From 0f577d1fbc2b0c15d85f18cc38eb14e3cbf6c6a2 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Fri, 22 May 2015 14:36:42 +0200 Subject: Fix optomo reconstruction for 1D input --- python/astra/optomo.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'python') diff --git a/python/astra/optomo.py b/python/astra/optomo.py index 2937d9c..0108674 100644 --- a/python/astra/optomo.py +++ b/python/astra/optomo.py @@ -164,7 +164,7 @@ class OpTomo(scipy.sparse.linalg.LinearOperator): :param extraOptions: Extra options to use during reconstruction (i.e. for cfg['option']). :type extraOptions: :class:`dict` """ - self.__checkArray(s, self.sshape) + s = self.__checkArray(s, self.sshape) sid = self.data_mod.link('-sino',self.pg,s) v = np.zeros(self.vshape,dtype=np.float32) vid = self.data_mod.link('-vol',self.vg,v) -- cgit v1.2.3 From ef47dca509c1c26c5037b9b9024a6a84a3b7fe0b Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Sat, 20 Jun 2015 00:31:15 +0200 Subject: Fix wrong module name in documentation --- python/docSRC/operator.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'python') diff --git a/python/docSRC/operator.rst b/python/docSRC/operator.rst index f5369fa..65a5a99 100644 --- a/python/docSRC/operator.rst +++ b/python/docSRC/operator.rst @@ -1,7 +1,7 @@ OpTomo class: the :mod:`operator` module ============================================== -.. automodule:: astra.operator +.. automodule:: astra.optomo :members: :undoc-members: :show-inheritance: -- cgit v1.2.3 From 26198f7e1fbed9d294fc2856f796f408c85b66f3 Mon Sep 17 00:00:00 2001 From: Valerii Sokolov Date: Tue, 9 Jun 2015 11:26:42 +0200 Subject: Don't take address of temporary. --- python/astra/utils.pyx | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'python') diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx index ddb37aa..a8e9e4e 100644 --- a/python/astra/utils.pyx +++ b/python/astra/utils.pyx @@ -95,7 +95,8 @@ cdef void readDict(XMLNode root, _dc): if val.size == 0: break listbase = root.addChildNode(item) - data = np.PyArray_DATA(np.ascontiguousarray(val,dtype=np.float64)) + contig_data = np.ascontiguousarray(val,dtype=np.float64) + data = np.PyArray_DATA(contig_data) if val.ndim == 2: listbase.setContent(data, val.shape[1], val.shape[0], False) elif val.ndim == 1: @@ -129,7 +130,8 @@ cdef void readOptions(XMLNode node, dc): break listbase = node.addChildNode(six.b('Option')) listbase.addAttribute(< string > six.b('key'), < string > item) - data = np.PyArray_DATA(np.ascontiguousarray(val,dtype=np.float64)) + contig_data = np.ascontiguousarray(val,dtype=np.float64) + data = np.PyArray_DATA(contig_data) if val.ndim == 2: listbase.setContent(data, val.shape[1], val.shape[0], False) elif val.ndim == 1: -- cgit v1.2.3 From a9ea08c4a11592378b320cac45be8eede8addd6f Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Mon, 22 Jun 2015 17:54:23 +0200 Subject: Additional module name fix in documentation --- python/docSRC/operator.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'python') diff --git a/python/docSRC/operator.rst b/python/docSRC/operator.rst index 65a5a99..fe500ba 100644 --- a/python/docSRC/operator.rst +++ b/python/docSRC/operator.rst @@ -1,4 +1,4 @@ -OpTomo class: the :mod:`operator` module +OpTomo class: the :mod:`optomo` module ============================================== .. automodule:: astra.optomo -- cgit v1.2.3 From 63d78fbaafa7d247347f9052db86f575d89260b7 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Wed, 24 Jun 2015 20:28:46 +0200 Subject: Fix config to struct/dict translation for array options --- python/astra/utils.pyx | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'python') diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx index a8e9e4e..260c308 100644 --- a/python/astra/utils.pyx +++ b/python/astra/utils.pyx @@ -204,7 +204,10 @@ cdef XMLNode2dict(XMLNode node): while it != nodes.end(): subnode = deref(it) if castString(subnode.getName())=="Option": - opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getAttribute('value')) + if subnode.hasAttribute('value'): + opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getAttribute('value')) + else: + opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getContent()) else: dct[castString(subnode.getName())] = stringToPythonValue(subnode.getContent()) inc(it) -- cgit v1.2.3 From 9e3472ea9041b8755050427d8bdb8a4701019c55 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Thu, 25 Jun 2015 21:52:07 +0200 Subject: Fix memory leak in configuration code --- python/astra/projector3d_c.pyx | 10 ++++++++-- python/astra/projector_c.pyx | 10 ++++++++-- 2 files changed, 16 insertions(+), 4 deletions(-) (limited to 'python') diff --git a/python/astra/projector3d_c.pyx b/python/astra/projector3d_c.pyx index 8b978d7..aec9cde 100644 --- a/python/astra/projector3d_c.pyx +++ b/python/astra/projector3d_c.pyx @@ -87,12 +87,18 @@ cdef CProjector3D * getObject(i) except NULL: def projection_geometry(i): cdef CProjector3D * proj = getObject(i) - return utils.configToDict(proj.getProjectionGeometry().getConfiguration()) + cdef Config * cfg = proj.getProjectionGeometry().getConfiguration() + dct = utils.configToDict(cfg) + del cfg + return dct def volume_geometry(i): cdef CProjector3D * proj = getObject(i) - return utils.configToDict(proj.getVolumeGeometry().getConfiguration()) + cdef Config * cfg = proj.getVolumeGeometry().getConfiguration() + dct = utils.configToDict(cfg) + del cfg + return dct def weights_single_ray(i, projection_index, detector_index): diff --git a/python/astra/projector_c.pyx b/python/astra/projector_c.pyx index 9aa868e..77c64a4 100644 --- a/python/astra/projector_c.pyx +++ b/python/astra/projector_c.pyx @@ -91,12 +91,18 @@ cdef CProjector2D * getObject(i) except NULL: def projection_geometry(i): cdef CProjector2D * proj = getObject(i) - return utils.configToDict(proj.getProjectionGeometry().getConfiguration()) + cdef Config * cfg = proj.getProjectionGeometry().getConfiguration() + dct = utils.configToDict(cfg) + del cfg + return dct def volume_geometry(i): cdef CProjector2D * proj = getObject(i) - return utils.configToDict(proj.getVolumeGeometry().getConfiguration()) + cdef Config * cfg = proj.getVolumeGeometry().getConfiguration() + dct = utils.configToDict(cfg) + del cfg + return dct def weights_single_ray(i, projection_index, detector_index): -- cgit v1.2.3 From 4d39c35d6c9124c26de64c9d227a25f612903a2a Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Fri, 17 Jul 2015 13:44:59 +0200 Subject: Fix formatting when passing strings to log from high-level code --- python/astra/log_c.pyx | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'python') diff --git a/python/astra/log_c.pyx b/python/astra/log_c.pyx index f16329f..55c63e6 100644 --- a/python/astra/log_c.pyx +++ b/python/astra/log_c.pyx @@ -53,19 +53,19 @@ cdef extern from "astra/Logging.h" namespace "astra::CLogger": def log_debug(sfile, sline, message): cstr = list(map(six.b,(sfile,message))) - debug(cstr[0],sline,cstr[1]) + debug(cstr[0],sline,"%s",cstr[1]) def log_info(sfile, sline, message): cstr = list(map(six.b,(sfile,message))) - info(cstr[0],sline,cstr[1]) + info(cstr[0],sline,"%s",cstr[1]) def log_warn(sfile, sline, message): cstr = list(map(six.b,(sfile,message))) - warn(cstr[0],sline,cstr[1]) + warn(cstr[0],sline,"%s",cstr[1]) def log_error(sfile, sline, message): cstr = list(map(six.b,(sfile,message))) - error(cstr[0],sline,cstr[1]) + error(cstr[0],sline,"%s",cstr[1]) def log_enable(): enable() -- 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 --- 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 ++++ 6 files changed, 169 insertions(+), 67 deletions(-) create mode 100644 python/astra/plugin.py create mode 100644 python/astra/plugin_c.pyx create mode 100644 python/docSRC/plugins.rst (limited to 'python') 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: + -- cgit v1.2.3 From 11af4b554df9a8a5c31d9dcbc1ea849b32394ba3 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Wed, 24 Jun 2015 18:36:03 +0200 Subject: Better way of passing options to Python plugin using inspect --- python/astra/plugin.py | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) (limited to 'python') diff --git a/python/astra/plugin.py b/python/astra/plugin.py index ccdb2cb..891f6c9 100644 --- a/python/astra/plugin.py +++ b/python/astra/plugin.py @@ -26,22 +26,20 @@ from . import plugin_c as p from . import log +import inspect 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 = {} + args, varargs, varkw, defaults = inspect.getargspec(self.initialize) + nopt = len(defaults) + if nopt>0: + req = args[2:-nopt] + opt = args[-nopt:] + else: + req = args[2:] + opt = [] try: optDict = cfg['options'] @@ -60,7 +58,9 @@ class base(object): if not cfgKeys.issubset(reqKeys | optKeys): log.warn(self.__class__.__name__ + ": unused configuration option: " + str(list(cfgKeys.difference(reqKeys | optKeys)))) - self.initialize(cfg) + 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 as e: log.error(str(e)) raise -- cgit v1.2.3 From 385865d6ad7a54ee294b4086d4679747f49cff2e Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Wed, 24 Jun 2015 21:04:22 +0200 Subject: Fix passing a python list as option --- python/astra/utils.pyx | 2 ++ 1 file changed, 2 insertions(+) (limited to 'python') diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx index 3746b8e..08ee67b 100644 --- a/python/astra/utils.pyx +++ b/python/astra/utils.pyx @@ -128,6 +128,8 @@ cdef void readOptions(XMLNode node, dc): val = dc[item] if node.hasOption(item): raise Exception('Duplicate Option: %s' % item) + if isinstance(val, list): + val = np.array(val,dtype=np.float64) if isinstance(val, np.ndarray): if val.size == 0: break -- cgit v1.2.3 From edae78481cf0e9cbffe335de1e541821758c5da1 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Wed, 24 Jun 2015 21:36:04 +0200 Subject: Log error when running Python plugin algorithm --- python/astra/plugin.py | 7 +++++++ 1 file changed, 7 insertions(+) (limited to 'python') diff --git a/python/astra/plugin.py b/python/astra/plugin.py index 891f6c9..bbbc450 100644 --- a/python/astra/plugin.py +++ b/python/astra/plugin.py @@ -65,6 +65,13 @@ class base(object): log.error(str(e)) raise + def astra_run(self, its): + try: + self.run(its) + except Exception as e: + log.error(str(e)) + raise + def register(name, className): """Register plugin with ASTRA. -- cgit v1.2.3 From 58af62f543bbb0e66247a37dae36698d9fa5d338 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Thu, 9 Jul 2015 23:13:44 +0200 Subject: Allow plugins without keywords --- python/astra/plugin.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'python') diff --git a/python/astra/plugin.py b/python/astra/plugin.py index bbbc450..be5c155 100644 --- a/python/astra/plugin.py +++ b/python/astra/plugin.py @@ -33,7 +33,10 @@ class base(object): def astra_init(self, cfg): try: args, varargs, varkw, defaults = inspect.getargspec(self.initialize) - nopt = len(defaults) + if not defaults is None: + nopt = len(defaults) + else: + nopt = 0 if nopt>0: req = args[2:-nopt] opt = args[-nopt:] -- cgit v1.2.3 From c4d227e4d8fd8809fb3c3bded5540cc1e82746ef Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Fri, 10 Jul 2015 00:23:18 +0200 Subject: Show more useful information when a plugin raises an exception --- python/astra/plugin.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) (limited to 'python') diff --git a/python/astra/plugin.py b/python/astra/plugin.py index be5c155..f8fc3bd 100644 --- a/python/astra/plugin.py +++ b/python/astra/plugin.py @@ -27,6 +27,7 @@ from . import plugin_c as p from . import log import inspect +import traceback class base(object): @@ -64,15 +65,15 @@ class base(object): 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 as e: - log.error(str(e)) + except Exception: + log.error(traceback.format_exc().replace("%","%%")) raise def astra_run(self, its): try: self.run(its) - except Exception as e: - log.error(str(e)) + except Exception: + log.error(traceback.format_exc().replace("%","%%")) raise def register(name, className): -- cgit v1.2.3 From f79f072b9bbc5719fbfa3d5c75e886a2bbb7f1ce Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Fri, 10 Jul 2015 00:30:23 +0200 Subject: Also allow tuples to be passed in a config dict --- python/astra/utils.pyx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'python') diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx index 08ee67b..9d2e9ab 100644 --- a/python/astra/utils.pyx +++ b/python/astra/utils.pyx @@ -93,7 +93,7 @@ cdef void readDict(XMLNode root, _dc): dc = convert_item(_dc) for item in dc: val = dc[item] - if isinstance(val, list): + if isinstance(val, list) or isinstance(val, tuple): val = np.array(val,dtype=np.float64) if isinstance(val, np.ndarray): if val.size == 0: @@ -128,7 +128,7 @@ cdef void readOptions(XMLNode node, dc): val = dc[item] if node.hasOption(item): raise Exception('Duplicate Option: %s' % item) - if isinstance(val, list): + if isinstance(val, list) or isinstance(val, tuple): val = np.array(val,dtype=np.float64) if isinstance(val, np.ndarray): if val.size == 0: -- 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 --- python/astra/plugin.py | 71 +++++++++++++++++++---------------------------- python/astra/plugin_c.pyx | 14 ++++++++-- 2 files changed, 40 insertions(+), 45 deletions(-) (limited to 'python') 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() -- cgit v1.2.3 From e509cd013f691acded3dc0d87732ba5257cb0ae4 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Mon, 20 Jul 2015 15:14:50 +0200 Subject: Add ReconstructionAlgorithm2D/3D classes for plugins (matching C++ classes) --- python/astra/PyIncludes.pxd | 2 ++ python/astra/data2d_c.pyx | 27 ++++++++++++++++++++++++++- python/astra/plugin.py | 27 +++++++++++++++++++++++++++ 3 files changed, 55 insertions(+), 1 deletion(-) (limited to 'python') diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd index 909f58f..a099c31 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": 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 = PyData2DManager.getSingletonPtr() +cdef CProjector2DManager * manProj = 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 = pDataObject + return pDataObject2.getGeometry().isEqual(proj.getProjectionGeometry()) + elif pDataObject.getType() == TWOVOLUME: + pDataObject3 = 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/plugin.py b/python/astra/plugin.py index 4b32e6e..11cc5cc 100644 --- a/python/astra/plugin.py +++ b/python/astra/plugin.py @@ -26,6 +26,10 @@ 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 @@ -65,6 +69,29 @@ class base(object): 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.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. -- cgit v1.2.3 From 14ce794a1654f82fe8ac414e56e842242bece729 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Tue, 21 Jul 2015 13:51:50 +0200 Subject: Also use ProjectorId in ReconstructionAlgorithm3D plugin base --- python/astra/plugin.py | 1 + 1 file changed, 1 insertion(+) (limited to 'python') diff --git a/python/astra/plugin.py b/python/astra/plugin.py index 11cc5cc..3e3528d 100644 --- a/python/astra/plugin.py +++ b/python/astra/plugin.py @@ -86,6 +86,7 @@ class ReconstructionAlgorithm2D(base): 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']) -- cgit v1.2.3 From 43155c03488ca98c24f8f369e5c8699efa20cca3 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Thu, 30 Jul 2015 15:28:16 +0200 Subject: Fix Python OpTomo for scipy 0.16 scipy 0.16 also uses .T to define a transpose, which conflicts with the old OpTomo implementation. OpTomo now also defines the _transpose() method, which .T will call in scipy 0.16. --- python/astra/optomo.py | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) (limited to 'python') diff --git a/python/astra/optomo.py b/python/astra/optomo.py index 0108674..19b07e3 100644 --- a/python/astra/optomo.py +++ b/python/astra/optomo.py @@ -86,7 +86,15 @@ class OpTomo(scipy.sparse.linalg.LinearOperator): self.proj_id = proj_id - self.T = OpTomoTranspose(self) + self.transposeOpTomo = OpTomoTranspose(self) + try: + self.T = self.transposeOpTomo + except AttributeError: + # Scipy >= 0.16 defines self.T using self._transpose() + pass + + def _transpose(self): + return self.transposeOpTomo def __checkArray(self, arr, shp): if len(arr.shape)==1: -- cgit v1.2.3 From b4bd441549ea71dd6c34a9f2158bbebc39ba4e9e Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Thu, 30 Jul 2015 15:34:10 +0200 Subject: Define a transpose for the OpTomo transpose as well Allows for chaining .T calls. --- python/astra/optomo.py | 8 ++++++++ 1 file changed, 8 insertions(+) (limited to 'python') diff --git a/python/astra/optomo.py b/python/astra/optomo.py index 19b07e3..4a64150 100644 --- a/python/astra/optomo.py +++ b/python/astra/optomo.py @@ -197,6 +197,11 @@ class OpTomoTranspose(scipy.sparse.linalg.LinearOperator): self.parent = parent self.dtype = np.float32 self.shape = (parent.shape[1], parent.shape[0]) + try: + self.T = self.parent + except AttributeError: + # Scipy >= 0.16 defines self.T using self._transpose() + pass def _matvec(self, s): return self.parent.rmatvec(s) @@ -204,6 +209,9 @@ class OpTomoTranspose(scipy.sparse.linalg.LinearOperator): def rmatvec(self, v): return self.parent.matvec(v) + def _transpose(self): + return self.parent + def __mul__(self,s): # Catch the case of a backprojection of 2D/3D data if isinstance(s, np.ndarray) and s.shape==self.parent.sshape: -- cgit v1.2.3 From ee790c305942675e94ee66bfd24896d1ef61335a Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Mon, 10 Aug 2015 16:22:19 +0200 Subject: Release the gil in algorithm.run --- python/astra/PyIncludes.pxd | 2 +- python/astra/algorithm_c.pyx | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) (limited to 'python') diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd index 909f58f..35dea5f 100644 --- a/python/astra/PyIncludes.pxd +++ b/python/astra/PyIncludes.pxd @@ -143,7 +143,7 @@ cdef extern from "astra/Float32ProjectionData2D.h" namespace "astra": cdef extern from "astra/Algorithm.h" namespace "astra": cdef cppclass CAlgorithm: bool initialize(Config) - void run(int) + void run(int) nogil bool isInitialized() cdef extern from "astra/ReconstructionAlgorithm2D.h" namespace "astra": diff --git a/python/astra/algorithm_c.pyx b/python/astra/algorithm_c.pyx index 966d3d7..3231c1f 100644 --- a/python/astra/algorithm_c.pyx +++ b/python/astra/algorithm_c.pyx @@ -73,7 +73,9 @@ cdef CAlgorithm * getAlg(i) except NULL: def run(i, iterations=0): cdef CAlgorithm * alg = getAlg(i) - alg.run(iterations) + cdef int its = iterations + with nogil: + alg.run(its) def get_res_norm(i): -- cgit v1.2.3 From c39b12fc42a7254bad1e68cbdb948eee0421ad81 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 16 Sep 2015 16:44:10 +0200 Subject: Let astra_create_vol_geom also generate flexible volume geometries --- python/astra/creators.py | 15 +++++++++++++++ 1 file changed, 15 insertions(+) (limited to 'python') 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 -- cgit v1.2.3 From c335c53178cf63374599682dfbd7e08d318a20f2 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 2 Dec 2015 17:48:02 +0100 Subject: Detect ASTRA_CUDA in Windows CL flags for Python as well --- python/builder.py | 6 ++++++ 1 file changed, 6 insertions(+) (limited to 'python') diff --git a/python/builder.py b/python/builder.py index cfdb7d1..44d9c3b 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 -- cgit v1.2.3 From 4621453bb753f17614b8ac4b6314a142ecbe278c Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Thu, 3 Dec 2015 15:14:25 +0100 Subject: Reduce dependency of python code on libastra --- python/astra/utils.pyx | 82 +++++++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 77 insertions(+), 5 deletions(-) (limited to 'python') diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx index 9871ac6..07727ce 100644 --- a/python/astra/utils.pyx +++ b/python/astra/utils.pyx @@ -29,8 +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.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 @@ -39,9 +44,6 @@ 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() @@ -93,7 +95,7 @@ cdef void readDict(XMLNode root, _dc): dc = convert_item(_dc) for item in dc: val = dc[item] - if isinstance(val, list) or isinstance(val, tuple): + if isinstance(val, __builtins__.list) or isinstance(val, tuple): val = np.array(val,dtype=np.float64) if isinstance(val, np.ndarray): if val.size == 0: @@ -129,7 +131,7 @@ cdef void readOptions(XMLNode node, dc): val = dc[item] if node.hasOption(item): raise Exception('Duplicate Option: %s' % item) - if isinstance(val, list) or isinstance(val, tuple): + if isinstance(val, __builtins__.list) or isinstance(val, tuple): val = np.array(val,dtype=np.float64) if isinstance(val, np.ndarray): if val.size == 0: @@ -149,3 +151,73 @@ 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": + if subnode.hasAttribute('value'): + opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getAttribute('value')) + else: + opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getContent()) + else: + dct[castString(subnode.getName())] = stringToPythonValue(subnode.getContent()) + inc(it) + if len(opts)>0: dct['options'] = opts + return dct -- cgit v1.2.3 From e07449189a05e3bcdc8ad4a9fbb95c0751f567bb Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Fri, 4 Dec 2015 15:15:16 +0100 Subject: Add sample for experimental composite geometry code --- python/astra/PyIncludes.pxd | 2 ++ python/astra/experimental.pyx | 84 +++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 python/astra/experimental.pyx (limited to 'python') diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd index 35dea5f..e9e2bdb 100644 --- a/python/astra/PyIncludes.pxd +++ b/python/astra/PyIncludes.pxd @@ -224,6 +224,7 @@ cdef extern from "astra/Float32VolumeData3DMemory.h" namespace "astra": int getRowCount() int getColCount() int getSliceCount() + bool isInitialized() @@ -255,6 +256,7 @@ 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/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 . +# +#----------------------------------------------------------------------- + +# 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" (CFloat32Data3D * ) except NULL + CFloat32ProjectionData3DMemory * dynamic_cast_proj_mem "dynamic_cast" (CFloat32Data3D * ) except NULL + +cimport PyProjector3DManager +from .PyProjector3DManager cimport CProjector3DManager +cimport PyData3DManager +from .PyData3DManager cimport CData3DManager + +cdef CProjector3DManager * manProj = PyProjector3DManager.getSingletonPtr() +cdef CData3DManager * man3d = 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") -- cgit v1.2.3 From b7c5deba2182514ffd6af61bac65ec9e0c0ebfd7 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Wed, 10 Jun 2015 12:45:52 -0500 Subject: Add conda build scripts --- python/conda/build.sh | 16 ++++++++++++++++ python/conda/meta.yaml | 40 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 python/conda/build.sh create mode 100644 python/conda/meta.yaml (limited to 'python') 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 == '' ] + 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..45ea812 --- /dev/null +++ b/python/conda/meta.yaml @@ -0,0 +1,40 @@ +package: + name: astra-toolbox + version: '1.6' + +source: + git_url: https://github.com/astra-toolbox/astra-toolbox.git + git_tag: v1.6 + +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 -- cgit v1.2.3 From 8603f9a768c99b18eb74aff13a015fc60fa57ea6 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Fri, 4 Dec 2015 16:20:35 +0100 Subject: Update version to 1.7 --- python/builder.py | 2 +- python/conda/meta.yaml | 4 ++-- python/docSRC/conf.py | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) (limited to 'python') diff --git a/python/builder.py b/python/builder.py index 44d9c3b..5322182 100644 --- a/python/builder.py +++ b/python/builder.py @@ -71,7 +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/meta.yaml b/python/conda/meta.yaml index 45ea812..e1adc83 100644 --- a/python/conda/meta.yaml +++ b/python/conda/meta.yaml @@ -1,10 +1,10 @@ package: name: astra-toolbox - version: '1.6' + version: '1.7' source: git_url: https://github.com/astra-toolbox/astra-toolbox.git - git_tag: v1.6 + git_tag: v1.7 build: number: 0 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. -- cgit v1.2.3 From 7362fccf97014538320f79cd4b58fc69ab04d648 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Thu, 10 Dec 2015 15:11:04 +0100 Subject: Use less ambiguous letters for create_vol_geom docs --- python/astra/creators.py | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) (limited to 'python') diff --git a/python/astra/creators.py b/python/astra/creators.py index f3474d8..bcacf00 100644 --- a/python/astra/creators.py +++ b/python/astra/creators.py @@ -57,23 +57,23 @@ This method can be called in a number of ways: ``create_vol_geom(N)``: :returns: A 2D volume geometry of size :math:`N \\times N`. -``create_vol_geom((M, N))``: - :returns: A 2D volume geometry of size :math:`M \\times N`. +``create_vol_geom((Y, X))``: + :returns: A 2D volume geometry of size :math:`Y \\times X`. -``create_vol_geom(M, N)``: - :returns: A 2D volume geometry of size :math:`M \\times N`. +``create_vol_geom(Y, X)``: + :returns: A 2D volume geometry of size :math:`Y \\times X`. -``create_vol_geom(M, N, minx, maxx, miny, maxy)``: - :returns: A 2D volume geometry of size :math:`M \\times N`, windowed as :math:`minx \\leq x \\leq maxx` and :math:`miny \\leq y \\leq maxy`. +``create_vol_geom(Y, X, minx, maxx, miny, maxy)``: + :returns: A 2D volume geometry of size :math:`Y \\times X`, windowed as :math:`minx \\leq x \\leq maxx` and :math:`miny \\leq y \\leq maxy`. -``create_vol_geom((M, N, Z))``: - :returns: A 3D volume geometry of size :math:`M \\times N \\times Z`. +``create_vol_geom((Y, X, Z))``: + :returns: A 3D volume geometry of size :math:`Y \\times X \\times Z`. -``create_vol_geom(M, N, Z)``: - :returns: A 3D volume geometry of size :math:`M \\times N \\times Z`. +``create_vol_geom(Y, X, Z)``: + :returns: A 3D volume geometry of size :math:`Y \\times X \\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` . +``create_vol_geom(Y, X, Z, minx, maxx, miny, maxy, minz, maxz)``: + :returns: A 3D volume geometry of size :math:`Y \\times X \\times Z`, windowed as :math:`minx \\leq x \\leq maxx` and :math:`miny \\leq y \\leq maxy` and :math:`minz \\leq z \\leq maxz` . """ -- cgit v1.2.3 From 823bdc90b6d4ebf5acade43ad909805053c8974e Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 16 Dec 2015 18:09:38 +0100 Subject: Fix origin_det name in create_proj_geom docs --- python/astra/creators.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) (limited to 'python') diff --git a/python/astra/creators.py b/python/astra/creators.py index bcacf00..18504ea 100644 --- a/python/astra/creators.py +++ b/python/astra/creators.py @@ -156,7 +156,7 @@ This method can be called in a number of ways: :returns: A parallel projection geometry. -``create_proj_geom('fanflat', det_width, det_count, angles, source_origin, source_det)``: +``create_proj_geom('fanflat', det_width, det_count, angles, source_origin, origin_det)``: :param det_width: Size of a detector pixel. :type det_width: :class:`float` @@ -165,7 +165,7 @@ This method can be called in a number of ways: :param angles: Array of angles in radians. :type angles: :class:`numpy.ndarray` :param source_origin: Position of the source. -:param source_det: Position of the detector +:param origin_det: Position of the detector :returns: A fan-beam projection geometry. ``create_proj_geom('fanflat_vec', det_count, V)``: @@ -188,7 +188,7 @@ This method can be called in a number of ways: :type angles: :class:`numpy.ndarray` :returns: A parallel projection geometry. -``create_proj_geom('cone', detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles, source_origin, source_det)``: +``create_proj_geom('cone', detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles, source_origin, origin_det)``: :param detector_spacing_*: Distance between two adjacent detector pixels. :type detector_spacing_*: :class:`float` @@ -200,8 +200,8 @@ This method can be called in a number of ways: :type angles: :class:`numpy.ndarray` :param source_origin: Distance between point source and origin. :type source_origin: :class:`float` -:param source_det: Distance between the detector and origin. -:type source_det: :class:`float` +:param origin_det: Distance between the detector and origin. +:type origin_det: :class:`float` :returns: A cone-beam projection geometry. ``create_proj_geom('cone_vec', det_row_count, det_col_count, V)``: @@ -244,7 +244,7 @@ This method can be called in a number of ways: return {'type': 'parallel', 'DetectorWidth': args[0], 'DetectorCount': args[1], 'ProjectionAngles': args[2]} elif intype == 'fanflat': if len(args) < 5: - raise Exception('not enough variables: astra_create_proj_geom(fanflat, det_width, det_count, angles, source_origin, source_det)') + raise Exception('not enough variables: astra_create_proj_geom(fanflat, det_width, det_count, angles, source_origin, origin_det)') return {'type': 'fanflat', 'DetectorWidth': args[0], 'DetectorCount': args[1], 'ProjectionAngles': args[2], 'DistanceOriginSource': args[3], 'DistanceOriginDetector': args[4]} elif intype == 'fanflat_vec': if len(args) < 2: @@ -258,7 +258,7 @@ This method can be called in a number of ways: return {'type':'parallel3d', 'DetectorSpacingX':args[0], 'DetectorSpacingY':args[1], 'DetectorRowCount':args[2], 'DetectorColCount':args[3],'ProjectionAngles':args[4]} elif intype == 'cone': if len(args) < 7: - raise Exception('not enough variables: astra_create_proj_geom(cone, detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles, source_origin, source_det)') + raise Exception('not enough variables: astra_create_proj_geom(cone, detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles, source_origin, origin_det)') return {'type': 'cone','DetectorSpacingX':args[0], 'DetectorSpacingY':args[1], 'DetectorRowCount':args[2],'DetectorColCount':args[3],'ProjectionAngles':args[4],'DistanceOriginSource': args[5],'DistanceOriginDetector':args[6]} elif intype == 'cone_vec': if len(args) < 3: -- cgit v1.2.3 From 3aabe41914a93d4c9afbc1a6cc498156924cbf18 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 23 Dec 2015 10:47:37 +0100 Subject: Update version to 1.7.1 --- python/builder.py | 2 +- python/conda/meta.yaml | 4 ++-- python/docSRC/conf.py | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) (limited to 'python') diff --git a/python/builder.py b/python/builder.py index 5322182..018b26b 100644 --- a/python/builder.py +++ b/python/builder.py @@ -71,7 +71,7 @@ ext_modules = cythonize("astra/*.pyx", language_level=2) cmdclass = { 'build_ext': build_ext } setup (name = 'PyASTRAToolbox', - version = '1.7', + version = '1.7.1', description = 'Python interface to the ASTRA-Toolbox', author='D.M. Pelt', author_email='D.M.Pelt@cwi.nl', diff --git a/python/conda/meta.yaml b/python/conda/meta.yaml index e1adc83..41250dc 100644 --- a/python/conda/meta.yaml +++ b/python/conda/meta.yaml @@ -1,10 +1,10 @@ package: name: astra-toolbox - version: '1.7' + version: '1.7.1' source: git_url: https://github.com/astra-toolbox/astra-toolbox.git - git_tag: v1.7 + git_tag: v1.7.1 build: number: 0 diff --git a/python/docSRC/conf.py b/python/docSRC/conf.py index cc95a80..78f7d42 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 = '1.7' +version = '1.7.1' # The full version, including alpha/beta/rc tags. -release = '1.7' +release = '1.7.1' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. -- cgit v1.2.3 From 62f66d27fc4d2b3c61e3f18ad14eeac742cb96ec Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Tue, 5 Jan 2016 16:32:26 +0100 Subject: Update credits --- python/astra/astra_c.pyx | 28 +++++++++++++--------------- 1 file changed, 13 insertions(+), 15 deletions(-) (limited to 'python') diff --git a/python/astra/astra_c.pyx b/python/astra/astra_c.pyx index 342a214..6b246b6 100644 --- a/python/astra/astra_c.pyx +++ b/python/astra/astra_c.pyx @@ -45,21 +45,19 @@ ELSE: pass def credits(): - six.print_(""" -All Scale Tomographic Reconstruction Antwerp Toolbox (ASTRA-Toolbox) -was developed at the University of Antwerp by - * Prof. dr. Joost Batenburg - * Andrei Dabravolski - * Gert Merckx - * Willem Jan Palenstijn - * Tom Roelandts - * Prof. dr. Jan Sijbers - * dr. Wim van Aarle - * Sander van der Maar - * dr. Gert Van Gompel - -Python interface written by - * Daniel M. Pelt (CWI, Amsterdam)""") + six.print_("""The ASTRA Toolbox has been developed at the University of Antwerp and CWI, Amsterdam by + * Prof. dr. Joost Batenburg + * Prof. dr. Jan Sijbers + * Dr. Jeroen Bedorf + * Dr. Folkert Bleichrodt + * Dr. Andrei Dabravolski + * Dr. Willem Jan Palenstijn + * Dr. Tom Roelandts + * Dr. Wim van Aarle + * Dr. Gert Van Gompel + * Sander van der Maar, MSc. + * Gert Merckx, MSc. + * Daan Pelt, MSc.""") def use_cuda(): -- cgit v1.2.3 From bf01d83ac9e57aacbc5d0a99d026327a7239c501 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Tue, 19 Jan 2016 13:24:03 +0100 Subject: Fix experimental.pyx for non-CUDA compilation --- python/astra/experimental.pyx | 96 ++++++++++++++++++++++--------------------- 1 file changed, 49 insertions(+), 47 deletions(-) (limited to 'python') diff --git a/python/astra/experimental.pyx b/python/astra/experimental.pyx index da27504..aafc002 100644 --- a/python/astra/experimental.pyx +++ b/python/astra/experimental.pyx @@ -28,57 +28,59 @@ include "config.pxi" -import six -from .PyIncludes cimport * -from libcpp.vector cimport vector +IF HAVE_CUDA==True: -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 *]) + import six + from .PyIncludes cimport * + from libcpp.vector cimport vector -cdef extern from *: - CFloat32VolumeData3DMemory * dynamic_cast_vol_mem "dynamic_cast" (CFloat32Data3D * ) except NULL - CFloat32ProjectionData3DMemory * dynamic_cast_proj_mem "dynamic_cast" (CFloat32Data3D * ) except NULL + 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 *]) -cimport PyProjector3DManager -from .PyProjector3DManager cimport CProjector3DManager -cimport PyData3DManager -from .PyData3DManager cimport CData3DManager + cdef extern from *: + CFloat32VolumeData3DMemory * dynamic_cast_vol_mem "dynamic_cast" (CFloat32Data3D * ) except NULL + CFloat32ProjectionData3DMemory * dynamic_cast_proj_mem "dynamic_cast" (CFloat32Data3D * ) except NULL -cdef CProjector3DManager * manProj = PyProjector3DManager.getSingletonPtr() -cdef CData3DManager * man3d = PyData3DManager.getSingletonPtr() + cimport PyProjector3DManager + from .PyProjector3DManager cimport CProjector3DManager + cimport PyData3DManager + from .PyData3DManager cimport CData3DManager -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") + cdef CProjector3DManager * manProj = PyProjector3DManager.getSingletonPtr() + cdef CData3DManager * man3d = PyData3DManager.getSingletonPtr() -def do_composite_FP(projector_id, vol_ids, proj_ids): - do_composite(projector_id, vol_ids, proj_ids, "FP") + 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_BP(projector_id, vol_ids, proj_ids): - do_composite(projector_id, vol_ids, proj_ids, "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") -- cgit v1.2.3 From 943fed8b702b80dad720a285679efd837c257f7b Mon Sep 17 00:00:00 2001 From: "Daniel M. 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Navigation

