diff options
101 files changed, 2196 insertions, 1304 deletions
diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..ec0eafb --- /dev/null +++ b/.gitignore @@ -0,0 +1,31 @@ +.*.swp +.*.swo +*~ +*.orig +*.rej +.nfs* + +/python/build/* +/python/finalbuild/* +/python/dist/* +/python/astra/*.pyc +/python/astra/*.cpp +/python/astra/*.c +/python/astra/config.pxi + +/build/linux/.libs/* +/build/linux/Makefile +/build/linux/aclocal.m4 +/build/linux/autom4te.cache/* +/build/linux/config.guess +/build/linux/config.log +/build/linux/config.status +/build/linux/config.sub +/build/linux/configure +/build/linux/cuda/* +/build/linux/install-sh +/build/linux/libastra.la +/build/linux/libtool +/build/linux/ltmain.sh +/build/linux/src/* +/build/linux/matlab/* @@ -9,6 +9,12 @@ Contact: astra@uantwerpen.be Website: http://sf.net/projects/astra-toolbox ----------------------------------------------------------------------- +1.6 (2015-05-29) + * integrate and improve python interface + * integrate opSpot-based opTomo operator + * build fixes for newer platforms + * various consistency and bug fixes + 1.5 (2015-01-30) * add support for fan beam FBP * remove limits on number of angles in GPU code @@ -23,12 +23,14 @@ Add the mex and tools subdirectories to your matlab path. ### Linux, from source -Requirements: g++, boost, CUDA (driver+toolkit), matlab +Requirements: g++, boost, CUDA (driver+toolkit), Matlab and/or Python (2.7 or 3.x) ``` cd build/linux +./autogen.sh # when building a git version ./configure --with-cuda=/usr/local/cuda \ --with-matlab=/usr/local/MATLAB/R2012a \ + --with-python --prefix=/usr/local/astra make make install @@ -36,6 +38,7 @@ make install Add /usr/local/astra/lib to your LD_LIBRARY_PATH. Add /usr/local/astra/matlab and its subdirectories (tools, mex) to your matlab path. +Add /usr/local/astra/python to your PYTHONPATH. NB: Each matlab version only supports a specific range of g++ versions. @@ -64,9 +67,14 @@ Install by copying AstraCuda32.dll or AstraCuda64.dll from bin/ and ## References -If you use parallel beam GPU code for your research, we would appreciate it if you would refer to the following paper: +If you use the ASTRA Toolbox for your research, we would appreciate it if you would refer to the following paper: + +W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K J. Batenburg, and J. Sijbers, "The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography", Ultramicroscopy (2015), http://dx.doi.org/10.1016/j.ultramic.2015.05.002 + +Additionally, if you use parallel beam GPU code, we would appreciate it if you would refer to the following paper: + +W. J. Palenstijn, K J. Batenburg, and J. Sijbers, "Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)", Journal of Structural Biology, vol. 176, issue 2, pp. 250-253, 2011, http://dx.doi.org/10.1016/j.jsb.2011.07.017 -W. J. Palenstijn, K J. Batenburg, and J. Sijbers, "Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)", Journal of Structural Biology, vol. 176, issue 2, pp. 250-253, 2011. ## License @@ -79,4 +87,4 @@ website: http://sf.net/projects/astra-toolbox Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp 2014-2015, CWI, Amsterdam - http://visielab.uantwerpen.be/ and http://www.cwi.nl/
\ No newline at end of file + http://visielab.uantwerpen.be/ and http://www.cwi.nl/ @@ -49,17 +49,20 @@ Add the mex and tools subdirectories to your matlab path. Linux, from source: -------------------- -Requirements: g++, boost, CUDA (driver+toolkit), matlab +Requirements: g++, boost, CUDA (driver+toolkit), Matlab and/or Python (2.7 or 3.x) cd build/linux +./autogen.sh # when building a git version ./configure --with-cuda=/usr/local/cuda \ --with-matlab=/usr/local/MATLAB/R2012a \ + --with-python \ --prefix=/usr/local/astra make make install Add /usr/local/astra/lib to your LD_LIBRARY_PATH. Add /usr/local/astra/matlab and its subdirectories (tools, mex) to your matlab path. +Add /usr/local/astra/python to your PYTHONPATH. NB: Each matlab version only supports a specific range of g++ versions. @@ -90,11 +93,14 @@ Install by copying AstraCuda32.dll or AstraCuda64.dll from bin/ and References: ------------ -If you use parallel beam GPU code for your research, we would appreciate it if -you would refer to the following paper: +If you use the ASTRA Toolbox for your research, we would appreciate it if you would refer to the following paper: + +W. van Aarle, W. J. Palenstijn, J. De Beenhouwer, T. Altantzis, S. Bals, K J. Batenburg, and J. Sijbers, "The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography", Ultramicroscopy (2015), http://dx.doi.org/10.1016/j.ultramic.2015.05.002 + +Additionally, if you use parallel beam GPU code, we would appreciate it if you would refer to the following paper: W. J. Palenstijn, K J. Batenburg, and J. Sijbers, "Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)", Journal of Structural Biology, vol. 176, issue 2, pp. 250-253, -2011 +2011, http://dx.doi.org/10.1016/j.jsb.2011.07.017 diff --git a/astra_vc09.vcproj b/astra_vc09.vcproj index a56e4bc..e5d7731 100644 --- a/astra_vc09.vcproj +++ b/astra_vc09.vcproj @@ -102,7 +102,8 @@ Arch3="35" TargetMachinePlatform="0" Runtime="3" - Defines="-DASTRA_CUDA -DDLL_EXPORTS" + ExtraCppOptions="-Iinclude -Ilib/include" + Defines="ASTRA_CUDA;DLL_EXPORTS" /> </Configuration> <Configuration @@ -186,7 +187,8 @@ Arch3="35" TargetMachinePlatform="1" Runtime="3" - Defines="-DASTRA_CUDA -DDLL_EXPORTS" + ExtraCppOptions="-Iinclude -Ilib/include" + Defines="ASTRA_CUDA;DLL_EXPORTS" /> </Configuration> <Configuration @@ -270,7 +272,8 @@ Arch3="35" TargetMachinePlatform="0" Runtime="3" - Defines="-DDLL_EXPORTS" + ExtraCppOptions="-Iinclude -Ilib/include" + Defines="DLL_EXPORTS" /> </Configuration> <Configuration @@ -353,7 +356,8 @@ Arch3="35" TargetMachinePlatform="1" Runtime="3" - Defines="-DDLL_EXPORTS" + ExtraCppOptions="-Iinclude -Ilib/include" + Defines="DLL_EXPORTS" /> </Configuration> <Configuration @@ -435,7 +439,8 @@ Arch3="35" TargetMachinePlatform="0" Runtime="2" - Defines="-DASTRA_CUDA -DDLL_EXPORTS" + ExtraCppOptions="-Iinclude -Ilib/include" + Defines="ASTRA_CUDA;DLL_EXPORTS" /> </Configuration> <Configuration @@ -516,7 +521,8 @@ Arch3="35" TargetMachinePlatform="1" Runtime="2" - Defines="-DASTRA_CUDA -DDLL_EXPORTS" + ExtraCppOptions="-Iinclude -Ilib/include" + Defines="ASTRA_CUDA;DLL_EXPORTS" /> </Configuration> <Configuration @@ -597,7 +603,8 @@ Arch3="35" TargetMachinePlatform="0" Runtime="2" - Defines="-DDLL_EXPORTS" + ExtraCppOptions="-Iinclude -Ilib/include" + Defines="DLL_EXPORTS" /> </Configuration> <Configuration @@ -677,7 +684,8 @@ Arch3="35" TargetMachinePlatform="1" Runtime="2" - Defines="-DDLL_EXPORTS" + ExtraCppOptions="-Iinclude -Ilib/include" + Defines="DLL_EXPORTS" /> </Configuration> </Configurations> diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 0dfa15a..2d862f2 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -28,7 +28,7 @@ CXXFLAGS=@SAVED_CXXFLAGS@ LDFLAGS=@SAVED_LDFLAGS@ LIBS=@SAVED_LIBS@ -CPPFLAGS+=-I../.. -I../../include -I../../lib/include/rapidxml +CPPFLAGS+=-I../.. -I../../include -I../../lib/include CXXFLAGS+=-g -O3 -Wall -Wshadow LIBS+=-lpthread LDFLAGS+=-g diff --git a/build/linux/README.txt b/build/linux/README.txt index 9dd7a7a..7208d45 100644 --- a/build/linux/README.txt +++ b/build/linux/README.txt @@ -1,15 +1,17 @@ -Requirements: g++, boost, CUDA (driver+toolkit), -matlab +Requirements: g++, boost, CUDA (driver+toolkit), Matlab and/or Python (2.7 or 3.x) cd build/linux +./autogen.sh # when building a git version ./configure --with-cuda=/usr/local/cuda \ --with-matlab=/usr/local/MATLAB/R2012a \ + --with-python \ --prefix=/usr/local/astra make make install Add /usr/local/astra/lib to your LD_LIBRARY_PATH. Add /usr/local/astra/matlab and its subdirectories (tools, mex) to your matlab path. +Add /usr/local/astra/python to your PYTHONPATH. NB: Each matlab version only supports a specific range of g++ versions. diff --git a/build/linux/config.guess.dist b/build/linux/config.guess.dist index dc84c68..b79252d 100755 --- a/build/linux/config.guess.dist +++ b/build/linux/config.guess.dist @@ -1,14 +1,12 @@ #! /bin/sh # Attempt to guess a canonical system name. -# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, -# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 -# Free Software Foundation, Inc. +# Copyright 1992-2013 Free Software Foundation, Inc. -timestamp='2009-11-20' +timestamp='2013-06-10' # This file 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 2 of the License, or +# the Free Software Foundation; either version 3 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, but @@ -17,26 +15,22 @@ timestamp='2009-11-20' # General Public License for more details. # # You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA -# 02110-1301, USA. +# along with this program; if not, see <http://www.gnu.org/licenses/>. # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under -# the same distribution terms that you use for the rest of that program. - - -# Originally written by Per Bothner. Please send patches (context -# diff format) to <config-patches@gnu.org> and include a ChangeLog -# entry. +# the same distribution terms that you use for the rest of that +# program. This Exception is an additional permission under section 7 +# of the GNU General Public License, version 3 ("GPLv3"). # -# This script attempts to guess a canonical system name similar to -# config.sub. If it succeeds, it prints the system name on stdout, and -# exits with 0. Otherwise, it exits with 1. +# Originally written by Per Bothner. # # You can get the latest version of this script from: # http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD +# +# Please send patches with a ChangeLog entry to config-patches@gnu.org. + me=`echo "$0" | sed -e 's,.*/,,'` @@ -56,8 +50,7 @@ version="\ GNU config.guess ($timestamp) Originally written by Per Bothner. -Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, -2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. +Copyright 1992-2013 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." @@ -139,12 +132,33 @@ UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown +case "${UNAME_SYSTEM}" in +Linux|GNU|GNU/*) + # If the system lacks a compiler, then just pick glibc. + # We could probably try harder. + LIBC=gnu + + eval $set_cc_for_build + cat <<-EOF > $dummy.c + #include <features.h> + #if defined(__UCLIBC__) + LIBC=uclibc + #elif defined(__dietlibc__) + LIBC=dietlibc + #else + LIBC=gnu + #endif + EOF + eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'` + ;; +esac + # Note: order is significant - the case branches are not exclusive. case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in *:NetBSD:*:*) # NetBSD (nbsd) targets should (where applicable) match one or - # more of the tupples: *-*-netbsdelf*, *-*-netbsdaout*, + # more of the tuples: *-*-netbsdelf*, *-*-netbsdaout*, # *-*-netbsdecoff* and *-*-netbsd*. For targets that recently # switched to ELF, *-*-netbsd* would select the old # object file format. This provides both forward @@ -180,7 +194,7 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in fi ;; *) - os=netbsd + os=netbsd ;; esac # The OS release @@ -201,6 +215,10 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used. echo "${machine}-${os}${release}" exit ;; + *:Bitrig:*:*) + UNAME_MACHINE_ARCH=`arch | sed 's/Bitrig.//'` + echo ${UNAME_MACHINE_ARCH}-unknown-bitrig${UNAME_RELEASE} + exit ;; *:OpenBSD:*:*) UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'` echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE} @@ -223,7 +241,7 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'` ;; *5.*) - UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'` + UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'` ;; esac # According to Compaq, /usr/sbin/psrinfo has been available on @@ -269,7 +287,10 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in # A Xn.n version is an unreleased experimental baselevel. # 1.2 uses "1.2" for uname -r. echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` - exit ;; + # Reset EXIT trap before exiting to avoid spurious non-zero exit code. + exitcode=$? + trap '' 0 + exit $exitcode ;; Alpha\ *:Windows_NT*:*) # How do we know it's Interix rather than the generic POSIX subsystem? # Should we change UNAME_MACHINE based on the output of uname instead @@ -295,12 +316,12 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in echo s390-ibm-zvmoe exit ;; *:OS400:*:*) - echo powerpc-ibm-os400 + echo powerpc-ibm-os400 exit ;; arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*) echo arm-acorn-riscix${UNAME_RELEASE} exit ;; - arm:riscos:*:*|arm:RISCOS:*:*) + arm*:riscos:*:*|arm*:RISCOS:*:*) echo arm-unknown-riscos exit ;; SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*) @@ -394,23 +415,23 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in # MiNT. But MiNT is downward compatible to TOS, so this should # be no problem. atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*) - echo m68k-atari-mint${UNAME_RELEASE} + echo m68k-atari-mint${UNAME_RELEASE} exit ;; atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} - exit ;; + exit ;; *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*) - echo m68k-atari-mint${UNAME_RELEASE} + echo m68k-atari-mint${UNAME_RELEASE} exit ;; milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*) - echo m68k-milan-mint${UNAME_RELEASE} - exit ;; + echo m68k-milan-mint${UNAME_RELEASE} + exit ;; hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*) - echo m68k-hades-mint${UNAME_RELEASE} - exit ;; + echo m68k-hades-mint${UNAME_RELEASE} + exit ;; *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*) - echo m68k-unknown-mint${UNAME_RELEASE} - exit ;; + echo m68k-unknown-mint${UNAME_RELEASE} + exit ;; m68k:machten:*:*) echo m68k-apple-machten${UNAME_RELEASE} exit ;; @@ -480,8 +501,8 @@ EOF echo m88k-motorola-sysv3 exit ;; AViiON:dgux:*:*) - # DG/UX returns AViiON for all architectures - UNAME_PROCESSOR=`/usr/bin/uname -p` + # DG/UX returns AViiON for all architectures + UNAME_PROCESSOR=`/usr/bin/uname -p` if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ] then if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \ @@ -494,7 +515,7 @@ EOF else echo i586-dg-dgux${UNAME_RELEASE} fi - exit ;; + exit ;; M88*:DolphinOS:*:*) # DolphinOS (SVR3) echo m88k-dolphin-sysv3 exit ;; @@ -551,7 +572,7 @@ EOF echo rs6000-ibm-aix3.2 fi exit ;; - *:AIX:*:[456]) + *:AIX:*:[4567]) IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'` if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then IBM_ARCH=rs6000 @@ -594,52 +615,52 @@ EOF 9000/[678][0-9][0-9]) if [ -x /usr/bin/getconf ]; then sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null` - sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null` - case "${sc_cpu_version}" in - 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0 - 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1 - 532) # CPU_PA_RISC2_0 - case "${sc_kernel_bits}" in - 32) HP_ARCH="hppa2.0n" ;; - 64) HP_ARCH="hppa2.0w" ;; + sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null` + case "${sc_cpu_version}" in + 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0 + 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1 + 532) # CPU_PA_RISC2_0 + case "${sc_kernel_bits}" in + 32) HP_ARCH="hppa2.0n" ;; + 64) HP_ARCH="hppa2.0w" ;; '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20 - esac ;; - esac + esac ;; + esac fi if [ "${HP_ARCH}" = "" ]; then eval $set_cc_for_build - sed 's/^ //' << EOF >$dummy.c + sed 's/^ //' << EOF >$dummy.c - #define _HPUX_SOURCE - #include <stdlib.h> - #include <unistd.h> + #define _HPUX_SOURCE + #include <stdlib.h> + #include <unistd.h> - int main () - { - #if defined(_SC_KERNEL_BITS) - long bits = sysconf(_SC_KERNEL_BITS); - #endif - long cpu = sysconf (_SC_CPU_VERSION); + int main () + { + #if defined(_SC_KERNEL_BITS) + long bits = sysconf(_SC_KERNEL_BITS); + #endif + long cpu = sysconf (_SC_CPU_VERSION); - switch (cpu) - { - case CPU_PA_RISC1_0: puts ("hppa1.0"); break; - case CPU_PA_RISC1_1: puts ("hppa1.1"); break; - case CPU_PA_RISC2_0: - #if defined(_SC_KERNEL_BITS) - switch (bits) - { - case 64: puts ("hppa2.0w"); break; - case 32: puts ("hppa2.0n"); break; - default: puts ("hppa2.0"); break; - } break; - #else /* !defined(_SC_KERNEL_BITS) */ - puts ("hppa2.0"); break; - #endif - default: puts ("hppa1.0"); break; - } - exit (0); - } + switch (cpu) + { + case CPU_PA_RISC1_0: puts ("hppa1.0"); break; + case CPU_PA_RISC1_1: puts ("hppa1.1"); break; + case CPU_PA_RISC2_0: + #if defined(_SC_KERNEL_BITS) + switch (bits) + { + case 64: puts ("hppa2.0w"); break; + case 32: puts ("hppa2.0n"); break; + default: puts ("hppa2.0"); break; + } break; + #else /* !defined(_SC_KERNEL_BITS) */ + puts ("hppa2.0"); break; + #endif + default: puts ("hppa1.0"); break; + } + exit (0); + } EOF (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy` test -z "$HP_ARCH" && HP_ARCH=hppa @@ -730,22 +751,22 @@ EOF exit ;; C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) echo c1-convex-bsd - exit ;; + exit ;; C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) if getsysinfo -f scalar_acc then echo c32-convex-bsd else echo c2-convex-bsd fi - exit ;; + exit ;; C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) echo c34-convex-bsd - exit ;; + exit ;; C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) echo c38-convex-bsd - exit ;; + exit ;; C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) echo c4-convex-bsd - exit ;; + exit ;; CRAY*Y-MP:*:*:*) echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; @@ -769,14 +790,14 @@ EOF exit ;; F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` - FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` - FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'` - echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" - exit ;; + FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` + FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'` + echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" + exit ;; 5000:UNIX_System_V:4.*:*) - FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` - FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'` - echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" + FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` + FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'` + echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" exit ;; i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE} @@ -788,30 +809,35 @@ EOF echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE} exit ;; *:FreeBSD:*:*) - case ${UNAME_MACHINE} in - pc98) - echo i386-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; + UNAME_PROCESSOR=`/usr/bin/uname -p` + case ${UNAME_PROCESSOR} in amd64) echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; *) - echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; + echo ${UNAME_PROCESSOR}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; esac exit ;; i*:CYGWIN*:*) echo ${UNAME_MACHINE}-pc-cygwin exit ;; + *:MINGW64*:*) + echo ${UNAME_MACHINE}-pc-mingw64 + exit ;; *:MINGW*:*) echo ${UNAME_MACHINE}-pc-mingw32 exit ;; + i*:MSYS*:*) + echo ${UNAME_MACHINE}-pc-msys + exit ;; i*:windows32*:*) - # uname -m includes "-pc" on this system. - echo ${UNAME_MACHINE}-mingw32 + # uname -m includes "-pc" on this system. + echo ${UNAME_MACHINE}-mingw32 exit ;; i*:PW*:*) echo ${UNAME_MACHINE}-pc-pw32 exit ;; *:Interix*:*) - case ${UNAME_MACHINE} in + case ${UNAME_MACHINE} in x86) echo i586-pc-interix${UNAME_RELEASE} exit ;; @@ -848,15 +874,22 @@ EOF exit ;; *:GNU:*:*) # the GNU system - echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'` + echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-${LIBC}`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'` exit ;; *:GNU/*:*:*) # other systems with GNU libc and userland - echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu + echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-${LIBC} exit ;; i*86:Minix:*:*) echo ${UNAME_MACHINE}-pc-minix exit ;; + aarch64:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-${LIBC} + exit ;; + aarch64_be:Linux:*:*) + UNAME_MACHINE=aarch64_be + echo ${UNAME_MACHINE}-unknown-linux-${LIBC} + exit ;; alpha:Linux:*:*) case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in EV5) UNAME_MACHINE=alphaev5 ;; @@ -866,52 +899,56 @@ EOF EV6) UNAME_MACHINE=alphaev6 ;; EV67) UNAME_MACHINE=alphaev67 ;; EV68*) UNAME_MACHINE=alphaev68 ;; - esac + esac objdump --private-headers /bin/sh | grep -q ld.so.1 - if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi - echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} + if test "$?" = 0 ; then LIBC="gnulibc1" ; fi + echo ${UNAME_MACHINE}-unknown-linux-${LIBC} + exit ;; + arc:Linux:*:* | arceb:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-${LIBC} exit ;; arm*:Linux:*:*) eval $set_cc_for_build if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \ | grep -q __ARM_EABI__ then - echo ${UNAME_MACHINE}-unknown-linux-gnu + echo ${UNAME_MACHINE}-unknown-linux-${LIBC} else - echo ${UNAME_MACHINE}-unknown-linux-gnueabi + if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \ + | grep -q __ARM_PCS_VFP + then + echo ${UNAME_MACHINE}-unknown-linux-${LIBC}eabi + else + echo ${UNAME_MACHINE}-unknown-linux-${LIBC}eabihf + fi fi exit ;; avr32*:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu + echo ${UNAME_MACHINE}-unknown-linux-${LIBC} exit ;; cris:Linux:*:*) - echo cris-axis-linux-gnu + echo ${UNAME_MACHINE}-axis-linux-${LIBC} exit ;; crisv32:Linux:*:*) - echo crisv32-axis-linux-gnu + echo ${UNAME_MACHINE}-axis-linux-${LIBC} exit ;; frv:Linux:*:*) - echo frv-unknown-linux-gnu + echo ${UNAME_MACHINE}-unknown-linux-${LIBC} + exit ;; + hexagon:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-${LIBC} exit ;; i*86:Linux:*:*) - LIBC=gnu - eval $set_cc_for_build - sed 's/^ //' << EOF >$dummy.c - #ifdef __dietlibc__ - LIBC=dietlibc - #endif -EOF - eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'` - echo "${UNAME_MACHINE}-pc-linux-${LIBC}" + echo ${UNAME_MACHINE}-pc-linux-${LIBC} exit ;; ia64:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu + echo ${UNAME_MACHINE}-unknown-linux-${LIBC} exit ;; m32r*:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu + echo ${UNAME_MACHINE}-unknown-linux-${LIBC} exit ;; m68*:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu + echo ${UNAME_MACHINE}-unknown-linux-${LIBC} exit ;; mips:Linux:*:* | mips64:Linux:*:*) eval $set_cc_for_build @@ -930,51 +967,63 @@ EOF #endif EOF eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'` - test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } + test x"${CPU}" != x && { echo "${CPU}-unknown-linux-${LIBC}"; exit; } ;; + or1k:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-${LIBC} + exit ;; or32:Linux:*:*) - echo or32-unknown-linux-gnu + echo ${UNAME_MACHINE}-unknown-linux-${LIBC} exit ;; padre:Linux:*:*) - echo sparc-unknown-linux-gnu + echo sparc-unknown-linux-${LIBC} exit ;; parisc64:Linux:*:* | hppa64:Linux:*:*) - echo hppa64-unknown-linux-gnu + echo hppa64-unknown-linux-${LIBC} exit ;; parisc:Linux:*:* | hppa:Linux:*:*) # Look for CPU level case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in - PA7*) echo hppa1.1-unknown-linux-gnu ;; - PA8*) echo hppa2.0-unknown-linux-gnu ;; - *) echo hppa-unknown-linux-gnu ;; + PA7*) echo hppa1.1-unknown-linux-${LIBC} ;; + PA8*) echo hppa2.0-unknown-linux-${LIBC} ;; + *) echo hppa-unknown-linux-${LIBC} ;; esac exit ;; ppc64:Linux:*:*) - echo powerpc64-unknown-linux-gnu + echo powerpc64-unknown-linux-${LIBC} exit ;; ppc:Linux:*:*) - echo powerpc-unknown-linux-gnu + echo powerpc-unknown-linux-${LIBC} + exit ;; + ppc64le:Linux:*:*) + echo powerpc64le-unknown-linux-${LIBC} + exit ;; + ppcle:Linux:*:*) + echo powerpcle-unknown-linux-${LIBC} exit ;; s390:Linux:*:* | s390x:Linux:*:*) - echo ${UNAME_MACHINE}-ibm-linux + echo ${UNAME_MACHINE}-ibm-linux-${LIBC} exit ;; sh64*:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu + echo ${UNAME_MACHINE}-unknown-linux-${LIBC} exit ;; sh*:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu + echo ${UNAME_MACHINE}-unknown-linux-${LIBC} exit ;; sparc:Linux:*:* | sparc64:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu + echo ${UNAME_MACHINE}-unknown-linux-${LIBC} + exit ;; + tile*:Linux:*:*) + echo ${UNAME_MACHINE}-unknown-linux-${LIBC} exit ;; vax:Linux:*:*) - echo ${UNAME_MACHINE}-dec-linux-gnu + echo ${UNAME_MACHINE}-dec-linux-${LIBC} exit ;; x86_64:Linux:*:*) - echo x86_64-unknown-linux-gnu + echo ${UNAME_MACHINE}-unknown-linux-${LIBC} exit ;; xtensa*:Linux:*:*) - echo ${UNAME_MACHINE}-unknown-linux-gnu + echo ${UNAME_MACHINE}-unknown-linux-${LIBC} exit ;; i*86:DYNIX/ptx:4*:*) # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. @@ -983,11 +1032,11 @@ EOF echo i386-sequent-sysv4 exit ;; i*86:UNIX_SV:4.2MP:2.*) - # Unixware is an offshoot of SVR4, but it has its own version - # number series starting with 2... - # I am not positive that other SVR4 systems won't match this, + # Unixware is an offshoot of SVR4, but it has its own version + # number series starting with 2... + # I am not positive that other SVR4 systems won't match this, # I just have to hope. -- rms. - # Use sysv4.2uw... so that sysv4* matches it. + # Use sysv4.2uw... so that sysv4* matches it. echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION} exit ;; i*86:OS/2:*:*) @@ -1019,7 +1068,7 @@ EOF fi exit ;; i*86:*:5:[678]*) - # UnixWare 7.x, OpenUNIX and OpenServer 6. + # UnixWare 7.x, OpenUNIX and OpenServer 6. case `/bin/uname -X | grep "^Machine"` in *486*) UNAME_MACHINE=i486 ;; *Pentium) UNAME_MACHINE=i586 ;; @@ -1047,13 +1096,13 @@ EOF exit ;; pc:*:*:*) # Left here for compatibility: - # uname -m prints for DJGPP always 'pc', but it prints nothing about - # the processor, so we play safe by assuming i586. + # uname -m prints for DJGPP always 'pc', but it prints nothing about + # the processor, so we play safe by assuming i586. # Note: whatever this is, it MUST be the same as what config.sub # prints for the "djgpp" host, or else GDB configury will decide that # this is a cross-build. echo i586-pc-msdosdjgpp - exit ;; + exit ;; Intel:Mach:3*:*) echo i386-pc-mach3 exit ;; @@ -1088,8 +1137,8 @@ EOF /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;; 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) - /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ - && { echo i486-ncr-sysv4; exit; } ;; + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && { echo i486-ncr-sysv4; exit; } ;; NCR*:*:4.2:* | MPRAS*:*:4.2:*) OS_REL='.3' test -r /etc/.relid \ @@ -1132,10 +1181,10 @@ EOF echo ns32k-sni-sysv fi exit ;; - PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort - # says <Richard.M.Bartel@ccMail.Census.GOV> - echo i586-unisys-sysv4 - exit ;; + PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort + # says <Richard.M.Bartel@ccMail.Census.GOV> + echo i586-unisys-sysv4 + exit ;; *:UNIX_System_V:4*:FTX*) # From Gerald Hewes <hewes@openmarket.com>. # How about differentiating between stratus architectures? -djm @@ -1161,11 +1210,11 @@ EOF exit ;; R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) if [ -d /usr/nec ]; then - echo mips-nec-sysv${UNAME_RELEASE} + echo mips-nec-sysv${UNAME_RELEASE} else - echo mips-unknown-sysv${UNAME_RELEASE} + echo mips-unknown-sysv${UNAME_RELEASE} fi - exit ;; + exit ;; BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. echo powerpc-be-beos exit ;; @@ -1178,6 +1227,9 @@ EOF BePC:Haiku:*:*) # Haiku running on Intel PC compatible. echo i586-pc-haiku exit ;; + x86_64:Haiku:*:*) + echo x86_64-unknown-haiku + exit ;; SX-4:SUPER-UX:*:*) echo sx4-nec-superux${UNAME_RELEASE} exit ;; @@ -1204,19 +1256,21 @@ EOF exit ;; *:Darwin:*:*) UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown - case $UNAME_PROCESSOR in - i386) - eval $set_cc_for_build - if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then - if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \ - (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \ - grep IS_64BIT_ARCH >/dev/null - then - UNAME_PROCESSOR="x86_64" - fi - fi ;; - unknown) UNAME_PROCESSOR=powerpc ;; - esac + eval $set_cc_for_build + if test "$UNAME_PROCESSOR" = unknown ; then + UNAME_PROCESSOR=powerpc + fi + if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then + if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \ + (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_64BIT_ARCH >/dev/null + then + case $UNAME_PROCESSOR in + i386) UNAME_PROCESSOR=x86_64 ;; + powerpc) UNAME_PROCESSOR=powerpc64 ;; + esac + fi + fi echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE} exit ;; *:procnto*:*:* | *:QNX:[0123456789]*:*) @@ -1230,7 +1284,10 @@ EOF *:QNX:*:4*) echo i386-pc-qnx exit ;; - NSE-?:NONSTOP_KERNEL:*:*) + NEO-?:NONSTOP_KERNEL:*:*) + echo neo-tandem-nsk${UNAME_RELEASE} + exit ;; + NSE-*:NONSTOP_KERNEL:*:*) echo nse-tandem-nsk${UNAME_RELEASE} exit ;; NSR-?:NONSTOP_KERNEL:*:*) @@ -1275,13 +1332,13 @@ EOF echo pdp10-unknown-its exit ;; SEI:*:*:SEIUX) - echo mips-sei-seiux${UNAME_RELEASE} + echo mips-sei-seiux${UNAME_RELEASE} exit ;; *:DragonFly:*:*) echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` exit ;; *:*VMS:*:*) - UNAME_MACHINE=`(uname -p) 2>/dev/null` + UNAME_MACHINE=`(uname -p) 2>/dev/null` case "${UNAME_MACHINE}" in A*) echo alpha-dec-vms ; exit ;; I*) echo ia64-dec-vms ; exit ;; @@ -1299,11 +1356,11 @@ EOF i*86:AROS:*:*) echo ${UNAME_MACHINE}-pc-aros exit ;; + x86_64:VMkernel:*:*) + echo ${UNAME_MACHINE}-unknown-esx + exit ;; esac -#echo '(No uname command or uname output not recognized.)' 