From 8f37932efdbf7585c85ba1e7653e7080e17d7714 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Thu, 23 Jul 2015 11:39:28 +0200 Subject: Reduce code duplication --- include/astra/AstraObjectFactory.h | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) (limited to 'include') diff --git a/include/astra/AstraObjectFactory.h b/include/astra/AstraObjectFactory.h index 1ed4955..efe997d 100644 --- a/include/astra/AstraObjectFactory.h +++ b/include/astra/AstraObjectFactory.h @@ -109,14 +109,11 @@ T* CAstraObjectFactory::create(std::string _sType) template T* CAstraObjectFactory::create(const Config& _cfg) { - functor_find finder = functor_find(); - finder.tofind = _cfg.self.getAttribute("type"); - CreateObject::find(finder); - if (finder.res == NULL) return NULL; - if (finder.res->initialize(_cfg)) - return finder.res; - - delete finder.res; + T* object = create(_cfg.self.getAttribute("type")); + if (object == NULL) return NULL; + if (object->initialize(_cfg)) + return object; + delete object; return NULL; } //---------------------------------------------------------------------------------------- -- cgit v1.2.3 From 2f800d5c1a305a23906783ecaa075e3d5274ef26 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Thu, 23 Jul 2015 11:49:39 +0200 Subject: Fix comments --- include/astra/AstraObjectFactory.h | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) (limited to 'include') diff --git a/include/astra/AstraObjectFactory.h b/include/astra/AstraObjectFactory.h index efe997d..c935a7c 100644 --- a/include/astra/AstraObjectFactory.h +++ b/include/astra/AstraObjectFactory.h @@ -59,16 +59,16 @@ public: */ ~CAstraObjectFactory(); - /** Create, but don't initialize, a new projector object. + /** Create, but don't initialize, a new object. * - * @param _sType Type of the new projector. - * @return Pointer to a new, unitialized projector. + * @param _sType Type of the new object. + * @return Pointer to a new, uninitialized object. */ T* create(std::string _sType); - /** Create and initialize a new projector object. + /** Create and initialize a new object. * - * @param _cfg Configuration object to create and initialize a new projector. + * @param _cfg Configuration object to create and initialize a new object. * @return Pointer to a new, initialized projector. */ T* create(const Config& _cfg); -- cgit v1.2.3 From 9e077994b382b2df63e4b79dd2afebc50366d419 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Thu, 23 Jul 2015 11:43:47 +0200 Subject: Add hooks for plugin support to AstraObjectFactory To use these hooks, add a specialization of findPlugin for the desired type of object (e.g., Algorithms). --- include/astra/AstraObjectFactory.h | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) (limited to 'include') diff --git a/include/astra/AstraObjectFactory.h b/include/astra/AstraObjectFactory.h index c935a7c..356acf9 100644 --- a/include/astra/AstraObjectFactory.h +++ b/include/astra/AstraObjectFactory.h @@ -73,6 +73,13 @@ public: */ T* create(const Config& _cfg); + /** Find a plugin. + * + * @param _sType Name of plugin to find. + * @return Pointer to a new, uninitialized object, or NULL if not found. + */ + T* findPlugin(std::string _sType); + }; @@ -93,6 +100,15 @@ CAstraObjectFactory::~CAstraObjectFactory() } + +//---------------------------------------------------------------------------------------- +// Hook for finding plugin in registered plugins. +template +T* CAstraObjectFactory::findPlugin(std::string _sType) +{ + return NULL; +} + //---------------------------------------------------------------------------------------- // Create template @@ -101,6 +117,9 @@ T* CAstraObjectFactory::create(std::string _sType) functor_find finder = functor_find(); finder.tofind = _sType; CreateObject::find(finder); + if (finder.res == NULL) { + finder.res = findPlugin(_sType); + } return finder.res; } -- cgit v1.2.3 From 18b6d25f7e4f0943b3592f3bb4f6ca5ed9c285d3 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Fri, 19 Jun 2015 22:28:06 +0200 Subject: Add support for Python algorithm plugins --- build/linux/Makefile.in | 16 +- include/astra/AstraObjectFactory.h | 13 ++ include/astra/PluginAlgorithm.h | 85 +++++++++++ matlab/mex/astra_mex_plugin_c.cpp | 139 ++++++++++++++++++ python/astra/__init__.py | 1 + python/astra/plugin.py | 95 ++++++++++++ python/astra/plugin_c.pyx | 59 ++++++++ python/astra/utils.pyx | 72 +-------- python/docSRC/index.rst | 1 + python/docSRC/plugins.rst | 8 + samples/python/s018_plugin.py | 138 +++++++++++++++++ src/PluginAlgorithm.cpp | 294 +++++++++++++++++++++++++++++++++++++ 12 files changed, 851 insertions(+), 70 deletions(-) create mode 100644 include/astra/PluginAlgorithm.h create mode 100644 matlab/mex/astra_mex_plugin_c.cpp create mode 100644 python/astra/plugin.py create mode 100644 python/astra/plugin_c.pyx create mode 100644 python/docSRC/plugins.rst create mode 100644 samples/python/s018_plugin.py create mode 100644 src/PluginAlgorithm.cpp (limited to 'include') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 2d862f2..e209fa7 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -50,11 +50,17 @@ LDFLAGS+=-fopenmp endif ifeq ($(python),yes) -PYCPPFLAGS = ${CPPFLAGS} +PYTHON = @PYTHON@ +PYLIBDIR = $(shell $(PYTHON) -c 'from distutils.sysconfig import get_config_var; import six; six.print_(get_config_var("LIBDIR"))') +PYINCDIR = $(shell $(PYTHON) -c 'from distutils.sysconfig import get_python_inc; import six; six.print_(get_python_inc())') +PYLIBVER = `basename $(PYINCDIR)` +CPPFLAGS += -DASTRA_PYTHON -I$(PYINCDIR) +PYCPPFLAGS = $(CPPFLAGS) PYCPPFLAGS += -I../include -PYLDFLAGS = ${LDFLAGS} +PYLDFLAGS = $(LDFLAGS) PYLDFLAGS += -L../build/linux/.libs -PYTHON = @PYTHON@ +LIBS += -l$(PYLIBVER) +LDFLAGS += -L$(PYLIBDIR) endif BOOST_CPPFLAGS= @@ -234,6 +240,10 @@ MATLAB_MEX=\ matlab/mex/astra_mex_log_c.