From 3cae1d138c53a3fd042de3d2c9d9a07cf0650e0f Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Tue, 24 Feb 2015 12:35:45 +0100 Subject: Added Python interface --- build/linux/Makefile.in | 45 +- build/linux/configure.ac | 31 +- python/COPYING | 674 +++++++++++++++++ python/LICENSE | 1 + python/astra/ASTRAProjector.py | 138 ++++ python/astra/PyAlgorithmFactory.pxd | 36 + python/astra/PyAlgorithmManager.pxd | 40 + python/astra/PyData2DManager.pxd | 39 + python/astra/PyData3DManager.pxd | 39 + python/astra/PyIncludes.pxd | 215 ++++++ python/astra/PyMatrixManager.pxd | 39 + python/astra/PyProjector2DFactory.pxd | 35 + python/astra/PyProjector2DManager.pxd | 39 + python/astra/PyXMLDocument.pxd | 65 ++ python/astra/__init__.py | 42 ++ python/astra/algorithm.py | 76 ++ python/astra/algorithm_c.pyx | 106 +++ python/astra/astra.py | 58 ++ python/astra/astra_c.pyx | 79 ++ python/astra/creators.py | 563 ++++++++++++++ python/astra/data2d.py | 120 +++ python/astra/data2d_c.pyx | 241 ++++++ python/astra/data3d.py | 108 +++ python/astra/data3d_c.pyx | 188 +++++ python/astra/extrautils.pyx | 43 ++ python/astra/functions.py | 270 +++++++ python/astra/matlab.py | 112 +++ python/astra/matrix.py | 86 +++ python/astra/matrix_c.pyx | 116 +++ python/astra/projector.py | 100 +++ python/astra/projector_c.pyx | 119 +++ python/astra/utils.pxd | 37 + python/astra/utils.pyx | 260 +++++++ python/builder.py | 70 ++ python/doc | 1 + python/docSRC/ASTRAProjector.rst | 8 + python/docSRC/Makefile | 153 ++++ .../docSRC/_build/doctrees/ASTRAProjector.doctree | Bin 0 -> 40455 bytes python/docSRC/_build/doctrees/algorithm.doctree | Bin 0 -> 26360 bytes python/docSRC/_build/doctrees/astra.doctree | Bin 0 -> 18750 bytes python/docSRC/_build/doctrees/creators.doctree | Bin 0 -> 147449 bytes python/docSRC/_build/doctrees/data2d.doctree | Bin 0 -> 48456 bytes python/docSRC/_build/doctrees/data3d.doctree | Bin 0 -> 43583 bytes python/docSRC/_build/doctrees/environment.pickle | Bin 0 -> 2590052 bytes python/docSRC/_build/doctrees/functions.doctree | Bin 0 -> 35085 bytes python/docSRC/_build/doctrees/index.doctree | Bin 0 -> 7240 bytes python/docSRC/_build/doctrees/matlab.doctree | Bin 0 -> 28503 bytes python/docSRC/_build/doctrees/matrix.doctree | Bin 0 -> 30783 bytes python/docSRC/_build/doctrees/projector.doctree | Bin 0 -> 36968 bytes python/docSRC/_build/html/.buildinfo | 4 + python/docSRC/_build/html/ASTRAProjector.html | 235 ++++++ .../_build/html/_modules/astra/ASTRAProjector.html | 243 +++++++ .../_build/html/_modules/astra/algorithm.html | 181 +++++ .../docSRC/_build/html/_modules/astra/astra.html | 163 +++++ .../_build/html/_modules/astra/creators.html | 668 +++++++++++++++++ .../docSRC/_build/html/_modules/astra/data2d.html | 225 ++++++ .../docSRC/_build/html/_modules/astra/data3d.html | 213 ++++++ .../_build/html/_modules/astra/functions.html | 375 ++++++++++ .../docSRC/_build/html/_modules/astra/matlab.html | 217 ++++++ .../docSRC/_build/html/_modules/astra/matrix.html | 191 +++++ .../_build/html/_modules/astra/projector.html | 205 ++++++ python/docSRC/_build/html/_modules/index.html | 112 +++ .../docSRC/_build/html/_sources/ASTRAProjector.txt | 8 + python/docSRC/_build/html/_sources/algorithm.txt | 8 + python/docSRC/_build/html/_sources/astra.txt | 8 + python/docSRC/_build/html/_sources/creators.txt | 8 + python/docSRC/_build/html/_sources/data2d.txt | 8 + python/docSRC/_build/html/_sources/data3d.txt | 8 + python/docSRC/_build/html/_sources/functions.txt | 8 + python/docSRC/_build/html/_sources/index.txt | 34 + python/docSRC/_build/html/_sources/matlab.txt | 8 + python/docSRC/_build/html/_sources/matrix.txt | 8 + python/docSRC/_build/html/_sources/projector.txt | 8 + python/docSRC/_build/html/_static/ajax-loader.gif | Bin 0 -> 673 bytes python/docSRC/_build/html/_static/basic.css | 537 ++++++++++++++ .../docSRC/_build/html/_static/comment-bright.png | Bin 0 -> 3500 bytes .../docSRC/_build/html/_static/comment-close.png | Bin 0 -> 3578 bytes python/docSRC/_build/html/_static/comment.png | Bin 0 -> 3445 bytes python/docSRC/_build/html/_static/default.css | 256 +++++++ python/docSRC/_build/html/_static/doctools.js | 238 ++++++ python/docSRC/_build/html/_static/down-pressed.png | Bin 0 -> 368 bytes python/docSRC/_build/html/_static/down.png | Bin 0 -> 363 bytes python/docSRC/_build/html/_static/file.png | Bin 0 -> 392 bytes python/docSRC/_build/html/_static/jquery.js | 2 + python/docSRC/_build/html/_static/minus.png | Bin 0 -> 199 bytes python/docSRC/_build/html/_static/plus.png | Bin 0 -> 199 bytes python/docSRC/_build/html/_static/pygments.css | 63 ++ python/docSRC/_build/html/_static/searchtools.js | 622 ++++++++++++++++ python/docSRC/_build/html/_static/sidebar.js | 159 ++++ python/docSRC/_build/html/_static/underscore.js | 31 + python/docSRC/_build/html/_static/up-pressed.png | Bin 0 -> 372 bytes python/docSRC/_build/html/_static/up.png | Bin 0 -> 363 bytes python/docSRC/_build/html/_static/websupport.js | 808 +++++++++++++++++++++ python/docSRC/_build/html/algorithm.html | 205 ++++++ python/docSRC/_build/html/astra.html | 169 +++++ python/docSRC/_build/html/creators.html | 520 +++++++++++++ python/docSRC/_build/html/data2d.html | 277 +++++++ python/docSRC/_build/html/data3d.html | 259 +++++++ python/docSRC/_build/html/functions.html | 236 ++++++ python/docSRC/_build/html/genindex.html | 575 +++++++++++++++ python/docSRC/_build/html/index.html | 148 ++++ python/docSRC/_build/html/matlab.html | 184 +++++ python/docSRC/_build/html/matrix.html | 221 ++++++ python/docSRC/_build/html/objects.inv | Bin 0 -> 928 bytes python/docSRC/_build/html/projector.html | 234 ++++++ python/docSRC/_build/html/py-modindex.html | 172 +++++ python/docSRC/_build/html/search.html | 118 +++ python/docSRC/_build/html/searchindex.js | 1 + python/docSRC/_templates/layout.html | 15 + python/docSRC/algorithm.rst | 8 + python/docSRC/astra.rst | 8 + python/docSRC/conf.py | 287 ++++++++ python/docSRC/creators.rst | 8 + python/docSRC/data2d.rst | 8 + python/docSRC/data3d.rst | 8 + python/docSRC/functions.rst | 8 + python/docSRC/index.rst | 34 + python/docSRC/make.bat | 190 +++++ python/docSRC/matlab.rst | 8 + python/docSRC/matrix.rst | 8 + python/docSRC/projector.rst | 8 + samples/matlab/s001_sinogram_par2d.m | 33 + samples/matlab/s002_data2d.m | 60 ++ samples/matlab/s003_gpu_reconstruction.m | 52 ++ samples/matlab/s004_cpu_reconstruction.m | 60 ++ samples/matlab/s005_3d_geometry.m | 98 +++ samples/matlab/s006_3d_data.m | 62 ++ samples/matlab/s007_3d_reconstruction.m | 53 ++ samples/matlab/s008_gpu_selection.m | 37 + samples/matlab/s009_projection_matrix.m | 45 ++ samples/matlab/s010_supersampling.m | 58 ++ samples/matlab/s011_object_info.m | 36 + samples/matlab/s012_masks.m | 60 ++ samples/matlab/s013_constraints.m | 47 ++ samples/matlab/s014_FBP.m | 47 ++ samples/matlab/s015_fp_bp.m | 62 ++ samples/matlab/s016_plots.m | 54 ++ samples/python/phantom.mat | Bin 0 -> 5583 bytes samples/python/s001_sinogram_par2d.py | 60 ++ samples/python/s002_data2d.py | 77 ++ samples/python/s003_gpu_reconstruction.py | 75 ++ samples/python/s004_cpu_reconstruction.py | 81 +++ samples/python/s005_3d_geometry.py | 114 +++ samples/python/s006_3d_data.py | 76 ++ samples/python/s007_3d_reconstruction.py | 77 ++ samples/python/s008_gpu_selection.py | 61 ++ samples/python/s009_projection_matrix.py | 65 ++ samples/python/s010_supersampling.py | 85 +++ samples/python/s011_object_info.py | 54 ++ samples/python/s012_masks.py | 92 +++ samples/python/s013_constraints.py | 77 ++ samples/python/s014_FBP.py | 76 ++ samples/python/s015_fp_bp.py | 86 +++ samples/python/s016_plots.py | 86 +++ samples/s001_sinogram_par2d.m | 33 - samples/s002_data2d.m | 60 -- samples/s003_gpu_reconstruction.m | 52 -- samples/s004_cpu_reconstruction.m | 60 -- samples/s005_3d_geometry.m | 98 --- samples/s006_3d_data.m | 62 -- samples/s007_3d_reconstruction.m | 53 -- samples/s008_gpu_selection.m | 37 - samples/s009_projection_matrix.m | 45 -- samples/s010_supersampling.m | 58 -- samples/s011_object_info.m | 36 - samples/s012_masks.m | 60 -- samples/s013_constraints.m | 47 -- samples/s014_FBP.m | 47 -- samples/s015_fp_bp.m | 62 -- samples/s016_plots.m | 54 -- 170 files changed, 16268 insertions(+), 873 deletions(-) create mode 100644 python/COPYING create mode 120000 python/LICENSE create mode 100644 python/astra/ASTRAProjector.py create mode 100644 python/astra/PyAlgorithmFactory.pxd create mode 100644 python/astra/PyAlgorithmManager.pxd create mode 100644 python/astra/PyData2DManager.pxd create mode 100644 python/astra/PyData3DManager.pxd create mode 100644 python/astra/PyIncludes.pxd create mode 100644 python/astra/PyMatrixManager.pxd create mode 100644 python/astra/PyProjector2DFactory.pxd create mode 100644 python/astra/PyProjector2DManager.pxd create mode 100644 python/astra/PyXMLDocument.pxd create mode 100644 python/astra/__init__.py create mode 100644 python/astra/algorithm.py create mode 100644 python/astra/algorithm_c.pyx create mode 100644 python/astra/astra.py create mode 100644 python/astra/astra_c.pyx create mode 100644 python/astra/creators.py create mode 100644 python/astra/data2d.py create mode 100644 python/astra/data2d_c.pyx create mode 100644 python/astra/data3d.py create mode 100644 python/astra/data3d_c.pyx create mode 100644 python/astra/extrautils.pyx create mode 100644 python/astra/functions.py create mode 100644 python/astra/matlab.py create mode 100644 python/astra/matrix.py create mode 100644 python/astra/matrix_c.pyx create mode 100644 python/astra/projector.py create mode 100644 python/astra/projector_c.pyx create mode 100644 python/astra/utils.pxd create mode 100644 python/astra/utils.pyx create mode 100644 python/builder.py create mode 120000 python/doc create mode 100644 python/docSRC/ASTRAProjector.rst create mode 100644 python/docSRC/Makefile create mode 100644 python/docSRC/_build/doctrees/ASTRAProjector.doctree create mode 100644 python/docSRC/_build/doctrees/algorithm.doctree create mode 100644 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python/docSRC/matlab.rst create mode 100644 python/docSRC/matrix.rst create mode 100644 python/docSRC/projector.rst create mode 100644 samples/matlab/s001_sinogram_par2d.m create mode 100644 samples/matlab/s002_data2d.m create mode 100644 samples/matlab/s003_gpu_reconstruction.m create mode 100644 samples/matlab/s004_cpu_reconstruction.m create mode 100644 samples/matlab/s005_3d_geometry.m create mode 100644 samples/matlab/s006_3d_data.m create mode 100644 samples/matlab/s007_3d_reconstruction.m create mode 100644 samples/matlab/s008_gpu_selection.m create mode 100644 samples/matlab/s009_projection_matrix.m create mode 100644 samples/matlab/s010_supersampling.m create mode 100644 samples/matlab/s011_object_info.m create mode 100644 samples/matlab/s012_masks.m create mode 100644 samples/matlab/s013_constraints.m create mode 100644 samples/matlab/s014_FBP.m create mode 100644 samples/matlab/s015_fp_bp.m create mode 100644 samples/matlab/s016_plots.m create mode 100644 samples/python/phantom.mat create mode 100644 samples/python/s001_sinogram_par2d.py create mode 100644 samples/python/s002_data2d.py create mode 100644 samples/python/s003_gpu_reconstruction.py create mode 100644 samples/python/s004_cpu_reconstruction.py create mode 100644 samples/python/s005_3d_geometry.py create mode 100644 samples/python/s006_3d_data.py create mode 100644 samples/python/s007_3d_reconstruction.py create mode 100644 samples/python/s008_gpu_selection.py create mode 100644 samples/python/s009_projection_matrix.py create mode 100644 samples/python/s010_supersampling.py create mode 100644 samples/python/s011_object_info.py create mode 100644 samples/python/s012_masks.py create mode 100644 samples/python/s013_constraints.py create mode 100644 samples/python/s014_FBP.py create mode 100644 samples/python/s015_fp_bp.py create mode 100644 samples/python/s016_plots.py delete mode 100644 samples/s001_sinogram_par2d.m delete mode 100644 samples/s002_data2d.m delete mode 100644 samples/s003_gpu_reconstruction.m delete mode 100644 samples/s004_cpu_reconstruction.m delete mode 100644 samples/s005_3d_geometry.m delete mode 100644 samples/s006_3d_data.m delete mode 100644 samples/s007_3d_reconstruction.m delete mode 100644 samples/s008_gpu_selection.m delete mode 100644 samples/s009_projection_matrix.m delete mode 100644 samples/s010_supersampling.m delete mode 100644 samples/s011_object_info.m delete mode 100644 samples/s012_masks.m delete mode 100644 samples/s013_constraints.m delete mode 100644 samples/s014_FBP.m delete mode 100644 samples/s015_fp_bp.m delete mode 100644 samples/s016_plots.m diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 685e1e5..fe1ba91 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -1,5 +1,7 @@ cuda=@HAVECUDA@ matlab=@HAVEMATLAB@ +python=@HAVEPYTHON@ + MATLAB_ROOT=@MATLAB_ROOT@ @@ -9,6 +11,10 @@ ifeq ($(matlab),yes) TARGETS+=mex endif +ifeq ($(python),yes) +TARGETS+=py +endif + all: $(TARGETS) prefix=@prefix@ @@ -39,6 +45,14 @@ CXXFLAGS+=-fopenmp LDFLAGS+=-fopenmp endif +ifeq ($(python),yes) +PYCPPFLAGS = ${CPPFLAGS} +PYCPPFLAGS += -I../include +PYLDFLAGS = ${LDFLAGS} +PYLDFLAGS += -L../build/linux/.libs +PYTHON = @PYTHON@ +endif + BOOST_CPPFLAGS= BOOST_LDFLAGS= @@ -53,7 +67,7 @@ LD=@CXX@ SHELL=@SHELL@ ifeq ($(matlab),yes) -MEXFLAGS = -cxx +MEXFLAGS = -cxx MEXLDFLAGS='$$LDFLAGS $(LDFLAGS)' MEXLIBS = -L.libs -lut MEXSUFFIX = @MEXSUFFIX@ @@ -226,6 +240,14 @@ mex: $(MATLAB_MEX) $(MEX) LDFLAGS=$(MEXLDFLAGS) $(MEXFLAGS) $(LIBS) $(MEXLIBS) -lastra -output $* $*.o $(MATLAB_CXX_OBJECTS) endif +ifeq ($(python),yes) +py: libastra.la + cd ../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py install \ + --install-base=./finalbuild --install-headers=./finalbuild --install-purelib=./finalbuild \ + --install-platlib=./finalbuild --install-scripts=./finalbuild --install-data=./finalbuild +endif + + libastra.la: $(ALL_OBJECTS) ./libtool --mode=link --tag=CXX $(LD) -rpath $(LIBDIR) -o $@ $(LDFLAGS) $(LIBS) $+ @@ -278,6 +300,8 @@ clean: rm -f $(addsuffix /*.d,$(DEPDIRS)) rm -f $(addsuffix /*,$(LIBDIRS)) rm -f $(TEST_OBJECTS) test.bin + rm -fr ../../python/finalbuild/ + rm -fr ../../python/build/ distclean: clean rm -f config.guess config.sub ltmain.sh libtool install-sh @@ -286,7 +310,7 @@ distclean: clean rm -rf autom4te.cache rm -f configure Makefile -install: install-libraries install-matlab +install: install-libraries install-matlab install-python install-libraries: libastra.la ./install-sh -m 755 -d @libdir@ @@ -306,6 +330,23 @@ else install-matlab: endif +ifeq ($(python),yes) +# TODO: This install location doesn't work well for /usr or /usr/local +install-python: py + ./install-sh -m 755 -d @prefix@/python + ./install-sh -m 755 -d @prefix@/python/astra + ./install-sh -m 644 ../../python/finalbuild/astra/*.so @prefix@/python/astra + ./install-sh -m 644 ../../python/finalbuild/astra/*.py @prefix@/python/astra + ./install-sh -m 644 ../../python/finalbuild/*.egg-info @prefix@/python/ + @echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++" + @echo "To use ASTRA in Python, add @prefix@/python/ to your PYTHONPATH" + @echo "and @libdir@ to your LD_LIBRARY_PATH." + @echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++" +# TODO: docs +else +install-python: +endif + Makefile: Makefile.in config.status CONFIG_HEADERS= CONFIG_LINKS= CONFIG_FILES=$@ $(SHELL) ./config.status diff --git a/build/linux/configure.ac b/build/linux/configure.ac index f99c4d3..7ad03c3 100644 --- a/build/linux/configure.ac +++ b/build/linux/configure.ac @@ -1,26 +1,26 @@ dnl ----------------------------------------------------------------------- dnl Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp dnl 2014-2015, CWI, Amsterdam -dnl +dnl dnl Contact: astra@uantwerpen.be dnl Website: http://sf.net/projects/astra-toolbox -dnl +dnl dnl This file is part of the ASTRA Toolbox. -dnl -dnl +dnl +dnl dnl The ASTRA Toolbox is free software: you can redistribute it and/or modify dnl it under the terms of the GNU General Public License as published by dnl the Free Software Foundation, either version 3 of the License, or dnl (at your option) any later version. -dnl +dnl dnl The ASTRA Toolbox is distributed in the hope that it will be useful, dnl but WITHOUT ANY WARRANTY; without even the implied warranty of dnl MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the dnl GNU General Public License for more details. -dnl +dnl dnl You should have received a copy of the GNU General Public License dnl along with the ASTRA Toolbox. If not, see . -dnl +dnl dnl ----------------------------------------------------------------------- dnl $Id$ @@ -166,6 +166,23 @@ fi AC_SUBST(HAVEMATLAB) +# python + +AC_ARG_WITH(python, [[ --with-python=path path of Python (optional)]],,) + +PY_PATH=$PATH +HAVEPYTHON=no +if test x"$with_python" != x; then + PY_PATH="$with_python:$PY_PATH" + AC_PATH_PROG([PYTHON], [python], [no], [$PY_PATH]) + if test x"$PYTHON" != xno; then + HAVEPYTHON=yes + AC_SUBST(PYTHON) + fi +fi + +AC_SUBST(HAVEPYTHON) + # TODO: diff --git a/python/COPYING b/python/COPYING new file mode 100644 index 0000000..94a9ed0 --- /dev/null +++ b/python/COPYING @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. We, the Free Software Foundation, use the +GNU General Public License for most of our software; it applies also to +any other work released this way by its authors. You can apply it to +your programs, too. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + + To protect your rights, we need to prevent others from denying you +these rights or asking you to surrender the rights. Therefore, you have +certain responsibilities if you distribute copies of the software, or if +you modify it: responsibilities to respect the freedom of others. + + For example, if you distribute copies of such a program, whether +gratis or for a fee, you must pass on to the recipients the same +freedoms that you received. You must make sure that they, too, receive +or can get the source code. And you must show them these terms so they +know their rights. + + Developers that use the GNU GPL protect your rights with two steps: +(1) assert copyright on the software, and (2) offer you this License +giving you legal permission to copy, distribute and/or modify it. + + For the developers' and authors' protection, the GPL clearly explains +that there is no warranty for this free software. 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If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/python/LICENSE b/python/LICENSE new file mode 120000 index 0000000..d24842f --- /dev/null +++ b/python/LICENSE @@ -0,0 +1 @@ +COPYING \ No newline at end of file diff --git a/python/astra/ASTRAProjector.py b/python/astra/ASTRAProjector.py new file mode 100644 index 0000000..96acb10 --- /dev/null +++ b/python/astra/ASTRAProjector.py @@ -0,0 +1,138 @@ +#----------------------------------------------------------------------- +#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 . +# +#----------------------------------------------------------------------- + +import math +from . import creators as ac +from . import data2d + + +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) + + +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) + + 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 + + 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 + + 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) diff --git a/python/astra/PyAlgorithmFactory.pxd b/python/astra/PyAlgorithmFactory.pxd new file mode 100644 index 0000000..256d7b2 --- /dev/null +++ b/python/astra/PyAlgorithmFactory.pxd @@ -0,0 +1,36 @@ +#----------------------------------------------------------------------- +#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 libcpp.string cimport string +from libcpp cimport bool +from .PyIncludes cimport * + +cdef extern from "astra/AstraObjectFactory.h" namespace "astra": + cdef cppclass CAlgorithmFactory: + CAlgorithmFactory() + CAlgorithm *create(string) + +cdef extern from "astra/AstraObjectFactory.h" namespace "astra::CAlgorithmFactory": + cdef CAlgorithmFactory* getSingletonPtr() diff --git a/python/astra/PyAlgorithmManager.pxd b/python/astra/PyAlgorithmManager.pxd new file mode 100644 index 0000000..a99a807 --- /dev/null +++ b/python/astra/PyAlgorithmManager.pxd @@ -0,0 +1,40 @@ +#----------------------------------------------------------------------- +#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 libcpp.string cimport string +from libcpp cimport bool +from .PyIncludes cimport * + +cdef extern from "astra/AstraObjectManager.h" namespace "astra": + cdef cppclass CAlgorithmManager: + int store(CAlgorithm *) + CAlgorithm * get(int) + void remove(int) + void clear() + string info() + +cdef extern from "astra/AstraObjectManager.h" namespace "astra::CAlgorithmManager": + cdef CAlgorithmManager* getSingletonPtr() + diff --git a/python/astra/PyData2DManager.pxd b/python/astra/PyData2DManager.pxd new file mode 100644 index 0000000..db8ec84 --- /dev/null +++ b/python/astra/PyData2DManager.pxd @@ -0,0 +1,39 @@ +#----------------------------------------------------------------------- +#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 libcpp.string cimport string + +from .PyIncludes cimport * + +cdef extern from "astra/AstraObjectManager.h" namespace "astra": + cdef cppclass CData2DManager: + string info() + void clear() + void remove(int i) + int store(CFloat32Data2D *) + CFloat32Data2D * get(int i) + +cdef extern from "astra/AstraObjectManager.h" namespace "astra::CData2DManager": + cdef CData2DManager* getSingletonPtr() diff --git a/python/astra/PyData3DManager.pxd b/python/astra/PyData3DManager.pxd new file mode 100644 index 0000000..9264a82 --- /dev/null +++ b/python/astra/PyData3DManager.pxd @@ -0,0 +1,39 @@ +#----------------------------------------------------------------------- +#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 libcpp.string cimport string + +from .PyIncludes cimport * + +cdef extern from "astra/AstraObjectManager.h" namespace "astra": + cdef cppclass CData3DManager: + string info() + void clear() + void remove(int i) + int store(CFloat32Data3D *) + CFloat32Data3D * get(int i) + +cdef extern from "astra/AstraObjectManager.h" namespace "astra::CData3DManager": + cdef CData3DManager* getSingletonPtr() diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd new file mode 100644 index 0000000..fc5980f --- /dev/null +++ b/python/astra/PyIncludes.pxd @@ -0,0 +1,215 @@ +#----------------------------------------------------------------------- +#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 libcpp cimport bool +from libcpp.string cimport string +from .PyXMLDocument cimport XMLNode + +cdef extern from "astra/Globals.h" namespace "astra": + ctypedef float float32 + ctypedef double float64 + ctypedef unsigned short int uint16 + ctypedef signed short int sint16 + ctypedef unsigned char uchar8 + ctypedef signed char schar8 + ctypedef int int32 + ctypedef short int int16 + +cdef extern from "astra/Config.h" namespace "astra": + cdef cppclass Config: + Config() + XMLNode *self + +cdef extern from "astra/VolumeGeometry2D.h" namespace "astra": + cdef cppclass CVolumeGeometry2D: + bool initialize(Config) + int getGridColCount() + int getGridRowCount() + int getGridTotCount() + float32 getWindowLengthX() + float32 getWindowLengthY() + float32 getWindowArea() + float32 getPixelLengthX() + float32 getPixelLengthY() + float32 getPixelArea() + float32 getWindowMinX() + float32 getWindowMinY() + float32 getWindowMaxX() + float32 getWindowMaxY() + + +cdef extern from "astra/Float32VolumeData2D.h" namespace "astra": + cdef cppclass CFloat32VolumeData2D: + CFloat32VolumeData2D(CVolumeGeometry2D*) + CVolumeGeometry2D * getGeometry() + int getWidth() + int getHeight() + void changeGeometry(CVolumeGeometry2D*) + + + +cdef extern from "astra/ProjectionGeometry2D.h" namespace "astra": + cdef cppclass CProjectionGeometry2D: + CProjectionGeometry2D() + bool initialize(Config) + int getDetectorCount() + int getProjectionAngleCount() + bool isOfType(string) + float32 getProjectionAngle(int) + float32 getDetectorWidth() + +cdef extern from "astra/Float32Data2D.h" namespace "astra::CFloat32Data2D": + cdef enum EDataType: + BASE,PROJECTION,VOLUME + +cdef extern from "astra/Float32Data2D.h" namespace "astra": + cdef cppclass CFloat32Data2D: + bool isInitialized() + int getSize() + float32 *getData() + float32 **getData2D() + int getWidth() + int getHeight() + EDataType getType() + + + + +cdef extern from "astra/SparseMatrixProjectionGeometry2D.h" namespace "astra": + cdef cppclass CSparseMatrixProjectionGeometry2D: + CSparseMatrixProjectionGeometry2D() + +cdef extern from "astra/FanFlatProjectionGeometry2D.h" namespace "astra": + cdef cppclass CFanFlatProjectionGeometry2D: + CFanFlatProjectionGeometry2D() + +cdef extern from "astra/FanFlatVecProjectionGeometry2D.h" namespace "astra": + cdef cppclass CFanFlatVecProjectionGeometry2D: + CFanFlatVecProjectionGeometry2D() + +cdef extern from "astra/ParallelProjectionGeometry2D.h" namespace "astra": + cdef cppclass