1>&2 -#echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2 - eval $set_cc_for_build cat >$dummy.c <<EOF #ifdef _SEQUENT_ @@ -1321,11 +1378,11 @@ main () #include <sys/param.h> printf ("m68k-sony-newsos%s\n", #ifdef NEWSOS4 - "4" + "4" #else - "" + "" #endif - ); exit (0); + ); exit (0); #endif #endif diff --git a/build/linux/config.sub.dist b/build/linux/config.sub.dist index 2a55a50..d2a9613 100755 --- a/build/linux/config.sub.dist +++ b/build/linux/config.sub.dist @@ -1,38 +1,31 @@ #! /bin/sh # Configuration validation subroutine script. -# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, -# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 -# Free Software Foundation, Inc. +# Copyright 1992-2013 Free Software Foundation, Inc. -timestamp='2009-11-20' +timestamp='2013-08-10' -# This file is (in principle) common to ALL GNU software. -# The presence of a machine in this file suggests that SOME GNU software -# can handle that machine. It does not imply ALL GNU software can. -# -# This file 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 2 of the License, or +# This file 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. # -# This program 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. +# This program 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 this program; if not, write to the Free Software -# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA -# 02110-1301, USA. +# along with this program; if not, see <http://www.gnu.org/licenses/>. # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under -# the same distribution terms that you use for the rest of that program. +# the same distribution terms that you use for the rest of that +# program. This Exception is an additional permission under section 7 +# of the GNU General Public License, version 3 ("GPLv3"). -# Please send patches to <config-patches@gnu.org>. Submit a context -# diff and a properly formatted GNU ChangeLog entry. +# Please send patches with a ChangeLog entry to config-patches@gnu.org. # # Configuration subroutine to validate and canonicalize a configuration type. # Supply the specified configuration type as an argument. @@ -75,8 +68,7 @@ Report bugs and patches to <config-patches@gnu.org>." version="\ GNU config.sub ($timestamp) -Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, -2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. +Copyright 1992-2013 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." @@ -123,13 +115,18 @@ esac # Here we must recognize all the valid KERNEL-OS combinations. maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'` case $maybe_os in - nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \ - uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \ + nto-qnx* | linux-gnu* | linux-android* | linux-dietlibc | linux-newlib* | \ + linux-musl* | linux-uclibc* | uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | \ + knetbsd*-gnu* | netbsd*-gnu* | \ kopensolaris*-gnu* | \ storm-chaos* | os2-emx* | rtmk-nova*) os=-$maybe_os basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'` ;; + android-linux) + os=-linux-android + basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`-unknown + ;; *) basic_machine=`echo $1 | sed 's/-[^-]*$//'` if [ $basic_machine != $1 ] @@ -152,12 +149,12 @@ case $os in -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\ -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \ -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \ - -apple | -axis | -knuth | -cray | -microblaze) + -apple | -axis | -knuth | -cray | -microblaze*) os= basic_machine=$1 ;; - -bluegene*) - os=-cnk + -bluegene*) + os=-cnk ;; -sim | -cisco | -oki | -wec | -winbond) os= @@ -173,10 +170,10 @@ case $os in os=-chorusos basic_machine=$1 ;; - -chorusrdb) - os=-chorusrdb + -chorusrdb) + os=-chorusrdb basic_machine=$1 - ;; + ;; -hiux*) os=-hiuxwe2 ;; @@ -221,6 +218,12 @@ case $os in -isc*) basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; + -lynx*178) + os=-lynxos178 + ;; + -lynx*5) + os=-lynxos5 + ;; -lynx*) os=-lynxos ;; @@ -245,20 +248,27 @@ case $basic_machine in # Some are omitted here because they have special meanings below. 1750a | 580 \ | a29k \ + | aarch64 | aarch64_be \ | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \ | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \ | am33_2.0 \ - | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr | avr32 \ + | arc | arceb \ + | arm | arm[bl]e | arme[lb] | armv[2-8] | armv[3-8][lb] | armv7[arm] \ + | avr | avr32 \ + | be32 | be64 \ | bfin \ - | c4x | clipper \ + | c4x | c8051 | clipper \ | d10v | d30v | dlx | dsp16xx \ + | epiphany \ | fido | fr30 | frv \ | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ + | hexagon \ | i370 | i860 | i960 | ia64 \ | ip2k | iq2000 \ + | le32 | le64 \ | lm32 \ | m32c | m32r | m32rle | m68000 | m68k | m88k \ - | maxq | mb | microblaze | mcore | mep | metag \ + | maxq | mb | microblaze | microblazeel | mcore | mep | metag \ | mips | mipsbe | mipseb | mipsel | mipsle \ | mips16 \ | mips64 | mips64el \ @@ -276,34 +286,45 @@ case $basic_machine in | mipsisa64r2 | mipsisa64r2el \ | mipsisa64sb1 | mipsisa64sb1el \ | mipsisa64sr71k | mipsisa64sr71kel \ + | mipsr5900 | mipsr5900el \ | mipstx39 | mipstx39el \ | mn10200 | mn10300 \ | moxie \ | mt \ | msp430 \ - | nios | nios2 \ + | nds32 | nds32le | nds32be \ + | nios | nios2 | nios2eb | nios2el \ | ns16k | ns32k \ - | or32 \ + | open8 \ + | or1k | or32 \ | pdp10 | pdp11 | pj | pjl \ - | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \ + | powerpc | powerpc64 | powerpc64le | powerpcle \ | pyramid \ - | rx \ + | rl78 | rx \ | score \ | sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \ | sh64 | sh64le \ | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \ | sparcv8 | sparcv9 | sparcv9b | sparcv9v \ - | spu | strongarm \ - | tahoe | thumb | tic4x | tic80 | tron \ + | spu \ + | tahoe | tic4x | tic54x | tic55x | tic6x | tic80 | tron \ | ubicom32 \ - | v850 | v850e \ + | v850 | v850e | v850e1 | v850e2 | v850es | v850e2v3 \ | we32k \ - | x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \ + | x86 | xc16x | xstormy16 | xtensa \ | z8k | z80) basic_machine=$basic_machine-unknown ;; - m6811 | m68hc11 | m6812 | m68hc12 | picochip) - # Motorola 68HC11/12. + c54x) + basic_machine=tic54x-unknown + ;; + c55x) + basic_machine=tic55x-unknown + ;; + c6x) + basic_machine=tic6x-unknown + ;; + m6811 | m68hc11 | m6812 | m68hc12 | m68hcs12x | picochip) basic_machine=$basic_machine-unknown os=-none ;; @@ -313,6 +334,21 @@ case $basic_machine in basic_machine=mt-unknown ;; + strongarm | thumb | xscale) + basic_machine=arm-unknown + ;; + xgate) + basic_machine=$basic_machine-unknown + os=-none + ;; + xscaleeb) + basic_machine=armeb-unknown + ;; + + xscaleel) + basic_machine=armel-unknown + ;; + # We use `pc' rather than `unknown' # because (1) that's what they normally are, and # (2) the word "unknown" tends to confuse beginning users. @@ -327,25 +363,30 @@ case $basic_machine in # Recognize the basic CPU types with company name. 580-* \ | a29k-* \ + | aarch64-* | aarch64_be-* \ | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \ | alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \ - | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \ + | alphapca5[67]-* | alpha64pca5[67]-* | arc-* | arceb-* \ | arm-* | armbe-* | armle-* | armeb-* | armv*-* \ | avr-* | avr32-* \ + | be32-* | be64-* \ | bfin-* | bs2000-* \ - | c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \ - | clipper-* | craynv-* | cydra-* \ + | c[123]* | c30-* | [cjt]90-* | c4x-* \ + | c8051-* | clipper-* | craynv-* | cydra-* \ | d10v-* | d30v-* | dlx-* \ | elxsi-* \ | f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \ | h8300-* | h8500-* \ | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \ + | hexagon-* \ | i*86-* | i860-* | i960-* | ia64-* \ | ip2k-* | iq2000-* \ + | le32-* | le64-* \ | lm32-* \ | m32c-* | m32r-* | m32rle-* \ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \ - | m88110-* | m88k-* | maxq-* | mcore-* | metag-* | microblaze-* \ + | m88110-* | m88k-* | maxq-* | mcore-* | metag-* \ + | microblaze-* | microblazeel-* \ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \ | mips16-* \ | mips64-* | mips64el-* \ @@ -363,29 +404,34 @@ case $basic_machine in | mipsisa64r2-* | mipsisa64r2el-* \ | mipsisa64sb1-* | mipsisa64sb1el-* \ | mipsisa64sr71k-* | mipsisa64sr71kel-* \ + | mipsr5900-* | mipsr5900el-* \ | mipstx39-* | mipstx39el-* \ | mmix-* \ | mt-* \ | msp430-* \ - | nios-* | nios2-* \ + | nds32-* | nds32le-* | nds32be-* \ + | nios-* | nios2-* | nios2eb-* | nios2el-* \ | none-* | np1-* | ns16k-* | ns32k-* \ + | open8-* \ | orion-* \ | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \ - | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \ + | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* \ | pyramid-* \ - | romp-* | rs6000-* | rx-* \ + | rl78-* | romp-* | rs6000-* | rx-* \ | sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \ | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \ | sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \ | sparclite-* \ - | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \ - | tahoe-* | thumb-* \ - | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* | tile-* \ + | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | sv1-* | sx?-* \ + | tahoe-* \ + | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \ + | tile*-* \ | tron-* \ | ubicom32-* \ - | v850-* | v850e-* | vax-* \ + | v850-* | v850e-* | v850e1-* | v850es-* | v850e2-* | v850e2v3-* \ + | vax-* \ | we32k-* \ - | x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \ + | x86-* | x86_64-* | xc16x-* | xps100-* \ | xstormy16-* | xtensa*-* \ | ymp-* \ | z8k-* | z80-*) @@ -410,7 +456,7 @@ case $basic_machine in basic_machine=a29k-amd os=-udi ;; - abacus) + abacus) basic_machine=abacus-unknown ;; adobe68k) @@ -480,11 +526,20 @@ case $basic_machine in basic_machine=powerpc-ibm os=-cnk ;; + c54x-*) + basic_machine=tic54x-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + c55x-*) + basic_machine=tic55x-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; + c6x-*) + basic_machine=tic6x-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; c90) basic_machine=c90-cray os=-unicos ;; - cegcc) + cegcc) basic_machine=arm-unknown os=-cegcc ;; @@ -516,7 +571,7 @@ case $basic_machine in basic_machine=craynv-cray os=-unicosmp ;; - cr16) + cr16 | cr16-*) basic_machine=cr16-unknown os=-elf ;; @@ -674,7 +729,6 @@ case $basic_machine in i370-ibm* | ibm*) basic_machine=i370-ibm ;; -# I'm not sure what "Sysv32" means. Should this be sysv3.2? i*86v32) basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'` os=-sysv32 @@ -732,11 +786,15 @@ case $basic_machine in basic_machine=ns32k-utek os=-sysv ;; - microblaze) + microblaze*) basic_machine=microblaze-xilinx ;; + mingw64) + basic_machine=x86_64-pc + os=-mingw64 + ;; mingw32) - basic_machine=i386-pc + basic_machine=i686-pc os=-mingw32 ;; mingw32ce) @@ -771,10 +829,18 @@ case $basic_machine in ms1-*) basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'` ;; + msys) + basic_machine=i686-pc + os=-msys + ;; mvs) basic_machine=i370-ibm os=-mvs ;; + nacl) + basic_machine=le32-unknown + os=-nacl + ;; ncr3000) basic_machine=i486-ncr os=-sysv4 @@ -839,6 +905,12 @@ case $basic_machine in np1) basic_machine=np1-gould ;; + neo-tandem) + basic_machine=neo-tandem + ;; + nse-tandem) + basic_machine=nse-tandem + ;; nsr-tandem) basic_machine=nsr-tandem ;; @@ -921,9 +993,10 @@ case $basic_machine in ;; power) basic_machine=power-ibm ;; - ppc) basic_machine=powerpc-unknown + ppc | ppcbe) basic_machine=powerpc-unknown ;; - ppc-*) basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'` + ppc-* | ppcbe-*) + basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ppcle | powerpclittle | ppc-le | powerpc-little) basic_machine=powerpcle-unknown @@ -933,7 +1006,7 @@ case $basic_machine in ;; ppc64) basic_machine=powerpc64-unknown ;; - ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'` + ppc64-* | ppc64p7-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ppc64le | powerpc64little | ppc64-le | powerpc64-little) basic_machine=powerpc64le-unknown @@ -948,7 +1021,11 @@ case $basic_machine in basic_machine=i586-unknown os=-pw32 ;; - rdos) + rdos | rdos64) + basic_machine=x86_64-pc + os=-rdos + ;; + rdos32) basic_machine=i386-pc os=-rdos ;; @@ -1017,6 +1094,9 @@ case $basic_machine in basic_machine=i860-stratus os=-sysv4 ;; + strongarm-* | thumb-*) + basic_machine=arm-`echo $basic_machine | sed 's/^[^-]*-//'` + ;; sun2) basic_machine=m68000-sun ;; @@ -1073,20 +1153,8 @@ case $basic_machine in basic_machine=t90-cray os=-unicos ;; - tic54x | c54x*) - basic_machine=tic54x-unknown - os=-coff - ;; - tic55x | c55x*) - basic_machine=tic55x-unknown - os=-coff - ;; - tic6x | c6x*) - basic_machine=tic6x-unknown - os=-coff - ;; tile*) - basic_machine=tile-unknown + basic_machine=$basic_machine-unknown os=-linux-gnu ;; tx39) @@ -1156,6 +1224,9 @@ case $basic_machine in xps | xps100) basic_machine=xps100-honeywell ;; + xscale-* | xscalee[bl]-*) + basic_machine=`echo $basic_machine | sed 's/^xscale/arm/'` + ;; ymp) basic_machine=ymp-cray os=-unicos @@ -1253,11 +1324,11 @@ esac if [ x"$os" != x"" ] then case $os in - # First match some system type aliases - # that might get confused with valid system types. + # First match some system type aliases + # that might get confused with valid system types. # -solaris* is a basic system type, with this one exception. - -auroraux) - os=-auroraux + -auroraux) + os=-auroraux ;; -solaris1 | -solaris1.*) os=`echo $os | sed -e 's|solaris1|sunos4|'` @@ -1281,20 +1352,21 @@ case $os in -gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \ | -*vms* | -sco* | -esix* | -isc* | -aix* | -cnk* | -sunos | -sunos[34]*\ | -hpux* | -unos* | -osf* | -luna* | -dgux* | -auroraux* | -solaris* \ - | -sym* | -kopensolaris* \ + | -sym* | -kopensolaris* | -plan9* \ | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \ | -aos* | -aros* \ | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \ | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \ | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \ - | -openbsd* | -solidbsd* \ + | -bitrig* | -openbsd* | -solidbsd* \ | -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \ | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \ | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \ | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \ | -chorusos* | -chorusrdb* | -cegcc* \ - | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \ - | -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \ + | -cygwin* | -msys* | -pe* | -psos* | -moss* | -proelf* | -rtems* \ + | -mingw32* | -mingw64* | -linux-gnu* | -linux-android* \ + | -linux-newlib* | -linux-musl* | -linux-uclibc* \ | -uxpv* | -beos* | -mpeix* | -udk* \ | -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \ | -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \ @@ -1341,7 +1413,7 @@ case $os in -opened*) os=-openedition ;; - -os400*) + -os400*) os=-os400 ;; -wince*) @@ -1390,7 +1462,7 @@ case $os in -sinix*) os=-sysv4 ;; - -tpf*) + -tpf*) os=-tpf ;; -triton*) @@ -1426,15 +1498,14 @@ case $os in -aros*) os=-aros ;; - -kaos*) - os=-kaos - ;; -zvmoe) os=-zvmoe ;; -dicos*) os=-dicos ;; + -nacl*) + ;; -none) ;; *) @@ -1457,10 +1528,10 @@ else # system, and we'll never get to this point. case $basic_machine in - score-*) + score-*) os=-elf ;; - spu-*) + spu-*) os=-elf ;; *-acorn) @@ -1472,8 +1543,23 @@ case $basic_machine in arm*-semi) os=-aout ;; - c4x-* | tic4x-*) - os=-coff + c4x-* | tic4x-*) + os=-coff + ;; + c8051-*) + os=-elf + ;; + hexagon-*) + os=-elf + ;; + tic54x-*) + os=-coff + ;; + tic55x-*) + os=-coff + ;; + tic6x-*) + os=-coff ;; # This must come before the *-dec entry. pdp10-*) @@ -1493,14 +1579,11 @@ case $basic_machine in ;; m68000-sun) os=-sunos3 - # This also exists in the configure program, but was not the - # default. - # os=-sunos4 ;; m68*-cisco) os=-aout ;; - mep-*) + mep-*) os=-elf ;; mips*-cisco) @@ -1509,6 +1592,9 @@ case $basic_machine in mips*-*) os=-elf ;; + or1k-*) + os=-elf + ;; or32-*) os=-coff ;; @@ -1527,7 +1613,7 @@ case $basic_machine in *-ibm) os=-aix ;; - *-knuth) + *-knuth) os=-mmixware ;; *-wec) diff --git a/build/linux/configure.ac b/build/linux/configure.ac index d9e1f1a..7c314f3 100644 --- a/build/linux/configure.ac +++ b/build/linux/configure.ac @@ -24,7 +24,7 @@ dnl dnl ----------------------------------------------------------------------- dnl $Id$ -AC_INIT(astra_toolbox, 1.5.0) +AC_INIT(astra_toolbox, 1.6.0) AC_CONFIG_SRCDIR([Makefile.in]) LT_INIT([disable-static]) @@ -190,7 +190,7 @@ if test x"$with_python" != x -a x"$with_python" != xno; then AC_MSG_CHECKING(for python) ASTRA_RUN_LOGOUTPUT(echo 'import sys' | $PYTHON -) if test $? -ne 0; then - AC_MSG_ERROR(Python binary not found)] + AC_MSG_ERROR(Python binary not found) fi AC_MSG_RESULT([$PYTHON]) HAVEPYTHON=yes diff --git a/build/linux/install-sh.dist b/build/linux/install-sh.dist index a5897de..a9244eb 100755 --- a/build/linux/install-sh.dist +++ b/build/linux/install-sh.dist @@ -1,7 +1,7 @@ #!/bin/sh # install - install a program, script, or datafile -scriptversion=2006-12-25.00 +scriptversion=2011-01-19.21; # UTC # This originates from X11R5 (mit/util/scripts/install.sh), which was # later released in X11R6 (xc/config/util/install.sh) with the @@ -156,6 +156,10 @@ while test $# -ne 0; do -s) stripcmd=$stripprog;; -t) dst_arg=$2 + # Protect names problematic for `test' and other utilities. + case $dst_arg in + -* | [=\(\)!]) dst_arg=./$dst_arg;; + esac shift;; -T) no_target_directory=true;; @@ -186,6 +190,10 @@ if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then fi shift # arg dst_arg=$arg + # Protect names problematic for `test' and other utilities. + case $dst_arg in + -* | [=\(\)!]) dst_arg=./$dst_arg;; + esac done fi @@ -200,7 +208,11 @@ if test $# -eq 0; then fi if test -z "$dir_arg"; then - trap '(exit $?); exit' 1 2 13 15 + do_exit='(exit $ret); exit $ret' + trap "ret=129; $do_exit" 1 + trap "ret=130; $do_exit" 2 + trap "ret=141; $do_exit" 13 + trap "ret=143; $do_exit" 15 # Set umask so as not to create temps with too-generous modes. # However, 'strip' requires both read and write access to temps. @@ -228,9 +240,9 @@ fi for src do - # Protect names starting with `-'. + # Protect names problematic for `test' and other utilities. case $src in - -*) src=./$src;; + -* | [=\(\)!]) src=./$src;; esac if test -n "$dir_arg"; then @@ -252,12 +264,7 @@ do echo "$0: no destination specified." >&2 exit 1 fi - dst=$dst_arg - # Protect names starting with `-'. - case $dst in - -*) dst=./$dst;; - esac # If destination is a directory, append the input filename; won't work # if double slashes aren't ignored. @@ -385,7 +392,7 @@ do case $dstdir in /*) prefix='/';; - -*) prefix='./';; + [-=\(\)!]*) prefix='./';; *) prefix='';; esac @@ -403,7 +410,7 @@ do for d do - test -z "$d" && continue + test X"$d" = X && continue prefix=$prefix$d if test -d "$prefix"; then @@ -515,5 +522,6 @@ done # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" -# time-stamp-end: "$" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" # End: diff --git a/build/msvc/gen.py b/build/msvc/gen.py index 9f5e367..aeca3b0 100644 --- a/build/msvc/gen.py +++ b/build/msvc/gen.py @@ -946,10 +946,11 @@ def write_main_project09(): print('\t\t\t\tRuntime="3"', file=F) # MDD else: print('\t\t\t\tRuntime="2"', file=F) # MD + print('\t\t\t\tExtraCppOptions="-Iinclude -Ilib/include"', file=F) if c.cuda: - print('\t\t\t\tDefines="-DASTRA_CUDA -DDLL_EXPORTS"', file=F) + print('\t\t\t\tDefines="ASTRA_CUDA;DLL_EXPORTS"', file=F) else: # This 'else' doesn't make much sense - print('\t\t\t\tDefines="-DDLL_EXPORTS"', file=F) + print('\t\t\t\tDefines="DLL_EXPORTS"', file=F) # TODO!!! print('\t\t\t/>', file=F) print('\t\t</Configuration>', file=F) diff --git a/include/astra/AstraObjectFactory.h b/include/astra/AstraObjectFactory.h index ba4ec11..1ed4955 100644 --- a/include/astra/AstraObjectFactory.h +++ b/include/astra/AstraObjectFactory.h @@ -110,7 +110,7 @@ template <typename T, typename TypeList> T* CAstraObjectFactory<T, TypeList>::create(const Config& _cfg) { functor_find<T> finder = functor_find<T>(); - finder.tofind = _cfg.self->getAttribute("type"); + finder.tofind = _cfg.self.getAttribute("type"); CreateObject<TypeList>::find(finder); if (finder.res == NULL) return NULL; if (finder.res->initialize(_cfg)) diff --git a/include/astra/Config.h b/include/astra/Config.h index 9893c90..c10a16e 100644 --- a/include/astra/Config.h +++ b/include/astra/Config.h @@ -44,13 +44,14 @@ namespace astra { struct _AstraExport Config { Config(); - Config(XMLNode* _self); + Config(XMLNode _self); ~Config(); void initialize(std::string rootname); - XMLNode* self; - XMLNode* global; + XMLNode self; + + XMLDocument *_doc; }; struct ConfigCheckData { diff --git a/include/astra/CudaProjector2D.h b/include/astra/CudaProjector2D.h index a571851..ecfca41 100644 --- a/include/astra/CudaProjector2D.h +++ b/include/astra/CudaProjector2D.h @@ -121,9 +121,15 @@ public: virtual std::string description() const; + Cuda2DProjectionKernel getProjectionKernel() const { return m_projectionKernel; } + int getVoxelSuperSampling() const { return m_iVoxelSuperSampling; } + int getDetectorSuperSampling() const { return m_iDetectorSuperSampling; } + protected: Cuda2DProjectionKernel m_projectionKernel; + int m_iVoxelSuperSampling; + int m_iDetectorSuperSampling; }; //---------------------------------------------------------------------------------------- diff --git a/include/astra/CudaProjector3D.h b/include/astra/CudaProjector3D.h index a181531..1d570fe 100644 --- a/include/astra/CudaProjector3D.h +++ b/include/astra/CudaProjector3D.h @@ -115,11 +115,14 @@ public: Cuda3DProjectionKernel getProjectionKernel() const { return m_projectionKernel; } + int getVoxelSuperSampling() const { return m_iVoxelSuperSampling; } + int getDetectorSuperSampling() const { return m_iDetectorSuperSampling; } protected: Cuda3DProjectionKernel m_projectionKernel; - + int m_iVoxelSuperSampling; + int m_iDetectorSuperSampling; }; diff --git a/include/astra/Globals.h b/include/astra/Globals.h index 9c8ddfb..4de07d1 100644 --- a/include/astra/Globals.h +++ b/include/astra/Globals.h @@ -61,9 +61,9 @@ $Id$ // macro's #define ASTRA_TOOLBOXVERSION_MAJOR 1 -#define ASTRA_TOOLBOXVERSION_MINOR 5 +#define ASTRA_TOOLBOXVERSION_MINOR 6 #define ASTRA_TOOLBOXVERSION ((ASTRA_TOOLBOXVERSION_MAJOR)*100 + (ASTRA_TOOLBOXVERSION_MINOR)) -#define ASTRA_TOOLBOXVERSION_STRING "1.5" +#define ASTRA_TOOLBOXVERSION_STRING "1.6" #define ASTRA_ASSERT(a) assert(a) diff --git a/include/astra/XMLDocument.h b/include/astra/XMLDocument.h index 869e1a3..eddd908 100644 --- a/include/astra/XMLDocument.h +++ b/include/astra/XMLDocument.h @@ -78,7 +78,7 @@ public: * * @return first XML node of the document */ - XMLNode* getRootNode(); + XMLNode getRootNode(); /** Save an XML DOM tree to an XML file * diff --git a/include/astra/XMLNode.h b/include/astra/XMLNode.h index eceffe1..4d29d5c 100644 --- a/include/astra/XMLNode.h +++ b/include/astra/XMLNode.h @@ -64,71 +64,68 @@ public: /** Deconstructor */ ~XMLNode(); - + + /** Check validity + */ + operator bool() const { return fDOMElement != 0; } /** Get a single child XML node. If there are more, the first one is returned * * @param _sName tagname of the requested child node * @return first child node with the correct tagname, null pointer if it doesn't exist */ - XMLNode* getSingleNode(string _sName); + XMLNode getSingleNode(string _sName) const; /** Get all child XML nodes that have the tagname name * * @param _sName tagname of the requested child nodes * @return list with all child nodes with the correct tagname */ - std::list<XMLNode*> getNodes(string _sName); + std::list<XMLNode> getNodes(string _sName) const; /** Get all child XML nodes * * @return list with all child nodes */ - std::list<XMLNode*> getNodes(); + std::list<XMLNode> getNodes() const; /** Get the name of this node * * @return name of node */ - std::string getName(); + std::string getName() const; /** Get the content of the XML node as a single string. * * @return node content */ - string getContent(); + string getContent() const; /** Get the content of the XML node as a numerical. * * @return node content */ - float32 getContentNumerical(); + float32 getContentNumerical() const; /** Get the content of the XML node as a boolean. * * @return node content */ - bool getContentBool(); + bool getContentBool() const; /** Get the content of the XML node as a vector of strings. * * @return node content */ - vector<string> getContentArray(); - - /** Get the content of the XML node as a c-array of float32 data. - * - * @param _pfData data array, shouldn't be initialized already. - * @param _iSize number of elements stored in _pfData - */ - void getContentNumericalArray(float32*& _pfData, int& _iSize); + vector<string> getContentArray() const; /** Get the content of the XML node as a stl container of float32 data. + * NB: A 2D matrix is returned as a linear list * * @return node content */ - vector<float32> getContentNumericalArray(); - vector<double> getContentNumericalArrayDouble(); + vector<float32> getContentNumericalArray() const; + vector<double> getContentNumericalArrayDouble() const; @@ -137,7 +134,7 @@ public: * @param _sName of the attribute. * @return attribute value, empty string if it doesn't exist. */ - bool hasAttribute(string _sName); + bool hasAttribute(string _sName) const; /** Get the value of an attribute. * @@ -145,7 +142,7 @@ public: * @param _sDefaultValue value to return if the attribute isn't found * @return attribute value, _sDefaultValue if it doesn't exist. */ - string getAttribute(string _sName, string _sDefaultValue = ""); + string getAttribute(string _sName, string _sDefaultValue = "") const; /** Get the value of a numerical attribute. * @@ -153,8 +150,8 @@ public: * @param _fDefaultValue value to return if the attribute isn't found * @return attribute value, _fDefaultValue if it doesn't exist. */ - float32 getAttributeNumerical(string _sName, float32 _fDefaultValue = 0); - double getAttributeNumericalDouble(string _sName, double _fDefaultValue = 0); + float32 getAttributeNumerical(string _sName, float32 _fDefaultValue = 0) const; + double getAttributeNumericalDouble(string _sName, double _fDefaultValue = 0) const; /** Get the value of a boolean attribute. * @@ -162,7 +159,7 @@ public: * @param _bDefaultValue value to return if the attribute isn't found * @return attribute value, _bDefaultValue if it doesn't exist. */ - bool getAttributeBool(string _sName, bool _bDefaultValue = false); + bool getAttributeBool(string _sName, bool _bDefaultValue = false) const; @@ -172,7 +169,7 @@ public: * @param _sKey option key * @return true if option does exist */ - bool hasOption(string _sKey); + bool hasOption(string _sKey) const; /** Get the value of an option within this XML Node * @@ -180,7 +177,7 @@ public: * @param _sDefaultValue value to return if key isn't found * @return option value, _sDefaultValue if the option doesn't exist */ - string getOption(string _sKey, string _sDefaultValue = ""); + string getOption(string _sKey, string _sDefaultValue = "") const; /** Get the value of an option within this XML Node * @@ -188,7 +185,7 @@ public: * @param _fDefaultValue value to return if key isn't found * @return option value, _fDefaultValue if the option doesn't exist */ - float32 getOptionNumerical(string _sKey, float32 _fDefaultValue = 0); + float32 getOptionNumerical(string _sKey, float32 _fDefaultValue = 0) const; /** Get the value of an option within this XML Node * @@ -196,14 +193,14 @@ public: * @param _bDefaultValue value to return if key isn't found * @return option value, _bDefaultValue if the option doesn't exist */ - bool getOptionBool(string _sKey, bool _bDefaultValue = false); + bool getOptionBool(string _sKey, bool _bDefaultValue = false) const; /** Get the value of an option within this XML Node * * @param _sKey option key * @return numerical array */ - vector<float32> getOptionNumericalArray(string _sKey); + vector<float32> getOptionNumericalArray(string _sKey) const; @@ -214,7 +211,7 @@ public: * @param _sNodeName the name of the new childnode * @return new child node */ - XMLNode* addChildNode(string _sNodeName); + XMLNode addChildNode(string _sNodeName); /** Create a new XML node as a child to this one, also add some content: * <...