From 0bcde21948d619e9803de229ea40499b5e1dd873 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 27 May 2015 11:54:04 +0200 Subject: Update README, NEWS --- build/linux/README.txt | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'build') 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. -- cgit v1.2.3 From 91d1cf7c8c75218939fcf1972966c84290c095e1 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Fri, 29 May 2015 11:44:58 +0200 Subject: Update utility files --- build/linux/config.guess.dist | 405 ++++++++++++++++++++++++------------------ build/linux/config.sub.dist | 288 +++++++++++++++++++----------- build/linux/install-sh.dist | 32 ++-- 3 files changed, 438 insertions(+), 287 deletions(-) (limited to 'build') 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 . # # 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 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 > $dummy.c + #include + #if defined(__UCLIBC__) + LIBC=uclibc + #elif defined(__dietlibc__) + LIBC=dietlibc + #else + LIBC=gnu + #endif + EOF + eval `$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 - #include + #define _HPUX_SOURCE + #include + #include - 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${OS_REL}; exit; } ;; 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) - /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ - && { echo i486-ncr-sysv4; exit; } ;; + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && { echo i486-ncr-sysv4; exit; } ;; NCR*:*:4.2:* | MPRAS*:*:4.2:*) OS_REL='.3' test -r /etc/.relid \ @@ -1132,10 +1181,10 @@ EOF echo ns32k-sni-sysv fi exit ;; - PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort - # says - echo i586-unisys-sysv4 - exit ;; + PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort + # says + echo i586-unisys-sysv4 + exit ;; *:UNIX_System_V:4*:FTX*) # From Gerald Hewes . # How about differentiating between stratus architectures? -djm @@ -1161,11 +1210,11 @@ EOF exit ;; R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) if [ -d /usr/nec ]; then - echo mips-nec-sysv${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 < 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 . # # 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 . 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 ." 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/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: -- cgit v1.2.3 From 33467f990312c393e5d4113fe86a3c850c66e4b7 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Fri, 29 May 2015 13:13:59 +0200 Subject: Fix vs2008 build --- astra_vc09.vcproj | 24 ++++++++++++++++-------- build/msvc/gen.py | 5 +++-- 2 files changed, 19 insertions(+), 10 deletions(-) (limited to 'build') 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" /> 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', file=F) -- cgit v1.2.3 From 7a4cfe2e5fe384691f0516020b2fcd48b35a7f63 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 27 May 2015 11:54:15 +0200 Subject: Increment version to 1.6 --- build/linux/configure.ac | 2 +- include/astra/Globals.h | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) (limited to 'build') diff --git a/build/linux/configure.ac b/build/linux/configure.ac index 58a3f4c..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]) 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) -- cgit v1.2.3 From 18b6d25f7e4f0943b3592f3bb4f6ca5ed9c285d3 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Fri, 19 Jun 2015 22:28:06 +0200 Subject: Add support for Python algorithm plugins --- build/linux/Makefile.in | 16 +- include/astra/AstraObjectFactory.h | 13 ++ include/astra/PluginAlgorithm.h | 85 +++++++++++ matlab/mex/astra_mex_plugin_c.cpp | 139 ++++++++++++++++++ python/astra/__init__.py | 1 + python/astra/plugin.py | 95 ++++++++++++ python/astra/plugin_c.pyx | 59 ++++++++ python/astra/utils.pyx | 72 +-------- python/docSRC/index.rst | 1 + python/docSRC/plugins.rst | 8 + samples/python/s018_plugin.py | 138 +++++++++++++++++ src/PluginAlgorithm.cpp | 294 +++++++++++++++++++++++++++++++++++++ 12 files changed, 851 insertions(+), 70 deletions(-) create mode 100644 include/astra/PluginAlgorithm.h create mode 100644 matlab/mex/astra_mex_plugin_c.cpp create mode 100644 python/astra/plugin.py create mode 100644 python/astra/plugin_c.pyx create mode 100644 python/docSRC/plugins.rst create mode 100644 samples/python/s018_plugin.py create mode 100644 src/PluginAlgorithm.cpp (limited to 'build') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 2d862f2..e209fa7 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -50,11 +50,17 @@ LDFLAGS+=-fopenmp endif ifeq ($(python),yes) -PYCPPFLAGS = ${CPPFLAGS} +PYTHON = @PYTHON@ +PYLIBDIR = $(shell $(PYTHON) -c 'from distutils.sysconfig import get_config_var; import six; six.print_(get_config_var("LIBDIR"))') +PYINCDIR = $(shell $(PYTHON) -c 'from distutils.sysconfig import get_python_inc; import six; six.print_(get_python_inc())') +PYLIBVER = `basename $(PYINCDIR)` +CPPFLAGS += -DASTRA_PYTHON -I$(PYINCDIR) +PYCPPFLAGS = $(CPPFLAGS) PYCPPFLAGS += -I../include -PYLDFLAGS = ${LDFLAGS} +PYLDFLAGS = $(LDFLAGS) PYLDFLAGS += -L../build/linux/.libs -PYTHON = @PYTHON@ +LIBS += -l$(PYLIBVER) +LDFLAGS += -L$(PYLIBDIR) endif BOOST_CPPFLAGS= @@ -234,6 +240,10 @@ MATLAB_MEX=\ matlab/mex/astra_mex_log_c.$(MEXSUFFIX) \ matlab/mex/astra_mex_data3d_c.$(MEXSUFFIX) +ifeq ($(python),yes) +ALL_OBJECTS+=src/PluginAlgorithm.lo +MATLAB_MEX+=matlab/mex/astra_mex_plugin_c.$(MEXSUFFIX) +endif OBJECT_DIRS = src/ tests/ cuda/2d/ cuda/3d/ matlab/mex/ ./ DEPDIRS = $(addsuffix $(DEPDIR),$(OBJECT_DIRS)) diff --git a/include/astra/AstraObjectFactory.h b/include/astra/AstraObjectFactory.h index 356acf9..325989e 100644 --- a/include/astra/AstraObjectFactory.h +++ b/include/astra/AstraObjectFactory.h @@ -40,6 +40,10 @@ $Id$ #include "AlgorithmTypelist.h" +#ifdef ASTRA_PYTHON +#include "PluginAlgorithm.h" +#endif + namespace astra { @@ -147,6 +151,15 @@ T* CAstraObjectFactory::create(const Config& _cfg) */ class _AstraExport CAlgorithmFactory : public CAstraObjectFactory {}; +#ifdef ASTRA_PYTHON +template <> +inline CAlgorithm* CAstraObjectFactory::findPlugin(std::string _sType) + { + CPluginAlgorithmFactory *fac = CPluginAlgorithmFactory::getSingletonPtr(); + return fac->getPlugin(_sType); + } +#endif + /** * Class used to create 2D projectors from a string or a config object */ diff --git a/include/astra/PluginAlgorithm.h b/include/astra/PluginAlgorithm.h new file mode 100644 index 0000000..7d6c64a --- /dev/null +++ b/include/astra/PluginAlgorithm.h @@ -0,0 +1,85 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the ASTRA Toolbox. + + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see . + +----------------------------------------------------------------------- +$Id$ +*/ + +#ifndef _INC_ASTRA_PLUGINALGORITHM +#define _INC_ASTRA_PLUGINALGORITHM + +#ifdef ASTRA_PYTHON + +#include +#include "bytesobject.h" +#include "astra/Algorithm.h" +#include "astra/Singleton.h" +#include "astra/XMLDocument.h" +#include "astra/XMLNode.h" + +namespace astra { +class _AstraExport CPluginAlgorithm : public CAlgorithm { + +public: + + CPluginAlgorithm(PyObject* pyclass); + ~CPluginAlgorithm(); + + bool initialize(const Config& _cfg); + void run(int _iNrIterations); + +private: + PyObject * instance; + +}; + +class _AstraExport CPluginAlgorithmFactory : public Singleton { + +public: + + CPluginAlgorithmFactory(); + ~CPluginAlgorithmFactory(); + + CPluginAlgorithm * getPlugin(std::string name); + + bool registerPlugin(std::string name, std::string className); + bool registerPluginClass(std::string name, PyObject * className); + + PyObject * getRegistered(); + + std::string getHelp(std::string name); + +private: + PyObject * pluginDict; + PyObject *ospath, *inspect, *six, *astra; + std::vector getPluginPathList(); +}; + +PyObject* XMLNode2dict(XMLNode node); + +} + +#endif + +#endif \ No newline at end of file diff --git a/matlab/mex/astra_mex_plugin_c.cpp b/matlab/mex/astra_mex_plugin_c.cpp new file mode 100644 index 0000000..2d9b9a0 --- /dev/null +++ b/matlab/mex/astra_mex_plugin_c.cpp @@ -0,0 +1,139 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the ASTRA Toolbox. + + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see . + +----------------------------------------------------------------------- +$Id$ +*/ + +/** \file astra_mex_plugin_c.cpp + * + * \brief Manages Python plugins. + */ + +#include +#include "mexHelpFunctions.h" +#include "mexInitFunctions.h" + +#include "astra/PluginAlgorithm.h" + +#include "Python.h" +#include "bytesobject.h" + +using namespace std; +using namespace astra; + + +//----------------------------------------------------------------------------------------- +/** astra_mex_plugin('get_registered'); + * + * Print registered plugins. + */ +void astra_mex_plugin_get_registered(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) +{ + astra::CPluginAlgorithmFactory *fact = astra::CPluginAlgorithmFactory::getSingletonPtr(); + PyObject *dict = fact->getRegistered(); + PyObject *key, *value; + Py_ssize_t pos = 0; + while (PyDict_Next(dict, &pos, &key, &value)) { + mexPrintf("%s: %s\n",PyBytes_AsString(key),PyBytes_AsString(value)); + } + Py_DECREF(dict); +} + +//----------------------------------------------------------------------------------------- +/** astra_mex_plugin('register', name, class_name); + * + * Register plugin. + */ +void astra_mex_plugin_register(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) +{ + if (3 <= nrhs) { + string name = mexToString(prhs[1]); + string class_name = mexToString(prhs[2]); + astra::CPluginAlgorithmFactory *fact = astra::CPluginAlgorithmFactory::getSingletonPtr(); + fact->registerPlugin(name, class_name); + }else{ + mexPrintf("astra_mex_plugin('register', name, class_name);\n"); + } +} + +//----------------------------------------------------------------------------------------- +/** astra_mex_plugin('get_help', name); + * + * Get help about plugin. + */ +void astra_mex_plugin_get_help(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) +{ + if (2 <= nrhs) { + string name = mexToString(prhs[1]); + astra::CPluginAlgorithmFactory *fact = astra::CPluginAlgorithmFactory::getSingletonPtr(); + mexPrintf((fact->getHelp(name)+"\n").c_str()); + }else{ + mexPrintf("astra_mex_plugin('get_help', name);\n"); + } +} + + +//----------------------------------------------------------------------------------------- + +static void printHelp() +{ + mexPrintf("Please specify a mode of operation.\n"); + mexPrintf(" Valid modes: register, get_registered, get_help\n"); +} + +//----------------------------------------------------------------------------------------- +/** + * ... = astra_mex(type,...); + */ +void mexFunction(int nlhs, mxArray* plhs[], + int nrhs, const mxArray* prhs[]) +{ + + // INPUT0: Mode + string sMode = ""; + if (1 <= nrhs) { + sMode = mexToString(prhs[0]); + } else { + printHelp(); + return; + } + + initASTRAMex(); + + // SWITCH (MODE) + if (sMode == std::string("get_registered")) { + astra_mex_plugin_get_registered(nlhs, plhs, nrhs, prhs); + }else if (sMode == std::string("get_help")) { + astra_mex_plugin_get_help(nlhs, plhs, nrhs, prhs); + }else if (sMode == std::string("register")) { + astra_mex_plugin_register(nlhs, plhs, nrhs, prhs); + } else { + printHelp(); + } + + return; +} + + diff --git a/python/astra/__init__.py b/python/astra/__init__.py index 6c15d30..10ed74d 100644 --- a/python/astra/__init__.py +++ b/python/astra/__init__.py @@ -34,6 +34,7 @@ from . import algorithm from . import projector from . import projector3d from . import matrix +from . import plugin from . import log from .optomo import OpTomo diff --git a/python/astra/plugin.py b/python/astra/plugin.py new file mode 100644 index 0000000..ccdb2cb --- /dev/null +++ b/python/astra/plugin.py @@ -0,0 +1,95 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see . +# +#----------------------------------------------------------------------- + +from . import plugin_c as p +from . import log + +class base(object): + + def astra_init(self, cfg): + try: + try: + req = self.required_options + except AttributeError: + log.warn("Plugin '" + self.__class__.__name__ + "' does not specify required options") + req = {} + + try: + opt = self.optional_options + except AttributeError: + log.warn("Plugin '" + self.__class__.__name__ + "' does not specify optional options") + opt = {} + + try: + optDict = cfg['options'] + except KeyError: + optDict = {} + + cfgKeys = set(optDict.keys()) + reqKeys = set(req) + optKeys = set(opt) + + if not reqKeys.issubset(cfgKeys): + for key in reqKeys.difference(cfgKeys): + log.error("Required option '" + key + "' for plugin '" + self.__class__.__name__ + "' not specified") + raise ValueError("Missing required options") + + if not cfgKeys.issubset(reqKeys | optKeys): + log.warn(self.__class__.__name__ + ": unused configuration option: " + str(list(cfgKeys.difference(reqKeys | optKeys)))) + + self.initialize(cfg) + except Exception as e: + log.error(str(e)) + raise + +def register(name, className): + """Register plugin with ASTRA. + + :param name: Plugin name to register + :type name: :class:`str` + :param className: Class name or class object to register + :type className: :class:`str` or :class:`class` + + """ + p.register(name,className) + +def get_registered(): + """Get dictionary of registered plugins. + + :returns: :class:`dict` -- Registered plugins. + + """ + return p.get_registered() + +def get_help(name): + """Get help for registered plugin. + + :param name: Plugin name to get help for + :type name: :class:`str` + :returns: :class:`str` -- Help string (docstring). + + """ + return p.get_help(name) \ No newline at end of file diff --git a/python/astra/plugin_c.pyx b/python/astra/plugin_c.pyx new file mode 100644 index 0000000..91b3cd5 --- /dev/null +++ b/python/astra/plugin_c.pyx @@ -0,0 +1,59 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see . +# +#----------------------------------------------------------------------- +# distutils: language = c++ +# distutils: libraries = astra + +import six +import inspect + +from libcpp.string cimport string +from libcpp cimport bool + +cdef CPluginAlgorithmFactory *fact = getSingletonPtr() + +from . import utils + +cdef extern from "astra/PluginAlgorithm.h" namespace "astra": + cdef cppclass CPluginAlgorithmFactory: + bool registerPlugin(string name, string className) + bool registerPluginClass(string name, object className) + object getRegistered() + string getHelp(string name) + +cdef extern from "astra/PluginAlgorithm.h" namespace "astra::CPluginAlgorithmFactory": + cdef CPluginAlgorithmFactory* getSingletonPtr() + +def register(name, className): + if inspect.isclass(className): + fact.registerPluginClass(six.b(name), className) + else: + fact.registerPlugin(six.b(name), six.b(className)) + +def get_registered(): + return fact.getRegistered() + +def get_help(name): + return utils.wrap_from_bytes(fact.getHelp(six.b(name))) diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx index ddb37aa..3746b8e 100644 --- a/python/astra/utils.pyx +++ b/python/astra/utils.pyx @@ -30,7 +30,6 @@ cimport numpy as np import numpy as np import six from libcpp.string cimport string -from libcpp.list cimport list from libcpp.vector cimport vector from cython.operator cimport dereference as deref, preincrement as inc from cpython.version cimport PY_MAJOR_VERSION @@ -40,6 +39,9 @@ from .PyXMLDocument cimport XMLDocument from .PyXMLDocument cimport XMLNode from .PyIncludes cimport * +cdef extern from "astra/PluginAlgorithm.h" namespace "astra": + object XMLNode2dict(XMLNode) + cdef Config * dictToConfig(string rootname, dc): cdef Config * cfg = new Config() @@ -91,6 +93,8 @@ cdef void readDict(XMLNode root, _dc): dc = convert_item(_dc) for item in dc: val = dc[item] + if isinstance(val, list): + val = np.array(val,dtype=np.float64) if isinstance(val, np.ndarray): if val.size == 0: break @@ -142,69 +146,3 @@ cdef void readOptions(XMLNode node, dc): cdef configToDict(Config *cfg): return XMLNode2dict(cfg.self) -def castString3(input): - return input.decode('utf-8') - -def castString2(input): - return input - -if six.PY3: - castString = castString3 -else: - castString = castString2 - -def stringToPythonValue(inputIn): - input = castString(inputIn) - # matrix - if ';' in input: - row_strings = input.split(';') - col_strings = row_strings[0].split(',') - nRows = len(row_strings) - nCols = len(col_strings) - - out = np.empty((nRows,nCols)) - for ridx, row in enumerate(row_strings): - col_strings = row.split(',') - for cidx, col in enumerate(col_strings): - out[ridx,cidx] = float(col) - return out - - # vector - if ',' in input: - items = input.split(',') - out = np.empty(len(items)) - for idx,item in enumerate(items): - out[idx] = float(item) - return out - - try: - # integer - return int(input) - except ValueError: - try: - #float - return float(input) - except ValueError: - # string - return str(input) - - -cdef XMLNode2dict(XMLNode node): - cdef XMLNode subnode - cdef list[XMLNode] nodes - cdef list[XMLNode].iterator it - dct = {} - opts = {} - if node.hasAttribute(six.b('type')): - dct['type'] = castString(node.getAttribute(six.b('type'))) - nodes = node.getNodes() - it = nodes.begin() - while it != nodes.end(): - subnode = deref(it) - if castString(subnode.getName())=="Option": - opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getAttribute('value')) - else: - dct[castString(subnode.getName())] = stringToPythonValue(subnode.getContent()) - inc(it) - if len(opts)>0: dct['options'] = opts - return dct diff --git a/python/docSRC/index.rst b/python/docSRC/index.rst index b7cc6d6..dcc6590 100644 --- a/python/docSRC/index.rst +++ b/python/docSRC/index.rst @@ -19,6 +19,7 @@ Contents: creators functions operator + plugins matlab astra .. astra diff --git a/python/docSRC/plugins.rst b/python/docSRC/plugins.rst new file mode 100644 index 0000000..dc7c607 --- /dev/null +++ b/python/docSRC/plugins.rst @@ -0,0 +1,8 @@ +Plugins: the :mod:`plugin` module +========================================= + +.. automodule:: astra.plugin + :members: + :undoc-members: + :show-inheritance: + diff --git a/samples/python/s018_plugin.py b/samples/python/s018_plugin.py new file mode 100644 index 0000000..6677930 --- /dev/null +++ b/samples/python/s018_plugin.py @@ -0,0 +1,138 @@ +#----------------------------------------------------------------------- +#Copyright 2015 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see . +# +#----------------------------------------------------------------------- + +import astra +import numpy as np +import six + +# Define the plugin class (has to subclass astra.plugin.base) +# Note that usually, these will be defined in a separate package/module +class SIRTPlugin(astra.plugin.base): + """Example of an ASTRA plugin class, implementing a simple 2D SIRT algorithm. + + Optional options: + + 'rel_factor': relaxation factor + """ + required_options=[] + optional_options=['rel_factor'] + + def initialize(self,cfg): + self.W = astra.OpTomo(cfg['ProjectorId']) + self.vid = cfg['ReconstructionDataId'] + self.sid = cfg['ProjectionDataId'] + try: + self.rel = cfg['option']['rel_factor'] + except KeyError: + self.rel = 1 + + def run(self, its): + v = astra.data2d.get_shared(self.vid) + s = astra.data2d.get_shared(self.sid) + W = self.W + for i in range(its): + v[:] += self.rel*(W.T*(s - (W*v).reshape(s.shape))).reshape(v.shape)/s.size + +if __name__=='__main__': + + vol_geom = astra.create_vol_geom(256, 256) + proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + + # As before, create a sinogram from a phantom + import scipy.io + P = scipy.io.loadmat('phantom.mat')['phantom256'] + proj_id = astra.create_projector('cuda',proj_geom,vol_geom) + + # construct the OpTomo object + W = astra.OpTomo(proj_id) + + sinogram = W * P + sinogram = sinogram.reshape([180, 384]) + + # Register the plugin with ASTRA + # A default set of plugins to load can be defined in: + # - /etc/astra-toolbox/plugins.txt + # - [ASTRA_INSTALL_PATH]/python/astra/plugins.txt + # - [USER_HOME_PATH]/.astra-toolbox/plugins.txt + # - [ASTRA_PLUGIN_PATH environment variable]/plugins.txt + # In these files, create a separate line for each plugin with: + # [PLUGIN_ASTRA_NAME] [FULL_PLUGIN_CLASS] + # + # So in this case, it would be a line: + # SIRT-PLUGIN s018_plugin.SIRTPlugin + # + astra.plugin.register('SIRT-PLUGIN','s018_plugin.SIRTPlugin') + + # To get help on a registered plugin, use get_help + six.print_(astra.plugin.get_help('SIRT-PLUGIN')) + + # Create data structures + sid = astra.data2d.create('-sino', proj_geom, sinogram) + vid = astra.data2d.create('-vol', vol_geom) + + # Create config using plugin name + cfg = astra.astra_dict('SIRT-PLUGIN') + cfg['ProjectorId'] = proj_id + cfg['ProjectionDataId'] = sid + cfg['ReconstructionDataId'] = vid + + # Create algorithm object + alg_id = astra.algorithm.create(cfg) + + # Run algorithm for 100 iterations + astra.algorithm.run(alg_id, 100) + + # Get reconstruction + rec = astra.data2d.get(vid) + + # Options for the plugin go in cfg['option'] + cfg = astra.astra_dict('SIRT-PLUGIN') + cfg['ProjectorId'] = proj_id + cfg['ProjectionDataId'] = sid + cfg['ReconstructionDataId'] = vid + cfg['option'] = {} + cfg['option']['rel_factor'] = 1.5 + alg_id_rel = astra.algorithm.create(cfg) + astra.algorithm.run(alg_id_rel, 100) + rec_rel = astra.data2d.get(vid) + + # We can also use OpTomo to call the plugin + rec_op = W.reconstruct('SIRT-PLUGIN', sinogram, 100, extraOptions={'rel_factor':1.5}) + + import pylab as pl + pl.gray() + pl.figure(1) + pl.imshow(rec,vmin=0,vmax=1) + pl.figure(2) + pl.imshow(rec_rel,vmin=0,vmax=1) + pl.figure(3) + pl.imshow(rec_op,vmin=0,vmax=1) + pl.show() + + # Clean up. + astra.projector.delete(proj_id) + astra.algorithm.delete([alg_id, alg_id_rel]) + astra.data2d.delete([vid, sid]) diff --git a/src/PluginAlgorithm.cpp b/src/PluginAlgorithm.cpp new file mode 100644 index 0000000..df13f31 --- /dev/null +++ b/src/PluginAlgorithm.cpp @@ -0,0 +1,294 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the ASTRA Toolbox. + + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see . + +----------------------------------------------------------------------- +$Id$ +*/ + +#ifdef ASTRA_PYTHON + +#include "astra/PluginAlgorithm.h" +#include +#include +#include +#include +#include +#include + +namespace astra { + +CPluginAlgorithm::CPluginAlgorithm(PyObject* pyclass){ + instance = PyObject_CallObject(pyclass, NULL); +} + +CPluginAlgorithm::~CPluginAlgorithm(){ + if(instance!