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-

Helper class: the ASTRAProjector module¶

-
-
-class astra.ASTRAProjector.ASTRAProjector2D(proj_geom, vol_geom, proj_type, useCUDA=False)[source]¶
-

Bases: builtins.object

-

Helps with various common ASTRA Toolbox 2D operations.

-

This class can perform several often used toolbox operations, such as:

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  • Forward projecting
    • -
  • Back projecting
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  • Reconstructing
    • -
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Note that this class has a some computational overhead, because it -copies a lot of data. If you use many repeated operations, directly -using the PyAstraToolbox methods directly is faster.

-

You can use this class as an abstracted weight matrix \(W\): multiplying an instance -proj of this class by an image results in a forward projection of the image, and multiplying -proj.T by a sinogram results in a backprojection of the sinogram:

-
proj = ASTRAProjector2D(...)
-fp = proj*image
-bp = proj.T*sinogram
-
-
- --- - - - -
Parameters:
    -
  • proj_geom (dict) – The projection geometry.
    • -
  • vol_geom (dict) – The volume geometry.
    • -
  • proj_type (string) – Projector type, such as 'line', 'linear', ...
    • -
  • useCUDA (bool) – If True, use CUDA for calculations, when possible.
    • -
-
-
-
-backProject(data)[source]¶
-

Backproject a sinogram.

- --- - - - - - -
Parameters:data (numpy.ndarray or int) – The sinogram data or ID.
Returns:numpy.ndarray – The backprojection.
-
- -
-
-forwardProject(data)[source]¶
-

Forward project an image.

- --- - - - - - -
Parameters:data (numpy.ndarray or int) – The image data or ID.
Returns:numpy.ndarray – The forward projection.
-
- -
-
-reconstruct(data, method, **kwargs)[source]¶
-

Reconstruct an image from a sinogram.

- --- - - - - - -
Parameters: -
Returns:

numpy.ndarray – The reconstruction.

-
-

Example of a SIRT reconstruction using CUDA:

-
proj = ASTRAProjector2D(...)
-rec = proj.reconstruct(sinogram,'SIRT_CUDA',iterations=1000)
-
-
-
- -
- -
-
-class astra.ASTRAProjector.ASTRAProjector2DTranspose(parentProj)[source]¶
-

Bases: builtins.object

-

Implements the proj.T functionality.

-

Do not use directly, since it can be accessed as member .T of -an ASTRAProjector2D object.

-
- -
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-

Additional functions: the functions module

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Source code for astra.ASTRAProjector

-#-----------------------------------------------------------------------
-#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/>.
-#
-#-----------------------------------------------------------------------
-
-import math
-from . import creators as ac
-from . import data2d
-
-
-
[docs]class ASTRAProjector2DTranspose():
-    """Implements the ``proj.T`` functionality.
-
-    Do not use directly, since it can be accessed as member ``.T`` of
-    an :class:`ASTRAProjector2D` object.
-
-    """
-    def __init__(self, parentProj):
-        self.parentProj = parentProj
-
-    def __mul__(self, data):
-        return self.parentProj.backProject(data)
-
-

-
[docs]class ASTRAProjector2D(object):
-    """Helps with various common ASTRA Toolbox 2D operations.
-
-    This class can perform several often used toolbox operations, such as:
-
-    * Forward projecting
-    * Back projecting
-    * Reconstructing
-
-    Note that this class has a some computational overhead, because it
-    copies a lot of data. If you use many repeated operations, directly
-    using the PyAstraToolbox methods directly is faster.
-
-    You can use this class as an abstracted weight matrix :math:`W`: multiplying an instance
-    ``proj`` of this class by an image results in a forward projection of the image, and multiplying
-    ``proj.T`` by a sinogram results in a backprojection of the sinogram::
-
-        proj = ASTRAProjector2D(...)
-        fp = proj*image
-        bp = proj.T*sinogram
-
-    :param proj_geom: The projection geometry.
-    :type proj_geom: :class:`dict`
-    :param vol_geom: The volume geometry.
-    :type vol_geom: :class:`dict`
-    :param proj_type: Projector type, such as ``'line'``, ``'linear'``, ...
-    :type proj_type: :class:`string`
-    :param useCUDA: If ``True``, use CUDA for calculations, when possible.
-    :type useCUDA: :class:`bool`
-    """
-
-    def __init__(self, proj_geom, vol_geom, proj_type, useCUDA=False):
-        self.vol_geom = vol_geom
-        self.recSize = vol_geom['GridColCount']
-        self.angles = proj_geom['ProjectionAngles']
-        self.nDet = proj_geom['DetectorCount']
-        nexpow = int(pow(2, math.ceil(math.log(2 * self.nDet, 2))))
-        self.filterSize = nexpow / 2 + 1
-        self.nProj = self.angles.shape[0]
-        self.proj_geom = proj_geom
-        self.proj_id = ac.create_projector(proj_type, proj_geom, vol_geom)
-        self.useCUDA = useCUDA
-        self.T = ASTRAProjector2DTranspose(self)
-
-
[docs]    def backProject(self, data):
-        """Backproject a sinogram.
-
-        :param data: The sinogram data or ID.
-        :type data: :class:`numpy.ndarray` or :class:`int`
-        :returns: :class:`numpy.ndarray` -- The backprojection.
-
-        """
-        vol_id, vol = ac.create_backprojection(
-            data, self.proj_id, useCUDA=self.useCUDA, returnData=True)
-        data2d.delete(vol_id)
-        return vol
-

-
[docs]    def forwardProject(self, data):
-        """Forward project an image.
-
-        :param data: The image data or ID.
-        :type data: :class:`numpy.ndarray` or :class:`int`
-        :returns: :class:`numpy.ndarray` -- The forward projection.
-
-        """
-        sin_id, sino = ac.create_sino(data, self.proj_id, useCUDA=self.useCUDA, returnData=True)
-        data2d.delete(sin_id)
-        return sino
-

-
[docs]    def reconstruct(self, data, method, **kwargs):
-        """Reconstruct an image from a sinogram.
-
-        :param data: The sinogram data or ID.
-        :type data: :class:`numpy.ndarray` or :class:`int`
-        :param method: Name of the reconstruction algorithm.
-        :type method: :class:`string`
-        :param kwargs: Additional named parameters to pass to :func:`astra.creators.create_reconstruction`.
-        :returns: :class:`numpy.ndarray` -- The reconstruction.
-
-        Example of a SIRT reconstruction using CUDA::
-
-            proj = ASTRAProjector2D(...)
-            rec = proj.reconstruct(sinogram,'SIRT_CUDA',iterations=1000)
-
-        """
-        kwargs['returnData'] = True
-        rec_id, rec = ac.create_reconstruction(
-            method, self.proj_id, data, **kwargs)
-        data2d.delete(rec_id)
-        return rec
-

-    def __mul__(self, data):
-        return self.forwardProject(data)

-
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- - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/algorithm.html b/python/docSRC/_build/html/_modules/astra/algorithm.html deleted file mode 100644 index 39816fd..0000000 --- a/python/docSRC/_build/html/_modules/astra/algorithm.html +++ /dev/null @@ -1,181 +0,0 @@ - - - - - - - - astra.algorithm — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - -
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Source code for astra.algorithm

-#-----------------------------------------------------------------------
-#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 algorithm_c as a
-
-
[docs]def create(config):
-    """Create algorithm object.
-    
-    :param config: Algorithm options.
-    :type config: :class:`dict`
-    :returns: :class:`int` -- the ID of the constructed object.
-    
-    """
-    return a.create(config)
-

-
[docs]def run(i, iterations=1):
-    """Run an algorithm.
-    
-    :param i: ID of object.
-    :type i: :class:`int`
-    :param iterations: Number of iterations to run.
-    :type iterations: :class:`int`
-    
-    """
-    return a.run(i,iterations)
-

-
[docs]def get_res_norm(i):
-    """Get residual norm of algorithm.
-    
-    :param i: ID of object.
-    :type i: :class:`int`
-    :returns: :class:`float` -- The residual norm.
-    
-    """
-    
-    return a.get_res_norm(i)
-    

-
[docs]def delete(ids):
-    """Delete a matrix object.
-    
-    :param ids: ID or list of ID's to delete.
-    :type ids: :class:`int` or :class:`list`
-    
-    """
-    return a.delete(ids)
-

-
[docs]def clear():
-    """Clear all matrix objects."""
-    return a.clear()
-

-
[docs]def info():
-    """Print info on matrix objects in memory."""
-    return a.info()

-
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- - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/astra.html b/python/docSRC/_build/html/_modules/astra/astra.html deleted file mode 100644 index 53fac8e..0000000 --- a/python/docSRC/_build/html/_modules/astra/astra.html +++ /dev/null @@ -1,163 +0,0 @@ - - - - - - - - astra.astra — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - -
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Source code for astra.astra

-#-----------------------------------------------------------------------
-#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 astra_c as a
-
-
[docs]def credits():
-    """Print credits of the ASTRA Toolbox."""
-    return a.credits()
-
-

-
[docs]def use_cuda():
-    """Test if CUDA is enabled.
-    
-    :returns: :class:`bool` -- ``True`` if CUDA is enabled.
-    """
-    return a.use_cuda()
-
-

-
[docs]def version(printToScreen=False):
-    """Check version of the ASTRA Toolbox.
-    
-    :param printToScreen: If ``True``, print version string. If ``False``, return version integer.
-    :type printToScreen: :class:`bool`
-    :returns: :class:`string` or :class:`int` -- The version string or integer.
-    
-    """
-    return a.version(printToScreen)
-

-
[docs]def set_gpu_index(idx):
-    """Set default GPU index to use.
-    
-    :param idx: GPU index
-    :type idx: :class:`int`
-    """
-    a.set_gpu_index(idx)

-
- -
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-

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Source code for astra.creators

-#-----------------------------------------------------------------------
-#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/>.
-#
-#-----------------------------------------------------------------------
-
-import six
-import numpy as np
-import math
-from . import data2d
-from . import data3d
-from . import projector
-from . import algorithm
-
-
[docs]def astra_dict(intype):
-    """Creates a dict to use with the ASTRA Toolbox.
-    
-    :param intype: Type of the ASTRA object.
-    :type intype: :class:`string`
-    :returns: :class:`dict` -- An ASTRA dict of type ``intype``.
-    
-    """
-    if intype == 'SIRT_CUDA2':
-        intype = 'SIRT_CUDA'
-        six.print_('SIRT_CUDA2 has been deprecated. Use SIRT_CUDA instead.')
-    elif intype == 'FP_CUDA2':
-        intype = 'FP_CUDA'
-        six.print_('FP_CUDA2 has been deprecated. Use FP_CUDA instead.')
-    return {'type': intype}
-

-
[docs]def create_vol_geom(*varargin):
-    """Create a volume geometry structure.
-
-This method can be called in a number of ways:
-
-``create_vol_geom(N)``:
-    :returns: A 2D volume geometry of size :math:`N \\times N`.
-
-``create_vol_geom((M, N))``:
-    :returns: A 2D volume geometry of size :math:`M \\times N`.
-
-``create_vol_geom(M, N)``:
-    :returns: A 2D volume geometry of size :math:`M \\times N`.
-
-``create_vol_geom(M, N, minx, maxx, miny, maxy)``:
-    :returns: A 2D volume geometry of size :math:`M \\times N`, windowed as :math:`minx \\leq x \\leq maxx` and :math:`miny \\leq y \\leq maxy`.
-
-``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)``:
-    :returns: A 3D volume geometry of size :math:`M \\times N \\times Z`.
-
-"""
-    vol_geom = {'option': {}}
-    # astra_create_vol_geom(row_count)
-    if len(varargin) == 1 and isinstance(varargin[0], int) == 1:
-        vol_geom['GridRowCount'] = varargin[0]
-        vol_geom['GridColCount'] = varargin[0]
-        vol_geom['option']['WindowMinX'] = -varargin[0] / 2.
-        vol_geom['option']['WindowMaxX'] = varargin[0] / 2.
-        vol_geom['option']['WindowMinY'] = -varargin[0] / 2.
-        vol_geom['option']['WindowMaxY'] = varargin[0] / 2.
-    # astra_create_vol_geom([row_count col_count])
-    elif len(varargin) == 1 and len(varargin[0]) == 2:
-        vol_geom['GridRowCount'] = varargin[0][0]
-        vol_geom['GridColCount'] = varargin[0][1]
-        vol_geom['option']['WindowMinX'] = -varargin[0][1] / 2.
-        vol_geom['option']['WindowMaxX'] = varargin[0][1] / 2.
-        vol_geom['option']['WindowMinY'] = -varargin[0][0] / 2.
-        vol_geom['option']['WindowMaxY'] = varargin[0][0] / 2.
-    # astra_create_vol_geom([row_count col_count slice_count])
-    elif len(varargin) == 1 and len(varargin[0]) == 3:
-        vol_geom['GridRowCount'] = varargin[0][0]
-        vol_geom['GridColCount'] = varargin[0][1]
-        vol_geom['GridSliceCount'] = varargin[0][2]
-        vol_geom['option']['WindowMinX'] = -varargin[0][1] / 2.
-        vol_geom['option']['WindowMaxX'] = varargin[0][1] / 2.
-        vol_geom['option']['WindowMinY'] = -varargin[0][0] / 2.
-        vol_geom['option']['WindowMaxY'] = varargin[0][0] / 2.
-        vol_geom['option']['WindowMinZ'] = -varargin[0][2] / 2.
-        vol_geom['option']['WindowMaxZ'] = varargin[0][2] / 2.
-    # astra_create_vol_geom(row_count, col_count)
-    elif len(varargin) == 2:
-        vol_geom['GridRowCount'] = varargin[0]
-        vol_geom['GridColCount'] = varargin[1]
-        vol_geom['option']['WindowMinX'] = -varargin[1] / 2.
-        vol_geom['option']['WindowMaxX'] = varargin[1] / 2.
-        vol_geom['option']['WindowMinY'] = -varargin[0] / 2.
-        vol_geom['option']['WindowMaxY'] = varargin[0] / 2.
-    # astra_create_vol_geom(row_count, col_count, min_x, max_x, min_y, max_y)
-    elif len(varargin) == 6:
-        vol_geom['GridRowCount'] = varargin[0]
-        vol_geom['GridColCount'] = varargin[1]
-        vol_geom['option']['WindowMinX'] = varargin[2]
-        vol_geom['option']['WindowMaxX'] = varargin[3]
-        vol_geom['option']['WindowMinY'] = varargin[4]
-        vol_geom['option']['WindowMaxY'] = varargin[5]
-    # astra_create_vol_geom(row_count, col_count, slice_count)
-    elif len(varargin) == 3:
-        vol_geom['GridRowCount'] = varargin[0]
-        vol_geom['GridColCount'] = varargin[1]
-        vol_geom['GridSliceCount'] = varargin[2]
-    return vol_geom
-
-