CParallelProjectionGeometry2D: + CParallelProjectionGeometry2D() + + +cdef extern from "astra/Float32ProjectionData2D.h" namespace "astra": + cdef cppclass CFloat32ProjectionData2D: + CFloat32ProjectionData2D(CProjectionGeometry2D*) + CProjectionGeometry2D * getGeometry() + void changeGeometry(CProjectionGeometry2D*) + int getDetectorCount() + int getAngleCount() + +cdef extern from "astra/Algorithm.h" namespace "astra": + cdef cppclass CAlgorithm: + bool initialize(Config) + void run(int) + bool isInitialized() + +cdef extern from "astra/ReconstructionAlgorithm2D.h" namespace "astra": + cdef cppclass CReconstructionAlgorithm2D: + bool getResidualNorm(float32&) + +cdef extern from "astra/Projector2D.h" namespace "astra": + cdef cppclass CProjector2D: + bool isInitialized() + CProjectionGeometry2D* getProjectionGeometry() + CVolumeGeometry2D* getVolumeGeometry() + CSparseMatrix* getMatrix() + +cdef extern from "astra/SparseMatrix.h" namespace "astra": + cdef cppclass CSparseMatrix: + CSparseMatrix(unsigned int,unsigned int,unsigned long) + unsigned int m_iWidth + unsigned int m_iHeight + unsigned long m_lSize + bool isInitialized() + float32* m_pfValues + unsigned int* m_piColIndices + unsigned long* m_plRowStarts + +cdef extern from "astra/Float32Data3DMemory.h" namespace "astra": + cdef cppclass CFloat32Data3DMemory: + CFloat32Data3DMemory() + bool isInitialized() + int getSize() + int getWidth() + int getHeight() + int getDepth() + void updateStatistics() + float32 *getData() + float32 ***getData3D() + + +cdef extern from "astra/VolumeGeometry3D.h" namespace "astra": + cdef cppclass CVolumeGeometry3D: + CVolumeGeometry3D() + bool initialize(Config) + +cdef extern from "astra/ProjectionGeometry3D.h" namespace "astra": + cdef cppclass CProjectionGeometry3D: + CProjectionGeometry3D() + bool initialize(Config) + + +cdef extern from "astra/Float32VolumeData3DMemory.h" namespace "astra": + cdef cppclass CFloat32VolumeData3DMemory: + CFloat32VolumeData3DMemory(CVolumeGeometry3D*) + + +cdef extern from "astra/ParallelProjectionGeometry3D.h" namespace "astra": + cdef cppclass CParallelProjectionGeometry3D: + CParallelProjectionGeometry3D() + +cdef extern from "astra/ParallelVecProjectionGeometry3D.h" namespace "astra": + cdef cppclass CParallelVecProjectionGeometry3D: + CParallelVecProjectionGeometry3D() + +cdef extern from "astra/ConeProjectionGeometry3D.h" namespace "astra": + cdef cppclass CConeProjectionGeometry3D: + CConeProjectionGeometry3D() + bool initialize(Config) + +cdef extern from "astra/ConeVecProjectionGeometry3D.h" namespace "astra": + cdef cppclass CConeVecProjectionGeometry3D: + CConeVecProjectionGeometry3D() + +cdef extern from "astra/Float32ProjectionData3DMemory.h" namespace "astra": + cdef cppclass CFloat32ProjectionData3DMemory: + CFloat32ProjectionData3DMemory(CProjectionGeometry3D*) + CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*) + +cdef extern from "astra/Float32Data3D.h" namespace "astra": + cdef cppclass CFloat32Data3D: + CFloat32Data3D() + bool isInitialized() + int getSize() + int getWidth() + int getHeight() + int getDepth() + void updateStatistics() + + + diff --git a/python/astra/PyMatrixManager.pxd b/python/astra/PyMatrixManager.pxd new file mode 100644 index 0000000..b2b84c4 --- /dev/null +++ b/python/astra/PyMatrixManager.pxd @@ -0,0 +1,39 @@ +#----------------------------------------------------------------------- +#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 libcpp.string cimport string + +from .PyIncludes cimport * + +cdef extern from "astra/AstraObjectManager.h" namespace "astra": + cdef cppclass CMatrixManager: + string info() + void clear() + void remove(int i) + int store(CSparseMatrix *) + CSparseMatrix * get(int i) + +cdef extern from "astra/AstraObjectManager.h" namespace "astra::CMatrixManager": + cdef CMatrixManager* getSingletonPtr() diff --git a/python/astra/PyProjector2DFactory.pxd b/python/astra/PyProjector2DFactory.pxd new file mode 100644 index 0000000..3314544 --- /dev/null +++ b/python/astra/PyProjector2DFactory.pxd @@ -0,0 +1,35 @@ +#----------------------------------------------------------------------- +#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 libcpp.string cimport string +from libcpp cimport bool +from .PyIncludes cimport * + +cdef extern from "astra/AstraObjectFactory.h" namespace "astra": + cdef cppclass CProjector2DFactory: + CProjector2D *create(Config) + +cdef extern from "astra/AstraObjectFactory.h" namespace "astra::CProjector2DFactory": + cdef CProjector2DFactory* getSingletonPtr() diff --git a/python/astra/PyProjector2DManager.pxd b/python/astra/PyProjector2DManager.pxd new file mode 100644 index 0000000..92176ba --- /dev/null +++ b/python/astra/PyProjector2DManager.pxd @@ -0,0 +1,39 @@ +#----------------------------------------------------------------------- +#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 libcpp.string cimport string + +from .PyIncludes cimport * + +cdef extern from "astra/AstraObjectManager.h" namespace "astra": + cdef cppclass CProjector2DManager: + string info() + void clear() + void remove(int i) + int store(CProjector2D *) + CProjector2D * get(int i) + +cdef extern from "astra/AstraObjectManager.h" namespace "astra::CProjector2DManager": + cdef CProjector2DManager* getSingletonPtr() diff --git a/python/astra/PyXMLDocument.pxd b/python/astra/PyXMLDocument.pxd new file mode 100644 index 0000000..69781f1 --- /dev/null +++ b/python/astra/PyXMLDocument.pxd @@ -0,0 +1,65 @@ +#----------------------------------------------------------------------- +#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 + +from libcpp.string cimport string +from libcpp cimport bool +from libcpp.list cimport list +from libcpp.vector cimport vector + +cdef extern from "astra/Globals.h" namespace "astra": + ctypedef float float32 + ctypedef double float64 + ctypedef unsigned short int uint16 + ctypedef signed short int sint16 + ctypedef unsigned char uchar8 + ctypedef signed char schar8 + ctypedef int int32 + ctypedef short int int16 + +cdef extern from "astra/XMLNode.h" namespace "astra": + cdef cppclass XMLNode: + string getName() + XMLNode *addChildNode(string name) + XMLNode *addChildNode(string, string) + void addAttribute(string, string) + void addAttribute(string, float32) + void addOption(string, string) + bool hasOption(string) + string getAttribute(string) + list[XMLNode *] getNodes() + vector[float32] getContentNumericalArray() + string getContent() + bool hasAttribute(string) + +cdef extern from "astra/XMLDocument.h" namespace "astra": + cdef cppclass XMLDocument: + void saveToFile(string sFilename) + XMLNode *getRootNode() + +cdef extern from "astra/XMLDocument.h" namespace "astra::XMLDocument": + cdef XMLDocument *createDocument(string rootname) diff --git a/python/astra/__init__.py b/python/astra/__init__.py new file mode 100644 index 0000000..a61aafc --- /dev/null +++ b/python/astra/__init__.py @@ -0,0 +1,42 @@ +#----------------------------------------------------------------------- +#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 matlab as m +from .creators import astra_dict,create_vol_geom, create_proj_geom, create_backprojection, create_sino, create_reconstruction, create_projector,create_sino3d_gpu, create_backprojection3d_gpu +from .functions import data_op, add_noise_to_sino, clear, move_vol_geom +from .extrautils import clipCircle +from .ASTRAProjector import ASTRAProjector2D +from . import data2d +from . import astra +from . import data3d +from . import algorithm +from . import projector +from . import matrix + +import os +try: + astra.set_gpu_index(int(os.environ['ASTRA_GPU_INDEX'])) +except KeyError: + pass diff --git a/python/astra/algorithm.py b/python/astra/algorithm.py new file mode 100644 index 0000000..46cfccc --- /dev/null +++ b/python/astra/algorithm.py @@ -0,0 +1,76 @@ +#----------------------------------------------------------------------- +#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 algorithm_c as a + +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) + +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) + +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) + +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) + +def clear(): + """Clear all matrix objects.""" + return a.clear() + +def info(): + """Print info on matrix objects in memory.""" + return a.info() diff --git a/python/astra/algorithm_c.pyx b/python/astra/algorithm_c.pyx new file mode 100644 index 0000000..0c2999c --- /dev/null +++ b/python/astra/algorithm_c.pyx @@ -0,0 +1,106 @@ +#----------------------------------------------------------------------- +#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 +from .PyIncludes cimport * + +cimport PyAlgorithmManager +from .PyAlgorithmManager cimport CAlgorithmManager + +cimport PyAlgorithmFactory +from .PyAlgorithmFactory cimport CAlgorithmFactory + +cimport PyXMLDocument +from .PyXMLDocument cimport XMLDocument + +cimport utils +from .utils import wrap_from_bytes + +cdef CAlgorithmManager * manAlg = PyAlgorithmManager.getSingletonPtr() + +cdef extern from *: + CReconstructionAlgorithm2D * dynamic_cast_recAlg "dynamic_cast" (CAlgorithm * ) except NULL + + +def create(config): + cdef XMLDocument * xml = utils.dict2XML(six.b('Algorithm'), config) + cdef Config cfg + cdef CAlgorithm * alg + cfg.self = xml.getRootNode() + alg = PyAlgorithmFactory.getSingletonPtr().create(cfg.self.getAttribute(six.b('type'))) + if alg == NULL: + del xml + raise Exception("Unknown algorithm.") + if not alg.initialize(cfg): + del xml + del alg + raise Exception("Algorithm not initialized.") + del xml + return manAlg.store(alg) + +cdef CAlgorithm * getAlg(i) except NULL: + cdef CAlgorithm * alg = manAlg.get(i) + if alg == NULL: + raise Exception("Unknown algorithm.") + if not alg.isInitialized(): + raise Exception("Algorithm not initialized.") + return alg + + +def run(i, iterations=0): + cdef CAlgorithm * alg = getAlg(i) + alg.run(iterations) + + +def get_res_norm(i): + cdef CReconstructionAlgorithm2D * pAlg2D + cdef CAlgorithm * alg = getAlg(i) + cdef float32 res = 0.0 + pAlg2D = dynamic_cast_recAlg(alg) + if pAlg2D == NULL: + raise Exception("Operation not supported.") + if not pAlg2D.getResidualNorm(res): + raise Exception("Operation not supported.") + return res + + +def delete(ids): + try: + for i in ids: + manAlg.remove(i) + except TypeError: + manAlg.remove(ids) + + +def clear(): + manAlg.clear() + + +def info(): + six.print_(wrap_from_bytes(manAlg.info())) diff --git a/python/astra/astra.py b/python/astra/astra.py new file mode 100644 index 0000000..26b1ff0 --- /dev/null +++ b/python/astra/astra.py @@ -0,0 +1,58 @@ +#----------------------------------------------------------------------- +#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 astra_c as a + +def credits(): + """Print credits of the ASTRA Toolbox.""" + return a.credits() + + +def use_cuda(): + """Test if CUDA is enabled. + + :returns: :class:`bool` -- ``True`` if CUDA is enabled. + """ + return a.use_cuda() + + +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) + +def set_gpu_index(idx): + """Set default GPU index to use. + + :param idx: GPU index + :type idx: :class:`int` + """ + a.set_gpu_index(idx) diff --git a/python/astra/astra_c.pyx b/python/astra/astra_c.pyx new file mode 100644 index 0000000..342a214 --- /dev/null +++ b/python/astra/astra_c.pyx @@ -0,0 +1,79 @@ +#----------------------------------------------------------------------- +#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 + +include "config.pxi" +import six +from .utils import wrap_from_bytes + +from libcpp.string cimport string +from libcpp cimport bool +cdef extern from "astra/Globals.h" namespace "astra": + int getVersion() + string getVersionString() + bool cudaEnabled() + +IF HAVE_CUDA==True: + cdef extern from "../cuda/2d/darthelper.h" namespace "astraCUDA": + bool setGPUIndex(int) +ELSE: + def setGPUIndex(): + 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)""") + + +def use_cuda(): + return cudaEnabled() + + +def version(printToScreen=False): + if printToScreen: + six.print_(wrap_from_bytes(getVersionString())) + else: + return getVersion() + +def set_gpu_index(idx): + if use_cuda()==True: + ret = setGPUIndex(idx) + if not ret: + six.print_("Failed to set GPU " + str(idx)) diff --git a/python/astra/creators.py b/python/astra/creators.py new file mode 100644 index 0000000..9aba464 --- /dev/null +++ b/python/astra/creators.py @@ -0,0 +1,563 @@ +#----------------------------------------------------------------------- +#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 . +# +#----------------------------------------------------------------------- + +import six +import numpy as np +import math +from . import data2d +from . import data3d +from . import projector +from . import algorithm + +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} + +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 + + +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) + + +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 + +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 + + +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 + + + +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 + + +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 + + +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) diff --git a/python/astra/data2d.py b/python/astra/data2d.py new file mode 100644 index 0000000..8c4be03 --- /dev/null +++ b/python/astra/data2d.py @@ -0,0 +1,120 @@ +#----------------------------------------------------------------------- +#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 data2d_c as d + +def clear(): + """Clear all 2D data objects.""" + return d.clear() + +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) + +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) + +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) + +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) + +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) + +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) + +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) + + +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) + +def info(): + """Print info on 2D objects in memory.""" + return d.info() diff --git a/python/astra/data2d_c.pyx b/python/astra/data2d_c.pyx new file mode 100644 index 0000000..ec1b478 --- /dev/null +++ b/python/astra/data2d_c.pyx @@ -0,0 +1,241 @@ +#----------------------------------------------------------------------- +#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 + +cimport cython +from cython cimport view + +cimport PyData2DManager +from .PyData2DManager cimport CData2DManager + +cimport PyXMLDocument +from .PyXMLDocument cimport XMLDocument + +import numpy as np + +cimport numpy as np +np.import_array() + + +from .PyIncludes cimport * +cimport utils +from .utils import wrap_from_bytes + + +cdef CData2DManager * man2d = PyData2DManager.getSingletonPtr() + + +def clear(): + man2d.clear() + + +def delete(ids): + try: + for i in ids: + man2d.remove(i) + except TypeError: + man2d.remove(ids) + + +def create(datatype, geometry, data=None): + cdef XMLDocument * xml + cdef Config cfg + cdef CVolumeGeometry2D * pGeometry + cdef CProjectionGeometry2D * ppGeometry + cdef CFloat32Data2D * pDataObject2D + if datatype == '-vol': + xml = utils.dict2XML(six.b('VolumeGeometry'), geometry) + cfg.self = xml.getRootNode() + pGeometry = new CVolumeGeometry2D() + if not pGeometry.initialize(cfg): + del xml + del pGeometry + raise Exception('Geometry class not initialized.') + pDataObject2D = new CFloat32VolumeData2D(pGeometry) + del xml + del pGeometry + elif datatype == '-sino': + xml = utils.dict2XML(six.b('ProjectionGeometry'), geometry) + cfg.self = xml.getRootNode() + tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type'))) + if (tpe == 'sparse_matrix'): + ppGeometry = new CSparseMatrixProjectionGeometry2D() + elif (tpe == 'fanflat'): + ppGeometry = new CFanFlatProjectionGeometry2D() + elif (tpe == 'fanflat_vec'): + ppGeometry = new CFanFlatVecProjectionGeometry2D() + else: + ppGeometry = new CParallelProjectionGeometry2D() + if not ppGeometry.initialize(cfg): + del xml + del ppGeometry + raise Exception('Geometry class not initialized.') + pDataObject2D = new CFloat32ProjectionData2D(ppGeometry) + del ppGeometry + del xml + else: + raise Exception("Invalid datatype. Please specify '-vol' or '-sino'.") + + if not pDataObject2D.isInitialized(): + del pDataObject2D + raise Exception("Couldn't initialize data object.") + + fillDataObject(pDataObject2D, data) + + return man2d.store(pDataObject2D) + +cdef fillDataObject(CFloat32Data2D * obj, data): + if data is None: + fillDataObjectScalar(obj, 0) + else: + if isinstance(data, np.ndarray): + fillDataObjectArray(obj, np.ascontiguousarray(data,dtype=np.float32)) + else: + fillDataObjectScalar(obj, np.float32(data)) + +cdef fillDataObjectScalar(CFloat32Data2D * obj, float s): + cdef int i + for i in range(obj.getSize()): + obj.getData()[i] = s + +@cython.boundscheck(False) +@cython.wraparound(False) +cdef fillDataObjectArray(CFloat32Data2D * obj, float [:,::1] data): + if (not data.shape[0] == obj.getHeight()) or (not data.shape[1] == obj.getWidth()): + raise Exception( + "The dimensions of the data do not match those specified in the geometry.") + cdef float [:,::1] cView = obj.getData2D()[0] + cView[:] = data + +cdef CFloat32Data2D * getObject(i) except NULL: + cdef CFloat32Data2D * pDataObject = man2d.get(i) + if pDataObject == NULL: + raise Exception("Data object not found") + if not pDataObject.isInitialized(): + raise Exception("Data object not initialized properly.") + return pDataObject + + +def store(i, data): + cdef CFloat32Data2D * pDataObject = getObject(i) + fillDataObject(pDataObject, data) + + +def get_geometry(i): + cdef CFloat32Data2D * pDataObject = getObject(i) + cdef CFloat32ProjectionData2D * pDataObject2 + cdef CFloat32VolumeData2D * pDataObject3 + if pDataObject.getType() == PROJECTION: + pDataObject2 = pDataObject + geom = utils.createProjectionGeometryStruct(pDataObject2.getGeometry()) + elif pDataObject.getType() == VOLUME: + pDataObject3 = pDataObject + geom = utils.createVolumeGeometryStruct(pDataObject3.getGeometry()) + else: + raise Exception("Not a known data object") + return geom + + +def change_geometry(i, geom): + cdef XMLDocument * xml + cdef Config cfg + cdef CVolumeGeometry2D * pGeometry + cdef CProjectionGeometry2D * ppGeometry + cdef CFloat32Data2D * pDataObject = getObject(i) + cdef CFloat32ProjectionData2D * pDataObject2 + cdef CFloat32VolumeData2D * pDataObject3 + if pDataObject.getType() == PROJECTION: + pDataObject2 = pDataObject + xml = utils.dict2XML(six.b('ProjectionGeometry'), geom) + cfg.self = xml.getRootNode() + tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type'))) + if (tpe == 'sparse_matrix'): + ppGeometry = new CSparseMatrixProjectionGeometry2D() + elif (tpe == 'fanflat'): + ppGeometry = new CFanFlatProjectionGeometry2D() + elif (tpe == 'fanflat_vec'): + ppGeometry = new CFanFlatVecProjectionGeometry2D() + else: + ppGeometry = new CParallelProjectionGeometry2D() + if not ppGeometry.initialize(cfg): + del xml + del ppGeometry + raise Exception('Geometry class not initialized.') + if (ppGeometry.getDetectorCount() != pDataObject2.getDetectorCount() or ppGeometry.getProjectionAngleCount() != pDataObject2.getAngleCount()): + del ppGeometry + del xml + raise Exception( + "The dimensions of the data do not match those specified in the geometry.") + pDataObject2.changeGeometry(ppGeometry) + del ppGeometry + del xml + elif pDataObject.getType() == VOLUME: + pDataObject3 = pDataObject + xml = utils.dict2XML(six.b('VolumeGeometry'), geom) + cfg.self = xml.getRootNode() + pGeometry = new CVolumeGeometry2D() + if not pGeometry.initialize(cfg): + del xml + del pGeometry + raise Exception('Geometry class not initialized.') + if (pGeometry.getGridColCount() != pDataObject3.getWidth() or pGeometry.getGridRowCount() != pDataObject3.getHeight()): + del xml + del pGeometry + raise Exception( + 'The dimensions of the data do not match those specified in the geometry.') + pDataObject3.changeGeometry(pGeometry) + del xml + del pGeometry + else: + raise Exception("Not a known data object") + +@cython.boundscheck(False) +@cython.wraparound(False) +def get(i): + cdef CFloat32Data2D * pDataObject = getObject(i) + outArr = np.empty((pDataObject.getHeight(), pDataObject.getWidth()),dtype=np.float32,order='C') + cdef float [:,::1] mView = outArr + cdef float [:,::1] cView = pDataObject.getData2D()[0] + mView[:] = cView + return outArr + +def get_shared(i): + cdef CFloat32Data2D * pDataObject = getObject(i) + cdef np.npy_intp shape[2] + shape[0] = pDataObject.getHeight() + shape[1] = pDataObject.getWidth() + return np.PyArray_SimpleNewFromData(2,shape,np.NPY_FLOAT32,pDataObject.getData2D()[0]) + + +def get_single(i): + raise Exception("Not yet implemented") + + +def info(): + six.print_(wrap_from_bytes(man2d.info())) diff --git a/python/astra/data3d.py b/python/astra/data3d.py new file mode 100644 index 0000000..33bde51 --- /dev/null +++ b/python/astra/data3d.py @@ -0,0 +1,108 @@ +#----------------------------------------------------------------------- +#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 data3d_c as d + +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) + +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) + +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) + +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) + +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) + +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) + +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) + +def clear(): + """Clear all 3D data objects.""" + return d.clear() + +def info(): + """Print info on 3D objects in memory.""" + return d.info() diff --git a/python/astra/data3d_c.pyx b/python/astra/data3d_c.pyx new file mode 100644 index 0000000..f821aaf --- /dev/null +++ b/python/astra/data3d_c.pyx @@ -0,0 +1,188 @@ +#----------------------------------------------------------------------- +#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 + +cimport cython + +cimport PyData3DManager +from .PyData3DManager cimport CData3DManager + +from .PyIncludes cimport * +import numpy as np + +cimport numpy as np +np.import_array() + +cimport PyXMLDocument +from .PyXMLDocument cimport XMLDocument + +cimport utils +from .utils import wrap_from_bytes + +cdef CData3DManager * man3d = PyData3DManager.getSingletonPtr() + +cdef extern from *: + CFloat32Data3DMemory * dynamic_cast_mem "dynamic_cast" (CFloat32Data3D * ) except NULL + +def create(datatype,geometry,data=None): + cdef XMLDocument * xml + cdef Config cfg + cdef CVolumeGeometry3D * pGeometry + cdef CProjectionGeometry3D * ppGeometry + cdef CFloat32Data3DMemory * pDataObject3D + cdef CConeProjectionGeometry3D* pppGeometry + if datatype == '-vol': + xml = utils.dict2XML(six.b('VolumeGeometry'), geometry) + cfg.self = xml.getRootNode() + pGeometry = new CVolumeGeometry3D() + if not pGeometry.initialize(cfg): + del xml + del pGeometry + raise Exception('Geometry class not initialized.') + pDataObject3D = new CFloat32VolumeData3DMemory(pGeometry) + del xml + del pGeometry + elif datatype == '-sino' or datatype == '-proj3d': + xml = utils.dict2XML(six.b('ProjectionGeometry'), geometry) + cfg.self = xml.getRootNode() + tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type'))) + if (tpe == "parallel3d"): + ppGeometry = new CParallelProjectionGeometry3D(); + elif (tpe == "parallel3d_vec"): + ppGeometry = new CParallelVecProjectionGeometry3D(); + elif (tpe == "cone"): + ppGeometry = new CConeProjectionGeometry3D(); + elif (tpe == "cone_vec"): + ppGeometry = new CConeVecProjectionGeometry3D(); + else: + raise Exception("Invalid geometry type.") + + if not ppGeometry.initialize(cfg): + del xml + del ppGeometry + raise Exception('Geometry class not initialized.') + pDataObject3D = new CFloat32ProjectionData3DMemory(ppGeometry) + del ppGeometry + del xml + elif datatype == "-sinocone": + xml = utils.dict2XML(six.b('ProjectionGeometry'), geometry) + cfg.self = xml.getRootNode() + pppGeometry = new CConeProjectionGeometry3D() + if not pppGeometry.initialize(cfg): + del xml + del pppGeometry + raise Exception('Geometry class not initialized.') + pDataObject3D = new CFloat32ProjectionData3DMemory(pppGeometry) + else: + raise Exception("Invalid datatype. Please specify '-vol' or '-proj3d'.") + + if not pDataObject3D.isInitialized(): + del pDataObject3D + raise Exception("Couldn't initialize data object.") + + fillDataObject(pDataObject3D, data) + + pDataObject3D.updateStatistics() + + return man3d.store(pDataObject3D) + + +cdef fillDataObject(CFloat32Data3DMemory * obj, data): + if data is None: + fillDataObjectScalar(obj, 0) + else: + if isinstance(data, np.ndarray): + fillDataObjectArray(obj, np.ascontiguousarray(data,dtype=np.float32)) + else: + fillDataObjectScalar(obj, np.float32(data)) + +cdef fillDataObjectScalar(CFloat32Data3DMemory * obj, float s): + cdef int i + for i in range(obj.getSize()): + obj.getData()[i] = s + +@cython.boundscheck(False) +@cython.wraparound(False) +cdef fillDataObjectArray(CFloat32Data3DMemory * obj, float [:,:,::1] data): + if (not data.shape[0] == obj.getDepth()) or (not data.shape[1] == obj.getHeight()) or (not data.shape[2] == obj.getWidth()): + raise Exception( + "The dimensions of the data do not match those specified in the geometry.") + cdef float [:,:,::1] cView = obj.getData3D()[0][0] + cView[:] = data + +cdef CFloat32Data3D * getObject(i) except NULL: + cdef CFloat32Data3D * pDataObject = man3d.get(i) + if pDataObject == NULL: + raise Exception("Data object not found") + if not pDataObject.isInitialized(): + raise Exception("Data object not initialized properly.") + return pDataObject + +@cython.boundscheck(False) +@cython.wraparound(False) +def get(i): + cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem(getObject(i)) + outArr = np.empty((pDataObject.getDepth(),pDataObject.getHeight(), pDataObject.getWidth()),dtype=np.float32,order='C') + cdef float [:,:,::1] mView = outArr + cdef float [:,:,::1] cView = pDataObject.getData3D()[0][0] + mView[:] = cView + return outArr + +def get_shared(i): + cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem(getObject(i)) + outArr = np.empty((pDataObject.getDepth(),pDataObject.getHeight(), pDataObject.getWidth()),dtype=np.float32,order='C') + cdef np.npy_intp shape[3] + shape[0] = pDataObject.getDepth() + shape[1] = pDataObject.getHeight() + shape[2] = pDataObject.getWidth() + return np.PyArray_SimpleNewFromData(3,shape,np.NPY_FLOAT32,pDataObject.getData3D()[0][0]) + +def get_single(i): + raise Exception("Not yet implemented") + +def store(i,data): + cdef CFloat32Data3D * pDataObject = getObject(i) + fillDataObject(dynamic_cast_mem(pDataObject), data) + +def dimensions(i): + cdef CFloat32Data3D * pDataObject = getObject(i) + return (pDataObject.getWidth(),pDataObject.getHeight(),pDataObject.getDepth()) + +def delete(ids): + try: + for i in ids: + man3d.remove(i) + except TypeError: + man3d.remove(ids) + +def clear(): + man3d.clear() + +def info(): + six.print_(wrap_from_bytes(man3d.info())) diff --git a/python/astra/extrautils.pyx b/python/astra/extrautils.pyx new file mode 100644 index 0000000..998f5cb --- /dev/null +++ b/python/astra/extrautils.pyx @@ -0,0 +1,43 @@ +#----------------------------------------------------------------------- +#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 . +# +#----------------------------------------------------------------------- + +def clipCircle(img): + cdef int i,j + cdef double x2,y2,mid,bnd + cdef long sz,sz2 + sz = img.shape[0] + sz2 = sz*sz + bnd = sz2/4. + mid = (sz-1.)