><_sNodeName>_sValue</_sNodeName></...> @@ -223,7 +220,7 @@ public: * @param _sValue some node content * @return new child node */ - XMLNode* addChildNode(string _sNodeName, string _sValue); + XMLNode addChildNode(string _sNodeName, string _sValue); /** Create a new XML node as a child to this one, also add some numerical content: * <...><_sNodeName>_sValue</_sNodeName></...> @@ -232,7 +229,7 @@ public: * @param _fValue some node content * @return new child node */ - XMLNode* addChildNode(string _sNodeName, float32 _fValue); + XMLNode addChildNode(string _sNodeName, float32 _fValue); /** Create a new XML node as a child to this one, also add a list of numerical content: * <...><_sNodeName>_sValue</_sNodeName></...> @@ -242,7 +239,7 @@ public: * @param _iSize number of elements in _pfList * @return new child node */ - XMLNode* addChildNode(string _sNodeName, float32* _pfList, int _iSize); + XMLNode addChildNode(string _sNodeName, float32* _pfList, int _iSize); /** Add some text to the node: <...>_sText</...> * @@ -256,13 +253,38 @@ public: */ void setContent(float32 _fValue); - /** Add a list of numerical data to the node: <...>_sText</...> + /** Add a list of numerical data to the node * * @param _pfList data * @param _iSize number of elements in the list */ void setContent(float32* _pfList, int _iSize); + /** Add a list of numerical data to the node + * + * @param _pfList data + * @param _iSize number of elements in the list + */ + void setContent(double* _pfList, int _iSize); + + /** Add a (2D) matrix of numerical data to the node + * + * @param _pfMatrix data + * @param _iWidth width of the matrix + * @param _iHeight height of the matrix + * @param transposed true is C order, false is Fortran order + */ + void setContent(float32* _pfMatrix, int _iWidth, int _iHeight, bool transposed); + + /** Add a (2D) matrix of numerical data to the node + * + * @param _pfMatrix data + * @param _iWidth width of the matrix + * @param _iHeight height of the matrix + * @param transposed true is C order, false is Fortran order + */ + void setContent(double* _pfMatrix, int _iWidth, int _iHeight, bool transposed); + /** Add an attribute to this node: <... _sName="_sValue"> * * @param _sName name of the attribute @@ -294,11 +316,11 @@ public: /** Print to String */ - std::string toString(); + std::string toString() const; /** Print the node */ - void print(); + void print() const; protected: diff --git a/matlab/mex/astra_mex_algorithm_c.cpp b/matlab/mex/astra_mex_algorithm_c.cpp index e4afa63..ec7aa72 100644 --- a/matlab/mex/astra_mex_algorithm_c.cpp +++ b/matlab/mex/astra_mex_algorithm_c.cpp @@ -81,7 +81,7 @@ void astra_mex_algorithm_create(int nlhs, mxArray* plhs[], int nrhs, const mxArr // turn MATLAB struct to an XML-based Config object Config* cfg = structToConfig("Algorithm", prhs[1]); - CAlgorithm* pAlg = CAlgorithmFactory::getSingleton().create(cfg->self->getAttribute("type")); + CAlgorithm* pAlg = CAlgorithmFactory::getSingleton().create(cfg->self.getAttribute("type")); if (!pAlg) { delete cfg; mexErrMsgTxt("Unknown algorithm. \n"); diff --git a/matlab/mex/astra_mex_c.cpp b/matlab/mex/astra_mex_c.cpp index 4a331f5..a9b9654 100644 --- a/matlab/mex/astra_mex_c.cpp +++ b/matlab/mex/astra_mex_c.cpp @@ -36,9 +36,9 @@ $Id$ #include "mexInitFunctions.h" #include "astra/Globals.h" - +#ifdef ASTRA_CUDA #include "../cuda/2d/darthelper.h" - +#endif using namespace std; using namespace astra; diff --git a/matlab/mex/astra_mex_data2d_c.cpp b/matlab/mex/astra_mex_data2d_c.cpp index 9576896..909d229 100644 --- a/matlab/mex/astra_mex_data2d_c.cpp +++ b/matlab/mex/astra_mex_data2d_c.cpp @@ -149,7 +149,7 @@ void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra Config* cfg = structToConfig("ProjectionGeometry", prhs[2]); // FIXME: Change how the base class is created. (This is duplicated // in 'change_geometry' and Projector2D.cpp.) - std::string type = cfg->self->getAttribute("type"); + std::string type = cfg->self.getAttribute("type"); CProjectionGeometry2D* pGeometry; if (type == "sparse_matrix") { pGeometry = new CSparseMatrixProjectionGeometry2D(); @@ -438,7 +438,7 @@ void astra_mex_data2d_change_geometry(int nlhs, mxArray* plhs[], int nrhs, const Config* cfg = structToConfig("ProjectionGeometry2D", prhs[2]); // FIXME: Change how the base class is created. (This is duplicated // in 'create' and Projector2D.cpp.) - std::string type = cfg->self->getAttribute("type"); + std::string type = cfg->self.getAttribute("type"); CProjectionGeometry2D* pGeometry; if (type == "sparse_matrix") { pGeometry = new CSparseMatrixProjectionGeometry2D(); diff --git a/matlab/mex/astra_mex_data3d_c.cpp b/matlab/mex/astra_mex_data3d_c.cpp index 6096adc..fe4ce37 100644 --- a/matlab/mex/astra_mex_data3d_c.cpp +++ b/matlab/mex/astra_mex_data3d_c.cpp @@ -346,7 +346,7 @@ void astra_mex_data3d_change_geometry(int nlhs, mxArray* plhs[], int nrhs, const astra::Config* cfg = structToConfig("ProjectionGeometry3D", geometry); // FIXME: Change how the base class is created. (This is duplicated // in Projector3D.cpp.) - std::string type = cfg->self->getAttribute("type"); + std::string type = cfg->self.getAttribute("type"); astra::CProjectionGeometry3D* pGeometry = 0; if (type == "parallel3d") { pGeometry = new astra::CParallelProjectionGeometry3D(); diff --git a/matlab/mex/astra_mex_log_c.cpp b/matlab/mex/astra_mex_log_c.cpp index ea4621e..905612c 100644 --- a/matlab/mex/astra_mex_log_c.cpp +++ b/matlab/mex/astra_mex_log_c.cpp @@ -55,7 +55,7 @@ void astra_mex_log_debug(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prh string filename = mexToString(prhs[1]); int linenumber = (int)mxGetScalar(prhs[2]); string message = mexToString(prhs[3]); - astra::CLogger::debug(filename.c_str(),linenumber,message.c_str()); + astra::CLogger::debug(filename.c_str(),linenumber,"%s",message.c_str()); } //----------------------------------------------------------------------------------------- @@ -75,7 +75,7 @@ void astra_mex_log_info(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs string filename = mexToString(prhs[1]); int linenumber = (int)mxGetScalar(prhs[2]); string message = mexToString(prhs[3]); - astra::CLogger::info(filename.c_str(),linenumber,message.c_str()); + astra::CLogger::info(filename.c_str(),linenumber,"%s",message.c_str()); } //----------------------------------------------------------------------------------------- @@ -95,7 +95,7 @@ void astra_mex_log_warn(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs string filename = mexToString(prhs[1]); int linenumber = (int)mxGetScalar(prhs[2]); string message = mexToString(prhs[3]); - astra::CLogger::warn(filename.c_str(),linenumber,message.c_str()); + astra::CLogger::warn(filename.c_str(),linenumber,"%s",message.c_str()); } //----------------------------------------------------------------------------------------- @@ -115,7 +115,7 @@ void astra_mex_log_error(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prh string filename = mexToString(prhs[1]); int linenumber = (int)mxGetScalar(prhs[2]); string message = mexToString(prhs[3]); - astra::CLogger::error(filename.c_str(),linenumber,message.c_str()); + astra::CLogger::error(filename.c_str(),linenumber,"%s",message.c_str()); } //----------------------------------------------------------------------------------------- diff --git a/matlab/mex/astra_mex_projector3d_c.cpp b/matlab/mex/astra_mex_projector3d_c.cpp index c3b547f..e25802c 100644 --- a/matlab/mex/astra_mex_projector3d_c.cpp +++ b/matlab/mex/astra_mex_projector3d_c.cpp @@ -137,7 +137,9 @@ void astra_mex_projector3d_get_projection_geometry(int nlhs, mxArray* plhs[], in // step3: get projection_geometry and turn it into a MATLAB struct if (1 <= nlhs) { - plhs[0] = configToStruct(pProjector->getProjectionGeometry()->getConfiguration()); + Config *cfg = pProjector->getProjectionGeometry()->getConfiguration(); + plhs[0] = configToStruct(cfg); + delete cfg; } } @@ -163,7 +165,9 @@ void astra_mex_projector3d_get_volume_geometry(int nlhs, mxArray* plhs[], int nr // step3: get projection_geometry and turn it into a MATLAB struct if (1 <= nlhs) { - plhs[0] = configToStruct(pProjector->getVolumeGeometry()->getConfiguration()); + Config *cfg = pProjector->getVolumeGeometry()->getConfiguration(); + plhs[0] = configToStruct(cfg); + delete cfg; } } diff --git a/matlab/mex/astra_mex_projector_c.cpp b/matlab/mex/astra_mex_projector_c.cpp index 204ba8e..bf701af 100644 --- a/matlab/mex/astra_mex_projector_c.cpp +++ b/matlab/mex/astra_mex_projector_c.cpp @@ -160,7 +160,9 @@ void astra_mex_projector_projection_geometry(int nlhs, mxArray* plhs[], int nrhs // step3: get projection_geometry and turn it into a MATLAB struct if (1 <= nlhs) { - plhs[0] = configToStruct(pProjector->getProjectionGeometry()->getConfiguration()); + Config *cfg = pProjector->getProjectionGeometry()->getConfiguration(); + plhs[0] = configToStruct(cfg); + delete cfg; } } @@ -189,8 +191,9 @@ void astra_mex_projector_volume_geometry(int nlhs, mxArray* plhs[], int nrhs, co // step3: get projection_geometry and turn it into a MATLAB struct if (1 <= nlhs) { - plhs[0] = configToStruct(pProjector->getVolumeGeometry()->getConfiguration()); - + Config *cfg = pProjector->getVolumeGeometry()->getConfiguration(); + plhs[0] = configToStruct(cfg); + delete cfg; } } diff --git a/matlab/mex/mexDataManagerHelpFunctions.cpp b/matlab/mex/mexDataManagerHelpFunctions.cpp index d482428..1794abb 100644 --- a/matlab/mex/mexDataManagerHelpFunctions.cpp +++ b/matlab/mex/mexDataManagerHelpFunctions.cpp @@ -285,7 +285,7 @@ allocateDataObject(const std::string & sDataType, astra::Config* cfg = structToConfig("ProjectionGeometry3D", geometry); // FIXME: Change how the base class is created. (This is duplicated // in Projector3D.cpp.) - std::string type = cfg->self->getAttribute("type"); + std::string type = cfg->self.getAttribute("type"); astra::CProjectionGeometry3D* pGeometry = 0; if (type == "parallel3d") { pGeometry = new astra::CParallelProjectionGeometry3D(); diff --git a/matlab/mex/mexHelpFunctions.cpp b/matlab/mex/mexHelpFunctions.cpp index c0ac711..58e84d2 100644 --- a/matlab/mex/mexHelpFunctions.cpp +++ b/matlab/mex/mexHelpFunctions.cpp @@ -185,7 +185,7 @@ Config* structToConfig(string rootname, const mxArray* pStruct) } //----------------------------------------------------------------------------------------- -bool structToXMLNode(XMLNode* node, const mxArray* pStruct) +bool structToXMLNode(XMLNode node, const mxArray* pStruct) { // loop all fields int nfields = mxGetNumberOfFields(pStruct); @@ -199,16 +199,16 @@ bool structToXMLNode(XMLNode* node, const mxArray* pStruct) if (mxIsChar(pField)) { string sValue = mexToString(pField); if (sFieldName == "type") { - node->addAttribute("type", sValue); + node.addAttribute("type", sValue); } else { - delete node->addChildNode(sFieldName, sValue); + node.addChildNode(sFieldName, sValue); } } // scalar else if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) == 1) { string sValue = mexToString(pField); - delete node->addChildNode(sFieldName, sValue); + node.addChildNode(sFieldName, sValue); } // numerical array @@ -217,20 +217,9 @@ bool structToXMLNode(XMLNode* node, const mxArray* pStruct) mexErrMsgTxt("Numeric input must be double."); return false; } - XMLNode* listbase = node->addChildNode(sFieldName); - listbase->addAttribute("listsize", mxGetM(pField)*mxGetN(pField)); + XMLNode listbase = node.addChildNode(sFieldName); double* pdValues = mxGetPr(pField); - int index = 0; - for (unsigned int row = 0; row < mxGetM(pField); row++) { - for (unsigned int col = 0; col < mxGetN(pField); col++) { - XMLNode* item = listbase->addChildNode("ListItem"); - item->addAttribute("index", index); - item->addAttribute("value", pdValues[col*mxGetM(pField)+row]); - index++; - delete item; - } - } - delete listbase; + listbase.setContent(pdValues, mxGetN(pField), mxGetM(pField), true); } // not castable to a single string @@ -240,9 +229,8 @@ bool structToXMLNode(XMLNode* node, const mxArray* pStruct) if (!ret) return false; } else { - XMLNode* newNode = node->addChildNode(sFieldName); + XMLNode newNode = node.addChildNode(sFieldName); bool ret = structToXMLNode(newNode, pField); - delete newNode; if (!ret) return false; } @@ -254,7 +242,7 @@ bool structToXMLNode(XMLNode* node, const mxArray* pStruct) } //----------------------------------------------------------------------------------------- // Options struct to xml node -bool optionsToXMLNode(XMLNode* node, const mxArray* pOptionStruct) +bool optionsToXMLNode(XMLNode node, const mxArray* pOptionStruct) { // loop all fields int nfields = mxGetNumberOfFields(pOptionStruct); @@ -262,7 +250,7 @@ bool optionsToXMLNode(XMLNode* node, const mxArray* pOptionStruct) std::string sFieldName = std::string(mxGetFieldNameByNumber(pOptionStruct, i)); const mxArray* pField = mxGetFieldByNumber(pOptionStruct, 0, i); - if (node->hasOption(sFieldName)) { + if (node.hasOption(sFieldName)) { mexErrMsgTxt("Duplicate option"); return false; } @@ -270,7 +258,7 @@ bool optionsToXMLNode(XMLNode* node, const mxArray* pOptionStruct) // string or scalar if (mxIsChar(pField) || mexIsScalar(pField)) { string sValue = mexToString(pField); - node->addOption(sFieldName, sValue); + node.addOption(sFieldName, sValue); } // numerical array else if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) > 1) { @@ -279,21 +267,10 @@ bool optionsToXMLNode(XMLNode* node, const mxArray* pOptionStruct) return false; } - XMLNode* listbase = node->addChildNode("Option"); - listbase->addAttribute("key", sFieldName); - listbase->addAttribute("listsize", mxGetM(pField)*mxGetN(pField)); + XMLNode listbase = node.addChildNode("Option"); + listbase.addAttribute("key", sFieldName); double* pdValues = mxGetPr(pField); - int index = 0; - for (unsigned int row = 0; row < mxGetM(pField); row++) { - for (unsigned int col = 0; col < mxGetN(pField); col++) { - XMLNode* item = listbase->addChildNode("ListItem"); - item->addAttribute("index", index); - item->addAttribute("value", pdValues[col*mxGetM(pField)+row]); - index++; - delete item; - } - } - delete listbase; + listbase.setContent(pdValues, mxGetN(pField), mxGetM(pField), true); } else { mexErrMsgTxt("Unsupported option type"); return false; @@ -343,30 +320,33 @@ mxArray* configToStruct(astra::Config* cfg) } //----------------------------------------------------------------------------------------- -mxArray* XMLNodeToStruct(astra::XMLNode* node) +mxArray* XMLNodeToStruct(astra::XMLNode node) { std::map<std::string, mxArray*> mList; std::map<std::string, mxArray*> mOptions; // type_attribute - if (node->hasAttribute("type")) { - mList["type"] = mxCreateString(node->getAttribute("type").c_str()); + if (node.hasAttribute("type")) { + mList["type"] = mxCreateString(node.getAttribute("type").c_str()); } - list<XMLNode*> nodes = node->getNodes(); - for (list<XMLNode*>::iterator it = nodes.begin(); it != nodes.end(); it++) { - XMLNode* subnode = (*it); + list<XMLNode> nodes = node.getNodes(); + for (list<XMLNode>::iterator it = nodes.begin(); it != nodes.end(); it++) { + XMLNode subnode = (*it); // option - if (subnode->getName() == "Option") { - mOptions[subnode->getAttribute("key")] = stringToMxArray(subnode->getAttribute("value")); + if (subnode.getName() == "Option") { + if(subnode.hasAttribute("value")){ + mOptions[subnode.getAttribute("key")] = stringToMxArray(subnode.getAttribute("value")); + }else{ + mOptions[subnode.getAttribute("key")] = stringToMxArray(subnode.getContent()); + } } // regular content else { - mList[subnode->getName()] = stringToMxArray(subnode->getContent()); + mList[subnode.getName()] = stringToMxArray(subnode.getContent()); } - delete subnode; } if (mOptions.size() > 0) mList["options"] = buildStruct(mOptions); diff --git a/matlab/mex/mexHelpFunctions.h b/matlab/mex/mexHelpFunctions.h index f9ffcf2..3ac5bd8 100644 --- a/matlab/mex/mexHelpFunctions.h +++ b/matlab/mex/mexHelpFunctions.h @@ -58,13 +58,13 @@ mxArray* anyToMxArray(boost::any _any); // turn a MATLAB struct into a Config object astra::Config* structToConfig(string rootname, const mxArray* pStruct); -bool structToXMLNode(astra::XMLNode* node, const mxArray* pStruct); -bool optionsToXMLNode(astra::XMLNode* node, const mxArray* pOptionStruct); +bool structToXMLNode(astra::XMLNode node, const mxArray* pStruct); +bool optionsToXMLNode(astra::XMLNode node, const mxArray* pOptionStruct); std::map<std::string, mxArray*> parseStruct(const mxArray* pInput); // turn a Config object into a MATLAB struct mxArray* configToStruct(astra::Config* cfg); -mxArray* XMLNodeToStruct(astra::XMLNode* xml); +mxArray* XMLNodeToStruct(astra::XMLNode xml); mxArray* stringToMxArray(std::string input); mxArray* buildStruct(std::map<std::string, mxArray*> mInput); diff --git a/matlab/mex/mexInitFunctions.cpp b/matlab/mex/mexInitFunctions.cpp index d8a50d7..89a31a1 100644 --- a/matlab/mex/mexInitFunctions.cpp +++ b/matlab/mex/mexInitFunctions.cpp @@ -8,7 +8,7 @@ bool mexIsInitialized=false; * */ void logCallBack(const char *msg, size_t len){ - mexPrintf(msg); + mexPrintf("%s",msg); } /** diff --git a/matlab/tools/astra_create_fbp_reconstruction.m b/matlab/tools/astra_create_fbp_reconstruction.m index 5540f27..a2561b7 100644 --- a/matlab/tools/astra_create_fbp_reconstruction.m +++ b/matlab/tools/astra_create_fbp_reconstruction.m @@ -19,6 +19,7 @@ cfg.ProjectorId = proj_id; cfg.Options.GPUindex = 0; alg_id = astra_mex_algorithm('create', cfg); astra_mex_algorithm('run', alg_id); +astra_mex_algorithm('delete', alg_id); if numel(sinogram) ~= 1 astra_mex_data2d('delete', sinogram_id); diff --git a/matlab/tools/astra_create_reconstruction_cuda.m b/matlab/tools/astra_create_reconstruction_cuda.m index 7d9e1dd..7d0421c 100644 --- a/matlab/tools/astra_create_reconstruction_cuda.m +++ b/matlab/tools/astra_create_reconstruction_cuda.m @@ -45,7 +45,7 @@ if strcmp(rec_type,'') end % configure -cfg = astra_struct('SIRT_CUDA'); +cfg = astra_struct(rec_type); cfg.ProjectionGeometry = proj_geom; cfg.ReconstructionGeometry = vol_geom; cfg.ProjectionDataId = sinogram_id; diff --git a/matlab/tools/opTomo.m b/matlab/tools/opTomo.m new file mode 100644 index 0000000..14128d2 --- /dev/null +++ b/matlab/tools/opTomo.m @@ -0,0 +1,280 @@ +%OPTOMO Wrapper for ASTRA tomography projector +% +% OP = OPTOMO(TYPE, PROJ_GEOM, VOL_GEOM) generates a Spot operator OP for +% the ASTRA forward and backprojection operations. The string TYPE +% determines the model used for the projections. Possible choices are: +% TYPE: * using the CPU +% 'line' - use a line kernel +% 'linear' - use a Joseph kernel +% 'strip' - use the strip kernel +% * using the GPU +% 'cuda' - use a Joseph kernel, on the GPU, currently using +% 'cuda' is the only option in 3D. +% The PROJ_GEOM and VOL_GEOM structures are projection and volume +% geometries as used in the ASTRA toolbox. +% +% OP = OPTOMO(TYPE, PROJ_GEOM, VOL_GEOM, GPU_INDEX) also specify the +% index of the GPU that should be used, if multiple GPUs are present in +% the host system. By default GPU_INDEX is 0. +% +% Note: this code depends on the Matlab toolbox +% "Spot - A Linear-Operator Toolbox" which can be downloaded from +% http://www.cs.ubc.ca/labs/scl/spot/ +%-------------------------------------------------------------------------- +% This file is part of the ASTRA Toolbox +% +% Copyright: 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Author: Folkert Bleichrodt +% Contact: F.Bleichrodt@cwi.nl +% Website: http://sf.net/projects/astra-toolbox +%-------------------------------------------------------------------------- +% $Id$ + +classdef opTomo < opSpot + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + % Properties + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + properties ( Access = private ) + % multiplication function + funHandle + % ASTRA identifiers + sino_id + vol_id + fp_alg_id + bp_alg_id + % ASTRA IDs handle + astra_handle + % geometries + proj_geom; + vol_geom; + end % properties + + properties ( SetAccess = private, GetAccess = public ) + proj_size + vol_size + end % properties + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + % Methods - public + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + methods + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + % opTomo - constructor + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + function op = opTomo(type, proj_geom, vol_geom, gpu_index) + + if nargin < 4 || isempty(gpu_index), gpu_index = 0; end + + proj_size = astra_geom_size(proj_geom); + vol_size = astra_geom_size(vol_geom); + + % construct operator + op = op@opSpot('opTomo', prod(proj_size), prod(vol_size)); + + % determine the dimension + is2D = ~isfield(vol_geom, 'GridSliceCount'); + gpuEnabled = strcmpi(type, 'cuda'); + + if is2D + % create a projector + proj_id = astra_create_projector(type, proj_geom, vol_geom); + + % create a function handle + op.funHandle = @opTomo_intrnl2D; + + % Initialize ASTRA data objects. + % projection data + sino_id = astra_mex_data2d('create', '-sino', proj_geom, 0); + % image data + vol_id = astra_mex_data2d('create', '-vol', vol_geom, 0); + + % Setup forward and back projection algorithms. + if gpuEnabled + fp_alg = 'FP_CUDA'; + bp_alg = 'BP_CUDA'; + proj_id = []; + else + fp_alg = 'FP'; + bp_alg = 'BP'; + proj_id = astra_create_projector(type, proj_geom, vol_geom); + end + + % configuration for ASTRA fp algorithm + cfg_fp = astra_struct(fp_alg); + cfg_fp.ProjectorId = proj_id; + cfg_fp.ProjectionDataId = sino_id; + cfg_fp.VolumeDataId = vol_id; + + % configuration for ASTRA bp algorithm + cfg_bp = astra_struct(bp_alg); + cfg_bp.ProjectionDataId = sino_id; + cfg_bp.ProjectorId = proj_id; + cfg_bp.ReconstructionDataId = vol_id; + + % set GPU index + if gpuEnabled + cfg_fp.option.GPUindex = gpu_index; + cfg_bp.option.GPUindex = gpu_index; + end + + fp_alg_id = astra_mex_algorithm('create', cfg_fp); + bp_alg_id = astra_mex_algorithm('create', cfg_bp); + + % Create handle to ASTRA objects, so they will be deleted + % if opTomo is deleted. + op.astra_handle = opTomo_helper_handle([sino_id, ... + vol_id, proj_id, fp_alg_id, bp_alg_id]); + + op.fp_alg_id = fp_alg_id; + op.bp_alg_id = bp_alg_id; + op.sino_id = sino_id; + op.vol_id = vol_id; + else + % 3D + % only gpu/cuda code for 3D + if ~gpuEnabled + error(['Only type ' 39 'cuda' 39 ' is supported ' ... + 'for 3D geometries.']) + end + + % create a function handle + op.funHandle = @opTomo_intrnl3D; + end + + + % pass object properties + op.proj_size = proj_size; + op.vol_size = vol_size; + op.proj_geom = proj_geom; + op.vol_geom = vol_geom; + op.cflag = false; + op.sweepflag = false; + + end % opTomo - constructor + + end % methods - public + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + % Methods - protected + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + methods( Access = protected ) + + % multiplication + function y = multiply(op,x,mode) + + % ASTRA cannot handle sparse vectors + if issparse(x) + x = full(x); + end + + % convert input to single + if isa(x, 'single') == false + x = single(x); + end + + % the multiplication + y = op.funHandle(op, x, mode); + + % make sure output is column vector + y = y(:); + + end % multiply + + end % methods - protected + + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + % Methods - private + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + methods( Access = private ) + + % 2D projection code + function y = opTomo_intrnl2D(op,x,mode) + + if mode == 1 + % X is passed as a vector, reshape it into an image. + x = reshape(x, op.vol_size); + + % Matlab data copied to ASTRA data + astra_mex_data2d('store', op.vol_id, x); + + % forward projection + astra_mex_algorithm('iterate', op.fp_alg_id); + + % retrieve Matlab array + y = astra_mex_data2d('get_single', op.sino_id); + else + % X is passed as a vector, reshape it into a sinogram. + x = reshape(x, op.proj_size); + + % Matlab data copied to ASTRA data + astra_mex_data2d('store', op.sino_id, x); + + % backprojection + astra_mex_algorithm('iterate', op.bp_alg_id); + + % retrieve Matlab array + y = astra_mex_data2d('get_single', op.vol_id); + end + end % opTomo_intrnl2D + + + % 3D projection code + function y = opTomo_intrnl3D(op,x,mode) + + if mode == 1 + % X is passed as a vector, reshape it into an image + x = reshape(x, op.vol_size); + + % initialize output + y = zeros(op.proj_size, 'single'); + + % link matlab array to ASTRA + vol_id = astra_mex_data3d_c('link', '-vol', op.vol_geom, x, 0); + sino_id = astra_mex_data3d_c('link', '-sino', op.proj_geom, y, 1); + + % initialize fp algorithm + cfg = astra_struct('FP3D_CUDA'); + cfg.ProjectionDataId = sino_id; + cfg.VolumeDataId = vol_id; + + alg_id = astra_mex_algorithm('create', cfg); + + % forward projection + astra_mex_algorithm('iterate', alg_id); + + % cleanup + astra_mex_data3d('delete', vol_id); + astra_mex_data3d('delete', sino_id); + else + % X is passed as a vector, reshape it into projection data + x = reshape(x, op.proj_size); + + % initialize output + y = zeros(op.vol_size,'single'); + + % link matlab array to ASTRA + vol_id = astra_mex_data3d_c('link', '-vol', op.vol_geom, y, 1); + sino_id = astra_mex_data3d_c('link', '-sino', op.proj_geom, x, 0); + + % initialize bp algorithm + cfg = astra_struct('BP3D_CUDA'); + cfg.ProjectionDataId = sino_id; + cfg.ReconstructionDataId = vol_id; + + alg_id = astra_mex_algorithm('create', cfg); + + % backprojection + astra_mex_algorithm('iterate', alg_id); + + % cleanup + astra_mex_data3d('delete', vol_id); + astra_mex_data3d('delete', sino_id); + end + end % opTomo_intrnl3D + + end % methods - private + +end % classdef diff --git a/matlab/tools/opTomo_helper_handle.m b/matlab/tools/opTomo_helper_handle.m new file mode 100644 index 0000000..d9be51f --- /dev/null +++ b/matlab/tools/opTomo_helper_handle.m @@ -0,0 +1,29 @@ +classdef opTomo_helper_handle < handle + %ASTRA.OPTOMO_HELPER_HANDLE Handle class around an astra identifier + % Automatically deletes the data when object is deleted. + % Multiple id's can be passed as an array as input to + % the constructor. + + properties + id + end + + methods + function obj = opTomo_helper_handle(id) + obj.id = id; + end + function delete(obj) + for i = 1:numel(obj.id) + % delete any kind of object + astra_mex_data2d('delete', obj.id(i)); + astra_mex_data3d('delete', obj.id(i)); + astra_mex_algorithm('delete', obj.id(i)); + astra_mex_matrix('delete', obj.id(i)); + astra_mex_projector('delete', obj.id(i)); + astra_mex_projector3d('delete', obj.id(i)) + end + end + end + +end + diff --git a/python/astra/ASTRAProjector.py b/python/astra/ASTRAProjector.py deleted file mode 100644 index f282618..0000000 --- a/python/astra/ASTRAProjector.py +++ /dev/null @@ -1,135 +0,0 @@ -#----------------------------------------------------------------------- -#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 - - -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` - """ - - def __init__(self, proj_geom, vol_geom, proj_type): - 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.