-
[docs]def create_proj_geom(intype, *args):
-    """Create a projection geometry.
-
-This method can be called in a number of ways:
-
-``create_proj_geom('parallel', detector_spacing, det_count, angles)``:
-
-:param detector_spacing: Distance between two adjacent detector pixels.
-:type detector_spacing: :class:`float`
-:param det_count: Number of detector pixels.
-:type det_count: :class:`int`
-:param angles: Array of angles in radians.
-:type angles: :class:`numpy.ndarray`
-:returns: A parallel projection geometry.
-
-
-``create_proj_geom('fanflat', det_width, det_count, angles, source_origin, source_det)``:
-
-:param det_width: Size of a detector pixel.
-:type det_width: :class:`float`
-:param det_count: Number of detector pixels.
-:type det_count: :class:`int`
-:param angles: Array of angles in radians.
-:type angles: :class:`numpy.ndarray`
-:param source_origin: Position of the source.
-:param source_det: Position of the detector
-:returns: A fan-beam projection geometry.
-
-``create_proj_geom('fanflat_vec', det_count, V)``:
-
-:param det_count: Number of detector pixels.
-:type det_count: :class:`int`
-:param V: Vector array.
-:type V: :class:`numpy.ndarray`
-:returns: A fan-beam projection geometry.
-
-``create_proj_geom('parallel3d', detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles)``:
-
-:param detector_spacing_*: Distance between two adjacent detector pixels.
-:type detector_spacing_*: :class:`float`
-:param det_row_count: Number of detector pixel rows.
-:type det_row_count: :class:`int`
-:param det_col_count: Number of detector pixel columns.
-:type det_col_count: :class:`int`
-:param angles: Array of angles in radians.
-:type angles: :class:`numpy.ndarray`
-:returns: A parallel projection geometry.
-
-``create_proj_geom('cone', detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles, source_origin, source_det)``:
-
-:param detector_spacing_*: Distance between two adjacent detector pixels.
-:type detector_spacing_*: :class:`float`
-:param det_row_count: Number of detector pixel rows.
-:type det_row_count: :class:`int`
-:param det_col_count: Number of detector pixel columns.
-:type det_col_count: :class:`int`
-:param angles: Array of angles in radians.
-:type angles: :class:`numpy.ndarray`
-:param source_origin: Distance between point source and origin.
-:type source_origin: :class:`float`
-:param source_det: Distance between the detector and origin.
-:type source_det: :class:`float`
-:returns: A cone-beam projection geometry.
-
-``create_proj_geom('cone_vec', det_row_count, det_col_count, V)``:
-
-:param det_row_count: Number of detector pixel rows.
-:type det_row_count: :class:`int`
-:param det_col_count: Number of detector pixel columns.
-:type det_col_count: :class:`int`
-:param V: Vector array.
-:type V: :class:`numpy.ndarray`
-:returns: A cone-beam projection geometry.
-
-``create_proj_geom('parallel3d_vec', det_row_count, det_col_count, V)``:
-
-:param det_row_count: Number of detector pixel rows.
-:type det_row_count: :class:`int`
-:param det_col_count: Number of detector pixel columns.
-:type det_col_count: :class:`int`
-:param V: Vector array.
-:type V: :class:`numpy.ndarray`
-:returns: A parallel projection geometry.
-
-``create_proj_geom('sparse_matrix', det_width, det_count, angles, matrix_id)``:
-
-:param det_width: Size of a detector pixel.
-:type det_width: :class:`float`
-:param det_count: Number of detector pixels.
-:type det_count: :class:`int`
-:param angles: Array of angles in radians.
-:type angles: :class:`numpy.ndarray`
-:param matrix_id: ID of the sparse matrix.
-:type matrix_id: :class:`int`
-:returns: A projection geometry based on a sparse matrix.
-
-"""
-    if intype == 'parallel':
-        if len(args) < 3:
-            raise Exception(
-                'not enough variables: astra_create_proj_geom(parallel, detector_spacing, det_count, angles)')
-        return {'type': 'parallel', 'DetectorWidth': args[0], 'DetectorCount': args[1], 'ProjectionAngles': args[2]}
-    elif intype == 'fanflat':
-        if len(args) < 5:
-            raise Exception('not enough variables: astra_create_proj_geom(fanflat, det_width, det_count, angles, source_origin, source_det)')
-        return {'type': 'fanflat', 'DetectorWidth': args[0], 'DetectorCount': args[1], 'ProjectionAngles': args[2], 'DistanceOriginSource': args[3], 'DistanceOriginDetector': args[4]}
-    elif intype == 'fanflat_vec':
-        if len(args) < 2:
-            raise Exception('not enough variables: astra_create_proj_geom(fanflat_vec, det_count, V)')
-        if not args[1].shape[1] == 6:
-            raise Exception('V should be a Nx6 matrix, with N the number of projections')
-        return {'type':'fanflat_vec', 'DetectorCount':args[0], 'Vectors':args[1]}
-    elif intype == 'parallel3d':
-        if len(args) < 5:
-            raise Exception('not enough variables: astra_create_proj_geom(parallel3d, detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles)')
-        return {'type':'parallel3d', 'DetectorSpacingX':args[0], 'DetectorSpacingY':args[1], 'DetectorRowCount':args[2], 'DetectorColCount':args[3],'ProjectionAngles':args[4]}
-    elif intype == 'cone':
-        if len(args) < 7:
-            raise Exception('not enough variables: astra_create_proj_geom(cone, detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles, source_origin, source_det)')
-        return {'type':	'cone','DetectorSpacingX':args[0], 'DetectorSpacingY':args[1], 'DetectorRowCount':args[2],'DetectorColCount':args[3],'ProjectionAngles':args[4],'DistanceOriginSource':	args[5],'DistanceOriginDetector':args[6]}
-    elif intype == 'cone_vec':
-        if len(args) < 3:
-            raise Exception('not enough variables: astra_create_proj_geom(cone_vec, det_row_count, det_col_count, V)')
-        if not args[2].shape[1] == 12:
-            raise Exception('V should be a Nx12 matrix, with N the number of projections')
-        return {'type': 'cone_vec','DetectorRowCount':args[0],'DetectorColCount':args[1],'Vectors':args[2]}
-    elif intype == 'parallel3d_vec':
-        if len(args) < 3:
-            raise Exception('not enough variables: astra_create_proj_geom(parallel3d_vec, det_row_count, det_col_count, V)')
-        if not args[2].shape[1] == 12:
-            raise Exception('V should be a Nx12 matrix, with N the number of projections')
-        return {'type': 'parallel3d_vec','DetectorRowCount':args[0],'DetectorColCount':args[1],'Vectors':args[2]}    
-    elif intype == 'sparse_matrix':
-        if len(args) < 4:
-            raise Exception(
-                'not enough variables: astra_create_proj_geom(sparse_matrix, det_width, det_count, angles, matrix_id)')
-        return {'type': 'sparse_matrix', 'DetectorWidth': args[0], 'DetectorCount': args[1], 'ProjectionAngles': args[2], 'MatrixID': args[3]}
-    else:
-        raise Exception('Error: unknown type ' + intype) 
-
-

-
[docs]def create_backprojection(data, proj_id, useCUDA=False, returnData=True):
-    """Create a backprojection of a sinogram (2D).
-
-:param data: Sinogram data or ID.
-:type data: :class:`numpy.ndarray` or :class:`int`
-:param proj_id: ID of the projector to use.
-:type proj_id: :class:`int`
-:param useCUDA: If ``True``, use CUDA for the calculation.
-:type useCUDA: :class:`bool`
-:param returnData: If False, only return the ID of the backprojection.
-:type returnData: :class:`bool`
-:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order.
-
-"""
-    proj_geom = projector.projection_geometry(proj_id)
-    vol_geom = projector.volume_geometry(proj_id)
-    if isinstance(data, np.ndarray):
-        sino_id = data2d.create('-sino', proj_geom, data)
-    else:
-        sino_id = data
-    vol_id = data2d.create('-vol', vol_geom, 0)
-
-    algString = 'BP'
-    if useCUDA:
-        algString = algString + '_CUDA'
-
-    cfg = astra_dict(algString)
-    if not useCUDA:
-        cfg['ProjectorId'] = proj_id
-    cfg['ProjectionDataId'] = sino_id
-    cfg['ReconstructionDataId'] = vol_id
-    alg_id = algorithm.create(cfg)
-    algorithm.run(alg_id)
-    algorithm.delete(alg_id)
-
-    if isinstance(data, np.ndarray):
-        data2d.delete(sino_id)
-
-    if returnData:
-        return vol_id, data2d.get(vol_id)
-    else:
-        return vol_id
-

-
[docs]def create_backprojection3d_gpu(data, proj_geom, vol_geom, returnData=True):
-    """Create a backprojection of a sinogram (3D) using CUDA.
-
-:param data: Sinogram data or ID.
-:type data: :class:`numpy.ndarray` or :class:`int`
-:param proj_geom: Projection geometry.
-:type proj_geom: :class:`dict`
-:param vol_geom: Volume geometry.
-:type vol_geom: :class:`dict`
-:param returnData: If False, only return the ID of the backprojection.
-:type returnData: :class:`bool`
-:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order.
-
-"""
-    if isinstance(data, np.ndarray):
-        sino_id = data3d.create('-sino', proj_geom, data)
-    else:
-        sino_id = data
-
-    vol_id = data3d.create('-vol', vol_geom, 0)
-
-    cfg = astra_dict('BP3D_CUDA')
-    cfg['ProjectionDataId'] = sino_id
-    cfg['ReconstructionDataId'] = vol_id
-    alg_id = algorithm.create(cfg)
-    algorithm.run(alg_id)
-    algorithm.delete(alg_id)
-
-    if isinstance(data, np.ndarray):
-        data3d.delete(sino_id)
-
-    if returnData:
-        return vol_id, data3d.get(vol_id)
-    else:
-        return vol_id
-
-

-
[docs]def create_sino(data, proj_id=None, proj_geom=None, vol_geom=None,
-                useCUDA=False, returnData=True, gpuIndex=None):
-    """Create a forward projection of an image (2D).
-
-    :param data: Image data or ID.
-    :type data: :class:`numpy.ndarray` or :class:`int`
-    :param proj_id: ID of the projector to use.
-    :type proj_id: :class:`int`
-    :param proj_geom: Projection geometry.
-    :type proj_geom: :class:`dict`
-    :param vol_geom: Volume geometry.
-    :type vol_geom: :class:`dict`
-    :param useCUDA: If ``True``, use CUDA for the calculation.
-    :type useCUDA: :class:`bool`
-    :param returnData: If False, only return the ID of the forward projection.
-    :type returnData: :class:`bool`
-    :param gpuIndex: Optional GPU index.
-    :type gpuIndex: :class:`int`
-    :returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`)
-
-    If ``returnData=False``, returns the ID of the forward
-    projection. Otherwise, returns a tuple containing the ID of the
-    forward projection and the forward projection itself, in that
-    order.
-
-    The geometry of setup is defined by ``proj_id`` or with
-    ``proj_geom`` and ``vol_geom``. If ``proj_id`` is given, then
-    ``proj_geom`` and ``vol_geom`` must be None and vice versa.
-"""
-    if proj_id is not None:
-        proj_geom = projector.projection_geometry(proj_id)
-        vol_geom = projector.volume_geometry(proj_id)
-    elif proj_geom is not None and vol_geom is not None:
-        if not useCUDA:
-            # We need more parameters to create projector.
-            raise ValueError(
-                """A ``proj_id`` is needed when CUDA is not used.""")
-    else:
-        raise Exception("""The geometry setup is not defined.
-        The geometry of setup is defined by ``proj_id`` or with
-        ``proj_geom`` and ``vol_geom``. If ``proj_id`` is given, then
-        ``proj_geom`` and ``vol_geom`` must be None and vice versa.""")
-
-    if isinstance(data, np.ndarray):
-        volume_id = data2d.create('-vol', vol_geom, data)
-    else:
-        volume_id = data
-    sino_id = data2d.create('-sino', proj_geom, 0)
-    algString = 'FP'
-    if useCUDA:
-        algString = algString + '_CUDA'
-    cfg = astra_dict(algString)
-    if not useCUDA:
-        cfg['ProjectorId'] = proj_id
-    if gpuIndex is not None:
-        cfg['option'] = {'GPUindex': gpuIndex}
-    cfg['ProjectionDataId'] = sino_id
-    cfg['VolumeDataId'] = volume_id
-    alg_id = algorithm.create(cfg)
-    algorithm.run(alg_id)
-    algorithm.delete(alg_id)
-
-    if isinstance(data, np.ndarray):
-        data2d.delete(volume_id)
-    if returnData:
-        return sino_id, data2d.get(sino_id)
-    else:
-        return sino_id
-
-
-

-
[docs]def create_sino3d_gpu(data, proj_geom, vol_geom, returnData=True, gpuIndex=None):
-    """Create a forward projection of an image (3D).
-
-:param data: Image data or ID.
-:type data: :class:`numpy.ndarray` or :class:`int`
-:param proj_geom: Projection geometry.
-:type proj_geom: :class:`dict`
-:param vol_geom: Volume geometry.
-:type vol_geom: :class:`dict`
-:param returnData: If False, only return the ID of the forward projection.
-:type returnData: :class:`bool`
-:param gpuIndex: Optional GPU index.
-:type gpuIndex: :class:`int`
-:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the forward projection. Otherwise, returns a tuple containing the ID of the forward projection and the forward projection itself, in that order.
-
-"""
-
-    if isinstance(data, np.ndarray):
-        volume_id = data3d.create('-vol', vol_geom, data)
-    else:
-        volume_id = data
-    sino_id = data3d.create('-sino', proj_geom, 0)
-    algString = 'FP3D_CUDA'
-    cfg = astra_dict(algString)
-    if not gpuIndex==None:
-        cfg['option']={'GPUindex':gpuIndex}
-    cfg['ProjectionDataId'] = sino_id
-    cfg['VolumeDataId'] = volume_id
-    alg_id = algorithm.create(cfg)
-    algorithm.run(alg_id)
-    algorithm.delete(alg_id)
-
-    if isinstance(data, np.ndarray):
-        data3d.delete(volume_id)
-    if returnData:
-        return sino_id, data3d.get(sino_id)
-    else:
-        return sino_id
-
-

-
[docs]def create_reconstruction(rec_type, proj_id, sinogram, iterations=1, use_mask='no', mask=np.array([]), use_minc='no', minc=0, use_maxc='no', maxc=255, returnData=True, filterType=None, filterData=None):
-    """Create a reconstruction of a sinogram (2D).
-
-:param rec_type: Name of the reconstruction algorithm.
-:type rec_type: :class:`string`
-:param proj_id: ID of the projector to use.
-:type proj_id: :class:`int`
-:param sinogram: Sinogram data or ID.
-:type sinogram: :class:`numpy.ndarray` or :class:`int`
-:param iterations: Number of iterations to run.
-:type iterations: :class:`int`
-:param use_mask: Whether to use a mask.
-:type use_mask: ``'yes'`` or ``'no'``
-:param mask: Mask data or ID
-:type mask: :class:`numpy.ndarray` or :class:`int`
-:param use_minc: Whether to force a minimum value on the reconstruction pixels.
-:type use_minc: ``'yes'`` or ``'no'``
-:param minc: Minimum value to use.
-:type minc: :class:`float`
-:param use_maxc: Whether to force a maximum value on the reconstruction pixels.
-:type use_maxc: ``'yes'`` or ``'no'``
-:param maxc: Maximum value to use.
-:type maxc: :class:`float`
-:param returnData: If False, only return the ID of the reconstruction.
-:type returnData: :class:`bool`
-:param filterType: Which type of filter to use for filter-based methods.
-:type filterType: :class:`string`
-:param filterData: Optional filter data for filter-based methods.
-:type filterData: :class:`numpy.ndarray`
-:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the reconstruction. Otherwise, returns a tuple containing the ID of the reconstruction and reconstruction itself, in that order.
-
-"""
-    proj_geom = projector.projection_geometry(proj_id)
-    if isinstance(sinogram, np.ndarray):
-        sino_id = data2d.create('-sino', proj_geom, sinogram)
-    else:
-        sino_id = sinogram
-    vol_geom = projector.volume_geometry(proj_id)
-    recon_id = data2d.create('-vol', vol_geom, 0)
-    cfg = astra_dict(rec_type)
-    if not 'CUDA' in rec_type:
-        cfg['ProjectorId'] = proj_id
-    cfg['ProjectionDataId'] = sino_id
-    cfg['ReconstructionDataId'] = recon_id
-    cfg['options'] = {}
-    if use_mask == 'yes':
-        if isinstance(mask, np.ndarray):
-            mask_id = data2d.create('-vol', vol_geom, mask)
-        else:
-            mask_id = mask
-        cfg['options']['ReconstructionMaskId'] = mask_id
-    if not filterType == None:
-        cfg['FilterType'] = filterType
-    if not filterData == None:
-        if isinstance(filterData, np.ndarray):
-            nexpow = int(
-                pow(2, math.ceil(math.log(2 * proj_geom['DetectorCount'], 2))))
-            filtSize = nexpow / 2 + 1
-            filt_proj_geom = create_proj_geom(
-                'parallel', 1.0, filtSize, proj_geom['ProjectionAngles'])
-            filt_id = data2d.create('-sino', filt_proj_geom, filterData)
-        else:
-            filt_id = filterData
-        cfg['FilterSinogramId'] = filt_id
-    cfg['options']['UseMinConstraint'] = use_minc
-    cfg['options']['MinConstraintValue'] = minc
-    cfg['options']['UseMaxConstraint'] = use_maxc
-    cfg['options']['MaxConstraintValue'] = maxc
-    cfg['options']['ProjectionOrder'] = 'random'
-    alg_id = algorithm.create(cfg)
-    algorithm.run(alg_id, iterations)
-
-    algorithm.delete(alg_id)
-
-    if isinstance(sinogram, np.ndarray):
-        data2d.delete(sino_id)
-    if use_mask == 'yes' and isinstance(mask, np.ndarray):
-        data2d.delete(mask_id)
-    if not filterData == None:
-        if isinstance(filterData, np.ndarray):
-            data2d.delete(filt_id)
-    if returnData:
-        return recon_id, data2d.get(recon_id)
-    else:
-        return recon_id
-
-

-
[docs]def create_projector(proj_type, proj_geom, vol_geom):
-    """Create a 2D projector.
-
-:param proj_type: Projector type, such as ``'line'``, ``'linear'``, ...
-:type proj_type: :class:`string`
-:param proj_geom: Projection geometry.
-:type proj_geom: :class:`dict`
-:param vol_geom: Volume geometry.
-:type vol_geom: :class:`dict`
-:returns: :class:`int` -- The ID of the projector.
-
-"""
-    if proj_type == 'blob':
-        raise Exception('Blob type not yet implemented')
-    cfg = astra_dict(proj_type)
-    cfg['ProjectionGeometry'] = proj_geom
-    cfg['VolumeGeometry'] = vol_geom
-    return projector.create(cfg)

-
- -
-
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- - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/data2d.html b/python/docSRC/_build/html/_modules/astra/data2d.html deleted file mode 100644 index d77cddd..0000000 --- a/python/docSRC/_build/html/_modules/astra/data2d.html +++ /dev/null @@ -1,225 +0,0 @@ - - - - - - - - astra.data2d — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - -
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Source code for astra.data2d

-#-----------------------------------------------------------------------
-#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 data2d_c as d
-
-
[docs]def clear():
-    """Clear all 2D data objects."""
-    return d.clear()
-

-
[docs]def delete(ids):
-    """Delete a 2D object.
-    
-    :param ids: ID or list of ID's to delete.
-    :type ids: :class:`int` or :class:`list`
-    
-    """
-    return d.delete(ids)
-

-
[docs]def create(datatype, geometry, data=None):
-    """Create a 2D object.
-        
-    :param datatype: Data object type, '-vol' or '-sino'.
-    :type datatype: :class:`string`
-    :param geometry: Volume or projection geometry.
-    :type geometry: :class:`dict`
-    :param data: Data to fill the constructed object with, either a scalar or array.
-    :type data: :class:`float` or :class:`numpy.ndarray`
-    :returns: :class:`int` -- the ID of the constructed object.
-    
-    """
-    return d.create(datatype,geometry,data)
-

-
[docs]def store(i, data):
-    """Fill existing 2D object with data.
-    
-    :param i: ID of object to fill.
-    :type i: :class:`int`
-    :param data: Data to fill the object with, either a scalar or array.
-    :type data: :class:`float` or :class:`numpy.ndarray`
-    
-    """
-    return d.store(i, data)
-    

-
[docs]def get_geometry(i):
-    """Get the geometry of a 2D object.
-    
-    :param i: ID of object.
-    :type i: :class:`int`
-    :returns: :class:`dict` -- The geometry of object with ID ``i``.
-    
-    """
-    return d.get_geometry(i)
-

-
[docs]def change_geometry(i, geom):
-    """Change the geometry of a 2D object.
-    
-    :param i: ID of object.
-    :type i: :class:`int`
-    :param geom: new geometry.
-    :type geom: :class:`dict`
-    
-    """
-    return d.change_geometry(i, geom)
-    

-
[docs]def get(i):
-    """Get a 2D object.
-    
-    :param i: ID of object to get.
-    :type i: :class:`int`
-    :returns: :class:`numpy.ndarray` -- The object data.
-    
-    """
-    return d.get(i)
-

-
[docs]def get_shared(i):
-    """Get a 2D object with memory shared between the ASTRA toolbox and numpy array.
-    
-    :param i: ID of object to get.
-    :type i: :class:`int`
-    :returns: :class:`numpy.ndarray` -- The object data.
-    
-    """
-    return d.get_shared(i)
-
-

-
[docs]def get_single(i):
-    """Get a 2D object in single precision.
-    
-    :param i: ID of object to get.
-    :type i: :class:`int`
-    :returns: :class:`numpy.ndarray` -- The object data.
-    
-    """
-    return d.get_single(i)
-

-
[docs]def info():
-    """Print info on 2D objects in memory."""
-    return d.info()

-
- -
-
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-

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- -
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- © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
- - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/data3d.html b/python/docSRC/_build/html/_modules/astra/data3d.html deleted file mode 100644 index 674d6d1..0000000 --- a/python/docSRC/_build/html/_modules/astra/data3d.html +++ /dev/null @@ -1,213 +0,0 @@ - - - - - - - - astra.data3d — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - -
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Source code for astra.data3d

-#-----------------------------------------------------------------------
-#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 data3d_c as d
-
-
[docs]def create(datatype,geometry,data=None):
-    """Create a 3D object.
-        
-    :param datatype: Data object type, '-vol' or '-sino'.
-    :type datatype: :class:`string`
-    :param geometry: Volume or projection geometry.
-    :type geometry: :class:`dict`
-    :param data: Data to fill the constructed object with, either a scalar or array.
-    :type data: :class:`float` or :class:`numpy.ndarray`
-    :returns: :class:`int` -- the ID of the constructed object.
-    
-    """
-    return d.create(datatype,geometry,data)
-

-
[docs]def get(i):
-    """Get a 3D object.
-    
-    :param i: ID of object to get.
-    :type i: :class:`int`
-    :returns: :class:`numpy.ndarray` -- The object data.
-    
-    """
-    return d.get(i)
-

-
[docs]def get_shared(i):
-    """Get a 3D object with memory shared between the ASTRA toolbox and numpy array.
-    
-    :param i: ID of object to get.
-    :type i: :class:`int`
-    :returns: :class:`numpy.ndarray` -- The object data.
-    
-    """
-    return d.get_shared(i)
-

-
[docs]def get_single(i):
-    """Get a 3D object in single precision.
-    
-    :param i: ID of object to get.
-    :type i: :class:`int`
-    :returns: :class:`numpy.ndarray` -- The object data.
-    
-    """
-    return g.get_single(i)
-

-
[docs]def store(i,data):
-    """Fill existing 3D object with data.
-    
-    :param i: ID of object to fill.
-    :type i: :class:`int`
-    :param data: Data to fill the object with, either a scalar or array.
-    :type data: :class:`float` or :class:`numpy.ndarray`
-    
-    """
-    return d.store(i,data)
-

-
[docs]def dimensions(i):
-    """Get dimensions of a 3D object.
-    
-    :param i: ID of object.
-    :type i: :class:`int`
-    :returns: :class:`tuple` -- dimensions of object with ID ``i``.
-    
-    """
-    return d.dimensions(i)
-

-
[docs]def delete(ids):
-    """Delete a 2D object.
-    
-    :param ids: ID or list of ID's to delete.
-    :type ids: :class:`int` or :class:`list`
-    
-    """
-    return d.delete(ids)
-

-
[docs]def clear():
-    """Clear all 3D data objects."""
-    return d.clear()
-

-
[docs]def info():
-    """Print info on 3D objects in memory."""
-    return d.info()

-
- -
-
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-
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-

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- -
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- © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
- - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/functions.html b/python/docSRC/_build/html/_modules/astra/functions.html deleted file mode 100644 index 336431f..0000000 --- a/python/docSRC/_build/html/_modules/astra/functions.html +++ /dev/null @@ -1,375 +0,0 @@ - - - - - - - - astra.functions — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - -
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Source code for astra.functions

-#-----------------------------------------------------------------------
-# 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/>.
-#
-#-----------------------------------------------------------------------
-"""Additional functions for PyAstraToolbox.
-
-.. moduleauthor:: Daniel M. Pelt <D.M.Pelt@cwi.nl>
-
-
-"""
-
-from . import creators as ac
-import numpy as np
-from six.moves import range
-
-from . import data2d
-from . import data3d
-from . import projector
-from . import algorithm
-
-
-
-
[docs]def clear():
-    """Clears all used memory of the ASTRA Toolbox.
-
-    .. note::
-        This is irreversible.
-
-    """
-    data2d.clear()
-    data3d.clear()
-    projector.clear()
-    algorithm.clear()
-
-