$(MEXSUFFIX) \ matlab/mex/astra_mex_data3d_c.$(MEXSUFFIX) +ifeq ($(python),yes) +ALL_OBJECTS+=src/PluginAlgorithm.lo +MATLAB_MEX+=matlab/mex/astra_mex_plugin_c.$(MEXSUFFIX) +endif OBJECT_DIRS = src/ tests/ cuda/2d/ cuda/3d/ matlab/mex/ ./ DEPDIRS = $(addsuffix $(DEPDIR),$(OBJECT_DIRS)) diff --git a/include/astra/AstraObjectFactory.h b/include/astra/AstraObjectFactory.h index 356acf9..325989e 100644 --- a/include/astra/AstraObjectFactory.h +++ b/include/astra/AstraObjectFactory.h @@ -40,6 +40,10 @@ $Id$ #include "AlgorithmTypelist.h" +#ifdef ASTRA_PYTHON +#include "PluginAlgorithm.h" +#endif + namespace astra { @@ -147,6 +151,15 @@ T* CAstraObjectFactory::create(const Config& _cfg) */ class _AstraExport CAlgorithmFactory : public CAstraObjectFactory {}; +#ifdef ASTRA_PYTHON +template <> +inline CAlgorithm* CAstraObjectFactory::findPlugin(std::string _sType) + { + CPluginAlgorithmFactory *fac = CPluginAlgorithmFactory::getSingletonPtr(); + return fac->getPlugin(_sType); + } +#endif + /** * Class used to create 2D projectors from a string or a config object */ diff --git a/include/astra/PluginAlgorithm.h b/include/astra/PluginAlgorithm.h new file mode 100644 index 0000000..7d6c64a --- /dev/null +++ b/include/astra/PluginAlgorithm.h @@ -0,0 +1,85 @@ +/* +----------------------------------------------------------------------- +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 . + +----------------------------------------------------------------------- +$Id$ +*/ + +#ifndef _INC_ASTRA_PLUGINALGORITHM +#define _INC_ASTRA_PLUGINALGORITHM + +#ifdef ASTRA_PYTHON + +#include +#include "bytesobject.h" +#include "astra/Algorithm.h" +#include "astra/Singleton.h" +#include "astra/XMLDocument.h" +#include "astra/XMLNode.h" + +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 _AstraExport CPluginAlgorithmFactory : public Singleton { + +public: + + CPluginAlgorithmFactory(); + ~CPluginAlgorithmFactory(); + + CPluginAlgorithm * getPlugin(std::string name); + + bool registerPlugin(std::string name, std::string className); + bool registerPluginClass(std::string name, PyObject * className); + + PyObject * getRegistered(); + + std::string getHelp(std::string name); + +private: + PyObject * pluginDict; + PyObject *ospath, *inspect, *six, *astra; + std::vector getPluginPathList(); +}; + +PyObject* XMLNode2dict(XMLNode node); + +} + +#endif + +#endif \ No newline at end of file diff --git a/matlab/mex/astra_mex_plugin_c.cpp b/matlab/mex/astra_mex_plugin_c.cpp new file mode 100644 index 0000000..2d9b9a0 --- /dev/null +++ b/matlab/mex/astra_mex_plugin_c.cpp @@ -0,0 +1,139 @@ +/* +----------------------------------------------------------------------- +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 . + +----------------------------------------------------------------------- +$Id$ +*/ + +/** \file astra_mex_plugin_c.cpp + * + * \brief Manages Python plugins. + */ + +#include +#include "mexHelpFunctions.h" +#include "mexInitFunctions.h" + +#include "astra/PluginAlgorithm.h" + +#include "Python.h" +#include "bytesobject.h" + +using namespace std; +using namespace astra; + + +//----------------------------------------------------------------------------------------- +/** astra_mex_plugin('get_registered'); + * + * Print registered plugins. + */ +void astra_mex_plugin_get_registered(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) +{ + astra::CPluginAlgorithmFactory *fact = astra::CPluginAlgorithmFactory::getSingletonPtr(); + PyObject *dict = fact->getRegistered(); + PyObject *key, *value; + Py_ssize_t pos = 0; + while (PyDict_Next(dict, &pos, &key, &value)) { + mexPrintf("%s: %s\n",PyBytes_AsString(key),PyBytes_AsString(value)); + } + Py_DECREF(dict); +} + +//----------------------------------------------------------------------------------------- +/** astra_mex_plugin('register', name, class_name); + * + * Register plugin. + */ +void astra_mex_plugin_register(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) +{ + if (3 <= nrhs) { + string name = mexToString(prhs[1]); + string class_name = mexToString(prhs[2]); + astra::CPluginAlgorithmFactory *fact = astra::CPluginAlgorithmFactory::getSingletonPtr(); + fact->registerPlugin(name, class_name); + }else{ + mexPrintf("astra_mex_plugin('register', name, class_name);\n"); + } +} + +//----------------------------------------------------------------------------------------- +/** astra_mex_plugin('get_help', name); + * + * Get help about plugin. + */ +void astra_mex_plugin_get_help(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) +{ + 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"); + } +} + + +//----------------------------------------------------------------------------------------- + +static void printHelp() +{ + mexPrintf("Please specify a mode of operation.