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, 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, 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/PyIncludes.pxd b/python/astra/PyIncludes.pxd index 1d8285b..35dea5f 100644 --- a/python/astra/PyIncludes.pxd +++ b/python/astra/PyIncludes.pxd @@ -43,7 +43,7 @@ cdef extern from "astra/Config.h" namespace "astra": cdef cppclass Config: Config() void initialize(string rootname) - XMLNode *self + XMLNode self cdef extern from "astra/VolumeGeometry2D.h" namespace "astra": cdef cppclass CVolumeGeometry2D: @@ -143,7 +143,7 @@ cdef extern from "astra/Float32ProjectionData2D.h" namespace "astra": cdef extern from "astra/Algorithm.h" namespace "astra": cdef cppclass CAlgorithm: bool initialize(Config) - void run(int) + void run(int) nogil bool isInitialized() cdef extern from "astra/ReconstructionAlgorithm2D.h" namespace "astra": diff --git a/python/astra/PyXMLDocument.pxd b/python/astra/PyXMLDocument.pxd index 69781f1..033b8ef 100644 --- a/python/astra/PyXMLDocument.pxd +++ b/python/astra/PyXMLDocument.pxd @@ -44,22 +44,24 @@ cdef extern from "astra/Globals.h" namespace "astra": cdef extern from "astra/XMLNode.h" namespace "astra": cdef cppclass XMLNode: string getName() - XMLNode *addChildNode(string name) - XMLNode *addChildNode(string, string) + 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() + list[XMLNode] getNodes() vector[float32] getContentNumericalArray() + void setContent(double*, int, int, bool) + void setContent(double*, int) string getContent() bool hasAttribute(string) cdef extern from "astra/XMLDocument.h" namespace "astra": cdef cppclass XMLDocument: void saveToFile(string sFilename) - XMLNode *getRootNode() + 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 index 063dc16..6c15d30 100644 --- a/python/astra/__init__.py +++ b/python/astra/__init__.py @@ -27,7 +27,6 @@ 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 @@ -36,6 +35,7 @@ from . import projector from . import projector3d from . import matrix from . import log +from .optomo import OpTomo import os try: diff --git a/python/astra/algorithm_c.pyx b/python/astra/algorithm_c.pyx index 966d3d7..3231c1f 100644 --- a/python/astra/algorithm_c.pyx +++ b/python/astra/algorithm_c.pyx @@ -73,7 +73,9 @@ cdef CAlgorithm * getAlg(i) except NULL: def run(i, iterations=0): cdef CAlgorithm * alg = getAlg(i) - alg.run(iterations) + cdef int its = iterations + with nogil: + alg.run(its) def get_res_norm(i): diff --git a/python/astra/data2d_c.pyx b/python/astra/data2d_c.pyx index ac54898..4919bf2 100644 --- a/python/astra/data2d_c.pyx +++ b/python/astra/data2d_c.pyx @@ -47,6 +47,12 @@ from .PyIncludes cimport * cimport utils from .utils import wrap_from_bytes +from .pythonutils import geom_size + +import operator + +from six.moves import reduce + cdef CData2DManager * man2d = <CData2DManager * >PyData2DManager.getSingletonPtr() cdef extern from "CFloat32CustomPython.h": @@ -71,6 +77,10 @@ def create(datatype, geometry, data=None, link=False): cdef CProjectionGeometry2D * ppGeometry cdef CFloat32Data2D * pDataObject2D cdef CFloat32CustomMemory * pCustom + + if link and data.shape!=geom_size(geometry): + raise Exception("The dimensions of the data do not match those specified in the geometry.") + if datatype == '-vol': cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry) pGeometry = new CVolumeGeometry2D() diff --git a/python/astra/data3d_c.pyx b/python/astra/data3d_c.pyx index 84472c1..3b27ab7 100644 --- a/python/astra/data3d_c.pyx +++ b/python/astra/data3d_c.pyx @@ -45,6 +45,13 @@ from .PyXMLDocument cimport XMLDocument cimport utils from .utils import wrap_from_bytes +from .pythonutils import geom_size + +import operator + +from six.moves import reduce + + cdef CData3DManager * man3d = <CData3DManager * >PyData3DManager.getSingletonPtr() cdef extern from *: @@ -61,6 +68,10 @@ def create(datatype,geometry,data=None, link=False): cdef CFloat32Data3DMemory * pDataObject3D cdef CConeProjectionGeometry3D* pppGeometry cdef CFloat32CustomMemory * pCustom + + if link and data.shape!=geom_size(geometry): + raise Exception("The dimensions of the data do not match those specified in the geometry.") + if datatype == '-vol': cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry) pGeometry = new CVolumeGeometry3D() diff --git a/python/astra/functions.py b/python/astra/functions.py index 4025468..e38b5bc 100644 --- a/python/astra/functions.py +++ b/python/astra/functions.py @@ -32,12 +32,17 @@ from . import creators as ac import numpy as np -from six.moves import range +try: + from six.moves import range +except ImportError: + # six 1.3.0 + from six.moves import xrange as range from . import data2d from . import data3d from . import projector from . import algorithm +from . import pythonutils @@ -158,29 +163,7 @@ def geom_size(geom, dim=None): :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 + return pythonutils.geom_size(geom,dim) def geom_2vec(proj_geom): diff --git a/python/astra/log_c.pyx b/python/astra/log_c.pyx index 969cc06..55c63e6 100644 --- a/python/astra/log_c.pyx +++ b/python/astra/log_c.pyx @@ -52,16 +52,20 @@ cdef extern from "astra/Logging.h" namespace "astra::CLogger": void setFormatScreen(const char *fmt) def log_debug(sfile, sline, message): - debug(six.b(sfile),sline,six.b(message)) + cstr = list(map(six.b,(sfile,message))) + debug(cstr[0],sline,"%s",<char*>cstr[1]) def log_info(sfile, sline, message): - info(six.b(sfile),sline,six.b(message)) + cstr = list(map(six.b,(sfile,message))) + info(cstr[0],sline,"%s",<char*>cstr[1]) def log_warn(sfile, sline, message): - warn(six.b(sfile),sline,six.b(message)) + cstr = list(map(six.b,(sfile,message))) + warn(cstr[0],sline,"%s",<char*>cstr[1]) def log_error(sfile, sline, message): - error(six.b(sfile),sline,six.b(message)) + cstr = list(map(six.b,(sfile,message))) + error(cstr[0],sline,"%s",<char*>cstr[1]) def log_enable(): enable() @@ -82,10 +86,12 @@ def log_disableFile(): disableFile() def log_setFormatFile(fmt): - setFormatFile(six.b(fmt)) + cstr = six.b(fmt) + setFormatFile(cstr) def log_setFormatScreen(fmt): - setFormatScreen(six.b(fmt)) + cstr = six.b(fmt) + setFormatScreen(cstr) enumList = [LOG_DEBUG,LOG_INFO,LOG_WARN,LOG_ERROR] @@ -93,4 +99,5 @@ def log_setOutputScreen(fd, level): setOutputScreen(fd, enumList[level]) def log_setOutputFile(filename, level): - setOutputFile(six.b(filename), enumList[level])
\ No newline at end of file + cstr = six.b(filename) + setOutputFile(cstr, enumList[level]) diff --git a/python/astra/matrix_c.pyx b/python/astra/matrix_c.pyx index b0d8bc4..d099a75 100644 --- a/python/astra/matrix_c.pyx +++ b/python/astra/matrix_c.pyx @@ -27,7 +27,12 @@ # distutils: libraries = astra import six -from six.moves import range +try: + from six.moves import range +except ImportError: + # six 1.3.0 + from six.moves import xrange as range + import numpy as np import scipy.sparse as ss diff --git a/python/astra/optomo.py b/python/astra/optomo.py new file mode 100644 index 0000000..4a64150 --- /dev/null +++ b/python/astra/optomo.py @@ -0,0 +1,219 @@ +#----------------------------------------------------------------------- +#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 +from . import data3d +from . import projector +from . import projector3d +from . import creators +from . import algorithm +from . import functions +import numpy as np +from six.moves import reduce +try: + from six.moves import range +except ImportError: + # six 1.3.0 + from six.moves import xrange as range + +import operator +import scipy.sparse.linalg + +class OpTomo(scipy.sparse.linalg.LinearOperator): + """Object that imitates a projection matrix with a given projector. + + This object can do forward projection by using the ``*`` operator:: + + W = astra.OpTomo(proj_id) + fp = W*image + bp = W.T*sinogram + + It can also be used in minimization methods of the :mod:`scipy.sparse.linalg` module:: + + W = astra.OpTomo(proj_id) + output = scipy.sparse.linalg.lsqr(W,sinogram) + + :param proj_id: ID to a projector. + :type proj_id: :class:`int` + """ + + def __init__(self,proj_id): + self.dtype = np.float32 + try: + self.vg = projector.volume_geometry(proj_id) + self.pg = projector.projection_geometry(proj_id) + self.data_mod = data2d + self.appendString = "" + if projector.is_cuda(proj_id): + self.appendString += "_CUDA" + except Exception: + self.vg = projector3d.volume_geometry(proj_id) + self.pg = projector3d.projection_geometry(proj_id) + self.data_mod = data3d + self.appendString = "3D" + if projector3d.is_cuda(proj_id): + self.appendString += "_CUDA" + + self.vshape = functions.geom_size(self.vg) + self.vsize = reduce(operator.mul,self.vshape) + self.sshape = functions.geom_size(self.pg) + self.ssize = reduce(operator.mul,self.sshape) + + self.shape = (self.ssize, self.vsize) + + self.proj_id = proj_id + + self.transposeOpTomo = OpTomoTranspose(self) + try: + self.T = self.transposeOpTomo + except AttributeError: + # Scipy >= 0.16 defines self.T using self._transpose() + pass + + def _transpose(self): + return self.transposeOpTomo + + def __checkArray(self, arr, shp): + if len(arr.shape)==1: + arr = arr.reshape(shp) + if arr.dtype != np.float32: + arr = arr.astype(np.float32) + if arr.flags['C_CONTIGUOUS']==False: + arr = np.ascontiguousarray(arr) + return arr + + def _matvec(self,v): + """Implements the forward operator. + + :param v: Volume to forward project. + :type v: :class:`numpy.ndarray` + """ + v = self.__checkArray(v, self.vshape) + vid = self.data_mod.link('-vol',self.vg,v) + s = np.zeros(self.sshape,dtype=np.float32) + sid = self.data_mod.link('-sino',self.pg,s) + + cfg = creators.astra_dict('FP'+self.appendString) + cfg['ProjectionDataId'] = sid + cfg['VolumeDataId'] = vid + cfg['ProjectorId'] = self.proj_id + fp_id = algorithm.create(cfg) + algorithm.run(fp_id) + + algorithm.delete(fp_id) + self.data_mod.delete([vid,sid]) + return s.flatten() + + def rmatvec(self,s): + """Implements the transpose operator. + + :param s: The projection data. + :type s: :class:`numpy.ndarray` + """ + s = self.__checkArray(s, self.sshape) + sid = self.data_mod.link('-sino',self.pg,s) + v = np.zeros(self.vshape,dtype=np.float32) + vid = self.data_mod.link('-vol',self.vg,v) + + cfg = creators.astra_dict('BP'+self.appendString) + cfg['ProjectionDataId'] = sid + cfg['ReconstructionDataId'] = vid + cfg['ProjectorId'] = self.proj_id + bp_id = algorithm.create(cfg) + algorithm.run(bp_id) + + algorithm.delete(bp_id) + self.data_mod.delete([vid,sid]) + return v.flatten() + + def __mul__(self,v): + """Provides easy forward operator by *. + + :param v: Volume to forward project. + :type v: :class:`numpy.ndarray` + """ + # Catch the case of a forward projection of a 2D/3D image + if isinstance(v, np.ndarray) and v.shape==self.vshape: + return self._matvec(v) + return scipy.sparse.linalg.LinearOperator.__mul__(self, v) + + def reconstruct(self, method, s, iterations=1, extraOptions = {}): + """Reconstruct an object. + + :param method: Method to use for reconstruction. + :type method: :class:`string` + :param s: The projection data. + :type s: :class:`numpy.ndarray` + :param iterations: Number of iterations to use. + :type iterations: :class:`int` + :param extraOptions: Extra options to use during reconstruction (i.e. for cfg['option']). + :type extraOptions: :class:`dict` + """ + s = self.__checkArray(s, self.sshape) + sid = self.data_mod.link('-sino',self.pg,s) + v = np.zeros(self.vshape,dtype=np.float32) + vid = self.data_mod.link('-vol',self.vg,v) + cfg = creators.astra_dict(method) + cfg['ProjectionDataId'] = sid + cfg['ReconstructionDataId'] = vid + cfg['ProjectorId'] = self.proj_id + cfg['option'] = extraOptions + alg_id = algorithm.create(cfg) + algorithm.run(alg_id,iterations) + algorithm.delete(alg_id) + self.data_mod.delete([vid,sid]) + return v + +class OpTomoTranspose(scipy.sparse.linalg.LinearOperator): + """This object provides the transpose operation (``.T``) of the OpTomo object. + + Do not use directly, since it can be accessed as member ``.T`` of + an :class:`OpTomo` object. + """ + def __init__(self,parent): + self.parent = parent + self.dtype = np.float32 + self.shape = (parent.shape[1], parent.shape[0]) + try: + self.T = self.parent + except AttributeError: + # Scipy >= 0.16 defines self.T using self._transpose() + pass + + def _matvec(self, s): + return self.parent.rmatvec(s) + + def rmatvec(self, v): + return self.parent.matvec(v) + + def _transpose(self): + return self.parent + + def __mul__(self,s): + # Catch the case of a backprojection of 2D/3D data + if isinstance(s, np.ndarray) and s.shape==self.parent.sshape: + return self._matvec(s) + return scipy.sparse.linalg.LinearOperator.__mul__(self, s) diff --git a/python/astra/projector3d_c.pyx b/python/astra/projector3d_c.pyx index 8b978d7..aec9cde 100644 --- a/python/astra/projector3d_c.pyx +++ b/python/astra/projector3d_c.pyx @@ -87,12 +87,18 @@ cdef CProjector3D * getObject(i) except NULL: def projection_geometry(i): cdef CProjector3D * proj = getObject(i) - return utils.configToDict(proj.getProjectionGeometry().getConfiguration()) + cdef Config * cfg = proj.getProjectionGeometry().getConfiguration() + dct = utils.configToDict(cfg) + del cfg + return dct def volume_geometry(i): cdef CProjector3D * proj = getObject(i) - return utils.configToDict(proj.getVolumeGeometry().getConfiguration()) + cdef Config * cfg = proj.getVolumeGeometry().getConfiguration() + dct = utils.configToDict(cfg) + del cfg + return dct def weights_single_ray(i, projection_index, detector_index): diff --git a/python/astra/projector_c.pyx b/python/astra/projector_c.pyx index 9aa868e..77c64a4 100644 --- a/python/astra/projector_c.pyx +++ b/python/astra/projector_c.pyx @@ -91,12 +91,18 @@ cdef CProjector2D * getObject(i) except NULL: def projection_geometry(i): cdef CProjector2D * proj = getObject(i) - return utils.configToDict(proj.getProjectionGeometry().getConfiguration()) + cdef Config * cfg = proj.getProjectionGeometry().getConfiguration() + dct = utils.configToDict(cfg) + del cfg + return dct def volume_geometry(i): cdef CProjector2D * proj = getObject(i) - return utils.configToDict(proj.getVolumeGeometry().getConfiguration()) + cdef Config * cfg = proj.getVolumeGeometry().getConfiguration() + dct = utils.configToDict(cfg) + del cfg + return dct def weights_single_ray(i, projection_index, detector_index): diff --git a/python/astra/pythonutils.py b/python/astra/pythonutils.py new file mode 100644 index 0000000..8ea4af5 --- /dev/null +++ b/python/astra/pythonutils.py @@ -0,0 +1,63 @@ +#----------------------------------------------------------------------- +# 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 purely Python functions for PyAstraToolbox. + +.. moduleauthor:: Daniel M. Pelt <D.M.Pelt@cwi.nl> + + +""" + +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 diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx index 0439f1b..260c308 100644 --- a/python/astra/utils.pyx +++ b/python/astra/utils.pyx @@ -26,6 +26,7 @@ # distutils: language = c++ # distutils: libraries = astra +cimport numpy as np import numpy as np import six from libcpp.string cimport string @@ -80,11 +81,12 @@ def wrap_from_bytes(value): return s -cdef void readDict(XMLNode * root, _dc): - cdef XMLNode * listbase - cdef XMLNode * itm +cdef void readDict(XMLNode root, _dc): + cdef XMLNode listbase + cdef XMLNode itm cdef int i cdef int j + cdef double* data dc = convert_item(_dc) for item in dc: @@ -93,45 +95,32 @@ cdef void readDict(XMLNode * root, _dc): if val.size == 0: break listbase = root.addChildNode(item) - listbase.addAttribute(< string > six.b('listsize'), < float32 > val.size) - index = 0 + contig_data = np.ascontiguousarray(val,dtype=np.float64) + data = <double*>np.PyArray_DATA(contig_data) 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 + listbase.setContent(data, val.shape[1], val.shape[0], False) 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 + listbase.setContent(data, val.shape[0]) 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'), <string> 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 void readOptions(XMLNode node, dc): + cdef XMLNode listbase + cdef XMLNode itm cdef int i cdef int j + cdef double* data for item in dc: val = dc[item] if node.hasOption(item): @@ -141,26 +130,14 @@ cdef void readOptions(XMLNode * node, dc): 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 + contig_data = np.ascontiguousarray(val,dtype=np.float64) + data = <double*>np.PyArray_DATA(contig_data) 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 + listbase.setContent(data, val.shape[1], val.shape[0], False) 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 + listbase.setContent(data, val.shape[0]) else: raise Exception("Only 1 or 2 dimensions are allowed") - del listbase else: node.addOption(item, wrap_to_bytes(val)) @@ -214,10 +191,10 @@ def stringToPythonValue(inputIn): return str(input) -cdef XMLNode2dict(XMLNode * node): - cdef XMLNode * subnode - cdef list[XMLNode * ] nodes - cdef list[XMLNode * ].iterator it +cdef XMLNode2dict(XMLNode node): + cdef XMLNode subnode + cdef list[XMLNode] nodes + cdef list[XMLNode].iterator it dct = {} opts = {} if node.hasAttribute(six.b('type')): @@ -227,10 +204,12 @@ cdef XMLNode2dict(XMLNode * node): while it != nodes.end(): subnode = deref(it) if castString(subnode.getName())=="Option": - opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getAttribute('value')) + if subnode.hasAttribute('value'): + opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getAttribute('value')) + else: + opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getContent()) else: dct[castString(subnode.getName())] = stringToPythonValue(subnode.getContent()) - del subnode inc(it) if len(opts)>0: dct['options'] = opts return dct diff --git a/python/docSRC/index.rst b/python/docSRC/index.rst index 8d17a4a..b7cc6d6 100644 --- a/python/docSRC/index.rst +++ b/python/docSRC/index.rst @@ -18,7 +18,7 @@ Contents: matrix creators functions - ASTRAProjector + operator matlab astra .. astra diff --git a/python/docSRC/ASTRAProjector.rst b/python/docSRC/operator.rst index 1c267e3..fe500ba 100644 --- a/python/docSRC/ASTRAProjector.rst +++ b/python/docSRC/operator.rst @@ -1,7 +1,7 @@ -Helper class: the :mod:`ASTRAProjector` module +OpTomo class: the :mod:`optomo` module ============================================== -.. automodule:: astra.ASTRAProjector +.. automodule:: astra.optomo :members: :undoc-members: :show-inheritance: diff --git a/samples/matlab/s010_supersampling.m b/samples/matlab/s010_supersampling.m index 80f6f56..148f6ad 100644 --- a/samples/matlab/s010_supersampling.m +++ b/samples/matlab/s010_supersampling.m @@ -12,23 +12,15 @@ 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; +% We create a projector set up to use 3 rays per detector element +cfg_proj = astra_struct('cuda'); +cfg_proj.option.DetectorSuperSampling = 3; +cfg_proj.ProjectionGeometry = proj_geom; +cfg_proj.VolumeGeometry = vol_geom; +proj_id = astra_mex_projector('create', cfg_proj); -% 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); +[sinogram3 sinogram_id] = astra_create_sino(P, proj_id); figure(1); imshow(P, []); figure(2); imshow(sinogram3, []); @@ -39,14 +31,14 @@ 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; +cfg.ProjectorId = proj_id; + % 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; +% cfg_proj.option.PixelSuperSampling = 2; alg_id = astra_mex_algorithm('create', cfg); diff --git a/samples/matlab/s017_opTomo.m b/samples/matlab/s017_opTomo.m new file mode 100644 index 0000000..891a93d --- /dev/null +++ b/samples/matlab/s017_opTomo.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 sample illustrates the use of opTomo. +% +% opTomo is a wrapper around the FP and BP operations of the ASTRA Toolbox, +% to allow you to use them as you would a matrix. +% +% This class requires the Spot Linear-Operator Toolbox to be installed. +% You can download this at http://www.cs.ubc.ca/labs/scl/spot/ + +% load a phantom image +im = phantom(256); +% and flatten it to a vector +x = im(:); + +%% Setting up the geometry +% projection geometry +proj_geom = astra_create_proj_geom('parallel', 1, 256, linspace2(0,pi,180)); +% object dimensions +vol_geom = astra_create_vol_geom(256,256); + +%% Generate projection data +% Create the Spot operator for ASTRA using the GPU. +W = opTomo('cuda', proj_geom, vol_geom); + +p = W*x; + +% reshape the vector into a sinogram +sinogram = reshape(p, W.proj_size); +imshow(sinogram, []); + + +%% Reconstruction +% We use a least squares solver lsqr from Matlab to solve the +% equation W*x = p. +% Max number of iterations is 100, convergence tolerance of 1e-6. +y = lsqr(W, p, 1e-6, 100); + +% the output is a vector, so we reshape it into an image +reconstruction = reshape(y, W.vol_size); + +subplot(1,3,1); +imshow(reconstruction, []); +title('Reconstruction'); + +subplot(1,3,2); +imshow(im, []); +title('Ground truth'); + +% The transpose of the operator corresponds to the backprojection. +backProjection = W'*p; +subplot(1,3,3); +imshow(reshape(backProjection, W.vol_size), []); +title('Backprojection'); diff --git a/samples/python/s005_3d_geometry.py b/samples/python/s005_3d_geometry.py index f43fc7e..a7f7a3d 100644 --- a/samples/python/s005_3d_geometry.py +++ b/samples/python/s005_3d_geometry.py @@ -24,7 +24,11 @@ # #----------------------------------------------------------------------- -from six.moves import range +try: + from six.moves import range +except ImportError: + # six 1.3.0 + from six.moves import xrange as range import astra import numpy as np diff --git a/samples/python/s016_plots.py b/samples/python/s016_plots.py index cd4d98c..8a8ba64 100644 --- a/samples/python/s016_plots.py +++ b/samples/python/s016_plots.py @@ -24,7 +24,11 @@ # #----------------------------------------------------------------------- -from six.moves import range +try: + from six.moves import range +except ImportError: + # six 1.3.0 + from six.moves import xrange as range import astra import numpy as np @@ -35,8 +39,8 @@ proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180 # 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) +proj_id = astra.create_projector('cuda',proj_geom,vol_geom) +sinogram_id, sinogram = astra.create_sino(P, proj_id) import pylab pylab.gray() diff --git a/samples/python/s017_OpTomo.py b/samples/python/s017_OpTomo.py new file mode 100644 index 0000000..967fa64 --- /dev/null +++ b/samples/python/s017_OpTomo.