=NULL){ + Py_DECREF(instance); + instance = NULL; + } +} + +bool CPluginAlgorithm::initialize(const Config& _cfg){ + if(instance==NULL) return false; + PyObject *cfgDict = XMLNode2dict(_cfg.self); + PyObject *retVal = PyObject_CallMethod(instance, "astra_init", "O",cfgDict); + Py_DECREF(cfgDict); + if(retVal==NULL) return false; + m_bIsInitialized = true; + Py_DECREF(retVal); + return m_bIsInitialized; +} + +void CPluginAlgorithm::run(int _iNrIterations){ + if(instance==NULL) return; + PyObject *retVal = PyObject_CallMethod(instance, "run", "i",_iNrIterations); + if(retVal==NULL) return; + Py_DECREF(retVal); +} + +const char ps = +#ifdef _WIN32 + '\\'; +#else + '/'; +#endif + +std::vector CPluginAlgorithmFactory::getPluginPathList(){ + std::vector list; + list.push_back("/etc/astra-toolbox"); + PyObject *ret, *retb; + ret = PyObject_CallMethod(inspect,"getfile","O",astra); + if(ret!=NULL){ + retb = PyObject_CallMethod(six,"b","O",ret); + Py_DECREF(ret); + if(retb!=NULL){ + std::string astra_inst (PyBytes_AsString(retb)); + Py_DECREF(retb); + ret = PyObject_CallMethod(ospath,"dirname","s",astra_inst.c_str()); + if(ret!=NULL){ + retb = PyObject_CallMethod(six,"b","O",ret); + Py_DECREF(ret); + if(retb!=NULL){ + list.push_back(std::string(PyBytes_AsString(retb))); + Py_DECREF(retb); + } + } + } + } + ret = PyObject_CallMethod(ospath,"expanduser","s","~"); + if(ret!=NULL){ + retb = PyObject_CallMethod(six,"b","O",ret); + Py_DECREF(ret); + if(retb!=NULL){ + list.push_back(std::string(PyBytes_AsString(retb)) + ps + ".astra-toolbox"); + Py_DECREF(retb); + } + } + const char *envval = getenv("ASTRA_PLUGIN_PATH"); + if(envval!=NULL){ + list.push_back(std::string(envval)); + } + return list; +} + +CPluginAlgorithmFactory::CPluginAlgorithmFactory(){ + Py_Initialize(); + pluginDict = PyDict_New(); + ospath = PyImport_ImportModule("os.path"); + inspect = PyImport_ImportModule("inspect"); + six = PyImport_ImportModule("six"); + astra = PyImport_ImportModule("astra"); + std::vector fls = getPluginPathList(); + std::vector items; + for(unsigned int i=0;i items; + boost::split(items, str, boost::is_any_of(".")); + PyObject *pyclass = PyImport_ImportModule(items[0].c_str()); + if(pyclass==NULL) return NULL; + PyObject *submod = pyclass; + for(unsigned int i=1;i= 3 +PyObject * pyStringFromString(std::string str){ + return PyUnicode_FromString(str.c_str()); +} +#else +PyObject * pyStringFromString(std::string str){ + return PyBytes_FromString(str.c_str()); +} +#endif + +PyObject* stringToPythonValue(std::string str){ + if(str.find(";")!=std::string::npos){ + std::vector rows, row; + boost::split(rows, str, boost::is_any_of(";")); + PyObject *mat = PyList_New(rows.size()); + for(unsigned int i=0; i(row[j]))); + } + PyList_SetItem(mat, i, rowlist); + } + return mat; + } + if(str.find(",")!=std::string::npos){ + std::vector vec; + boost::split(vec, str, boost::is_any_of(",")); + PyObject *veclist = PyList_New(vec.size()); + for(unsigned int i=0;i(vec[i]))); + } + return veclist; + } + try{ + return PyLong_FromLong(boost::lexical_cast(str)); + }catch(const boost::bad_lexical_cast &){ + try{ + return PyFloat_FromDouble(boost::lexical_cast(str)); + }catch(const boost::bad_lexical_cast &){ + return pyStringFromString(str); + } + } +} + +PyObject* XMLNode2dict(XMLNode node){ + PyObject *dct = PyDict_New(); + PyObject *opts = PyDict_New(); + if(node.hasAttribute("type")){ + PyObject *obj = pyStringFromString(node.getAttribute("type").c_str()); + PyDict_SetItemString(dct, "type", obj); + Py_DECREF(obj); + } + std::list nodes = node.getNodes(); + std::list::iterator it = nodes.begin(); + while(it!=nodes.end()){ + XMLNode subnode = *it; + if(subnode.getName()=="Option"){ + PyObject *obj = stringToPythonValue(subnode.getAttribute("value")); + PyDict_SetItemString(opts, subnode.getAttribute("key").c_str(), obj); + Py_DECREF(obj); + }else{ + PyObject *obj = stringToPythonValue(subnode.getContent()); + PyDict_SetItemString(dct, subnode.getName().c_str(), obj); + Py_DECREF(obj); + } + ++it; + } + PyDict_SetItemString(dct, "options", opts); + Py_DECREF(opts); + return dct; +} + +} +#endif \ No newline at end of file -- cgit v1.2.3 From 1cc67c1e4d9b6b24c096f52d6f086a3f224ece8a Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 7 Oct 2015 17:29:20 +0200 Subject: Add astra_mex_direct('FP3D'/'BP3D', ...) --- build/linux/Makefile.in | 3 +- matlab/mex/astra_mex_direct_c.cpp | 332 ++++++++++++++++++++++++++++++++++++++ matlab/tools/astra_mex_direct.m | 24 +++ 3 files changed, 358 insertions(+), 1 deletion(-) create mode 100755 matlab/mex/astra_mex_direct_c.cpp create mode 100644 matlab/tools/astra_mex_direct.m (limited to 'build') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 2d862f2..abbebe2 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -232,7 +232,8 @@ MATLAB_MEX=\ matlab/mex/astra_mex_projector_c.$(MEXSUFFIX) \ matlab/mex/astra_mex_projector3d_c.$(MEXSUFFIX) \ matlab/mex/astra_mex_log_c.$(MEXSUFFIX) \ - matlab/mex/astra_mex_data3d_c.$(MEXSUFFIX) + matlab/mex/astra_mex_data3d_c.$(MEXSUFFIX) \ + matlab/mex/astra_mex_direct_c.$(MEXSUFFIX) OBJECT_DIRS = src/ tests/ cuda/2d/ cuda/3d/ matlab/mex/ ./ diff --git a/matlab/mex/astra_mex_direct_c.cpp b/matlab/mex/astra_mex_direct_c.cpp new file mode 100755 index 0000000..94eb1cd --- /dev/null +++ b/matlab/mex/astra_mex_direct_c.cpp @@ -0,0 +1,332 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the ASTRA Toolbox. + + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see . + +----------------------------------------------------------------------- +$Id$ +*/ + +/** \file astra_mex_direct_c.cpp + * + * \brief Utility functions for low-overhead FP and BP calls. + */ +#include +#include "mexHelpFunctions.h" +#include "mexCopyDataHelpFunctions.h" +#include "mexDataManagerHelpFunctions.h" + +#include + +#include "astra/Globals.h" + +#include "astra/AstraObjectManager.h" + +#include "astra/Float32ProjectionData2D.h" +#include "astra/Float32VolumeData2D.h" +#include "astra/CudaProjector3D.h" +#include "astra/Projector3D.h" +#include "astra/Float32ProjectionData3DMemory.h" +#include "astra/Float32VolumeData3DMemory.h" + +#include "astra/CudaForwardProjectionAlgorithm3D.h" + +#include "astra/CudaBackProjectionAlgorithm3D.h" + +using namespace std; +using namespace astra; + +#define USE_MATLAB_UNDOCUMENTED + + +class CFloat32CustomMemory_simple : public astra::CFloat32CustomMemory { +public: + CFloat32CustomMemory_simple(float *ptr) { m_fPtr = ptr; } + ~CFloat32CustomMemory_simple() { } +}; + +#ifdef ASTRA_CUDA + +//----------------------------------------------------------------------------------------- +/** + * projection = astra_mex_direct_c('FP3D', projector_id, volume); + * Both 'projection' and 'volume' are Matlab arrays. + */ +void astra_mex_direct_fp3d(int& nlhs, mxArray* plhs[], int& nrhs, const mxArray* prhs[]) +{ + // TODO: Add an optional way of specifying extra options + + if (nrhs < 3) { + mexErrMsgTxt("Not enough arguments. Syntax: astra_mex_direct_c('FP3D', projector_id, data)"); + return; + } + + int