-
[docs]def data_op(op, data, scalar, gpu_core, mask=None):
-    """Perform data operation on data.
-
-    :param op: Operation to perform.
-    :param data: Data to perform operation on.
-    :param scalar: Scalar argument to data operation.
-    :param gpu_core: GPU core to perform operation on.
-    :param mask: Optional mask.
-
-    """
-
-    cfg = ac.astra_dict('DataOperation_CUDA')
-    cfg['Operation'] = op
-    cfg['Scalar'] = scalar
-    cfg['DataId'] = data
-    if not mask == None:
-        cfg['MaskId'] = mask
-    cfg['option']['GPUindex'] = gpu_core
-    alg_id = algorithm.create(cfg)
-    algorithm.run(alg_id)
-    algorithm.delete(alg_id)
-
-

-
[docs]def add_noise_to_sino(sinogram_in, I0, seed=None):
-    """Adds Poisson noise to a sinogram.
-
-    :param sinogram_in: Sinogram to add noise to.
-    :type sinogram_in: :class:`numpy.ndarray`
-    :param I0: Background intensity. Lower values lead to higher noise.
-    :type I0: :class:`float`
-    :returns:  :class:`numpy.ndarray` -- the sinogram with added noise.
-
-    """
-
-    if not seed==None:
-        curstate = np.random.get_state()
-        np.random.seed(seed)
-
-    if isinstance(sinogram_in, np.ndarray):
-        sinogramRaw = sinogram_in
-    else:
-        sinogramRaw = data2d.get(sinogram_in)
-    max_sinogramRaw = sinogramRaw.max()
-    sinogramRawScaled = sinogramRaw / max_sinogramRaw
-    # to detector count
-    sinogramCT = I0 * np.exp(-sinogramRawScaled)
-    # add poison noise
-    sinogramCT_C = np.zeros_like(sinogramCT)
-    for i in range(sinogramCT_C.shape[0]):
-        for j in range(sinogramCT_C.shape[1]):
-            sinogramCT_C[i, j] = np.random.poisson(sinogramCT[i, j])
-    # to density
-    sinogramCT_D = sinogramCT_C / I0
-    sinogram_out = -max_sinogramRaw * np.log(sinogramCT_D)
-
-    if not isinstance(sinogram_in, np.ndarray):
-        at.data2d.store(sinogram_in, sinogram_out)
-
-    if not seed==None:
-        np.random.set_state(curstate)
-
-    return sinogram_out
-

-
[docs]def move_vol_geom(geom, pos, is_relative=False):
-    """Moves center of volume geometry to new position.
-
-    :param geom: Input volume geometry
-    :type geom: :class:`dict`
-    :param pos: Tuple (x,y[,z]) for new position, with the center of the image at (0,0[,0])
-    :type pos: :class:`tuple`
-    :param is_relative: Whether new position is relative to the old position
-    :type is_relative: :class:`bool`
-    :returns: :class:`dict` -- Volume geometry with the new center
-    """
-
-    ret_geom = geom.copy()
-    ret_geom['option'] = geom['option'].copy()
-
-    if not is_relative:
-        ret_geom['option']['WindowMinX'] = -geom['GridColCount']/2.
-        ret_geom['option']['WindowMaxX'] = geom['GridColCount']/2.
-        ret_geom['option']['WindowMinY'] = -geom['GridRowCount']/2.
-        ret_geom['option']['WindowMaxY'] = geom['GridRowCount']/2.
-        if len(pos)>2:
-            ret_geom['option']['WindowMinZ'] = -geom['GridSliceCount']/2.
-            ret_geom['option']['WindowMaxZ'] = geom['GridSliceCount']/2.
-    ret_geom['option']['WindowMinX'] += pos[0]
-    ret_geom['option']['WindowMaxX'] += pos[0]
-    ret_geom['option']['WindowMinY'] += pos[1]
-    ret_geom['option']['WindowMaxY'] += pos[1]
-    if len(pos)>2:
-        ret_geom['option']['WindowMinZ'] += pos[2]
-        ret_geom['option']['WindowMaxZ'] += pos[2]
-    return ret_geom
-
-

-
[docs]def geom_size(geom, dim=None):
-    """Returns the size of a volume or sinogram, based on the projection or volume geometry.
-
-    :param geom: Geometry to calculate size from
-    :type geometry: :class:`dict`
-    :param dim: Optional axis index to return
-    :type dim: :class:`int`
-    """
-
-    if 'GridSliceCount' in geom:
-        # 3D Volume geometry?
-        s = (geom['GridSliceCount'], geom[
-             'GridRowCount'], geom['GridColCount'])
-    elif 'GridColCount' in geom:
-        # 2D Volume geometry?
-        s = (geom['GridRowCount'], geom['GridColCount'])
-    elif geom['type'] == 'parallel' or geom['type'] == 'fanflat':
-        s = (len(geom['ProjectionAngles']), geom['DetectorCount'])
-    elif geom['type'] == 'parallel3d' or geom['type'] == 'cone':
-        s = (geom['DetectorRowCount'], len(
-            geom['ProjectionAngles']), geom['DetectorColCount'])
-    elif geom['type'] == 'fanflat_vec':
-        s = (geom['Vectors'].shape[0], geom['DetectorCount'])
-    elif geom['type'] == 'parallel3d_vec' or geom['type'] == 'cone_vec':
-        s = (geom['DetectorRowCount'], geom[
-             'Vectors'].shape[0], geom['DetectorColCount'])
-
-    if dim != None:
-        s = s[dim]
-
-    return s
-
-

-
[docs]def geom_2vec(proj_geom):
-    """Returns a vector-based projection geometry from a basic projection geometry.
-
-    :param proj_geom: Projection geometry to convert
-    :type proj_geom: :class:`dict`
-    """
-    if proj_geom['type'] == 'fanflat':
-        angles = proj_geom['ProjectionAngles']
-        vectors = np.zeros((len(angles), 6))
-        for i in range(len(angles)):
-
-            # source
-            vectors[i, 0] = np.sin(angles[i]) * proj_geom['DistanceOriginSource']
-            vectors[i, 1] = -np.cos(angles[i]) * proj_geom['DistanceOriginSource']
-
-            # center of detector
-            vectors[i, 2] = -np.sin(angles[i]) * proj_geom['DistanceOriginDetector']
-            vectors[i, 3] = np.cos(angles[i]) * proj_geom['DistanceOriginDetector']
-
-            # vector from detector pixel 0 to 1
-            vectors[i, 4] = np.cos(angles[i]) * proj_geom['DetectorWidth']
-            vectors[i, 5] = np.sin(angles[i]) * proj_geom['DetectorWidth']
-        proj_geom_out = ac.create_proj_geom(
-        'fanflat_vec', proj_geom['DetectorCount'], vectors)
-
-    elif proj_geom['type'] == 'cone':
-        angles = proj_geom['ProjectionAngles']
-        vectors = np.zeros((len(angles), 12))
-        for i in range(len(angles)):
-            # source
-            vectors[i, 0] = np.sin(angles[i]) * proj_geom['DistanceOriginSource']
-            vectors[i, 1] = -np.cos(angles[i]) * proj_geom['DistanceOriginSource']
-            vectors[i, 2] = 0
-
-            # center of detector
-            vectors[i, 3] = -np.sin(angles[i]) * proj_geom['DistanceOriginDetector']
-            vectors[i, 4] = np.cos(angles[i]) * proj_geom['DistanceOriginDetector']
-            vectors[i, 5] = 0
-
-            # vector from detector pixel (0,0) to (0,1)
-            vectors[i, 6] = np.cos(angles[i]) * proj_geom['DetectorSpacingX']
-            vectors[i, 7] = np.sin(angles[i]) * proj_geom['DetectorSpacingX']
-            vectors[i, 8] = 0
-
-            # vector from detector pixel (0,0) to (1,0)
-            vectors[i, 9] = 0
-            vectors[i, 10] = 0
-            vectors[i, 11] = proj_geom['DetectorSpacingY']
-
-        proj_geom_out = ac.create_proj_geom(
-        'cone_vec', proj_geom['DetectorRowCount'], proj_geom['DetectorColCount'], vectors)
-
-    # PARALLEL
-    elif proj_geom['type'] == 'parallel3d':
-        angles = proj_geom['ProjectionAngles']
-        vectors = np.zeros((len(angles), 12))
-        for i in range(len(angles)):
-
-            # ray direction
-            vectors[i, 0] = np.sin(angles[i])
-            vectors[i, 1] = -np.cos(angles[i])
-            vectors[i, 2] = 0
-
-            # center of detector
-            vectors[i, 3] = 0
-            vectors[i, 4] = 0
-            vectors[i, 5] = 0
-
-            # vector from detector pixel (0,0) to (0,1)
-            vectors[i, 6] = np.cos(angles[i]) * proj_geom['DetectorSpacingX']
-            vectors[i, 7] = np.sin(angles[i]) * proj_geom['DetectorSpacingX']
-            vectors[i, 8] = 0
-
-            # vector from detector pixel (0,0) to (1,0)
-            vectors[i, 9] = 0
-            vectors[i, 10] = 0
-            vectors[i, 11] = proj_geom['DetectorSpacingY']
-
-        proj_geom_out = ac.create_proj_geom(
-        'parallel3d_vec', proj_geom['DetectorRowCount'], proj_geom['DetectorColCount'], vectors)
-
-    else:
-        raise ValueError(
-        'No suitable vector geometry found for type: ' + proj_geom['type'])
-    return proj_geom_out

-
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Source code for astra.matlab

-#-----------------------------------------------------------------------
-#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/>.
-#
-#-----------------------------------------------------------------------
-"""This module implements a MATLAB-like interface to the ASTRA Toolbox.
-
-Note that all functions are called with a :class:`string` as the first
-argument, specifying the operation to perform. This un-pythonic way
-is used to make transitioning from MATLAB code to Python code easier, as
-the MATLAB interface uses the same type of method calling.
-
-After an initial ``import astra``, these functions can be accessed in the
-``astra.m`` module.
-
-"""
-
-from . import astra_c
-from . import data2d_c
-from . import data3d_c
-from . import projector_c
-from . import algorithm_c
-from . import matrix_c
-import numpy as np
-
-
-
[docs]def astra(command, *args):
-    """MATLAB-like interface to the :mod:`astra.astra` module
-    
-    For example:
-    
-    ``astra.m.astra('use_cuda')`` -- Check if CUDA is enabled.
-    
-    """
-    return getattr(astra_c, command)(*args)
-
-

-
[docs]def data2d(command, *args):
-    """MATLAB-like interface to the :mod:`astra.data2d` module
-    
-    For example:
-    
-    ``astra.m.data2d('create',type,geometry,data)`` -- Create a 2D object.
-    
-    """
-    return getattr(data2d_c, command)(*args)
-
-

-
[docs]def data3d(command, *args):
-    """MATLAB-like interface to the :mod:`astra.data3d` module
-    
-    For example:
-    
-    ``astra.m.data3d('get',i)`` -- Get 3D object data.
-    
-    """
-    return getattr(data3d_c, command)(*args)
-
-

-
[docs]def projector(command, *args):
-    """MATLAB-like interface to the :mod:`astra.projector` module
-    
-    For example:
-    
-    ``astra.m.projector('volume_geometry',i)`` -- Get volume geometry.
-    
-    """
-    return getattr(projector_c, command)(*args)
-
-

-
[docs]def matrix(command, *args):
-    """MATLAB-like interface to the :mod:`astra.matrix` module
-    
-    For example:
-    
-    ``astra.m.matrix('delete',i)`` -- Delete a matrix.
-    
-    """
-    return getattr(matrix_c, command)(*args)
-
-

-
[docs]def algorithm(command, *args):
-    """MATLAB-like interface to the :mod:`astra.algorithm` module
-    
-    For example:
-    
-    ``astra.m.algorithm('run',i,1000)`` -- Run an algorithm with 1000 iterations.
-    
-    """
-    if command == 'iterate':
-        command = 'run'
-    return getattr(algorithm_c, command)(*args)

-
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- - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/matrix.html b/python/docSRC/_build/html/_modules/astra/matrix.html deleted file mode 100644 index 5f75455..0000000 --- a/python/docSRC/_build/html/_modules/astra/matrix.html +++ /dev/null @@ -1,191 +0,0 @@ - - - - - - - - astra.matrix — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - -
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Source code for astra.matrix

-#-----------------------------------------------------------------------
-#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 matrix_c as m
-
-
[docs]def delete(ids):
-    """Delete a matrix object.
-    
-    :param ids: ID or list of ID's to delete.
-    :type ids: :class:`int` or :class:`list`
-    
-    """
-    return m.delete(ids)
-

-
[docs]def clear():
-    """Clear all matrix objects."""
-    return m.clear()
-

-
[docs]def create(data):
-    """Create matrix object with data.
-    
-    :param data: Data to fill the created object with.
-    :type data: :class:`scipy.sparse.csr_matrix`
-    :returns: :class:`int` -- the ID of the constructed object.
-    
-    """
-    return m.create(data)
-
-    

-
[docs]def store(i,data):
-    """Fill existing matrix object with data.
-    
-    :param i: ID of object to fill.
-    :type i: :class:`int`
-    :param data: Data to fill the object with.
-    :type data: :class:`scipy.sparse.csr_matrix`
-    
-    """
-    return m.store(i,data)
-

-
[docs]def get_size(i):
-    """Get matrix dimensions.
-    
-    :param i: ID of object.
-    :type i: :class:`int`
-    :returns: :class:`tuple` -- matrix dimensions.
-    """
-    return m.get_size(i)
-    

-
[docs]def get(i):
-    """Get a matrix object.
-    
-    :param i: ID of object to get.
-    :type i: :class:`int`
-    :returns: :class:`scipy.sparse.csr_matrix` --  The object data.
-    
-    """
-    return m.get(i)
-

-
[docs]def info():
-    """Print info on matrix objects in memory."""
-    return m.info()
-    
-        

-
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Source code for astra.projector

-#-----------------------------------------------------------------------
-#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 projector_c as p
-
-
[docs]def create(config):
-    """Create projector object.
-    
-    :param config: Projector options.
-    :type config: :class:`dict`
-    :returns: :class:`int` -- the ID of the constructed object.
-    
-    """
-    return p.create(config)
-
-

-
[docs]def delete(ids):
-    """Delete a projector object.
-    
-    :param ids: ID or list of ID's to delete.
-    :type ids: :class:`int` or :class:`list`
-    
-    """
-    return p.delete(ids)
-
-

-
[docs]def clear():
-    """Clear all projector objects."""
-    return p.clear()
-
-

-
[docs]def info():
-    """Print info on projector objects in memory."""
-    return p.info()
-

-
[docs]def projection_geometry(i):
-    """Get projection geometry of a projector.
-    
-    :param i: ID of projector.
-    :type i: :class:`int`
-    :returns: :class:`dict` -- projection geometry
-    
-    """
-    return p.projection_geometry(i)
-
-

-
[docs]def volume_geometry(i):
-    """Get volume geometry of a projector.
-    
-    :param i: ID of projector.
-    :type i: :class:`int`
-    :returns: :class:`dict` -- volume geometry
-    
-    """
-    return p.volume_geometry(i)
-
-

-
[docs]def weights_single_ray(i, projection_index, detector_index):
-    return p.weights_single_ray(i, projection_index, detector_index)
-
-

-
[docs]def weights_projection(i, projection_index):
-    return p.weights_projection(i, projection_index)
-
-

-
[docs]def splat(i, row, col):
-    return p.splat(i, row, col)
-
-

-
[docs]def matrix(i):
-    """Get sparse matrix of a projector.
-    
-    :param i: ID of projector.
-    :type i: :class:`int`
-    :returns: :class:`int` -- ID of sparse matrix.
-    
-    """
-    return p.matrix(i)

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- - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/_sources/ASTRAProjector.txt b/python/docSRC/_build/html/_sources/ASTRAProjector.txt deleted file mode 100644 index 1c267e3..0000000 --- a/python/docSRC/_build/html/_sources/ASTRAProjector.txt +++ /dev/null @@ -1,8 +0,0 @@ -Helper class: the :mod:`ASTRAProjector` module -============================================== - -.. automodule:: astra.ASTRAProjector - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_sources/algorithm.txt b/python/docSRC/_build/html/_sources/algorithm.txt deleted file mode 100644 index 83752bd..0000000 --- a/python/docSRC/_build/html/_sources/algorithm.txt +++ /dev/null @@ -1,8 +0,0 @@ -Algorithms: the :mod:`algorithm` module -======================================= - -.. automodule:: astra.algorithm - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_sources/astra.txt b/python/docSRC/_build/html/_sources/astra.txt deleted file mode 100644 index 5d5fdf0..0000000 --- a/python/docSRC/_build/html/_sources/astra.txt +++ /dev/null @@ -1,8 +0,0 @@ -Additional ASTRA methods: the :mod:`astra` module -======================================================== - -.. automodule:: astra.astra - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_sources/creators.txt b/python/docSRC/_build/html/_sources/creators.txt deleted file mode 100644 index d6249c3..0000000 --- a/python/docSRC/_build/html/_sources/creators.txt +++ /dev/null @@ -1,8 +0,0 @@ -Creation of objects: the :mod:`creators` module -=============================================== - -.. automodule:: astra.creators - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_sources/data2d.txt b/python/docSRC/_build/html/_sources/data2d.txt deleted file mode 100644 index 342cbec..0000000 --- a/python/docSRC/_build/html/_sources/data2d.txt +++ /dev/null @@ -1,8 +0,0 @@ -2D data objects: the :mod:`data2d` module -========================================= - -.. automodule:: astra.data2d - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_sources/data3d.txt b/python/docSRC/_build/html/_sources/data3d.txt deleted file mode 100644 index 5b7de23..0000000 --- a/python/docSRC/_build/html/_sources/data3d.txt +++ /dev/null @@ -1,8 +0,0 @@ -3D data objects: the :mod:`data3d` module -========================================= - -.. automodule:: astra.data3d - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_sources/functions.txt b/python/docSRC/_build/html/_sources/functions.txt deleted file mode 100644 index 749eb27..0000000 --- a/python/docSRC/_build/html/_sources/functions.txt +++ /dev/null @@ -1,8 +0,0 @@ -Additional functions: the :mod:`functions` module -================================================= - -.. automodule:: astra.functions - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_sources/index.txt b/python/docSRC/_build/html/_sources/index.txt deleted file mode 100644 index 8d17a4a..0000000 --- a/python/docSRC/_build/html/_sources/index.txt +++ /dev/null @@ -1,34 +0,0 @@ -.. .. documentation master file, created by - sphinx-quickstart on Wed Mar 13 16:36:32 2013. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -Welcome to PyASTRAToolbox's documentation! -========================================== - -Contents: - -.. toctree:: - :maxdepth: 4 - - data2d - data3d - projector - algorithm - matrix - creators - functions - ASTRAProjector - matlab - astra -.. astra -.. builder - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` - diff --git a/python/docSRC/_build/html/_sources/matlab.txt b/python/docSRC/_build/html/_sources/matlab.txt deleted file mode 100644 index fb7033e..0000000 --- a/python/docSRC/_build/html/_sources/matlab.txt +++ /dev/null @@ -1,8 +0,0 @@ -MATLAB compatibility interface: the :mod:`matlab` module -======================================================== - -.. automodule:: astra.matlab - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_sources/matrix.txt b/python/docSRC/_build/html/_sources/matrix.txt deleted file mode 100644 index 6f11d8a..0000000 --- a/python/docSRC/_build/html/_sources/matrix.txt +++ /dev/null @@ -1,8 +0,0 @@ -Sparse matrices: the :mod:`matrix` module -========================================= - -.. automodule:: astra.matrix - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_sources/projector.txt b/python/docSRC/_build/html/_sources/projector.txt deleted file mode 100644 index b0854e8..0000000 --- a/python/docSRC/_build/html/_sources/projector.txt +++ /dev/null @@ -1,8 +0,0 @@ -Projector object: the :mod:`projector` module -============================================= - -.. automodule:: astra.projector - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/_build/html/_static/ajax-loader.gif b/python/docSRC/_build/html/_static/ajax-loader.gif deleted file mode 100644 index 61faf8c..0000000 Binary files a/python/docSRC/_build/html/_static/ajax-loader.gif and /dev/null differ diff --git a/python/docSRC/_build/html/_static/basic.css b/python/docSRC/_build/html/_static/basic.css deleted file mode 100644 index 967e36c..0000000 --- a/python/docSRC/_build/html/_static/basic.css +++ /dev/null @@ -1,537 +0,0 @@ -/* - * basic.css - 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'ous', - ization: 'ize', - ation: 'ate', - ator: 'ate', - alism: 'al', - iveness: 'ive', - fulness: 'ful', - ousness: 'ous', - aliti: 'al', - iviti: 'ive', - biliti: 'ble', - logi: 'log' - }; - - var step3list = { - icate: 'ic', - ative: '', - alize: 'al', - iciti: 'ic', - ical: 'ic', - ful: '', - ness: '' - }; - - var c = "[^aeiou]"; // consonant - var v = "[aeiouy]"; // vowel - var C = c + "[^aeiouy]*"; // consonant sequence - var V = v + "[aeiou]*"; // vowel sequence - - var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 - var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 - var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 - var s_v = "^(" + C + ")?" + v; // vowel in stem - - this.stemWord = function (w) { - var stem; - var suffix; - var firstch; - var origword = w; - - if (w.length < 3) - return w; - - var re; - var re2; - var re3; - var re4; - - firstch = w.substr(0,1); - if (firstch == "y") - w = firstch.toUpperCase() + w.substr(1); - - // Step 1a - re = /^(.+?)(ss|i)es$/; - re2 = /^(.+?)([^s])s$/; - - if (re.test(w)) - w = w.replace(re,"$1$2"); - else if (re2.test(w)) - w = w.replace(re2,"$1$2"); - - // Step 1b - re = /^(.+?)eed$/; - re2 = /^(.+?)(ed|ing)$/; - if (re.test(w)) { - var fp = re.exec(w); - re = new RegExp(mgr0); - if (re.test(fp[1])) { - re = /.$/; - w = w.replace(re,""); - } - } - else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1]; - re2 = new RegExp(s_v); - if (re2.test(stem)) { - w = stem; - re2 = /(at|bl|iz)$/; - re3 = new RegExp("([^aeiouylsz])\\1$"); - re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - if (re2.test(w)) - w = w + "e"; - else if (re3.test(w)) { - re = /.$/; - w = w.replace(re,""); - } - else if (re4.test(w)) - w = w + "e"; - } - } - - // Step 1c - re = /^(.+?)y$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(s_v); - if (re.test(stem)) - w = stem + "i"; - } - - // Step 2 - re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = new RegExp(mgr0); - if (re.test(stem)) - w = stem + step2list[suffix]; - } - - // Step 3 - re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - suffix = fp[2]; - re = new RegExp(mgr0); - if (re.test(stem)) - w = stem + step3list[suffix]; - } - - // Step 4 - re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; - re2 = /^(.+?)(s|t)(ion)$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(mgr1); - if (re.test(stem)) - w = stem; - } - else if (re2.test(w)) { - var fp = re2.exec(w); - stem = fp[1] + fp[2]; - re2 = new RegExp(mgr1); - if (re2.test(stem)) - w = stem; - } - - // Step 5 - re = /^(.+?)e$/; - if (re.test(w)) { - var fp = re.exec(w); - stem = fp[1]; - re = new RegExp(mgr1); - re2 = new RegExp(meq1); - re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); - if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) - w = stem; - } - re = /ll$/; - re2 = new RegExp(mgr1); - if (re.test(w) && re2.test(w)) { - re = /.$/; - w = w.replace(re,""); - } - - // and turn initial Y back to y - if (firstch == "y") - w = firstch.toLowerCase() + w.substr(1); - return w; - } -} - - - -/** - * Simple result scoring code. - */ -var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [filename, title, anchor, descr, score] - // and returns the new score. - /* - score: function(result) { - return result[4]; - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: {0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5}, // used to be unimportantResults - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - // query found in terms - term: 5 -}; - - -/** - * Search Module - */ -var Search = { - - _index : null, - _queued_query : null, - _pulse_status : -1, - - init : function() { - var params = $.getQueryParameters(); - if (params.q) { - var query = params.q[0]; - $('input[name="q"]')[0].value = query; - this.performSearch(query); - } - }, - - loadIndex : function(url) { - $.ajax({type: "GET", url: url, data: null, - dataType: "script", cache: true, - complete: function(jqxhr, textstatus) { - if (textstatus != "success") { - document.getElementById("searchindexloader").src = url; - } - }}); - }, - - setIndex : function(index) { - var q; - this._index = index; - if ((q = this._queued_query) !== null) { - this._queued_query = null; - Search.query(q); - } - }, - - hasIndex : function() { - return this._index !== null; - }, - - deferQuery : function(query) { - this._queued_query = query; - }, - - stopPulse : function() { - this._pulse_status = 0; - }, - - startPulse : function() { - if (this._pulse_status >= 0) - return; - function pulse() { - var i; - Search._pulse_status = (Search._pulse_status + 1) % 4; - var dotString = ''; - for (i = 0; i < Search._pulse_status; i++) - dotString += '.'; - Search.dots.text(dotString); - if (Search._pulse_status > -1) - window.setTimeout(pulse, 500); - } - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch : function(query) { - // create the required interface elements - this.out = $('#search-results'); - this.title = $('

' + _('Searching') + '

').appendTo(this.out); - this.dots = $('').appendTo(this.title); - this.status = $('

