ, (void*)sub); + +			double shift = pGeom->getPixelLengthX() * newsubX; + +			sub->pData = pData; +			sub->pGeom = new CVolumeGeometry3D(size, +			                                   pGeom->getGridRowCount(), +			                                   pGeom->getGridSliceCount(), +			                                   pGeom->getWindowMinX() + shift, +			                                   pGeom->getWindowMinY(), +			                                   pGeom->getWindowMinZ(), +			                                   pGeom->getWindowMinX() + shift + size * pGeom->getPixelLengthX(), +			                                   pGeom->getWindowMaxY(), +			                                   pGeom->getWindowMaxZ()); + +			out.push_back(boost::shared_ptr<CPart>(sub)); +		} +	} +} + +void CCompositeGeometryManager::CVolumePart::splitY(CCompositeGeometryManager::TPartList& out, size_t maxSize, size_t maxDim, int div)  { -	TPartList ret; +	if (true) { +		// Split in vertical direction only at first, until we figure out +		// a model for splitting in other directions + +		size_t sliceSize = ((size_t) pGeom->getGridColCount()) * pGeom->getGridSliceCount(); +		int sliceCount = pGeom->getGridRowCount(); +		size_t m = std::min(maxSize / sliceSize, maxDim); +		size_t blockSize = computeLinearSplit(m, div, sliceCount); + +		int rem = sliceCount % blockSize; + +		ASTRA_DEBUG("From %d to %d step %d", -(rem / 2), sliceCount, blockSize); + +		for (int y = -(rem / 2); y < sliceCount; y += blockSize) { +			int newsubY = y; +			if (newsubY < 0) newsubY = 0; +			int endY = y + blockSize; +			if (endY > sliceCount) endY = sliceCount; +			int size = endY - newsubY; +			CVolumePart *sub = new CVolumePart(); +			sub->subX = this->subX; +			sub->subY = this->subY + newsubY; +			sub->subZ = this->subZ; + +			ASTRA_DEBUG("VolumePart split %d %d %d -> %p", sub->subX, sub->subY, sub->subZ, (void*)sub); + +			double shift = pGeom->getPixelLengthY() * newsubY; + +			sub->pData = pData; +			sub->pGeom = new CVolumeGeometry3D(pGeom->getGridColCount(), +			                                   size, +			                                   pGeom->getGridSliceCount(), +			                                   pGeom->getWindowMinX(), +			                                   pGeom->getWindowMinY() + shift, +			                                   pGeom->getWindowMinZ(), +			                                   pGeom->getWindowMaxX(), +			                                   pGeom->getWindowMinY() + shift + size * pGeom->getPixelLengthY(), +			                                   pGeom->getWindowMaxZ()); + +			out.push_back(boost::shared_ptr<CPart>(sub)); +		} +	} +} + +void CCompositeGeometryManager::CVolumePart::splitZ(CCompositeGeometryManager::TPartList& out, size_t maxSize, size_t maxDim, int div) +{  	if (true) {  		// Split in vertical direction only at first, until we figure out  		// a model for splitting in other directions  		size_t sliceSize = ((size_t) pGeom->getGridColCount()) * pGeom->getGridRowCount();  		int sliceCount = pGeom->getGridSliceCount(); -		size_t blockSize = computeVerticalSplit(maxSize / sliceSize, div, sliceCount); +		size_t m = std::min(maxSize / sliceSize, maxDim); +		size_t blockSize = computeLinearSplit(m, div, sliceCount);  		int rem = sliceCount % blockSize; @@ -519,11 +708,9 @@ CCompositeGeometryManager::TPartList CCompositeGeometryManager::CVolumePart::spl  			                                   pGeom->getWindowMaxY(),  			                                   pGeom->getWindowMinZ() + shift + size * pGeom->getPixelLengthZ()); -			ret.push_back(boost::shared_ptr<CPart>(sub)); +			out.push_back(boost::shared_ptr<CPart>(sub));  		}  	} - -	return ret;  }  CCompositeGeometryManager::CVolumePart* CCompositeGeometryManager::CVolumePart::clone() const @@ -630,7 +817,7 @@ CCompositeGeometryManager::CPart* CCompositeGeometryManager::CProjectionPart::re  	if (_vmin == _vmax) {  		sub->pGeom = 0;  	} else { -		sub->pGeom = getSubProjectionGeometry(pGeom, _vmin, _vmax - _vmin); +		sub->pGeom = getSubProjectionGeometryV(pGeom, _vmin, _vmax - _vmin);  	}  	ASTRA_DEBUG("Reduce projection from %d - %d to %d - %d", this->subZ, this->subZ + pGeom->getDetectorRowCount(), this->subZ + _vmin, this->subZ + _vmax); @@ -639,17 +826,58 @@ CCompositeGeometryManager::CPart* CCompositeGeometryManager::CProjectionPart::re  } -CCompositeGeometryManager::TPartList CCompositeGeometryManager::CProjectionPart::split(size_t