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 <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +import astra +import numpy as np +import scipy.sparse.linalg + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + +# As before, create a sinogram from a phantom +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] +proj_id = astra.create_projector('cuda',proj_geom,vol_geom) + +# construct the OpTomo object +W = astra.OpTomo(proj_id) + +sinogram = W * P +sinogram = sinogram.reshape([180, 384]) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(P) +pylab.figure(2) +pylab.imshow(sinogram) + +# Run the lsqr linear solver +output = scipy.sparse.linalg.lsqr(W, sinogram.flatten(), iter_lim=150) +rec = output[0].reshape([256, 256]) + +pylab.figure(3) +pylab.imshow(rec) +pylab.show() + +# Clean up. +astra.projector.delete(proj_id) diff --git a/src/ArtAlgorithm.cpp b/src/ArtAlgorithm.cpp index 8f058a3..6a699ec 100644 --- a/src/ArtAlgorithm.cpp +++ b/src/ArtAlgorithm.cpp @@ -132,7 +132,7 @@ bool CArtAlgorithm::initialize(const Config& _cfg) } // ray order - string projOrder = _cfg.self->getOption("RayOrder", "sequential"); + string projOrder = _cfg.self.getOption("RayOrder", "sequential"); CC.markOptionParsed("RayOrder"); m_iCurrentRay = 0; m_iRayCount = m_pProjector->getProjectionGeometry()->getProjectionAngleCount() * @@ -145,7 +145,7 @@ bool CArtAlgorithm::initialize(const Config& _cfg) m_piDetectorOrder[i] = i % m_pProjector->getProjectionGeometry()->getDetectorCount(); } } else if (projOrder == "custom") { - vector<float32> rayOrderList = _cfg.self->getOptionNumericalArray("RayOrderList"); + vector<float32> rayOrderList = _cfg.self.getOptionNumericalArray("RayOrderList"); m_iRayCount = rayOrderList.size() / 2; m_piProjectionOrder = new int[m_iRayCount]; m_piDetectorOrder = new int[m_iRayCount]; @@ -158,7 +158,7 @@ bool CArtAlgorithm::initialize(const Config& _cfg) return false; } - m_fLambda = _cfg.self->getOptionNumerical("Lambda", 1.0f); + m_fLambda = _cfg.self.getOptionNumerical("Lambda", 1.0f); CC.markOptionParsed("Lambda"); // success diff --git a/src/ConeProjectionGeometry3D.cpp b/src/ConeProjectionGeometry3D.cpp index 1976901..dd22eba 100644 --- a/src/ConeProjectionGeometry3D.cpp +++ b/src/ConeProjectionGeometry3D.cpp @@ -87,17 +87,15 @@ bool CConeProjectionGeometry3D::initialize(const Config& _cfg) CProjectionGeometry3D::initialize(_cfg); // Required: DistanceOriginDetector - XMLNode* node = _cfg.self->getSingleNode("DistanceOriginDetector"); + XMLNode node = _cfg.self.getSingleNode("DistanceOriginDetector"); ASTRA_CONFIG_CHECK(node, "ConeProjectionGeometry3D", "No DistanceOriginDetector tag specified."); - m_fOriginDetectorDistance = boost::lexical_cast<float32>(node->getContent()); - ASTRA_DELETE(node); + m_fOriginDetectorDistance = boost::lexical_cast<float32>(node.getContent()); CC.markNodeParsed("DistanceOriginDetector"); // Required: DetectorOriginSource - node = _cfg.self->getSingleNode("DistanceOriginSource"); + node = _cfg.self.getSingleNode("DistanceOriginSource"); ASTRA_CONFIG_CHECK(node, "ConeProjectionGeometry3D", "No DistanceOriginSource tag specified."); - m_fOriginSourceDistance = boost::lexical_cast<float32>(node->getContent()); - ASTRA_DELETE(node); + m_fOriginSourceDistance = boost::lexical_cast<float32>(node.getContent()); CC.markNodeParsed("DistanceOriginSource"); // success @@ -193,14 +191,14 @@ Config* CConeProjectionGeometry3D::getConfiguration() const { Config* cfg = new Config(); cfg->initialize("ProjectionGeometry3D"); - cfg->self->addAttribute("type", "cone"); - cfg->self->addChildNode("DetectorSpacingX", m_fDetectorSpacingX); - cfg->self->addChildNode("DetectorSpacingY", m_fDetectorSpacingY); - cfg->self->addChildNode("DetectorRowCount", m_iDetectorRowCount); - cfg->self->addChildNode("DetectorColCount", m_iDetectorColCount); - cfg->self->addChildNode("DistanceOriginDetector", m_fOriginDetectorDistance); - cfg->self->addChildNode("DistanceOriginSource", m_fOriginSourceDistance); - cfg->self->addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); + cfg->self.addAttribute("type", "cone"); + cfg->self.addChildNode("DetectorSpacingX", m_fDetectorSpacingX); + cfg->self.addChildNode("DetectorSpacingY", m_fDetectorSpacingY); + cfg->self.addChildNode("DetectorRowCount", m_iDetectorRowCount); + cfg->self.addChildNode("DetectorColCount", m_iDetectorColCount); + cfg->self.addChildNode("DistanceOriginDetector", m_fOriginDetectorDistance); + cfg->self.addChildNode("DistanceOriginSource", m_fOriginSourceDistance); + cfg->self.addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); return cfg; } diff --git a/src/ConeVecProjectionGeometry3D.cpp b/src/ConeVecProjectionGeometry3D.cpp index 9dc273d..47ed630 100644 --- a/src/ConeVecProjectionGeometry3D.cpp +++ b/src/ConeVecProjectionGeometry3D.cpp @@ -73,33 +73,30 @@ bool CConeVecProjectionGeometry3D::initialize(const Config& _cfg) ASTRA_ASSERT(_cfg.self); ConfigStackCheck<CProjectionGeometry3D> CC("ConeVecProjectionGeometry3D", this, _cfg); - XMLNode* node; + XMLNode node; // TODO: Fix up class hierarchy... this class doesn't fit very well. // initialization of parent class //CProjectionGeometry3D::initialize(_cfg); // Required: DetectorRowCount - node = _cfg.self->getSingleNode("DetectorRowCount"); + node = _cfg.self.getSingleNode("DetectorRowCount"); ASTRA_CONFIG_CHECK(node, "ConeVecProjectionGeometry3D", "No DetectorRowCount tag specified."); - m_iDetectorRowCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iDetectorRowCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("DetectorRowCount"); // Required: DetectorColCount - node = _cfg.self->getSingleNode("DetectorColCount"); + node = _cfg.self.getSingleNode("DetectorColCount"); ASTRA_CONFIG_CHECK(node, "ConeVecProjectionGeometry3D", "No DetectorColCount tag specified."); - m_iDetectorColCount = boost::lexical_cast<int>(node->getContent()); + m_iDetectorColCount = boost::lexical_cast<int>(node.getContent()); m_iDetectorTotCount = m_iDetectorRowCount * m_iDetectorColCount; - ASTRA_DELETE(node); CC.markNodeParsed("DetectorColCount"); // Required: Vectors - node = _cfg.self->getSingleNode("Vectors"); + node = _cfg.self.getSingleNode("Vectors"); ASTRA_CONFIG_CHECK(node, "ConeVecProjectionGeometry3D", "No Vectors tag specified."); - vector<double> data = node->getContentNumericalArrayDouble(); + vector<double> data = node.getContentNumericalArrayDouble(); CC.markNodeParsed("Vectors"); - ASTRA_DELETE(node); ASTRA_CONFIG_CHECK(data.size() % 12 == 0, "ConeVecProjectionGeometry3D", "Vectors doesn't consist of 12-tuples."); m_iProjectionAngleCount = data.size() / 12; m_pProjectionAngles = new SConeProjection[m_iProjectionAngleCount]; @@ -208,9 +205,9 @@ Config* CConeVecProjectionGeometry3D::getConfiguration() const Config* cfg = new Config(); cfg->initialize("ProjectionGeometry3D"); - cfg->self->addAttribute("type", "cone_vec"); - cfg->self->addChildNode("DetectorRowCount", m_iDetectorRowCount); - cfg->self->addChildNode("DetectorColCount", m_iDetectorColCount); + cfg->self.addAttribute("type", "cone_vec"); + cfg->self.addChildNode("DetectorRowCount", m_iDetectorRowCount); + cfg->self.addChildNode("DetectorColCount", m_iDetectorColCount); std::string vectors = ""; for (int i = 0; i < m_iProjectionAngleCount; ++i) { @@ -229,7 +226,7 @@ Config* CConeVecProjectionGeometry3D::getConfiguration() const vectors += boost::lexical_cast<string>(p.fDetVZ); if (i < m_iProjectionAngleCount-1) vectors += ';'; } - cfg->self->addChildNode("Vectors", vectors); + cfg->self.addChildNode("Vectors", vectors); return cfg; } diff --git a/src/Config.cpp b/src/Config.cpp index d860638..395080b 100644 --- a/src/Config.cpp +++ b/src/Config.cpp @@ -45,31 +45,33 @@ using namespace std; //----------------------------------------------------------------------------- // default constructor -Config::Config() +Config::Config() : self() { - self = 0; + _doc = 0; } //----------------------------------------------------------------------------- // not so default constructor -Config::Config(XMLNode* _self) +Config::Config(XMLNode _self) { self = _self; + _doc = 0; } //----------------------------------------------------------------------------- Config::~Config() { - delete self; - self = 0; + delete _doc; + _doc = 0; } //----------------------------------------------------------------------------- void Config::initialize(std::string rootname) { - if (self == 0) { + if (!self) { XMLDocument* doc = XMLDocument::createDocument(rootname); self = doc->getRootNode(); + _doc = doc; } } @@ -124,13 +126,13 @@ bool ConfigStackCheck<T>::stopParsing() std::string errors; - std::list<XMLNode*> nodes = cfg->self->getNodes(); - for (std::list<XMLNode*>::iterator i = nodes.begin(); i != nodes.end(); ++i) + std::list<XMLNode> nodes = cfg->self.getNodes(); + for (std::list<XMLNode>::iterator i = nodes.begin(); i != nodes.end(); ++i) { - std::string nodeName = (*i)->getName(); + std::string nodeName = i->getName(); if (nodeName == "Option") { - nodeName = (*i)->getAttribute("key", ""); + nodeName = i->getAttribute("key", ""); if (object->configCheckData->parsedOptions.find(nodeName) == object->configCheckData->parsedOptions.end()) { if (!errors.empty()) errors += ", "; errors += nodeName; @@ -142,8 +144,6 @@ bool ConfigStackCheck<T>::stopParsing() } } } - for (std::list<XMLNode*>::iterator i = nodes.begin(); i != nodes.end(); ++i) - delete (*i); nodes.clear(); if (!errors.empty()) { diff --git a/src/CudaBackProjectionAlgorithm3D.cpp b/src/CudaBackProjectionAlgorithm3D.cpp index a8a1b0a..a5c3445 100644 --- a/src/CudaBackProjectionAlgorithm3D.cpp +++ b/src/CudaBackProjectionAlgorithm3D.cpp @@ -32,6 +32,7 @@ $Id$ #include "astra/AstraObjectManager.h" +#include "astra/CudaProjector3D.h" #include "astra/ConeProjectionGeometry3D.h" #include "astra/ParallelProjectionGeometry3D.h" #include "astra/ParallelVecProjectionGeometry3D.h" @@ -102,12 +103,23 @@ bool CCudaBackProjectionAlgorithm3D::initialize(const Config& _cfg) return false; } - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); + CCudaProjector3D* pCudaProjector = 0; + pCudaProjector = dynamic_cast<CCudaProjector3D*>(m_pProjector); + if (!pCudaProjector) { + // TODO: Report + } + + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); CC.markOptionParsed("GPUindex"); - m_iVoxelSuperSampling = (int)_cfg.self->getOptionNumerical("VoxelSuperSampling", 1); + + + m_iVoxelSuperSampling = 1; + if (pCudaProjector) + m_iVoxelSuperSampling = pCudaProjector->getVoxelSuperSampling(); + m_iVoxelSuperSampling = (int)_cfg.self.getOptionNumerical("VoxelSuperSampling", m_iVoxelSuperSampling); CC.markOptionParsed("VoxelSuperSampling"); - m_bSIRTWeighting = _cfg.self->getOptionBool("SIRTWeighting", false); + m_bSIRTWeighting = _cfg.self.getOptionBool("SIRTWeighting", false); CC.markOptionParsed("SIRTWeighting"); // success diff --git a/src/CudaCglsAlgorithm3D.cpp b/src/CudaCglsAlgorithm3D.cpp index 3677458..2d28964 100644 --- a/src/CudaCglsAlgorithm3D.cpp +++ b/src/CudaCglsAlgorithm3D.cpp @@ -32,6 +32,7 @@ $Id$ #include "astra/AstraObjectManager.h" +#include "astra/CudaProjector3D.h" #include "astra/ConeProjectionGeometry3D.h" #include "astra/ParallelVecProjectionGeometry3D.h" #include "astra/ConeVecProjectionGeometry3D.h" @@ -106,12 +107,27 @@ bool CCudaCglsAlgorithm3D::initialize(const Config& _cfg) return false; } - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); + CCudaProjector3D* pCudaProjector = 0; + pCudaProjector = dynamic_cast<CCudaProjector3D*>(m_pProjector); + if (!pCudaProjector) { + // TODO: Report + } + + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); CC.markOptionParsed("GPUindex"); - m_iDetectorSuperSampling = (int)_cfg.self->getOptionNumerical("DetectorSuperSampling", 1); - CC.markOptionParsed("DetectorSuperSampling"); - m_iVoxelSuperSampling = (int)_cfg.self->getOptionNumerical("VoxelSuperSampling", 1); + + m_iVoxelSuperSampling = 1; + m_iDetectorSuperSampling = 1; + if (pCudaProjector) { + // New interface + m_iVoxelSuperSampling = pCudaProjector->getVoxelSuperSampling(); + m_iDetectorSuperSampling = pCudaProjector->getDetectorSuperSampling(); + } + // Deprecated options + m_iVoxelSuperSampling = (int)_cfg.self.getOptionNumerical("VoxelSuperSampling", m_iVoxelSuperSampling); + m_iDetectorSuperSampling = (int)_cfg.self.getOptionNumerical("DetectorSuperSampling", m_iDetectorSuperSampling); CC.markOptionParsed("VoxelSuperSampling"); + CC.markOptionParsed("DetectorSuperSampling"); m_pCgls = new AstraCGLS3d(); diff --git a/src/CudaDartMaskAlgorithm.cpp b/src/CudaDartMaskAlgorithm.cpp index dcdefcc..950b428 100644 --- a/src/CudaDartMaskAlgorithm.cpp +++ b/src/CudaDartMaskAlgorithm.cpp @@ -65,38 +65,36 @@ bool CCudaDartMaskAlgorithm::initialize(const Config& _cfg) ConfigStackCheck<CAlgorithm> CC("CudaDartMaskAlgorithm", this, _cfg); // reconstruction data - XMLNode* node = _cfg.self->getSingleNode("SegmentationDataId"); + XMLNode node = _cfg.self.getSingleNode("SegmentationDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No SegmentationDataId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pSegmentation = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("SegmentationDataId"); // reconstruction data - node = _cfg.self->getSingleNode("MaskDataId"); + node = _cfg.self.getSingleNode("MaskDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No MaskDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pMask = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("MaskDataId"); // Option: GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUIndex", m_iGPUIndex); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUIndex", m_iGPUIndex); CC.markOptionParsed("GPUindex"); - if (!_cfg.self->hasOption("GPUindex")) + if (!_cfg.self.hasOption("GPUindex")) CC.markOptionParsed("GPUIndex"); // Option: Connectivity - m_iConn = (unsigned int)_cfg.self->getOptionNumerical("Connectivity", 8); + m_iConn = (unsigned int)_cfg.self.getOptionNumerical("Connectivity", 8); CC.markOptionParsed("Connectivity"); // Option: Threshold - m_iThreshold = (unsigned int)_cfg.self->getOptionNumerical("Threshold", 1); + m_iThreshold = (unsigned int)_cfg.self.getOptionNumerical("Threshold", 1); CC.markOptionParsed("Threshold"); // Option: Radius - m_iRadius = (unsigned int)_cfg.self->getOptionNumerical("Radius", 1); + m_iRadius = (unsigned int)_cfg.self.getOptionNumerical("Radius", 1); CC.markOptionParsed("Radius"); _check(); diff --git a/src/CudaDartMaskAlgorithm3D.cpp b/src/CudaDartMaskAlgorithm3D.cpp index f3500b9..b0dfc5b 100644 --- a/src/CudaDartMaskAlgorithm3D.cpp +++ b/src/CudaDartMaskAlgorithm3D.cpp @@ -65,38 +65,36 @@ bool CCudaDartMaskAlgorithm3D::initialize(const Config& _cfg) ConfigStackCheck<CAlgorithm> CC("CudaDartMaskAlgorithm", this, _cfg); // reconstruction data - XMLNode* node = _cfg.self->getSingleNode("SegmentationDataId"); + XMLNode node = _cfg.self.getSingleNode("SegmentationDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No SegmentationDataId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pSegmentation = dynamic_cast<CFloat32VolumeData3DMemory*>(CData3DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("SegmentationDataId"); // reconstruction data - node = _cfg.self->getSingleNode("MaskDataId"); + node = _cfg.self.getSingleNode("MaskDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No MaskDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pMask = dynamic_cast<CFloat32VolumeData3DMemory*>(CData3DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("MaskDataId"); // Option: GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUIndex", m_iGPUIndex); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUIndex", m_iGPUIndex); CC.markOptionParsed("GPUindex"); - if (!_cfg.self->hasOption("GPUindex")) + if (!_cfg.self.hasOption("GPUindex")) CC.markOptionParsed("GPUIndex"); // Option: Connectivity - m_iConn = (unsigned int)_cfg.self->getOptionNumerical("Connectivity", 8); + m_iConn = (unsigned int)_cfg.self.getOptionNumerical("Connectivity", 8); CC.markOptionParsed("Connectivity"); // Option: Threshold - m_iThreshold = (unsigned int)_cfg.self->getOptionNumerical("Threshold", 1); + m_iThreshold = (unsigned int)_cfg.self.getOptionNumerical("Threshold", 1); CC.markOptionParsed("Threshold"); // Option: Radius - m_iRadius = (unsigned int)_cfg.self->getOptionNumerical("Radius", 1); + m_iRadius = (unsigned int)_cfg.self.getOptionNumerical("Radius", 1); CC.markOptionParsed("Radius"); _check(); diff --git a/src/CudaDartSmoothingAlgorithm.cpp b/src/CudaDartSmoothingAlgorithm.cpp index 2f2103f..7e22809 100644 --- a/src/CudaDartSmoothingAlgorithm.cpp +++ b/src/CudaDartSmoothingAlgorithm.cpp @@ -65,34 +65,32 @@ bool CCudaDartSmoothingAlgorithm::initialize(const Config& _cfg) ConfigStackCheck<CAlgorithm> CC("CudaDartSmoothingAlgorithm", this, _cfg); // reconstruction data - XMLNode* node = _cfg.self->getSingleNode("InDataId"); + XMLNode node = _cfg.self.getSingleNode("InDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No InDataId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pIn = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("InDataId"); // reconstruction data - node = _cfg.self->getSingleNode("OutDataId"); + node = _cfg.self.getSingleNode("OutDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No OutDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pOut = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("OutDataId"); // Option: GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUIndex", m_iGPUIndex); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUIndex", m_iGPUIndex); CC.markOptionParsed("GPUindex"); - if (!_cfg.self->hasOption("GPUindex")) + if (!_cfg.self.hasOption("GPUindex")) CC.markOptionParsed("GPUIndex"); // Option: Radius - m_fB = (float)_cfg.self->getOptionNumerical("Intensity", 0.3f); + m_fB = (float)_cfg.self.getOptionNumerical("Intensity", 0.3f); CC.markOptionParsed("Intensity"); // Option: Radius - m_iRadius = (unsigned int)_cfg.self->getOptionNumerical("Radius", 1); + m_iRadius = (unsigned int)_cfg.self.getOptionNumerical("Radius", 1); CC.markOptionParsed("Radius"); diff --git a/src/CudaDartSmoothingAlgorithm3D.cpp b/src/CudaDartSmoothingAlgorithm3D.cpp index f3cf015..9c4437a 100644 --- a/src/CudaDartSmoothingAlgorithm3D.cpp +++ b/src/CudaDartSmoothingAlgorithm3D.cpp @@ -65,34 +65,32 @@ bool CCudaDartSmoothingAlgorithm3D::initialize(const Config& _cfg) ConfigStackCheck<CAlgorithm> CC("CudaDartSmoothingAlgorithm", this, _cfg); // reconstruction data - XMLNode* node = _cfg.self->getSingleNode("InDataId"); + XMLNode node = _cfg.self.getSingleNode("InDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No InDataId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pIn = dynamic_cast<CFloat32VolumeData3DMemory*>(CData3DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("InDataId"); // reconstruction data - node = _cfg.self->getSingleNode("OutDataId"); + node = _cfg.self.getSingleNode("OutDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No OutDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pOut = dynamic_cast<CFloat32VolumeData3DMemory*>(CData3DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("OutDataId"); // Option: GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUIndex", m_iGPUIndex); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUIndex", m_iGPUIndex); CC.markOptionParsed("GPUindex"); - if (!_cfg.self->hasOption("GPUindex")) + if (!_cfg.self.hasOption("GPUindex")) CC.markOptionParsed("GPUIndex"); // Option: Intensity - m_fB = (float)_cfg.self->getOptionNumerical("Intensity", 0.3f); + m_fB = (float)_cfg.self.getOptionNumerical("Intensity", 0.3f); CC.markOptionParsed("Intensity"); // Option: Radius - m_iRadius = (unsigned int)_cfg.self->getOptionNumerical("Radius", 1); + m_iRadius = (unsigned int)_cfg.self.getOptionNumerical("Radius", 1); CC.markOptionParsed("Radius"); _check(); diff --git a/src/CudaDataOperationAlgorithm.cpp b/src/CudaDataOperationAlgorithm.cpp index 79a9d7f..ae133c2 100644 --- a/src/CudaDataOperationAlgorithm.cpp +++ b/src/CudaDataOperationAlgorithm.cpp @@ -67,40 +67,37 @@ bool CCudaDataOperationAlgorithm::initialize(const Config& _cfg) ConfigStackCheck<CAlgorithm> CC("CCudaDataOperationAlgorithm", this, _cfg); // operation - XMLNode* node = _cfg.self->getSingleNode("Operation"); + XMLNode node = _cfg.self.getSingleNode("Operation"); ASTRA_CONFIG_CHECK(node, "CCudaDataOperationAlgorithm", "No Operation tag specified."); - m_sOperation = node->getContent(); + m_sOperation = node.getContent(); m_sOperation.erase(std::remove(m_sOperation.begin(), m_sOperation.end(), ' '), m_sOperation.end()); - ASTRA_DELETE(node); CC.markNodeParsed("Operation"); // data - node = _cfg.self->getSingleNode("DataId"); + node = _cfg.self.getSingleNode("DataId"); ASTRA_CONFIG_CHECK(node, "CCudaDataOperationAlgorithm", "No DataId tag specified."); - vector<string> data = node->getContentArray(); + vector<string> data = node.getContentArray(); for (vector<string>::iterator it = data.begin(); it != data.end(); it++){ int id = boost::lexical_cast<int>(*it); m_pData.push_back(dynamic_cast<CFloat32Data2D*>(CData2DManager::getSingleton().get(id))); } - ASTRA_DELETE(node); CC.markNodeParsed("DataId"); // scalar - node = _cfg.self->getSingleNode("Scalar"); + node = _cfg.self.getSingleNode("Scalar"); ASTRA_CONFIG_CHECK(node, "CCudaDataOperationAlgorithm", "No Scalar tag specified."); - m_fScalar = node->getContentNumericalArray(); - ASTRA_DELETE(node); + m_fScalar = node.getContentNumericalArray(); CC.markNodeParsed("Scalar"); // Option: GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUIndex", m_iGPUIndex); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUIndex", m_iGPUIndex); CC.markOptionParsed("GPUindex"); - if (!_cfg.self->hasOption("GPUindex")) + if (!_cfg.self.hasOption("GPUindex")) CC.markOptionParsed("GPUIndex"); - if (_cfg.self->hasOption("MaskId")) { - int id = boost::lexical_cast<int>(_cfg.self->getOption("MaskId")); + if (_cfg.self.hasOption("MaskId")) { + int id = boost::lexical_cast<int>(_cfg.self.getOption("MaskId")); m_pMask = dynamic_cast<CFloat32Data2D*>(CData2DManager::getSingleton().get(id)); } CC.markOptionParsed("MaskId"); diff --git a/src/CudaFDKAlgorithm3D.cpp b/src/CudaFDKAlgorithm3D.cpp index 0a46ff6..e700945 100644 --- a/src/CudaFDKAlgorithm3D.cpp +++ b/src/CudaFDKAlgorithm3D.cpp @@ -32,6 +32,7 @@ $Id$ #include "astra/AstraObjectManager.h" +#include "astra/CudaProjector3D.h" #include "astra/ConeProjectionGeometry3D.h" #include "../cuda/3d/astra3d.h" @@ -100,12 +101,22 @@ bool CCudaFDKAlgorithm3D::initialize(const Config& _cfg) return false; } - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); + CCudaProjector3D* pCudaProjector = 0; + pCudaProjector = dynamic_cast<CCudaProjector3D*>(m_pProjector); + if (!pCudaProjector) { + // TODO: Report + } + + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); CC.markOptionParsed("GPUindex"); - m_iVoxelSuperSampling = (int)_cfg.self->getOptionNumerical("VoxelSuperSampling", 1); + + m_iVoxelSuperSampling = 1; + if (pCudaProjector) + m_iVoxelSuperSampling = pCudaProjector->getVoxelSuperSampling(); + m_iVoxelSuperSampling = (int)_cfg.self.getOptionNumerical("VoxelSuperSampling", m_iVoxelSuperSampling); CC.markOptionParsed("VoxelSuperSampling"); - m_bShortScan = _cfg.self->getOptionBool("ShortScan", false); + m_bShortScan = _cfg.self.getOptionBool("ShortScan", false); CC.markOptionParsed("ShortScan"); // success diff --git a/src/CudaFilteredBackProjectionAlgorithm.cpp b/src/CudaFilteredBackProjectionAlgorithm.cpp index 0badc20..aac96d6 100644 --- a/src/CudaFilteredBackProjectionAlgorithm.cpp +++ b/src/CudaFilteredBackProjectionAlgorithm.cpp @@ -32,6 +32,7 @@ $Id$ #include <cstring> #include "astra/AstraObjectManager.h" +#include "astra/CudaProjector2D.h" #include "../cuda/2d/astra.h" #include "astra/Logging.h" @@ -77,40 +78,51 @@ bool CCudaFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) clear(); } + // Projector + XMLNode node = _cfg.self.getSingleNode("ProjectorId"); + CCudaProjector2D* pCudaProjector = 0; + if (node) { + int id = boost::lexical_cast<int>(node.getContent()); + CProjector2D *projector = CProjector2DManager::getSingleton().get(id); + pCudaProjector = dynamic_cast<CCudaProjector2D*>(projector); + if (!pCudaProjector) { + ASTRA_WARN("non-CUDA Projector2D passed"); + } + } + CC.markNodeParsed("ProjectorId"); + + // sinogram data - XMLNode* node = _cfg.self->getSingleNode("ProjectionDataId"); + node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "CudaFBP", "No ProjectionDataId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pSinogram = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ProjectionDataId"); // reconstruction data - node = _cfg.self->getSingleNode("ReconstructionDataId"); + node = _cfg.self.getSingleNode("ReconstructionDataId"); ASTRA_CONFIG_CHECK(node, "CudaFBP", "No ReconstructionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pReconstruction = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ReconstructionDataId"); // filter type - node = _cfg.self->getSingleNode("FilterType"); - if(node != NULL) + node = _cfg.self.getSingleNode("FilterType"); + if (node) { - m_eFilter = _convertStringToFilter(node->getContent().c_str()); + m_eFilter = _convertStringToFilter(node.getContent().c_str()); } else { m_eFilter = FILTER_RAMLAK; } CC.markNodeParsed("FilterType"); - ASTRA_DELETE(node); // filter - node = _cfg.self->getSingleNode("FilterSinogramId"); - if(node != NULL) + node = _cfg.self.getSingleNode("FilterSinogramId"); + if (node) { - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); const CFloat32ProjectionData2D * pFilterData = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); m_iFilterWidth = pFilterData->getGeometry()->getDetectorCount(); int iFilterProjectionCount = pFilterData->getGeometry()->getProjectionAngleCount(); @@ -124,13 +136,12 @@ bool CCudaFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) m_pfFilter = NULL; } CC.markNodeParsed("FilterSinogramId"); // TODO: Only for some types! - ASTRA_DELETE(node); // filter parameter - node = _cfg.self->getSingleNode("FilterParameter"); - if(node != NULL) + node = _cfg.self.getSingleNode("FilterParameter"); + if (node) { - float fParameter = boost::lexical_cast<float>(node->getContent()); + float fParameter = boost::lexical_cast<float>(node.getContent()); m_fFilterParameter = fParameter; } else @@ -138,13 +149,12 @@ bool CCudaFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) m_fFilterParameter = -1.0f; } CC.markNodeParsed("FilterParameter"); // TODO: Only for some types! - ASTRA_DELETE(node); // D value - node = _cfg.self->getSingleNode("FilterD"); - if(node != NULL) + node = _cfg.self.getSingleNode("FilterD"); + if (node) { - float fD = boost::lexical_cast<float>(node->getContent()); + float fD = boost::lexical_cast<float>(node.getContent()); m_fFilterD = fD; } else @@ -152,19 +162,24 @@ bool CCudaFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) m_fFilterD = 1.0f; } CC.markNodeParsed("FilterD"); // TODO: Only for some types! - ASTRA_DELETE(node); // GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); CC.markOptionParsed("GPUindex"); - // Pixel supersampling factor - m_iPixelSuperSampling = (int)_cfg.self->getOptionNumerical("PixelSuperSampling", 1); + m_iPixelSuperSampling = 1; + if (pCudaProjector) { + // New interface + m_iPixelSuperSampling = pCudaProjector->getVoxelSuperSampling(); + } + // Deprecated options + m_iPixelSuperSampling = (int)_cfg.self.getOptionNumerical("PixelSuperSampling", m_iPixelSuperSampling); CC.markOptionParsed("PixelSuperSampling"); + // Fan beam short scan mode if (m_pSinogram && dynamic_cast<CFanFlatProjectionGeometry2D*>(m_pSinogram->getGeometry())) { - m_bShortScan = (int)_cfg.self->getOptionBool("ShortScan", false); + m_bShortScan = (int)_cfg.self.getOptionBool("ShortScan", false); CC.markOptionParsed("ShortScan"); } diff --git a/src/CudaForwardProjectionAlgorithm.cpp b/src/CudaForwardProjectionAlgorithm.cpp index 95abb62..b382f2e 100644 --- a/src/CudaForwardProjectionAlgorithm.cpp +++ b/src/CudaForwardProjectionAlgorithm.cpp @@ -71,47 +71,52 @@ bool CCudaForwardProjectionAlgorithm::initialize(const Config& _cfg) { ASTRA_ASSERT(_cfg.self); ConfigStackCheck<CAlgorithm> CC("CudaForwardProjectionAlgorithm", this, _cfg); + + // Projector + XMLNode node = _cfg.self.getSingleNode("ProjectorId"); + CCudaProjector2D* pCudaProjector = 0; + if (node) { + int id = boost::lexical_cast<int>(node.getContent()); + CProjector2D *projector = CProjector2DManager::getSingleton().get(id); + pCudaProjector = dynamic_cast<CCudaProjector2D*>(projector); + if (!pCudaProjector) { + ASTRA_WARN("non-CUDA Projector2D passed to FP_CUDA"); + } + } + CC.markNodeParsed("ProjectorId"); + + // sinogram data - XMLNode* node = _cfg.self->getSingleNode("ProjectionDataId"); + node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "FP_CUDA", "No ProjectionDataId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pSinogram = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ProjectionDataId"); // volume data - node = _cfg.self->getSingleNode("VolumeDataId"); + node = _cfg.self.getSingleNode("VolumeDataId"); ASTRA_CONFIG_CHECK(node, "FP_CUDA", "No VolumeDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pVolume = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("VolumeDataId"); // GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUIndex", m_iGPUIndex); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUIndex", m_iGPUIndex); CC.markOptionParsed("GPUindex"); - if (!