').appendTo(this.out); - this.output = $('
'); - } - // Prettify the comment rating. - comment.pretty_rating = comment.rating + ' point' + - (comment.rating == 1 ? '' : 's'); - // Make a class (for displaying not yet moderated comments differently) - comment.css_class = comment.displayed ? '' : ' moderate'; - // Create a div for this comment. - var context = $.extend({}, opts, comment); - var div = $(renderTemplate(commentTemplate, context)); - - // If the user has voted on this comment, highlight the correct arrow. - if (comment.vote) { - var direction = (comment.vote == 1) ? 'u' : 'd'; - div.find('#' + direction + 'v' + comment.id).hide(); - div.find('#' + direction + 'u' + comment.id).show(); - } - - if (opts.moderator || comment.text != '[deleted]') { - div.find('a.reply').show(); - if (comment.proposal_diff) - div.find('#sp' + comment.id).show(); - if (opts.moderator && !comment.displayed) - div.find('#cm' + comment.id).show(); - if (opts.moderator || (opts.username == comment.username)) - div.find('#dc' + comment.id).show(); - } - return div; - } - - /** - * A simple template renderer. Placeholders such as <%id%> are replaced - * by context['id'] with items being escaped. Placeholders such as <#id#> - * are not escaped. - */ - function renderTemplate(template, context) { - var esc = $(document.createElement('div')); - - function handle(ph, escape) { - var cur = context; - $.each(ph.split('.'), function() { - cur = cur[this]; - }); - return escape ? esc.text(cur || "").html() : cur; - } - - return template.replace(/<([%#])([\w\.]*)\1>/g, function() { - return handle(arguments[2], arguments[1] == '%' ? true : false); - }); - } - - /** Flash an error message briefly. */ - function showError(message) { - $(document.createElement('div')).attr({'class': 'popup-error'}) - .append($(document.createElement('div')) - .attr({'class': 'error-message'}).text(message)) - .appendTo('body') - .fadeIn("slow") - .delay(2000) - .fadeOut("slow"); - } - - /** Add a link the user uses to open the comments popup. */ - $.fn.comment = function() { - return this.each(function() { - var id = $(this).attr('id').substring(1); - var count = COMMENT_METADATA[id]; - var title = count + ' comment' + (count == 1 ? '' : 's'); - var image = count > 0 ? opts.commentBrightImage : opts.commentImage; - var addcls = count == 0 ? ' nocomment' : ''; - $(this) - .append( - $(document.createElement('a')).attr({ - href: '#', - 'class': 'sphinx-comment-open' + addcls, - id: 'ao' + id - }) - .append($(document.createElement('img')).attr({ - src: image, - alt: 'comment', - title: title - })) - .click(function(event) { - event.preventDefault(); - show($(this).attr('id').substring(2)); - }) - ) - .append( - $(document.createElement('a')).attr({ - href: '#', - 'class': 'sphinx-comment-close hidden', - id: 'ah' + id - }) - .append($(document.createElement('img')).attr({ - src: opts.closeCommentImage, - alt: 'close', - title: 'close' - })) - .click(function(event) { - event.preventDefault(); - hide($(this).attr('id').substring(2)); - }) - ); - }); - }; - - var opts = { - processVoteURL: '/_process_vote', - addCommentURL: '/_add_comment', - getCommentsURL: '/_get_comments', - acceptCommentURL: '/_accept_comment', - deleteCommentURL: '/_delete_comment', - commentImage: '/static/_static/comment.png', - closeCommentImage: '/static/_static/comment-close.png', - loadingImage: '/static/_static/ajax-loader.gif', - commentBrightImage: '/static/_static/comment-bright.png', - upArrow: '/static/_static/up.png', - downArrow: '/static/_static/down.png', - upArrowPressed: '/static/_static/up-pressed.png', - downArrowPressed: '/static/_static/down-pressed.png', - voting: false, - moderator: false - }; - - if (typeof COMMENT_OPTIONS != "undefined") { - opts = jQuery.extend(opts, COMMENT_OPTIONS); - } - - var popupTemplate = '\ -
\ -

\ - Sort by:\ - best rated\ - newest\ - oldest\ -

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    Add a comment\ - (markup):

    \ -
    \ - reStructured text markup: *emph*, **strong**, \ - ``code``, \ - code blocks: :: and an indented block after blank line
    \ -
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    \ - \ - Propose a change ▹\ - \ - \ - Propose a change ▿\ - \ -

    \ - \ - \ - \ - \ - \ -
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    '; - - var commentTemplate = '\ -
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    \ -
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    \ - <%username%>\ - <%pretty_rating%>\ - <%time.delta%>\ -

    \ -
    <#text#>
    \ -

    \ - \ - reply ▿\ - proposal ▹\ - proposal ▿\ - \ - \ -

    \ - 
    \
-<#proposal_diff#>\
-
    \ -
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    • \ -
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      • '; - - $(document).ready(function() { - init(); - }); -})(jQuery); - -$(document).ready(function() { - // add comment anchors for all paragraphs that are commentable - $('.sphinx-has-comment').comment(); - - // highlight search words in search results - $("div.context").each(function() { - var params = $.getQueryParameters(); - var terms = (params.q) ? params.q[0].split(/\s+/) : []; - var result = $(this); - $.each(terms, function() { - result.highlightText(this.toLowerCase(), 'highlighted'); - }); - }); - - // directly open comment window if requested - var anchor = document.location.hash; - if (anchor.substring(0, 9) == '#comment-') { - $('#ao' + anchor.substring(9)).click(); - document.location.hash = '#s' + anchor.substring(9); - } -}); diff --git a/python/docSRC/_build/html/algorithm.html b/python/docSRC/_build/html/algorithm.html deleted file mode 100644 index bf4b90f..0000000 --- a/python/docSRC/_build/html/algorithm.html +++ /dev/null @@ -1,205 +0,0 @@ - - - - - - - - Algorithms: the algorithm module — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - - -
      -

      Navigation

      - -
      - -
      -
      -
      -
      - -
      -

      Algorithms: the algorithm module¶

      -
      -
      -astra.algorithm.clear()[source]¶
      -

      Clear all matrix objects.

      -
      - -
      -
      -astra.algorithm.create(config)[source]¶
      -

      Create algorithm object.

      -
      --- - - - - - -
      Parameters:config (dict) – Algorithm options.
      Returns:int – the ID of the constructed object.
      - - -
      -
      -astra.algorithm.delete(ids)[source]¶
      -

      Delete a matrix object.

      - --- - - - -
      Parameters:ids (int or list) – ID or list of ID’s to delete.
      -
      - -
      -
      -astra.algorithm.get_res_norm(i)[source]¶
      -

      Get residual norm of algorithm.

      - --- - - - - - -
      Parameters:i (int) – ID of object.
      Returns:float – The residual norm.
      -
      - -
      -
      -astra.algorithm.info()[source]¶
      -

      Print info on matrix objects in memory.

      -
      - -
      -
      -astra.algorithm.run(i, iterations=1)[source]¶
      -

      Run an algorithm.

      - --- - - - -
      Parameters:
        -
      • i (int) – ID of object.
        • -
      • iterations (int) – Number of iterations to run.
        • -
      -
      -
      - - - - - - - -
      -
      -

      Previous topic

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      Projector object: the projector module

      -

      Next topic

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      Sparse matrices: the matrix module

      -

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      Navigation

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      - © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
      - - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/astra.html b/python/docSRC/_build/html/astra.html deleted file mode 100644 index 42d68b8..0000000 --- a/python/docSRC/_build/html/astra.html +++ /dev/null @@ -1,169 +0,0 @@ - - - - - - - - Additional ASTRA methods: the astra module — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - -
      -

      Navigation

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      -

      Additional ASTRA methods: the astra module¶

      -
      -
      -astra.astra.credits()[source]¶
      -

      Print credits of the ASTRA Toolbox.

      -
      - -
      -
      -astra.astra.set_gpu_index(idx)[source]¶
      -

      Set default GPU index to use.

      - --- - - - -
      Parameters:idx (int) – GPU index
      -
      - -
      -
      -astra.astra.use_cuda()[source]¶
      -

      Test if CUDA is enabled.

      - --- - - - -
      Returns:bool – True if CUDA is enabled.
      -
      - -
      -
      -astra.astra.version(printToScreen=False)[source]¶
      -

      Check version of the ASTRA Toolbox.

      - --- - - - - - -
      Parameters:printToScreen (bool) – If True, print version string. If False, return version integer.
      Returns:string or int – The version string or integer.
      -
      - -
      - - -
      -
      -
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      Previous topic

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      MATLAB compatibility interface: the matlab module

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      - © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
      - - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/creators.html b/python/docSRC/_build/html/creators.html deleted file mode 100644 index 2f29232..0000000 --- a/python/docSRC/_build/html/creators.html +++ /dev/null @@ -1,520 +0,0 @@ - - - - - - - - Creation of objects: the creators module — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - - -
      -

      Navigation

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      Creation of objects: the creators module¶

      -
      -
      -astra.creators.astra_dict(intype)[source]¶
      -

      Creates a dict to use with the ASTRA Toolbox.

      - --- - - - - - -
      Parameters:intype (string) – Type of the ASTRA object.
      Returns:dict – An ASTRA dict of type intype.
      -
      - -
      -
      -astra.creators.create_backprojection(data, proj_id, useCUDA=False, returnData=True)[source]¶
      -

      Create a backprojection of a sinogram (2D).

      - --- - - - - - -
      Parameters:
        -
      • data (numpy.ndarray or int) – Sinogram data or ID.
        • -
      • proj_id (int) – ID of the projector to use.
        • -
      • useCUDA (bool) – If True, use CUDA for the calculation.
        • -
      • returnData (bool) – If False, only return the ID of the backprojection.
        • -
      -
      Returns:

      int or (int, numpy.ndarray) – If returnData=False, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order.

      -
      -
      - -
      -
      -astra.creators.create_backprojection3d_gpu(data, proj_geom, vol_geom, returnData=True)[source]¶
      -

      Create a backprojection of a sinogram (3D) using CUDA.

      - --- - - - - - -
      Parameters:
        -
      • data (numpy.ndarray or int) – Sinogram data or ID.
        • -
      • proj_geom (dict) – Projection geometry.
        • -
      • vol_geom (dict) – Volume geometry.
        • -
      • returnData (bool) – If False, only return the ID of the backprojection.
        • -
      -
      Returns:

      int or (int, numpy.ndarray) – If returnData=False, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order.

      -
      -
      - -
      -
      -astra.creators.create_proj_geom(intype, *args)[source]¶
      -

      Create a projection geometry.

      -

      This method can be called in a number of ways:

      -

      create_proj_geom('parallel', detector_spacing, det_count, angles):

      - --- - - - - - -
      Parameters:
        -
      • detector_spacing (float) – Distance between two adjacent detector pixels.
        • -
      • det_count (int) – Number of detector pixels.
        • -
      • angles (numpy.ndarray) – Array of angles in radians.
        • -
      -
      Returns:

      A parallel projection geometry.

      -
      -

      create_proj_geom('fanflat', det_width, det_count, angles, source_origin, source_det):

      - --- - - - - - -
      Parameters:
        -
      • det_width (float) – Size of a detector pixel.
        • -
      • det_count (int) – Number of detector pixels.
        • -
      • angles (numpy.ndarray) – Array of angles in radians.
        • -
      • source_origin – Position of the source.
        • -
      • source_det – Position of the detector
        • -
      -
      Returns:

      A fan-beam projection geometry.

      -
      -

      create_proj_geom('fanflat_vec', det_count, V):

      - --- - - - - - -
      Parameters:
        -
      • det_count (int) – Number of detector pixels.
        • -
      • V (numpy.ndarray) – Vector array.
        • -
      -
      Returns:

      A fan-beam projection geometry.

      -
      -

      create_proj_geom('parallel3d', detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles):

      - --- - - - - - -
      Parameters:
        -
      • detector_spacing_* (float) – Distance between two adjacent detector pixels.
        • -
      • det_row_count (int) – Number of detector pixel rows.
        • -
      • det_col_count (int) – Number of detector pixel columns.
        • -
      • angles (numpy.ndarray) – Array of angles in radians.
        • -
      -
      Returns:

      A parallel projection geometry.

      -
      -

      create_proj_geom('cone', detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles, source_origin, source_det):

      - --- - - - - - -
      Parameters:
        -
      • detector_spacing_* (float) – Distance between two adjacent detector pixels.
        • -
      • det_row_count (int) – Number of detector pixel rows.
        • -
      • det_col_count (int) – Number of detector pixel columns.
        • -
      • angles (numpy.ndarray) – Array of angles in radians.
        • -
      • source_origin (float) – Distance between point source and origin.
        • -
      • source_det (float) – Distance between the detector and origin.
        • -
      -
      Returns:

      A cone-beam projection geometry.

      -
      -

      create_proj_geom('cone_vec', det_row_count, det_col_count, V):

      - --- - - - - - -
      Parameters:
        -
      • det_row_count (int) – Number of detector pixel rows.
        • -
      • det_col_count (int) – Number of detector pixel columns.
        • -
      • V (numpy.ndarray) – Vector array.
        • -
      -
      Returns:

      A cone-beam projection geometry.

      -
      -

      create_proj_geom('parallel3d_vec', det_row_count, det_col_count, V):

      - --- - - - - - -
      Parameters:
        -
      • det_row_count (int) – Number of detector pixel rows.
        • -
      • det_col_count (int) – Number of detector pixel columns.
        • -
      • V (numpy.ndarray) – Vector array.
        • -
      -
      Returns:

      A parallel projection geometry.

      -
      -

      create_proj_geom('sparse_matrix', det_width, det_count, angles, matrix_id):

      - --- - - - - - -
      Parameters:
        -
      • det_width (float) – Size of a detector pixel.
        • -
      • det_count (int) – Number of detector pixels.
        • -
      • angles (numpy.ndarray) – Array of angles in radians.
        • -
      • matrix_id (int) – ID of the sparse matrix.
        • -
      -
      Returns:

      A projection geometry based on a sparse matrix.

      -
      -
      - -
      -
      -astra.creators.create_projector(proj_type, proj_geom, vol_geom)[source]¶
      -

      Create a 2D projector.

      - --- - - - - - -
      Parameters:
        -
      • proj_type (string) – Projector type, such as 'line', 'linear', ...
        • -
      • proj_geom (dict) – Projection geometry.
        • -
      • vol_geom (dict) – Volume geometry.
        • -
      -
      Returns:

      int – The ID of the projector.

      -
      -
      - -
      -
      -astra.creators.create_reconstruction(rec_type, proj_id, sinogram, iterations=1, use_mask='no', mask=array([], dtype=float64), use_minc='no', minc=0, use_maxc='no', maxc=255, returnData=True, filterType=None, filterData=None)[source]¶
      -

      Create a reconstruction of a sinogram (2D).

      - --- - - - - - -
      Parameters:
        -
      • rec_type (string) – Name of the reconstruction algorithm.
        • -
      • proj_id (int) – ID of the projector to use.
        • -
      • sinogram (numpy.ndarray or int) – Sinogram data or ID.
        • -
      • iterations (int) – Number of iterations to run.
        • -
      • use_mask ('yes' or 'no') – Whether to use a mask.
        • -
      • mask (numpy.ndarray or int) – Mask data or ID
        • -
      • use_minc ('yes' or 'no') – Whether to force a minimum value on the reconstruction pixels.
        • -
      • minc (float) – Minimum value to use.
        • -
      • use_maxc ('yes' or 'no') – Whether to force a maximum value on the reconstruction pixels.
        • -
      • maxc (float) – Maximum value to use.
        • -
      • returnData (bool) – If False, only return the ID of the reconstruction.
        • -
      • filterType (string) – Which type of filter to use for filter-based methods.
        • -
      • filterData (numpy.ndarray) – Optional filter data for filter-based methods.
        • -
      -
      Returns:

      int or (int, numpy.ndarray) – If returnData=False, returns the ID of the reconstruction. Otherwise, returns a tuple containing the ID of the reconstruction and reconstruction itself, in that order.

      -
      -
      - -
      -
      -astra.creators.create_sino(data, proj_id=None, proj_geom=None, vol_geom=None, useCUDA=False, returnData=True, gpuIndex=None)[source]¶
      -

      Create a forward projection of an image (2D).

      - --- - - - - - -
      Parameters:
        -
      • data (numpy.ndarray or int) – Image data or ID.
        • -
      • proj_id (int) – ID of the projector to use.
        • -
      • proj_geom (dict) – Projection geometry.
        • -
      • vol_geom (dict) – Volume geometry.
        • -
      • useCUDA (bool) – If True, use CUDA for the calculation.
        • -
      • returnData (bool) – If False, only return the ID of the forward projection.
        • -
      • gpuIndex (int) – Optional GPU index.
        • -
      -
      Returns:

      int or (int, numpy.ndarray)

      -
      -

      If returnData=False, returns the ID of the forward -projection. Otherwise, returns a tuple containing the ID of the -forward projection and the forward projection itself, in that -order.

      -

      The geometry of setup is defined by proj_id or with -proj_geom and vol_geom. If proj_id is given, then -proj_geom and vol_geom must be None and vice versa.

      -
      - -
      -
      -astra.creators.create_sino3d_gpu(data, proj_geom, vol_geom, returnData=True, gpuIndex=None)[source]¶
      -

      Create a forward projection of an image (3D).

      - --- - - - - - -
      Parameters:
        -
      • data (numpy.ndarray or int) – Image data or ID.
        • -
      • proj_geom (dict) – Projection geometry.
        • -
      • vol_geom (dict) – Volume geometry.
        • -
      • returnData (bool) – If False, only return the ID of the forward projection.
        • -
      • gpuIndex (int) – Optional GPU index.
        • -
      -
      Returns:

      int or (int, numpy.ndarray) – If returnData=False, returns the ID of the forward projection. Otherwise, returns a tuple containing the ID of the forward projection and the forward projection itself, in that order.

      -
      -
      - -
      -
      -astra.creators.create_vol_geom(*varargin)[source]¶
      -

      Create a volume geometry structure.

      -

      This method can be called in a number of ways:

      -
      -
      create_vol_geom(N):
      -
      --- - - - -
      returns:A 2D volume geometry of size \(N \times N\).
      -
      -
      create_vol_geom((M, N)):
      -
      --- - - - -
      returns:A 2D volume geometry of size \(M \times N\).
      -
      -
      create_vol_geom(M, N):
      -
      --- - - - -
      returns:A 2D volume geometry of size \(M \times N\).
      -
      -
      create_vol_geom(M, N, minx, maxx, miny, maxy):
      -
      --- - - - -
      returns:A 2D volume geometry of size \(M \times N\), windowed as \(minx \leq x \leq maxx\) and \(miny \leq y \leq maxy\).
      -
      -
      create_vol_geom((M, N, Z)):
      -
      --- - - - -
      returns:A 3D volume geometry of size \(M \times N \times Z\).
      -
      -
      create_vol_geom(M, N, Z):
      -
      --- - - - -
      returns:A 3D volume geometry of size \(M \times N \times Z\).
      -
      -
      -
      - -
      - - -
      -
      -
      -
      -
      -

      Previous topic

      -

      Sparse matrices: the matrix module

      -

      Next topic

      -

      Additional functions: the functions module

      -

      This Page

      - - - -
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      -

      Navigation

      - -
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      - © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
      - - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/data2d.html b/python/docSRC/_build/html/data2d.html deleted file mode 100644 index 6b01d41..0000000 --- a/python/docSRC/_build/html/data2d.html +++ /dev/null @@ -1,277 +0,0 @@ - - - - - - - - 2D data objects: the data2d module — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - - -
      -

      Navigation

      - -
      - -
      -
      -
      -
      - -
      -

      2D data objects: the data2d module¶

      -
      -
      -astra.data2d.change_geometry(i, geom)[source]¶
      -

      Change the geometry of a 2D object.

      - --- - - - -
      Parameters:
        -
      • i (int) – ID of object.
        • -
      • geom (dict) – new geometry.
        • -
      -
      -
      - -
      -
      -astra.data2d.clear()[source]¶
      -

      Clear all 2D data objects.

      -
      - -
      -
      -astra.data2d.create(datatype, geometry, data=None)[source]¶
      -

      Create a 2D object.

      - --- - - - - - -
      Parameters:
        -
      • datatype (string) – Data object type, ‘-vol’ or ‘-sino’.
        • -
      • geometry (dict) – Volume or projection geometry.
        • -
      • data (float or numpy.ndarray) – Data to fill the constructed object with, either a scalar or array.
        • -
      -
      Returns:

      int – the ID of the constructed object.

      -
      -
      - -
      -
      -astra.data2d.delete(ids)[source]¶
      -

      Delete a 2D object.

      - --- - - - -
      Parameters:ids (int or list) – ID or list of ID’s to delete.
      -
      - -
      -
      -astra.data2d.get(i)[source]¶
      -

      Get a 2D object.

      - --- - - - - - -
      Parameters:i (int) – ID of object to get.
      Returns:numpy.ndarray – The object data.
      -
      - -
      -
      -astra.data2d.get_geometry(i)[source]¶
      -

      Get the geometry of a 2D object.

      - --- - - - - - -
      Parameters:i (int) – ID of object.
      Returns:dict – The geometry of object with ID i.
      -
      - -
      -
      -astra.data2d.get_shared(i)[source]¶
      -

      Get a 2D object with memory shared between the ASTRA toolbox and numpy array.

      - --- - - - - - -
      Parameters:i (int) – ID of object to get.
      Returns:numpy.ndarray – The object data.
      -
      - -
      -
      -astra.data2d.get_single(i)[source]¶
      -

      Get a 2D object in single precision.

      - --- - - - - - -
      Parameters:i (int) – ID of object to get.
      Returns:numpy.ndarray – The object data.
      -
      - -
      -
      -astra.data2d.info()[source]¶
      -

      Print info on 2D objects in memory.

      -
      - -
      -
      -astra.data2d.store(i, data)[source]¶
      -

      Fill existing 2D object with data.

      - --- - - - -
      Parameters:
        -
      • i (int) – ID of object to fill.
        • -
      • data (float or numpy.ndarray) – Data to fill the object with, either a scalar or array.
        • -
      -
      -
      - -
      - - -
      -
      -
      -
      -
      -

      Previous topic

      -

      Welcome to PyASTRAToolbox’s documentation!

      -

      Next topic

      -

      3D data objects: the data3d module

      -

      This Page

      - - - -
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      Navigation

      - -
      - -
      - © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
      - - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/data3d.html b/python/docSRC/_build/html/data3d.html deleted file mode 100644 index 926bd6e..0000000 --- a/python/docSRC/_build/html/data3d.html +++ /dev/null @@ -1,259 +0,0 @@ - - - - - - - - 3D data objects: the data3d module — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - - -
      -

      Navigation

      - -
      - -
      -
      -
      -
      - -
      -

      3D data objects: the data3d module¶

      -
      -
      -astra.data3d.clear()[source]¶
      -

      Clear all 3D data objects.

      -
      - -
      -
      -astra.data3d.create(datatype, geometry, data=None)[source]¶
      -

      Create a 3D object.

      - --- - - - - - -
      Parameters:
        -
      • datatype (string) – Data object type, ‘-vol’ or ‘-sino’.
        • -
      • geometry (dict) – Volume or projection geometry.
        • -
      • data (float or numpy.ndarray) – Data to fill the constructed object with, either a scalar or array.
        • -
      -
      Returns:

      int – the ID of the constructed object.

      -
      -
      - -
      -
      -astra.data3d.delete(ids)[source]¶
      -

      Delete a 2D object.

      - --- - - - -
      Parameters:ids (int or list) – ID or list of ID’s to delete.
      -
      - -
      -
      -astra.data3d.dimensions(i)[source]¶
      -

      Get dimensions of a 3D object.

      - --- - - - - - -
      Parameters:i (int) – ID of object.
      Returns:tuple – dimensions of object with ID i.
      -
      - -
      -
      -astra.data3d.get(i)[source]¶
      -

      Get a 3D object.

      - --- - - - - - -
      Parameters:i (int) – ID of object to get.
      Returns:numpy.ndarray – The object data.
      -
      - -
      -
      -astra.data3d.get_shared(i)[source]¶
      -

      Get a 3D object with memory shared between the ASTRA toolbox and numpy array.

      - --- - - - - - -
      Parameters:i (int) – ID of object to get.
      Returns:numpy.ndarray – The object data.
      -
      - -
      -
      -astra.data3d.get_single(i)[source]¶
      -

      Get a 3D object in single precision.

      - --- - - - - - -
      Parameters:i (int) – ID of object to get.
      Returns:numpy.ndarray – The object data.
      -
      - -
      -
      -astra.data3d.info()[source]¶
      -

      Print info on 3D objects in memory.

      -
      - -
      -
      -astra.data3d.store(i, data)[source]¶
      -

      Fill existing 3D object with data.

      - --- - - - -
      Parameters:
        -
      • i (int) – ID of object to fill.
        • -
      • data (float or numpy.ndarray) – Data to fill the object with, either a scalar or array.
        • -
      -
      -
      - -
      - - -
      -
      -
      -
      -
      -

      Previous topic

      -

      2D data objects: the data2d module

      -

      Next topic

      -

      Projector object: the projector module

      -

      This Page

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      -
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      -

      Navigation

      - -
      - -
      - © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
      - - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/functions.html b/python/docSRC/_build/html/functions.html deleted file mode 100644 index 7ec397e..0000000 --- a/python/docSRC/_build/html/functions.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - - - Additional functions: the functions module — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - - -
      -

      Navigation

      - -
      - -
      -
      -
      -
      - -
      -

      Additional functions: the functions module¶

      -

      Additional functions for PyAstraToolbox.

      -
      -
      -astra.functions.add_noise_to_sino(sinogram_in, I0, seed=None)[source]¶
      -

      Adds Poisson noise to a sinogram.

      - --- - - - - - -
      Parameters:
        -
      • sinogram_in (numpy.ndarray) – Sinogram to add noise to.
        • -
      • I0 (float) – Background intensity. Lower values lead to higher noise.
        • -
      -
      Returns:

      numpy.ndarray – the sinogram with added noise.