\n"); + mexPrintf(" Valid modes: register, get_registered, get_help\n"); +} + +//----------------------------------------------------------------------------------------- +/** + * ... = astra_mex(type,...); + */ +void mexFunction(int nlhs, mxArray* plhs[], + int nrhs, const mxArray* prhs[]) +{ + + // INPUT0: Mode + string sMode = ""; + if (1 <= nrhs) { + sMode = mexToString(prhs[0]); + } else { + printHelp(); + return; + } + + 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); + } else { + printHelp(); + } + + return; +} + + diff --git a/python/astra/__init__.py b/python/astra/__init__.py index 6c15d30..10ed74d 100644 --- a/python/astra/__init__.py +++ b/python/astra/__init__.py @@ -34,6 +34,7 @@ from . import algorithm from . import projector from . import projector3d from . import matrix +from . import plugin from . import log from .optomo import OpTomo diff --git a/python/astra/plugin.py b/python/astra/plugin.py new file mode 100644 index 0000000..ccdb2cb --- /dev/null +++ b/python/astra/plugin.py @@ -0,0 +1,95 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#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 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. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see . +# +#----------------------------------------------------------------------- + +from . import plugin_c as p +from . import log + +class base(object): + + def astra_init(self, cfg): + try: + try: + req = self.required_options + except AttributeError: + log.warn("Plugin '" + self.__class__.__name__ + "' does not specify required options") + req = {} + + try: + opt = self.optional_options + except AttributeError: + log.warn("Plugin '" + self.__class__.__name__ + "' does not specify optional options") + opt = {} + + try: + optDict = cfg['options'] + except KeyError: + optDict = {} + + cfgKeys = set(optDict.keys()) + reqKeys = set(req) + optKeys = set(opt) + + if not reqKeys.issubset(cfgKeys): + for key in reqKeys.difference(cfgKeys): + log.error("Required option '" + key + "' for plugin '" + self.__class__.__name__ + "' not specified") + raise ValueError("Missing required options") + + if not cfgKeys.issubset(reqKeys | optKeys): + log.warn(self.__class__.__name__ + ": unused configuration option: " + str(list(cfgKeys.difference(reqKeys | optKeys)))) + + self.initialize(cfg) + except Exception as e: + log.error(str(e)) + raise + +def register(name, className): + """Register plugin with ASTRA. + + :param name: Plugin name to register + :type name: :class:`str` + :param className: Class name or class object to register + :type className: :class:`str` or :class:`class` + + """ + p.register(name,className) + +def get_registered(): + """Get dictionary of registered plugins. + + :returns: :class:`dict` -- Registered plugins. + + """ + return p.get_registered() + +def get_help(name): + """Get help for registered plugin. + + :param name: Plugin name to get help for + :type name: :class:`str` + :returns: :class:`str` -- Help string (docstring). + + """ + return p.get_help(name) \ No newline at end of file diff --git a/python/astra/plugin_c.pyx b/python/astra/plugin_c.pyx new file mode 100644 index 0000000..91b3cd5 --- /dev/null +++ b/python/astra/plugin_c.pyx @@ -0,0 +1,59 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#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 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. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see . +# +#----------------------------------------------------------------------- +# distutils: language = c++ +# distutils: libraries = astra + +import six +import inspect + +from libcpp.string cimport string +from libcpp cimport bool + +cdef CPluginAlgorithmFactory *fact = getSingletonPtr() + +from . import utils + +cdef extern from "astra/PluginAlgorithm.h" namespace "astra": + cdef cppclass CPluginAlgorithmFactory: + bool registerPlugin(string name, string className) + bool registerPluginClass(string name, object className) + object getRegistered() + string getHelp(string name) + +cdef extern from "astra/PluginAlgorithm.h" namespace "astra::CPluginAlgorithmFactory": + cdef CPluginAlgorithmFactory* getSingletonPtr() + +def register(name, className): + if inspect.isclass(className): + fact.registerPluginClass(six.b(name), className) + else: + fact.registerPlugin(six.b(name), six.b(className)) + +def get_registered(): + return fact.getRegistered() + +def get_help(name): + return utils.wrap_from_bytes(fact.getHelp(six.b(name))) diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx index ddb37aa..3746b8e 100644 --- a/python/astra/utils.pyx +++ b/python/astra/utils.pyx @@ -30,7 +30,6 @@ cimport numpy as np import numpy as np import six from libcpp.string cimport string -from libcpp.list cimport list from libcpp.vector cimport vector from cython.operator cimport dereference as deref, preincrement as inc from cpython.version cimport PY_MAJOR_VERSION @@ -40,6 +39,9 @@ from .PyXMLDocument cimport XMLDocument from .PyXMLDocument cimport XMLNode from .PyIncludes cimport * +cdef extern from "astra/PluginAlgorithm.h" namespace "astra": + object XMLNode2dict(XMLNode) + cdef Config * dictToConfig(string rootname, dc): cdef Config * cfg = new Config() @@ -91,6 +93,8 @@ cdef void readDict(XMLNode root, _dc): dc = convert_item(_dc) for item in dc: val = dc[item] + if isinstance(val, list): + val = np.array(val,dtype=np.float64) if isinstance(val, np.ndarray): if val.size == 0: break @@ -142,69 +146,3 @@ cdef void readOptions(XMLNode node, dc): cdef