/2. + nDel=0 + for i in range(sz): + for j in range(sz): + x2 = (i-mid)*(i-mid) + y2 = (j-mid)*(j-mid) + if x2+y2>bnd: + img[i,j]=0 + nDel=nDel+1 + return nDel diff --git a/python/astra/functions.py b/python/astra/functions.py new file mode 100644 index 0000000..4025468 --- /dev/null +++ b/python/astra/functions.py @@ -0,0 +1,270 @@ +#----------------------------------------------------------------------- +# 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 . +# +#----------------------------------------------------------------------- +"""Additional functions for PyAstraToolbox. + +.. moduleauthor:: Daniel M. Pelt + + +""" + +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 + + + +def clear(): + """Clears all used memory of the ASTRA Toolbox. + + .. note:: + This is irreversible. + + """ + data2d.clear() + data3d.clear() + projector.clear() + algorithm.clear() + + +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) + + +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 + +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 + + +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 + + +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 diff --git a/python/astra/matlab.py b/python/astra/matlab.py new file mode 100644 index 0000000..83b345d --- /dev/null +++ b/python/astra/matlab.py @@ -0,0 +1,112 @@ +#----------------------------------------------------------------------- +#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 . +# +#----------------------------------------------------------------------- +"""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 + + +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) + + +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) + + +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) + + +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) + + +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) + + +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) diff --git a/python/astra/matrix.py b/python/astra/matrix.py new file mode 100644 index 0000000..27e4823 --- /dev/null +++ b/python/astra/matrix.py @@ -0,0 +1,86 @@ +#----------------------------------------------------------------------- +#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 matrix_c as m + +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) + +def clear(): + """Clear all matrix objects.""" + return m.clear() + +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) + + +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) + +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) + +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) + +def info(): + """Print info on matrix objects in memory.""" + return m.info() + + diff --git a/python/astra/matrix_c.pyx b/python/astra/matrix_c.pyx new file mode 100644 index 0000000..b0d8bc4 --- /dev/null +++ b/python/astra/matrix_c.pyx @@ -0,0 +1,116 @@ +#----------------------------------------------------------------------- +#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 +from six.moves import range +import numpy as np +import scipy.sparse as ss + +from libcpp cimport bool + +cimport PyMatrixManager +from .PyMatrixManager cimport CMatrixManager +from .PyIncludes cimport * +from .utils import wrap_from_bytes + +cdef CMatrixManager * manM = PyMatrixManager.getSingletonPtr() + + +def delete(ids): + try: + for i in ids: + manM.remove(i) + except TypeError: + manM.remove(ids) + +def clear(): + manM.clear() + +cdef int csr_matrix_to_astra(data,CSparseMatrix *mat) except -1: + if isinstance(data,ss.csr_matrix): + csrD = data + else: + csrD = data.tocsr() + if not mat.isInitialized(): + raise Exception("Couldn't initialize data object.") + if csrD.nnz > mat.m_lSize or csrD.shape[0] > mat.m_iHeight: + raise Exception("Matrix too large to store in this object.") + for i in range(len(csrD.indptr)): + mat.m_plRowStarts[i] = csrD.indptr[i] + for i in range(csrD.nnz): + mat.m_piColIndices[i] = csrD.indices[i] + mat.m_pfValues[i] = csrD.data[i] + +cdef astra_to_csr_matrix(CSparseMatrix *mat): + indptr = np.zeros(mat.m_iHeight+1,dtype=np.int) + indices = np.zeros(mat.m_plRowStarts[mat.m_iHeight],dtype=np.int) + data = np.zeros(mat.m_plRowStarts[mat.m_iHeight]) + for i in range(mat.m_iHeight+1): + indptr[i] = mat.m_plRowStarts[i] + for i in range(mat.m_plRowStarts[mat.m_iHeight]): + indices[i] = mat.m_piColIndices[i] + data[i] = mat.m_pfValues[i] + return ss.csr_matrix((data,indices,indptr),shape=(mat.m_iHeight,mat.m_iWidth)) + +def create(data): + cdef CSparseMatrix* pMatrix + pMatrix = new CSparseMatrix(data.shape[0], data.shape[1], data.nnz) + if not pMatrix.isInitialized(): + del pMatrix + raise Exception("Couldn't initialize data object.") + try: + csr_matrix_to_astra(data,pMatrix) + except: + del pMatrix + raise Exception("Failed to create data object.") + + return manM.store(pMatrix) + +cdef CSparseMatrix * getObject(i) except NULL: + cdef CSparseMatrix * pDataObject = manM.get(i) + if pDataObject == NULL: + raise Exception("Data object not found") + if not pDataObject.isInitialized(): + raise Exception("Data object not initialized properly.") + return pDataObject + + +def store(i,data): + cdef CSparseMatrix * pDataObject = getObject(i) + csr_matrix_to_astra(data,pDataObject) + +def get_size(i): + cdef CSparseMatrix * pDataObject = getObject(i) + return (pDataObject.m_iHeight,pDataObject.m_iWidth) + +def get(i): + cdef CSparseMatrix * pDataObject = getObject(i) + return astra_to_csr_matrix(pDataObject) + +def info(): + six.print_(wrap_from_bytes(manM.info())) diff --git a/python/astra/projector.py b/python/astra/projector.py new file mode 100644 index 0000000..c916c52 --- /dev/null +++ b/python/astra/projector.py @@ -0,0 +1,100 @@ +#----------------------------------------------------------------------- +#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 projector_c as p + +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) + + +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) + + +def clear(): + """Clear all projector objects.""" + return p.clear() + + +def info(): + """Print info on projector objects in memory.""" + return p.info() + +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) + + +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) + + +def weights_single_ray(i, projection_index, detector_index): + return p.weights_single_ray(i, projection_index, detector_index) + + +def weights_projection(i, projection_index): + return p.weights_projection(i, projection_index) + + +def splat(i, row, col): + return p.splat(i, row, col) + + +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) diff --git a/python/astra/projector_c.pyx b/python/astra/projector_c.pyx new file mode 100644 index 0000000..978ca09 --- /dev/null +++ b/python/astra/projector_c.pyx @@ -0,0 +1,119 @@ +#----------------------------------------------------------------------- +#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 +from .PyIncludes cimport * + +cimport utils +from .utils import wrap_from_bytes + +cimport PyProjector2DFactory +from .PyProjector2DFactory cimport CProjector2DFactory + +cimport PyProjector2DManager +from .PyProjector2DManager cimport CProjector2DManager + +cimport PyXMLDocument +from .PyXMLDocument cimport XMLDocument + +cimport PyMatrixManager +from .PyMatrixManager cimport CMatrixManager + +cdef CProjector2DManager * manProj = PyProjector2DManager.getSingletonPtr() +cdef CMatrixManager * manM = PyMatrixManager.getSingletonPtr() + + +def create(config): + cdef XMLDocument * xml = utils.dict2XML(six.b('Projector2D'), config) + cdef Config cfg + cdef CProjector2D * proj + cfg.self = xml.getRootNode() + proj = PyProjector2DFactory.getSingletonPtr().create(cfg) + if proj == NULL: + del xml + raise Exception("Error creating projector.") + del xml + return manProj.store(proj) + + +def delete(ids): + try: + for i in ids: + manProj.remove(i) + except TypeError: + manProj.remove(ids) + + +def clear(): + manProj.clear() + + +def info(): + six.print_(wrap_from_bytes(manProj.info())) + +cdef CProjector2D * getObject(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 projection_geometry(i): + cdef CProjector2D * proj = getObject(i) + return utils.createProjectionGeometryStruct(proj.getProjectionGeometry()) + + +def volume_geometry(i): + cdef CProjector2D * proj = getObject(i) + return utils.createVolumeGeometryStruct(proj.getVolumeGeometry()) + + +def weights_single_ray(i, projection_index, detector_index): + raise Exception("Not yet implemented") + + +def weights_projection(i, projection_index): + raise Exception("Not yet implemented") + + +def splat(i, row, col): + raise Exception("Not yet implemented") + + +def matrix(i): + cdef CProjector2D * proj = getObject(i) + cdef CSparseMatrix * mat = proj.getMatrix() + if mat == NULL: + del mat + raise Exception("Data object not found") + if not mat.isInitialized(): + del mat + raise Exception("Data object not initialized properly.") + return manM.store(mat) diff --git a/python/astra/utils.pxd b/python/astra/utils.pxd new file mode 100644 index 0000000..55db9d3 --- /dev/null +++ b/python/astra/utils.pxd @@ -0,0 +1,37 @@ +#----------------------------------------------------------------------- +#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 libcpp.string cimport string + +cimport PyXMLDocument +from .PyXMLDocument cimport XMLDocument +from .PyXMLDocument cimport XMLNode + +from .PyIncludes cimport * + +cdef XMLDocument *dict2XML(string rootname, dc) +cdef XML2dict(XMLDocument *) +cdef createVolumeGeometryStruct(CVolumeGeometry2D* geom) +cdef createProjectionGeometryStruct(CProjectionGeometry2D* geom) diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx new file mode 100644 index 0000000..53e84a9 --- /dev/null +++ b/python/astra/utils.pyx @@ -0,0 +1,260 @@ +#----------------------------------------------------------------------- +#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 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 +from cpython.version cimport PY_MAJOR_VERSION + +cimport PyXMLDocument +from .PyXMLDocument cimport XMLDocument +from .PyXMLDocument cimport XMLNode +from .PyIncludes cimport * + + +cdef XMLDocument * dict2XML(string rootname, dc): + cdef XMLDocument * doc = PyXMLDocument.createDocument(rootname) + cdef XMLNode * node = doc.getRootNode() + try: + readDict(node, dc) + except: + six.print_('Error reading XML') + del doc + doc = NULL + finally: + del node + return doc + +def convert_item(item): + if isinstance(item, six.string_types): + return item.encode('ascii') + + if type(item) is not dict: + return item + + out_dict = {} + for k in item: + out_dict[convert_item(k)] = convert_item(item[k]) + return out_dict + + +def wrap_to_bytes(value): + if isinstance(value, six.binary_type): + return value + s = str(value) + if PY_MAJOR_VERSION == 3: + s = s.encode('ascii') + return s + + +def wrap_from_bytes(value): + s = value + if PY_MAJOR_VERSION == 3: + s = s.decode('ascii') + return s + + +cdef void readDict(XMLNode * root, _dc): + cdef XMLNode * listbase + cdef XMLNode * itm + cdef int i + cdef int j + + dc = convert_item(_dc) + for item in dc: + val = dc[item] + if isinstance(val, np.ndarray): + if val.size == 0: + break + listbase = root.addChildNode(item) + listbase.addAttribute(< string > six.b('listsize'), < float32 > val.size) + index = 0 + if val.ndim == 2: + for i in range(val.shape[0]): + for j in range(val.shape[1]): + itm = listbase.addChildNode(six.b('ListItem')) + itm.addAttribute(< string > six.b('index'), < float32 > index) + itm.addAttribute( < string > six.b('value'), < float32 > val[i, j]) + index += 1 + del itm + elif val.ndim == 1: + for i in range(val.shape[0]): + itm = listbase.addChildNode(six.b('ListItem')) + itm.addAttribute(< string > six.b('index'), < float32 > index) + itm.addAttribute(< string > six.b('value'), < float32 > val[i]) + index += 1 + del itm + else: + raise Exception("Only 1 or 2 dimensions are allowed") + del listbase + elif isinstance(val, dict): + if item == six.b('option') or item == six.b('options') or item == six.b('Option') or item == six.b('Options'): + readOptions(root, val) + else: + itm = root.addChildNode(item) + readDict(itm, val) + del itm + else: + if item == six.b('type'): + root.addAttribute(< string > six.b('type'), wrap_to_bytes(val)) + else: + itm = root.addChildNode(item, wrap_to_bytes(val)) + del itm + +cdef void readOptions(XMLNode * node, dc): + cdef XMLNode * listbase + cdef XMLNode * itm + cdef int i + cdef int j + for item in dc: + val = dc[item] + if node.hasOption(item): + raise Exception('Duplicate Option: %s' % item) + if isinstance(val, np.ndarray): + if val.size == 0: + break + listbase = node.addChildNode(six.b('Option')) + listbase.addAttribute(< string > six.b('key'), < string > item) + listbase.addAttribute(< string > six.b('listsize'), < float32 > val.size) + index = 0 + if val.ndim == 2: + for i in range(val.shape[0]): + for j in range(val.shape[1]): + itm = listbase.addChildNode(six.b('ListItem')) + itm.addAttribute(< string > six.b('index'), < float32 > index) + itm.addAttribute( < string > six.b('value'), < float32 > val[i, j]) + index += 1 + del itm + elif val.ndim == 1: + for i in range(val.shape[0]): + itm = listbase.addChildNode(six.b('ListItem')) + itm.addAttribute(< string > six.b('index'), < float32 > index) + itm.addAttribute(< string > six.b('value'), < float32 > val[i]) + index += 1 + del itm + else: + raise Exception("Only 1 or 2 dimensions are allowed") + del listbase + else: + node.addOption(item, wrap_to_bytes(val)) + +cdef vectorToNumpy(vector[float32] inp): + cdef int i + cdef int sz = inp.size() + ret = np.empty(sz) + for i in range(sz): + ret[i] = inp[i] + return ret + +cdef XMLNode2dict(XMLNode * node): + cdef XMLNode * subnode + cdef list[XMLNode * ] nodes + cdef list[XMLNode * ].iterator it + dct = {} + if node.hasAttribute(six.b('type')): + dct['type'] = node.getAttribute(six.b('type')) + nodes = node.getNodes() + it = nodes.begin() + while it != nodes.end(): + subnode = deref(it) + if subnode.hasAttribute(six.b('listsize')): + dct[subnode.getName( + )] = vectorToNumpy(subnode.getContentNumericalArray()) + else: + dct[subnode.getName()] = subnode.getContent() + del subnode + return dct + +cdef XML2dict(XMLDocument * xml): + cdef XMLNode * node = xml.getRootNode() + dct = XMLNode2dict(node) + del node; + return dct; + +cdef createProjectionGeometryStruct(CProjectionGeometry2D * geom): + cdef int i + cdef CFanFlatVecProjectionGeometry2D * fanvecGeom + # cdef SFanProjection* p + dct = {} + dct['DetectorCount'] = geom.getDetectorCount() + if not geom.isOfType(< string > six.b('fanflat_vec')): + dct['DetectorWidth'] = geom.getDetectorWidth() + angles = np.empty(geom.getProjectionAngleCount()) + for i in range(geom.getProjectionAngleCount()): + angles[i] = geom.getProjectionAngle(i) + dct['ProjectionAngles'] = angles + else: + raise Exception("Not yet implemented") + # fanvecGeom = geom + # vecs = np.empty(fanvecGeom.getProjectionAngleCount()*6) + # iDetCount = pVecGeom.getDetectorCount() + # for i in range(fanvecGeom.getProjectionAngleCount()): + # p = &fanvecGeom.getProjectionVectors()[i]; + # out[6*i + 0] = p.fSrcX + # out[6*i + 1] = p.fSrcY + # out[6*i + 2] = p.fDetSX + 0.5f*iDetCount*p.fDetUX + # out[6*i + 3] = p.fDetSY + 0.5f*iDetCount*p.fDetUY + # out[6*i + 4] = p.fDetUX + # out[6*i + 5] = p.fDetUY + # dct['Vectors'] = vecs + if (geom.isOfType(< string > six.b('parallel'))): + dct["type"] = "parallel" + elif (geom.isOfType(< string > six.b('fanflat'))): + raise Exception("Not yet implemented") + # astra::CFanFlatProjectionGeometry2D* pFanFlatGeom = dynamic_cast(_pProjGeom) + # mGeometryInfo["DistanceOriginSource"] = mxCreateDoubleScalar(pFanFlatGeom->getOriginSourceDistance()) + # mGeometryInfo["DistanceOriginDetector"] = + # mxCreateDoubleScalar(pFanFlatGeom->getOriginDetectorDistance()) + dct["type"] = "fanflat" + elif (geom.isOfType(< string > six.b('sparse_matrix'))): + raise Exception("Not yet implemented") + # astra::CSparseMatrixProjectionGeometry2D* pSparseMatrixGeom = + # dynamic_cast(_pProjGeom); + dct["type"] = "sparse_matrix" + # dct["MatrixID"] = + # mxCreateDoubleScalar(CMatrixManager::getSingleton().getIndex(pSparseMatrixGeom->getMatrix())) + elif(geom.isOfType(< string > six.b('fanflat_vec'))): + dct["type"] = "fanflat_vec" + return dct + +cdef createVolumeGeometryStruct(CVolumeGeometry2D * geom): + mGeometryInfo = {} + mGeometryInfo["GridColCount"] = geom.getGridColCount() + mGeometryInfo["GridRowCount"] = geom.getGridRowCount() + + mGeometryOptions = {} + mGeometryOptions["WindowMinX"] = geom.getWindowMinX() + mGeometryOptions["WindowMaxX"] = geom.getWindowMaxX() + mGeometryOptions["WindowMinY"] = geom.getWindowMinY() + mGeometryOptions["WindowMaxY"] = geom.getWindowMaxY() + + mGeometryInfo["option"] = mGeometryOptions + return mGeometryInfo diff --git a/python/builder.py b/python/builder.py new file mode 100644 index 0000000..bdfd092 --- /dev/null +++ b/python/builder.py @@ -0,0 +1,70 @@ +#----------------------------------------------------------------------- +#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 . +# +#----------------------------------------------------------------------- +import sys +import os +import numpy as np + +from distutils.version import LooseVersion +from distutils.core import setup +from distutils.extension import Extension + +from Cython.Distutils import build_ext +from Cython.Build import cythonize +import Cython +if LooseVersion(Cython.__version__)' 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 " latexpdf to make LaTeX files and run them through pdflatex" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of 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)" + +clean: + -rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @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/.qhc" + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/" + @echo "# devhelp" + +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +latexpdf: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through pdflatex..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. The text files are in $(BUILDDIR)/text." + +man: + $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man + @echo + @echo "Build finished. The manual pages are in $(BUILDDIR)/man." + +texinfo: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo + @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." + @echo "Run \`make' in that directory to run these through makeinfo" \ + "(use \`make info' here to do that automatically)." + +info: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo "Running Texinfo files through makeinfo..." + make -C $(BUILDDIR)/texinfo info + @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." + +gettext: + $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale + @echo + @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." diff --git a/python/docSRC/_build/doctrees/ASTRAProjector.doctree b/python/docSRC/_build/doctrees/ASTRAProjector.doctree new file mode 100644 index 0000000..c93e5bb Binary files /dev/null and b/python/docSRC/_build/doctrees/ASTRAProjector.doctree differ diff --git a/python/docSRC/_build/doctrees/algorithm.doctree b/python/docSRC/_build/doctrees/algorithm.doctree new file mode 100644 index 0000000..1cb6d80 Binary files /dev/null and b/python/docSRC/_build/doctrees/algorithm.doctree differ diff --git a/python/docSRC/_build/doctrees/astra.doctree b/python/docSRC/_build/doctrees/astra.doctree new file mode 100644 index 0000000..948d05e Binary files /dev/null and b/python/docSRC/_build/doctrees/astra.doctree differ diff --git a/python/docSRC/_build/doctrees/creators.doctree b/python/docSRC/_build/doctrees/creators.doctree new file mode 100644 index 0000000..72c82fd Binary files /dev/null and b/python/docSRC/_build/doctrees/creators.doctree differ diff --git a/python/docSRC/_build/doctrees/data2d.doctree b/python/docSRC/_build/doctrees/data2d.doctree new file mode 100644 index 0000000..bfe67d5 Binary files /dev/null and b/python/docSRC/_build/doctrees/data2d.doctree differ diff --git a/python/docSRC/_build/doctrees/data3d.doctree b/python/docSRC/_build/doctrees/data3d.doctree new file mode 100644 index 0000000..4025c09 Binary files /dev/null and b/python/docSRC/_build/doctrees/data3d.doctree differ diff --git a/python/docSRC/_build/doctrees/environment.pickle b/python/docSRC/_build/doctrees/environment.pickle new file mode 100644 index 0000000..d17f654 Binary files /dev/null and b/python/docSRC/_build/doctrees/environment.pickle differ diff --git a/python/docSRC/_build/doctrees/functions.doctree b/python/docSRC/_build/doctrees/functions.doctree new file mode 100644 index 0000000..9ee097d Binary files /dev/null and b/python/docSRC/_build/doctrees/functions.doctree differ diff --git a/python/docSRC/_build/doctrees/index.doctree b/python/docSRC/_build/doctrees/index.doctree new file mode 100644 index 0000000..f0925c9 Binary files /dev/null and b/python/docSRC/_build/doctrees/index.doctree differ diff --git a/python/docSRC/_build/doctrees/matlab.doctree b/python/docSRC/_build/doctrees/matlab.doctree new file mode 100644 index 0000000..fc443e9 Binary files /dev/null and b/python/docSRC/_build/doctrees/matlab.doctree differ diff --git a/python/docSRC/_build/doctrees/matrix.doctree b/python/docSRC/_build/doctrees/matrix.doctree new file mode 100644 index 0000000..847c0c7 Binary files /dev/null and b/python/docSRC/_build/doctrees/matrix.doctree differ diff --git a/python/docSRC/_build/doctrees/projector.doctree b/python/docSRC/_build/doctrees/projector.doctree new file mode 100644 index 0000000..cb7e640 Binary files /dev/null and b/python/docSRC/_build/doctrees/projector.doctree differ diff --git a/python/docSRC/_build/html/.buildinfo b/python/docSRC/_build/html/.buildinfo new file mode 100644 index 0000000..aecd9dc --- /dev/null +++ b/python/docSRC/_build/html/.buildinfo @@ -0,0 +1,4 @@ +# Sphinx build info version 1 +# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. +config: 613726d7ead289eb5bc59a5d50e806e0 +tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/python/docSRC/_build/html/ASTRAProjector.html b/python/docSRC/_build/html/ASTRAProjector.html new file mode 100644 index 0000000..61c6a2f --- /dev/null +++ b/python/docSRC/_build/html/ASTRAProjector.html @@ -0,0 +1,235 @@ + + + + + + + + Helper class: the ASTRAProjector module — PyASTRAToolbox 1.6 documentation + + + + + + + + + + + + + + +
+

