diff options
Diffstat (limited to 'python')
| -rw-r--r-- | python/astra/PyIncludes.pxd | 4 | ||||
| -rw-r--r-- | python/astra/__init__.py | 1 | ||||
| -rw-r--r-- | python/astra/creators.py | 15 | ||||
| -rw-r--r-- | python/astra/data2d_c.pyx | 27 | ||||
| -rw-r--r-- | python/astra/experimental.pyx | 84 | ||||
| -rw-r--r-- | python/astra/plugin.py | 121 | ||||
| -rw-r--r-- | python/astra/plugin_c.pyx | 67 | ||||
| -rw-r--r-- | python/astra/utils.pyx | 10 | ||||
| -rw-r--r-- | python/builder.py | 8 | ||||
| -rw-r--r-- | python/conda/build.sh | 16 | ||||
| -rw-r--r-- | python/conda/meta.yaml | 40 | ||||
| -rw-r--r-- | python/docSRC/conf.py | 4 | ||||
| -rw-r--r-- | python/docSRC/index.rst | 1 | ||||
| -rw-r--r-- | python/docSRC/plugins.rst | 8 |
14 files changed, 401 insertions, 5 deletions
diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd index 35dea5f..4a4ce43 100644 --- a/python/astra/PyIncludes.pxd +++ b/python/astra/PyIncludes.pxd @@ -62,6 +62,7 @@ cdef extern from "astra/VolumeGeometry2D.h" namespace "astra": float32 getWindowMaxX() float32 getWindowMaxY() Config* getConfiguration() + bool isEqual(CVolumeGeometry2D*) cdef extern from "astra/Float32Data2D.h" namespace "astra": cdef cppclass CFloat32CustomMemory: @@ -89,6 +90,7 @@ cdef extern from "astra/ProjectionGeometry2D.h" namespace "astra": float32 getProjectionAngle(int) float32 getDetectorWidth() Config* getConfiguration() + bool isEqual(CProjectionGeometry2D*) cdef extern from "astra/Float32Data2D.h" namespace "astra::CFloat32Data2D": cdef enum TWOEDataType "astra::CFloat32Data2D::EDataType": @@ -224,6 +226,7 @@ cdef extern from "astra/Float32VolumeData3DMemory.h" namespace "astra": int getRowCount() int getColCount() int getSliceCount() + bool isInitialized() @@ -255,6 +258,7 @@ cdef extern from "astra/Float32ProjectionData3DMemory.h" namespace "astra": int getDetectorColCount() int getDetectorRowCount() int getAngleCount() + bool isInitialized() cdef extern from "astra/Float32Data3D.h" namespace "astra": cdef cppclass CFloat32Data3D: 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/creators.py b/python/astra/creators.py index 68bc8a2..f3474d8 100644 --- a/python/astra/creators.py +++ b/python/astra/creators.py @@ -72,6 +72,10 @@ This method can be called in a number of ways: ``create_vol_geom(M, N, Z)``: :returns: A 3D volume geometry of size :math:`M \\times N \\times Z`. +``create_vol_geom(M, N, Z, minx, maxx, miny, maxy, minz, maxz)``: + :returns: A 3D volume geometry of size :math:`M \\times N \\times Z`, windowed as :math:`minx \\leq x \\leq maxx` and :math:`miny \\leq y \\leq maxy` and :math:`minz \\leq z \\leq maxz` . + + """ vol_geom = {'option': {}} # astra_create_vol_geom(row_count) @@ -122,6 +126,17 @@ This method can be called in a number of ways: vol_geom['GridRowCount'] = varargin[0] vol_geom['GridColCount'] = varargin[1] vol_geom['GridSliceCount'] = varargin[2] + # astra_create_vol_geom(row_count, col_count, slice_count, min_x, max_x, min_y, max_y, min_z, max_z) + elif len(varargin) == 9: + vol_geom['GridRowCount'] = varargin[0] + vol_geom['GridColCount'] = varargin[1] + vol_geom['GridSliceCount'] = varargin[2] + vol_geom['option']['WindowMinX'] = varargin[3] + vol_geom['option']['WindowMaxX'] = varargin[4] + vol_geom['option']['WindowMinY'] = varargin[5] + vol_geom['option']['WindowMaxY'] = varargin[6] + vol_geom['option']['WindowMinZ'] = varargin[7] + vol_geom['option']['WindowMaxZ'] = varargin[8] return vol_geom diff --git a/python/astra/data2d_c.pyx b/python/astra/data2d_c.pyx index 4919bf2..801fd8e 100644 --- a/python/astra/data2d_c.pyx +++ b/python/astra/data2d_c.pyx @@ -34,6 +34,9 @@ from cython cimport view cimport PyData2DManager from .PyData2DManager cimport