configToDict(Config *cfg): return XMLNode2dict(cfg.self) -def castString3(input): - return input.decode('utf-8') - -def castString2(input): - return input - -if six.PY3: - castString = castString3 -else: - castString = castString2 - -def stringToPythonValue(inputIn): - input = castString(inputIn) - # matrix - if ';' in input: - row_strings = input.split(';') - col_strings = row_strings[0].split(',') - nRows = len(row_strings) - nCols = len(col_strings) - - out = np.empty((nRows,nCols)) - for ridx, row in enumerate(row_strings): - col_strings = row.split(',') - for cidx, col in enumerate(col_strings): - out[ridx,cidx] = float(col) - return out - - # vector - if ',' in input: - items = input.split(',') - out = np.empty(len(items)) - for idx,item in enumerate(items): - out[idx] = float(item) - return out - - try: - # integer - return int(input) - except ValueError: - try: - #float - return float(input) - except ValueError: - # string - return str(input) - - -cdef XMLNode2dict(XMLNode node): - cdef XMLNode subnode - cdef list[XMLNode] nodes - cdef list[XMLNode].iterator it - dct = {} - opts = {} - if node.hasAttribute(six.b('type')): - dct['type'] = castString(node.getAttribute(six.b('type'))) - nodes = node.getNodes() - it = nodes.begin() - while it != nodes.end(): - subnode = deref(it) - if castString(subnode.getName())=="Option": - opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getAttribute('value')) - else: - dct[castString(subnode.getName())] = stringToPythonValue(subnode.getContent()) - inc(it) - if len(opts)>0: dct['options'] = opts - return dct diff --git a/python/docSRC/index.rst b/python/docSRC/index.rst index b7cc6d6..dcc6590 100644 --- a/python/docSRC/index.rst +++ b/python/docSRC/index.rst @@ -19,6 +19,7 @@ Contents: creators functions operator + plugins matlab astra .. astra diff --git a/python/docSRC/plugins.rst b/python/docSRC/plugins.rst new file mode 100644 index 0000000..dc7c607 --- /dev/null +++ b/python/docSRC/plugins.rst @@ -0,0 +1,8 @@ +Plugins: the :mod:`plugin` module +========================================= + +.. automodule:: astra.plugin + :members: + :undoc-members: + :show-inheritance: + diff --git a/samples/python/s018_plugin.py b/samples/python/s018_plugin.py new file mode 100644 index 0000000..6677930 --- /dev/null +++ b/samples/python/s018_plugin.py @@ -0,0 +1,138 @@ +#----------------------------------------------------------------------- +#Copyright 2015 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#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 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. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see . +# +#----------------------------------------------------------------------- + +import astra +import numpy as np +import six + +# Define the plugin class (has to subclass astra.plugin.base) +# Note that usually, these will be defined in a separate package/module +class SIRTPlugin(astra.plugin.base): + """Example of an ASTRA plugin class, implementing a simple 2D SIRT algorithm. + + Optional options: + + 'rel_factor': relaxation factor + """ + required_options=[] + optional_options=['rel_factor'] + + def initialize(self,cfg): + self.W = astra.OpTomo(cfg['ProjectorId']) + self.vid = cfg['ReconstructionDataId'] + self.sid = cfg['ProjectionDataId'] + try: + self.rel = cfg['option']['rel_factor'] + except KeyError: + self.rel = 1 + + def run(self, its): + v = astra.data2d.get_shared(self.vid) + s = astra.data2d.get_shared(self.sid) + W = self.W + for i in range(its): + v[:] += self.rel*(W.T*(s - (W*v).reshape(s.shape))).reshape(v.shape)/s.size + +if __name__=='__main__': + + vol_geom = astra.create_vol_geom(256, 256) + proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + + # As before, create a sinogram from a phantom + import scipy.io + P = scipy.io.loadmat('phantom.mat')['phantom256'] + proj_id = astra.create_projector('cuda',proj_geom,vol_geom) + + # construct the OpTomo object + W = astra.OpTomo(proj_id) + + sinogram = W * P + sinogram = sinogram.reshape([180, 384]) + + # Register the plugin with ASTRA + # A default set of plugins to load can be defined in: + # - /etc/astra-toolbox/plugins.txt + # - [ASTRA_INSTALL_PATH]/python/astra/plugins.txt + # - [USER_HOME_PATH]/.astra-toolbox/plugins.txt + # - [ASTRA_PLUGIN_PATH environment variable]/plugins.txt + # In these files, create a separate line for each plugin with: + # [PLUGIN_ASTRA_NAME] [FULL_PLUGIN_CLASS] + # + # So in this case, it would be a line: + # SIRT-PLUGIN s018_plugin.SIRTPlugin + # + astra.plugin.register('SIRT-PLUGIN','s018_plugin.SIRTPlugin') + + # To get help on a registered plugin, use get_help + six.print_(astra.plugin.get_help('SIRT-PLUGIN')) + + # Create data structures + sid = astra.data2d.create('-sino', proj_geom, sinogram) + vid = astra.data2d.create('-vol', vol_geom) + + # Create config using plugin name + cfg = astra.astra_dict('SIRT-PLUGIN') + cfg['ProjectorId'] = proj_id + cfg['ProjectionDataId'] = sid + cfg['ReconstructionDataId'] = vid + + # Create algorithm object + alg_id = astra.algorithm.create(cfg) + + # Run algorithm for 100 iterations + astra.algorithm.run(alg_id, 100) + + # Get reconstruction + rec = astra.data2d.get(vid) + + # Options for the plugin go in cfg['option'] + cfg = astra.astra_dict('SIRT-PLUGIN') + cfg['ProjectorId'] = proj_id + cfg['ProjectionDataId'] = sid + cfg['ReconstructionDataId'] = vid + cfg['option'] = {} + cfg['option']['rel_factor'] = 1.5 + alg_id_rel = astra.algorithm.create(cfg) + astra.algorithm.run(alg_id_rel, 100) + rec_rel = astra.data2d.get(vid) + + # We can also use OpTomo to call the plugin + rec_op = W.reconstruct('SIRT-PLUGIN', sinogram, 100, extraOptions={'rel_factor':1.5}) + + import pylab as pl + pl.gray() + pl.figure(1) + pl.imshow(rec,vmin=0,vmax=1) + pl.figure(2) + pl.imshow(rec_rel,vmin=0,vmax=1) + pl.figure(3) + pl.imshow(rec_op,vmin=0,vmax=1) + pl.show() + + # Clean up. + astra.projector.delete(proj_id) + astra.algorithm.delete([alg_id, alg_id_rel]) + astra.data2d.delete([vid, sid]) diff --git a/src/PluginAlgorithm.cpp b/src/PluginAlgorithm.cpp new file mode 100644 index 0000000..df13f31 --- /dev/null +++ b/src/PluginAlgorithm.cpp @@ -0,0 +1,294 @@ +/* +----------------------------------------------------------------------- +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 . + +----------------------------------------------------------------------- +$Id$ +*/ + +#ifdef ASTRA_PYTHON + +#include "astra/PluginAlgorithm.h" +#include +#include +#include +#include +#include +#include + +namespace astra { + +CPluginAlgorithm::CPluginAlgorithm(PyObject* pyclass){ + instance = PyObject_CallObject(pyclass, NULL); +} + +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) return false; + m_bIsInitialized = true; + Py_DECREF(retVal); + return m_bIsInitialized; +} + +void CPluginAlgorithm::run(int _iNrIterations){ + if(instance==NULL) return; + PyObject *retVal = PyObject_CallMethod(instance, "run", "i",_iNrIterations); + if(retVal==NULL) return; + Py_DECREF(retVal); +} + +const char ps = +#ifdef _WIN32 + '\\'; +#else + '/'; +#endif + +std::vector CPluginAlgorithmFactory::getPluginPathList(){ + std::vector list; + list.push_back("/etc/astra-toolbox"); + PyObject *ret, *retb; + ret = PyObject_CallMethod(inspect,"getfile","O",astra); + if(ret!=NULL){ + retb = PyObject_CallMethod(six,"b","O",ret); + Py_DECREF(ret); + if(retb!=NULL){ + std::string astra_inst (PyBytes_AsString(retb)); + Py_DECREF(retb); + ret = PyObject_CallMethod(ospath,"dirname","s",astra_inst.c_str()); + if(ret!=NULL){ + retb = PyObject_CallMethod(six,"b","O",ret); + Py_DECREF(ret); + if(retb!=NULL){ + list.push_back(std::string(PyBytes_AsString(retb))); + Py_DECREF(retb); + } + } + } + } + ret = PyObject_CallMethod(ospath,"expanduser","s","~"); + if(ret!=NULL){ + retb = PyObject_CallMethod(six,"b","O",ret); + Py_DECREF(ret); + if(retb!=NULL){ + list.push_back(std::string(PyBytes_AsString(retb)) + ps + ".astra-toolbox"); + Py_DECREF(retb); + } + } + const char *envval = getenv("ASTRA_PLUGIN_PATH"); + if(envval!=NULL){ + list.push_back(std::string(envval)); + } + return list; +} + +CPluginAlgorithmFactory::CPluginAlgorithmFactory(){ + Py_Initialize(); + pluginDict = PyDict_New(); + ospath = PyImport_ImportModule("os.path"); + inspect = PyImport_ImportModule("inspect"); + six = PyImport_ImportModule("six"); + astra = PyImport_ImportModule("astra"); + std::vector fls = getPluginPathList(); + std::vector items; + for(unsigned int i=0;i items; + boost::split(items, str, boost::is_any_of(".")); + PyObject *pyclass = PyImport_ImportModule(items[0].c_str()); + if(pyclass==NULL) return NULL; + PyObject *submod = pyclass; + for(unsigned int i=1;i= 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 rows, row; + boost::split(rows, str, boost::is_any_of(";")); + PyObject *mat = PyList_New(rows.size()); + for(unsigned int i=0; i(row[j]))); + } + PyList_SetItem(mat, i, rowlist); + } + return mat; + } + if(str.find(",")!=std::string::npos){ + std::vector vec; + boost::split(vec, str, boost::is_any_of(",")); + PyObject *veclist = PyList_New(vec.size()); + for(unsigned int i=0;i(vec[i]))); + } + return veclist; + } + try{ + return PyLong_FromLong(boost::lexical_cast(str)); + }catch(const boost::bad_lexical_cast &){ + try{ + return PyFloat_FromDouble(boost::lexical_cast(str)); + }catch(const boost::bad_lexical_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 nodes = node.getNodes(); + std::list::iterator it = nodes.begin(); + while(it!=nodes.end()){ + XMLNode subnode = *it; + if(subnode.getName()=="Option"){ + PyObject *obj = stringToPythonValue(subnode.getAttribute("value")); + 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 \ No newline at end of file -- cgit v1.2.3 From 2f871bc7068d6c87a7d950ae044ba66b0b8dcd3f Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Fri, 17 Jul 2015 12:05:46 +0200 Subject: Remove config text file loading for plugins --- include/astra/PluginAlgorithm.h | 3 +- src/PluginAlgorithm.cpp | 72 +++-------------------------------------- 2 files changed, 6 insertions(+), 69 deletions(-) (limited to 'include') diff --git a/include/astra/PluginAlgorithm.h b/include/astra/PluginAlgorithm.h index 7d6c64a..a82c579 100644 --- a/include/astra/PluginAlgorithm.h +++ b/include/astra/PluginAlgorithm.h @@ -72,8 +72,7 @@ public: private: PyObject * pluginDict; - PyObject *ospath, *inspect, *six, *astra; - std::vector getPluginPathList(); + PyObject *inspect, *six; }; PyObject* XMLNode2dict(XMLNode node); diff --git a/src/PluginAlgorithm.cpp b/src/PluginAlgorithm.cpp index 7dcaf68..8ba6631 100644 --- a/src/PluginAlgorithm.cpp +++ b/src/PluginAlgorithm.cpp @@ -67,79 +67,19 @@ void CPluginAlgorithm::run(int _iNrIterations){ Py_DECREF(retVal); } -const char ps = -#ifdef _WIN32 - '\\'; -#else - '/'; -#endif - -std::vector CPluginAlgorithmFactory::getPluginPathList(){ - std::vector list; - list.push_back("/etc/astra-toolbox"); - PyObject *ret, *retb; - ret = PyObject_CallMethod(inspect,"getfile","O",astra); - if(ret!