maxSize, int div) +void CCompositeGeometryManager::CProjectionPart::splitX(CCompositeGeometryManager::TPartList &out, size_t maxSize, size_t maxDim, int div) +{ +	if (true) { +		// Split in vertical direction only at first, until we figure out +		// a model for splitting in other directions + +		size_t sliceSize = ((size_t) pGeom->getDetectorRowCount()) * pGeom->getProjectionCount(); +		int sliceCount = pGeom->getDetectorColCount(); +		size_t m = std::min(maxSize / sliceSize, maxDim); +		size_t blockSize = computeLinearSplit(m, div, sliceCount); + +		int rem = sliceCount % blockSize; + +		for (int x = -(rem / 2); x < sliceCount; x += blockSize) { +			int newsubX = x; +			if (newsubX < 0) newsubX = 0; +			int endX = x + blockSize; +			if (endX > sliceCount) endX = sliceCount; +			int size = endX - newsubX; + +			CProjectionPart *sub = new CProjectionPart(); +			sub->subX = this->subX + newsubX; +			sub->subY = this->subY; +			sub->subZ = this->subZ; + +			ASTRA_DEBUG("ProjectionPart split %d %d %d -> %p", sub->subX, sub->subY, sub->subZ, (void*)sub); + +			sub->pData = pData; + +			sub->pGeom = getSubProjectionGeometryU(pGeom, newsubX, size); + +			out.push_back(boost::shared_ptr<CPart>(sub)); +		} +	} +} + +void CCompositeGeometryManager::CProjectionPart::splitY(CCompositeGeometryManager::TPartList &out, size_t maxSize, size_t maxDim, int div)  { -	TPartList ret; +	// TODO +	out.push_back(boost::shared_ptr<CPart>(clone())); +} +void CCompositeGeometryManager::CProjectionPart::splitZ(CCompositeGeometryManager::TPartList &out, size_t maxSize, size_t maxDim, int div) +{  	if (true) {  		// Split in vertical direction only at first, until we figure out  		// a model for splitting in other directions  		size_t sliceSize = ((size_t) pGeom->getDetectorColCount()) * pGeom->getProjectionCount();  		int sliceCount = pGeom->getDetectorRowCount(); -		size_t blockSize = computeVerticalSplit(maxSize / sliceSize, div, sliceCount); +		size_t m = std::min(maxSize / sliceSize, maxDim); +		size_t blockSize = computeLinearSplit(m, div, sliceCount);  		int rem = sliceCount % blockSize; @@ -669,14 +897,12 @@ CCompositeGeometryManager::TPartList CCompositeGeometryManager::CProjectionPart:  			sub->pData = pData; -			sub->pGeom = getSubProjectionGeometry(pGeom, newsubZ, size); +			sub->pGeom = getSubProjectionGeometryV(pGeom, newsubZ, size); -			ret.push_back(boost::shared_ptr<CPart>(sub)); +			out.push_back(boost::shared_ptr<CPart>(sub));  		}  	} -	return ret; -  }  CCompositeGeometryManager::CProjectionPart* CCompositeGeometryManager::CProjectionPart::clone() const diff --git a/src/PluginAlgorithm.cpp b/src/PluginAlgorithm.cpp index 9fc511a..1bcfbdb 100644 --- a/src/PluginAlgorithm.cpp +++ b/src/PluginAlgorithm.cpp @@ -26,376 +26,11 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.  $Id$  */ -#ifdef ASTRA_PYTHON -  #include "astra/PluginAlgorithm.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 { +CPluginAlgorithmFactory *CPluginAlgorithmFactory::m_factory = 0; - -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); -    } -} - -CPluginAlgorithmFactory::CPluginAlgorithmFactory(){ -    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"); -} - -CPluginAlgorithmFactory::~CPluginAlgorithmFactory(){ -    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 CPluginAlgorithmFactory::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 CPluginAlgorithmFactory::registerPlugin(std::string className){ -    PyObject *pyclass = getClassFromString(className); -    if(pyclass==NULL) return false; -    bool ret = registerPluginClass(pyclass); -    Py_DECREF(pyclass); -    return ret; -} - -bool CPluginAlgorithmFactory::registerPluginClass(std::string name, PyObject * className){ -    PyDict_SetItemString(pluginDict, name.c_str(), className); -    return true; -} - -bool CPluginAlgorithmFactory::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; -} - -CPluginAlgorithm * CPluginAlgorithmFactory::getPlugin(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 * CPluginAlgorithmFactory::getRegistered(){ -    Py_INCREF(pluginDict); -    return pluginDict; -} - -std::map<std::string, std::string> CPluginAlgorithmFactory::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 CPluginAlgorithmFactory::getHelp(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(CPluginAlgorithmFactory); - -#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 | 