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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:

+
    +
  • 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 \(W\): 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.

+
+ +
+ + +
+
+
+
+
+

Previous topic

+

Additional functions: the functions module

+

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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/_modules/astra/ASTRAProjector.html b/python/docSRC/_build/html/_modules/astra/ASTRAProjector.html new file mode 100644 index 0000000..08789f2 --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/ASTRAProjector.html @@ -0,0 +1,243 @@ + + + + + + + + astra.ASTRAProjector — PyASTRAToolbox 1.6 documentation + + + + + + + + + + + + + +
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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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+ © 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/algorithm.html b/python/docSRC/_build/html/_modules/astra/algorithm.html new file mode 100644 index 0000000..39816fd --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/algorithm.html @@ -0,0 +1,181 @@ + + + + + + + + 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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+ © 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/astra.html b/python/docSRC/_build/html/_modules/astra/astra.html new file mode 100644 index 0000000..53fac8e --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/astra.html @@ -0,0 +1,163 @@ + + + + + + + + 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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+ +
+ +
+ © 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/creators.html b/python/docSRC/_build/html/_modules/astra/creators.html new file mode 100644 index 0000000..c43978a --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/creators.html @@ -0,0 +1,668 @@ + + + + + + + + astra.creators — PyASTRAToolbox 1.6 documentation + + + + + + + + + + + + + +
+

Navigation

+ +
+ +
+
+
+
+ +

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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+ +
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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/data2d.html b/python/docSRC/_build/html/_modules/astra/data2d.html new file mode 100644 index 0000000..d77cddd --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/data2d.html @@ -0,0 +1,225 @@ + + + + + + + + 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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+ +
+ +
+ © 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 new file mode 100644 index 0000000..674d6d1 --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/data3d.html @@ -0,0 +1,213 @@ + + + + + + + + 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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+ +
+ +
+ © 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 new file mode 100644 index 0000000..336431f --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/functions.html @@ -0,0 +1,375 @@ + + + + + + + + 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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+ © 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/matlab.html b/python/docSRC/_build/html/_modules/astra/matlab.html new file mode 100644 index 0000000..b58ff06 --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/matlab.html @@ -0,0 +1,217 @@ + + + + + + + + astra.matlab — PyASTRAToolbox 1.6 documentation + + + + + + + + + + + + + +
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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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+ © 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/matrix.html b/python/docSRC/_build/html/_modules/astra/matrix.html new file mode 100644 index 0000000..5f75455 --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/matrix.html @@ -0,0 +1,191 @@ + + + + + + + + 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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+ © 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/projector.html b/python/docSRC/_build/html/_modules/astra/projector.html new file mode 100644 index 0000000..5982b54 --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/projector.html @@ -0,0 +1,205 @@ + + + + + + + + astra.projector — PyASTRAToolbox 1.6 documentation + + + + + + + + + + + + + +
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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/_modules/index.html b/python/docSRC/_build/html/_modules/index.html new file mode 100644 index 0000000..a844d93 --- /dev/null +++ b/python/docSRC/_build/html/_modules/index.html @@ -0,0 +1,112 @@ + + + + + + + + Overview: module code — PyASTRAToolbox 1.6 documentation + + + + + + + + + + + + +
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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/_sources/ASTRAProjector.txt b/python/docSRC/_build/html/_sources/ASTRAProjector.txt new file mode 100644 index 0000000..1c267e3 --- /dev/null +++ b/python/docSRC/_build/html/_sources/ASTRAProjector.txt @@ -0,0 +1,8 @@ +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 new file mode 100644 index 0000000..83752bd --- /dev/null +++ b/python/docSRC/_build/html/_sources/algorithm.txt @@ -0,0 +1,8 @@ +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 new file mode 100644 index 0000000..5d5fdf0 --- /dev/null +++ b/python/docSRC/_build/html/_sources/astra.txt @@ -0,0 +1,8 @@ +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 new file mode 100644 index 0000000..d6249c3 --- /dev/null +++ b/python/docSRC/_build/html/_sources/creators.txt @@ -0,0 +1,8 @@ +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 new file mode 100644 index 0000000..342cbec --- /dev/null +++ b/python/docSRC/_build/html/_sources/data2d.txt @@ -0,0 +1,8 @@ +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 new file mode 100644 index 0000000..5b7de23 --- /dev/null +++ b/python/docSRC/_build/html/_sources/data3d.txt @@ -0,0 +1,8 @@ +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 new file mode 100644 index 0000000..749eb27 --- /dev/null +++ b/python/docSRC/_build/html/_sources/functions.txt @@ -0,0 +1,8 @@ +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 new file mode 100644 index 0000000..8d17a4a --- /dev/null +++ b/python/docSRC/_build/html/_sources/index.txt @@ -0,0 +1,34 @@ +.. .. 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 new file mode 100644 index 0000000..fb7033e --- /dev/null +++ b/python/docSRC/_build/html/_sources/matlab.txt @@ -0,0 +1,8 @@ +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 new file mode 100644 index 0000000..6f11d8a --- /dev/null +++ b/python/docSRC/_build/html/_sources/matrix.txt @@ -0,0 +1,8 @@ +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 new file mode 100644 index 0000000..b0854e8 --- /dev/null +++ b/python/docSRC/_build/html/_sources/projector.txt @@ -0,0 +1,8 @@ +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 new file mode 100644 index 0000000..61faf8c Binary files /dev/null and b/python/docSRC/_build/html/_static/ajax-loader.gif differ diff --git a/python/docSRC/_build/html/_static/basic.css b/python/docSRC/_build/html/_static/basic.css new file mode 100644 index 0000000..967e36c --- /dev/null +++ b/python/docSRC/_build/html/_static/basic.css @@ -0,0 +1,537 @@ +/* + * basic.css + * ~~~~~~~~~ + * + * Sphinx stylesheet -- basic theme. + * + * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +/* -- main layout ----------------------------------------------------------- */ + +div.clearer { + clear: both; +} + +/* -- relbar 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+h6:hover > a.headerlink, +dt:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.field-list ul { + padding-left: 1em; +} + +.first { + margin-top: 0 !important; +} + +p.rubric { + margin-top: 30px; + font-weight: bold; +} + +img.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- sidebars -------------------------------------------------------------- */ + +div.sidebar { + margin: 0 0 0.5em 1em; + border: 1px solid #ddb; + padding: 7px 7px 0 7px; + background-color: #ffe; + width: 40%; + float: right; +} + +p.sidebar-title { + font-weight: bold; +} + +/* -- topics ---------------------------------------------------------------- */ + +div.topic { + border: 1px solid #ccc; + padding: 7px 7px 0 7px; + margin: 10px 0 10px 0; +} + +p.topic-title { + font-size: 1.1em; + font-weight: bold; + margin-top: 10px; +} + +/* -- admonitions ----------------------------------------------------------- */ + +div.admonition { + margin-top: 10px; + margin-bottom: 10px; + padding: 7px; +} + +div.admonition dt { + font-weight: bold; +} + +div.admonition dl { + margin-bottom: 0; +} + +p.admonition-title { + margin: 0px 10px 5px 0px; + font-weight: bold; +} + +div.body p.centered { + text-align: center; + margin-top: 25px; +} + +/* -- tables ---------------------------------------------------------------- */ + +table.docutils { + border: 0; + border-collapse: collapse; +} + +table.docutils td, table.docutils th { + padding: 1px 8px 1px 5px; + border-top: 0; + 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'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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\ +
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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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    \ + <%username%>\ + <%pretty_rating%>\ + <%time.delta%>\ +

    \ +
    <#text#>
    \ +

    \ + \ + reply ▿\ + proposal ▹\ + proposal ▿\ + \ + \ +

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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 new file mode 100644 index 0000000..bf4b90f --- /dev/null +++ b/python/docSRC/_build/html/algorithm.html @@ -0,0 +1,205 @@ + + + + + + + + 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

      +

      Projector object: the projector module

      +

      Next topic

      +

      Sparse matrices: the matrix 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/astra.html b/python/docSRC/_build/html/astra.html new file mode 100644 index 0000000..42d68b8 --- /dev/null +++ b/python/docSRC/_build/html/astra.html @@ -0,0 +1,169 @@ + + + + + + + + Additional ASTRA methods: the astra module — PyASTRAToolbox 1.6 documentation + + + + + + + + + + + + + +
      +

      Navigation

      + +
      + +
      +
      +
      +
      + +
      +

      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.
      +
      + +
      + + +
      +
      +
      +
      +
      +

      Previous topic

      +

      MATLAB compatibility interface: the matlab 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/creators.html b/python/docSRC/_build/html/creators.html new file mode 100644 index 0000000..2f29232 --- /dev/null +++ b/python/docSRC/_build/html/creators.html @@ -0,0 +1,520 @@ + + + + + + + + Creation of objects: the creators module — PyASTRAToolbox 1.6 documentation + + + + + + + + + + + + + + +
      +

      Navigation

      + +
      + +
      +
      +
      +
      + +
      +

      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

      + +
      + +
      + © 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 new file mode 100644 index 0000000..6b01d41 --- /dev/null +++ b/python/docSRC/_build/html/data2d.html @@ -0,0 +1,277 @@ + + + + + + + + 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

      + + + +
      +
      +
      +
      +
      +

      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 new file mode 100644 index 0000000..926bd6e --- /dev/null +++ b/python/docSRC/_build/html/data3d.html @@ -0,0 +1,259 @@ + + + + + + + + 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

      + + + +
      +
      +
      +
      +
      +

      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 new file mode 100644 index 0000000..7ec397e --- /dev/null +++ b/python/docSRC/_build/html/functions.html @@ -0,0 +1,236 @@ + + + + + + + + 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 new file mode 100644 index 0000000..3099bfa --- /dev/null +++ b/python/docSRC/_build/html/genindex.html @@ -0,0 +1,575 @@ + + + + + + + + + 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) +
      + +
      +
      + +

      U

      + + +
      + +
      use_cuda() (in module astra.astra) +
      + +
      + +

      V

      + + + +
      + +
      version() (in module astra.astra) +
      + +
      + +
      volume_geometry() (in module astra.projector) +
      + +
      + +

      W

      + + + +
      + +
      weights_projection() (in module astra.projector) +
      + +
      + +
      weights_single_ray() (in module astra.projector) +
      + +
      + + + +
      +
      +
      +
      +
      + + + + + +
      +
      +
      +
      +
      +

      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/index.html b/python/docSRC/_build/html/index.html new file mode 100644 index 0000000..817e07f --- /dev/null +++ b/python/docSRC/_build/html/index.html @@ -0,0 +1,148 @@ + + + + + + + + Welcome to PyASTRAToolbox’s documentation! — PyASTRAToolbox 1.6 documentation + + + + + + + + + + + + + +
      +

      Navigation

      + +
      + +
      +
      +
      +
      + + +
      +

      Indices and tables¶

      + +
      + + +
      +
      +
      +
      +
      +

      Table Of Contents

      + + +

      Next topic

      +

      2D data objects: the data2d 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/matlab.html b/python/docSRC/_build/html/matlab.html new file mode 100644 index 0000000..8b4bf31 --- /dev/null +++ b/python/docSRC/_build/html/matlab.html @@ -0,0 +1,184 @@ + + + + + + + + MATLAB compatibility interface: the matlab module — PyASTRAToolbox 1.6 documentation + + + + + + + + + + + + + + +
      +

      Navigation

      + +
      + +
      +
      +
      +
      + +
      +

      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.

      +
      + +
      + + +
      +
      +
      +
      +
      +

      Previous topic

      +

      Helper class: the ASTRAProjector module

      +

      Next topic

      +

      Additional ASTRA methods: the astra 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/matrix.html b/python/docSRC/_build/html/matrix.html new file mode 100644 index 0000000..1df4c30 --- /dev/null +++ b/python/docSRC/_build/html/matrix.html @@ -0,0 +1,221 @@ + + + + + + + + Sparse matrices: the matrix module — PyASTRAToolbox 1.6 documentation + + + + + + + + + + + + + + +
      +

      Navigation

      + +
      + +
      +
      +
      +
      + +
      +

      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.
        • +
      +
      +
      + +
      + + +
      +
      +
      +
      +
      +

      Previous topic

      +

      Algorithms: the algorithm module

      +

      Next topic

      +

      Creation of objects: the creators 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/objects.inv b/python/docSRC/_build/html/objects.inv new file mode 100644 index 0000000..54bab0b Binary files /dev/null and b/python/docSRC/_build/html/objects.inv differ diff --git a/python/docSRC/_build/html/projector.html b/python/docSRC/_build/html/projector.html new file mode 100644 index 0000000..9df5d0b --- /dev/null +++ b/python/docSRC/_build/html/projector.html @@ -0,0 +1,234 @@ + + + + + + + + Projector object: the projector module — PyASTRAToolbox 1.6 documentation + + + + + + + + + + + + + + +
      +

      Navigation

      + +
      + +
      +
      +
      +
      + +
      +

      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]¶
      +
      + +
      + + +
      +
      +
      +
      +
      +

      Previous topic

      +

      3D data objects: the data3d module

      +

      Next topic

      +

      Algorithms: the algorithm 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/py-modindex.html b/python/docSRC/_build/html/py-modindex.html new file mode 100644 index 0000000..b0e4888 --- /dev/null +++ b/python/docSRC/_build/html/py-modindex.html @@ -0,0 +1,172 @@ + + + + + + + + Python Module Index — PyASTRAToolbox 1.6 documentation + + + + + + + + + + + + + + + +
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      + + +