iPid = (int)(mxGetScalar(prhs[1])); + astra::CProjector3D* pProjector; + pProjector = astra::CProjector3DManager::getSingleton().get(iPid); + if (!pProjector) { + mexErrMsgTxt("Projector not found."); + return; + } + if (!pProjector->isInitialized()) { + mexErrMsgTxt("Projector not initialized."); + return; + } + bool isCuda = false; + if (dynamic_cast(pProjector)) + isCuda = true; + if (!isCuda) { + mexErrMsgTxt("Only CUDA projectors are currently supported."); + return; + } + + astra::CVolumeGeometry3D* pVolGeom = pProjector->getVolumeGeometry(); + astra::CProjectionGeometry3D* pProjGeom = pProjector->getProjectionGeometry(); + + const mxArray* const data = prhs[2]; + if (!checkDataType(data)) { + mexErrMsgTxt("Data must be single or double."); + return; + } + + if (!checkDataSize(data, pVolGeom)) { + mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry."); + return; + } + + + // Allocate input data + astra::CFloat32VolumeData3DMemory* pInput; + if (mxIsSingle(data)) { + astra::CFloat32CustomMemory* m = new CFloat32CustomMemory_simple((float *)mxGetData(data)); + pInput = new astra::CFloat32VolumeData3DMemory(pVolGeom, m); + } else { + pInput = new astra::CFloat32VolumeData3DMemory(pVolGeom); + copyMexToCFloat32Array(data, pInput->getData(), pInput->getSize()); + } + + + // Allocate output data + // If the input is single, we also allocate single output. + // Otherwise, double. + astra::CFloat32ProjectionData3DMemory* pOutput; + mxArray *pOutputMx; + if (mxIsSingle(data)) { + mwSize dims[3]; + dims[0] = pProjGeom->getDetectorColCount(); + dims[1] = pProjGeom->getProjectionCount(); + dims[2] = pProjGeom->getDetectorRowCount(); + pOutputMx = mxCreateNumericArray(3, dims, mxSINGLE_CLASS, mxREAL); + + astra::CFloat32CustomMemory* m = new CFloat32CustomMemory_simple((float *)mxGetData(pOutputMx)); + pOutput = new astra::CFloat32ProjectionData3DMemory(pProjGeom, m); + } else { + pOutput = new astra::CFloat32ProjectionData3DMemory(pProjGeom); + } + + // Perform FP + + astra::CCudaForwardProjectionAlgorithm3D* pAlg; + pAlg = new astra::CCudaForwardProjectionAlgorithm3D(); + pAlg->initialize(pProjector, pOutput, pInput); + + if (!pAlg->isInitialized()) { + mexErrMsgTxt("Error initializing algorithm."); + // TODO: Delete pOutputMx? + delete pAlg; + delete pInput; + delete pOutput; + return; + } + + pAlg->run(); + + delete pAlg; + + + if (mxIsSingle(data)) { + + } else { + pOutputMx = createEquivMexArray(pOutput); + copyCFloat32ArrayToMex(pOutput->getData(), pOutputMx); + } + plhs[0] = pOutputMx; + + delete pOutput; + delete pInput; +} +//----------------------------------------------------------------------------------------- +/** + * projection = astra_mex_direct_c('BP3D', projector_id, volume); + * Both 'projection' and 'volume' are Matlab arrays. + */ +void astra_mex_direct_bp3d(int& nlhs, mxArray* plhs[], int& nrhs, const mxArray* prhs[]) +{ + // TODO: Add an optional way of specifying extra options + + if (nrhs < 3) { + mexErrMsgTxt("Not enough arguments. Syntax: astra_mex_direct_c('BP3D', projector_id, data)"); + return; + } + + int iPid = (int)(mxGetScalar(prhs[1])); + astra::CProjector3D* pProjector; + pProjector = astra::CProjector3DManager::getSingleton().get(iPid); + if (!pProjector) { + mexErrMsgTxt("Projector not found."); + return; + } + if (!pProjector->isInitialized()) { + mexErrMsgTxt("Projector not initialized."); + return; + } + bool isCuda = false; + if (dynamic_cast(pProjector)) + isCuda = true; + if (!isCuda) { + mexErrMsgTxt("Only CUDA projectors are currently supported."); + return; + } + + astra::CVolumeGeometry3D* pVolGeom = pProjector->getVolumeGeometry(); + astra::CProjectionGeometry3D* pProjGeom = pProjector->getProjectionGeometry(); + + const mxArray* const data = prhs[2]; + if (!checkDataType(data)) { + mexErrMsgTxt("Data must be single or double."); + return; + } + + if (!checkDataSize(data, pProjGeom)) { + mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry."); + return; + } + + + // Allocate input data + astra::CFloat32ProjectionData3DMemory* pInput; + if (mxIsSingle(data)) { + astra::CFloat32CustomMemory* m = new CFloat32CustomMemory_simple((float *)mxGetData(data)); + pInput = new astra::CFloat32ProjectionData3DMemory(pProjGeom, m); + } else { + pInput = new astra::CFloat32ProjectionData3DMemory(pProjGeom); + copyMexToCFloat32Array(data, pInput->getData(), pInput->getSize()); + } + + + // Allocate output data + // If the input is single, we also allocate single output. + // Otherwise, double. + astra::CFloat32VolumeData3DMemory* pOutput; + mxArray *pOutputMx; + if (mxIsSingle(data)) { + mwSize dims[3]; + dims[0] = pVolGeom->getGridColCount(); + dims[1] = pVolGeom->getGridRowCount(); + dims[2] = pVolGeom->getGridSliceCount(); + pOutputMx = mxCreateNumericArray(3, dims, mxSINGLE_CLASS, mxREAL); + + astra::CFloat32CustomMemory* m = new CFloat32CustomMemory_simple((float *)mxGetData(pOutputMx)); + pOutput = new astra::CFloat32VolumeData3DMemory(pVolGeom, m); + } else { + pOutput = new astra::CFloat32VolumeData3DMemory(pVolGeom); + } + + // Perform BP + + astra::CCudaBackProjectionAlgorithm3D* pAlg; + pAlg = new astra::CCudaBackProjectionAlgorithm3D(); + pAlg->initialize(pProjector, pInput, pOutput); + + if (!pAlg->isInitialized()) { + mexErrMsgTxt("Error initializing algorithm."); + // TODO: Delete pOutputMx? + delete pAlg; + delete pInput; + delete pOutput; + return; + } + + pAlg->run(); + + delete pAlg; + + + if (mxIsSingle(data)) { + + } else { + pOutputMx = createEquivMexArray(pOutput); + copyCFloat32ArrayToMex(pOutput->getData(), pOutputMx); + } + plhs[0] = pOutputMx; + + delete pOutput; + delete pInput; +} + +#endif + +//----------------------------------------------------------------------------------------- + +static void printHelp() +{ + mexPrintf("Please specify a mode of operation.\n"); + mexPrintf("Valid modes: FP3D, BP3D\n"); +} + + +//----------------------------------------------------------------------------------------- +/** + * ... = astra_mex_direct_c(mode,...); + */ +void mexFunction(int nlhs, mxArray* plhs[], + int nrhs, const mxArray* prhs[]) +{ + + // INPUT: Mode + string sMode; + if (1 <= nrhs) { + sMode = mexToString(prhs[0]); + } else { + printHelp(); + return; + } + +#ifndef ASTRA_CUDA + mexErrMsgTxt("Only CUDA projectors are currently supported."); + return; +#else + + // 3D data + if (sMode == "FP3D") { + astra_mex_direct_fp3d(nlhs, plhs, nrhs, prhs); + } else if (sMode == "BP3D") { + astra_mex_direct_bp3d(nlhs, plhs, nrhs, prhs); + } else { + printHelp(); + } +#endif + + return; +} + + diff --git a/matlab/tools/astra_mex_direct.m b/matlab/tools/astra_mex_direct.m new file mode 100644 index 0000000..58c4fd2 --- /dev/null +++ b/matlab/tools/astra_mex_direct.m @@ -0,0 +1,24 @@ +function [varargout] = astra_mex_direct(varargin) +%------------------------------------------------------------------------ +% Reference page in Help browser +% astra_mex_data3d. +%------------------------------------------------------------------------ +%------------------------------------------------------------------------ +% 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 +%------------------------------------------------------------------------ +% $Id$ +if nargout == 0 + astra_mex_direct_c(varargin{:}); + if exist('ans','var') + varargout{1} = ans; + end +else + varargout = cell(1,nargout); + [varargout{:}] = astra_mex_direct_c(varargin{:}); +end -- cgit v1.2.3 From 793afbc3fa1cca64292716869e503cb66942606d Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 7 Oct 2015 17:29:40 +0200 Subject: Build astra_mex_direct in MSVC --- astra_vc09.sln | 22 ++ astra_vc11.sln | 22 ++ build/msvc/gen.py | 15 +- matlab/mex/astra_mex_direct_vc09.vcproj | 612 +++++++++++++++++++++++++++++++ matlab/mex/astra_mex_direct_vc11.vcxproj | 306 ++++++++++++++++ 5 files changed, 975 insertions(+), 2 deletions(-) create mode 100644 matlab/mex/astra_mex_direct_vc09.vcproj create mode 100644 matlab/mex/astra_mex_direct_vc11.vcxproj (limited to 'build') diff --git a/astra_vc09.sln b/astra_vc09.sln index 9b93a0f..371e9b1 100644 --- a/astra_vc09.sln +++ b/astra_vc09.sln @@ -48,6 +48,11 @@ Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "astra_mex_log", "matlab\mex {12926444-6723-46A8-B388-12E65E0577FA} = {12926444-6723-46A8-B388-12E65E0577FA} EndProjectSection EndProject +Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "astra_mex_direct", "matlab\mex\astra_mex_direct_vc09.vcproj", "{85FE09A6-FA49-4314-A2B1-59D77C7442A8}" + ProjectSection(ProjectDependencies) = postProject + {12926444-6723-46A8-B388-12E65E0577FA} = {12926444-6723-46A8-B388-12E65E0577FA} + EndProjectSection +EndProject Global GlobalSection(SolutionConfigurationPlatforms) = preSolution Debug_CUDA|Win32 = Debug_CUDA|Win32 @@ -204,6 +209,22 @@ Global {CA2840B3-DA68-41B5-AC57-F5DFD20ED8F8}.Release|Win32.Build.0 = Release|Win32 {CA2840B3-DA68-41B5-AC57-F5DFD20ED8F8}.Release|x64.ActiveCfg = Release|x64 {CA2840B3-DA68-41B5-AC57-F5DFD20ED8F8}.Release|x64.Build.0 = Release|x64 + {85FE09A6-FA49-4314-A2B1-59D77C7442A8}.Debug_CUDA|Win32.ActiveCfg = Debug_CUDA|Win32 + {85FE09A6-FA49-4314-A2B1-59D77C7442A8}.Debug_CUDA|Win32.Build.0 = Debug_CUDA|Win32 + {85FE09A6-FA49-4314-A2B1-59D77C7442A8}.Debug_CUDA|x64.ActiveCfg = Debug_CUDA|x64 + {85FE09A6-FA49-4314-A2B1-59D77C7442A8}.Debug_CUDA|x64.Build.0 = Debug_CUDA|x64 + {85FE09A6-FA49-4314-A2B1-59D77C7442A8}.Debug|Win32.ActiveCfg = Debug|Win32 + {85FE09A6-FA49-4314-A2B1-59D77C7442A8}.Debug|Win32.Build.0 = Debug|Win32 + {85FE09A6-FA49-4314-A2B1-59D77C7442A8}.Debug|x64.ActiveCfg = Debug|x64 + {85FE09A6-FA49-4314-A2B1-59D77C7442A8}.Debug|x64.Build.0 = Debug|x64 + {85FE09A6-FA49-4314-A2B1-59D77C7442A8}.Release_CUDA|Win32.ActiveCfg = Release_CUDA|Win32 + {85FE09A6-FA49-4314-A2B1-59D77C7442A8}.Release_CUDA|Win32.Build.0 = Release_CUDA|Win32 + {85FE09A6-FA49-4314-A2B1-59D77C7442A8}.Release_CUDA|x64.ActiveCfg = Release_CUDA|x64 + {85FE09A6-FA49-4314-A2B1-59D77C7442A8}.Release_CUDA|x64.Build.0 = Release_CUDA|x64 + {85FE09A6-FA49-4314-A2B1-59D77C7442A8}.Release|Win32.ActiveCfg = Release|Win32 + {85FE09A6-FA49-4314-A2B1-59D77C7442A8}.Release|Win32.Build.0 = Release|Win32 + {85FE09A6-FA49-4314-A2B1-59D77C7442A8}.Release|x64.ActiveCfg = Release|x64 + {85FE09A6-FA49-4314-A2B1-59D77C7442A8}.Release|x64.Build.0 = Release|x64 EndGlobalSection GlobalSection(SolutionProperties) = preSolution HideSolutionNode = FALSE @@ -217,5 +238,6 @@ Global {4DD6056F-8EEE-4C9A-B2A9-923F01A32E97} = {33EF0AC5-B475-40BF-BAE5-67075B204D10} {F94CCD79-AA11-42DF-AC8A-6C9D2238A883} = {33EF0AC5-B475-40BF-BAE5-67075B204D10} {CA2840B3-DA68-41B5-AC57-F5DFD20ED8F8} = {33EF0AC5-B475-40BF-BAE5-67075B204D10} + {85FE09A6-FA49-4314-A2B1-59D77C7442A8} = {33EF0AC5-B475-40BF-BAE5-67075B204D10} EndGlobalSection EndGlobal diff --git a/astra_vc11.sln b/astra_vc11.sln index 2832eab..92fb584 100644 --- a/astra_vc11.sln +++ b/astra_vc11.sln @@ -48,6 +48,11 @@ Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "astra_mex_log", "matlab\mex {BE9F1326-527C-4284-AE2C-D1E25D539CEA} = {BE9F1326-527C-4284-AE2C-D1E25D539CEA} EndProjectSection EndProject +Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "astra_mex_direct", "matlab\mex\astra_mex_direct_vc11.vcxproj", "{0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7}" + ProjectSection(ProjectDependencies) = postProject + {BE9F1326-527C-4284-AE2C-D1E25D539CEA} = {BE9F1326-527C-4284-AE2C-D1E25D539CEA} + EndProjectSection +EndProject Global GlobalSection(SolutionConfigurationPlatforms) = preSolution Debug_CUDA|Win32 = Debug_CUDA|Win32 @@ -204,6 +209,22 @@ Global {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}.Release|Win32.Build.0 = Release|Win32 {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}.Release|x64.ActiveCfg = Release|x64 {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}.Release|x64.Build.0 = Release|x64 + {0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7}.Debug_CUDA|Win32.ActiveCfg = Debug_CUDA|Win32 + {0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7}.Debug_CUDA|Win32.Build.0 = Debug_CUDA|Win32 + {0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7}.Debug_CUDA|x64.ActiveCfg = Debug_CUDA|x64 + {0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7}.Debug_CUDA|x64.Build.0 = Debug_CUDA|x64 + {0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7}.Debug|Win32.ActiveCfg = Debug|Win32 + {0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7}.Debug|Win32.Build.0 = Debug|Win32 + {0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7}.Debug|x64.ActiveCfg = Debug|x64 + {0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7}.Debug|x64.Build.0 = Debug|x64 + {0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7}.Release_CUDA|Win32.ActiveCfg = Release_CUDA|Win32 + {0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7}.Release_CUDA|Win32.Build.0 = Release_CUDA|Win32 + {0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7}.Release_CUDA|x64.ActiveCfg = Release_CUDA|x64 + {0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7}.Release_CUDA|x64.Build.0 = Release_CUDA|x64 + {0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7}.Release|Win32.ActiveCfg = Release|Win32 + {0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7}.Release|Win32.Build.0 = Release|Win32 + {0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7}.Release|x64.ActiveCfg = Release|x64 + {0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7}.Release|x64.Build.0 = Release|x64 EndGlobalSection GlobalSection(SolutionProperties) = preSolution HideSolutionNode = FALSE @@ -217,5 +238,6 @@ Global {4DD6056F-8EEE-4C9A-B2A9-923F01A32E97} = {5E99A109-374E-4102-BE9B-99BA1FA8AA30} {F94CCD79-AA11-42DF-AC8A-6C9D2238A883} = {5E99A109-374E-4102-BE9B-99BA1FA8AA30} {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E} = {5E99A109-374E-4102-BE9B-99BA1FA8AA30} + {0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7} = {5E99A109-374E-4102-BE9B-99BA1FA8AA30} EndGlobalSection EndGlobal diff --git a/build/msvc/gen.py b/build/msvc/gen.py index aeca3b0..a9bc494 100644 --- a/build/msvc/gen.py +++ b/build/msvc/gen.py @@ -24,6 +24,7 @@ P4 = create_mex_project("astra_mex_matrix", "9D041710-2119-4230-BCF2-5FBE753FDE4 P5 = create_mex_project("astra_mex_projector", "4DD6056F-8EEE-4C9A-B2A9-923F01A32E97", "4DD6056F-8EEE-4C9A-B2A9-923F01A32E97") P6 = create_mex_project("astra_mex_projector3d", "F94CCD79-AA11-42DF-AC8A-6C9D2238A883", "F94CCD79-AA11-42DF-AC8A-6C9D2238A883") P7 = create_mex_project("astra_mex_log", "03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E", "CA2840B3-DA68-41B5-AC57-F5DFD20ED8F8") +P8 = create_mex_project("astra_mex_direct", "0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7", "85FE09A6-FA49-4314-A2B1-59D77C7442A8") F_astra_mex = { "type": siguid, "name": "astra_mex", @@ -31,7 +32,7 @@ F_astra_mex = { "type": siguid, "file09": "astra_mex", "uuid11": "5E99A109-374E-4102-BE9B-99BA1FA8AA30", "uuid09": "33EF0AC5-B475-40BF-BAE5-67075B204D10", - "entries": [ P0, P1, P2, P3, P4, P5, P6, P7 ] } + "entries": [ P0, P1, P2, P3, P4, P5, P6, P7, P8 ] } P0["files"] = [ @@ -98,6 +99,14 @@ P7["files"] = [ "mexInitFunctions.cpp", "mexInitFunctions.h", ] +P8["files"] = [ +"astra_mex_direct_c.cpp", +"mexHelpFunctions.cpp", +"mexHelpFunctions.h", +"mexInitFunctions.cpp", +"mexInitFunctions.h", +] + @@ -407,7 +416,7 @@ for f in P_astra["filters"]: P_astra["files"].extend(P_astra["filters"][f][1:]) P_astra["files"].sort() -projects = [ P_astra, F_astra_mex, P0, P1, P2, P3, P4, P5, P6, P7 ] +projects = [ P_astra, F_astra_mex, P0, P1, P2, P3, P4, P5, P6, P7, P8 ] bom = "\xef\xbb\xbf" @@ -1111,6 +1120,7 @@ if sys.argv[1] in ["vc11", "all"]: write_mex_project11(P5) write_mex_project11(P6) write_mex_project11(P7) + write_mex_project11(P8) if sys.argv[1] in ["vc09", "all"]: # HACK @@ -1126,3 +1136,4 @@ if sys.argv[1] in ["vc09", "all"]: write_mex_project09(P5) write_mex_project09(P6) write_mex_project09(P7) + write_mex_project09(P8) diff --git a/matlab/mex/astra_mex_direct_vc09.vcproj b/matlab/mex/astra_mex_direct_vc09.vcproj new file mode 100644 index 0000000..04b49ac --- /dev/null +++ b/matlab/mex/astra_mex_direct_vc09.vcproj @@ -0,0 +1,612 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/matlab/mex/astra_mex_direct_vc11.vcxproj b/matlab/mex/astra_mex_direct_vc11.vcxproj new file mode 100644 index 0000000..15c3c06 --- /dev/null +++ b/matlab/mex/astra_mex_direct_vc11.vcxproj @@ -0,0 +1,306 @@ + + + + + Debug_CUDA + Win32 + + + Debug_CUDA + x64 + + + Debug + Win32 + + + Debug + x64 + + + Release_CUDA + Win32 + + + Release_CUDA + x64 + + + Release + Win32 + + + Release + x64 + + + + astra_mex_direct + {0F68F4E2-BE1B-4A9A-B101-AECF4C069CC7} + astraMatlab + + + + DynamicLibrary + v110 + + + DynamicLibrary + v110 + + + DynamicLibrary + v110 + + + DynamicLibrary + v110 + + + DynamicLibrary + v110 + + + DynamicLibrary + v110 + + + DynamicLibrary + v110 + + + DynamicLibrary + v110 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + <_ProjectFileVersion>11.0.60610.1 + + + $(SolutionDir)bin\$(Platform)\$(Configuration)\ + $(OutDir)obj\$(ProjectName)\ + $(ProjectName)_c + .mexw32 + + + $(SolutionDir)bin\$(Platform)\$(Configuration)\ + $(OutDir)obj\$(ProjectName)\ + $(ProjectName)_c + .mexw64 + + + $(SolutionDir)bin\$(Platform)\$(Configuration)\ + $(OutDir)obj\$(ProjectName)\ + $(ProjectName)_c + .mexw32 + + + $(SolutionDir)bin\$(Platform)\$(Configuration)\ + $(OutDir)obj\$(ProjectName)\ + $(ProjectName)_c + .mexw64 + + + $(SolutionDir)bin\$(Platform)\$(Configuration)\ + $(OutDir)obj\$(ProjectName)\ + $(ProjectName)_c + .mexw32 + + + $(SolutionDir)bin\$(Platform)\$(Configuration)\ + $(OutDir)obj\$(ProjectName)\ + $(ProjectName)_c + .mexw64 + + + $(SolutionDir)bin\$(Platform)\$(Configuration)\ + $(OutDir)obj\$(ProjectName)\ + $(ProjectName)_c + .mexw32 + + + $(SolutionDir)bin\$(Platform)\$(Configuration)\ + $(OutDir)obj\$(ProjectName)\ + $(ProjectName)_c + .mexw64 + + + + MultiThreadedDebugDLL + $(MATLAB_ROOT)\extern\include\;$(CUDA_PATH)\include;..\..\lib\include;..\..\include;%(AdditionalIncludeDirectories) + true + StreamingSIMDExtensions2 + Disabled + ASTRA_CUDA;__SSE2__;%(PreprocessorDefinitions) + true + + + $(OutDir)$(ProjectName)_c.mexw32 + AstraCuda32D.lib;libmex.lib;libmx.lib;libut.lib;%(AdditionalDependencies) + ..\..\lib\win32\;..\..\bin\win32\Debug_CUDA;$(MATLAB_ROOT)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories) + mex.def + true + + + + + MultiThreadedDebugDLL + $(MATLAB_ROOT)\extern\include\;$(CUDA_PATH)\include;..\..\lib\include;..\..\include;%(AdditionalIncludeDirectories) + true + Disabled + ASTRA_CUDA;__SSE2__;%(PreprocessorDefinitions) + true + + + $(OutDir)$(ProjectName)_c.mexw64 + AstraCuda64D.lib;libmex.lib;libmx.lib;libut.lib;%(AdditionalDependencies) + ..\..\lib\x64\;..\..\bin\x64\Debug_CUDA;$(MATLAB_ROOT)\extern\lib\win64\microsoft;%(AdditionalLibraryDirectories) + mex.def + true + + + + + MultiThreadedDebugDLL + $(MATLAB_ROOT)\extern\include\;$(CUDA_PATH)\include;..\..\lib\include;..\..\include;%(AdditionalIncludeDirectories) + true + StreamingSIMDExtensions2 + Disabled + __SSE2__;%(PreprocessorDefinitions) + true + + + $(OutDir)$(ProjectName)_c.mexw32 + Astra32D.lib;libmex.lib;libmx.lib;libut.lib;%(AdditionalDependencies) + ..\..\lib\win32\;..\..\bin\win32\Debug;$(MATLAB_ROOT)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories) + mex.def + true + + + + + MultiThreadedDebugDLL + $(MATLAB_ROOT)\extern\include\;$(CUDA_PATH)\include;..\..\lib\include;..\..\include;%(AdditionalIncludeDirectories) + true + Disabled + __SSE2__;%(PreprocessorDefinitions) + true + + + $(OutDir)$(ProjectName)_c.mexw64 + Astra64D.lib;libmex.lib;libmx.lib;libut.lib;%(AdditionalDependencies) + ..\..\lib\x64\;..\..\bin\x64\Debug;$(MATLAB_ROOT)\extern\lib\win64\microsoft;%(AdditionalLibraryDirectories) + mex.def + true + + + + + MultiThreadedDLL + $(MATLAB_ROOT)\extern\include\;$(CUDA_PATH)\include;..\..\lib\include;..\..\include;%(AdditionalIncludeDirectories) + true + StreamingSIMDExtensions2 + MaxSpeed + ASTRA_CUDA;__SSE2__;%(PreprocessorDefinitions) + true + + + $(OutDir)$(ProjectName)_c.mexw32 + AstraCuda32.lib;libmex.lib;libmx.lib;libut.lib;%(AdditionalDependencies) + ..\..\lib\win32\;..\..\bin\win32\Release_CUDA;$(MATLAB_ROOT)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories) + mex.def + true + + + + + MultiThreadedDLL + $(MATLAB_ROOT)\extern\include\;$(CUDA_PATH)\include;..\..\lib\include;..\..\include;%(AdditionalIncludeDirectories) + true + MaxSpeed + ASTRA_CUDA;__SSE2__;%(PreprocessorDefinitions) + true + + + $(OutDir)$(ProjectName)_c.mexw64 + AstraCuda64.lib;libmex.lib;libmx.lib;libut.lib;%(AdditionalDependencies) + ..\..\lib\x64\;..\..\bin\x64\Release_CUDA;$(MATLAB_ROOT)\extern\lib\win64\microsoft;%(AdditionalLibraryDirectories) + mex.def + true + + + + + MultiThreadedDLL + $(MATLAB_ROOT)\extern\include\;$(CUDA_PATH)\include;..\..\lib\include;..\..\include;%(AdditionalIncludeDirectories) + true + StreamingSIMDExtensions2 + MaxSpeed + __SSE2__;%(PreprocessorDefinitions) + true + + + $(OutDir)$(ProjectName)_c.mexw32 + Astra32.lib;libmex.lib;libmx.lib;libut.lib;%(AdditionalDependencies) + ..\..\lib\win32\;..\..\bin\win32\Release;$(MATLAB_ROOT)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories) + mex.def + true + + + + + MultiThreadedDLL + $(MATLAB_ROOT)\extern\include\;$(CUDA_PATH)\include;..\..\lib\include;..\..\include;%(AdditionalIncludeDirectories) + true + MaxSpeed + __SSE2__;%(PreprocessorDefinitions) + true + + + $(OutDir)$(ProjectName)_c.mexw64 + Astra64.lib;libmex.lib;libmx.lib;libut.lib;%(AdditionalDependencies) + ..\..\lib\x64\;..\..