      -
      -
      - -
      -
      -astra.functions.clear()[source]¶
      -

      Clears all used memory of the ASTRA Toolbox.

      -
      -

      Note

      -

      This is irreversible.

      -
      -
      - -
      -
      -astra.functions.data_op(op, data, scalar, gpu_core, mask=None)[source]¶
      -

      Perform data operation on data.

      - --- - - - -
      Parameters:
        -
      • op – Operation to perform.
        • -
      • data – Data to perform operation on.
        • -
      • scalar – Scalar argument to data operation.
        • -
      • gpu_core – GPU core to perform operation on.
        • -
      • mask – Optional mask.
        • -
      -
      -
      - -
      -
      -astra.functions.geom_2vec(proj_geom)[source]¶
      -

      Returns a vector-based projection geometry from a basic projection geometry.

      - --- - - - -
      Parameters:proj_geom (dict) – Projection geometry to convert
      -
      - -
      -
      -astra.functions.geom_size(geom, dim=None)[source]¶
      -

      Returns the size of a volume or sinogram, based on the projection or volume geometry.

      - --- - - - -
      Parameters:
        -
      • geom – Geometry to calculate size from
        • -
      • dim (int) – Optional axis index to return
        • -
      -
      -
      - -
      -
      -astra.functions.move_vol_geom(geom, pos, is_relative=False)[source]¶
      -

      Moves center of volume geometry to new position.

      - --- - - - - - -
      Parameters:
        -
      • geom (dict) – Input volume geometry
        • -
      • pos (tuple) – Tuple (x,y[,z]) for new position, with the center of the image at (0,0[,0])
        • -
      • is_relative (bool) – Whether new position is relative to the old position
        • -
      -
      Returns:

      dict – Volume geometry with the new center

      -
      -
      - -
      - - -
      -
      -
      -
      -
      -

      Previous topic

      -

      Creation of objects: the creators module

      -

      Next topic

      -

      Helper class: the ASTRAProjector module

      -

      This Page

      - - - -
      -
      -
      -
      -
      -

      Navigation

      - -
      - -
      - © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
      - - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/genindex.html b/python/docSRC/_build/html/genindex.html deleted file mode 100644 index 3099bfa..0000000 --- a/python/docSRC/_build/html/genindex.html +++ /dev/null @@ -1,575 +0,0 @@ - - - - - - - - - Index — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - -
      -

      Navigation

      - -
      - -
      -
      -
      -
      - - -

      Index

      - -
      - A - | B - | C - | D - | F - | G - | I - | M - | P - | R - | S - | U - | V - | W - -
      -

      A

      - - - -
      - -
      add_noise_to_sino() (in module astra.functions) -
      - - -
      algorithm() (in module astra.matlab) -
      - - -
      astra() (in module astra.matlab) -
      - - -
      astra.algorithm (module) -
      - - -
      astra.astra (module) -
      - - -
      astra.ASTRAProjector (module) -
      - - -
      astra.creators (module) -
      - - -
      astra.data2d (module) -
      - -
      - -
      astra.data3d (module) -
      - - -
      astra.functions (module) -
      - - -
      astra.matlab (module) -
      - - -
      astra.matrix (module) -
      - - -
      astra.projector (module) -
      - - -
      astra_dict() (in module astra.creators) -
      - - -
      ASTRAProjector2D (class in astra.ASTRAProjector) -
      - - -
      ASTRAProjector2DTranspose (class in astra.ASTRAProjector) -
      - -
      - -

      B

      - - -
      - -
      backProject() (astra.ASTRAProjector.ASTRAProjector2D method) -
      - -
      - -

      C

      - - - -
      - -
      change_geometry() (in module astra.data2d) -
      - - -
      clear() (in module astra.algorithm) -
      - -
      - -
      (in module astra.data2d) -
      - - -
      (in module astra.data3d) -
      - - -
      (in module astra.functions) -
      - - -
      (in module astra.matrix) -
      - - -
      (in module astra.projector) -
      - -
      - -
      create() (in module astra.algorithm) -
      - -
      - -
      (in module astra.data2d) -
      - - -
      (in module astra.data3d) -
      - - -
      (in module astra.matrix) -
      - - -
      (in module astra.projector) -
      - -
      - -
      create_backprojection() (in module astra.creators) -
      - - -
      create_backprojection3d_gpu() (in module astra.creators) -
      - - -
      create_proj_geom() (in module astra.creators) -
      - -
      - -
      create_projector() (in module astra.creators) -
      - - -
      create_reconstruction() (in module astra.creators) -
      - - -
      create_sino() (in module astra.creators) -
      - - -
      create_sino3d_gpu() (in module astra.creators) -
      - - -
      create_vol_geom() (in module astra.creators) -
      - - -
      credits() (in module astra.astra) -
      - -
      - -

      D

      - - - -
      - -
      data2d() (in module astra.matlab) -
      - - -
      data3d() (in module astra.matlab) -
      - - -
      data_op() (in module astra.functions) -
      - -
      - -
      delete() (in module astra.algorithm) -
      - -
      - -
      (in module astra.data2d) -
      - - -
      (in module astra.data3d) -
      - - -
      (in module astra.matrix) -
      - - -
      (in module astra.projector) -
      - -
      - -
      dimensions() (in module astra.data3d) -
      - -
      - -

      F

      - - -
      - -
      forwardProject() (astra.ASTRAProjector.ASTRAProjector2D method) -
      - -
      - -

      G

      - - - -
      - -
      geom_2vec() (in module astra.functions) -
      - - -
      geom_size() (in module astra.functions) -
      - - -
      get() (in module astra.data2d) -
      - -
      - -
      (in module astra.data3d) -
      - - -
      (in module astra.matrix) -
      - -
      - -
      get_geometry() (in module astra.data2d) -
      - -
      - -
      get_res_norm() (in module astra.algorithm) -
      - - -
      get_shared() (in module astra.data2d) -
      - -
      - -
      (in module astra.data3d) -
      - -
      - -
      get_single() (in module astra.data2d) -
      - -
      - -
      (in module astra.data3d) -
      - -
      - -
      get_size() (in module astra.matrix) -
      - -
      - -

      I

      - - -
      - -
      info() (in module astra.algorithm) -
      - -
      - -
      (in module astra.data2d) -
      - - -
      (in module astra.data3d) -
      - - -
      (in module astra.matrix) -
      - - -
      (in module astra.projector) -
      - -
      -
      - -

      M

      - - - -
      - -
      matrix() (in module astra.matlab) -
      - -
      - -
      (in module astra.projector) -
      - -
      -
      - -
      move_vol_geom() (in module astra.functions) -
      - -
      - -

      P

      - - - -
      - -
      projection_geometry() (in module astra.projector) -
      - -
      - -
      projector() (in module astra.matlab) -
      - -
      - -

      R

      - - - -
      - -
      reconstruct() (astra.ASTRAProjector.ASTRAProjector2D method) -
      - -
      - -
      run() (in module astra.algorithm) -
      - -
      - -

      S

      - - - -
      - -
      set_gpu_index() (in module astra.astra) -
      - - -
      splat() (in module astra.projector) -
      - -
      - -
      store() (in module astra.data2d) -
      - -
      - -
      (in module astra.data3d) -
      - - -
      (in module astra.matrix) -
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      U

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      use_cuda() (in module astra.astra) -
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      V

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      version() (in module astra.astra) -
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      W

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      weights_projection() (in module astra.projector) -
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      weights_single_ray() (in module astra.projector) -
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      Indices and tables¶

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      Table Of Contents

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      2D data objects: the data2d module

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      MATLAB compatibility interface: the matlab module¶

      -

      This module implements a MATLAB-like interface to the ASTRA Toolbox.

      -

      Note that all functions are called with a string as the first -argument, specifying the operation to perform. This un-pythonic way -is used to make transitioning from MATLAB code to Python code easier, as -the MATLAB interface uses the same type of method calling.

      -

      After an initial import astra, these functions can be accessed in the -astra.m module.

      -
      -
      -astra.matlab.algorithm(command, *args)[source]¶
      -

      MATLAB-like interface to the astra.algorithm module

      -

      For example:

      -

      astra.m.algorithm('run',i,1000) – Run an algorithm with 1000 iterations.

      -
      - -
      -
      -astra.matlab.astra(command, *args)[source]¶
      -

      MATLAB-like interface to the astra.astra module

      -

      For example:

      -

      astra.m.astra('use_cuda') – Check if CUDA is enabled.

      -
      - -
      -
      -astra.matlab.data2d(command, *args)[source]¶
      -

      MATLAB-like interface to the astra.data2d module

      -

      For example:

      -

      astra.m.data2d('create',type,geometry,data) – Create a 2D object.

      -
      - -
      -
      -astra.matlab.data3d(command, *args)[source]¶
      -

      MATLAB-like interface to the astra.data3d module

      -

      For example:

      -

      astra.m.data3d('get',i) – Get 3D object data.

      -
      - -
      -
      -astra.matlab.matrix(command, *args)[source]¶
      -

      MATLAB-like interface to the astra.matrix module

      -

      For example:

      -

      astra.m.matrix('delete',i) – Delete a matrix.

      -
      - -
      -
      -astra.matlab.projector(command, *args)[source]¶
      -

      MATLAB-like interface to the astra.projector module

      -

      For example:

      -

      astra.m.projector('volume_geometry',i) – Get volume geometry.

      -
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      Previous topic

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      Helper class: the ASTRAProjector module

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      Additional ASTRA methods: the astra module

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      Sparse matrices: the matrix module¶

      -
      -
      -astra.matrix.clear()[source]¶
      -

      Clear all matrix objects.

      -
      - -
      -
      -astra.matrix.create(data)[source]¶
      -

      Create matrix object with data.

      - --- - - - - - -
      Parameters:data (scipy.sparse.csr_matrix) – Data to fill the created object with.
      Returns:int – the ID of the constructed object.
      -
      - -
      -
      -astra.matrix.delete(ids)[source]¶
      -

      Delete a matrix object.

      - --- - - - -
      Parameters:ids (int or list) – ID or list of ID’s to delete.
      -
      - -
      -
      -astra.matrix.get(i)[source]¶
      -

      Get a matrix object.

      - --- - - - - - -
      Parameters:i (int) – ID of object to get.
      Returns:scipy.sparse.csr_matrix – The object data.
      -
      - -
      -
      -astra.matrix.get_size(i)[source]¶
      -

      Get matrix dimensions.

      - --- - - - - - -
      Parameters:i (int) – ID of object.
      Returns:tuple – matrix dimensions.
      -
      - -
      -
      -astra.matrix.info()[source]¶
      -

      Print info on matrix objects in memory.

      -
      - -
      -
      -astra.matrix.store(i, data)[source]¶
      -

      Fill existing matrix object with data.

      - --- - - - -
      Parameters:
        -
      • i (int) – ID of object to fill.
        • -
      • data (scipy.sparse.csr_matrix) – Data to fill the object with.
        • -
      -
      -
      - -
      - - -
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      Previous topic

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      Algorithms: the algorithm module

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      Creation of objects: the creators module

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      - © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. - Created using Sphinx 1.2.3. -
      - - - - \ No newline at end of file diff --git a/python/docSRC/_build/html/objects.inv b/python/docSRC/_build/html/objects.inv deleted file mode 100644 index 54bab0b..0000000 Binary files a/python/docSRC/_build/html/objects.inv and /dev/null differ diff --git a/python/docSRC/_build/html/projector.html b/python/docSRC/_build/html/projector.html deleted file mode 100644 index 9df5d0b..0000000 --- a/python/docSRC/_build/html/projector.html +++ /dev/null @@ -1,234 +0,0 @@ - - - - - - - - Projector object: the projector module — PyASTRAToolbox 1.6 documentation - - - - - - - - - - - - - - -
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      Projector object: the projector module¶

      -
      -
      -astra.projector.clear()[source]¶
      -

      Clear all projector objects.

      -
      - -
      -
      -astra.projector.create(config)[source]¶
      -

      Create projector object.

      - --- - - - - - -
      Parameters:config (dict) – Projector options.
      Returns:int – the ID of the constructed object.
      -
      - -
      -
      -astra.projector.delete(ids)[source]¶
      -

      Delete a projector object.

      - --- - - - -
      Parameters:ids (int or list) – ID or list of ID’s to delete.
      -
      - -
      -
      -astra.projector.info()[source]¶
      -

      Print info on projector objects in memory.

      -
      - -
      -
      -astra.projector.matrix(i)[source]¶
      -

      Get sparse matrix of a projector.

      - --- - - - - - -
      Parameters:i (int) – ID of projector.
      Returns:int – ID of sparse matrix.
      -
      - -
      -
      -astra.projector.projection_geometry(i)[source]¶
      -

      Get projection geometry of a projector.

      - --- - - - - - -
      Parameters:i (int) – ID of projector.
      Returns:dict – projection geometry
      -
      - -
      -
      -astra.projector.splat(i, row, col)[source]¶
      -
      - -
      -
      -astra.projector.volume_geometry(i)[source]¶
      -

      Get volume geometry of a projector.

      - --- - - - - - -
      Parameters:i (int) – ID of projector.
      Returns:dict – volume geometry
      -
      - -
      -
      -astra.projector.weights_projection(i, projection_index)[source]¶
      -
      - -
      -
      -astra.projector.weights_single_ray(i, projection_index, detector_index)[source]¶
      -
      - -
      - - -
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      Previous topic

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      3D data objects: the data3d module