      Python Module Index

      + +
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      + a
      + astra +
          + astra.algorithm +
          + astra.astra +
          + astra.ASTRAProjector +
          + astra.creators +
          + astra.data2d +
          + astra.data3d +
          + astra.functions +
          + astra.matlab +
          + astra.matrix +
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\ No newline at end of file diff --git a/python/docSRC/_templates/layout.html b/python/docSRC/_templates/layout.html new file mode 100644 index 0000000..f30df11 --- /dev/null +++ b/python/docSRC/_templates/layout.html @@ -0,0 +1,15 @@ +{% extends "!layout.html" %} + +{% block footer %} +{{ super() }} + +{% endblock %} diff --git a/python/docSRC/algorithm.rst b/python/docSRC/algorithm.rst new file mode 100644 index 0000000..83752bd --- /dev/null +++ b/python/docSRC/algorithm.rst @@ -0,0 +1,8 @@ +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 new file mode 100644 index 0000000..5d5fdf0 --- /dev/null +++ b/python/docSRC/astra.rst @@ -0,0 +1,8 @@ +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 new file mode 100644 index 0000000..e54bbb8 --- /dev/null +++ b/python/docSRC/conf.py @@ -0,0 +1,287 @@ +# -*- 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 = '1.6' +# The full version, including alpha/beta/rc tags. +release = '1.6' + +# 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 new file mode 100644 index 0000000..d6249c3 --- /dev/null +++ b/python/docSRC/creators.rst @@ -0,0 +1,8 @@ +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 new file mode 100644 index 0000000..342cbec --- /dev/null +++ b/python/docSRC/data2d.rst @@ -0,0 +1,8 @@ +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 new file mode 100644 index 0000000..5b7de23 --- /dev/null +++ b/python/docSRC/data3d.rst @@ -0,0 +1,8 @@ +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 new file mode 100644 index 0000000..749eb27 --- /dev/null +++ b/python/docSRC/functions.rst @@ -0,0 +1,8 @@ +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 new file mode 100644 index 0000000..8d17a4a --- /dev/null +++ b/python/docSRC/index.rst @@ -0,0 +1,34 @@ +.. .. 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/make.bat b/python/docSRC/make.bat new file mode 100644 index 0000000..d70c604 --- /dev/null +++ b/python/docSRC/make.bat @@ -0,0 +1,190 @@ +@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 new file mode 100644 index 0000000..fb7033e --- /dev/null +++ b/python/docSRC/matlab.rst @@ -0,0 +1,8 @@ +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 new file mode 100644 index 0000000..6f11d8a --- /dev/null +++ b/python/docSRC/matrix.rst @@ -0,0 +1,8 @@ +Sparse matrices: the :mod:`matrix` module +========================================= + +.. automodule:: astra.matrix + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/projector.rst b/python/docSRC/projector.rst new file mode 100644 index 0000000..b0854e8 --- /dev/null +++ b/python/docSRC/projector.rst @@ -0,0 +1,8 @@ +Projector object: the :mod:`projector` module +============================================= + +.. automodule:: astra.projector + :members: + :undoc-members: + :show-inheritance: + diff --git a/samples/matlab/s001_sinogram_par2d.m b/samples/matlab/s001_sinogram_par2d.m new file mode 100644 index 0000000..4494e7b --- /dev/null +++ b/samples/matlab/s001_sinogram_par2d.m @@ -0,0 +1,33 @@ +% ----------------------------------------------------------------------- +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +% ----------------------------------------------------------------------- + +% Create a basic 256x256 square volume geometry +vol_geom = astra_create_vol_geom(256, 256); + +% Create a parallel beam geometry with 180 angles between 0 and pi, and +% 384 detector pixels of width 1. +% For more details on available geometries, see the online help of the +% function astra_create_proj_geom . +proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,180)); + +% Create a 256x256 phantom image using matlab's built-in phantom() function +P = phantom(256); + +% Create a sinogram using the GPU. +% Note that the first time the GPU is accessed, there may be a delay +% of up to 10 seconds for initialization. +[sinogram_id, sinogram] = astra_create_sino_gpu(P, proj_geom, vol_geom); + +figure(1); imshow(P, []); +figure(2); imshow(sinogram, []); + + +% Free memory +astra_mex_data2d('delete', sinogram_id); diff --git a/samples/matlab/s002_data2d.m b/samples/matlab/s002_data2d.m new file mode 100644 index 0000000..a91071f --- /dev/null +++ b/samples/matlab/s002_data2d.m @@ -0,0 +1,60 @@ +% ----------------------------------------------------------------------- +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +% ----------------------------------------------------------------------- + +vol_geom = astra_create_vol_geom(256, 256); + +proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,180)); + + +% Create volumes + +% initialized to zero +v0 = astra_mex_data2d('create', '-vol', vol_geom); + +% initialized to 3.0 +v1 = astra_mex_data2d('create', '-vol', vol_geom, 3.0); + +% initialized to a matrix. A may be a single, double or logical (0/1) array. +A = phantom(256); +v2 = astra_mex_data2d('create', '-vol', vol_geom, A); + + +% Projection data +s0 = astra_mex_data2d('create', '-sino', proj_geom); +% Initialization to a scalar or a matrix also works, exactly as with a volume. + + +% Update data + +% set to zero +astra_mex_data2d('store', v0, 0); + +% set to a matrix +astra_mex_data2d('store', v2, A); + + + +% Retrieve data + +R = astra_mex_data2d('get', v2); +imshow(R, []); + + +% Retrieve data as a single array. Since astra internally stores +% data as single precision, this is more efficient: + +R = astra_mex_data2d('get_single', v2); + + +% Free memory +astra_mex_data2d('delete', v0); +astra_mex_data2d('delete', v1); +astra_mex_data2d('delete', v2); +astra_mex_data2d('delete', s0); diff --git a/samples/matlab/s003_gpu_reconstruction.m b/samples/matlab/s003_gpu_reconstruction.m new file mode 100644 index 0000000..efb5c68 --- /dev/null +++ b/samples/matlab/s003_gpu_reconstruction.m @@ -0,0 +1,52 @@ +% ----------------------------------------------------------------------- +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +% ----------------------------------------------------------------------- + +vol_geom = astra_create_vol_geom(256, 256); +proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,180)); + +% As before, create a sinogram from a phantom +P = phantom(256); +[sinogram_id, sinogram] = astra_create_sino_gpu(P, proj_geom, vol_geom); +figure(1); imshow(P, []); +figure(2); imshow(sinogram, []); + +astra_mex_data2d('delete', sinogram_id); + +% We now re-create the sinogram data object as we would do when loading +% an external sinogram +sinogram_id = astra_mex_data2d('create', '-sino', proj_geom, sinogram); + +% Create a data object for the reconstruction +rec_id = astra_mex_data2d('create', '-vol', vol_geom); + +% Set up the parameters for a reconstruction algorithm using the GPU +cfg = astra_struct('SIRT_CUDA'); +cfg.ReconstructionDataId = rec_id; +cfg.ProjectionDataId = sinogram_id; + +% Available algorithms: +% SIRT_CUDA, SART_CUDA, EM_CUDA, FBP_CUDA (see the FBP sample) + + +% Create the algorithm object from the configuration structure +alg_id = astra_mex_algorithm('create', cfg); + +% Run 150 iterations of the algorithm +astra_mex_algorithm('iterate', alg_id, 150); + +% Get the result +rec = astra_mex_data2d('get', rec_id); +figure(3); imshow(rec, []); + +% Clean up. Note that GPU memory is tied up in the algorithm object, +% and main RAM in the data objects. +astra_mex_algorithm('delete', alg_id); +astra_mex_data2d('delete', rec_id); +astra_mex_data2d('delete', sinogram_id); diff --git a/samples/matlab/s004_cpu_reconstruction.m b/samples/matlab/s004_cpu_reconstruction.m new file mode 100644 index 0000000..f25cd2b --- /dev/null +++ b/samples/matlab/s004_cpu_reconstruction.m @@ -0,0 +1,60 @@ +% ----------------------------------------------------------------------- +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +% ----------------------------------------------------------------------- + +vol_geom = astra_create_vol_geom(256, 256); +proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,180)); + +% For CPU-based algorithms, a "projector" object specifies the projection +% model used. In this case, we use the "strip" model. +proj_id = astra_create_projector('strip', proj_geom, vol_geom); + +% Create a sinogram from a phantom +P = phantom(256); +[sinogram_id, sinogram] = astra_create_sino(P, proj_id); +figure(1); imshow(P, []); +figure(2); imshow(sinogram, []); + +astra_mex_data2d('delete', sinogram_id); + +% We now re-create the sinogram data object as we would do when loading +% an external sinogram +sinogram_id = astra_mex_data2d('create', '-sino', proj_geom, sinogram); + +% Create a data object for the reconstruction +rec_id = astra_mex_data2d('create', '-vol', vol_geom); + +% Set up the parameters for a reconstruction algorithm using the CPU +% The main difference with the configuration of a GPU algorithm is the +% extra ProjectorId setting. +cfg = astra_struct('SIRT'); +cfg.ReconstructionDataId = rec_id; +cfg.ProjectionDataId = sinogram_id; +cfg.ProjectorId = proj_id; + +% Available algorithms: +% ART, SART, SIRT, CGLS, FBP + + +% Create the algorithm object from the configuration structure +alg_id = astra_mex_algorithm('create', cfg); + +% Run 20 iterations of the algorithm +% This will have a runtime in the order of 10 seconds. +astra_mex_algorithm('iterate', alg_id, 20); + +% Get the result +rec = astra_mex_data2d('get', rec_id); +figure(3); imshow(rec, []); + +% Clean up. +astra_mex_projector('delete', proj_id); +astra_mex_algorithm('delete', alg_id); +astra_mex_data2d('delete', rec_id); +astra_mex_data2d('delete', sinogram_id); diff --git a/samples/matlab/s005_3d_geometry.m b/samples/matlab/s005_3d_geometry.m new file mode 100644 index 0000000..4b7360b --- /dev/null +++ b/samples/matlab/s005_3d_geometry.m @@ -0,0 +1,98 @@ +% ----------------------------------------------------------------------- +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +% ----------------------------------------------------------------------- + +vol_geom = astra_create_vol_geom(64, 64, 64); + + +% There are two main 3d projection geometry types: cone beam and parallel beam. +% Each has a regular variant, and a 'vec' variant. +% The 'vec' variants are completely free in the placement of source/detector, +% while the regular variants assume circular trajectories around the z-axis. + + +% ------------- +% Parallel beam +% ------------- + + +% Circular + +% Parameters: width of detector column, height of detector row, #rows, #columns +angles = linspace2(0, 2*pi, 48); +proj_geom = astra_create_proj_geom('parallel3d', 1.0, 1.0, 32, 64, angles); + + +% Free + +% We generate the same geometry as the circular one above. +vectors = zeros(numel(angles), 12); +for i = 1:numel(angles) + % ray direction + vectors(i,1) = sin(angles(i)); + vectors(i,2) = -cos(angles(i)); + vectors(i,3) = 0; + + % center of detector + vectors(i,4:6) = 0; + + % vector from detector pixel (0,0) to (0,1) + vectors(i,7) = cos(angles(i)); + vectors(i,8) = sin(angles(i)); + vectors(i,9) = 0; + + % vector from detector pixel (0,0) to (1,0) + vectors(i,10) = 0; + vectors(i,11) = 0; + vectors(i,12) = 1; +end + +% Parameters: #rows, #columns, vectors +proj_geom = astra_create_proj_geom('parallel3d_vec', 32, 64, vectors); + +% ---------- +% Cone beam +% ---------- + + +% Circular + +% Parameters: width of detector column, height of detector row, #rows, #columns, +% angles, distance source-origin, distance origin-detector +angles = linspace2(0, 2*pi, 48); +proj_geom = astra_create_proj_geom('cone', 1.0, 1.0, 32, 64, ... + angles, 1000, 0); + +% Free + +vectors = zeros(numel(angles), 12); +for i = 1:numel(angles) + + % source + vectors(i,1) = sin(angles(i)) * 1000; + vectors(i,2) = -cos(angles(i)) * 1000; + vectors(i,3) = 0; + + % center of detector + vectors(i,4:6) = 0; + + % vector from detector pixel (0,0) to (0,1) + vectors(i,7) = cos(angles(i)); + vectors(i,8) = sin(angles(i)); + vectors(i,9) = 0; + + % vector from detector pixel (0,0) to (1,0) + vectors(i,10) = 0; + vectors(i,11) = 0; + vectors(i,12) = 1; +end + +% Parameters: #rows, #columns, vectors +proj_geom = astra_create_proj_geom('cone_vec', 32, 64, vectors); + diff --git a/samples/matlab/s006_3d_data.m b/samples/matlab/s006_3d_data.m new file mode 100644 index 0000000..32d88cc --- /dev/null +++ b/samples/matlab/s006_3d_data.m @@ -0,0 +1,62 @@ +% ----------------------------------------------------------------------- +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +% ----------------------------------------------------------------------- + +% Create a 3D volume geometry. +% Parameter order: rows, colums, slices (y, x, z) +vol_geom = astra_create_vol_geom(64, 48, 32); + + +% Create volumes + +% initialized to zero +v0 = astra_mex_data3d('create', '-vol', vol_geom); + +% initialized to 3.0 +v1 = astra_mex_data3d('create', '-vol', vol_geom, 3.0); + +% initialized to a matrix. A may be a single or double array. +% Coordinate order: column, row, slice (x, y, z) +A = zeros(48, 64, 32); +v2 = astra_mex_data3d('create', '-vol', vol_geom, A); + + +% Projection data + +% 2 projection directions, along x and y axis resp. +V = [ 1 0 0 0 0 0 0 1 0 0 0 1 ; ... + 0 1 0 0 0 0 -1 0 0 0 0 1 ]; +% 32 rows (v), 64 columns (u) +proj_geom = astra_create_proj_geom('parallel3d_vec', 32, 64, V); + +s0 = astra_mex_data3d('create', '-proj3d', proj_geom); + +% Initialization to a scalar or zero works exactly as with a volume. + +% Initialized to a matrix: +% Coordinate order: column (u), angle, row (v) +A = zeros(64, 2, 32); +s1 = astra_mex_data3d('create', '-proj3d', proj_geom, A); + + +% Retrieve data: +R = astra_mex_data3d('get', v1); + +% Retrieve data as a single array. Since astra internally stores +% data as single precision, this is more efficient: +R = astra_mex_data3d('get_single', v1); + + + +% Delete all created data objects +astra_mex_data3d('delete', v0); +astra_mex_data3d('delete', v1); +astra_mex_data3d('delete', v2); +astra_mex_data3d('delete', s0); +astra_mex_data3d('delete', s1); diff --git a/samples/matlab/s007_3d_reconstruction.m b/samples/matlab/s007_3d_reconstruction.m new file mode 100644 index 0000000..fc9aca6 --- /dev/null +++ b/samples/matlab/s007_3d_reconstruction.m @@ -0,0 +1,53 @@ +% ----------------------------------------------------------------------- +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +% ----------------------------------------------------------------------- + +vol_geom = astra_create_vol_geom(128, 128, 128); + +angles = linspace2(0, pi, 180); +proj_geom = astra_create_proj_geom('parallel3d', 1.0, 1.0, 128, 192, angles); + +% Create a simple hollow cube phantom +cube = zeros(128,128,128); +cube(17:112,17:112,17:112) = 1; +cube(33:96,33:96,33:96) = 0; + +% Create projection data from this +[proj_id, proj_data] = astra_create_sino3d_cuda(cube, proj_geom, vol_geom); + +% Display a single projection image +figure, imshow(squeeze(proj_data(:,20,:))',[]) + +% Create a data object for the reconstruction +rec_id = astra_mex_data3d('create', '-vol', vol_geom); + +% Set up the parameters for a reconstruction algorithm using the GPU +cfg = astra_struct('SIRT3D_CUDA'); +cfg.ReconstructionDataId = rec_id; +cfg.ProjectionDataId = proj_id; + + +% Create the algorithm object from the configuration structure +alg_id = astra_mex_algorithm('create', cfg); + +% Run 150 iterations of the algorithm +% Note that this requires about 750MB of GPU memory, and has a runtime +% in the order of 10 seconds. +astra_mex_algorithm('iterate', alg_id, 150); + +% Get the result +rec = astra_mex_data3d('get', rec_id); +figure, imshow(squeeze(rec(:,:,65)),[]); + + +% Clean up. Note that GPU memory is tied up in the algorithm object, +% and main RAM in the data objects. +astra_mex_algorithm('delete', alg_id); +astra_mex_data3d('delete', rec_id); +astra_mex_data3d('delete', proj_id); diff --git a/samples/matlab/s008_gpu_selection.m b/samples/matlab/s008_gpu_selection.m new file mode 100644 index 0000000..a9e152d --- /dev/null +++ b/samples/matlab/s008_gpu_selection.m @@ -0,0 +1,37 @@ +% ----------------------------------------------------------------------- +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +% ----------------------------------------------------------------------- + +vol_geom = astra_create_vol_geom(256, 256); +proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,180)); +P = phantom(256); + +% Create a sinogram from a phantom, using GPU #1. (The default is #0) +[sinogram_id, sinogram] = astra_create_sino_gpu(P, proj_geom, vol_geom, 1); + + +% Set up the parameters for a reconstruction algorithm using the GPU +rec_id = astra_mex_data2d('create', '-vol', vol_geom); +cfg = astra_struct('SIRT_CUDA'); +cfg.ReconstructionDataId = rec_id; +cfg.ProjectionDataId = sinogram_id; + +% Use GPU #1 for the reconstruction. (The default is #0.) +cfg.option.GPUindex = 1; + +% Run 150 iterations of the algorithm +alg_id = astra_mex_algorithm('create', cfg); +astra_mex_algorithm('iterate', alg_id, 150); +rec = astra_mex_data2d('get', rec_id); + + +% Clean up. +astra_mex_algorithm('delete', alg_id); +astra_mex_data2d('delete', rec_id); +astra_mex_data2d('delete', sinogram_id); diff --git a/samples/matlab/s009_projection_matrix.m b/samples/matlab/s009_projection_matrix.m new file mode 100644 index 0000000..efda0d2 --- /dev/null +++ b/samples/matlab/s009_projection_matrix.m @@ -0,0 +1,45 @@ +% ----------------------------------------------------------------------- +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +% ----------------------------------------------------------------------- + +vol_geom = astra_create_vol_geom(256, 256); +proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,180)); + +% For CPU-based algorithms, a "projector" object specifies the projection +% model used. In this case, we use the "strip" model. +proj_id = astra_create_projector('strip', proj_geom, vol_geom); + +% Generate the projection matrix for this projection model. +% This creates a matrix W where entry w_{i,j} corresponds to the +% contribution of volume element j to detector element i. +matrix_id = astra_mex_projector('matrix', proj_id); + +% Get the projection matrix as a Matlab sparse matrix. +W = astra_mex_matrix('get', matrix_id); + + +% Manually use this projection matrix to do a projection: +P = phantom(256)'; +s = W * P(:); +s = reshape(s, [proj_geom.DetectorCount size(proj_geom.ProjectionAngles, 2)])'; +figure(1), imshow(s,[]); + +% Because Matlab's matrices are stored transposed in memory compared to C++, +% reshaping them to a vector doesn't give the right ordering for multiplication +% with W. We have to take the transpose of the input and output to get the same +% results (up to numerical noise) as using the toolbox directly. + +% Each row of the projection matrix corresponds to a detector element. +% Detector t for angle p is for row 1 + t + p*proj_geom.DetectorCount. +% Each column corresponds to a volume pixel. +% Pixel (x,y) corresponds to column 1 + x + y*vol_geom.GridColCount. + + +astra_mex_projector('delete', proj_id); +astra_mex_matrix('delete', matrix_id); diff --git a/samples/matlab/s010_supersampling.m b/samples/matlab/s010_supersampling.m new file mode 100644 index 0000000..80f6f56 --- /dev/null +++ b/samples/matlab/s010_supersampling.m @@ -0,0 +1,58 @@ +% ----------------------------------------------------------------------- +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +% ----------------------------------------------------------------------- + +vol_geom = astra_create_vol_geom(256, 256); +proj_geom = astra_create_proj_geom('parallel', 3.0, 128, linspace2(0,pi,180)); +P = phantom(256); + +% Because the astra_create_sino_gpu wrapper does not have support for +% all possible algorithm options, we manually create a sinogram +phantom_id = astra_mex_data2d('create', '-vol', vol_geom, P); +sinogram_id = astra_mex_data2d('create', '-sino', proj_geom); +cfg = astra_struct('FP_CUDA'); +cfg.VolumeDataId = phantom_id; +cfg.ProjectionDataId = sinogram_id; + +% Set up 3 rays per detector element +cfg.option.DetectorSuperSampling = 3; + +alg_id = astra_mex_algorithm('create', cfg); +astra_mex_algorithm('run', alg_id); +astra_mex_algorithm('delete', alg_id); +astra_mex_data2d('delete', phantom_id); + +sinogram3 = astra_mex_data2d('get', sinogram_id); + +figure(1); imshow(P, []); +figure(2); imshow(sinogram3, []); + + +% Create a reconstruction, also using supersampling +rec_id = astra_mex_data2d('create', '-vol', vol_geom); +cfg = astra_struct('SIRT_CUDA'); +cfg.ReconstructionDataId = rec_id; +cfg.ProjectionDataId = sinogram_id; +% Set up 3 rays per detector element +cfg.option.DetectorSuperSampling = 3; + +% There is also an option for supersampling during the backprojection step. +% This should be used if your detector pixels are smaller than the voxels. + +% Set up 2 rays per image pixel dimension, for 4 rays total per image pixel. +% cfg.option.PixelSuperSampling = 2; + + +alg_id = astra_mex_algorithm('create', cfg); +astra_mex_algorithm('iterate', alg_id, 150); +astra_mex_algorithm('delete', alg_id); + +rec = astra_mex_data2d('get', rec_id); +figure(3); imshow(rec, []); + diff --git a/samples/matlab/s011_object_info.m b/samples/matlab/s011_object_info.m new file mode 100644 index 0000000..61ecb83 --- /dev/null +++ b/samples/matlab/s011_object_info.m @@ -0,0 +1,36 @@ +% ----------------------------------------------------------------------- +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +% ----------------------------------------------------------------------- + +% Create two volume geometries +vol_geom1 = astra_create_vol_geom(256, 256); +vol_geom2 = astra_create_vol_geom(512, 256); + +% Create volumes +v0 = astra_mex_data2d('create', '-vol', vol_geom1); +v1 = astra_mex_data2d('create', '-vol', vol_geom2); +v2 = astra_mex_data2d('create', '-vol', vol_geom2); + +% Show the currently allocated volumes +astra_mex_data2d('info'); + + +astra_mex_data2d('delete', v2); +astra_mex_data2d('info'); + +astra_mex_data2d('clear'); +astra_mex_data2d('info'); + + + +% The same clear and info command also work for other object types: +astra_mex_algorithm('info'); +astra_mex_data3d('info'); +astra_mex_projector('info'); +astra_mex_matrix('info'); diff --git a/samples/matlab/s012_masks.m b/samples/matlab/s012_masks.m new file mode 100644 index 0000000..d3611a6 --- /dev/null +++ b/samples/matlab/s012_masks.m @@ -0,0 +1,60 @@ +% ----------------------------------------------------------------------- +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +% ----------------------------------------------------------------------- + + +% In this example we will create a reconstruction in a circular region, +% instead of the usual rectangle. + +% This is done by placing a circular mask on the square reconstruction volume: + +c = -127.5:127.5; +[x y] = meshgrid(-127.5:127.5,-127.5:127.5); +mask = (x.^2 + y.