_cfg.self->hasOption("GPUindex")) + if (!_cfg.self.hasOption("GPUindex")) CC.markOptionParsed("GPUIndex"); // Detector supersampling factor - m_iDetectorSuperSampling = (int)_cfg.self->getOptionNumerical("DetectorSuperSampling", 1); - CC.markOptionParsed("DetectorSuperSampling"); - - - // This isn't used yet, but passing it is not something to warn about - node = _cfg.self->getSingleNode("ProjectorId"); - if (node) { - id = boost::lexical_cast<int>(node->getContent()); - CProjector2D *projector = CProjector2DManager::getSingleton().get(id); - if (!dynamic_cast<CCudaProjector2D*>(projector)) { - ASTRA_WARN("non-CUDA Projector2D passed to FP_CUDA"); - } - delete node; + m_iDetectorSuperSampling = 1; + if (pCudaProjector) { + // New interface + m_iDetectorSuperSampling = pCudaProjector->getDetectorSuperSampling(); } - CC.markNodeParsed("ProjectorId"); - + // Deprecated option + m_iDetectorSuperSampling = (int)_cfg.self.getOptionNumerical("DetectorSuperSampling", m_iDetectorSuperSampling); + CC.markOptionParsed("DetectorSuperSampling"); // return success diff --git a/src/CudaForwardProjectionAlgorithm3D.cpp b/src/CudaForwardProjectionAlgorithm3D.cpp index aa36715..3da61ff 100644 --- a/src/CudaForwardProjectionAlgorithm3D.cpp +++ b/src/CudaForwardProjectionAlgorithm3D.cpp @@ -78,40 +78,47 @@ bool CCudaForwardProjectionAlgorithm3D::initialize(const Config& _cfg) ASTRA_ASSERT(_cfg.self); ConfigStackCheck<CAlgorithm> CC("CudaForwardProjectionAlgorithm3D", this, _cfg); - XMLNode* node; + XMLNode node; int id; // sinogram data - node = _cfg.self->getSingleNode("ProjectionDataId"); + node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "CudaForwardProjection3D", "No ProjectionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pProjections = dynamic_cast<CFloat32ProjectionData3DMemory*>(CData3DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ProjectionDataId"); // reconstruction data - node = _cfg.self->getSingleNode("VolumeDataId"); + node = _cfg.self.getSingleNode("VolumeDataId"); ASTRA_CONFIG_CHECK(node, "CudaForwardProjection3D", "No VolumeDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pVolume = dynamic_cast<CFloat32VolumeData3DMemory*>(CData3DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("VolumeDataId"); // optional: projector - node = _cfg.self->getSingleNode("ProjectorId"); + node = _cfg.self.getSingleNode("ProjectorId"); + CCudaProjector3D* pCudaProjector = 0; + m_pProjector = 0; if (node) { - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pProjector = CProjector3DManager::getSingleton().get(id); - ASTRA_DELETE(node); - } else { - m_pProjector = 0; // TODO: or manually construct default projector? + pCudaProjector = dynamic_cast<CCudaProjector3D*>(CProjector3DManager::getSingleton().get(id)); + m_pProjector = pCudaProjector; + if (!pCudaProjector) { + // TODO: Report + } } CC.markNodeParsed("ProjectorId"); // GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); CC.markOptionParsed("GPUindex"); - m_iDetectorSuperSampling = (int)_cfg.self->getOptionNumerical("DetectorSuperSampling", 1); + + + m_iDetectorSuperSampling = 1; + if (pCudaProjector) + m_iDetectorSuperSampling = pCudaProjector->getDetectorSuperSampling(); + m_iDetectorSuperSampling = (int)_cfg.self.getOptionNumerical("DetectorSuperSampling", m_iDetectorSuperSampling); CC.markOptionParsed("DetectorSuperSampling"); // success diff --git a/src/CudaProjector2D.cpp b/src/CudaProjector2D.cpp index 056ea3b..a26e32d 100644 --- a/src/CudaProjector2D.cpp +++ b/src/CudaProjector2D.cpp @@ -59,6 +59,8 @@ void CCudaProjector2D::_clear() m_bIsInitialized = false; m_projectionKernel = ker2d_default; + m_iVoxelSuperSampling = 1; + m_iDetectorSuperSampling = 1; } //---------------------------------------------------------------------------------------- @@ -104,10 +106,10 @@ bool CCudaProjector2D::initialize(const Config& _cfg) // TODO: Check the projection geometry is a supported type - XMLNode* node = _cfg.self->getSingleNode("ProjectionKernel"); + XMLNode node = _cfg.self.getSingleNode("ProjectionKernel"); m_projectionKernel = ker2d_default; if (node) { - std::string sProjKernel = node->getContent(); + std::string sProjKernel = node.getContent(); if (sProjKernel == "default") { @@ -115,9 +117,14 @@ bool CCudaProjector2D::initialize(const Config& _cfg) return false; } } - ASTRA_DELETE(node); CC.markNodeParsed("ProjectionKernel"); + m_iVoxelSuperSampling = (int)_cfg.self.getOptionNumerical("VoxelSuperSampling", 1); + CC.markOptionParsed("VoxelSuperSampling"); + + m_iDetectorSuperSampling = (int)_cfg.self.getOptionNumerical("DetectorSuperSampling", 1); + CC.markOptionParsed("DetectorSuperSampling"); + m_bIsInitialized = _check(); return m_bIsInitialized; } diff --git a/src/CudaProjector3D.cpp b/src/CudaProjector3D.cpp index 2f4c799..d2fd74c 100644 --- a/src/CudaProjector3D.cpp +++ b/src/CudaProjector3D.cpp @@ -62,6 +62,8 @@ void CCudaProjector3D::_clear() m_bIsInitialized = false; m_projectionKernel = ker3d_default; + m_iVoxelSuperSampling = 1; + m_iDetectorSuperSampling = 1; } //---------------------------------------------------------------------------------------- @@ -105,10 +107,10 @@ bool CCudaProjector3D::initialize(const Config& _cfg) return false; } - XMLNode* node = _cfg.self->getSingleNode("ProjectionKernel"); + XMLNode node = _cfg.self.getSingleNode("ProjectionKernel"); m_projectionKernel = ker3d_default; if (node) { - std::string sProjKernel = node->getContent(); + std::string sProjKernel = node.getContent(); if (sProjKernel == "default") { @@ -118,9 +120,14 @@ bool CCudaProjector3D::initialize(const Config& _cfg) return false; } } - ASTRA_DELETE(node); CC.markNodeParsed("ProjectionKernel"); + m_iVoxelSuperSampling = (int)_cfg.self.getOptionNumerical("VoxelSuperSampling", 1); + CC.markOptionParsed("VoxelSuperSampling"); + + m_iDetectorSuperSampling = (int)_cfg.self.getOptionNumerical("DetectorSuperSampling", 1); + CC.markOptionParsed("DetectorSuperSampling"); + m_bIsInitialized = _check(); return m_bIsInitialized; } diff --git a/src/CudaReconstructionAlgorithm2D.cpp b/src/CudaReconstructionAlgorithm2D.cpp index 1c6b763..71b6637 100644 --- a/src/CudaReconstructionAlgorithm2D.cpp +++ b/src/CudaReconstructionAlgorithm2D.cpp @@ -95,96 +95,101 @@ bool CCudaReconstructionAlgorithm2D::initialize(const Config& _cfg) clear(); } + // Projector + XMLNode node = _cfg.self.getSingleNode("ProjectorId"); + CCudaProjector2D* pCudaProjector = 0; + if (node) { + int id = boost::lexical_cast<int>(node.getContent()); + CProjector2D *projector = CProjector2DManager::getSingleton().get(id); + pCudaProjector = dynamic_cast<CCudaProjector2D*>(projector); + if (!pCudaProjector) { + ASTRA_WARN("non-CUDA Projector2D passed"); + } + } + CC.markNodeParsed("ProjectorId"); + + // sinogram data - XMLNode* node = _cfg.self->getSingleNode("ProjectionDataId"); + node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "CudaSirt2", "No ProjectionDataId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pSinogram = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ProjectionDataId"); // reconstruction data - node = _cfg.self->getSingleNode("ReconstructionDataId"); + node = _cfg.self.getSingleNode("ReconstructionDataId"); ASTRA_CONFIG_CHECK(node, "CudaSirt2", "No ReconstructionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pReconstruction = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ReconstructionDataId"); // fixed mask - if (_cfg.self->hasOption("ReconstructionMaskId")) { + if (_cfg.self.hasOption("ReconstructionMaskId")) { m_bUseReconstructionMask = true; - id = boost::lexical_cast<int>(_cfg.self->getOption("ReconstructionMaskId")); + id = boost::lexical_cast<int>(_cfg.self.getOption("ReconstructionMaskId")); m_pReconstructionMask = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); ASTRA_CONFIG_CHECK(m_pReconstructionMask, "CudaReconstruction2D", "Invalid ReconstructionMaskId."); } CC.markOptionParsed("ReconstructionMaskId"); // fixed mask - if (_cfg.self->hasOption("SinogramMaskId")) { + if (_cfg.self.hasOption("SinogramMaskId")) { m_bUseSinogramMask = true; - id = boost::lexical_cast<int>(_cfg.self->getOption("SinogramMaskId")); + id = boost::lexical_cast<int>(_cfg.self.getOption("SinogramMaskId")); m_pSinogramMask = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); ASTRA_CONFIG_CHECK(m_pSinogramMask, "CudaReconstruction2D", "Invalid SinogramMaskId."); } CC.markOptionParsed("SinogramMaskId"); // Constraints - NEW - if (_cfg.self->hasOption("MinConstraint")) { + if (_cfg.self.hasOption("MinConstraint")) { m_bUseMinConstraint = true; - m_fMinValue = _cfg.self->getOptionNumerical("MinConstraint", 0.0f); + m_fMinValue = _cfg.self.getOptionNumerical("MinConstraint", 0.0f); CC.markOptionParsed("MinConstraint"); } else { // Constraint - OLD - m_bUseMinConstraint = _cfg.self->getOptionBool("UseMinConstraint", false); + m_bUseMinConstraint = _cfg.self.getOptionBool("UseMinConstraint", false); CC.markOptionParsed("UseMinConstraint"); if (m_bUseMinConstraint) { - m_fMinValue = _cfg.self->getOptionNumerical("MinConstraintValue", 0.0f); + m_fMinValue = _cfg.self.getOptionNumerical("MinConstraintValue", 0.0f); CC.markOptionParsed("MinConstraintValue"); } } - if (_cfg.self->hasOption("MaxConstraint")) { + if (_cfg.self.hasOption("MaxConstraint")) { m_bUseMaxConstraint = true; - m_fMaxValue = _cfg.self->getOptionNumerical("MaxConstraint", 255.0f); + m_fMaxValue = _cfg.self.getOptionNumerical("MaxConstraint", 255.0f); CC.markOptionParsed("MaxConstraint"); } else { // Constraint - OLD - m_bUseMaxConstraint = _cfg.self->getOptionBool("UseMaxConstraint", false); + m_bUseMaxConstraint = _cfg.self.getOptionBool("UseMaxConstraint", false); CC.markOptionParsed("UseMaxConstraint"); if (m_bUseMaxConstraint) { - m_fMaxValue = _cfg.self->getOptionNumerical("MaxConstraintValue", 0.0f); + m_fMaxValue = _cfg.self.getOptionNumerical("MaxConstraintValue", 0.0f); CC.markOptionParsed("MaxConstraintValue"); } } // GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUIndex", m_iGPUIndex); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUIndex", m_iGPUIndex); CC.markOptionParsed("GPUindex"); - if (!_cfg.self->hasOption("GPUindex")) + if (!_cfg.self.hasOption("GPUindex")) CC.markOptionParsed("GPUIndex"); - // Detector supersampling factor - m_iDetectorSuperSampling = (int)_cfg.self->getOptionNumerical("DetectorSuperSampling", 1); + // Supersampling factors + m_iDetectorSuperSampling = 1; + m_iPixelSuperSampling = 1; + if (pCudaProjector) { + // New interface + m_iDetectorSuperSampling = pCudaProjector->getDetectorSuperSampling(); + m_iPixelSuperSampling = pCudaProjector->getVoxelSuperSampling(); + } + // Deprecated options + m_iDetectorSuperSampling = (int)_cfg.self.getOptionNumerical("DetectorSuperSampling", m_iDetectorSuperSampling); + m_iPixelSuperSampling = (int)_cfg.self.getOptionNumerical("PixelSuperSampling", m_iPixelSuperSampling); CC.markOptionParsed("DetectorSuperSampling"); - - // Pixel supersampling factor - m_iPixelSuperSampling = (int)_cfg.self->getOptionNumerical("PixelSuperSampling", 1); CC.markOptionParsed("PixelSuperSampling"); - // This isn't used yet, but passing it is not something to warn about - node = _cfg.self->getSingleNode("ProjectorId"); - if (node) { - id = boost::lexical_cast<int>(node->getContent()); - CProjector2D *projector = CProjector2DManager::getSingleton().get(id); - if (!dynamic_cast<CCudaProjector2D*>(projector)) { - ASTRA_WARN("non-CUDA Projector2D passed"); - } - delete node; - } - CC.markNodeParsed("ProjectorId"); - - return _check(); } diff --git a/src/CudaRoiSelectAlgorithm.cpp b/src/CudaRoiSelectAlgorithm.cpp index bfccb3a..7635c69 100644 --- a/src/CudaRoiSelectAlgorithm.cpp +++ b/src/CudaRoiSelectAlgorithm.cpp @@ -66,22 +66,21 @@ bool CCudaRoiSelectAlgorithm::initialize(const Config& _cfg) ConfigStackCheck<CAlgorithm> CC("CudaDartMaskAlgorithm", this, _cfg); // reconstruction data - XMLNode* node = _cfg.self->getSingleNode("DataId"); + XMLNode node = _cfg.self.getSingleNode("DataId"); ASTRA_CONFIG_CHECK(node, "CudaRoiSelect", "No DataId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pData = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("DataId"); // Option: GPU number - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUIndex", m_iGPUIndex); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUIndex", m_iGPUIndex); CC.markOptionParsed("GPUindex"); - if (!_cfg.self->hasOption("GPUindex")) + if (!_cfg.self.hasOption("GPUindex")) CC.markOptionParsed("GPUIndex"); // Option: Radius - m_fRadius = (unsigned int)_cfg.self->getOptionNumerical("Radius", 0.0f); + m_fRadius = (unsigned int)_cfg.self.getOptionNumerical("Radius", 0.0f); CC.markOptionParsed("Radius"); _check(); diff --git a/src/CudaSartAlgorithm.cpp b/src/CudaSartAlgorithm.cpp index 8e22c59..8c0c6d7 100644 --- a/src/CudaSartAlgorithm.cpp +++ b/src/CudaSartAlgorithm.cpp @@ -74,7 +74,7 @@ bool CCudaSartAlgorithm::initialize(const Config& _cfg) // projection order int projectionCount = m_pSinogram->getGeometry()->getProjectionAngleCount(); int* projectionOrder = NULL; - string projOrder = _cfg.self->getOption("ProjectionOrder", "random"); + string projOrder = _cfg.self.getOption("ProjectionOrder", "random"); CC.markOptionParsed("ProjectionOrder"); if (projOrder == "sequential") { projectionOrder = new int[projectionCount]; @@ -97,7 +97,7 @@ bool CCudaSartAlgorithm::initialize(const Config& _cfg) sart->setProjectionOrder(projectionOrder, projectionCount); delete[] projectionOrder; } else if (projOrder == "custom") { - vector<float32> projOrderList = _cfg.self->getOptionNumericalArray("ProjectionOrderList"); + vector<float32> projOrderList = _cfg.self.getOptionNumericalArray("ProjectionOrderList"); projectionOrder = new int[projOrderList.size()]; for (int i = 0; i < projOrderList.size(); i++) { projectionOrder[i] = static_cast<int>(projOrderList[i]); diff --git a/src/CudaSirtAlgorithm.cpp b/src/CudaSirtAlgorithm.cpp index f6eb79a..d424915 100644 --- a/src/CudaSirtAlgorithm.cpp +++ b/src/CudaSirtAlgorithm.cpp @@ -76,13 +76,13 @@ bool CCudaSirtAlgorithm::initialize(const Config& _cfg) return false; // min/max masks - if (_cfg.self->hasOption("MinMaskId")) { - int id = boost::lexical_cast<int>(_cfg.self->getOption("MinMaskId")); + if (_cfg.self.hasOption("MinMaskId")) { + int id = boost::lexical_cast<int>(_cfg.self.getOption("MinMaskId")); m_pMinMask = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); } CC.markOptionParsed("MinMaskId"); - if (_cfg.self->hasOption("MaxMaskId")) { - int id = boost::lexical_cast<int>(_cfg.self->getOption("MaxMaskId")); + if (_cfg.self.hasOption("MaxMaskId")) { + int id = boost::lexical_cast<int>(_cfg.self.getOption("MaxMaskId")); m_pMaxMask = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); } CC.markOptionParsed("MaxMaskId"); diff --git a/src/CudaSirtAlgorithm3D.cpp b/src/CudaSirtAlgorithm3D.cpp index d67778f..b833e07 100644 --- a/src/CudaSirtAlgorithm3D.cpp +++ b/src/CudaSirtAlgorithm3D.cpp @@ -36,6 +36,7 @@ $Id$ #include "astra/ParallelProjectionGeometry3D.h" #include "astra/ParallelVecProjectionGeometry3D.h" #include "astra/ConeVecProjectionGeometry3D.h" +#include "astra/CudaProjector3D.h" #include "../cuda/3d/astra3d.h" @@ -107,12 +108,28 @@ bool CCudaSirtAlgorithm3D::initialize(const Config& _cfg) return false; } - m_iGPUIndex = (int)_cfg.self->getOptionNumerical("GPUindex", -1); + CCudaProjector3D* pCudaProjector = 0; + pCudaProjector = dynamic_cast<CCudaProjector3D*>(m_pProjector); + if (!pCudaProjector) { + // TODO: Report + } + + m_iGPUIndex = (int)_cfg.self.getOptionNumerical("GPUindex", -1); CC.markOptionParsed("GPUindex"); - m_iDetectorSuperSampling = (int)_cfg.self->getOptionNumerical("DetectorSuperSampling", 1); - CC.markOptionParsed("DetectorSuperSampling"); - m_iVoxelSuperSampling = (int)_cfg.self->getOptionNumerical("VoxelSuperSampling", 1); + + + m_iVoxelSuperSampling = 1; + m_iDetectorSuperSampling = 1; + if (pCudaProjector) { + // New interface + m_iVoxelSuperSampling = pCudaProjector->getVoxelSuperSampling(); + m_iDetectorSuperSampling = pCudaProjector->getDetectorSuperSampling(); + } + // Deprecated options + m_iVoxelSuperSampling = (int)_cfg.self.getOptionNumerical("VoxelSuperSampling", m_iVoxelSuperSampling); + m_iDetectorSuperSampling = (int)_cfg.self.getOptionNumerical("DetectorSuperSampling", m_iDetectorSuperSampling); CC.markOptionParsed("VoxelSuperSampling"); + CC.markOptionParsed("DetectorSuperSampling"); m_pSirt = new AstraSIRT3d(); diff --git a/src/FanFlatProjectionGeometry2D.cpp b/src/FanFlatProjectionGeometry2D.cpp index d757f18..32a19bc 100644 --- a/src/FanFlatProjectionGeometry2D.cpp +++ b/src/FanFlatProjectionGeometry2D.cpp @@ -134,17 +134,15 @@ bool CFanFlatProjectionGeometry2D::initialize(const Config& _cfg) CProjectionGeometry2D::initialize(_cfg); // Required: DistanceOriginDetector - XMLNode* node = _cfg.self->getSingleNode("DistanceOriginDetector"); + XMLNode node = _cfg.self.getSingleNode("DistanceOriginDetector"); ASTRA_CONFIG_CHECK(node, "FanFlatProjectionGeometry2D", "No DistanceOriginDetector tag specified."); - m_fOriginDetectorDistance = boost::lexical_cast<float32>(node->getContent()); - ASTRA_DELETE(node); + m_fOriginDetectorDistance = boost::lexical_cast<float32>(node.getContent()); CC.markNodeParsed("DistanceOriginDetector"); // Required: DetectorOriginSource - node = _cfg.self->getSingleNode("DistanceOriginSource"); + node = _cfg.self.getSingleNode("DistanceOriginSource"); ASTRA_CONFIG_CHECK(node, "FanFlatProjectionGeometry2D", "No DistanceOriginSource tag specified."); - m_fOriginSourceDistance = boost::lexical_cast<float32>(node->getContent()); - ASTRA_DELETE(node); + m_fOriginSourceDistance = boost::lexical_cast<float32>(node.getContent()); CC.markNodeParsed("DistanceOriginSource"); // success @@ -209,12 +207,12 @@ Config* CFanFlatProjectionGeometry2D::getConfiguration() const { Config* cfg = new Config(); cfg->initialize("ProjectionGeometry2D"); - cfg->self->addAttribute("type", "fanflat"); - cfg->self->addChildNode("DetectorCount", getDetectorCount()); - cfg->self->addChildNode("DetectorWidth", getDetectorWidth()); - cfg->self->addChildNode("DistanceOriginSource", getOriginSourceDistance()); - cfg->self->addChildNode("DistanceOriginDetector", getOriginDetectorDistance()); - cfg->self->addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); + cfg->self.addAttribute("type", "fanflat"); + cfg->self.addChildNode("DetectorCount", getDetectorCount()); + cfg->self.addChildNode("DetectorWidth", getDetectorWidth()); + cfg->self.addChildNode("DistanceOriginSource", getOriginSourceDistance()); + cfg->self.addChildNode("DistanceOriginDetector", getOriginDetectorDistance()); + cfg->self.addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); return cfg; } //---------------------------------------------------------------------------------------- diff --git a/src/FanFlatVecProjectionGeometry2D.cpp b/src/FanFlatVecProjectionGeometry2D.cpp index 9c7b596..4104379 100644 --- a/src/FanFlatVecProjectionGeometry2D.cpp +++ b/src/FanFlatVecProjectionGeometry2D.cpp @@ -116,25 +116,23 @@ bool CFanFlatVecProjectionGeometry2D::initialize(const Config& _cfg) ASTRA_ASSERT(_cfg.self); ConfigStackCheck<CProjectionGeometry2D> CC("FanFlatVecProjectionGeometry2D", this, _cfg); - XMLNode* node; + XMLNode node; // TODO: Fix up class hierarchy... this class doesn't fit very well. // initialization of parent class //CProjectionGeometry2D::initialize(_cfg); // Required: DetectorCount - node = _cfg.self->getSingleNode("DetectorCount"); + node = _cfg.self.getSingleNode("DetectorCount"); ASTRA_CONFIG_CHECK(node, "FanFlatVecProjectionGeometry3D", "No DetectorRowCount tag specified."); - m_iDetectorCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iDetectorCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("DetectorCount"); // Required: Vectors - node = _cfg.self->getSingleNode("Vectors"); + node = _cfg.self.getSingleNode("Vectors"); ASTRA_CONFIG_CHECK(node, "FanFlatVecProjectionGeometry3D", "No Vectors tag specified."); - vector<float32> data = node->getContentNumericalArray(); + vector<float32> data = node.getContentNumericalArray(); CC.markNodeParsed("Vectors"); - ASTRA_DELETE(node); ASTRA_CONFIG_CHECK(data.size() % 6 == 0, "FanFlatVecProjectionGeometry3D", "Vectors doesn't consist of 6-tuples."); m_iProjectionAngleCount = data.size() / 6; m_pProjectionAngles = new SFanProjection[m_iProjectionAngleCount]; @@ -232,8 +230,8 @@ Config* CFanFlatVecProjectionGeometry2D::getConfiguration() const { Config* cfg = new Config(); cfg->initialize("ProjectionGeometry2D"); - cfg->self->addAttribute("type", "fanflat_vec"); - cfg->self->addChildNode("DetectorCount", getDetectorCount()); + cfg->self.addAttribute("type", "fanflat_vec"); + cfg->self.addChildNode("DetectorCount", getDetectorCount()); std::string vectors = ""; for (int i = 0; i < m_iProjectionAngleCount; ++i) { SFanProjection& p = m_pProjectionAngles[i]; @@ -245,7 +243,7 @@ Config* CFanFlatVecProjectionGeometry2D::getConfiguration() const vectors += boost::lexical_cast<string>(p.fDetUY); if (i < m_iProjectionAngleCount-1) vectors += ';'; } - cfg->self->addChildNode("Vectors", vectors); + cfg->self.addChildNode("Vectors", vectors); return cfg; } //---------------------------------------------------------------------------------------- diff --git a/src/FilteredBackProjectionAlgorithm.cpp b/src/FilteredBackProjectionAlgorithm.cpp index 4a8e5ac..f494d22 100644 --- a/src/FilteredBackProjectionAlgorithm.cpp +++ b/src/FilteredBackProjectionAlgorithm.cpp @@ -94,30 +94,27 @@ bool CFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) ASTRA_ASSERT(_cfg.self); // projector - XMLNode* node = _cfg.self->getSingleNode("ProjectorId"); + XMLNode node = _cfg.self.getSingleNode("ProjectorId"); ASTRA_CONFIG_CHECK(node, "FilteredBackProjection", "No ProjectorId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pProjector = CProjector2DManager::getSingleton().get(id); - ASTRA_DELETE(node); // sinogram data - node = _cfg.self->getSingleNode("ProjectionDataId"); + node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "FilteredBackProjection", "No ProjectionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pSinogram = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); // volume data - node = _cfg.self->getSingleNode("ReconstructionDataId"); + node = _cfg.self.getSingleNode("ReconstructionDataId"); ASTRA_CONFIG_CHECK(node, "FilteredBackProjection", "No ReconstructionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pReconstruction = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); - node = _cfg.self->getSingleNode("ProjectionIndex"); + node = _cfg.self.getSingleNode("ProjectionIndex"); if (node) { - vector<float32> projectionIndex = node->getContentNumericalArray(); + vector<float32> projectionIndex = node.getContentNumericalArray(); int angleCount = projectionIndex.size(); int detectorCount = m_pProjector->getProjectionGeometry()->getDetectorCount(); @@ -154,7 +151,6 @@ bool CFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) m_pProjector = new CParallelBeamLineKernelProjector2D(pg,m_pReconstruction->getGeometry()); m_pSinogram = new CFloat32ProjectionData2D(pg, sinogramData2D); } - ASTRA_DELETE(node); // TODO: check that the angles are linearly spaced between 0 and pi diff --git a/src/ForwardProjectionAlgorithm.cpp b/src/ForwardProjectionAlgorithm.cpp index b530491..f356824 100644 --- a/src/ForwardProjectionAlgorithm.cpp +++ b/src/ForwardProjectionAlgorithm.cpp @@ -126,37 +126,34 @@ bool CForwardProjectionAlgorithm::initialize(const Config& _cfg) } // projector - XMLNode* node = _cfg.self->getSingleNode("ProjectorId"); + XMLNode node = _cfg.self.getSingleNode("ProjectorId"); ASTRA_CONFIG_CHECK(node, "ForwardProjection", "No ProjectorId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pProjector = CProjector2DManager::getSingleton().get(id); - ASTRA_DELETE(node); // sinogram data - node = _cfg.self->getSingleNode("ProjectionDataId"); + node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "ForwardProjection", "No ProjectionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pSinogram = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); // volume data - node = _cfg.self->getSingleNode("VolumeDataId"); + node = _cfg.self.getSingleNode("VolumeDataId"); ASTRA_CONFIG_CHECK(node, "ForwardProjection", "No VolumeDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pVolume = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); // volume mask - if (_cfg.self->hasOption("VolumeMaskId")) { + if (_cfg.self.hasOption("VolumeMaskId")) { m_bUseVolumeMask = true; - id = boost::lexical_cast<int>(_cfg.self->getOption("VolumeMaskId")); + id = boost::lexical_cast<int>(_cfg.self.getOption("VolumeMaskId")); m_pVolumeMask = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); } // sino mask - if (_cfg.self->hasOption("SinogramMaskId")) { + if (_cfg.self.hasOption("SinogramMaskId")) { m_bUseSinogramMask = true; - id = boost::lexical_cast<int>(_cfg.self->getOption("SinogramMaskId")); + id = boost::lexical_cast<int>(_cfg.self.getOption("SinogramMaskId")); m_pSinogramMask = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); } diff --git a/src/ParallelBeamBlobKernelProjector2D.cpp b/src/ParallelBeamBlobKernelProjector2D.cpp index 3253f88..4559a48 100644 --- a/src/ParallelBeamBlobKernelProjector2D.cpp +++ b/src/ParallelBeamBlobKernelProjector2D.cpp @@ -128,28 +128,28 @@ bool CParallelBeamBlobKernelProjector2D::initialize(const Config& _cfg) } // required: Kernel - XMLNode* node = _cfg.self->getSingleNode("Kernel"); + XMLNode node = _cfg.self.getSingleNode("Kernel"); ASTRA_CONFIG_CHECK(node, "BlobProjector", "No Kernel tag specified."); { // Required: KernelSize - XMLNode* node2 = node->getSingleNode("KernelSize"); + XMLNode node2 = node.getSingleNode("KernelSize"); ASTRA_CONFIG_CHECK(node2, "BlobProjector", "No Kernel/KernelSize tag specified."); - m_fBlobSize = boost::lexical_cast<float32>(node2->getContent()); + m_fBlobSize = boost::lexical_cast<float32>(node2.getContent()); // Required: SampleRate - node2 = node->getSingleNode("SampleRate"); + node2 = node.getSingleNode("SampleRate"); ASTRA_CONFIG_CHECK(node2, "BlobProjector", "No Kernel/SampleRate tag specified."); - m_fBlobSampleRate = boost::lexical_cast<float32>(node2->getContent()); + m_fBlobSampleRate = boost::lexical_cast<float32>(node2.getContent()); // Required: SampleCount - node2 = node->getSingleNode("SampleCount"); + node2 = node.getSingleNode("SampleCount"); ASTRA_CONFIG_CHECK(node2, "BlobProjector", "No Kernel/SampleCount tag specified."); - m_iBlobSampleCount = boost::lexical_cast<int>(node2->getContent()); + m_iBlobSampleCount = boost::lexical_cast<int>(node2.getContent()); // Required: KernelValues - node2 = node->getSingleNode("KernelValues"); + node2 = node.getSingleNode("KernelValues"); ASTRA_CONFIG_CHECK(node2, "BlobProjector", "No Kernel/KernelValues tag specified."); - vector<float32> values = node2->getContentNumericalArray(); + vector<float32> values = node2.getContentNumericalArray(); ASTRA_CONFIG_CHECK(values.size() == (unsigned int)m_iBlobSampleCount, "BlobProjector", "Number of specified values doesn't match SampleCount."); m_pfBlobValues = new float32[m_iBlobSampleCount]; for (int i = 0; i < m_iBlobSampleCount; i++) { @@ -157,9 +157,9 @@ bool CParallelBeamBlobKernelProjector2D::initialize(const Config& _cfg) } // Required: KernelValues - node2 = node->getSingleNode("KernelValuesNeg"); + node2 = node.getSingleNode("KernelValuesNeg"); ASTRA_CONFIG_CHECK(node2, "BlobProjector", "No Kernel/KernelValuesNeg tag specified."); - vector<float32> values2 = node2->getContentNumericalArray(); + vector<float32> values2 = node2.getContentNumericalArray(); ASTRA_CONFIG_CHECK(values2.size() == (unsigned int)m_iBlobSampleCount, "BlobProjector", "Number of specified values doesn't match SampleCount."); m_pfBlobValuesNeg = new float32[m_iBlobSampleCount]; for (int i = 0; i < m_iBlobSampleCount; i++) { diff --git a/src/ParallelProjectionGeometry2D.cpp b/src/ParallelProjectionGeometry2D.cpp index cac8f30..7260b83 100644 --- a/src/ParallelProjectionGeometry2D.cpp +++ b/src/ParallelProjectionGeometry2D.cpp @@ -176,10 +176,15 @@ Config* CParallelProjectionGeometry2D::getConfiguration() const { Config* cfg = new Config(); cfg->initialize("ProjectionGeometry2D"); - cfg->self->addAttribute("type", "parallel"); - cfg->self->addChildNode("DetectorCount", getDetectorCount()); - cfg->self->addChildNode("DetectorWidth", getDetectorWidth()); - cfg->self->addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); + cfg->self.addAttribute("type", "parallel"); + cfg->self.addChildNode("DetectorCount", getDetectorCount()); + cfg->self.addChildNode("DetectorWidth", getDetectorWidth()); + cfg->self.addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); + if(m_pfExtraDetectorOffset!