CData2DManager +cimport PyProjector2DManager +from .PyProjector2DManager cimport CProjector2DManager + cimport PyXMLDocument from .PyXMLDocument cimport XMLDocument @@ -54,6 +57,8 @@ import operator from six.moves import reduce cdef CData2DManager * man2d = <CData2DManager * >PyData2DManager.getSingletonPtr() +cdef CProjector2DManager * manProj = <CProjector2DManager * >PyProjector2DManager.getSingletonPtr() + cdef extern from "CFloat32CustomPython.h": cdef cppclass CFloat32CustomPython: @@ -164,7 +169,6 @@ def store(i, data): cdef CFloat32Data2D * pDataObject = getObject(i) fillDataObject(pDataObject, data) - def get_geometry(i): cdef CFloat32Data2D * pDataObject = getObject(i) cdef CFloat32ProjectionData2D * pDataObject2 @@ -179,6 +183,27 @@ def get_geometry(i): raise Exception("Not a known data object") return geom +cdef CProjector2D * getProjector(i) except NULL: + cdef CProjector2D * proj = manProj.get(i) + if proj == NULL: + raise Exception("Projector not initialized.") + if not proj.isInitialized(): + raise Exception("Projector not initialized.") + return proj + +def check_compatible(i, proj_id): + cdef CProjector2D * proj = getProjector(proj_id) + cdef CFloat32Data2D * pDataObject = getObject(i) + cdef CFloat32ProjectionData2D * pDataObject2 + cdef CFloat32VolumeData2D * pDataObject3 + if pDataObject.getType() == TWOPROJECTION: + pDataObject2 = <CFloat32ProjectionData2D * >pDataObject + return pDataObject2.getGeometry().isEqual(proj.getProjectionGeometry()) + elif pDataObject.getType() == TWOVOLUME: + pDataObject3 = <CFloat32VolumeData2D * >pDataObject + return pDataObject3.getGeometry().isEqual(proj.getVolumeGeometry()) + else: + raise Exception("Not a known data object") def change_geometry(i, geom): cdef Config *cfg diff --git a/python/astra/experimental.pyx b/python/astra/experimental.pyx new file mode 100644 index 0000000..da27504 --- /dev/null +++ b/python/astra/experimental.pyx @@ -0,0 +1,84 @@ +#----------------------------------------------------------------------- +# Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +# 2014-2015, CWI, Amsterdam +# +# Contact: astra@uantwerpen.be +# Website: http://sf.net/projects/astra-toolbox +# +# This file is part of the ASTRA Toolbox. +# +# +# The ASTRA Toolbox is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# The ASTRA Toolbox is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +# distutils: language = c++ +# distutils: libraries = astra + +include "config.pxi" + +import six +from .PyIncludes cimport * +from libcpp.vector cimport vector + +cdef extern from "astra/CompositeGeometryManager.h" namespace "astra": + cdef cppclass CCompositeGeometryManager: + bool doFP(CProjector3D *, vector[CFloat32VolumeData3DMemory *], vector[CFloat32ProjectionData3DMemory *]) + bool doBP(CProjector3D *, vector[CFloat32VolumeData3DMemory *], vector[CFloat32ProjectionData3DMemory *]) + +cdef extern from *: + CFloat32VolumeData3DMemory * dynamic_cast_vol_mem "dynamic_cast<astra::CFloat32VolumeData3DMemory*>" (CFloat32Data3D * ) except NULL + CFloat32ProjectionData3DMemory * dynamic_cast_proj_mem "dynamic_cast<astra::CFloat32ProjectionData3DMemory*>" (CFloat32Data3D * ) except NULL + +cimport PyProjector3DManager +from .PyProjector3DManager cimport CProjector3DManager +cimport PyData3DManager +from .PyData3DManager cimport CData3DManager + +cdef CProjector3DManager * manProj = <CProjector3DManager * >PyProjector3DManager.getSingletonPtr() +cdef CData3DManager * man3d = <CData3DManager * >PyData3DManager.getSingletonPtr() + +def do_composite(projector_id, vol_ids, proj_ids, t): + cdef vector[CFloat32VolumeData3DMemory *] vol + cdef CFloat32VolumeData3DMemory * pVolObject + cdef CFloat32ProjectionData3DMemory * pProjObject + for v in vol_ids: + pVolObject = dynamic_cast_vol_mem(man3d.get(v)) + if pVolObject == NULL: + raise Exception("Data object not found") + if not pVolObject.isInitialized(): + raise Exception("Data object not initialized properly") + vol.push_back(pVolObject) + cdef vector[CFloat32ProjectionData3DMemory *] proj + for v in proj_ids: + pProjObject = dynamic_cast_proj_mem(man3d.get(v)) + if pProjObject == NULL: + raise Exception("Data object not found") + if not pProjObject.isInitialized(): + raise Exception("Data object not initialized properly") + proj.push_back(pProjObject) + cdef CCompositeGeometryManager m + cdef CProjector3D * projector = manProj.get(projector_id) # may be NULL + if t == "FP": + if not m.doFP(projector, vol, proj): + raise Exception("Failed to perform FP") + else: + if not m.doBP(projector, vol, proj): + raise Exception("Failed to perform BP") + +def do_composite_FP(projector_id, vol_ids, proj_ids): + do_composite(projector_id, vol_ids, proj_ids, "FP") + +def do_composite_BP(projector_id, vol_ids, proj_ids): + do_composite(projector_id, vol_ids, proj_ids, "BP") diff --git a/python/astra/plugin.py b/python/astra/plugin.py new file mode 100644 index 0000000..3e3528d --- /dev/null +++ b/python/astra/plugin.py @@ -0,0 +1,121 @@ +#----------------------------------------------------------------------- +#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 <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +from . import plugin_c as p +from . import log +from . import data2d +from . import data2d_c +from . import data3d +from . import projector +import inspect +import traceback + +class base(object): + + def astra_init(self, cfg): + 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 = {} + + 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)))) + + 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) + +class ReconstructionAlgorithm2D(base): + + def astra_init(self, cfg): + self.pid = cfg['ProjectorId'] + self.s = data2d.get_shared(cfg['ProjectionDataId']) + self.v = data2d.get_shared(cfg['ReconstructionDataId']) + self.vg = projector.volume_geometry(self.pid) + self.pg = projector.projection_geometry(self.pid) + if not data2d_c.check_compatible(cfg['ProjectionDataId'], self.pid): + raise ValueError("Projection data and projector not compatible") + if not data2d_c.check_compatible(cfg['ReconstructionDataId'], self.pid): + raise ValueError("Reconstruction data and projector not compatible") + super(ReconstructionAlgorithm2D,self).astra_init(cfg) + +class ReconstructionAlgorithm3D(base): + + def astra_init(self, cfg): + self.pid = cfg['ProjectorId'] + self.s = data3d.get_shared(cfg['ProjectionDataId']) + self.v = data3d.get_shared(cfg['ReconstructionDataId']) + self.vg = data3d.get_geometry(cfg['ReconstructionDataId']) + self.pg = data3d.get_geometry(cfg['ProjectionDataId']) + super(ReconstructionAlgorithm3D,self).astra_init(cfg) + +def register(className): + """Register plugin with ASTRA. + + :param className: Class name or class object to register + :type className: :class:`str` or :class:`class` + + """ + p.register(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..8d6816b --- /dev/null +++ b/python/astra/plugin_c.pyx @@ -0,0 +1,67 @@ +#----------------------------------------------------------------------- +#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 <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +# 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 className) + bool registerPlugin(string name, string className) + bool registerPluginClass(object 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(className, name=None): + if inspect.isclass(className): + if name==None: + fact.registerPluginClass(className) + else: + fact.registerPluginClass(six.b(name), className) + else: + if name==None: + fact.registerPlugin(six.b(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 260c308..07727ce 100644 --- a/python/astra/utils.pyx +++ b/python/astra/utils.pyx @@ -29,9 +29,13 @@ cimport numpy as np import numpy as np import six +if six.PY3: + import builtins +else: + import __builtin__ from libcpp.string cimport string -from libcpp.list cimport list from libcpp.vector cimport vector +from libcpp.list cimport list from cython.operator cimport dereference as deref, preincrement as inc from cpython.version cimport PY_MAJOR_VERSION @@ -91,6 +95,8 @@ cdef void readDict(XMLNode root, _dc): dc = convert_item(_dc) for item in dc: val = dc[item] + if isinstance(val, __builtins__.list) or isinstance(val, tuple): + val = np.array(val,dtype=np.float64) if isinstance(val, np.ndarray): if val.size == 0: break @@ -125,6 +131,8 @@ cdef void readOptions(XMLNode node, dc): val = dc[item] if node.hasOption(item): raise Exception('Duplicate Option: %s' % item) + if isinstance(val, __builtins__.list) or isinstance(val, tuple): + val = np.array(val,dtype=np.float64) if isinstance(val, np.ndarray): if val.size == 0: break diff --git a/python/builder.py b/python/builder.py index cfdb7d1..5322182 100644 --- a/python/builder.py +++ b/python/builder.py @@ -41,6 +41,12 @@ try: usecuda=True except KeyError: pass +try: + if os.environ['CL'].find('/DASTRA_CUDA')!=-1: + usecuda=True +except KeyError: + pass + cfgToWrite = 'DEF HAVE_CUDA=' + str(usecuda) + "\n" cfgHasToBeUpdated = True @@ -65,7 +71,7 @@ ext_modules = cythonize("astra/*.pyx", language_level=2) cmdclass = { 'build_ext': build_ext } setup (name = 'PyASTRAToolbox', - version = '1.6', + version = '1.7', description = 'Python interface to the ASTRA-Toolbox', author='D.M. Pelt', author_email='D.M.Pelt@cwi.nl', diff --git a/python/conda/build.sh b/python/conda/build.sh new file mode 100644 index 0000000..814ea7e --- /dev/null +++ b/python/conda/build.sh @@ -0,0 +1,16 @@ +cd build/linux +./autogen.sh +./configure --with-python --with-cuda=$CUDA_ROOT --prefix=$PREFIX +if [ $MAKEOPTS == '<UNDEFINED>' ] + then + MAKEOPTS="" +fi +make $MAKEOPTS install-libraries +make $MAKEOPTS python-root-install +LIBPATH=lib +if [ $ARCH == 64 ] + then + LIBPATH+=64 +fi +cp -P $CUDA_ROOT/$LIBPATH/libcudart.so.* $PREFIX/lib +cp -P $CUDA_ROOT/$LIBPATH/libcufft.so.* $PREFIX/lib diff --git a/python/conda/meta.yaml b/python/conda/meta.yaml new file mode 100644 index 0000000..e1adc83 --- /dev/null +++ b/python/conda/meta.yaml @@ -0,0 +1,40 @@ +package: + name: astra-toolbox + version: '1.7' + +source: + git_url: https://github.com/astra-toolbox/astra-toolbox.git + git_tag: v1.7 + +build: + number: 0 + script_env: + - CUDA_ROOT + - MAKEOPTS + +test: + imports: + - astra + +requirements: + build: + - python + - cython >=0.13 + - numpy + - six + + run: + - python + - numpy + - scipy + - six + + +about: + home: http://sourceforge.net/p/astra-toolbox/wiki/Home/ + license: GPLv3 + summary: 'The ASTRA Toolbox is a Python toolbox of high-performance GPU primitives for 2D and 3D tomography.' + +# See +# http://docs.continuum.io/conda/build.html for +# more information about meta.yaml diff --git a/python/docSRC/conf.py b/python/docSRC/conf.py index e54bbb8..cc95a80 100644 --- a/python/docSRC/conf.py +++ b/python/docSRC/conf.py @@ -48,9 +48,9 @@ copyright = u'2013, Centrum Wiskunde & Informatica, Amsterdam' # built documents. # # The short X.Y version. -version = '1.6' +version = '1.7' # The full version, including alpha/beta/rc tags. -release = '1.6' +release = '1.7' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. 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: + |