=NULL){ - retb = PyObject_CallMethod(six,"b","O",ret); - Py_DECREF(ret); - if(retb!=NULL){ - std::string astra_inst (PyBytes_AsString(retb)); - Py_DECREF(retb); - ret = PyObject_CallMethod(ospath,"dirname","s",astra_inst.c_str()); - if(ret!=NULL){ - retb = PyObject_CallMethod(six,"b","O",ret); - Py_DECREF(ret); - if(retb!=NULL){ - list.push_back(std::string(PyBytes_AsString(retb))); - Py_DECREF(retb); - } - } - } - } - ret = PyObject_CallMethod(ospath,"expanduser","s","~"); - if(ret!=NULL){ - retb = PyObject_CallMethod(six,"b","O",ret); - Py_DECREF(ret); - if(retb!=NULL){ - list.push_back(std::string(PyBytes_AsString(retb)) + ps + ".astra-toolbox"); - Py_DECREF(retb); - } - } - const char *envval = getenv("ASTRA_PLUGIN_PATH"); - if(envval!=NULL){ - list.push_back(std::string(envval)); - } - return list; -} - CPluginAlgorithmFactory::CPluginAlgorithmFactory(){ Py_Initialize(); pluginDict = PyDict_New(); - ospath = PyImport_ImportModule("os.path"); inspect = PyImport_ImportModule("inspect"); six = PyImport_ImportModule("six"); - astra = PyImport_ImportModule("astra"); - std::vector fls = getPluginPathList(); - std::vector items; - for(unsigned int i=0;i Date: Fri, 17 Jul 2015 16:22:05 +0200 Subject: Fix numpy lapack loading when running in Matlab --- include/astra/Globals.h | 2 ++ matlab/mex/mexInitFunctions.cpp | 3 +++ src/Globals.cpp | 3 +++ src/PluginAlgorithm.cpp | 29 +++++++++++++++++++++++++++++ 4 files changed, 37 insertions(+) (limited to 'include') diff --git a/include/astra/Globals.h b/include/astra/Globals.h index 4de07d1..dc2d7e6 100644 --- a/include/astra/Globals.h +++ b/include/astra/Globals.h @@ -146,6 +146,8 @@ namespace astra { const float32 PIdiv2 = PI / 2; const float32 PIdiv4 = PI / 4; const float32 eps = 1e-7f; + + extern bool running_in_matlab; } //---------------------------------------------------------------------------------------- diff --git a/matlab/mex/mexInitFunctions.cpp b/matlab/mex/mexInitFunctions.cpp index d8a50d7..c11c7d5 100644 --- a/matlab/mex/mexInitFunctions.cpp +++ b/matlab/mex/mexInitFunctions.cpp @@ -17,6 +17,9 @@ void logCallBack(const char *msg, size_t len){ */ void initASTRAMex(){ if(mexIsInitialized) return; + + astra::running_in_matlab=true; + if(!astra::CLogger::setCallbackScreen(&logCallBack)){ mexErrMsgTxt("Error initializing mex functions."); } diff --git a/src/Globals.cpp b/src/Globals.cpp index 813f9c9..904a459 100644 --- a/src/Globals.cpp +++ b/src/Globals.cpp @@ -28,5 +28,8 @@ $Id$ #include "astra/Globals.h" +namespace astra{ + bool running_in_matlab=false; +} // nothing to see here :) diff --git a/src/PluginAlgorithm.cpp b/src/PluginAlgorithm.cpp index 8ba6631..c26ee3f 100644 --- a/src/PluginAlgorithm.cpp +++ b/src/PluginAlgorithm.cpp @@ -67,8 +67,37 @@ void CPluginAlgorithm::run(int _iNrIterations){ Py_DECREF(retVal); } +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(){ Py_Initialize(); +#ifndef _MSC_VER + if(astra::running_in_matlab) fixLapackLoading(); +#endif pluginDict = PyDict_New(); inspect = PyImport_ImportModule("inspect"); six = PyImport_ImportModule("six"); -- cgit v1.2.3 From d91b51f6d58003de84a9d6dd8189fceba0e81a5a Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Mon, 20 Jul 2015 14:07:21 +0200 Subject: Allow registering plugins without explicit name, and fix exception handling when running in Matlab --- include/astra/PluginAlgorithm.h | 3 ++ matlab/mex/astra_mex_plugin_c.cpp | 23 ++++------ python/astra/plugin.py | 71 ++++++++++++----------------- python/astra/plugin_c.pyx | 14 ++++-- samples/python/s018_plugin.py | 23 +++++----- src/PluginAlgorithm.cpp | 95 +++++++++++++++++++++++++++++++-------- 6 files changed, 138 insertions(+), 91 deletions(-) (limited to 'include') diff --git a/include/astra/PluginAlgorithm.h b/include/astra/PluginAlgorithm.h index a82c579..b56228e 100644 --- a/include/astra/PluginAlgorithm.h +++ b/include/astra/PluginAlgorithm.h @@ -64,9 +64,12 @@ public: CPluginAlgorithm * getPlugin(std::string name); bool registerPlugin(std::string name, std::string className); + bool registerPlugin(std::string className); bool registerPluginClass(std::string name, PyObject * className); + bool registerPluginClass(PyObject * className); PyObject * getRegistered(); + std::map getRegisteredMap(); std::string getHelp(std::string name); diff --git a/matlab/mex/astra_mex_plugin_c.cpp b/matlab/mex/astra_mex_plugin_c.cpp index 2d9b9a0..177fcf4 100644 --- a/matlab/mex/astra_mex_plugin_c.cpp +++ b/matlab/mex/astra_mex_plugin_c.cpp @@ -37,9 +37,6 @@ $Id$ #include "astra/PluginAlgorithm.h" -#include "Python.h" -#include "bytesobject.h" - using namespace std; using namespace astra; @@ -52,29 +49,25 @@ using namespace astra; void astra_mex_plugin_get_registered(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) { astra::CPluginAlgorithmFactory *fact = astra::CPluginAlgorithmFactory::getSingletonPtr(); - PyObject *dict = fact->getRegistered(); - PyObject *key, *value; - Py_ssize_t pos = 0; - while (PyDict_Next(dict, &pos, &key, &value)) { - mexPrintf("%s: %s\n",PyBytes_AsString(key),PyBytes_AsString(value)); + std::map mp = fact->getRegisteredMap(); + for(std::map::iterator it=mp.begin();it!