=NULL){ + XMLNode opt = cfg->self.addChildNode("Option"); + opt.addAttribute("key","ExtraDetectorOffset"); + opt.setContent(m_pfExtraDetectorOffset, m_iProjectionAngleCount); + } return cfg; } //---------------------------------------------------------------------------------------- diff --git a/src/ParallelProjectionGeometry3D.cpp b/src/ParallelProjectionGeometry3D.cpp index eb200f9..1c87157 100644 --- a/src/ParallelProjectionGeometry3D.cpp +++ b/src/ParallelProjectionGeometry3D.cpp @@ -164,12 +164,12 @@ Config* CParallelProjectionGeometry3D::getConfiguration() const { Config* cfg = new Config(); cfg->initialize("ProjectionGeometry3D"); - cfg->self->addAttribute("type", "parallel3d"); - cfg->self->addChildNode("DetectorRowCount", m_iDetectorRowCount); - cfg->self->addChildNode("DetectorColCount", m_iDetectorColCount); - cfg->self->addChildNode("DetectorSpacingX", m_fDetectorSpacingX); - cfg->self->addChildNode("DetectorSpacingY", m_fDetectorSpacingY); - cfg->self->addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); + cfg->self.addAttribute("type", "parallel3d"); + cfg->self.addChildNode("DetectorRowCount", m_iDetectorRowCount); + cfg->self.addChildNode("DetectorColCount", m_iDetectorColCount); + cfg->self.addChildNode("DetectorSpacingX", m_fDetectorSpacingX); + cfg->self.addChildNode("DetectorSpacingY", m_fDetectorSpacingY); + cfg->self.addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); return cfg; } //---------------------------------------------------------------------------------------- diff --git a/src/ParallelVecProjectionGeometry3D.cpp b/src/ParallelVecProjectionGeometry3D.cpp index dc325e9..ffad6d0 100644 --- a/src/ParallelVecProjectionGeometry3D.cpp +++ b/src/ParallelVecProjectionGeometry3D.cpp @@ -73,33 +73,30 @@ bool CParallelVecProjectionGeometry3D::initialize(const Config& _cfg) ASTRA_ASSERT(_cfg.self); ConfigStackCheck<CProjectionGeometry3D> CC("ParallelVecProjectionGeometry3D", this, _cfg); - XMLNode* node; + XMLNode node; // TODO: Fix up class hierarchy... this class doesn't fit very well. // initialization of parent class //CProjectionGeometry3D::initialize(_cfg); // Required: DetectorRowCount - node = _cfg.self->getSingleNode("DetectorRowCount"); + node = _cfg.self.getSingleNode("DetectorRowCount"); ASTRA_CONFIG_CHECK(node, "ParallelVecProjectionGeometry3D", "No DetectorRowCount tag specified."); - m_iDetectorRowCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iDetectorRowCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("DetectorRowCount"); // Required: DetectorCount - node = _cfg.self->getSingleNode("DetectorColCount"); + node = _cfg.self.getSingleNode("DetectorColCount"); ASTRA_CONFIG_CHECK(node, "", "No DetectorColCount tag specified."); - m_iDetectorColCount = boost::lexical_cast<int>(node->getContent()); + m_iDetectorColCount = boost::lexical_cast<int>(node.getContent()); m_iDetectorTotCount = m_iDetectorRowCount * m_iDetectorColCount; - ASTRA_DELETE(node); CC.markNodeParsed("DetectorColCount"); // Required: Vectors - node = _cfg.self->getSingleNode("Vectors"); + node = _cfg.self.getSingleNode("Vectors"); ASTRA_CONFIG_CHECK(node, "ParallelVecProjectionGeometry3D", "No Vectors tag specified."); - vector<double> data = node->getContentNumericalArrayDouble(); + vector<double> data = node.getContentNumericalArrayDouble(); CC.markNodeParsed("Vectors"); - ASTRA_DELETE(node); ASTRA_CONFIG_CHECK(data.size() % 12 == 0, "ParallelVecProjectionGeometry3D", "Vectors doesn't consist of 12-tuples."); m_iProjectionAngleCount = data.size() / 12; m_pProjectionAngles = new SPar3DProjection[m_iProjectionAngleCount]; @@ -208,9 +205,9 @@ Config* CParallelVecProjectionGeometry3D::getConfiguration() const Config* cfg = new Config(); cfg->initialize("ProjectionGeometry3D"); - cfg->self->addAttribute("type", "parallel3d_vec"); - cfg->self->addChildNode("DetectorRowCount", m_iDetectorRowCount); - cfg->self->addChildNode("DetectorColCount", m_iDetectorColCount); + cfg->self.addAttribute("type", "parallel3d_vec"); + cfg->self.addChildNode("DetectorRowCount", m_iDetectorRowCount); + cfg->self.addChildNode("DetectorColCount", m_iDetectorColCount); std::string vectors = ""; for (int i = 0; i < m_iProjectionAngleCount; ++i) { @@ -229,7 +226,7 @@ Config* CParallelVecProjectionGeometry3D::getConfiguration() const vectors += boost::lexical_cast<string>(p.fDetVZ); if (i < m_iProjectionAngleCount-1) vectors += ';'; } - cfg->self->addChildNode("Vectors", vectors); + cfg->self.addChildNode("Vectors", vectors); return cfg; } diff --git a/src/ProjectionGeometry2D.cpp b/src/ProjectionGeometry2D.cpp index 89b5fe0..b89605b 100644 --- a/src/ProjectionGeometry2D.cpp +++ b/src/ProjectionGeometry2D.cpp @@ -124,24 +124,21 @@ bool CProjectionGeometry2D::initialize(const Config& _cfg) } // Required: DetectorWidth - XMLNode* node = _cfg.self->getSingleNode("DetectorWidth"); + XMLNode node = _cfg.self.getSingleNode("DetectorWidth"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry2D", "No DetectorWidth tag specified."); - m_fDetectorWidth = boost::lexical_cast<float32>(node->getContent()); - ASTRA_DELETE(node); + m_fDetectorWidth = boost::lexical_cast<float32>(node.getContent()); CC.markNodeParsed("DetectorWidth"); // Required: DetectorCount - node = _cfg.self->getSingleNode("DetectorCount"); + node = _cfg.self.getSingleNode("DetectorCount"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry2D", "No DetectorCount tag specified."); - m_iDetectorCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iDetectorCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("DetectorCount"); // Required: ProjectionAngles - node = _cfg.self->getSingleNode("ProjectionAngles"); + node = _cfg.self.getSingleNode("ProjectionAngles"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry2D", "No ProjectionAngles tag specified."); - vector<float32> angles = node->getContentNumericalArray(); - delete node; + vector<float32> angles = node.getContentNumericalArray(); m_iProjectionAngleCount = angles.size(); ASTRA_CONFIG_CHECK(m_iProjectionAngleCount > 0, "ProjectionGeometry2D", "Not enough ProjectionAngles specified."); m_pfProjectionAngles = new float32[m_iProjectionAngleCount]; @@ -150,7 +147,7 @@ bool CProjectionGeometry2D::initialize(const Config& _cfg) } CC.markNodeParsed("ProjectionAngles"); - vector<float32> offset = _cfg.self->getOptionNumericalArray("ExtraDetectorOffset"); + vector<float32> offset = _cfg.self.getOptionNumericalArray("ExtraDetectorOffset"); m_pfExtraDetectorOffset = new float32[m_iProjectionAngleCount]; if (offset.size() == (size_t)m_iProjectionAngleCount) { for (int i = 0; i < m_iProjectionAngleCount; i++) { diff --git a/src/ProjectionGeometry3D.cpp b/src/ProjectionGeometry3D.cpp index 5b77767..ef0246c 100644 --- a/src/ProjectionGeometry3D.cpp +++ b/src/ProjectionGeometry3D.cpp @@ -149,38 +149,34 @@ bool CProjectionGeometry3D::initialize(const Config& _cfg) ASTRA_ASSERT(_cfg.self); // Required: DetectorWidth - XMLNode* node = _cfg.self->getSingleNode("DetectorSpacingX"); + XMLNode node = _cfg.self.getSingleNode("DetectorSpacingX"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry3D", "No DetectorSpacingX tag specified."); - m_fDetectorSpacingX = boost::lexical_cast<float32>(node->getContent()); - ASTRA_DELETE(node); + m_fDetectorSpacingX = boost::lexical_cast<float32>(node.getContent()); CC.markNodeParsed("DetectorSpacingX"); // Required: DetectorHeight - node = _cfg.self->getSingleNode("DetectorSpacingY"); + node = _cfg.self.getSingleNode("DetectorSpacingY"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry3D", "No DetectorSpacingY tag specified."); - m_fDetectorSpacingY = boost::lexical_cast<float32>(node->getContent()); - ASTRA_DELETE(node); + m_fDetectorSpacingY = boost::lexical_cast<float32>(node.getContent()); CC.markNodeParsed("DetectorSpacingY"); // Required: DetectorRowCount - node = _cfg.self->getSingleNode("DetectorRowCount"); + node = _cfg.self.getSingleNode("DetectorRowCount"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry3D", "No DetectorRowCount tag specified."); - m_iDetectorRowCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iDetectorRowCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("DetectorRowCount"); // Required: DetectorCount - node = _cfg.self->getSingleNode("DetectorColCount"); + node = _cfg.self.getSingleNode("DetectorColCount"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry3D", "No DetectorColCount tag specified."); - m_iDetectorColCount = boost::lexical_cast<int>(node->getContent()); + m_iDetectorColCount = boost::lexical_cast<int>(node.getContent()); m_iDetectorTotCount = m_iDetectorRowCount * m_iDetectorColCount; - ASTRA_DELETE(node); CC.markNodeParsed("DetectorColCount"); // Required: ProjectionAngles - node = _cfg.self->getSingleNode("ProjectionAngles"); + node = _cfg.self.getSingleNode("ProjectionAngles"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry3D", "No ProjectionAngles tag specified."); - vector<float32> angles = node->getContentNumericalArray(); + vector<float32> angles = node.getContentNumericalArray(); m_iProjectionAngleCount = angles.size(); ASTRA_CONFIG_CHECK(m_iProjectionAngleCount > 0, "ProjectionGeometry3D", "Not enough ProjectionAngles specified."); m_pfProjectionAngles = new float32[m_iProjectionAngleCount]; @@ -188,7 +184,6 @@ bool CProjectionGeometry3D::initialize(const Config& _cfg) m_pfProjectionAngles[i] = angles[i]; } CC.markNodeParsed("ProjectionAngles"); - ASTRA_DELETE(node); // Interface class, so don't return true return false; diff --git a/src/Projector2D.cpp b/src/Projector2D.cpp index 32a2956..cf233a0 100644 --- a/src/Projector2D.cpp +++ b/src/Projector2D.cpp @@ -114,12 +114,12 @@ bool CProjector2D::initialize(const Config& _cfg) } // required: ProjectionGeometry - XMLNode* node = _cfg.self->getSingleNode("ProjectionGeometry"); + XMLNode node = _cfg.self.getSingleNode("ProjectionGeometry"); ASTRA_CONFIG_CHECK(node, "Projector2D", "No ProjectionGeometry tag specified."); // FIXME: Change how the base class is created. (This is duplicated // in astra_mex_data2d.cpp.) - std::string type = node->getAttribute("type"); + std::string type = node.getAttribute("type"); if (type == "sparse_matrix") { m_pProjectionGeometry = new CSparseMatrixProjectionGeometry2D(); m_pProjectionGeometry->initialize(Config(node)); @@ -141,7 +141,7 @@ bool CProjector2D::initialize(const Config& _cfg) // required: VolumeGeometry - node = _cfg.self->getSingleNode("VolumeGeometry"); + node = _cfg.self.getSingleNode("VolumeGeometry"); ASTRA_CONFIG_CHECK(node, "Projector2D", "No VolumeGeometry tag specified."); m_pVolumeGeometry = new CVolumeGeometry2D(); m_pVolumeGeometry->initialize(Config(node)); diff --git a/src/Projector3D.cpp b/src/Projector3D.cpp index 14cb16a..5e22105 100644 --- a/src/Projector3D.cpp +++ b/src/Projector3D.cpp @@ -92,11 +92,11 @@ bool CProjector3D::initialize(const Config& _cfg) assert(_cfg.self); ConfigStackCheck<CProjector3D> CC("Projector3D", this, _cfg); - XMLNode* node; + XMLNode node; - node = _cfg.self->getSingleNode("ProjectionGeometry"); + node = _cfg.self.getSingleNode("ProjectionGeometry"); ASTRA_CONFIG_CHECK(node, "Projector3D", "No ProjectionGeometry tag specified."); - std::string type = node->getAttribute("type"); + std::string type = node.getAttribute("type"); CProjectionGeometry3D* pProjGeometry = 0; if (type == "parallel3d") { pProjGeometry = new CParallelProjectionGeometry3D(); @@ -115,7 +115,7 @@ bool CProjector3D::initialize(const Config& _cfg) ASTRA_CONFIG_CHECK(m_pProjectionGeometry->isInitialized(), "Projector3D", "ProjectionGeometry not initialized."); CC.markNodeParsed("ProjectionGeometry"); - node = _cfg.self->getSingleNode("VolumeGeometry"); + node = _cfg.self.getSingleNode("VolumeGeometry"); ASTRA_CONFIG_CHECK(node, "Projector3D", "No VolumeGeometry tag specified."); CVolumeGeometry3D* pVolGeometry = new CVolumeGeometry3D(); pVolGeometry->initialize(Config(node)); // this deletes node diff --git a/src/ReconstructionAlgorithm2D.cpp b/src/ReconstructionAlgorithm2D.cpp index e089fac..767efe6 100644 --- a/src/ReconstructionAlgorithm2D.cpp +++ b/src/ReconstructionAlgorithm2D.cpp @@ -84,71 +84,68 @@ bool CReconstructionAlgorithm2D::initialize(const Config& _cfg) ConfigStackCheck<CAlgorithm> CC("ReconstructionAlgorithm2D", this, _cfg); // projector - XMLNode* node = _cfg.self->getSingleNode("ProjectorId"); + XMLNode node = _cfg.self.getSingleNode("ProjectorId"); ASTRA_CONFIG_CHECK(node, "Reconstruction2D", "No ProjectorId tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pProjector = CProjector2DManager::getSingleton().get(id); - ASTRA_DELETE(node); CC.markNodeParsed("ProjectorId"); // sinogram data - node = _cfg.self->getSingleNode("ProjectionDataId"); + node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "Reconstruction2D", "No ProjectionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pSinogram = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ProjectionDataId"); // reconstruction data - node = _cfg.self->getSingleNode("ReconstructionDataId"); + node = _cfg.self.getSingleNode("ReconstructionDataId"); ASTRA_CONFIG_CHECK(node, "Reconstruction2D", "No ReconstructionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pReconstruction = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ReconstructionDataId"); // fixed mask - if (_cfg.self->hasOption("ReconstructionMaskId")) { + if (_cfg.self.hasOption("ReconstructionMaskId")) { m_bUseReconstructionMask = true; - id = boost::lexical_cast<int>(_cfg.self->getOption("ReconstructionMaskId")); + id = boost::lexical_cast<int>(_cfg.self.getOption("ReconstructionMaskId")); m_pReconstructionMask = dynamic_cast<CFloat32VolumeData2D*>(CData2DManager::getSingleton().get(id)); ASTRA_CONFIG_CHECK(m_pReconstructionMask, "Reconstruction2D", "Invalid ReconstructionMaskId."); } CC.markOptionParsed("ReconstructionMaskId"); // fixed mask - if (_cfg.self->hasOption("SinogramMaskId")) { + if (_cfg.self.hasOption("SinogramMaskId")) { m_bUseSinogramMask = true; - id = boost::lexical_cast<int>(_cfg.self->getOption("SinogramMaskId")); + id = boost::lexical_cast<int>(_cfg.self.getOption("SinogramMaskId")); m_pSinogramMask = dynamic_cast<CFloat32ProjectionData2D*>(CData2DManager::getSingleton().get(id)); ASTRA_CONFIG_CHECK(m_pSinogramMask, "Reconstruction2D", "Invalid SinogramMaskId."); } CC.markOptionParsed("SinogramMaskId"); // Constraints - NEW - if (_cfg.self->hasOption("MinConstraint")) { + if (_cfg.self.hasOption("MinConstraint")) { m_bUseMinConstraint = true; - m_fMinValue = _cfg.self->getOptionNumerical("MinConstraint", 0.0f); + m_fMinValue = _cfg.self.getOptionNumerical("MinConstraint", 0.0f); CC.markOptionParsed("MinConstraint"); } else { // Constraint - OLD - m_bUseMinConstraint = _cfg.self->getOptionBool("UseMinConstraint", false); + m_bUseMinConstraint = _cfg.self.getOptionBool("UseMinConstraint", false); CC.markOptionParsed("UseMinConstraint"); if (m_bUseMinConstraint) { - m_fMinValue = _cfg.self->getOptionNumerical("MinConstraintValue", 0.0f); + m_fMinValue = _cfg.self.getOptionNumerical("MinConstraintValue", 0.0f); CC.markOptionParsed("MinConstraintValue"); } } - if (_cfg.self->hasOption("MaxConstraint")) { + if (_cfg.self.hasOption("MaxConstraint")) { m_bUseMaxConstraint = true; - m_fMaxValue = _cfg.self->getOptionNumerical("MaxConstraint", 255.0f); + m_fMaxValue = _cfg.self.getOptionNumerical("MaxConstraint", 255.0f); CC.markOptionParsed("MaxConstraint"); } else { // Constraint - OLD - m_bUseMaxConstraint = _cfg.self->getOptionBool("UseMaxConstraint", false); + m_bUseMaxConstraint = _cfg.self.getOptionBool("UseMaxConstraint", false); CC.markOptionParsed("UseMaxConstraint"); if (m_bUseMaxConstraint) { - m_fMaxValue = _cfg.self->getOptionNumerical("MaxConstraintValue", 0.0f); + m_fMaxValue = _cfg.self.getOptionNumerical("MaxConstraintValue", 0.0f); CC.markOptionParsed("MaxConstraintValue"); } } diff --git a/src/ReconstructionAlgorithm3D.cpp b/src/ReconstructionAlgorithm3D.cpp index 13d069d..f975ace 100644 --- a/src/ReconstructionAlgorithm3D.cpp +++ b/src/ReconstructionAlgorithm3D.cpp @@ -104,72 +104,74 @@ bool CReconstructionAlgorithm3D::initialize(const Config& _cfg) ASTRA_ASSERT(_cfg.self); ConfigStackCheck<CAlgorithm> CC("ReconstructionAlgorithm3D", this, _cfg); - XMLNode* node; + XMLNode node; int id; -#if 0 + // projector - node = _cfg.self->getSingleNode("ProjectorId"); - ASTRA_CONFIG_CHECK(node, "Reconstruction3D", "No ProjectorId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); - m_pProjector = CProjector3DManager::getSingleton().get(id); - ASTRA_DELETE(node); -#endif + node = _cfg.self.getSingleNode("ProjectorId"); + m_pProjector = 0; + if (node) { + id = boost::lexical_cast<int>(node.getContent()); + m_pProjector = CProjector3DManager::getSingleton().get(id); + if (!m_pProjector) { + // TODO: Report + } + } + CC.markNodeParsed("ProjectorId"); // sinogram data - node = _cfg.self->getSingleNode("ProjectionDataId"); + node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "Reconstruction3D", "No ProjectionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pSinogram = dynamic_cast<CFloat32ProjectionData3D*>(CData3DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ProjectionDataId"); // reconstruction data - node = _cfg.self->getSingleNode("ReconstructionDataId"); + node = _cfg.self.getSingleNode("ReconstructionDataId"); ASTRA_CONFIG_CHECK(node, "Reconstruction3D", "No ReconstructionDataId tag specified."); - id = boost::lexical_cast<int>(node->getContent()); + id = boost::lexical_cast<int>(node.getContent()); m_pReconstruction = dynamic_cast<CFloat32VolumeData3D*>(CData3DManager::getSingleton().get(id)); - ASTRA_DELETE(node); CC.markNodeParsed("ReconstructionDataId"); // fixed mask - if (_cfg.self->hasOption("ReconstructionMaskId")) { + if (_cfg.self.hasOption("ReconstructionMaskId")) { m_bUseReconstructionMask = true; - id = boost::lexical_cast<int>(_cfg.self->getOption("ReconstructionMaskId")); + id = boost::lexical_cast<int>(_cfg.self.getOption("ReconstructionMaskId")); m_pReconstructionMask = dynamic_cast<CFloat32VolumeData3D*>(CData3DManager::getSingleton().get(id)); } CC.markOptionParsed("ReconstructionMaskId"); // fixed mask - if (_cfg.self->hasOption("SinogramMaskId")) { + if (_cfg.self.hasOption("SinogramMaskId")) { m_bUseSinogramMask = true; - id = boost::lexical_cast<int>(_cfg.self->getOption("SinogramMaskId")); + id = boost::lexical_cast<int>(_cfg.self.getOption("SinogramMaskId")); m_pSinogramMask = dynamic_cast<CFloat32ProjectionData3D*>(CData3DManager::getSingleton().get(id)); } // Constraints - NEW - if (_cfg.self->hasOption("MinConstraint")) { + if (_cfg.self.hasOption("MinConstraint")) { m_bUseMinConstraint = true; - m_fMinValue = _cfg.self->getOptionNumerical("MinConstraint", 0.0f); + m_fMinValue = _cfg.self.getOptionNumerical("MinConstraint", 0.0f); CC.markOptionParsed("MinConstraint"); } else { // Constraint - OLD - m_bUseMinConstraint = _cfg.self->getOptionBool("UseMinConstraint", false); + m_bUseMinConstraint = _cfg.self.getOptionBool("UseMinConstraint", false); CC.markOptionParsed("UseMinConstraint"); if (m_bUseMinConstraint) { - m_fMinValue = _cfg.self->getOptionNumerical("MinConstraintValue", 0.0f); + m_fMinValue = _cfg.self.getOptionNumerical("MinConstraintValue", 0.0f); CC.markOptionParsed("MinConstraintValue"); } } - if (_cfg.self->hasOption("MaxConstraint")) { + if (_cfg.self.hasOption("MaxConstraint")) { m_bUseMaxConstraint = true; - m_fMaxValue = _cfg.self->getOptionNumerical("MaxConstraint", 255.0f); + m_fMaxValue = _cfg.self.getOptionNumerical("MaxConstraint", 255.0f); CC.markOptionParsed("MaxConstraint"); } else { // Constraint - OLD - m_bUseMaxConstraint = _cfg.self->getOptionBool("UseMaxConstraint", false); + m_bUseMaxConstraint = _cfg.self.getOptionBool("UseMaxConstraint", false); CC.markOptionParsed("UseMaxConstraint"); if (m_bUseMaxConstraint) { - m_fMaxValue = _cfg.self->getOptionNumerical("MaxConstraintValue", 0.0f); + m_fMaxValue = _cfg.self.getOptionNumerical("MaxConstraintValue", 0.0f); CC.markOptionParsed("MaxConstraintValue"); } } diff --git a/src/SartAlgorithm.cpp b/src/SartAlgorithm.cpp index f7a1677..e4dc5c7 100644 --- a/src/SartAlgorithm.cpp +++ b/src/SartAlgorithm.cpp @@ -126,7 +126,7 @@ bool CSartAlgorithm::initialize(const Config& _cfg) // projection order m_iCurrentProjection = 0; m_iProjectionCount = m_pProjector->getProjectionGeometry()->getProjectionAngleCount(); - string projOrder = _cfg.self->getOption("ProjectionOrder", "sequential"); + string projOrder = _cfg.self.getOption("ProjectionOrder", "sequential"); CC.markOptionParsed("ProjectionOrder"); if (projOrder == "sequential") { m_piProjectionOrder = new int[m_iProjectionCount]; @@ -145,7 +145,7 @@ bool CSartAlgorithm::initialize(const Config& _cfg) m_piProjectionOrder[i + k] = t; } } else if (projOrder == "custom") { - vector<float32> projOrderList = _cfg.self->getOptionNumericalArray("ProjectionOrderList"); + vector<float32> projOrderList = _cfg.self.getOptionNumericalArray("ProjectionOrderList"); m_piProjectionOrder = new int[projOrderList.size()]; for (int i = 0; i < m_iProjectionCount; i++) { m_piProjectionOrder[i] = static_cast<int>(projOrderList[i]); diff --git a/src/SparseMatrixProjectionGeometry2D.cpp b/src/SparseMatrixProjectionGeometry2D.cpp index 86357d2..073720f 100644 --- a/src/SparseMatrixProjectionGeometry2D.cpp +++ b/src/SparseMatrixProjectionGeometry2D.cpp @@ -98,11 +98,10 @@ bool CSparseMatrixProjectionGeometry2D::initialize(const Config& _cfg) CProjectionGeometry2D::initialize(_cfg); // get matrix - XMLNode* node = _cfg.self->getSingleNode("MatrixID"); + XMLNode node = _cfg.self.getSingleNode("MatrixID"); ASTRA_CONFIG_CHECK(node, "SparseMatrixProjectionGeometry2D", "No MatrixID tag specified."); - int id = boost::lexical_cast<int>(node->getContent()); + int id = boost::lexical_cast<int>(node.getContent()); m_pMatrix = CMatrixManager::getSingleton().get(id); - ASTRA_DELETE(node); CC.markNodeParsed("MatrixID"); // success @@ -194,11 +193,11 @@ Config* CSparseMatrixProjectionGeometry2D::getConfiguration() const { Config* cfg = new Config(); cfg->initialize("ProjectionGeometry2D"); - cfg->self->addAttribute("type", "sparse matrix"); - cfg->self->addChildNode("DetectorCount", getDetectorCount()); - cfg->self->addChildNode("DetectorWidth", getDetectorWidth()); - cfg->self->addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); - cfg->self->addChildNode("MatrixID", CMatrixManager::getSingleton().getIndex(m_pMatrix)); + cfg->self.addAttribute("type", "sparse matrix"); + cfg->self.addChildNode("DetectorCount", getDetectorCount()); + cfg->self.addChildNode("DetectorWidth", getDetectorWidth()); + cfg->self.addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); + cfg->self.addChildNode("MatrixID", CMatrixManager::getSingleton().getIndex(m_pMatrix)); return cfg; } diff --git a/src/VolumeGeometry2D.cpp b/src/VolumeGeometry2D.cpp index d412914..6eea1b2 100644 --- a/src/VolumeGeometry2D.cpp +++ b/src/VolumeGeometry2D.cpp @@ -164,24 +164,22 @@ bool CVolumeGeometry2D::initialize(const Config& _cfg) } // Required: GridColCount - XMLNode* node = _cfg.self->getSingleNode("GridColCount"); + XMLNode node = _cfg.self.getSingleNode("GridColCount"); ASTRA_CONFIG_CHECK(node, "ReconstructionGeometry2D", "No GridColCount tag specified."); - m_iGridColCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iGridColCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("GridColCount"); // Required: GridRowCount - node = _cfg.self->getSingleNode("GridRowCount"); + node = _cfg.self.getSingleNode("GridRowCount"); ASTRA_CONFIG_CHECK(node, "ReconstructionGeometry2D", "No GridRowCount tag specified."); - m_iGridRowCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iGridRowCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("GridRowCount"); // Optional: Window minima and maxima - m_fWindowMinX = _cfg.self->getOptionNumerical("WindowMinX", -m_iGridColCount/2.0f); - m_fWindowMaxX = _cfg.self->getOptionNumerical("WindowMaxX", m_iGridColCount/2.0f); - m_fWindowMinY = _cfg.self->getOptionNumerical("WindowMinY", -m_iGridRowCount/2.0f); - m_fWindowMaxY = _cfg.self->getOptionNumerical("WindowMaxY", m_iGridRowCount/2.0f); + m_fWindowMinX = _cfg.self.getOptionNumerical("WindowMinX", -m_iGridColCount/2.0f); + m_fWindowMaxX = _cfg.self.getOptionNumerical("WindowMaxX", m_iGridColCount/2.0f); + m_fWindowMinY = _cfg.self.getOptionNumerical("WindowMinY", -m_iGridRowCount/2.0f); + m_fWindowMaxY = _cfg.self.getOptionNumerical("WindowMaxY", m_iGridRowCount/2.0f); CC.markOptionParsed("WindowMinX"); CC.markOptionParsed("WindowMaxX"); CC.markOptionParsed("WindowMinY"); @@ -285,13 +283,13 @@ Config* CVolumeGeometry2D::getConfiguration() const Config* cfg = new Config(); cfg->initialize("VolumeGeometry2D"); - cfg->self->addChildNode("GridColCount", m_iGridColCount); - cfg->self->addChildNode("GridRowCount", m_iGridRowCount); + cfg->self.addChildNode("GridColCount", m_iGridColCount); + cfg->self.addChildNode("GridRowCount", m_iGridRowCount); - cfg->self->addOption("WindowMinX", m_fWindowMinX); - cfg->self->addOption("WindowMaxX", m_fWindowMaxX); - cfg->self->addOption("WindowMinY", m_fWindowMinY); - cfg->self->addOption("WindowMaxY", m_fWindowMaxY); + cfg->self.addOption("WindowMinX", m_fWindowMinX); + cfg->self.addOption("WindowMaxX", m_fWindowMaxX); + cfg->self.addOption("WindowMinY", m_fWindowMinY); + cfg->self.addOption("WindowMaxY", m_fWindowMaxY); return