^2 < 127.5^2); + +figure(1); imshow(mask, []); + + +vol_geom = astra_create_vol_geom(256, 256); +proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,50)); + +% As before, create a sinogram from a phantom +P = phantom(256); +[sinogram_id, sinogram] = astra_create_sino_gpu(P, proj_geom, vol_geom); +figure(2); imshow(P, []); +figure(3); imshow(sinogram, []); + +% Create a data object for the reconstruction +rec_id = astra_mex_data2d('create', '-vol', vol_geom); + +% Create a data object for the mask +mask_id = astra_mex_data2d('create', '-vol', vol_geom, mask); + +% Set up the parameters for a reconstruction algorithm using the GPU +cfg = astra_struct('SIRT_CUDA'); +cfg.ReconstructionDataId = rec_id; +cfg.ProjectionDataId = sinogram_id; +cfg.option.ReconstructionMaskId = mask_id; + +% Create the algorithm object from the configuration structure +alg_id = astra_mex_algorithm('create', cfg); + +% Run 150 iterations of the algorithm +astra_mex_algorithm('iterate', alg_id, 150); + +% Get the result +rec = astra_mex_data2d('get', rec_id); +figure(4); imshow(rec, []); + +% Clean up. Note that GPU memory is tied up in the algorithm object, +% and main RAM in the data objects. +astra_mex_algorithm('delete', alg_id); +astra_mex_data2d('delete', mask_id); +astra_mex_data2d('delete', rec_id); +astra_mex_data2d('delete', sinogram_id); diff --git a/samples/matlab/s013_constraints.m b/samples/matlab/s013_constraints.m new file mode 100644 index 0000000..d72195c --- /dev/null +++ b/samples/matlab/s013_constraints.m @@ -0,0 +1,47 @@ +% ----------------------------------------------------------------------- +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +% ----------------------------------------------------------------------- + +% In this example we will create a reconstruction constrained to +% greyvalues between 0 and 1 + +vol_geom = astra_create_vol_geom(256, 256); +proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,50)); + +% As before, create a sinogram from a phantom +P = phantom(256); +[sinogram_id, sinogram] = astra_create_sino_gpu(P, proj_geom, vol_geom); +figure(1); imshow(P, []); +figure(2); imshow(sinogram, []); + +% Create a data object for the reconstruction +rec_id = astra_mex_data2d('create', '-vol', vol_geom); + +% Set up the parameters for a reconstruction algorithm using the GPU +cfg = astra_struct('SIRT_CUDA'); +cfg.ReconstructionDataId = rec_id; +cfg.ProjectionDataId = sinogram_id; +cfg.option.MinConstraint = 0; +cfg.option.MaxConstraint = 1; + +% Create the algorithm object from the configuration structure +alg_id = astra_mex_algorithm('create', cfg); + +% Run 150 iterations of the algorithm +astra_mex_algorithm('iterate', alg_id, 150); + +% Get the result +rec = astra_mex_data2d('get', rec_id); +figure(3); imshow(rec, []); + +% Clean up. Note that GPU memory is tied up in the algorithm object, +% and main RAM in the data objects. +astra_mex_algorithm('delete', alg_id); +astra_mex_data2d('delete', rec_id); +astra_mex_data2d('delete', sinogram_id); diff --git a/samples/matlab/s014_FBP.m b/samples/matlab/s014_FBP.m new file mode 100644 index 0000000..b73149c --- /dev/null +++ b/samples/matlab/s014_FBP.m @@ -0,0 +1,47 @@ +% ----------------------------------------------------------------------- +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +% ----------------------------------------------------------------------- + +vol_geom = astra_create_vol_geom(256, 256); +proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,180)); + +% As before, create a sinogram from a phantom +P = phantom(256); +[sinogram_id, sinogram] = astra_create_sino_gpu(P, proj_geom, vol_geom); +figure(1); imshow(P, []); +figure(2); imshow(sinogram, []); + +% Create a data object for the reconstruction +rec_id = astra_mex_data2d('create', '-vol', vol_geom); + +% create configuration +cfg = astra_struct('FBP_CUDA'); +cfg.ReconstructionDataId = rec_id; +cfg.ProjectionDataId = sinogram_id; +cfg.FilterType = 'Ram-Lak'; + +% possible values for FilterType: +% none, ram-lak, shepp-logan, cosine, hamming, hann, tukey, lanczos, +% triangular, gaussian, barlett-hann, blackman, nuttall, blackman-harris, +% blackman-nuttall, flat-top, kaiser, parzen + + +% Create and run the algorithm object from the configuration structure +alg_id = astra_mex_algorithm('create', cfg); +astra_mex_algorithm('run', alg_id); + +% Get the result +rec = astra_mex_data2d('get', rec_id); +figure(3); imshow(rec, []); + +% Clean up. Note that GPU memory is tied up in the algorithm object, +% and main RAM in the data objects. +astra_mex_algorithm('delete', alg_id); +astra_mex_data2d('delete', rec_id); +astra_mex_data2d('delete', sinogram_id); diff --git a/samples/matlab/s015_fp_bp.m b/samples/matlab/s015_fp_bp.m new file mode 100644 index 0000000..8cc417e --- /dev/null +++ b/samples/matlab/s015_fp_bp.m @@ -0,0 +1,62 @@ +% ----------------------------------------------------------------------- +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +% ----------------------------------------------------------------------- + + +% This example demonstrates using the FP and BP primitives with Matlab's lsqr +% solver. Calls to FP (astra_create_sino_cuda) and +% BP (astra_create_backprojection_cuda) are wrapped in a function astra_wrap, +% and a handle to this function is passed to lsqr. + +% Because in this case the inputs/outputs of FP and BP have to be vectors +% instead of images (matrices), the calls require reshaping to and from vectors. + +function s015_fp_bp + + +% FP/BP wrapper function +function Y = astra_wrap(X,T) + if strcmp(T, 'notransp') + % X is passed as a vector. Reshape it into an image. + [sid, s] = astra_create_sino_cuda(reshape(X,[vol_geom.GridRowCount vol_geom.GridColCount])', proj_geom, vol_geom); + astra_mex_data2d('delete', sid); + % now s is the sinogram. Reshape it back into a vector + Y = reshape(s',[prod(size(s)) 1]); + else + % X is passed as a vector. Reshape it into a sinogram. + v = astra_create_backprojection_cuda(reshape(X, [proj_geom.DetectorCount size(proj_geom.ProjectionAngles,2)])', proj_geom, vol_geom); + % now v is the resulting volume. Reshape it back into a vector + Y = reshape(v',[prod(size(v)) 1]); + end +end + + +vol_geom = astra_create_vol_geom(256, 256); +proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,180)); + +% Create a 256x256 phantom image using matlab's built-in phantom() function +P = phantom(256); + +% Create a sinogram using the GPU. +[sinogram_id, sinogram] = astra_create_sino_gpu(P, proj_geom, vol_geom); + +% Reshape the sinogram into a vector +b = reshape(sinogram',[prod(size(sinogram)) 1]); + +% Call Matlab's lsqr with ASTRA FP and BP +Y = lsqr(@astra_wrap,b,1e-4,25); + +% Reshape the result into an image +Y = reshape(Y,[vol_geom.GridRowCount vol_geom.GridColCount])'; +imshow(Y,[]); + + +astra_mex_data2d('delete', sinogram_id); + +end diff --git a/samples/matlab/s016_plots.m b/samples/matlab/s016_plots.m new file mode 100644 index 0000000..1455c6d --- /dev/null +++ b/samples/matlab/s016_plots.m @@ -0,0 +1,54 @@ +% ----------------------------------------------------------------------- +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +% ----------------------------------------------------------------------- + +vol_geom = astra_create_vol_geom(256, 256); +proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,180)); + +% As before, create a sinogram from a phantom +P = phantom(256); +[sinogram_id, sinogram] = astra_create_sino_gpu(P, proj_geom, vol_geom); +figure(1); imshow(P, []); +figure(2); imshow(sinogram, []); + +% Create a data object for the reconstruction +rec_id = astra_mex_data2d('create', '-vol', vol_geom); + +% Set up the parameters for a reconstruction algorithm using the GPU +cfg = astra_struct('SIRT_CUDA'); +cfg.ReconstructionDataId = rec_id; +cfg.ProjectionDataId = sinogram_id; + +% Create the algorithm object from the configuration structure +alg_id = astra_mex_algorithm('create', cfg); + +% Run 1500 iterations of the algorithm one at a time, keeping track of errors +nIters = 1500; +phantom_error = zeros(1, nIters); +residual_error = zeros(1, nIters); +for i = 1:nIters; + % Run a single iteration + astra_mex_algorithm('iterate', alg_id, 1); + + residual_error(i) = astra_mex_algorithm('get_res_norm', alg_id); + rec = astra_mex_data2d('get', rec_id); + phantom_error(i) = sqrt(sumsqr(rec - P)); +end + +% Get the result +rec = astra_mex_data2d('get', rec_id); +figure(3); imshow(rec, []); + +figure(4); plot(residual_error) +figure(5); plot(phantom_error) + +% Clean up. +astra_mex_algorithm('delete', alg_id); +astra_mex_data2d('delete', rec_id); +astra_mex_data2d('delete', sinogram_id); diff --git a/samples/python/phantom.mat b/samples/python/phantom.mat new file mode 100644 index 0000000..c465bbe Binary files /dev/null and b/samples/python/phantom.mat differ diff --git a/samples/python/s001_sinogram_par2d.py b/samples/python/s001_sinogram_par2d.py new file mode 100644 index 0000000..009d9b3 --- /dev/null +++ b/samples/python/s001_sinogram_par2d.py @@ -0,0 +1,60 @@ +#----------------------------------------------------------------------- +#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 . +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +# Create a basic 256x256 square volume geometry +vol_geom = astra.create_vol_geom(256, 256) + +# Create a parallel beam geometry with 180 angles between 0 and pi, and +# 384 detector pixels of width 1. +# For more details on available geometries, see the online help of the +# function astra_create_proj_geom . +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + +# Load a 256x256 phantom image +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] + +# Create a sinogram using the GPU. +# Note that the first time the GPU is accessed, there may be a delay +# of up to 10 seconds for initialization. +proj_id = astra.create_projector('line',proj_geom,vol_geom) +sinogram_id, sinogram = astra.create_sino(P, proj_id,useCUDA=True) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(P) +pylab.figure(2) +pylab.imshow(sinogram) +pylab.show() + + +# Free memory +astra.data2d.delete(sinogram_id) +astra.projector.delete(proj_id) diff --git a/samples/python/s002_data2d.py b/samples/python/s002_data2d.py new file mode 100644 index 0000000..35fb91f --- /dev/null +++ b/samples/python/s002_data2d.py @@ -0,0 +1,77 @@ +#----------------------------------------------------------------------- +#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 . +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +vol_geom = astra.create_vol_geom(256, 256) + +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + + +# Create volumes + +# initialized to zero +v0 = astra.data2d.create('-vol', vol_geom) + +# initialized to 3.0 +v1 = astra.data2d.create('-vol', vol_geom, 3.0) + +# initialized to a matrix. A may be a single, double or logical (0/1) array. +import scipy.io +A = scipy.io.loadmat('phantom.mat')['phantom256'] +v2 = astra.data2d.create('-vol', vol_geom, A) + + +# Projection data +s0 = astra.data2d.create('-sino', proj_geom) +# Initialization to a scalar or a matrix also works, exactly as with a volume. + + +# Update data + +# set to zero +astra.data2d.store(v0, 0) + +# set to a matrix +astra.data2d.store(v2, A) + + + +# Retrieve data + +R = astra.data2d.get(v2) +import pylab +pylab.gray() +pylab.imshow(R) +pylab.show() + + +# Free memory +astra.data2d.delete(v0) +astra.data2d.delete(v1) +astra.data2d.delete(v2) +astra.data2d.delete(s0) diff --git a/samples/python/s003_gpu_reconstruction.py b/samples/python/s003_gpu_reconstruction.py new file mode 100644 index 0000000..4f6ec1f --- /dev/null +++ b/samples/python/s003_gpu_reconstruction.py @@ -0,0 +1,75 @@ +#----------------------------------------------------------------------- +#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 . +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + +# As before, create a sinogram from a phantom +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] +proj_id = astra.create_projector('line',proj_geom,vol_geom) +sinogram_id, sinogram = astra.create_sino(P, proj_id,useCUDA=True) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(P) +pylab.figure(2) +pylab.imshow(sinogram) + +# Create a data object for the reconstruction +rec_id = astra.data2d.create('-vol', vol_geom) + +# Set up the parameters for a reconstruction algorithm using the GPU +cfg = astra.astra_dict('SIRT_CUDA') +cfg['ReconstructionDataId'] = rec_id +cfg['ProjectionDataId'] = sinogram_id + +# Available algorithms: +# SIRT_CUDA, SART_CUDA, EM_CUDA, FBP_CUDA (see the FBP sample) + + +# Create the algorithm object from the configuration structure +alg_id = astra.algorithm.create(cfg) + +# Run 150 iterations of the algorithm +astra.algorithm.run(alg_id, 150) + +# Get the result +rec = astra.data2d.get(rec_id) +pylab.figure(3) +pylab.imshow(rec) +pylab.show() + +# Clean up. Note that GPU memory is tied up in the algorithm object, +# and main RAM in the data objects. +astra.algorithm.delete(alg_id) +astra.data2d.delete(rec_id) +astra.data2d.delete(sinogram_id) +astra.projector.delete(proj_id) diff --git a/samples/python/s004_cpu_reconstruction.py b/samples/python/s004_cpu_reconstruction.py new file mode 100644 index 0000000..8385cf8 --- /dev/null +++ b/samples/python/s004_cpu_reconstruction.py @@ -0,0 +1,81 @@ +#----------------------------------------------------------------------- +#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 . +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + +# For CPU-based algorithms, a "projector" object specifies the projection +# model used. In this case, we use the "strip" model. +proj_id = astra.create_projector('strip', proj_geom, vol_geom) + +# Create a sinogram from a phantom +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] +sinogram_id, sinogram = astra.create_sino(P, proj_id) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(P) +pylab.figure(2) +pylab.imshow(sinogram) + +# Create a data object for the reconstruction +rec_id = astra.data2d.create('-vol', vol_geom) + +# Set up the parameters for a reconstruction algorithm using the CPU +# The main difference with the configuration of a GPU algorithm is the +# extra ProjectorId setting. +cfg = astra.astra_dict('SIRT') +cfg['ReconstructionDataId'] = rec_id +cfg['ProjectionDataId'] = sinogram_id +cfg['ProjectorId'] = proj_id + +# Available algorithms: +# ART, SART, SIRT, CGLS, FBP + + +# Create the algorithm object from the configuration structure +alg_id = astra.algorithm.create(cfg) + +# Run 20 iterations of the algorithm +# This will have a runtime in the order of 10 seconds. +astra.algorithm.run(alg_id, 20) + +# Get the result +rec = astra.data2d.get(rec_id) +pylab.figure(3) +pylab.imshow(rec) +pylab.show() + +# Clean up. +astra.algorithm.delete(alg_id) +astra.data2d.delete(rec_id) +astra.data2d.delete(sinogram_id) +astra.projector.delete(proj_id) diff --git a/samples/python/s005_3d_geometry.py b/samples/python/s005_3d_geometry.py new file mode 100644 index 0000000..f43fc7e --- /dev/null +++ b/samples/python/s005_3d_geometry.py @@ -0,0 +1,114 @@ +#----------------------------------------------------------------------- +#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 six.moves import range +import astra +import numpy as np + +vol_geom = astra.create_vol_geom(64, 64, 64) + + +# There are two main 3d projection geometry types: cone beam and parallel beam. +# Each has a regular variant, and a 'vec' variant. +# The 'vec' variants are completely free in the placement of source/detector, +# while the regular variants assume circular trajectories around the z-axis. + + +# ------------- +# Parallel beam +# ------------- + + +# Circular + +# Parameters: width of detector column, height of detector row, #rows, #columns +angles = np.linspace(0, 2*np.pi, 48, False) +proj_geom = astra.create_proj_geom('parallel3d', 1.0, 1.0, 32, 64, angles) + + +# Free + +# We generate the same geometry as the circular one above. +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,3:6] = 0 + + # vector from detector pixel (0,0) to (0,1) + vectors[i,6] = np.cos(angles[i]) + vectors[i,7] = np.sin(angles[i]) + vectors[i,8] = 0; + + # vector from detector pixel (0,0) to (1,0) + vectors[i,9] = 0 + vectors[i,10] = 0 + vectors[i,11] = 1 + +# Parameters: #rows, #columns, vectors +proj_geom = astra.create_proj_geom('parallel3d_vec', 32, 64, vectors) + +# ---------- +# Cone beam +# ---------- + + +# Circular + +# Parameters: width of detector column, height of detector row, #rows, #columns, +# angles, distance source-origin, distance origin-detector +angles = np.linspace(0, 2*np.pi, 48, False) +proj_geom = astra.create_proj_geom('cone', 1.0, 1.0, 32, 64, angles, 1000, 0) + +# Free + +vectors = np.zeros((len(angles), 12)) +for i in range(len(angles)): + # source + vectors[i,0] = np.sin(angles[i]) * 1000 + vectors[i,1] = -np.cos(angles[i]) * 1000 + vectors[i,2] = 0 + + # center of detector + vectors[i,3:6] = 0 + + # vector from detector pixel (0,0) to (0,1) + vectors[i,6] = np.cos(angles[i]) + vectors[i,7] = np.sin(angles[i]) + vectors[i,8] = 0 + + # vector from detector pixel (0,0) to (1,0) + vectors[i,9] = 0 + vectors[i,10] = 0 + vectors[i,11] = 1 + +# Parameters: #rows, #columns, vectors +proj_geom = astra.create_proj_geom('cone_vec', 32, 64, vectors) + diff --git a/samples/python/s006_3d_data.py b/samples/python/s006_3d_data.py new file mode 100644 index 0000000..5178179 --- /dev/null +++ b/samples/python/s006_3d_data.py @@ -0,0 +1,76 @@ +#----------------------------------------------------------------------- +#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 . +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +# Create a 3D volume geometry. +# Parameter order: rows, colums, slices (y, x, z) +vol_geom = astra.create_vol_geom(64, 48, 32) + + +# Create volumes + +# initialized to zero +v0 = astra.data3d.create('-vol', vol_geom) + +# initialized to 3.0 +v1 = astra.data3d.create('-vol', vol_geom, 3.0) + +# initialized to a matrix. A may be a single or double array. +# Coordinate order: slice, row, column (z, y, x) +A = np.zeros((32, 64, 48)) +v2 = astra.data3d.create('-vol', vol_geom, A) + + +# Projection data + +# 2 projection directions, along x and y axis resp. +V = np.array([[ 1,0,0, 0,0,0, 0,1,0, 0,0,1], + [0,1,0, 0,0,0, -1,0,0, 0,0,1]],dtype=np.float) +# 32 rows (v), 64 columns (u) +proj_geom = astra.create_proj_geom('parallel3d_vec', 32, 64, V) + +s0 = astra.data3d.create('-proj3d', proj_geom) + +# Initialization to a scalar or zero works exactly as with a volume. + +# Initialized to a matrix: +# Coordinate order: row (v), angle, column (u) +A = np.zeros((32, 2, 64)) +s1 = astra.data3d.create('-proj3d', proj_geom, A) + + +# Retrieve data: +R = astra.data3d.get(v1) + + +# Delete all created data objects +astra.data3d.delete(v0) +astra.data3d.delete(v1) +astra.data3d.delete(v2) +astra.data3d.delete(s0) +astra.data3d.delete(s1) diff --git a/samples/python/s007_3d_reconstruction.py b/samples/python/s007_3d_reconstruction.py new file mode 100644 index 0000000..40e9556 --- /dev/null +++ b/samples/python/s007_3d_reconstruction.py @@ -0,0 +1,77 @@ +#----------------------------------------------------------------------- +#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 . +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +vol_geom = astra.create_vol_geom(128, 128, 128) + +angles = np.linspace(0, np.pi, 180,False) +proj_geom = astra.create_proj_geom('parallel3d', 1.0, 1.0, 128, 192, angles) + +# Create a simple hollow cube phantom +cube = np.zeros((128,128,128)) +cube[17:113,17:113,17:113] = 1 +cube[33:97,33:97,33:97] = 0 + +# Create projection data from this +proj_id, proj_data = astra.create_sino3d_gpu(cube, proj_geom, vol_geom) + +# Display a single projection image +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(proj_data[:,20,:]) + +# Create a data object for the reconstruction +rec_id = astra.data3d.create('-vol', vol_geom) + +# Set up the parameters for a reconstruction algorithm using the GPU +cfg = astra.astra_dict('SIRT3D_CUDA') +cfg['ReconstructionDataId'] = rec_id +cfg['ProjectionDataId'] = proj_id + + +# Create the algorithm object from the configuration structure +alg_id = astra.algorithm.create(cfg) + +# Run 150 iterations of the algorithm +# Note that this requires about 750MB of GPU memory, and has a runtime +# in the order of 10 seconds. +astra.algorithm.run(alg_id, 150) + +# Get the result +rec = astra.data3d.get(rec_id) +pylab.figure(2) +pylab.imshow(rec[:,:,65]) +pylab.show() + + +# Clean up. Note that GPU memory is tied up in the algorithm object, +# and main RAM in the data objects. +astra.algorithm.delete(alg_id) +astra.data3d.delete(rec_id) +astra.data3d.delete(proj_id) diff --git a/samples/python/s008_gpu_selection.py b/samples/python/s008_gpu_selection.py new file mode 100644 index 0000000..c42e53b --- /dev/null +++ b/samples/python/s008_gpu_selection.py @@ -0,0 +1,61 @@ +#----------------------------------------------------------------------- +#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 . +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] + +proj_id = astra.create_projector('line',proj_geom,vol_geom) + +# Create a sinogram from a phantom, using GPU #1. (The default is #0) +sinogram_id, sinogram = astra.create_sino(P, proj_id, useCUDA=True, gpuIndex=1) + + +# Set up the parameters for a reconstruction algorithm using the GPU +rec_id = astra.data2d.create('-vol', vol_geom) +cfg = astra.astra_dict('SIRT_CUDA') +cfg['ReconstructionDataId'] = rec_id +cfg['ProjectionDataId'] = sinogram_id + +# Use GPU #1 for the reconstruction. (The default is #0.) +cfg['option'] = {} +cfg['option']['GPUindex'] = 1 + +# Run 150 iterations of the algorithm +alg_id = astra.algorithm.create(cfg) +astra.algorithm.run(alg_id, 150) +rec = astra.data2d.get(rec_id) + + +# Clean up. +astra.algorithm.delete(alg_id) +astra.data2d.delete(rec_id) +astra.data2d.delete(sinogram_id) +astra.projector.delete(proj_id) diff --git a/samples/python/s009_projection_matrix.py b/samples/python/s009_projection_matrix.py new file mode 100644 index 0000000..c4c4557 --- /dev/null +++ b/samples/python/s009_projection_matrix.py @@ -0,0 +1,65 @@ +#----------------------------------------------------------------------- +#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 . +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + +# For CPU-based algorithms, a "projector" object specifies the projection +# model used. In this case, we use the "line" model. +proj_id = astra.create_projector('line', proj_geom, vol_geom) + +# Generate the projection matrix for this projection model. +# This creates a matrix W where entry w_{i,j} corresponds to the +# contribution of volume element j to detector element i. +matrix_id = astra.projector.matrix(proj_id) + +# Get the projection matrix as a Scipy sparse matrix. +W = astra.matrix.get(matrix_id) + + +# Manually use this projection matrix to do a projection: +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] +s = W.dot(P.flatten()) +s = np.reshape(s, (len(proj_geom['ProjectionAngles']),proj_geom['DetectorCount'])) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(s) +pylab.show() + +# Each row of the projection matrix corresponds to a detector element. +# Detector t for angle p is for row 1 + t + p*proj_geom.DetectorCount. +# Each column corresponds to a volume pixel. +# Pixel (x,y) corresponds to column 1 + x + y*vol_geom.GridColCount. + + +astra.projector.delete(proj_id) +astra.matrix.delete(matrix_id) diff --git a/samples/python/s010_supersampling.py b/samples/python/s010_supersampling.py new file mode 100644 index 0000000..1a337bc --- /dev/null +++ b/samples/python/s010_supersampling.py @@ -0,0 +1,85 @@ +#----------------------------------------------------------------------- +#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 . +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 3.0, 128, np.linspace(0,np.pi,180,False)) +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] + +# Because the astra.create_sino method does not have support for +# all possible algorithm options, we manually create a sinogram +phantom_id = astra.data2d.create('-vol', vol_geom, P) +sinogram_id = astra.data2d.create('-sino', proj_geom) +cfg = astra.astra_dict('FP_CUDA') +cfg['VolumeDataId'] = phantom_id +cfg['ProjectionDataId'] = sinogram_id + +# Set up 3 rays per detector element +cfg['option'] = {} +cfg['option']['DetectorSuperSampling'] = 3 + +alg_id = astra.algorithm.create(cfg) +astra.algorithm.run(alg_id) +astra.algorithm.delete(alg_id) +astra.data2d.delete(phantom_id) + +sinogram3 = astra.data2d.get(sinogram_id) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(P) +pylab.figure(2) +pylab.imshow(sinogram3) + +# Create a reconstruction, also using supersampling +rec_id = astra.data2d.create('-vol', vol_geom) +cfg = astra.astra_dict('SIRT_CUDA') +cfg['ReconstructionDataId'] = rec_id +cfg['ProjectionDataId'] = sinogram_id +# Set up 3 rays per detector element +cfg['option'] = {} +cfg['option']['DetectorSuperSampling'] = 3 + +# There is also an option for supersampling during the backprojection step. +# This should be used if your detector pixels are smaller than the voxels. + +# Set up 2 rays per image pixel dimension, for 4 rays total per image pixel. +# cfg['option']['PixelSuperSampling'] = 2 + + +alg_id = astra.algorithm.create(cfg) +astra.algorithm.run(alg_id, 150) +astra.algorithm.delete(alg_id) + +rec = astra.data2d.get(rec_id) +pylab.figure(3) +pylab.imshow(rec) +pylab.show() + diff --git a/samples/python/s011_object_info.py b/samples/python/s011_object_info.py new file mode 100644 index 0000000..02f387a --- /dev/null +++ b/samples/python/s011_object_info.py @@ -0,0 +1,54 @@ +#----------------------------------------------------------------------- +#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 . +# +#----------------------------------------------------------------------- + +import astra + +# Create two volume geometries +vol_geom1 = astra.create_vol_geom(256, 256) +vol_geom2 = astra.create_vol_geom(512, 256) + +# Create volumes +v0 = astra.data2d.create('-vol', vol_geom1) +v1 = astra.data2d.create('-vol', vol_geom2) +v2 = astra.data2d.create('-vol', vol_geom2) + +# Show the currently allocated volumes +astra.data2d.info() + + +astra.data2d.delete(v2) +astra.data2d.info() + +astra.data2d.clear() +astra.data2d.info() + + + +# The same clear and info command also work for other object types: +astra.algorithm.info() +astra.data3d.info() +astra.projector.info() +astra.matrix.info() diff --git a/samples/python/s012_masks.py b/samples/python/s012_masks.py new file mode 100644 index 0000000..441d11b --- /dev/null +++ b/samples/python/s012_masks.py @@ -0,0 +1,92 @@ +#----------------------------------------------------------------------- +#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 . +# +#----------------------------------------------------------------------- + + +import astra +import numpy as np + +# In this example we will create a reconstruction in a circular region, +# instead of the usual rectangle. + +# This is done by placing a circular mask on the square reconstruction volume: + +c = np.linspace(-127.5,127.5,256) +x, y = np.meshgrid(c,c) +mask = np.array((x**2 + y**2 < 127.5**2),dtype=np.float) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(mask) + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,50,False)) + +# As before, create a sinogram from a phantom +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] +proj_id = astra.create_projector('line',proj_geom,vol_geom) +sinogram_id, sinogram = astra.create_sino(P, proj_id,useCUDA=True) + +pylab.figure(2) +pylab.imshow(P) +pylab.figure(3) +pylab.imshow(sinogram) + +# Create a data object for the reconstruction +rec_id = astra.data2d.create('-vol', vol_geom) + +# Create a data object for the mask +mask_id = astra.data2d.create('-vol', vol_geom, mask) + +# Set up the parameters for a reconstruction algorithm using the GPU +cfg = astra.astra_dict('SIRT_CUDA') +cfg['ReconstructionDataId'] = rec_id +cfg['ProjectionDataId'] = sinogram_id +cfg['option'] = {} +cfg['option']['ReconstructionMaskId'] = mask_id + +# Create the algorithm object from the configuration structure +alg_id = astra.algorithm.create(cfg) + +# Run 150 iterations of the algorithm +astra.algorithm.run(alg_id, 150) + +# Get the result +rec = astra.data2d.get(rec_id) + +pylab.figure(4) +pylab.imshow(rec) + +pylab.show() + +# Clean up. Note that GPU memory is tied up in the algorithm object, +# and main RAM in the data objects. +astra.algorithm.delete(alg_id) +astra.data2d.delete(mask_id) +astra.data2d.delete(rec_id) +astra.data2d.delete(sinogram_id) +astra.projector.delete(proj_id) diff --git a/samples/python/s013_constraints.py b/samples/python/s013_constraints.py new file mode 100644 index 0000000..009360e --- /dev/null +++ b/samples/python/s013_constraints.py @@ -0,0 +1,77 @@ +#----------------------------------------------------------------------- +#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 . +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +# In this example we will create a reconstruction constrained to +# greyvalues between 0 and 1 + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,50,False)) + +# As before, create a sinogram from a phantom +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] +proj_id = astra.create_projector('line',proj_geom,vol_geom) +sinogram_id, sinogram = astra.create_sino(P, proj_id,useCUDA=True) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(P) +pylab.figure(2) +pylab.imshow(sinogram) + +# Create a data object for the reconstruction +rec_id = astra.data2d.create('-vol', vol_geom) + +# Set up the parameters for a reconstruction algorithm using the GPU +cfg = astra.astra_dict('SIRT_CUDA') +cfg['ReconstructionDataId'] = rec_id +cfg['ProjectionDataId'] = sinogram_id +cfg['option']={} +cfg['option']['MinConstraint'] = 0 +cfg['option']['MaxConstraint'] = 1 + +# Create the algorithm object from the configuration structure +alg_id = astra.algorithm.create(cfg) + +# Run 150 iterations of the algorithm +astra.algorithm.run(alg_id, 150) + +# Get the result +rec = astra.data2d.get(rec_id) +pylab.figure(3) +pylab.imshow(rec) +pylab.show() + +# Clean up. Note that GPU memory is tied up in the algorithm object, +# and main RAM in the data objects. +astra.algorithm.delete(alg_id) +astra.data2d.delete(rec_id) +astra.data2d.delete(sinogram_id) +astra.projector.delete(proj_id) diff --git a/samples/python/s014_FBP.py b/samples/python/s014_FBP.py new file mode 100644 index 0000000..ef4afc2 --- /dev/null +++ b/samples/python/s014_FBP.py @@ -0,0 +1,76 @@ +#----------------------------------------------------------------------- +#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 . +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + +# As before, create a sinogram from a phantom +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] +proj_id = astra.create_projector('line',proj_geom,vol_geom) +sinogram_id, sinogram = astra.create_sino(P, proj_id,useCUDA=True) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(P) +pylab.figure(2) +pylab.imshow(sinogram) + +# Create a data object for the reconstruction +rec_id = astra.data2d.create('-vol', vol_geom) + +# create configuration +cfg = astra.astra_dict('FBP_CUDA') +cfg['ReconstructionDataId'] = rec_id +cfg['ProjectionDataId'] = sinogram_id +cfg['FilterType'] = 'Ram-Lak' + +# possible values for FilterType: +# none, ram-lak, shepp-logan, cosine, hamming, hann, tukey, lanczos, +# triangular, gaussian, barlett-hann, blackman, nuttall, blackman-harris, +# blackman-nuttall, flat-top, kaiser, parzen + + +# Create and run the algorithm object from the configuration structure +alg_id = astra.algorithm.create(cfg) +astra.algorithm.run(alg_id) + +# Get the result +rec = astra.data2d.get(rec_id) +pylab.figure(3) +pylab.imshow(rec) +pylab.show() + +# Clean up. Note that GPU memory is tied up in the algorithm object, +# and main RAM in the data objects. +astra.algorithm.delete(alg_id) +astra.data2d.delete(rec_id) +astra.data2d.delete(sinogram_id) +astra.projector.delete(proj_id) diff --git a/samples/python/s015_fp_bp.py b/samples/python/s015_fp_bp.py new file mode 100644 index 0000000..10c238d --- /dev/null +++ b/samples/python/s015_fp_bp.py @@ -0,0 +1,86 @@ +#----------------------------------------------------------------------- +#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 . +# +#----------------------------------------------------------------------- + + +# This example demonstrates using the FP and BP primitives with Matlab's lsqr +# solver. Calls to FP (astra_create_sino_cuda) and +# BP (astra_create_backprojection_cuda) are wrapped in a function astra_wrap, +# and a handle to this function is passed to lsqr. + +# Because in this case the inputs/outputs of FP and BP have to be vectors +# instead of images (matrices), the calls require reshaping to and from vectors. + +import astra +import numpy as np + +# FP/BP wrapper class +class astra_wrap(object): + def __init__(self,proj_geom,vol_geom): + self.proj_id = astra.create_projector('line',proj_geom,vol_geom) + self.shape = (proj_geom['DetectorCount']*len(proj_geom['ProjectionAngles']),vol_geom['GridColCount']*vol_geom['GridRowCount']) + self.dtype = np.float + + def matvec(self,v): + sid, s = astra.create_sino(np.reshape(v,(vol_geom['GridRowCount'],vol_geom['GridColCount'])),self.proj_id,useCUDA=True) + astra.data2d.delete(sid) + return s.flatten() + + def rmatvec(self,v): + bid, b = astra.create_backprojection(np.reshape(v,(len(proj_geom['ProjectionAngles']),proj_geom['DetectorCount'],)),self.proj_id,useCUDA=True) + astra.data2d.delete(bid) + return b.flatten() + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + +# Create a 256x256 phantom image +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] + +# Create a sinogram using the GPU. +proj_id = astra.create_projector('line',proj_geom,vol_geom) +sinogram_id, sinogram = astra.create_sino(P, proj_id,useCUDA=True) + +# Reshape the sinogram into a vector +b = sinogram.flatten() + +# Call lsqr with ASTRA FP and BP +import scipy.sparse.linalg +wrapper = astra_wrap(proj_geom,vol_geom) +result = scipy.sparse.linalg.lsqr(wrapper,b,atol=1e-4,btol=1e-4,iter_lim=25) + +# Reshape the result into an image +Y = np.reshape(result[0],(vol_geom['GridRowCount'], vol_geom['GridColCount'])); + +import pylab +pylab.gray() +pylab.imshow(Y) +pylab.show() + +astra.data2d.delete(sinogram_id) +astra.projector.delete(proj_id) +astra.projector.delete(wrapper.proj_id) + diff --git a/samples/python/s016_plots.py b/samples/python/s016_plots.py new file mode 100644 index 0000000..cd4d98c --- /dev/null +++ b/samples/python/s016_plots.py @@ -0,0 +1,86 @@ +#----------------------------------------------------------------------- +#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 six.moves import range +import astra +import numpy as np + + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + +# As before, create a sinogram from a phantom +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] +proj_id = astra.create_projector('line',proj_geom,vol_geom) +sinogram_id, sinogram = astra.create_sino(P, proj_id,useCUDA=True) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(P) +pylab.figure(2) +pylab.imshow(sinogram) + +# Create a data object for the reconstruction +rec_id = astra.data2d.create('-vol', vol_geom) + +# Set up the parameters for a reconstruction algorithm using the GPU +cfg = astra.astra_dict('SIRT_CUDA') +cfg['ReconstructionDataId'] = rec_id +cfg['ProjectionDataId'] = sinogram_id + +# Create the algorithm object from the configuration structure +alg_id = astra.algorithm.create(cfg) + +# Run 1500 iterations of the algorithm one at a time, keeping track of errors +nIters = 1500 +phantom_error = np.zeros(nIters) +residual_error = np.zeros(nIters) +for i in range(nIters): + # Run a single iteration + astra.algorithm.run(alg_id, 1) + residual_error[i] = astra.algorithm.get_res_norm(alg_id) + rec = astra.data2d.get(rec_id) + phantom_error[i] = np.sqrt(((rec - P)**2).sum()) + +# Get the result +rec = astra.data2d.get(rec_id) +pylab.figure(3) +pylab.imshow(rec) + +pylab.figure(4) +pylab.plot(residual_error) +pylab.figure(5) +pylab.plot(phantom_error) + +pylab.show() + +# Clean up. +astra.algorithm.delete(alg_id) +astra.data2d.delete(rec_id) +astra.data2d.delete(sinogram_id) +astra.projector.delete(proj_id) diff --git a/samples/s001_sinogram_par2d.m b/samples/s001_sinogram_par2d.m deleted file mode 100644 index 4494e7b..0000000 --- a/samples/s001_sinogram_par2d.m +++ /dev/null @@ -1,33 +0,0 @@ -% ----------------------------------------------------------------------- -% This file is part of the ASTRA Toolbox -% -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam -% License: Open Source under GPLv3 -% Contact: astra@uantwerpen.be -% Website: http://sf.net/projects/astra-toolbox -% ----------------------------------------------------------------------- - -% Create a basic 256x256 square volume geometry -vol_geom = astra_create_vol_geom(256, 256); - -% Create a parallel beam geometry with 180 angles between 0 and pi, and -% 384 detector pixels of width 1. -% For more details on available geometries, see the online help of the -% function astra_create_proj_geom . -proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,180)); - -% Create a 256x256 phantom image using matlab's built-in phantom() function -P = phantom(256); - -% Create a sinogram using the GPU. -% Note that the first time the GPU is accessed, there may be a delay -% of up to 10 seconds for initialization. -[sinogram_id, sinogram] = astra_create_sino_gpu(P, proj_geom, vol_geom); - -figure(1); imshow(P, []); -figure(2); imshow(sinogram, []); - - -% Free memory -astra_mex_data2d('delete', sinogram_id); diff --git a/samples/s002_data2d.m b/samples/s002_data2d.m deleted file mode 100644 index a91071f..0000000 --- a/samples/s002_data2d.m +++ /dev/null @@ -1,60 +0,0 @@ -% ----------------------------------------------------------------------- -% This file is part of the ASTRA Toolbox -% -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam -% License: Open Source under GPLv3 -% Contact: astra@uantwerpen.be -% Website: http://sf.net/projects/astra-toolbox -% ----------------------------------------------------------------------- - -vol_geom = astra_create_vol_geom(256, 256); - -proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,180)); - - -% Create volumes - -% initialized to zero -v0 = astra_mex_data2d('create', '-vol', vol_geom); - -% initialized to 3.0 -v1 = astra_mex_data2d('create', '-vol', vol_geom, 3.0); - -% initialized to a matrix. A may be a single, double or logical (0/1) array. -A = phantom(256); -v2 = astra_mex_data2d('create', '-vol', vol_geom, A); - - -% Projection data -s0 = astra_mex_data2d('create', '-sino', proj_geom); -% Initialization to a scalar or a matrix also works, exactly as with a volume. - - -% Update data - -% set to zero -astra_mex_data2d('store', v0, 0); - -% set to a matrix -astra_mex_data2d('store', v2, A); - - - -% Retrieve data - -R = astra_mex_data2d('get', v2); -imshow(R, []); - - -% Retrieve data as a single array. Since astra internally stores -% data as single precision, this is more efficient: - -R = astra_mex_data2d('get_single', v2); - - -% Free memory -astra_mex_data2d('delete', v0); -astra_mex_data2d('delete', v1); -astra_mex_data2d('delete', v2); -astra_mex_data2d('delete', s0); diff --git a/samples/s003_gpu_reconstruction.m b/samples/s003_gpu_reconstruction.m deleted file mode 100644 index efb5c68..0000000 --- a/samples/s003_gpu_reconstruction.m +++ /dev/null @@ -1,52 +0,0 @@ -% ----------------------------------------------------------------------- -% This file is part of the ASTRA Toolbox -% -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam -% License: Open Source under GPLv3 -% Contact: astra@uantwerpen.be -% Website: http://sf.net/projects/astra-toolbox -% ----------------------------------------------------------------------- - -vol_geom = astra_create_vol_geom(256, 256); -proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,180)); - -% As before, create a sinogram from a phantom -P = phantom(256); -[sinogram_id, sinogram] = astra_create_sino_gpu(P, proj_geom, vol_geom); -figure(1); imshow(P, []); -figure(2); imshow(sinogram, []); - -astra_mex_data2d('delete', sinogram_id); - -% We now re-create the sinogram data object as we would do when loading -% an external sinogram -sinogram_id = astra_mex_data2d('create', '-sino', proj_geom, sinogram); - -% Create a data object for the reconstruction -rec_id = astra_mex_data2d('create', '-vol', vol_geom); - -% Set up the parameters for a reconstruction algorithm using the GPU -cfg = astra_struct('SIRT_CUDA'); -cfg.ReconstructionDataId = rec_id; -cfg.ProjectionDataId = sinogram_id; - -% Available algorithms: -% SIRT_CUDA, SART_CUDA, EM_CUDA, FBP_CUDA (see the FBP sample) - - -% Create the algorithm object from the configuration structure -alg_id = astra_mex_algorithm('create', cfg); - -% Run 150 iterations of the algorithm -astra_mex_algorithm('iterate', alg_id, 150); - -% Get the result -rec = astra_mex_data2d('get', rec_id); -figure(3); imshow(rec, []); - -% Clean up. Note that GPU memory is tied up in the algorithm object, -% and main RAM in the data objects. -astra_mex_algorithm('delete', alg_id); -astra_mex_data2d('delete', rec_id); -astra_mex_data2d('delete', sinogram_id); diff --git a/samples/s004_cpu_reconstruction.m b/samples/s004_cpu_reconstruction.m deleted file mode 100644 index f25cd2b..0000000 --- a/samples/s004_cpu_reconstruction.m +++ /dev/null @@ -1,60 +0,0 @@ -% ----------------------------------------------------------------------- -% This file is part of the ASTRA Toolbox -% -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam -% License: Open Source under GPLv3 -% Contact: astra@uantwerpen.be -% Website: http://sf.net/projects/astra-toolbox -% ----------------------------------------------------------------------- - -vol_geom = astra_create_vol_geom(256, 256); -proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,180)); - -% For CPU-based algorithms, a "projector" object specifies the projection -% model used. In this case, we use the "strip" model. -proj_id = astra_create_projector('strip', proj_geom, vol_geom); - -% Create a sinogram from a phantom -P = phantom(256); -[sinogram_id, sinogram] = astra_create_sino(P, proj_id); -figure(1); imshow(P, []); -figure(2); imshow(sinogram, []); - -astra_mex_data2d('delete', sinogram_id); - -% We now re-create the sinogram data object as we would do when loading -% an external sinogram -sinogram_id = astra_mex_data2d('create', '-sino', proj_geom, sinogram); - -% Create a data object for the reconstruction -rec_id = astra_mex_data2d('create', '-vol', vol_geom); - -% Set up the parameters for a reconstruction algorithm using the CPU -% The main difference with the configuration of a GPU algorithm is the -% extra ProjectorId setting. -cfg = astra_struct('SIRT'); -cfg.ReconstructionDataId = rec_id; -cfg.ProjectionDataId = sinogram_id; -cfg.ProjectorId = proj_id; - -% Available algorithms: -% ART, SART, SIRT, CGLS, FBP - - -% Create the algorithm object from the configuration structure -alg_id = astra_mex_algorithm('create', cfg); - -% Run 20 iterations of the algorithm -% This will have a runtime in the order of 10 seconds. -astra_mex_algorithm('iterate', alg_id, 20); - -% Get the result -rec = astra_mex_data2d('get', rec_id); -figure(3); imshow(rec, []); - -% Clean up. -astra_mex_projector('delete', proj_id); -astra_mex_algorithm('delete', alg_id); -astra_mex_data2d('delete', rec_id); -astra_mex_data2d('delete', sinogram_id); diff --git a/samples/s005_3d_geometry.m b/samples/s005_3d_geometry.m deleted file mode 100644 index 4b7360b..0000000 --- a/samples/s005_3d_geometry.m +++ /dev/null @@ -1,98 +0,0 @@ -% ----------------------------------------------------------------------- -% This file is part of the ASTRA Toolbox -% -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam -% License: Open Source under GPLv3 -% Contact: astra@uantwerpen.be -% Website: http://sf.net/projects/astra-toolbox -% ----------------------------------------------------------------------- - -vol_geom = astra_create_vol_geom(64, 64, 64); - - -% There are two main 3d projection geometry types: cone beam and parallel beam. -% Each has a regular variant, and a 'vec' variant. -% The 'vec' variants are completely free in the placement of source/detector, -% while the regular variants assume circular trajectories around the z-axis. - - -% ------------- -% Parallel beam -% ------------- - - -% Circular - -% Parameters: width of detector column, height of detector row, #rows, #columns -angles = linspace2(0, 2*pi, 48); -proj_geom = astra_create_proj_geom('parallel3d', 1.0, 1.0, 32, 64, angles); - - -% Free - -% We generate the same geometry as the circular one above. -vectors = zeros(numel(angles), 12); -for i = 1:numel(angles) - % ray direction - vectors(i,1) = sin(angles(i)); - vectors(i,2) = -cos(angles(i)); - vectors(i,3) = 0; - - % center of detector - vectors(i,4:6) = 0; - - % vector from detector pixel (0,0) to (0,1) - vectors(i,7) = cos(angles(i)); - vectors(i,8) = sin(angles(i)); - vectors(i,9) = 0; - - % vector from detector pixel (0,0) to (1,0) - vectors(i,10) = 0; - vectors(i,11) = 0; - vectors(i,12) = 1; -end - -% Parameters: #rows, #columns, vectors -proj_geom = astra_create_proj_geom('parallel3d_vec', 32, 64, vectors); - -% ---------- -% Cone beam -% ---------- - - -% Circular - -% Parameters: width of detector column, height of detector row, #rows, #columns, -% angles, distance source-origin, distance origin-detector -angles = linspace2(0, 2*pi, 48); -proj_geom = astra_create_proj_geom('cone', 1.0, 1.0, 32, 64, ... - angles, 1000, 0); - -% Free - -vectors = zeros(numel(angles), 12); -for i = 1:numel(angles) - - % source - vectors(i,1) = sin(angles(i)) * 1000; - vectors(i,2) = -cos(angles(i)) * 1000; - vectors(i,3) = 0; - - % center of detector - vectors(i,4:6) = 0; - - % vector from detector pixel (0,0) to (0,1) - vectors(i,7) = cos(angles(i)); - vectors(i,8) = sin(angles(i)); - vectors(i,9) = 0; - - % vector from detector pixel (0,0) to (1,0) - vectors(i,10) = 0; - vectors(i,11) = 0; - vectors(i,12) = 1; -end - -% Parameters: #rows, #columns, vectors -proj_geom = astra_create_proj_geom('cone_vec', 32, 64, vectors); - diff --git a/samples/s006_3d_data.m b/samples/s006_3d_data.m deleted file mode 100644 index 32d88cc..0000000 --- a/samples/s006_3d_data.m +++ /dev/null @@ -1,62 +0,0 @@ -% ----------------------------------------------------------------------- -% This file is part of the ASTRA Toolbox -% -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam -% License: Open Source under GPLv3 -% Contact: astra@uantwerpen.be -% Website: http://sf.net/projects/astra-toolbox -% ----------------------------------------------------------------------- - -% Create a 3D volume geometry. -% Parameter order: rows, colums, slices (y, x, z) -vol_geom = astra_create_vol_geom(64, 48, 32); - - -% Create volumes - -% initialized to zero -v0 = astra_mex_data3d('create', '-vol', vol_geom); - -% initialized to 3.0 -v1 = astra_mex_data3d('create', '-vol', vol_geom, 3.0); - -% initialized to a matrix. A may be a single or double array. -% Coordinate order: column, row, slice (x, y, z) -A = zeros(48, 64, 32); -v2 = astra_mex_data3d('create', '-vol', vol_geom, A); - - -% Projection data - -% 2 projection directions, along x and y axis resp. -V = [ 1 0 0 0 0 0 0 1 0 0 0 1 ; ... - 0 1 0 0 0 0 -1 0 0 0 0 1 ]; -% 32 rows (v), 64 columns (u) -proj_geom = astra_create_proj_geom('parallel3d_vec', 32, 64, V); - -s0 = astra_mex_data3d('create', '-proj3d', proj_geom); - -% Initialization to a scalar or zero works exactly as with a volume. - -% Initialized to a matrix: -% Coordinate order: column (u), angle, row (v) -A = zeros(64, 2, 32); -s1 = astra_mex_data3d('create', '-proj3d', proj_geom, A); - - -% Retrieve data: -R = astra_mex_data3d('get', v1); - -% Retrieve data as a single array. Since astra internally stores -% data as single precision, this is more efficient: -R = astra_mex_data3d('get_single', v1); - - - -% Delete all created data objects -astra_mex_data3d('delete', v0); -astra_mex_data3d('delete', v1); -astra_mex_data3d('delete', v2); -astra_mex_data3d('delete', s0); -astra_mex_data3d('delete', s1); diff --git a/samples/s007_3d_reconstruction.m b/samples/s007_3d_reconstruction.m deleted file mode 100644 index fc9aca6..0000000 --- a/samples/s007_3d_reconstruction.m +++ /dev/null @@ -1,53 +0,0 @@ -% ----------------------------------------------------------------------- -% This file is part of the ASTRA Toolbox -% -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam -% License: Open Source under GPLv3 -% Contact: astra@uantwerpen.be -% Website: http://sf.net/projects/astra-toolbox -% ----------------------------------------------------------------------- - -vol_geom = astra_create_vol_geom(128, 128, 128); - -angles = linspace2(0, pi, 