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\ No newline at end of file diff --git a/python/docSRC/_templates/layout.html b/python/docSRC/_templates/layout.html deleted file mode 100644 index f30df11..0000000 --- a/python/docSRC/_templates/layout.html +++ /dev/null @@ -1,15 +0,0 @@ -{% extends "!layout.html" %} - -{% block footer %} -{{ super() }} - -{% endblock %} diff --git a/python/docSRC/algorithm.rst b/python/docSRC/algorithm.rst deleted file mode 100644 index 83752bd..0000000 --- a/python/docSRC/algorithm.rst +++ /dev/null @@ -1,8 +0,0 @@ -Algorithms: the :mod:`algorithm` module -======================================= - -.. automodule:: astra.algorithm - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/astra.rst b/python/docSRC/astra.rst deleted file mode 100644 index 5d5fdf0..0000000 --- a/python/docSRC/astra.rst +++ /dev/null @@ -1,8 +0,0 @@ -Additional ASTRA methods: the :mod:`astra` module -======================================================== - -.. automodule:: astra.astra - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/conf.py b/python/docSRC/conf.py deleted file mode 100644 index 78f7d42..0000000 --- a/python/docSRC/conf.py +++ /dev/null @@ -1,287 +0,0 @@ -# -*- coding: utf-8 -*- -# -# .. documentation build configuration file, created by -# sphinx-quickstart on Wed Mar 13 16:36:32 2013. -# -# This file is execfile()d with the current directory set to its containing dir. -# -# Note that not all possible configuration values are present in this -# autogenerated file. -# -# All configuration values have a default; values that are commented out -# serve to show the default. - -import sys, os - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -#sys.path.insert(0, os.path.abspath('.')) - -# -- General configuration ----------------------------------------------------- - -# If your documentation needs a minimal Sphinx version, state it here. -#needs_sphinx = '1.0' - -# Add any Sphinx extension module names here, as strings. They can be extensions -# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. -extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode','sphinx.ext.mathjax','sphinx.ext.intersphinx'] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] - -# The suffix of source filenames. -source_suffix = '.rst' - -# The encoding of source files. -#source_encoding = 'utf-8-sig' - -# The master toctree document. -master_doc = 'index' - -# General information about the project. -project = u'PyASTRAToolbox' -copyright = u'2013, Centrum Wiskunde & Informatica, Amsterdam' - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# The short X.Y version. -version = '1.7.1' -# The full version, including alpha/beta/rc tags. -release = '1.7.1' - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -#language = None - -# There are two options for replacing |today|: either, you set today to some -# non-false value, then it is used: -#today = '' -# Else, today_fmt is used as the format for a strftime call. -#today_fmt = '%B %d, %Y' - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -exclude_patterns = ['_build'] - -# The reST default role (used for this markup: `text`) to use for all documents. -#default_role = None - -# If true, '()' will be appended to :func: etc. cross-reference text. -#add_function_parentheses = True - -# If true, the current module name will be prepended to all description -# unit titles (such as .. function::). -#add_module_names = True - -# If true, sectionauthor and moduleauthor directives will be shown in the -# output. They are ignored by default. -#show_authors = False - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' - -# A list of ignored prefixes for module index sorting. -#modindex_common_prefix = [] - - -# -- Options for HTML output --------------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -html_theme = 'default' - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -#html_theme_options = {} - -# Add any paths that contain custom themes here, relative to this directory. -#html_theme_path = [] - -# The name for this set of Sphinx documents. If None, it defaults to -# " v documentation". -#html_title = None - -# A shorter title for the navigation bar. Default is the same as html_title. -#html_short_title = None - -# The name of an image file (relative to this directory) to place at the top -# of the sidebar. -#html_logo = None - -# The name of an image file (within the static path) to use as favicon of the -# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 -# pixels large. -#html_favicon = None - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] - -# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, -# using the given strftime format. -#html_last_updated_fmt = '%b %d, %Y' - -# If true, SmartyPants will be used to convert quotes and dashes to -# typographically correct entities. -#html_use_smartypants = True - -# Custom sidebar templates, maps document names to template names. -#html_sidebars = {} - -# Additional templates that should be rendered to pages, maps page names to -# template names. -#html_additional_pages = {} - -# If false, no module index is generated. -#html_domain_indices = True - -# If false, no index is generated. -#html_use_index = True - -# If true, the index is split into individual pages for each letter. -#html_split_index = False - -# If true, links to the reST sources are added to the pages. -#html_show_sourcelink = True - -# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -#html_show_sphinx = True - -# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -#html_show_copyright = True - -# If true, an OpenSearch description file will be output, and all pages will -# contain a tag referring to it. The value of this option must be the -# base URL from which the finished HTML is served. -#html_use_opensearch = '' - -# This is the file name suffix for HTML files (e.g. ".xhtml"). -#html_file_suffix = None - -# Output file base name for HTML help builder. -htmlhelp_basename = 'doc' - - -# -- Options for LaTeX output -------------------------------------------------- - -latex_elements = { -# The paper size ('letterpaper' or 'a4paper'). -#'papersize': 'letterpaper', - -# The font size ('10pt', '11pt' or '12pt'). -#'pointsize': '10pt', - -# Additional stuff for the LaTeX preamble. -#'preamble': '', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, author, documentclass [howto/manual]). -latex_documents = [ - ('index', '.tex', u'.. Documentation', - u'Author', 'manual'), -] - -# The name of an image file (relative to this directory) to place at the top of -# the title page. -#latex_logo = None - -# For "manual" documents, if this is true, then toplevel headings are parts, -# not chapters. -#latex_use_parts = False - -# If true, show page references after internal links. -#latex_show_pagerefs = False - -# If true, show URL addresses after external links. -#latex_show_urls = False - -# Documents to append as an appendix to all manuals. -#latex_appendices = [] - -# If false, no module index is generated. -#latex_domain_indices = True - - -# -- Options for manual page output -------------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - ('index', '', u'.. Documentation', - [u'Author'], 1) -] - -# If true, show URL addresses after external links. -#man_show_urls = False - - -# -- Options for Texinfo output ------------------------------------------------ - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - ('index', '', u'.. Documentation', - u'Author', '', 'One line description of project.', - 'Miscellaneous'), -] - -# Documents to append as an appendix to all manuals. -#texinfo_appendices = [] - -# If false, no module index is generated. -#texinfo_domain_indices = True - -# How to display URL addresses: 'footnote', 'no', or 'inline'. -#texinfo_show_urls = 'footnote' - - -# -- Options for Epub output --------------------------------------------------- - -# Bibliographic Dublin Core info. -epub_title = u'..' -epub_author = u'Author' -epub_publisher = u'Author' -epub_copyright = u'2013, Author' - -# The language of the text. It defaults to the language option -# or en if the language is not set. -#epub_language = '' - -# The scheme of the identifier. Typical schemes are ISBN or URL. -#epub_scheme = '' - -# The unique identifier of the text. This can be a ISBN number -# or the project homepage. -#epub_identifier = '' - -# A unique identification for the text. -#epub_uid = '' - -# A tuple containing the cover image and cover page html template filenames. -#epub_cover = () - -# HTML files that should be inserted before the pages created by sphinx. -# The format is a list of tuples containing the path and title. -#epub_pre_files = [] - -# HTML files shat should be inserted after the pages created by sphinx. -# The format is a list of tuples containing the path and title. -#epub_post_files = [] - -# A list of files that should not be packed into the epub file. -#epub_exclude_files = [] - -# The depth of the table of contents in toc.ncx. -#epub_tocdepth = 3 - -# Allow duplicate toc entries. -#epub_tocdup = True - -intersphinx_mapping = {'python': ('http://docs.python.org/2.7', None), 'numpy':('http://docs.scipy.org/doc/numpy/',None)} diff --git a/python/docSRC/creators.rst b/python/docSRC/creators.rst deleted file mode 100644 index d6249c3..0000000 --- a/python/docSRC/creators.rst +++ /dev/null @@ -1,8 +0,0 @@ -Creation of objects: the :mod:`creators` module -=============================================== - -.. automodule:: astra.creators - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/data2d.rst b/python/docSRC/data2d.rst deleted file mode 100644 index 342cbec..0000000 --- a/python/docSRC/data2d.rst +++ /dev/null @@ -1,8 +0,0 @@ -2D data objects: the :mod:`data2d` module -========================================= - -.. automodule:: astra.data2d - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/data3d.rst b/python/docSRC/data3d.rst deleted file mode 100644 index 5b7de23..0000000 --- a/python/docSRC/data3d.rst +++ /dev/null @@ -1,8 +0,0 @@ -3D data objects: the :mod:`data3d` module -========================================= - -.. automodule:: astra.data3d - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/functions.rst b/python/docSRC/functions.rst deleted file mode 100644 index 749eb27..0000000 --- a/python/docSRC/functions.rst +++ /dev/null @@ -1,8 +0,0 @@ -Additional functions: the :mod:`functions` module -================================================= - -.. automodule:: astra.functions - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/index.rst b/python/docSRC/index.rst deleted file mode 100644 index dcc6590..0000000 --- a/python/docSRC/index.rst +++ /dev/null @@ -1,35 +0,0 @@ -.. .. documentation master file, created by - sphinx-quickstart on Wed Mar 13 16:36:32 2013. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -Welcome to PyASTRAToolbox's documentation! -========================================== - -Contents: - -.. toctree:: - :maxdepth: 4 - - data2d - data3d - projector - algorithm - matrix - creators - functions - operator - plugins - matlab - astra -.. astra -.. builder - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` - diff --git a/python/docSRC/make.bat b/python/docSRC/make.bat deleted file mode 100644 index d70c604..0000000 --- a/python/docSRC/make.bat +++ /dev/null @@ -1,190 +0,0 @@ -@ECHO OFF - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set BUILDDIR=_build -set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . -set I18NSPHINXOPTS=%SPHINXOPTS% . -if NOT "%PAPER%" == "" ( - set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% - set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% -) - -if "%1" == "" goto help - -if "%1" == "help" ( - :help - echo.Please use `make ^` where ^ is one of - echo. html to make standalone HTML files - echo. dirhtml to make HTML files named index.html in directories - echo. singlehtml to make a single large HTML file - echo. pickle to make pickle files - echo. json to make JSON files - echo. htmlhelp to make HTML files and a HTML help project - echo. qthelp to make HTML files and a qthelp project - echo. devhelp to make HTML files and a Devhelp project - echo. epub to make an epub - echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter - echo. text to make text files - echo. man to make manual pages - echo. texinfo to make Texinfo files - echo. gettext to make PO message catalogs - echo. changes to make an overview over all changed/added/deprecated items - echo. linkcheck to check all external links for integrity - echo. doctest to run all doctests embedded in the documentation if enabled - goto end -) - -if "%1" == "clean" ( - for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i - del /q /s %BUILDDIR%\* - goto end -) - -if "%1" == "html" ( - %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/html. - goto end -) - -if "%1" == "dirhtml" ( - %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. - goto end -) - -if "%1" == "singlehtml" ( - %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml. - goto end -) - -if "%1" == "pickle" ( - %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can process the pickle files. - goto end -) - -if "%1" == "json" ( - %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can process the JSON files. - goto end -) - -if "%1" == "htmlhelp" ( - %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can run HTML Help Workshop with the ^ -.hhp project file in %BUILDDIR%/htmlhelp. - goto end -) - -if "%1" == "qthelp" ( - %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; now you can run "qcollectiongenerator" with the ^ -.qhcp project file in %BUILDDIR%/qthelp, like this: - echo.^> qcollectiongenerator %BUILDDIR%\qthelp\.qhcp - echo.To view the help file: - echo.^> assistant -collectionFile %BUILDDIR%\qthelp\.ghc - goto end -) - -if "%1" == "devhelp" ( - %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. - goto end -) - -if "%1" == "epub" ( - %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The epub file is in %BUILDDIR%/epub. - goto end -) - -if "%1" == "latex" ( - %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex - if errorlevel 1 exit /b 1 - echo. - echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. - goto end -) - -if "%1" == "text" ( - %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The text files are in %BUILDDIR%/text. - goto end -) - -if "%1" == "man" ( - %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The manual pages are in %BUILDDIR%/man. - goto end -) - -if "%1" == "texinfo" ( - %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo. - goto end -) - -if "%1" == "gettext" ( - %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale - if errorlevel 1 exit /b 1 - echo. - echo.Build finished. The message catalogs are in %BUILDDIR%/locale. - goto end -) - -if "%1" == "changes" ( - %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes - if errorlevel 1 exit /b 1 - echo. - echo.The overview file is in %BUILDDIR%/changes. - goto end -) - -if "%1" == "linkcheck" ( - %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck - if errorlevel 1 exit /b 1 - echo. - echo.Link check complete; look for any errors in the above output ^ -or in %BUILDDIR%/linkcheck/output.txt. - goto end -) - -if "%1" == "doctest" ( - %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest - if errorlevel 1 exit /b 1 - echo. - echo.Testing of doctests in the sources finished, look at the ^ -results in %BUILDDIR%/doctest/output.txt. - goto end -) - -:end diff --git a/python/docSRC/matlab.rst b/python/docSRC/matlab.rst deleted file mode 100644 index fb7033e..0000000 --- a/python/docSRC/matlab.rst +++ /dev/null @@ -1,8 +0,0 @@ -MATLAB compatibility interface: the :mod:`matlab` module -======================================================== - -.. automodule:: astra.matlab - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/matrix.rst b/python/docSRC/matrix.rst deleted file mode 100644 index 6f11d8a..0000000 --- a/python/docSRC/matrix.rst +++ /dev/null @@ -1,8 +0,0 @@ -Sparse matrices: the :mod:`matrix` module -========================================= - -.. automodule:: astra.matrix - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/operator.rst b/python/docSRC/operator.rst deleted file mode 100644 index fe500ba..0000000 --- a/python/docSRC/operator.rst +++ /dev/null @@ -1,8 +0,0 @@ -OpTomo class: the :mod:`optomo` module -============================================== - -.. automodule:: astra.optomo - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/plugins.rst b/python/docSRC/plugins.rst deleted file mode 100644 index dc7c607..0000000 --- a/python/docSRC/plugins.rst +++ /dev/null @@ -1,8 +0,0 @@ -Plugins: the :mod:`plugin` module -========================================= - -.. automodule:: astra.plugin - :members: - :undoc-members: - :show-inheritance: - diff --git a/python/docSRC/projector.rst b/python/docSRC/projector.rst deleted file mode 100644 index b0854e8..0000000 --- a/python/docSRC/projector.rst +++ /dev/null @@ -1,8 +0,0 @@ -Projector object: the :mod:`projector` module -============================================= - -.. automodule:: astra.projector - :members: - :undoc-members: - :show-inheritance: - -- cgit v1.2.3 From 76d182ace088b7ab6d64019079c049a0f9a29e69 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 6 Jan 2016 16:40:26 +0100 Subject: Change python set_gpu_index to match --- python/astra/astra.py | 4 ++-- python/astra/astra_c.pyx | 21 ++++++++++++++++++--- 2 files changed, 20 insertions(+), 5 deletions(-) (limited to 'python') diff --git a/python/astra/astra.py b/python/astra/astra.py index 26b1ff0..9328b6b 100644 --- a/python/astra/astra.py +++ b/python/astra/astra.py @@ -49,10 +49,10 @@ def version(printToScreen=False): """ return a.version(printToScreen) -def set_gpu_index(idx): +def set_gpu_index(idx, memory=0): """Set default GPU index to use. :param idx: GPU index :type idx: :class:`int` """ - a.set_gpu_index(idx) + a.set_gpu_index(idx, memory) diff --git a/python/astra/astra_c.pyx b/python/astra/astra_c.pyx index 6b246b6..2a9c816 100644 --- a/python/astra/astra_c.pyx +++ b/python/astra/astra_c.pyx @@ -31,6 +31,7 @@ import six from .utils import wrap_from_bytes from libcpp.string cimport string +from libcpp.vector cimport vector from libcpp cimport bool cdef extern from "astra/Globals.h" namespace "astra": int getVersion() @@ -43,6 +44,12 @@ IF HAVE_CUDA==True: ELSE: def setGPUIndex(): pass +cdef extern from "astra/CompositeGeometryManager.h" namespace "astra": + cdef cppclass SGPUParams: + vector[int] GPUIndices + size_t memory +cdef extern from "astra/CompositeGeometryManager.h" namespace "astra::CCompositeGeometryManager": + void setGlobalGPUParams(SGPUParams&) def credits(): six.print_("""The ASTRA Toolbox has been developed at the University of Antwerp and CWI, Amsterdam by @@ -70,8 +77,16 @@ def version(printToScreen=False): else: return getVersion() -def set_gpu_index(idx): +def set_gpu_index(idx, memory=0): + import types + import collections + cdef SGPUParams params if use_cuda()==True: - ret = setGPUIndex(idx) + if not isinstance(idx, collections.Iterable) or isinstance(idx, types.StringTypes): + idx = (idx,) + params.memory = memory + params.GPUIndices = idx + setGlobalGPUParams(params) + ret = setGPUIndex(params.GPUIndices[0]) if not ret: - six.print_("Failed to set GPU " + str(idx)) + six.print_("Failed to set GPU " + str(params.GPUIndices[0])) -- cgit v1.2.3 From 5bc9c23c84a3e7f079b75d0bee50c570a7372920 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 6 Jan 2016 16:49:56 +0100 Subject: Allow multiple GPUs in ASTRA_GPU_INDEX envvar --- python/astra/__init__.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'python') diff --git a/python/astra/__init__.py b/python/astra/__init__.py index 10ed74d..515d9a2 100644 --- a/python/astra/__init__.py +++ b/python/astra/__init__.py @@ -39,7 +39,7 @@ from . import log from .optomo import OpTomo import os -try: - astra.set_gpu_index(int(os.environ['ASTRA_GPU_INDEX'])) -except KeyError: - pass + +if 'ASTRA_GPU_INDEX' in os.environ: + L = [ int(x) for x in os.environ['ASTRA_GPU_INDEX'].split(',') ] + astra.set_gpu_index(L) -- cgit v1.2.3 From 5c33826855a8d88889cdbbfc78b27c86549715d5 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 20 Jan 2016 13:02:36 +0100 Subject: Add check for scipy The module matrix_c.pyx uses it. --- python/conda/meta.yaml | 1 + 1 file changed, 1 insertion(+) (limited to 'python') diff --git a/python/conda/meta.yaml b/python/conda/meta.yaml index 41250dc..7e4679b 100644 --- a/python/conda/meta.yaml +++ b/python/conda/meta.yaml @@ -21,6 +21,7 @@ requirements: - python - cython >=0.13 - numpy + - scipy - six run: -- cgit v1.2.3 From 56809b0359af7e9108adeb1fd21823a225edf6fa Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 20 Jan 2016 18:08:59 +0100 Subject: Remove dependency of libastra on libpython by refactoring PluginAlgorithm --- python/astra/plugin_c.pyx | 17 +- python/astra/src/PythonPluginAlgorithm.cpp | 402 +++++++++++++++++++++++++++++ python/astra/src/PythonPluginAlgorithm.h | 89 +++++++ python/builder.py | 4 + 4 files changed, 507 insertions(+), 5 deletions(-) create mode 100644 python/astra/src/PythonPluginAlgorithm.cpp create mode 100644 python/astra/src/PythonPluginAlgorithm.h (limited to 'python') diff --git a/python/astra/plugin_c.pyx b/python/astra/plugin_c.pyx index 8d6816b..775ccd4 100644 --- a/python/astra/plugin_c.pyx +++ b/python/astra/plugin_c.pyx @@ -32,21 +32,25 @@ import inspect from libcpp.string cimport string from libcpp cimport bool -cdef CPluginAlgorithmFactory *fact = getSingletonPtr() +cdef CPythonPluginAlgorithmFactory *fact = getSingletonPtr() from . import utils -cdef extern from "astra/PluginAlgorithm.h" namespace "astra": - cdef cppclass CPluginAlgorithmFactory: +cdef extern from "src/PythonPluginAlgorithm.h" namespace "astra": + cdef cppclass CPythonPluginAlgorithmFactory: bool registerPlugin(string className) bool registerPlugin(string name, string className) bool registerPluginClass(object className) bool registerPluginClass(string name, object className) object getRegistered() - string getHelp(string name) + string getHelp(string &name) + +cdef extern from "src/PythonPluginAlgorithm.h" namespace "astra::CPythonPluginAlgorithmFactory": + cdef CPythonPluginAlgorithmFactory* getSingletonPtr() cdef extern from "astra/PluginAlgorithm.h" namespace "astra::CPluginAlgorithmFactory": - cdef CPluginAlgorithmFactory* getSingletonPtr() + # NB: Using wrong pointer type here for convenience + cdef void registerFactory(CPythonPluginAlgorithmFactory *) def register(className, name=None): if inspect.isclass(className): @@ -65,3 +69,6 @@ def get_registered(): def get_help(name): return utils.wrap_from_bytes(fact.getHelp(six.b(name))) + +# Register python plugin factory with astra +registerFactory(fact) diff --git a/python/astra/src/PythonPluginAlgorithm.cpp b/python/astra/src/PythonPluginAlgorithm.cpp new file mode 100644 index 0000000..1ea858d --- /dev/null +++ b/python/astra/src/PythonPluginAlgorithm.cpp @@ -0,0 +1,402 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the ASTRA Toolbox. + + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see . + +----------------------------------------------------------------------- +$Id$ +*/ + +#ifdef ASTRA_PYTHON + +#include "PythonPluginAlgorithm.h" + +#include "astra/Logging.h" +#include "astra/Utilities.h" +#include +#include +#include +#include +#include + +#include +#include "bytesobject.h" + +namespace astra { + + + +void logPythonError(){ + if(PyErr_Occurred()){ + PyObject *ptype, *pvalue, *ptraceback; + PyErr_Fetch(&ptype, &pvalue, &ptraceback); + PyErr_NormalizeException(&ptype, &pvalue, &ptraceback); + PyObject *traceback = PyImport_ImportModule("traceback"); + if(traceback!=NULL){ + PyObject *exc; + if(ptraceback==NULL){ + exc = PyObject_CallMethod(traceback,"format_exception_only","OO",ptype, pvalue); + }else{ + exc = PyObject_CallMethod(traceback,"format_exception","OOO",ptype, pvalue, ptraceback); + } + if(exc!=NULL){ + PyObject *six = PyImport_ImportModule("six"); + if(six!=NULL){ + PyObject *iter = PyObject_GetIter(exc); + if(iter!=NULL){ + PyObject *line; + std::string errStr = ""; + while(line = PyIter_Next(iter)){ + PyObject *retb = PyObject_CallMethod(six,"b","O",line); + if(retb!=NULL){ + errStr += std::string(PyBytes_AsString(retb)); + Py_DECREF(retb); + } + Py_DECREF(line); + } + ASTRA_ERROR("%s",errStr.c_str()); + Py_DECREF(iter); + } + Py_DECREF(six); + } + Py_DECREF(exc); + } + Py_DECREF(traceback); + } + if(ptype!=NULL) Py_DECREF(ptype); + if(pvalue!=NULL) Py_DECREF(pvalue); + if(ptraceback!=NULL) Py_DECREF(ptraceback); + } +} + + +CPluginAlgorithm::CPluginAlgorithm(PyObject* pyclass){ + instance = PyObject_CallObject(pyclass, NULL); + if(instance==NULL) logPythonError(); +} + +CPluginAlgorithm::~CPluginAlgorithm(){ + if(instance!=NULL){ + Py_DECREF(instance); + instance = NULL; + } +} + +bool CPluginAlgorithm::initialize(const Config& _cfg){ + if(instance==NULL) return false; + PyObject *cfgDict = XMLNode2dict(_cfg.self); + PyObject *retVal = PyObject_CallMethod(instance, "astra_init", "O",cfgDict); + Py_DECREF(cfgDict); + if(retVal==NULL){ + logPythonError(); + return false; + } + m_bIsInitialized = true; + Py_DECREF(retVal); + return m_bIsInitialized; +} + +void CPluginAlgorithm::run(int _iNrIterations){ + if(instance==NULL) return; + PyGILState_STATE state = PyGILState_Ensure(); + PyObject *retVal = PyObject_CallMethod(instance, "run", "i",_iNrIterations); + if(retVal==NULL){ + logPythonError(); + }else{ + Py_DECREF(retVal); + } + PyGILState_Release(state); +} + +void fixLapackLoading(){ + // When running in Matlab, we need to force numpy + // to use its internal lapack library instead of + // Matlab's MKL library to avoid errors. To do this, + // we set Python's dlopen flags to RTLD_NOW|RTLD_DEEPBIND + // and import 'numpy.linalg.lapack_lite' here. We reset + // Python's dlopen flags afterwards. + PyObject *sys = PyImport_ImportModule("sys"); + if(sys!=NULL){ + PyObject *curFlags = PyObject_CallMethod(sys,"getdlopenflags",NULL); + if(curFlags!=NULL){ + PyObject *retVal = PyObject_CallMethod(sys, "setdlopenflags", "i",10); + if(retVal!=NULL){ + PyObject *lapack = PyImport_ImportModule("numpy.linalg.lapack_lite"); + if(lapack!=NULL){ + Py_DECREF(lapack); + } + PyObject_CallMethod(sys, "setdlopenflags", "O",curFlags); + Py_DECREF(retVal); + } + Py_DECREF(curFlags); + } + Py_DECREF(sys); + } +} + +CPythonPluginAlgorithmFactory::CPythonPluginAlgorithmFactory(){ + if(!Py_IsInitialized()){ + Py_Initialize(); + PyEval_InitThreads(); + } +#ifndef _MSC_VER + if(astra::running_in_matlab) fixLapackLoading(); +#endif + pluginDict = PyDict_New(); + inspect = PyImport_ImportModule("inspect"); + six = PyImport_ImportModule("six"); +} + +CPythonPluginAlgorithmFactory::~CPythonPluginAlgorithmFactory(){ + if(pluginDict!=NULL){ + Py_DECREF(pluginDict); + } + if(inspect!=NULL) Py_DECREF(inspect); + if(six!=NULL) Py_DECREF(six); +} + +PyObject * getClassFromString(std::string str){ + std::vector 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 CPythonPluginAlgorithmFactory::getRegisteredMap(){ + std::map 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 rows, row; + boost::split(rows, str, boost::is_any_of(";")); + PyObject *mat = PyList_New(rows.size()); + for(unsigned int i=0; i vec; + boost::split(vec, str, boost::is_any_of(",")); + PyObject *veclist = PyList_New(vec.size()); + for(unsigned int i=0;i nodes = node.getNodes(); + std::list::iterator it = nodes.begin(); + while(it!=nodes.end()){ + XMLNode subnode = *it; + if(subnode.getName()=="Option"){ + PyObject *obj; + if(subnode.hasAttribute("value")){ + obj = stringToPythonValue(subnode.getAttribute("value")); + }else{ + obj = stringToPythonValue(subnode.getContent()); + } + PyDict_SetItemString(opts, subnode.getAttribute("key").c_str(), obj); + Py_DECREF(obj); + }else{ + PyObject *obj = stringToPythonValue(subnode.getContent()); + PyDict_SetItemString(dct, subnode.getName().c_str(), obj); + Py_DECREF(obj); + } + ++it; + } + PyDict_SetItemString(dct, "options", opts); + Py_DECREF(opts); + return dct; +} + +} +#endif diff --git a/python/astra/src/PythonPluginAlgorithm.h b/python/astra/src/PythonPluginAlgorithm.h new file mode 100644 index 0000000..0b1309e --- /dev/null +++ b/python/astra/src/PythonPluginAlgorithm.h @@ -0,0 +1,89 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the ASTRA Toolbox. + + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see . + +----------------------------------------------------------------------- +$Id$ +*/ + +#ifndef _INC_PYTHONPLUGINALGORITHM +#define _INC_PYTHONPLUGINALGORITHM + +#ifdef ASTRA_PYTHON + +#include "astra/Algorithm.h" +#include "astra/Singleton.h" +#include "astra/XMLDocument.h" +#include "astra/XMLNode.h" +#include "astra/PluginAlgorithm.h" + +#include + +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 { + +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 getRegisteredMap(); + + virtual std::string getHelp(const std::string &name); + +private: + PyObject * pluginDict; + PyObject *inspect, *six; +}; + +PyObject* XMLNode2dict(XMLNode node); + +} + + +#endif + +#endif diff --git a/python/builder.py b/python/builder.py index 018b26b..9a77ecc 100644 --- a/python/builder.py +++ b/python/builder.py @@ -70,6 +70,10 @@ ext_modules = [ ] ext_modules = cythonize("astra/*.pyx", language_level=2) cmdclass = { 'build_ext': build_ext } +for m in ext_modules: + if m.name == 'astra.plugin_c': + m.sources.append('astra/src/PythonPluginAlgorithm.cpp') + setup (name = 'PyASTRAToolbox', version = '1.7.1', description = 'Python interface to the ASTRA-Toolbox', -- cgit v1.2.3 From 7f11ed333cdc93e9e93d4677f857d97ffbbfec87 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Thu, 21 Jan 2016 12:14:44 +0100 Subject: Fix whitespace --- python/astra/src/PythonPluginAlgorithm.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'python') diff --git a/python/astra/src/PythonPluginAlgorithm.cpp b/python/astra/src/PythonPluginAlgorithm.cpp index 1ea858d..0100bed 100644 --- a/python/astra/src/PythonPluginAlgorithm.cpp +++ b/python/astra/src/PythonPluginAlgorithm.cpp @@ -238,7 +238,7 @@ CAlgorithm * CPythonPluginAlgorithmFactory::getPlugin(const std::string &name){ CPluginAlgorithm *alg = NULL; if(PyBytes_Check(className)){ std::string str = std::string(PyBytes_AsString(className)); - PyObject *pyclass = getClassFromString(str); + PyObject *pyclass = getClassFromString(str); if(pyclass!=NULL){ alg = new CPluginAlgorithm(pyclass); Py_DECREF(pyclass); -- cgit v1.2.3 From cf0eff7075d21ccfa985676eb3a5e30f8694fc4c Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 27 Jan 2016 09:48:25 +0100 Subject: Decrement refcount of CallMethod return value --- python/astra/src/PythonPluginAlgorithm.cpp | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'python') diff --git a/python/astra/src/PythonPluginAlgorithm.cpp b/python/astra/src/PythonPluginAlgorithm.cpp index 0100bed..61a56ea 100644 --- a/python/astra/src/PythonPluginAlgorithm.cpp +++ b/python/astra/src/PythonPluginAlgorithm.cpp @@ -144,7 +144,10 @@ void fixLapackLoading(){ if(lapack!=NULL){ Py_DECREF(lapack); } - PyObject_CallMethod(sys, "setdlopenflags", "O",curFlags); + PyObject *retVal2 = PyObject_CallMethod(sys, "setdlopenflags", "O",curFlags); + if(retVal2!=NULL){ + Py_DECREF(retVal2); + } Py_DECREF(retVal); } Py_DECREF(curFlags); -- cgit v1.2.3 From 4a75ab09962015d90acaa3e2be8357a1c917d5eb Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 27 Jan 2016 10:05:57 +0100 Subject: Move fixLapackLoading to astra_mex_plugin --- python/astra/src/PythonPluginAlgorithm.cpp | 32 ------------------------------ 1 file changed, 32 deletions(-) (limited to 'python') diff --git a/python/astra/src/PythonPluginAlgorithm.cpp b/python/astra/src/PythonPluginAlgorithm.cpp index 61a56ea..e34861a 100644 --- a/python/astra/src/PythonPluginAlgorithm.cpp +++ b/python/astra/src/PythonPluginAlgorithm.cpp @@ -127,43 +127,11 @@ void CPluginAlgorithm::run(int _iNrIterations){ PyGILState_Release(state); } -void fixLapackLoading(){ - // When running in Matlab, we need to force numpy - // to use its internal lapack library instead of - // Matlab's MKL library to avoid errors. To do this, - // we set Python's dlopen flags to RTLD_NOW|RTLD_DEEPBIND - // and import 'numpy.linalg.lapack_lite' here. We reset - // Python's dlopen flags afterwards. - PyObject *sys = PyImport_ImportModule("sys"); - if(sys!=NULL){ - PyObject *curFlags = PyObject_CallMethod(sys,"getdlopenflags",NULL); - if(curFlags!