cfg; } diff --git a/src/VolumeGeometry3D.cpp b/src/VolumeGeometry3D.cpp index 66e6f0c..a1cf424 100644 --- a/src/VolumeGeometry3D.cpp +++ b/src/VolumeGeometry3D.cpp @@ -192,33 +192,30 @@ bool CVolumeGeometry3D::initialize(const Config& _cfg) } // Required: GridColCount - XMLNode* node = _cfg.self->getSingleNode("GridColCount"); + XMLNode node = _cfg.self.getSingleNode("GridColCount"); ASTRA_CONFIG_CHECK(node, "ReconstructionGeometry2D", "No GridColCount tag specified."); - m_iGridColCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iGridColCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("GridColCount"); // Required: GridRowCount - node = _cfg.self->getSingleNode("GridRowCount"); + node = _cfg.self.getSingleNode("GridRowCount"); ASTRA_CONFIG_CHECK(node, "ReconstructionGeometry2D", "No GridRowCount tag specified."); - m_iGridRowCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iGridRowCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("GridRowCount"); // Required: GridRowCount - node = _cfg.self->getSingleNode("GridSliceCount"); + node = _cfg.self.getSingleNode("GridSliceCount"); ASTRA_CONFIG_CHECK(node, "ReconstructionGeometry2D", "No GridSliceCount tag specified."); - m_iGridSliceCount = boost::lexical_cast<int>(node->getContent()); - ASTRA_DELETE(node); + m_iGridSliceCount = boost::lexical_cast<int>(node.getContent()); CC.markNodeParsed("GridSliceCount"); // Optional: Window minima and maxima - m_fWindowMinX = _cfg.self->getOptionNumerical("WindowMinX", -m_iGridColCount/2.0f); - m_fWindowMaxX = _cfg.self->getOptionNumerical("WindowMaxX", m_iGridColCount/2.0f); - m_fWindowMinY = _cfg.self->getOptionNumerical("WindowMinY", -m_iGridRowCount/2.0f); - m_fWindowMaxY = _cfg.self->getOptionNumerical("WindowMaxY", m_iGridRowCount/2.0f); - m_fWindowMinZ = _cfg.self->getOptionNumerical("WindowMinZ", -m_iGridSliceCount/2.0f); - m_fWindowMaxZ = _cfg.self->getOptionNumerical("WindowMaxZ", m_iGridSliceCount/2.0f); + m_fWindowMinX = _cfg.self.getOptionNumerical("WindowMinX", -m_iGridColCount/2.0f); + m_fWindowMaxX = _cfg.self.getOptionNumerical("WindowMaxX", m_iGridColCount/2.0f); + m_fWindowMinY = _cfg.self.getOptionNumerical("WindowMinY", -m_iGridRowCount/2.0f); + m_fWindowMaxY = _cfg.self.getOptionNumerical("WindowMaxY", m_iGridRowCount/2.0f); + m_fWindowMinZ = _cfg.self.getOptionNumerical("WindowMinZ", -m_iGridSliceCount/2.0f); + m_fWindowMaxZ = _cfg.self.getOptionNumerical("WindowMaxZ", m_iGridSliceCount/2.0f); CC.markOptionParsed("WindowMinX"); CC.markOptionParsed("WindowMaxX"); CC.markOptionParsed("WindowMinY"); @@ -386,16 +383,16 @@ Config* CVolumeGeometry3D::getConfiguration() const Config* cfg = new Config(); cfg->initialize("VolumeGeometry3D"); - cfg->self->addChildNode("GridColCount", m_iGridColCount); - cfg->self->addChildNode("GridRowCount", m_iGridRowCount); - cfg->self->addChildNode("GridSliceCount", m_iGridSliceCount); + cfg->self.addChildNode("GridColCount", m_iGridColCount); + cfg->self.addChildNode("GridRowCount", m_iGridRowCount); + cfg->self.addChildNode("GridSliceCount", m_iGridSliceCount); - cfg->self->addOption("WindowMinX", m_fWindowMinX); - cfg->self->addOption("WindowMaxX", m_fWindowMaxX); - cfg->self->addOption("WindowMinY", m_fWindowMinY); - cfg->self->addOption("WindowMaxY", m_fWindowMaxY); - cfg->self->addOption("WindowMinZ", m_fWindowMinZ); - cfg->self->addOption("WindowMaxZ", m_fWindowMaxZ); + cfg->self.addOption("WindowMinX", m_fWindowMinX); + cfg->self.addOption("WindowMaxX", m_fWindowMaxX); + cfg->self.addOption("WindowMinY", m_fWindowMinY); + cfg->self.addOption("WindowMaxY", m_fWindowMaxY); + cfg->self.addOption("WindowMinZ", m_fWindowMinZ); + cfg->self.addOption("WindowMaxZ", m_fWindowMaxZ); return cfg; } diff --git a/src/XMLDocument.cpp b/src/XMLDocument.cpp index 406564f..716ed9e 100644 --- a/src/XMLDocument.cpp +++ b/src/XMLDocument.cpp @@ -32,13 +32,8 @@ $Id$ #include <iostream> #include <sstream> -#ifdef _MSC_VER #include "rapidxml/rapidxml.hpp" #include "rapidxml/rapidxml_print.hpp" -#else -#include "rapidxml.hpp" -#include "rapidxml_print.hpp" -#endif using namespace rapidxml; using namespace astra; @@ -94,10 +89,9 @@ XMLDocument* XMLDocument::createDocument(string sRootName) } //----------------------------------------------------------------------------- -XMLNode* XMLDocument::getRootNode() +XMLNode XMLDocument::getRootNode() { - // TODO: clean up: this 'new' requires callers to do memory management - return new XMLNode(fDOMDocument->first_node()); + return XMLNode(fDOMDocument->first_node()); } //----------------------------------------------------------------------------- diff --git a/src/XMLNode.cpp b/src/XMLNode.cpp index 4b2bdf4..0ec701f 100644 --- a/src/XMLNode.cpp +++ b/src/XMLNode.cpp @@ -28,15 +28,15 @@ $Id$ #include "astra/XMLNode.h" -#ifdef _MSC_VER #include "rapidxml/rapidxml.hpp" #include "rapidxml/rapidxml_print.hpp" -#else -#include "rapidxml.hpp" -#include "rapidxml_print.hpp" -#endif #include <boost/lexical_cast.hpp> +#include <boost/algorithm/string.hpp> +#include <boost/algorithm/string/split.hpp> +#include <boost/algorithm/string/classification.hpp> + + using namespace rapidxml; using namespace astra; @@ -44,21 +44,10 @@ using namespace std; //----------------------------------------------------------------------------- -// Utility function to delete a list of nodes -static void deleteNodes(list<XMLNode*>& nodes) -{ - for (list<XMLNode*>::iterator i = nodes.begin(); i != nodes.end(); ++i) - delete (*i); - - nodes.clear(); -} - - -//----------------------------------------------------------------------------- // default constructor XMLNode::XMLNode() { - + fDOMElement = 0; } //----------------------------------------------------------------------------- @@ -84,14 +73,14 @@ void XMLNode::setDOMNode(xml_node<>* n) //----------------------------------------------------------------------------- // print XML Node -void XMLNode::print() +void XMLNode::print() const { std::cout << fDOMElement; } //----------------------------------------------------------------------------- // print XML Node -std::string XMLNode::toString() +std::string XMLNode::toString() const { std::string s; ::print(std::back_inserter(s), *fDOMElement, 0); @@ -100,64 +89,61 @@ std::string XMLNode::toString() //----------------------------------------------------------------------------- // Get single node -XMLNode* XMLNode::getSingleNode(string name) +XMLNode XMLNode::getSingleNode(string name) const { xml_node<> *node = fDOMElement->first_node(name.c_str()); - if (node) - return new XMLNode(node); - else - return 0; + return XMLNode(node); } //----------------------------------------------------------------------------- // Get list of nodes -list<XMLNode*> XMLNode::getNodes(string name) +list<XMLNode> XMLNode::getNodes(string name) const { - list<XMLNode*> result; + list<XMLNode> result; xml_node<> *iter; for (iter = fDOMElement->first_node(name.c_str()); iter; iter = iter->next_sibling(name.c_str())) { - result.push_back(new XMLNode(iter)); + result.push_back(XMLNode(iter)); } return result; } //----------------------------------------------------------------------------- // Get list of nodes -list<XMLNode*> XMLNode::getNodes() +list<XMLNode> XMLNode::getNodes() const { - list<XMLNode*> result; + list<XMLNode> result; xml_node<> *iter; for (iter = fDOMElement->first_node(); iter; iter = iter->next_sibling()) { - result.push_back(new XMLNode(iter)); + result.push_back(XMLNode(iter)); } return result; } //----------------------------------------------------------------------------- // Get name of this node -std::string XMLNode::getName() +std::string XMLNode::getName() const { return fDOMElement->name(); } //----------------------------------------------------------------------------- // Get node content - STRING -string XMLNode::getContent() +string XMLNode::getContent() const { return fDOMElement->value(); } //----------------------------------------------------------------------------- // Get node content - NUMERICAL -float32 XMLNode::getContentNumerical() +float32 XMLNode::getContentNumerical() const { return boost::lexical_cast<float32>(getContent()); } //----------------------------------------------------------------------------- // Get node content - BOOLEAN -bool XMLNode::getContentBool() +bool XMLNode::getContentBool() const { string res = getContent(); return ((res == "1") || (res == "yes") || (res == "true") || (res == "on")); @@ -165,21 +151,20 @@ bool XMLNode::getContentBool() //----------------------------------------------------------------------------- // Get node content - STRING LIST -vector<string> XMLNode::getContentArray() +vector<string> XMLNode::getContentArray() const { // get listsize int iSize = boost::lexical_cast<int>(getAttribute("listsize")); // create result array vector<string> res(iSize); // loop all list item nodes - list<XMLNode*> nodes = getNodes("ListItem"); - for (list<XMLNode*>::iterator it = nodes.begin(); it != nodes.end(); it++) { - int iIndex = (*it)->getAttributeNumerical("index"); - string sValue = (*it)->getAttribute("value"); + list<XMLNode> nodes = getNodes("ListItem"); + for (list<XMLNode>::iterator it = nodes.begin(); it != nodes.end(); it++) { + int iIndex = it->getAttributeNumerical("index"); + string sValue = it->getAttribute("value"); ASTRA_ASSERT(iIndex < iSize); res[iIndex] = sValue; } - deleteNodes(nodes); // return return res; @@ -187,85 +172,48 @@ vector<string> XMLNode::getContentArray() //----------------------------------------------------------------------------- // Get node content - NUMERICAL LIST -vector<float32> XMLNode::getContentNumericalArray() +// NB: A 2D matrix is returned as a linear list +vector<float32> XMLNode::getContentNumericalArray() const { - // is scalar - if (!hasAttribute("listsize")) { - vector<float32> res(1); - res[0] = getContentNumerical(); - return res; - } + string input = getContent(); - int iSize = boost::lexical_cast<int>(getAttribute("listsize")); - // create result array - vector<float32> res(iSize); - // loop all list item nodes - list<XMLNode*> nodes = getNodes("ListItem"); - for (list<XMLNode*>::iterator it = nodes.begin(); it != nodes.end(); it++) { - int iIndex = (*it)->getAttributeNumerical("index"); - float32 fValue = (*it)->getAttributeNumerical("value"); - ASTRA_ASSERT(iIndex < iSize); - res[iIndex] = fValue; - } - deleteNodes(nodes); - // return - return res; -} + // split + std::vector<std::string> items; + boost::split(items, input, boost::is_any_of(",;")); -vector<double> XMLNode::getContentNumericalArrayDouble() -{ - // is scalar - if (!hasAttribute("listsize")) { - vector<double> res(1); - res[0] = getContentNumerical(); - return res; - } + // init list + vector<float32> out; + out.resize(items.size()); - int iSize = boost::lexical_cast<int>(getAttribute("listsize")); - // create result array - vector<double> res(iSize); - // loop all list item nodes - list<XMLNode*> nodes = getNodes("ListItem"); - for (list<XMLNode*>::iterator it = nodes.begin(); it != nodes.end(); it++) { - int iIndex = (*it)->getAttributeNumerical("index"); - double fValue = (*it)->getAttributeNumericalDouble("value"); - ASTRA_ASSERT(iIndex < iSize); - res[iIndex] = fValue; + // loop elements + for (unsigned int i = 0; i < items.size(); i++) { + out[i] = boost::lexical_cast<float32>(items[i]); } - deleteNodes(nodes); - // return - return res; + return out; } -//----------------------------------------------------------------------------- -// Get node content - NUMERICAL LIST 2 -void XMLNode::getContentNumericalArray(float32*& _pfData, int& _iSize) +vector<double> XMLNode::getContentNumericalArrayDouble() const { - // is scalar - if (!hasAttribute("listsize")) { - _iSize = 1; - _pfData = new float32[_iSize]; - _pfData[0] = getContentNumerical(); - return; - } - // get listsize - _iSize = boost::lexical_cast<int>(getAttribute("listsize")); - // create result array - _pfData = new float32[_iSize]; - // loop all list item nodes - list<XMLNode*> nodes = getNodes("ListItem"); - for (list<XMLNode*>::iterator it = nodes.begin(); it != nodes.end(); it++) { - int iIndex = (*it)->getAttributeNumerical("index"); - float32 fValue = (*it)->getAttributeNumerical("value"); - ASTRA_ASSERT(iIndex < _iSize); - _pfData[iIndex] = fValue; + string input = getContent(); + + // split + std::vector<std::string> items; + boost::split(items, input, boost::is_any_of(",;")); + + // init list + vector<double> out; + out.resize(items.size()); + + // loop elements + for (unsigned int i = 0; i < items.size(); i++) { + out[i] = boost::lexical_cast<double>(items[i]); } - deleteNodes(nodes); + return out; } //----------------------------------------------------------------------------- // Is attribute? -bool XMLNode::hasAttribute(string _sName) +bool XMLNode::hasAttribute(string _sName) const { xml_attribute<> *attr = fDOMElement->first_attribute(_sName.c_str()); return (attr != 0); @@ -273,7 +221,7 @@ bool XMLNode::hasAttribute(string _sName) //----------------------------------------------------------------------------- // Get attribute - STRING -string XMLNode::getAttribute(string _sName, string _sDefaultValue) +string XMLNode::getAttribute(string _sName, string _sDefaultValue) const { xml_attribute<> *attr = fDOMElement->first_attribute(_sName.c_str()); @@ -284,12 +232,12 @@ string XMLNode::getAttribute(string _sName, string _sDefaultValue) //----------------------------------------------------------------------------- // Get attribute - NUMERICAL -float32 XMLNode::getAttributeNumerical(string _sName, float32 _fDefaultValue) +float32 XMLNode::getAttributeNumerical(string _sName, float32 _fDefaultValue) const { if (!hasAttribute(_sName)) return _fDefaultValue; return boost::lexical_cast<float32>(getAttribute(_sName)); } -double XMLNode::getAttributeNumericalDouble(string _sName, double _fDefaultValue) +double XMLNode::getAttributeNumericalDouble(string _sName, double _fDefaultValue) const { if (!hasAttribute(_sName)) return _fDefaultValue; return boost::lexical_cast<double>(getAttribute(_sName)); @@ -297,7 +245,7 @@ double XMLNode::getAttributeNumericalDouble(string _sName, double _fDefaultValue //----------------------------------------------------------------------------- // Get attribute - BOOLEAN -bool XMLNode::getAttributeBool(string _sName, bool _bDefaultValue) +bool XMLNode::getAttributeBool(string _sName, bool _bDefaultValue) const { if (!hasAttribute(_sName)) return _bDefaultValue; string res = getAttribute(_sName); @@ -306,7 +254,7 @@ bool XMLNode::getAttributeBool(string _sName, bool _bDefaultValue) //----------------------------------------------------------------------------- // Has option? -bool XMLNode::hasOption(string _sKey) +bool XMLNode::hasOption(string _sKey) const { xml_node<> *iter; for (iter = fDOMElement->first_node("Option"); iter; iter = iter->next_sibling("Option")) { @@ -319,7 +267,7 @@ bool XMLNode::hasOption(string _sKey) //----------------------------------------------------------------------------- // Get option - STRING -string XMLNode::getOption(string _sKey, string _sDefaultValue) +string XMLNode::getOption(string _sKey, string _sDefaultValue) const { xml_node<> *iter; for (iter = fDOMElement->first_node("Option"); iter; iter = iter->next_sibling("Option")) { @@ -336,7 +284,7 @@ string XMLNode::getOption(string _sKey, string _sDefaultValue) //----------------------------------------------------------------------------- // Get option - NUMERICAL -float32 XMLNode::getOptionNumerical(string _sKey, float32 _fDefaultValue) +float32 XMLNode::getOptionNumerical(string _sKey, float32 _fDefaultValue) const { if (!hasOption(_sKey)) return _fDefaultValue; return boost::lexical_cast<float32>(getOption(_sKey)); @@ -344,7 +292,7 @@ float32 XMLNode::getOptionNumerical(string _sKey, float32 _fDefaultValue) //----------------------------------------------------------------------------- // Get option - BOOL -bool XMLNode::getOptionBool(string _sKey, bool _bDefaultValue) +bool XMLNode::getOptionBool(string _sKey, bool _bDefaultValue) const { bool bHasOption = hasOption(_sKey); if (!bHasOption) return _bDefaultValue; @@ -354,20 +302,18 @@ bool XMLNode::getOptionBool(string _sKey, bool _bDefaultValue) //----------------------------------------------------------------------------- // Get option - NUMERICAL ARRAY -vector<float32> XMLNode::getOptionNumericalArray(string _sKey) +vector<float32> XMLNode::getOptionNumericalArray(string _sKey) const { if (!hasOption(_sKey)) return vector<float32>(); - list<XMLNode*> nodes = getNodes("Option"); - for (list<XMLNode*>::iterator it = nodes.begin(); it != nodes.end(); it++) { - if ((*it)->getAttribute("key") == _sKey) { - vector<float32> vals = (*it)->getContentNumericalArray(); - deleteNodes(nodes); + list<XMLNode> nodes = getNodes("Option"); + for (list<XMLNode>::iterator it = nodes.begin(); it != nodes.end(); it++) { + if (it->getAttribute("key") == _sKey) { + vector<float32> vals = it->getContentNumericalArray(); return vals; } } - deleteNodes(nodes); return vector<float32>(); } @@ -390,41 +336,40 @@ vector<float32> XMLNode::getOptionNumericalArray(string _sKey) //----------------------------------------------------------------------------- // Add child node - EMPTY -XMLNode* XMLNode::addChildNode(string _sNodeName) +XMLNode XMLNode::addChildNode(string _sNodeName) { xml_document<> *doc = fDOMElement->document(); char *node_name = doc->allocate_string(_sNodeName.c_str()); xml_node<> *node = doc->allocate_node(node_element, node_name); fDOMElement->append_node(node); - // TODO: clean up: this 'new' requires callers to do memory management - return new XMLNode(node); + return XMLNode(node); } //----------------------------------------------------------------------------- // Add child node - STRING -XMLNode* XMLNode::addChildNode(string _sNodeName, string _sText) +XMLNode XMLNode::addChildNode(string _sNodeName, string _sText) { - XMLNode* res = addChildNode(_sNodeName); - res->setContent(_sText); + XMLNode res = addChildNode(_sNodeName); + res.setContent(_sText); return res; } //----------------------------------------------------------------------------- // Add child node - FLOAT -XMLNode* XMLNode::addChildNode(string _sNodeName, float32 _fValue) +XMLNode XMLNode::addChildNode(string _sNodeName, float32 _fValue) { - XMLNode* res = addChildNode(_sNodeName); - res->setContent(_fValue); + XMLNode res = addChildNode(_sNodeName); + res.setContent(_fValue); return res; } //----------------------------------------------------------------------------- // Add child node - LIST -XMLNode* XMLNode::addChildNode(string _sNodeName, float32* _pfList, int _iSize) +XMLNode XMLNode::addChildNode(string _sNodeName, float32* _pfList, int _iSize) { - XMLNode* res = addChildNode(_sNodeName); - res->setContent(_pfList, _iSize); + XMLNode res = addChildNode(_sNodeName); + res.setContent(_pfList, _iSize); return res; } @@ -446,15 +391,68 @@ void XMLNode::setContent(float32 _fValue) //----------------------------------------------------------------------------- // Set content - LIST -void XMLNode::setContent(float32* pfList, int _iSize) -{ + +template<typename T> +static std::string setContentList_internal(T* pfList, int _iSize) { std::string str = (_iSize > 0) ? boost::lexical_cast<std::string>(pfList[0]) : ""; for (int i = 1; i < _iSize; i++) { str += "," + boost::lexical_cast<std::string>(pfList[i]); } - setContent(str); + return str; +} + +void XMLNode::setContent(float32* pfList, int _iSize) +{ + setContent(setContentList_internal<float32>(pfList, _iSize)); +} + +void XMLNode::setContent(double* pfList, int _iSize) +{ + setContent(setContentList_internal<double>(pfList, _iSize)); +} + +//----------------------------------------------------------------------------- +// Set content - MATRIX + +template<typename T> +static std::string setContentMatrix_internal(T* _pfMatrix, int _iWidth, int _iHeight, bool transposed) +{ + std::string str = ""; + + int s1,s2; + + if (!transposed) { + s1 = 1; + s2 = _iWidth; + } else { + s1 = _iHeight; + s2 = 1; + } + + for (int y = 0; y < _iHeight; ++y) { + if (_iWidth > 0) + str += boost::lexical_cast<std::string>(_pfMatrix[0*s1 + y*s2]); + for (int x = 1; x < _iWidth; x++) + str += "," + boost::lexical_cast<std::string>(_pfMatrix[x*s1 + y*s2]); + + if (y != _iHeight-1) + str += ";"; + } + + return str; } +void XMLNode::setContent(float32* _pfMatrix, int _iWidth, int _iHeight, bool transposed) +{ + setContent(setContentMatrix_internal<float32>(_pfMatrix, _iWidth, _iHeight, transposed)); +} + +void XMLNode::setContent(double* _pfMatrix, int _iWidth, int _iHeight, bool transposed) +{ + setContent(setContentMatrix_internal<double>(_pfMatrix, _iWidth, _iHeight, transposed)); +} + + //----------------------------------------------------------------------------- // Add attribute - STRING void XMLNode::addAttribute(string _sName, string _sText) @@ -477,20 +475,18 @@ void XMLNode::addAttribute(string _sName, float32 _fValue) // Add option - STRING void XMLNode::addOption(string _sName, string _sText) { - XMLNode* node = addChildNode("Option"); - node->addAttribute("key", _sName); - node->addAttribute("value", _sText); - delete node; + XMLNode node = addChildNode("Option"); + node.addAttribute("key", _sName); + node.addAttribute("value", _sText); } //----------------------------------------------------------------------------- // Add option - FLOAT void XMLNode::addOption(string _sName, float32 _sText) { - XMLNode* node = addChildNode("Option"); - node->addAttribute("key", _sName); - node->addAttribute("value", _sText); - delete node; + XMLNode node = addChildNode("Option"); + node.addAttribute("key", _sName); + node.addAttribute("value", _sText); } //----------------------------------------------------------------------------- diff --git a/tests/test_Fourier.cpp b/tests/test_Fourier.cpp index 2602edb..ef12747 100644 --- a/tests/test_Fourier.cpp +++ b/tests/test_Fourier.cpp @@ -105,8 +105,8 @@ BOOST_AUTO_TEST_CASE( testFourier_FFT_1D_1 ) { astra::float32 inR[8] = { 1.0f, 1.0f, 1.0f, 0.0f, 0.0f, 0.0f, 1.0f, 1.0f }; astra::float32 inI[8] = { 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f }; - astra::float32 outR[5]; - astra::float32 outI[5]; + astra::float32 outR[8]; + astra::float32 outI[8]; astra::fastTwoPowerFourierTransform1D(8, inR, inI, outR, outI, 1, 1, false); diff --git a/tests/test_ParallelBeamLineKernelProjector2D.cpp b/tests/test_ParallelBeamLineKernelProjector2D.cpp index 86bc54f..c56ff37 100644 --- a/tests/test_ParallelBeamLineKernelProjector2D.cpp +++ b/tests/test_ParallelBeamLineKernelProjector2D.cpp @@ -77,6 +77,8 @@ BOOST_FIXTURE_TEST_CASE( testParallelBeamLineKernelProjector2D_Rectangle, TestPa fWeight += pPix[i].m_fWeight; BOOST_CHECK_SMALL(fWeight - 7.13037f, 0.00001f); + + delete[] pPix; } diff --git a/tests/test_XMLDocument.cpp b/tests/test_XMLDocument.cpp index adabdd6..95429cb 100644 --- a/tests/test_XMLDocument.cpp +++ b/tests/test_XMLDocument.cpp @@ -32,18 +32,22 @@ $Id$ #include <boost/test/auto_unit_test.hpp> #include "astra/XMLDocument.h" +#include "astra/Config.h" BOOST_AUTO_TEST_CASE( testXMLDocument_Constructor1 ) { astra::XMLDocument *doc = astra::XMLDocument::createDocument("test"); BOOST_REQUIRE(doc); - astra::XMLNode *root = doc->getRootNode(); + astra::XMLNode root = doc->getRootNode(); BOOST_REQUIRE(root); - BOOST_CHECK(root->getName() == "test"); - BOOST_CHECK(root->getContent().empty()); + BOOST_CHECK(root.getName() == "test"); + BOOST_CHECK(root.getContent().empty()); + + delete doc; + } BOOST_AUTO_TEST_CASE( testXMLDocument_FileIO ) @@ -53,12 +57,15 @@ BOOST_AUTO_TEST_CASE( testXMLDocument_FileIO ) doc->saveToFile("test.xml"); astra::XMLDocument *doc2 = astra::XMLDocument::readFromFile("test.xml"); - astra::XMLNode *root = doc2->getRootNode(); + astra::XMLNode root = doc2->getRootNode(); BOOST_REQUIRE(root); - BOOST_CHECK(root->getName() == "test"); - BOOST_CHECK(root->getContent().empty()); + BOOST_CHECK(root.getName() == "test"); + BOOST_CHECK(root.getContent().empty()); + + delete doc2; + delete doc; } @@ -67,32 +74,28 @@ BOOST_AUTO_TEST_CASE( testXMLDocument_CreateNodes ) astra::XMLDocument *doc = astra::XMLDocument::createDocument("test"); BOOST_REQUIRE(doc); - astra::XMLNode *root = doc->getRootNode(); + astra::XMLNode root = doc->getRootNode(); BOOST_REQUIRE(root); - astra::XMLNode *node = root->addChildNode("child"); + astra::XMLNode node = root.addChildNode("child"); BOOST_REQUIRE(node); - node->addAttribute("attr", "val"); + node.addAttribute("attr", "val"); doc->saveToFile("test2.xml"); - delete node; - delete root; delete doc; doc = astra::XMLDocument::readFromFile("test2.xml"); BOOST_REQUIRE(doc); root = doc->getRootNode(); BOOST_REQUIRE(node); - node = root->getSingleNode("child"); + node = root.getSingleNode("child"); BOOST_REQUIRE(node); - BOOST_CHECK(node->hasAttribute("attr")); - BOOST_CHECK(node->getAttribute("attr") == "val"); + BOOST_CHECK(node.hasAttribute("attr")); + BOOST_CHECK(node.getAttribute("attr") == "val"); - delete node; - delete root; delete doc; } @@ -101,16 +104,18 @@ BOOST_AUTO_TEST_CASE( testXMLDocument_Options ) astra::XMLDocument *doc = astra::XMLDocument::createDocument("test"); BOOST_REQUIRE(doc); - astra::XMLNode *root = doc->getRootNode(); + astra::XMLNode root = doc->getRootNode(); BOOST_REQUIRE(root); - BOOST_CHECK(!root->hasOption("opt")); + BOOST_CHECK(!root.hasOption("opt")); + + root.addOption("opt", "val"); - root->addOption("opt", "val"); + BOOST_CHECK(root.hasOption("opt")); - BOOST_CHECK(root->hasOption("opt")); + BOOST_CHECK(root.getOption("opt") == "val"); - BOOST_CHECK(root->getOption("opt") == "val"); + delete doc; } @@ -119,40 +124,51 @@ BOOST_AUTO_TEST_CASE( testXMLDocument_List ) astra::XMLDocument *doc = astra::XMLDocument::createDocument("test"); BOOST_REQUIRE(doc); - astra::XMLNode *root = doc->getRootNode(); + astra::XMLNode root = doc->getRootNode(); BOOST_REQUIRE(root); - astra::XMLNode *node = root->addChildNode("child"); + astra::XMLNode node = root.addChildNode("child"); BOOST_REQUIRE(node); float fl[] = { 1.0, 3.5, 2.0, 4.75 }; - node->setContent(fl, sizeof(fl)/sizeof(fl[0])); + node.setContent(fl, sizeof(fl)/sizeof(fl[0])); doc->saveToFile("test3.xml"); - delete node; - delete root; delete doc; doc = astra::XMLDocument::readFromFile("test3.xml"); BOOST_REQUIRE(doc); root = doc->getRootNode(); BOOST_REQUIRE(root); - node = root->getSingleNode("child"); + node = root.getSingleNode("child"); BOOST_REQUIRE(node); - std::vector<astra::float32> f = node->getContentNumericalArray(); + std::vector<astra::float32> f = node.getContentNumericalArray(); BOOST_CHECK(f[0] == fl[0]); BOOST_CHECK(f[1] == fl[1]); BOOST_CHECK(f[2] == fl[2]); BOOST_CHECK(f[3] == fl[3]); - delete node; - delete root; delete doc; } +BOOST_AUTO_TEST_CASE( testXMLDocument_Config ) +{ + astra::Config* cfg = new astra::Config(); + cfg->initialize("VolumeGeometry2D"); + + cfg->self.addChildNode("GridColCount", 1); + cfg->self.addChildNode("GridRowCount", 2); + + cfg->self.addOption("WindowMinX", 3); + cfg->self.addOption("WindowMaxX", 4); + cfg->self.addOption("WindowMinY", 5); + cfg->self.addOption("WindowMaxY", 6); + + delete cfg; +} |