180); -proj_geom = astra_create_proj_geom('parallel3d', 1.0, 1.0, 128, 192, angles); - -% Create a simple hollow cube phantom -cube = zeros(128,128,128); -cube(17:112,17:112,17:112) = 1; -cube(33:96,33:96,33:96) = 0; - -% Create projection data from this -[proj_id, proj_data] = astra_create_sino3d_cuda(cube, proj_geom, vol_geom); - -% Display a single projection image -figure, imshow(squeeze(proj_data(:,20,:))',[]) - -% Create a data object for the reconstruction -rec_id = astra_mex_data3d('create', '-vol', vol_geom); - -% Set up the parameters for a reconstruction algorithm using the GPU -cfg = astra_struct('SIRT3D_CUDA'); -cfg.ReconstructionDataId = rec_id; -cfg.ProjectionDataId = proj_id; - - -% Create the algorithm object from the configuration structure -alg_id = astra_mex_algorithm('create', cfg); - -% Run 150 iterations of the algorithm -% Note that this requires about 750MB of GPU memory, and has a runtime -% in the order of 10 seconds. -astra_mex_algorithm('iterate', alg_id, 150); - -% Get the result -rec = astra_mex_data3d('get', rec_id); -figure, imshow(squeeze(rec(:,:,65)),[]); - - -% Clean up. Note that GPU memory is tied up in the algorithm object, -% and main RAM in the data objects. -astra_mex_algorithm('delete', alg_id); -astra_mex_data3d('delete', rec_id); -astra_mex_data3d('delete', proj_id); diff --git a/samples/s008_gpu_selection.m b/samples/s008_gpu_selection.m deleted file mode 100644 index a9e152d..0000000 --- a/samples/s008_gpu_selection.m +++ /dev/null @@ -1,37 +0,0 @@ -% ----------------------------------------------------------------------- -% This file is part of the ASTRA Toolbox -% -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam -% License: Open Source under GPLv3 -% Contact: astra@uantwerpen.be -% Website: http://sf.net/projects/astra-toolbox -% ----------------------------------------------------------------------- - -vol_geom = astra_create_vol_geom(256, 256); -proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,180)); -P = phantom(256); - -% Create a sinogram from a phantom, using GPU #1. (The default is #0) -[sinogram_id, sinogram] = astra_create_sino_gpu(P, proj_geom, vol_geom, 1); - - -% Set up the parameters for a reconstruction algorithm using the GPU -rec_id = astra_mex_data2d('create', '-vol', vol_geom); -cfg = astra_struct('SIRT_CUDA'); -cfg.ReconstructionDataId = rec_id; -cfg.ProjectionDataId = sinogram_id; - -% Use GPU #1 for the reconstruction. (The default is #0.) -cfg.option.GPUindex = 1; - -% Run 150 iterations of the algorithm -alg_id = astra_mex_algorithm('create', cfg); -astra_mex_algorithm('iterate', alg_id, 150); -rec = astra_mex_data2d('get', rec_id); - - -% Clean up. -astra_mex_algorithm('delete', alg_id); -astra_mex_data2d('delete', rec_id); -astra_mex_data2d('delete', sinogram_id); diff --git a/samples/s009_projection_matrix.m b/samples/s009_projection_matrix.m deleted file mode 100644 index efda0d2..0000000 --- a/samples/s009_projection_matrix.m +++ /dev/null @@ -1,45 +0,0 @@ -% ----------------------------------------------------------------------- -% This file is part of the ASTRA Toolbox -% -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam -% License: Open Source under GPLv3 -% Contact: astra@uantwerpen.be -% Website: http://sf.net/projects/astra-toolbox -% ----------------------------------------------------------------------- - -vol_geom = astra_create_vol_geom(256, 256); -proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,180)); - -% For CPU-based algorithms, a "projector" object specifies the projection -% model used. In this case, we use the "strip" model. -proj_id = astra_create_projector('strip', proj_geom, vol_geom); - -% Generate the projection matrix for this projection model. -% This creates a matrix W where entry w_{i,j} corresponds to the -% contribution of volume element j to detector element i. -matrix_id = astra_mex_projector('matrix', proj_id); - -% Get the projection matrix as a Matlab sparse matrix. -W = astra_mex_matrix('get', matrix_id); - - -% Manually use this projection matrix to do a projection: -P = phantom(256)'; -s = W * P(:); -s = reshape(s, [proj_geom.DetectorCount size(proj_geom.ProjectionAngles, 2)])'; -figure(1), imshow(s,[]); - -% Because Matlab's matrices are stored transposed in memory compared to C++, -% reshaping them to a vector doesn't give the right ordering for multiplication -% with W. We have to take the transpose of the input and output to get the same -% results (up to numerical noise) as using the toolbox directly. - -% Each row of the projection matrix corresponds to a detector element. -% Detector t for angle p is for row 1 + t + p*proj_geom.DetectorCount. -% Each column corresponds to a volume pixel. -% Pixel (x,y) corresponds to column 1 + x + y*vol_geom.GridColCount. - - -astra_mex_projector('delete', proj_id); -astra_mex_matrix('delete', matrix_id); diff --git a/samples/s010_supersampling.m b/samples/s010_supersampling.m deleted file mode 100644 index 80f6f56..0000000 --- a/samples/s010_supersampling.m +++ /dev/null @@ -1,58 +0,0 @@ -% ----------------------------------------------------------------------- -% This file is part of the ASTRA Toolbox -% -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam -% License: Open Source under GPLv3 -% Contact: astra@uantwerpen.be -% Website: http://sf.net/projects/astra-toolbox -% ----------------------------------------------------------------------- - -vol_geom = astra_create_vol_geom(256, 256); -proj_geom = astra_create_proj_geom('parallel', 3.0, 128, linspace2(0,pi,180)); -P = phantom(256); - -% Because the astra_create_sino_gpu wrapper does not have support for -% all possible algorithm options, we manually create a sinogram -phantom_id = astra_mex_data2d('create', '-vol', vol_geom, P); -sinogram_id = astra_mex_data2d('create', '-sino', proj_geom); -cfg = astra_struct('FP_CUDA'); -cfg.VolumeDataId = phantom_id; -cfg.ProjectionDataId = sinogram_id; - -% Set up 3 rays per detector element -cfg.option.DetectorSuperSampling = 3; - -alg_id = astra_mex_algorithm('create', cfg); -astra_mex_algorithm('run', alg_id); -astra_mex_algorithm('delete', alg_id); -astra_mex_data2d('delete', phantom_id); - -sinogram3 = astra_mex_data2d('get', sinogram_id); - -figure(1); imshow(P, []); -figure(2); imshow(sinogram3, []); - - -% Create a reconstruction, also using supersampling -rec_id = astra_mex_data2d('create', '-vol', vol_geom); -cfg = astra_struct('SIRT_CUDA'); -cfg.ReconstructionDataId = rec_id; -cfg.ProjectionDataId = sinogram_id; -% Set up 3 rays per detector element -cfg.option.DetectorSuperSampling = 3; - -% There is also an option for supersampling during the backprojection step. -% This should be used if your detector pixels are smaller than the voxels. - -% Set up 2 rays per image pixel dimension, for 4 rays total per image pixel. -% cfg.option.PixelSuperSampling = 2; - - -alg_id = astra_mex_algorithm('create', cfg); -astra_mex_algorithm('iterate', alg_id, 150); -astra_mex_algorithm('delete', alg_id); - -rec = astra_mex_data2d('get', rec_id); -figure(3); imshow(rec, []); - diff --git a/samples/s011_object_info.m b/samples/s011_object_info.m deleted file mode 100644 index 61ecb83..0000000 --- a/samples/s011_object_info.m +++ /dev/null @@ -1,36 +0,0 @@ -% ----------------------------------------------------------------------- -% This file is part of the ASTRA Toolbox -% -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam -% License: Open Source under GPLv3 -% Contact: astra@uantwerpen.be -% Website: http://sf.net/projects/astra-toolbox -% ----------------------------------------------------------------------- - -% Create two volume geometries -vol_geom1 = astra_create_vol_geom(256, 256); -vol_geom2 = astra_create_vol_geom(512, 256); - -% Create volumes -v0 = astra_mex_data2d('create', '-vol', vol_geom1); -v1 = astra_mex_data2d('create', '-vol', vol_geom2); -v2 = astra_mex_data2d('create', '-vol', vol_geom2); - -% Show the currently allocated volumes -astra_mex_data2d('info'); - - -astra_mex_data2d('delete', v2); -astra_mex_data2d('info'); - -astra_mex_data2d('clear'); -astra_mex_data2d('info'); - - - -% The same clear and info command also work for other object types: -astra_mex_algorithm('info'); -astra_mex_data3d('info'); -astra_mex_projector('info'); -astra_mex_matrix('info'); diff --git a/samples/s012_masks.m b/samples/s012_masks.m deleted file mode 100644 index d3611a6..0000000 --- a/samples/s012_masks.m +++ /dev/null @@ -1,60 +0,0 @@ -% ----------------------------------------------------------------------- -% This file is part of the ASTRA Toolbox -% -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam -% License: Open Source under GPLv3 -% Contact: astra@uantwerpen.be -% Website: http://sf.net/projects/astra-toolbox -% ----------------------------------------------------------------------- - - -% In this example we will create a reconstruction in a circular region, -% instead of the usual rectangle. - -% This is done by placing a circular mask on the square reconstruction volume: - -c = -127.5:127.5; -[x y] = meshgrid(-127.5:127.5,-127.5:127.5); -mask = (x.^2 + y.^2 < 127.5^2); - -figure(1); imshow(mask, []); - - -vol_geom = astra_create_vol_geom(256, 256); -proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,50)); - -% As before, create a sinogram from a phantom -P = phantom(256); -[sinogram_id, sinogram] = astra_create_sino_gpu(P, proj_geom, vol_geom); -figure(2); imshow(P, []); -figure(3); imshow(sinogram, []); - -% Create a data object for the reconstruction -rec_id = astra_mex_data2d('create', '-vol', vol_geom); - -% Create a data object for the mask -mask_id = astra_mex_data2d('create', '-vol', vol_geom, mask); - -% Set up the parameters for a reconstruction algorithm using the GPU -cfg = astra_struct('SIRT_CUDA'); -cfg.ReconstructionDataId = rec_id; -cfg.ProjectionDataId = sinogram_id; -cfg.option.ReconstructionMaskId = mask_id; - -% Create the algorithm object from the configuration structure -alg_id = astra_mex_algorithm('create', cfg); - -% Run 150 iterations of the algorithm -astra_mex_algorithm('iterate', alg_id, 150); - -% Get the result -rec = astra_mex_data2d('get', rec_id); -figure(4); imshow(rec, []); - -% Clean up. Note that GPU memory is tied up in the algorithm object, -% and main RAM in the data objects. -astra_mex_algorithm('delete', alg_id); -astra_mex_data2d('delete', mask_id); -astra_mex_data2d('delete', rec_id); -astra_mex_data2d('delete', sinogram_id); diff --git a/samples/s013_constraints.m b/samples/s013_constraints.m deleted file mode 100644 index d72195c..0000000 --- a/samples/s013_constraints.m +++ /dev/null @@ -1,47 +0,0 @@ -% ----------------------------------------------------------------------- -% This file is part of the ASTRA Toolbox -% -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam -% License: Open Source under GPLv3 -% Contact: astra@uantwerpen.be -% Website: http://sf.net/projects/astra-toolbox -% ----------------------------------------------------------------------- - -% In this example we will create a reconstruction constrained to -% greyvalues between 0 and 1 - -vol_geom = astra_create_vol_geom(256, 256); -proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,50)); - -% As before, create a sinogram from a phantom -P = phantom(256); -[sinogram_id, sinogram] = astra_create_sino_gpu(P, proj_geom, vol_geom); -figure(1); imshow(P, []); -figure(2); imshow(sinogram, []); - -% Create a data object for the reconstruction -rec_id = astra_mex_data2d('create', '-vol', vol_geom); - -% Set up the parameters for a reconstruction algorithm using the GPU -cfg = astra_struct('SIRT_CUDA'); -cfg.ReconstructionDataId = rec_id; -cfg.ProjectionDataId = sinogram_id; -cfg.option.MinConstraint = 0; -cfg.option.MaxConstraint = 1; - -% Create the algorithm object from the configuration structure -alg_id = astra_mex_algorithm('create', cfg); - -% Run 150 iterations of the algorithm -astra_mex_algorithm('iterate', alg_id, 150); - -% Get the result -rec = astra_mex_data2d('get', rec_id); -figure(3); imshow(rec, []); - -% Clean up. Note that GPU memory is tied up in the algorithm object, -% and main RAM in the data objects. -astra_mex_algorithm('delete', alg_id); -astra_mex_data2d('delete', rec_id); -astra_mex_data2d('delete', sinogram_id); diff --git a/samples/s014_FBP.m b/samples/s014_FBP.m deleted file mode 100644 index b73149c..0000000 --- a/samples/s014_FBP.m +++ /dev/null @@ -1,47 +0,0 @@ -% ----------------------------------------------------------------------- -% This file is part of the ASTRA Toolbox -% -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam -% License: Open Source under GPLv3 -% Contact: astra@uantwerpen.be -% Website: http://sf.net/projects/astra-toolbox -% ----------------------------------------------------------------------- - -vol_geom = astra_create_vol_geom(256, 256); -proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,180)); - -% As before, create a sinogram from a phantom -P = phantom(256); -[sinogram_id, sinogram] = astra_create_sino_gpu(P, proj_geom, vol_geom); -figure(1); imshow(P, []); -figure(2); imshow(sinogram, []); - -% Create a data object for the reconstruction -rec_id = astra_mex_data2d('create', '-vol', vol_geom); - -% create configuration -cfg = astra_struct('FBP_CUDA'); -cfg.ReconstructionDataId = rec_id; -cfg.ProjectionDataId = sinogram_id; -cfg.FilterType = 'Ram-Lak'; - -% possible values for FilterType: -% none, ram-lak, shepp-logan, cosine, hamming, hann, tukey, lanczos, -% triangular, gaussian, barlett-hann, blackman, nuttall, blackman-harris, -% blackman-nuttall, flat-top, kaiser, parzen - - -% Create and run the algorithm object from the configuration structure -alg_id = astra_mex_algorithm('create', cfg); -astra_mex_algorithm('run', alg_id); - -% Get the result -rec = astra_mex_data2d('get', rec_id); -figure(3); imshow(rec, []); - -% Clean up. Note that GPU memory is tied up in the algorithm object, -% and main RAM in the data objects. -astra_mex_algorithm('delete', alg_id); -astra_mex_data2d('delete', rec_id); -astra_mex_data2d('delete', sinogram_id); diff --git a/samples/s015_fp_bp.m b/samples/s015_fp_bp.m deleted file mode 100644 index 8cc417e..0000000 --- a/samples/s015_fp_bp.m +++ /dev/null @@ -1,62 +0,0 @@ -% ----------------------------------------------------------------------- -% This file is part of the ASTRA Toolbox -% -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam -% License: Open Source under GPLv3 -% Contact: astra@uantwerpen.be -% Website: http://sf.net/projects/astra-toolbox -% ----------------------------------------------------------------------- - - -% This example demonstrates using the FP and BP primitives with Matlab's lsqr -% solver. Calls to FP (astra_create_sino_cuda) and -% BP (astra_create_backprojection_cuda) are wrapped in a function astra_wrap, -% and a handle to this function is passed to lsqr. - -% Because in this case the inputs/outputs of FP and BP have to be vectors -% instead of images (matrices), the calls require reshaping to and from vectors. - -function s015_fp_bp - - -% FP/BP wrapper function -function Y = astra_wrap(X,T) - if strcmp(T, 'notransp') - % X is passed as a vector. Reshape it into an image. - [sid, s] = astra_create_sino_cuda(reshape(X,[vol_geom.GridRowCount vol_geom.GridColCount])', proj_geom, vol_geom); - astra_mex_data2d('delete', sid); - % now s is the sinogram. Reshape it back into a vector - Y = reshape(s',[prod(size(s)) 1]); - else - % X is passed as a vector. Reshape it into a sinogram. - v = astra_create_backprojection_cuda(reshape(X, [proj_geom.DetectorCount size(proj_geom.ProjectionAngles,2)])', proj_geom, vol_geom); - % now v is the resulting volume. Reshape it back into a vector - Y = reshape(v',[prod(size(v)) 1]); - end -end - - -vol_geom = astra_create_vol_geom(256, 256); -proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,180)); - -% Create a 256x256 phantom image using matlab's built-in phantom() function -P = phantom(256); - -% Create a sinogram using the GPU. -[sinogram_id, sinogram] = astra_create_sino_gpu(P, proj_geom, vol_geom); - -% Reshape the sinogram into a vector -b = reshape(sinogram',[prod(size(sinogram)) 1]); - -% Call Matlab's lsqr with ASTRA FP and BP -Y = lsqr(@astra_wrap,b,1e-4,25); - -% Reshape the result into an image -Y = reshape(Y,[vol_geom.GridRowCount vol_geom.GridColCount])'; -imshow(Y,[]); - - -astra_mex_data2d('delete', sinogram_id); - -end diff --git a/samples/s016_plots.m b/samples/s016_plots.m deleted file mode 100644 index 1455c6d..0000000 --- a/samples/s016_plots.m +++ /dev/null @@ -1,54 +0,0 @@ -% ----------------------------------------------------------------------- -% This file is part of the ASTRA Toolbox -% -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam -% License: Open Source under GPLv3 -% Contact: astra@uantwerpen.be -% Website: http://sf.net/projects/astra-toolbox -% ----------------------------------------------------------------------- - -vol_geom = astra_create_vol_geom(256, 256); -proj_geom = astra_create_proj_geom('parallel', 1.0, 384, linspace2(0,pi,180)); - -% As before, create a sinogram from a phantom -P = phantom(256); -[sinogram_id, sinogram] = astra_create_sino_gpu(P, proj_geom, vol_geom); -figure(1); imshow(P, []); -figure(2); imshow(sinogram, []); - -% Create a data object for the reconstruction -rec_id = astra_mex_data2d('create', '-vol', vol_geom); - -% Set up the parameters for a reconstruction algorithm using the GPU -cfg = astra_struct('SIRT_CUDA'); -cfg.ReconstructionDataId = rec_id; -cfg.ProjectionDataId = sinogram_id; - -% Create the algorithm object from the configuration structure -alg_id = astra_mex_algorithm('create', cfg); - -% Run 1500 iterations of the algorithm one at a time, keeping track of errors -nIters = 1500; -phantom_error = zeros(1, nIters); -residual_error = zeros(1, nIters); -for i = 1:nIters; - % Run a single iteration - astra_mex_algorithm('iterate', alg_id, 1); - - residual_error(i) = astra_mex_algorithm('get_res_norm', alg_id); - rec = astra_mex_data2d('get', rec_id); - phantom_error(i) = sqrt(sumsqr(rec - P)); -end - -% Get the result -rec = astra_mex_data2d('get', rec_id); -figure(3); imshow(rec, []); - -figure(4); plot(residual_error) -figure(5); plot(phantom_error) - -% Clean up. -astra_mex_algorithm('delete', alg_id); -astra_mex_data2d('delete', rec_id); -astra_mex_data2d('delete', sinogram_id); -- cgit v1.2.3 From 153b480b267a2d62e3b2d671d8018ab6e55dc8c4 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Tue, 24 Feb 2015 14:19:34 +0100 Subject: Better Python configure checks --- build/linux/configure.ac | 31 ++++++++++++++++++++++++------- 1 file changed, 24 insertions(+), 7 deletions(-) diff --git a/build/linux/configure.ac b/build/linux/configure.ac index f4cc82e..f9755f9 100644 --- a/build/linux/configure.ac +++ b/build/linux/configure.ac @@ -162,17 +162,34 @@ AC_SUBST(HAVEMATLAB) # python -AC_ARG_WITH(python, [[ --with-python=path path of Python (optional)]],,) +AC_ARG_WITH(python, [[ --with-python=path path of Python binary (optional)]],,) -PY_PATH=$PATH HAVEPYTHON=no if test x"$with_python" != x; then - PY_PATH="$with_python:$PY_PATH" - AC_PATH_PROG([PYTHON], [python], [no], [$PY_PATH]) - if test x"$PYTHON" != xno; then - HAVEPYTHON=yes - AC_SUBST(PYTHON) + AC_CHECK_FILE([$with_python],[PYTHON=$with_python],[AC_PATH_PROG([PYTHON], [$with_python], [AC_MSG_ERROR(Python binary not found)], [$PATH])]) + HAVEPYTHON=yes + AC_SUBST(PYTHON) + AC_MSG_CHECKING(for numpy module) + echo "import numpy" | $PYTHON - + if test $? -ne 0 ; then + AC_MSG_RESULT(not found) + AC_MSG_ERROR(You need the numpy module to use the ASTRA toolbox in Python) fi + AC_MSG_RESULT(found) + AC_MSG_CHECKING(for Cython module) + echo "import Cython;from distutils.version import LooseVersion;assert(LooseVersion(Cython.__version__)>=LooseVersion('0.13'))" | $PYTHON - + if test $? -ne 0 ; then + AC_MSG_RESULT(not found) + AC_MSG_ERROR(You need the Cython module (version >=0.13) to use the ASTRA toolbox in Python) + fi + AC_MSG_RESULT(found) + AC_MSG_CHECKING(for six module) + echo "import six" | $PYTHON - + if test $? -ne 0 ; then + AC_MSG_RESULT(not found) + AC_MSG_ERROR(You need the six module to use the ASTRA toolbox in Python) + fi + AC_MSG_RESULT(found) fi AC_SUBST(HAVEPYTHON) -- cgit v1.2.3 From 22f0c35dd2576b0121992ab09fe89e68c6532459 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 25 Feb 2015 10:48:59 +0100 Subject: Simplify with-python handling --- build/linux/configure.ac | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/build/linux/configure.ac b/build/linux/configure.ac index f9755f9..525ca9d 100644 --- a/build/linux/configure.ac +++ b/build/linux/configure.ac @@ -165,8 +165,18 @@ AC_SUBST(HAVEMATLAB) AC_ARG_WITH(python, [[ --with-python=path path of Python binary (optional)]],,) HAVEPYTHON=no -if test x"$with_python" != x; then - AC_CHECK_FILE([$with_python],[PYTHON=$with_python],[AC_PATH_PROG([PYTHON], [$with_python], [AC_MSG_ERROR(Python binary not found)], [$PATH])]) +if test x"$with_python" != x -a x"$with_python" != xno; then + if test x"$with_python" = xyes; then + PYTHON=python + else + PYTHON="$with_python" + fi + AC_MSG_CHECKING(for python) + ASTRA_RUN_LOGOUTPUT(echo 'import sys' | $PYTHON -) + if test $? -ne 0; then + AC_MSG_ERROR(Python binary not found)] + fi + AC_MSG_RESULT([$PYTHON]) HAVEPYTHON=yes AC_SUBST(PYTHON) AC_MSG_CHECKING(for numpy module) @@ -215,6 +225,7 @@ echo echo "Summary of ASTRA Toolbox build options:" echo " CUDA : $HAVECUDA" echo " Matlab : $HAVEMATLAB" +echo " Python : $HAVEPYTHON" echo echo " prefix : $prefix" echo -- cgit v1.2.3 From e0aca18f687e9f49223ffb24b9be354bed4b150a Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 25 Feb 2015 10:49:08 +0100 Subject: Add logging for python module checks --- build/linux/acinclude.m4 | 12 ++++++++++++ build/linux/configure.ac | 28 ++++++++++++++++------------ 2 files changed, 28 insertions(+), 12 deletions(-) diff --git a/build/linux/acinclude.m4 b/build/linux/acinclude.m4 index 713b5d3..e4b6de7 100644 --- a/build/linux/acinclude.m4 +++ b/build/linux/acinclude.m4 @@ -70,6 +70,18 @@ AC_DEFUN([ASTRA_RUN_LOGOUTPUT],[{ }]) +dnl ASTRA_TRY_PYTHON(code, action-if-ok, action-if-not-ok) +AC_DEFUN([ASTRA_TRY_PYTHON],[ +cat >conftest.py <<_ACEOF +$1 +_ACEOF +ASTRA_RUN_LOGOUTPUT($PYTHON conftest.py) +AS_IF([test $? = 0],[$2],[ + AS_ECHO(["$as_me: failed program was:"]) >&AS_MESSAGE_LOG_FD + sed 's/^/| /' conftest.py >&AS_MESSAGE_LOG_FD + $3]) +]) + dnl ASTRA_CHECK_NVCC(variable-to-set,cppflags-to-set) AC_DEFUN([ASTRA_CHECK_NVCC],[ diff --git a/build/linux/configure.ac b/build/linux/configure.ac index 525ca9d..b97a7a0 100644 --- a/build/linux/configure.ac +++ b/build/linux/configure.ac @@ -180,26 +180,30 @@ if test x"$with_python" != x -a x"$with_python" != xno; then HAVEPYTHON=yes AC_SUBST(PYTHON) AC_MSG_CHECKING(for numpy module) - echo "import numpy" | $PYTHON - - if test $? -ne 0 ; then - AC_MSG_RESULT(not found) + ASTRA_TRY_PYTHON([import numpy],,HAVEPYTHON=no) + if test x$HAVEPYTHON = xno; then + AC_MSG_RESULT(no) AC_MSG_ERROR(You need the numpy module to use the ASTRA toolbox in Python) fi - AC_MSG_RESULT(found) + AC_MSG_RESULT(yes) AC_MSG_CHECKING(for Cython module) - echo "import Cython;from distutils.version import LooseVersion;assert(LooseVersion(Cython.__version__)>=LooseVersion('0.13'))" | $PYTHON - - if test $? -ne 0 ; then - AC_MSG_RESULT(not found) + ASTRA_TRY_PYTHON([ +import Cython +from distutils.version import LooseVersion +assert(LooseVersion(Cython.__version__)>=LooseVersion("0.13")) +],,HAVEPYTHON=no) + if test x$HAVEPYTHON = xno; then + AC_MSG_RESULT(no) AC_MSG_ERROR(You need the Cython module (version >=0.13) to use the ASTRA toolbox in Python) fi - AC_MSG_RESULT(found) + AC_MSG_RESULT(yes) AC_MSG_CHECKING(for six module) - echo "import six" | $PYTHON - - if test $? -ne 0 ; then - AC_MSG_RESULT(not found) + ASTRA_TRY_PYTHON([import six]) + if test x$HAVEPYTHON = xno; then + AC_MSG_RESULT(no) AC_MSG_ERROR(You need the six module to use the ASTRA toolbox in Python) fi - AC_MSG_RESULT(found) + AC_MSG_RESULT(yes) fi AC_SUBST(HAVEPYTHON) -- cgit v1.2.3