=mp.end();it++){ + mexPrintf("%s: %s\n",it->first.c_str(), it->second.c_str()); } - Py_DECREF(dict); } //----------------------------------------------------------------------------------------- -/** astra_mex_plugin('register', name, class_name); +/** astra_mex_plugin('register', class_name); * * Register plugin. */ void astra_mex_plugin_register(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) { - if (3 <= nrhs) { - string name = mexToString(prhs[1]); - string class_name = mexToString(prhs[2]); + if (2 <= nrhs) { + string class_name = mexToString(prhs[1]); astra::CPluginAlgorithmFactory *fact = astra::CPluginAlgorithmFactory::getSingletonPtr(); - fact->registerPlugin(name, class_name); + fact->registerPlugin(class_name); }else{ - mexPrintf("astra_mex_plugin('register', name, class_name);\n"); + mexPrintf("astra_mex_plugin('register', class_name);\n"); } } diff --git a/python/astra/plugin.py b/python/astra/plugin.py index f8fc3bd..4b32e6e 100644 --- a/python/astra/plugin.py +++ b/python/astra/plugin.py @@ -32,60 +32,47 @@ import traceback class base(object): def astra_init(self, cfg): - try: - args, varargs, varkw, defaults = inspect.getargspec(self.initialize) - if not defaults is None: - nopt = len(defaults) - else: - nopt = 0 - if nopt>0: - req = args[2:-nopt] - opt = args[-nopt:] - else: - req = args[2:] - opt = [] + args, varargs, varkw, defaults = inspect.getargspec(self.initialize) + if not defaults is None: + nopt = len(defaults) + else: + nopt = 0 + if nopt>0: + req = args[2:-nopt] + opt = args[-nopt:] + else: + req = args[2:] + opt = [] - try: - optDict = cfg['options'] - except KeyError: - optDict = {} + try: + optDict = cfg['options'] + except KeyError: + optDict = {} - cfgKeys = set(optDict.keys()) - reqKeys = set(req) - optKeys = set(opt) + cfgKeys = set(optDict.keys()) + reqKeys = set(req) + optKeys = set(opt) - if not reqKeys.issubset(cfgKeys): - for key in reqKeys.difference(cfgKeys): - log.error("Required option '" + key + "' for plugin '" + self.__class__.__name__ + "' not specified") - raise ValueError("Missing required options") + if not reqKeys.issubset(cfgKeys): + for key in reqKeys.difference(cfgKeys): + log.error("Required option '" + key + "' for plugin '" + self.__class__.__name__ + "' not specified") + raise ValueError("Missing required options") - if not cfgKeys.issubset(reqKeys | optKeys): - log.warn(self.__class__.__name__ + ": unused configuration option: " + str(list(cfgKeys.difference(reqKeys | optKeys)))) + if not cfgKeys.issubset(reqKeys | optKeys): + log.warn(self.__class__.__name__ + ": unused configuration option: " + str(list(cfgKeys.difference(reqKeys | optKeys)))) - args = [optDict[k] for k in req] - kwargs = dict((k,optDict[k]) for k in opt if k in optDict) - self.initialize(cfg, *args, **kwargs) - except Exception: - log.error(traceback.format_exc().replace("%","%%")) - raise + args = [optDict[k] for k in req] + kwargs = dict((k,optDict[k]) for k in opt if k in optDict) + self.initialize(cfg, *args, **kwargs) - def astra_run(self, its): - try: - self.run(its) - except Exception: - log.error(traceback.format_exc().replace("%","%%")) - raise - -def register(name, className): +def register(className): """Register plugin with ASTRA. - :param name: Plugin name to register - :type name: :class:`str` :param className: Class name or class object to register :type className: :class:`str` or :class:`class` """ - p.register(name,className) + p.register(className) def get_registered(): """Get dictionary of registered plugins. diff --git a/python/astra/plugin_c.pyx b/python/astra/plugin_c.pyx index 91b3cd5..8d6816b 100644 --- a/python/astra/plugin_c.pyx +++ b/python/astra/plugin_c.pyx @@ -38,7 +38,9 @@ from . import utils cdef extern from "astra/PluginAlgorithm.h" namespace "astra": cdef cppclass CPluginAlgorithmFactory: + 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) @@ -46,11 +48,17 @@ cdef extern from "astra/PluginAlgorithm.h" namespace "astra": cdef extern from "astra/PluginAlgorithm.h" namespace "astra::CPluginAlgorithmFactory": cdef CPluginAlgorithmFactory* getSingletonPtr() -def register(name, className): +def register(className, name=None): if inspect.isclass(className): - fact.registerPluginClass(six.b(name), className) + if name==None: + fact.registerPluginClass(className) + else: + fact.registerPluginClass(six.b(name), className) else: - fact.registerPlugin(six.b(name), six.b(className)) + if name==None: + fact.registerPlugin(six.b(className)) + else: + fact.registerPlugin(six.b(name), six.b(className)) def get_registered(): return fact.getRegistered() diff --git a/samples/python/s018_plugin.py b/samples/python/s018_plugin.py index 90e09ac..31cca95 100644 --- a/samples/python/s018_plugin.py +++ b/samples/python/s018_plugin.py @@ -38,6 +38,10 @@ class SIRTPlugin(astra.plugin.base): 'rel_factor': relaxation factor (optional) """ + # The astra_name variable defines the name to use to + # call the plugin from ASTRA + astra_name = "SIRT-PLUGIN" + def initialize(self,cfg, rel_factor = 1): self.W = astra.OpTomo(cfg['ProjectorId']) self.vid = cfg['ReconstructionDataId'] @@ -68,18 +72,13 @@ if __name__=='__main__': sinogram = sinogram.reshape([180, 384]) # Register the plugin with ASTRA - # A default set of plugins to load can be defined in: - # - /etc/astra-toolbox/plugins.txt - # - [ASTRA_INSTALL_PATH]/python/astra/plugins.txt - # - [USER_HOME_PATH]/.astra-toolbox/plugins.txt - # - [ASTRA_PLUGIN_PATH environment variable]/plugins.txt - # In these files, create a separate line for each plugin with: - # [PLUGIN_ASTRA_NAME] [FULL_PLUGIN_CLASS] - # - # So in this case, it would be a line: - # SIRT-PLUGIN s018_plugin.SIRTPlugin - # - astra.plugin.register('SIRT-PLUGIN','s018_plugin.SIRTPlugin') + # First we import the package that contains the plugin + import s018_plugin + # Then, we register the plugin class with ASTRA + astra.plugin.register(s018_plugin.SIRTPlugin) + + # Get a list of registered plugins + six.print_(astra.plugin.get_registered()) # To get help on a registered plugin, use get_help six.print_(astra.plugin.get_help('SIRT-PLUGIN')) diff --git a/src/PluginAlgorithm.cpp b/src/PluginAlgorithm.cpp index d6cf731..7f7ff61 100644 --- a/src/PluginAlgorithm.cpp +++ b/src/PluginAlgorithm.cpp @@ -100,7 +100,10 @@ bool CPluginAlgorithm::initialize(const Config& _cfg){ PyObject *cfgDict = XMLNode2dict(_cfg.self); PyObject *retVal = PyObject_CallMethod(instance, "astra_init", "O",cfgDict); Py_DECREF(cfgDict); - if(retVal==NULL) return false; + if(retVal==NULL){ + logPythonError(); + return false; + } m_bIsInitialized = true; Py_DECREF(retVal); return m_bIsInitialized; @@ -108,8 +111,11 @@ bool CPluginAlgorithm::initialize(const Config& _cfg){ void CPluginAlgorithm::run(int _iNrIterations){ if(instance==NULL) return; - PyObject *retVal = PyObject_CallMethod(instance, "astra_run", "i",_iNrIterations); - if(retVal==NULL) return; + PyObject *retVal = PyObject_CallMethod(instance, "run", "i",_iNrIterations); + if(retVal==NULL){ + logPythonError(); + return; + } Py_DECREF(retVal); } @@ -157,18 +163,6 @@ CPluginAlgorithmFactory::~CPluginAlgorithmFactory(){ if(six!=NULL) Py_DECREF(six); } -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::registerPluginClass(std::string name, PyObject * className){ - PyDict_SetItemString(pluginDict, name.c_str(), className); - return true; -} - PyObject * getClassFromString(std::string str){ std::vector items; boost::split(items, str, boost::is_any_of(".")); @@ -190,6 +184,43 @@ PyObject * getClassFromString(std::string str){ 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; @@ -212,12 +243,34 @@ PyObject * CPluginAlgorithmFactory::getRegistered(){ return pluginDict; } +std::map CPluginAlgorithmFactory::getRegisteredMap(){ + std::map ret; + PyObject *key, *value; + Py_ssize_t pos = 0; + while (PyDict_Next(pluginDict, &pos, &key, &value)) { + PyObject * keyb = PyObject_Bytes(key); + PyObject * valb = PyObject_Bytes(value); + ret[PyBytes_AsString(keyb)] = PyBytes_AsString(valb); + Py_DECREF(keyb); + Py_DECREF(valb); + } + return ret; +} + std::string CPluginAlgorithmFactory::getHelp(std::string name){ PyObject *className = PyDict_GetItemString(pluginDict, name.c_str()); - if(className==NULL) return ""; - std::string str = std::string(PyBytes_AsString(className)); + if(className==NULL){ + ASTRA_ERROR("Plugin %s not found!",name.c_str()); + return ""; + } std::string ret = ""; - PyObject *pyclass = getClassFromString(str); + 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); @@ -228,9 +281,13 @@ std::string CPluginAlgorithmFactory::getHelp(std::string name){ ret = std::string(PyBytes_AsString(retb)); Py_DECREF(retb); } + }else{ + logPythonError(); } } - Py_DECREF(pyclass); + if(PyBytes_Check(className)){ + Py_DECREF(pyclass); + } return ret; } -- cgit v1.2.3 From 07c31b932078544205d61551edd4a66f69be30ae Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 2 Dec 2015 11:25:59 +0100 Subject: Avoid unnecessary include in header --- include/astra/PluginAlgorithm.h | 9 ++++++--- src/PluginAlgorithm.cpp | 6 +++++- 2 files changed, 11 insertions(+), 4 deletions(-) (limited to 'include') diff --git a/include/astra/PluginAlgorithm.h b/include/astra/PluginAlgorithm.h index b56228e..667e813 100644 --- a/include/astra/PluginAlgorithm.h +++ b/include/astra/PluginAlgorithm.h @@ -31,13 +31,16 @@ $Id$ #ifdef ASTRA_PYTHON -#include -#include "bytesobject.h" #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; + + namespace astra { class _AstraExport CPluginAlgorithm : public CAlgorithm { @@ -84,4 +87,4 @@ PyObject* XMLNode2dict(XMLNode node); #endif -#endif \ No newline at end of file +#endif diff --git a/src/PluginAlgorithm.cpp b/src/PluginAlgorithm.cpp index e79c77b..8f7dfc5 100644 --- a/src/PluginAlgorithm.cpp +++ b/src/PluginAlgorithm.cpp @@ -37,9 +37,13 @@ $Id$ #include #include +#include +#include "bytesobject.h" + namespace astra { + void logPythonError(){ if(PyErr_Occurred()){ PyObject *ptype, *pvalue, *ptraceback; @@ -394,4 +398,4 @@ PyObject* XMLNode2dict(XMLNode node){ } } -#endif \ No newline at end of file +#endif -- cgit v1.2.3 From 5df8492fcca44965f87884509668c1b75509e584 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 2 Dec 2015 14:56:42 +0100 Subject: Fix Windows build --- include/astra/Globals.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'include') diff --git a/include/astra/Globals.h b/include/astra/Globals.h index dc2d7e6..f70c3a9 100644 --- a/include/astra/Globals.h +++ b/include/astra/Globals.h @@ -147,7 +147,7 @@ namespace astra { const float32 PIdiv4 = PI / 4; const float32 eps = 1e-7f; - extern bool running_in_matlab; + extern _AstraExport bool running_in_matlab; } //---------------------------------------------------------------------------------------- -- cgit v1.2.3