=NULL){ - PyObject *retVal = PyObject_CallMethod(sys, "setdlopenflags", "i",10); - if(retVal!=NULL){ - PyObject *lapack = PyImport_ImportModule("numpy.linalg.lapack_lite"); - if(lapack!=NULL){ - Py_DECREF(lapack); - } - PyObject *retVal2 = PyObject_CallMethod(sys, "setdlopenflags", "O",curFlags); - if(retVal2!=NULL){ - Py_DECREF(retVal2); - } - Py_DECREF(retVal); - } - Py_DECREF(curFlags); - } - Py_DECREF(sys); - } -} - CPythonPluginAlgorithmFactory::CPythonPluginAlgorithmFactory(){ if(!Py_IsInitialized()){ Py_Initialize(); PyEval_InitThreads(); } -#ifndef _MSC_VER - if(astra::running_in_matlab) fixLapackLoading(); -#endif pluginDict = PyDict_New(); inspect = PyImport_ImportModule("inspect"); six = PyImport_ImportModule("six"); -- cgit v1.2.3 From d2705f52766716b4d4627a62de92e7a2480b6b86 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Tue, 2 Feb 2016 14:12:41 +0100 Subject: Make copyright/license headers consistent with rest of astra --- python/astra/algorithm_c.pyx | 37 +++++++++++++++--------------- python/astra/astra_c.pyx | 36 ++++++++++++++--------------- python/astra/data2d_c.pyx | 36 ++++++++++++++--------------- python/astra/data3d_c.pyx | 36 ++++++++++++++--------------- python/astra/experimental.pyx | 10 ++++---- python/astra/extrautils.pyx | 35 ++++++++++++++-------------- python/astra/log_c.pyx | 36 ++++++++++++++--------------- python/astra/matrix_c.pyx | 36 ++++++++++++++--------------- python/astra/plugin_c.pyx | 36 ++++++++++++++--------------- python/astra/projector3d_c.pyx | 36 ++++++++++++++--------------- python/astra/projector_c.pyx | 36 ++++++++++++++--------------- python/astra/src/PythonPluginAlgorithm.cpp | 5 ++-- python/astra/src/PythonPluginAlgorithm.h | 5 ++-- python/astra/utils.pyx | 36 ++++++++++++++--------------- python/builder.py | 36 ++++++++++++++--------------- 15 files changed, 224 insertions(+), 228 deletions(-) (limited to 'python') 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 . +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see . +# +# ----------------------------------------------------------------------- # -#----------------------------------------------------------------------- - # distutils: language = c++ # distutils: libraries = astra diff --git a/python/astra/astra_c.pyx b/python/astra/astra_c.pyx index 6b246b6..5075fed 100644 --- a/python/astra/astra_c.pyx +++ b/python/astra/astra_c.pyx @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://sf.net/projects/astra-toolbox # +# This file is part of the ASTRA Toolbox. # -#This file is part of the Python interface to the -#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). # -#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify -#it under the terms of the GNU General Public License as published by -#the Free Software Foundation, either version 3 of the License, or -#(at your option) any later version. +# The ASTRA Toolbox is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. # -#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, -#but WITHOUT ANY WARRANTY; without even the implied warranty of -#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -#GNU General Public License for more details. +# The ASTRA Toolbox is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. # -#You should have received a copy of the GNU General Public License -#along with the Python interface to the ASTRA Toolbox. If not, see . +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see . +# +# ----------------------------------------------------------------------- # -#----------------------------------------------------------------------- # distutils: language = c++ # distutils: libraries = astra diff --git a/python/astra/data2d_c.pyx b/python/astra/data2d_c.pyx index 801fd8e..65e80ce 100644 --- a/python/astra/data2d_c.pyx +++ b/python/astra/data2d_c.pyx @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://sf.net/projects/astra-toolbox # +# This file is part of the ASTRA Toolbox. # -#This file is part of the Python interface to the -#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). # -#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify -#it under the terms of the GNU General Public License as published by -#the Free Software Foundation, either version 3 of the License, or -#(at your option) any later version. +# The ASTRA Toolbox is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. # -#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, -#but WITHOUT ANY WARRANTY; without even the implied warranty of -#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -#GNU General Public License for more details. +# The ASTRA Toolbox is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. # -#You should have received a copy of the GNU General Public License -#along with the Python interface to the ASTRA Toolbox. If not, see . +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see . +# +# ----------------------------------------------------------------------- # -#----------------------------------------------------------------------- # 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 . +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see . +# +# ----------------------------------------------------------------------- # -#----------------------------------------------------------------------- # 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 . # -#----------------------------------------------------------------------- - +# ----------------------------------------------------------------------- +# # 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 . +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see . # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- 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 . +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see . +# +# ----------------------------------------------------------------------- # -#----------------------------------------------------------------------- # 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 . +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see . +# +# ----------------------------------------------------------------------- # -#----------------------------------------------------------------------- # distutils: language = c++ # distutils: libraries = astra diff --git a/python/astra/plugin_c.pyx b/python/astra/plugin_c.pyx index 775ccd4..ee04853 100644 --- a/python/astra/plugin_c.pyx +++ b/python/astra/plugin_c.pyx @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://sf.net/projects/astra-toolbox # +# This file is part of the ASTRA Toolbox. # -#This file is part of the Python interface to the -#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). # -#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify -#it under the terms of the GNU General Public License as published by -#the Free Software Foundation, either version 3 of the License, or -#(at your option) any later version. +# The ASTRA Toolbox is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. # -#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, -#but WITHOUT ANY WARRANTY; without even the implied warranty of -#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -#GNU General Public License for more details. +# The ASTRA Toolbox is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. # -#You should have received a copy of the GNU General Public License -#along with the Python interface to the ASTRA Toolbox. If not, see . +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see . +# +# ----------------------------------------------------------------------- # -#----------------------------------------------------------------------- # distutils: language = c++ # distutils: libraries = astra diff --git a/python/astra/projector3d_c.pyx b/python/astra/projector3d_c.pyx index aec9cde..e355e38 100644 --- a/python/astra/projector3d_c.pyx +++ b/python/astra/projector3d_c.pyx @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://sf.net/projects/astra-toolbox # +# This file is part of the ASTRA Toolbox. # -#This file is part of the Python interface to the -#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). # -#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify -#it under the terms of the GNU General Public License as published by -#the Free Software Foundation, either version 3 of the License, or -#(at your option) any later version. +# The ASTRA Toolbox is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. # -#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, -#but WITHOUT ANY WARRANTY; without even the implied warranty of -#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -#GNU General Public License for more details. +# The ASTRA Toolbox is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. # -#You should have received a copy of the GNU General Public License -#along with the Python interface to the ASTRA Toolbox. If not, see . +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see . +# +# ----------------------------------------------------------------------- # -#----------------------------------------------------------------------- # 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 . +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see . +# +# ----------------------------------------------------------------------- # -#----------------------------------------------------------------------- # distutils: language = c++ # distutils: libraries = astra diff --git a/python/astra/src/PythonPluginAlgorithm.cpp b/python/astra/src/PythonPluginAlgorithm.cpp index e34861a..617c0f4 100644 --- a/python/astra/src/PythonPluginAlgorithm.cpp +++ b/python/astra/src/PythonPluginAlgorithm.cpp @@ -1,7 +1,7 @@ /* ----------------------------------------------------------------------- -Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp - 2014-2015, CWI, Amsterdam +Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp + 2014-2016, CWI, Amsterdam Contact: astra@uantwerpen.be Website: http://sf.net/projects/astra-toolbox @@ -23,7 +23,6 @@ You should have received a copy of the GNU General Public License along with the ASTRA Toolbox. If not, see . ----------------------------------------------------------------------- -$Id$ */ #ifdef ASTRA_PYTHON diff --git a/python/astra/src/PythonPluginAlgorithm.h b/python/astra/src/PythonPluginAlgorithm.h index 0b1309e..ea4c6fb 100644 --- a/python/astra/src/PythonPluginAlgorithm.h +++ b/python/astra/src/PythonPluginAlgorithm.h @@ -1,7 +1,7 @@ /* ----------------------------------------------------------------------- -Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp - 2014-2015, CWI, Amsterdam +Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp + 2014-2016, CWI, Amsterdam Contact: astra@uantwerpen.be Website: http://sf.net/projects/astra-toolbox @@ -23,7 +23,6 @@ You should have received a copy of the GNU General Public License along with the ASTRA Toolbox. If not, see . ----------------------------------------------------------------------- -$Id$ */ #ifndef _INC_PYTHONPLUGINALGORITHM diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx index 07727ce..52c2a8d 100644 --- a/python/astra/utils.pyx +++ b/python/astra/utils.pyx @@ -1,28 +1,28 @@ -#----------------------------------------------------------------------- -#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam # -#Author: Daniel M. Pelt -#Contact: D.M.Pelt@cwi.nl -#Website: http://dmpelt.github.io/pyastratoolbox/ +# Contact: astra@uantwerpen.be +# Website: http://sf.net/projects/astra-toolbox # +# This file is part of the ASTRA Toolbox. # -#This file is part of the Python interface to the -#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). # -#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify -#it under the terms of the GNU General Public License as published by -#the Free Software Foundation, either version 3 of the License, or -#(at your option) any later version. +# The ASTRA Toolbox is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. # -#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, -#but WITHOUT ANY WARRANTY; without even the implied warranty of -#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -#GNU General Public License for more details. +# The ASTRA Toolbox is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. # -#You should have received a copy of the GNU General Public License -#along with the Python interface to the ASTRA Toolbox. If not, see . +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see . +# +# ----------------------------------------------------------------------- # -#----------------------------------------------------------------------- # distutils: language = c++ # distutils: libraries = astra diff --git a/python/builder.py b/python/builder.py index 9a77ecc..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 . +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see . # #----------------------------------------------------------------------- + import sys import os import numpy as np @@ -79,7 +79,7 @@ setup (name = 'PyASTRAToolbox', 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', -- cgit v1.2.3 From 0884a3928395dd368aea61eeef768677018f9095 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 17 Feb 2016 16:18:23 +0100 Subject: Add python astra.astra delete/info based on index manager --- python/astra/PyIndexManager.pxd | 40 ++++++++++++++++++++++++++++++++++++++++ python/astra/astra.py | 20 ++++++++++++++++++++ python/astra/astra_c.pyx | 30 ++++++++++++++++++++++++++++-- 3 files changed, 88 insertions(+), 2 deletions(-) create mode 100644 python/astra/PyIndexManager.pxd (limited to 'python') diff --git a/python/astra/PyIndexManager.pxd b/python/astra/PyIndexManager.pxd new file mode 100644 index 0000000..c1ad502 --- /dev/null +++ b/python/astra/PyIndexManager.pxd @@ -0,0 +1,40 @@ +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, CWI, Amsterdam +# +# Contact: astra@uantwerpen.be +# Website: http://sf.net/projects/astra-toolbox +# +# This file is part of the ASTRA Toolbox. +# +# +# The ASTRA Toolbox is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# The ASTRA Toolbox is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with the ASTRA Toolbox. If not, see . +# +# ----------------------------------------------------------------------- + +from libcpp.string cimport string + +from .PyIncludes cimport * + +cdef extern from "astra/AstraObjectManager.h" namespace "astra": + cdef cppclass CAstraObjectManagerBase: + string getInfo(int) + void remove(int) + string getType() + cdef cppclass CAstraIndexManager: + CAstraObjectManagerBase* get(int) + +cdef extern from "astra/AstraObjectManager.h" namespace "astra::CAstraIndexManager": + cdef CAstraIndexManager* getSingletonPtr() + diff --git a/python/astra/astra.py b/python/astra/astra.py index 9328b6b..61c26ee 100644 --- a/python/astra/astra.py +++ b/python/astra/astra.py @@ -56,3 +56,23 @@ def set_gpu_index(idx, memory=0): :type idx: :class:`int` """ a.set_gpu_index(idx, memory) + +def delete(ids): + """Delete an astra object. + + :param ids: ID or list of ID's to delete. + :type ids: :class:`int` or :class:`list` + + """ + return a.delete(ids) + +def info(ids): + """Print info about an astra object. + + :param ids: ID or list of ID's to show. + :type ids: :class:`int` or :class:`list` + + """ + return a.info(ids) + + diff --git a/python/astra/astra_c.pyx b/python/astra/astra_c.pyx index 2a9c816..c70bb8e 100644 --- a/python/astra/astra_c.pyx +++ b/python/astra/astra_c.pyx @@ -33,6 +33,9 @@ from .utils import wrap_from_bytes from libcpp.string cimport string from libcpp.vector cimport vector from libcpp cimport bool +cimport PyIndexManager +from .PyIndexManager cimport CAstraObjectManagerBase + cdef extern from "astra/Globals.h" namespace "astra": int getVersion() string getVersionString() @@ -51,6 +54,7 @@ cdef extern from "astra/CompositeGeometryManager.h" namespace "astra": cdef extern from "astra/CompositeGeometryManager.h" namespace "astra::CCompositeGeometryManager": void setGlobalGPUParams(SGPUParams&) + def credits(): six.print_("""The ASTRA Toolbox has been developed at the University of Antwerp and CWI, Amsterdam by * Prof. dr. Joost Batenburg @@ -78,11 +82,10 @@ def version(printToScreen=False): return getVersion() def set_gpu_index(idx, memory=0): - import types import collections cdef SGPUParams params if use_cuda()==True: - if not isinstance(idx, collections.Iterable) or isinstance(idx, types.StringTypes): + if not isinstance(idx, collections.Iterable) or isinstance(idx, six.string_types + (six.text_type,six.binary_type)): idx = (idx,) params.memory = memory params.GPUIndices = idx @@ -90,3 +93,26 @@ def set_gpu_index(idx, memory=0): ret = setGPUIndex(params.GPUIndices[0]) if not ret: six.print_("Failed to set GPU " + str(params.GPUIndices[0])) + +def delete(ids): + import collections + cdef CAstraObjectManagerBase* ptr + if not isinstance(ids, collections.Iterable) or isinstance(ids, six.string_types + (six.text_type,six.binary_type)): + ids = (ids,) + for i in ids: + ptr = PyIndexManager.getSingletonPtr().get(i) + if ptr: + ptr.remove(i) + +def info(ids): + import collections + cdef CAstraObjectManagerBase* ptr + if not isinstance(ids, collections.Iterable) or isinstance(ids, six.string_types + (six.text_type,six.binary_type)): + ids = (ids,) + for i in ids: + ptr = PyIndexManager.getSingletonPtr().get(i) + if ptr: + s = ptr.getType() + six.b("\t") + ptr.getInfo(i) + six.print_(wrap_from_bytes(s)) + + -- cgit v1.2.3 From b74e64aef7845666d27cbf7e876a6a360eefed7f Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Mon, 29 Feb 2016 11:01:21 +0100 Subject: Disable astra.set_gpu_index when building without CUDA --- python/astra/astra_c.pyx | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) (limited to 'python') diff --git a/python/astra/astra_c.pyx b/python/astra/astra_c.pyx index 65192b5..baad853 100644 --- a/python/astra/astra_c.pyx +++ b/python/astra/astra_c.pyx @@ -77,7 +77,8 @@ def version(printToScreen=False): else: return getVersion() -def set_gpu_index(idx, memory=0): +IF HAVE_CUDA==True: + def set_gpu_index(idx, memory=0): import types import collections cdef SGPUParams params @@ -90,3 +91,6 @@ def set_gpu_index(idx, memory=0): ret = setGPUIndex(params.GPUIndices[0]) if not ret: six.print_("Failed to set GPU " + str(params.GPUIndices[0])) +ELSE: + def set_gpu_index(idx, memory=0): + raise NotImplementedError("CUDA support is not enabled in ASTRA") -- cgit v1.2.3 From 0fb04ca6fb4fca23b9d1b885b9f075a90542997b Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Wed, 2 Mar 2016 13:49:40 +0100 Subject: Fix small Python errors --- python/astra/data3d.py | 2 +- python/astra/functions.py | 2 +- python/astra/optomo.py | 4 +++- 3 files changed, 5 insertions(+), 3 deletions(-) (limited to 'python') diff --git a/python/astra/data3d.py b/python/astra/data3d.py index e5ef6b0..f143659 100644 --- a/python/astra/data3d.py +++ b/python/astra/data3d.py @@ -89,7 +89,7 @@ def get_single(i): :returns: :class:`numpy.ndarray` -- The object data. """ - return g.get_single(i) + return d.get_single(i) def store(i,data): """Fill existing 3D object with data. diff --git a/python/astra/functions.py b/python/astra/functions.py index e38b5bc..3f4aa82 100644 --- a/python/astra/functions.py +++ b/python/astra/functions.py @@ -115,7 +115,7 @@ def add_noise_to_sino(sinogram_in, I0, seed=None): sinogram_out = -max_sinogramRaw * np.log(sinogramCT_D) if not isinstance(sinogram_in, np.ndarray): - at.data2d.store(sinogram_in, sinogram_out) + data2d.store(sinogram_in, sinogram_out) if not seed==None: np.random.set_state(curstate) diff --git a/python/astra/optomo.py b/python/astra/optomo.py index 4a64150..dd10713 100644 --- a/python/astra/optomo.py +++ b/python/astra/optomo.py @@ -160,7 +160,7 @@ class OpTomo(scipy.sparse.linalg.LinearOperator): return self._matvec(v) return scipy.sparse.linalg.LinearOperator.__mul__(self, v) - def reconstruct(self, method, s, iterations=1, extraOptions = {}): + def reconstruct(self, method, s, iterations=1, extraOptions = None): """Reconstruct an object. :param method: Method to use for reconstruction. @@ -172,6 +172,8 @@ class OpTomo(scipy.sparse.linalg.LinearOperator): :param extraOptions: Extra options to use during reconstruction (i.e. for cfg['option']). :type extraOptions: :class:`dict` """ + if extraOptions is None: + extraOptions={} s = self.__checkArray(s, self.sshape) sid = self.data_mod.link('-sino',self.pg,s) v = np.zeros(self.vshape,dtype=np.float32) -- cgit v1.2.3 From 7acb21aa87fdc98c725f72db456270c63c15b96a Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Thu, 3 Mar 2016 12:23:58 +0100 Subject: Split conda package into c++ lib and python parts --- python/conda/build.sh | 10 +--------- python/conda/libastra/build.sh | 15 +++++++++++++++ python/conda/libastra/meta.yaml | 22 ++++++++++++++++++++++ python/conda/meta.yaml | 7 ++++--- 4 files changed, 42 insertions(+), 12 deletions(-) create mode 100644 python/conda/libastra/build.sh create mode 100644 python/conda/libastra/meta.yaml (limited to 'python') diff --git a/python/conda/build.sh b/python/conda/build.sh index 814ea7e..13ae3f8 100644 --- a/python/conda/build.sh +++ b/python/conda/build.sh @@ -5,12 +5,4 @@ if [ $MAKEOPTS == '' ] 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 +make $MAKEOPTS python-root-install \ No newline at end of file diff --git a/python/conda/libastra/build.sh b/python/conda/libastra/build.sh new file mode 100644 index 0000000..a80b9c4 --- /dev/null +++ b/python/conda/libastra/build.sh @@ -0,0 +1,15 @@ +cd build/linux +./autogen.sh +./configure --with-python --with-cuda=$CUDA_ROOT --prefix=$PREFIX +if [ $MAKEOPTS == '' ] + then + MAKEOPTS="" +fi +make $MAKEOPTS install-libraries +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.* $PREFIX/lib diff --git a/python/conda/libastra/meta.yaml b/python/conda/libastra/meta.yaml new file mode 100644 index 0000000..73fa0d7 --- /dev/null +++ b/python/conda/libastra/meta.yaml @@ -0,0 +1,22 @@ +package: + name: libastra + version: '1.8b' + +source: + git_url: https://github.com/astra-toolbox/astra-toolbox.git + #git_tag: v1.7.1 # Change to 1.8 after release + +build: + number: 0 + script_env: + - CUDA_ROOT + - MAKEOPTS + +about: + home: http://www.astra-toolbox.com + license: GPLv3 + summary: 'The ASTRA Toolbox is a Python toolbox of high-performance GPU primitives for 2D and 3D tomography.' + +# See +# http://docs.continuum.io/conda/build.html for +# more information about meta.yaml diff --git a/python/conda/meta.yaml b/python/conda/meta.yaml index 7e4679b..e6a7f52 100644 --- a/python/conda/meta.yaml +++ b/python/conda/meta.yaml @@ -1,10 +1,10 @@ package: name: astra-toolbox - version: '1.7.1' + version: '1.8b' source: git_url: https://github.com/astra-toolbox/astra-toolbox.git - git_tag: v1.7.1 + #git_tag: v1.7.1 # Change to 1.8 after release build: number: 0 @@ -29,10 +29,11 @@ requirements: - numpy - scipy - six + - libastra ==1.8b about: - home: http://sourceforge.net/p/astra-toolbox/wiki/Home/ + home: http://www.astra-toolbox.com license: GPLv3 summary: 'The ASTRA Toolbox is a Python toolbox of high-performance GPU primitives for 2D and 3D tomography.' -- cgit v1.2.3 From 57b2a752a458266066c1048b9cfacafd7692b943 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Thu, 3 Mar 2016 13:01:38 +0100 Subject: Remove with-python from libastra conda build --- python/conda/libastra/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'python') diff --git a/python/conda/libastra/build.sh b/python/conda/libastra/build.sh index a80b9c4..e1d9700 100644 --- a/python/conda/libastra/build.sh +++ b/python/conda/libastra/build.sh @@ -1,6 +1,6 @@ cd build/linux ./autogen.sh -./configure --with-python --with-cuda=$CUDA_ROOT --prefix=$PREFIX +./configure --with-cuda=$CUDA_ROOT --prefix=$PREFIX if [ $MAKEOPTS == '' ] then MAKEOPTS="" -- cgit v1.2.3 From a3b742fd2dc8ea253addd7342388c73a40f6fd59 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Fri, 4 Mar 2016 18:09:06 +0100 Subject: Encode Python bool as int in XML instead of str --- python/astra/utils.pyx | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) (limited to 'python') diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx index 52c2a8d..34d1902 100644 --- a/python/astra/utils.pyx +++ b/python/astra/utils.pyx @@ -32,7 +32,7 @@ import six if six.PY3: import builtins else: - import __builtin__ + import __builtin__ as builtins from libcpp.string cimport string from libcpp.vector cimport vector from libcpp.list cimport list @@ -95,14 +95,14 @@ cdef void readDict(XMLNode root, _dc): dc = convert_item(_dc) for item in dc: val = dc[item] - if isinstance(val, __builtins__.list) or isinstance(val, tuple): + if isinstance(val, builtins.list) or isinstance(val, tuple): val = np.array(val,dtype=np.float64) if isinstance(val, np.ndarray): if val.size == 0: break listbase = root.addChildNode(item) contig_data = np.ascontiguousarray(val,dtype=np.float64) - data = np.PyArray_DATA(contig_data) + data = np.PyArray_DATA(contig_data) if val.ndim == 2: listbase.setContent(data, val.shape[1], val.shape[0], False) elif val.ndim == 1: @@ -119,6 +119,8 @@ cdef void readDict(XMLNode root, _dc): if item == six.b('type'): root.addAttribute(< string > six.b('type'), wrap_to_bytes(val)) else: + if isinstance(val, builtins.bool): + val = int(val) itm = root.addChildNode(item, wrap_to_bytes(val)) cdef void readOptions(XMLNode node, dc): @@ -131,7 +133,7 @@ cdef void readOptions(XMLNode node, dc): val = dc[item] if node.hasOption(item): raise Exception('Duplicate Option: %s' % item) - if isinstance(val, __builtins__.list) or isinstance(val, tuple): + if isinstance(val, builtins.list) or isinstance(val, tuple): val = np.array(val,dtype=np.float64) if isinstance(val, np.ndarray): if val.size == 0: @@ -147,6 +149,8 @@ cdef void readOptions(XMLNode node, dc): else: raise Exception("Only 1 or 2 dimensions are allowed") else: + if isinstance(val, builtins.bool): + val = int(val) node.addOption(item, wrap_to_bytes(val)) cdef configToDict(Config *cfg): -- cgit v1.2.3 From c58929ca7d0201335b5036773b26f82361793f25 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Tue, 19 Apr 2016 16:40:14 +0200 Subject: Use CXX for Python compilation as well --- python/astra/extrautils.pyx | 2 ++ 1 file changed, 2 insertions(+) (limited to 'python') diff --git a/python/astra/extrautils.pyx b/python/astra/extrautils.pyx index 5bc315f..2c7771e 100644 --- a/python/astra/extrautils.pyx +++ b/python/astra/extrautils.pyx @@ -22,6 +22,8 @@ # along with the ASTRA Toolbox. If not, see . # # ----------------------------------------------------------------------- +# distutils: language = c++ + def clipCircle(img): cdef int i,j -- cgit v1.2.3 From 1e26f7602b6685c584fd4d857353f390622e3a34 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Mon, 25 Apr 2016 10:47:59 +0200 Subject: Change flatten to ravel in Python code --- python/astra/optomo.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'python') diff --git a/python/astra/optomo.py b/python/astra/optomo.py index dd10713..5a92998 100644 --- a/python/astra/optomo.py +++ b/python/astra/optomo.py @@ -125,7 +125,7 @@ class OpTomo(scipy.sparse.linalg.LinearOperator): algorithm.delete(fp_id) self.data_mod.delete([vid,sid]) - return s.flatten() + return s.ravel() def rmatvec(self,s): """Implements the transpose operator. @@ -147,7 +147,7 @@ class OpTomo(scipy.sparse.linalg.LinearOperator): algorithm.delete(bp_id) self.data_mod.delete([vid,sid]) - return v.flatten() + return v.ravel() def __mul__(self,v): """Provides easy forward operator by *. -- cgit v1.2.3 From a33b2a0e4e0663145fb0d4d67a9145948f90341a Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Mon, 25 Apr 2016 11:03:18 +0200 Subject: Reverse output of astra.data3d.dimensions This makes the output directly usable in numpy commands like zeros, reshape. We were not using data3d.dimensions ourselves, as far as I can tell. --- python/astra/data3d_c.pyx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'python') diff --git a/python/astra/data3d_c.pyx b/python/astra/data3d_c.pyx index 207d9a5..811d1e4 100644 --- a/python/astra/data3d_c.pyx +++ b/python/astra/data3d_c.pyx @@ -264,7 +264,7 @@ def store(i,data): def dimensions(i): cdef CFloat32Data3D * pDataObject = getObject(i) - return (pDataObject.getWidth(),pDataObject.getHeight(),pDataObject.getDepth()) + return (pDataObject.getDepth(),pDataObject.getHeight(),pDataObject.getWidth()) def delete(ids): try: -- cgit v1.2.3 From 63e22423350089a37b188a53164867eedab781ac Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Thu, 21 Apr 2016 11:39:51 +0200 Subject: Give OpTomo FP/BP functions with optional out argument This allows more efficient use of allocated arrays. --- python/astra/optomo.py | 96 ++++++++++++++++++++++++++++++++++---------------- 1 file changed, 66 insertions(+), 30 deletions(-) (limited to 'python') diff --git a/python/astra/optomo.py b/python/astra/optomo.py index 5a92998..dde719e 100644 --- a/python/astra/optomo.py +++ b/python/astra/optomo.py @@ -111,21 +111,7 @@ class OpTomo(scipy.sparse.linalg.LinearOperator): :param v: Volume to forward project. :type v: :class:`numpy.ndarray` """ - v = self.__checkArray(v, self.vshape) - vid = self.data_mod.link('-vol',self.vg,v) - s = np.zeros(self.sshape,dtype=np.float32) - sid = self.data_mod.link('-sino',self.pg,s) - - cfg = creators.astra_dict('FP'+self.appendString) - cfg['ProjectionDataId'] = sid - cfg['VolumeDataId'] = vid - cfg['ProjectorId'] = self.proj_id - fp_id = algorithm.create(cfg) - algorithm.run(fp_id) - - algorithm.delete(fp_id) - self.data_mod.delete([vid,sid]) - return s.ravel() + return self.FP(v, out=None).ravel() def rmatvec(self,s): """Implements the transpose operator. @@ -133,21 +119,7 @@ class OpTomo(scipy.sparse.linalg.LinearOperator): :param s: The projection data. :type s: :class:`numpy.ndarray` """ - s = self.__checkArray(s, self.sshape) - sid = self.data_mod.link('-sino',self.pg,s) - v = np.zeros(self.vshape,dtype=np.float32) - vid = self.data_mod.link('-vol',self.vg,v) - - cfg = creators.astra_dict('BP'+self.appendString) - cfg['ProjectionDataId'] = sid - cfg['ReconstructionDataId'] = vid - cfg['ProjectorId'] = self.proj_id - bp_id = algorithm.create(cfg) - algorithm.run(bp_id) - - algorithm.delete(bp_id) - self.data_mod.delete([vid,sid]) - return v.ravel() + return self.BP(s, out=None).ravel() def __mul__(self,v): """Provides easy forward operator by *. @@ -189,6 +161,70 @@ class OpTomo(scipy.sparse.linalg.LinearOperator): self.data_mod.delete([vid,sid]) return v + def FP(self,v,out=None): + """Perform forward projection. + + Output must have the right 2D/3D shape. Input may also be flattened. + + Output must also be contiguous and float32. This isn't required for the + input, but it is more efficient if it is. + + :param v: Volume to forward project. + :type v: :class:`numpy.ndarray` + :param out: Array to store result in. + :type out: :class:`numpy.ndarray` + """ + + v = self.__checkArray(v, self.vshape) + vid = self.data_mod.link('-vol',self.vg,v) + if out is None: + out = np.zeros(self.sshape,dtype=np.float32) + sid = self.data_mod.link('-sino',self.pg,out) + + cfg = creators.astra_dict('FP'+self.appendString) + cfg['ProjectionDataId'] = sid + cfg['VolumeDataId'] = vid + cfg['ProjectorId'] = self.proj_id + fp_id = algorithm.create(cfg) + algorithm.run(fp_id) + + algorithm.delete(fp_id) + self.data_mod.delete([vid,sid]) + return out + + def BP(self,s,out=None): + """Perform backprojection. + + Output must have the right 2D/3D shape. Input may also be flattened. + + Output must also be contiguous and float32. This isn't required for the + input, but it is more efficient if it is. + + :param : The projection data. + :type s: :class:`numpy.ndarray` + :param out: Array to store result in. + :type out: :class:`numpy.ndarray` + """ + s = self.__checkArray(s, self.sshape) + sid = self.data_mod.link('-sino',self.pg,s) + if out is None: + out = np.zeros(self.vshape,dtype=np.float32) + vid = self.data_mod.link('-vol',self.vg,out) + + cfg = creators.astra_dict('BP'+self.appendString) + cfg['ProjectionDataId'] = sid + cfg['ReconstructionDataId'] = vid + cfg['ProjectorId'] = self.proj_id + bp_id = algorithm.create(cfg) + algorithm.run(bp_id) + + algorithm.delete(bp_id) + self.data_mod.delete([vid,sid]) + return out + + + + class OpTomoTranspose(scipy.sparse.linalg.LinearOperator): """This object provides the transpose operation (``.T``) of the OpTomo object. -- cgit v1.2.3