\bin\x64\Release;$(MATLAB_ROOT)\extern\lib\win64\microsoft;%(AdditionalLibraryDirectories) + mex.def + true + + + + + + + + + + + + + + + \ No newline at end of file -- cgit v1.2.3 From 6d57f7874713e6632c2e49590538c6a48ddcc311 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 2 Dec 2015 14:53:36 +0100 Subject: Fix Windows builds of astra_mex_direct --- build/msvc/gen.py | 4 ++++ matlab/mex/astra_mex_direct_vc09.vcproj | 16 ++++++++++++++++ matlab/mex/astra_mex_direct_vc11.vcxproj | 4 ++++ 3 files changed, 24 insertions(+) (limited to 'build') diff --git a/build/msvc/gen.py b/build/msvc/gen.py index a9bc494..72d4582 100644 --- a/build/msvc/gen.py +++ b/build/msvc/gen.py @@ -103,6 +103,10 @@ P8["files"] = [ "astra_mex_direct_c.cpp", "mexHelpFunctions.cpp", "mexHelpFunctions.h", +"mexCopyDataHelpFunctions.cpp", +"mexCopyDataHelpFunctions.h", +"mexDataManagerHelpFunctions.cpp", +"mexDataManagerHelpFunctions.h", "mexInitFunctions.cpp", "mexInitFunctions.h", ] diff --git a/matlab/mex/astra_mex_direct_vc09.vcproj b/matlab/mex/astra_mex_direct_vc09.vcproj index 04b49ac..5d27c65 100644 --- a/matlab/mex/astra_mex_direct_vc09.vcproj +++ b/matlab/mex/astra_mex_direct_vc09.vcproj @@ -598,6 +598,22 @@ RelativePath=".\mexHelpFunctions.h" > + + + + + + + + diff --git a/matlab/mex/astra_mex_direct_vc11.vcxproj b/matlab/mex/astra_mex_direct_vc11.vcxproj index 15c3c06..bc2db62 100644 --- a/matlab/mex/astra_mex_direct_vc11.vcxproj +++ b/matlab/mex/astra_mex_direct_vc11.vcxproj @@ -294,10 +294,14 @@ + + + + -- cgit v1.2.3 From b14fb531ad9ae3d565f2cf28f5506408ab10dbed Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 18 Nov 2015 11:26:15 +0100 Subject: Add CompositeGeometryManager This handles FP and BP operations on multiple data objects at once, splitting them to fit in GPU memory where necessary. --- astra_vc09.vcproj | 48 ++ astra_vc11.vcxproj | 9 + astra_vc11.vcxproj.filters | 12 + build/linux/Makefile.in | 4 +- build/msvc/gen.py | 4 + cuda/3d/astra3d.cu | 82 --- cuda/3d/astra3d.h | 9 + cuda/3d/mem3d.cu | 270 ++++++++ cuda/3d/mem3d.h | 99 +++ include/astra/CompositeGeometryManager.h | 150 ++++ include/astra/ConeProjectionGeometry3D.h | 10 +- include/astra/ConeVecProjectionGeometry3D.h | 11 +- include/astra/GeometryUtil3D.h | 17 + include/astra/ParallelProjectionGeometry3D.h | 11 +- include/astra/ParallelVecProjectionGeometry3D.h | 10 +- include/astra/ProjectionGeometry3D.h | 19 +- src/CompositeGeometryManager.cpp | 884 ++++++++++++++++++++++++ src/ConeProjectionGeometry3D.cpp | 92 ++- src/ConeVecProjectionGeometry3D.cpp | 58 +- src/CudaBackProjectionAlgorithm3D.cpp | 8 + src/CudaForwardProjectionAlgorithm3D.cpp | 9 + src/GeometryUtil3D.cpp | 172 +++++ src/ParallelProjectionGeometry3D.cpp | 81 ++- src/ParallelVecProjectionGeometry3D.cpp | 61 +- 24 files changed, 2023 insertions(+), 107 deletions(-) create mode 100644 cuda/3d/mem3d.cu create mode 100644 cuda/3d/mem3d.h create mode 100644 include/astra/CompositeGeometryManager.h create mode 100644 src/CompositeGeometryManager.cpp (limited to 'build') diff --git a/astra_vc09.vcproj b/astra_vc09.vcproj index e5d7731..b928662 100644 --- a/astra_vc09.vcproj +++ b/astra_vc09.vcproj @@ -932,6 +932,10 @@ RelativePath=".\include\astra\clog.h" > + + @@ -988,6 +992,10 @@ RelativePath=".\src\AstraObjectManager.cpp" > + + @@ -2228,6 +2236,10 @@ RelativePath=".\cuda\3d\fdk.h" > + + @@ -3040,6 +3052,42 @@ /> + + + + + + + + + + + + + + diff --git a/astra_vc11.vcxproj b/astra_vc11.vcxproj index bc11b23..fc8b9ce 100644 --- a/astra_vc11.vcxproj +++ b/astra_vc11.vcxproj @@ -380,6 +380,7 @@ + @@ -582,6 +583,7 @@ + @@ -594,6 +596,7 @@ + @@ -804,6 +807,12 @@ true true + + true + true + true + true + true true diff --git a/astra_vc11.vcxproj.filters b/astra_vc11.vcxproj.filters index a597962..af8ca39 100644 --- a/astra_vc11.vcxproj.filters +++ b/astra_vc11.vcxproj.filters @@ -67,6 +67,9 @@ CUDA\cuda source + + CUDA\cuda source + CUDA\cuda source @@ -153,6 +156,9 @@ Global & Other\source + + Global & Other\source + Global & Other\source @@ -398,6 +404,9 @@ Global & Other\headers + + Global & Other\headers + Global & Other\headers @@ -641,6 +650,9 @@ CUDA\cuda headers + + CUDA\cuda headers + CUDA\cuda headers diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index abbebe2..c555bca 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -99,6 +99,7 @@ BASE_OBJECTS=\ src/AstraObjectManager.lo \ src/BackProjectionAlgorithm.lo \ src/CglsAlgorithm.lo \ + src/CompositeGeometryManager.lo \ src/ConeProjectionGeometry3D.lo \ src/ConeVecProjectionGeometry3D.lo \ src/Config.lo \ @@ -197,7 +198,8 @@ CUDA_OBJECTS=\ cuda/3d/sirt3d.lo \ cuda/3d/astra3d.lo \ cuda/3d/util3d.lo \ - cuda/3d/arith3d.lo + cuda/3d/arith3d.lo \ + cuda/3d/mem3d.lo ALL_OBJECTS=$(BASE_OBJECTS) ifeq ($(cuda),yes) diff --git a/build/msvc/gen.py b/build/msvc/gen.py index 72d4582..c18c1e8 100644 --- a/build/msvc/gen.py +++ b/build/msvc/gen.py @@ -168,6 +168,7 @@ P_astra["filters"]["CUDA\\cuda source"] = [ "cuda\\3d\\cone_fp.cu", "cuda\\3d\\darthelper3d.cu", "cuda\\3d\\fdk.cu", +"cuda\\3d\\mem3d.cu", "cuda\\3d\\par3d_bp.cu", "cuda\\3d\\par3d_fp.cu", "cuda\\3d\\sirt3d.cu", @@ -205,6 +206,7 @@ P_astra["filters"]["Global & Other\\source"] = [ "1546cb47-7e5b-42c2-b695-ef172024c14b", "src\\AstraObjectFactory.cpp", "src\\AstraObjectManager.cpp", +"src\\CompositeGeometryManager.cpp", "src\\Config.cpp", "src\\Fourier.cpp", "src\\Globals.cpp", @@ -295,6 +297,7 @@ P_astra["filters"]["CUDA\\cuda headers"] = [ "cuda\\3d\\darthelper3d.h", "cuda\\3d\\dims3d.h", "cuda\\3d\\fdk.h", +"cuda\\3d\\mem3d.h", "cuda\\3d\\par3d_bp.h", "cuda\\3d\\par3d_fp.h", "cuda\\3d\\sirt3d.h", @@ -336,6 +339,7 @@ P_astra["filters"]["Global & Other\\headers"] = [ "include\\astra\\AstraObjectFactory.h", "include\\astra\\AstraObjectManager.h", "include\\astra\\clog.h", +"include\\astra\\CompositeGeometryManager.h", "include\\astra\\Config.h", "include\\astra\\Fourier.h", "include\\astra\\Globals.h", diff --git a/cuda/3d/astra3d.cu b/cuda/3d/astra3d.cu index 3815a1a..8328229 100644 --- a/cuda/3d/astra3d.cu +++ b/cuda/3d/astra3d.cu @@ -58,88 +58,6 @@ enum CUDAProjectionType3d { }; -static SConeProjection* genConeProjections(unsigned int iProjAngles, - unsigned int iProjU, - unsigned int iProjV, - double fOriginSourceDistance, - double fOriginDetectorDistance, - double fDetUSize, - double fDetVSize, - const float *pfAngles) -{ - SConeProjection base; - base.fSrcX = 0.0f; - base.fSrcY = -fOriginSourceDistance; - base.fSrcZ = 0.0f; - - base.fDetSX = iProjU * fDetUSize * -0.5f; - base.fDetSY = fOriginDetectorDistance; - base.fDetSZ = iProjV * fDetVSize * -0.5f; - - base.fDetUX = fDetUSize; - base.fDetUY = 0.0f; - base.fDetUZ = 0.0f; - - base.fDetVX = 0.0f; - base.fDetVY = 0.0f; - base.fDetVZ = fDetVSize; - - SConeProjection* p = new SConeProjection[iProjAngles]; - -#define ROTATE0(name,i,alpha) do { p[i].f##name##X = base.f##name##X * cos(alpha) - base.f##name##Y * sin(alpha); p[i].f##name##Y = base.f##name##X * sin(alpha) + base.f##name##Y * cos(alpha); p[i].f##name##Z = base.f##name##Z; } while(0) - - for (unsigned int i = 0; i < iProjAngles; ++i) { - ROTATE0(Src, i, pfAngles[i]); - ROTATE0(DetS, i, pfAngles[i]); - ROTATE0(DetU, i, pfAngles[i]); - ROTATE0(DetV, i, pfAngles[i]); - } - -#undef ROTATE0 - - return p; -} - -static SPar3DProjection* genPar3DProjections(unsigned int iProjAngles, - unsigned int iProjU, - unsigned int iProjV, - double fDetUSize, - double fDetVSize, - const float *pfAngles) -{ - SPar3DProjection base; - base.fRayX = 0.0f; - base.fRayY = 1.0f; - base.fRayZ = 0.0f; - - base.fDetSX = iProjU * fDetUSize * -0.5f; - base.fDetSY = 0.0f; - base.fDetSZ = iProjV * fDetVSize * -0.5f; - - base.fDetUX = fDetUSize; - base.fDetUY = 0.0f; - base.fDetUZ = 0.0f; - - base.fDetVX = 0.0f; - base.fDetVY = 0.0f; - base.fDetVZ = fDetVSize; - - SPar3DProjection* p = new SPar3DProjection[iProjAngles]; - -#define ROTATE0(name,i,alpha) do { p[i].f##name##X = base.f##name##X * cos(alpha) - base.f##name##Y * sin(alpha); p[i].f##name##Y = base.f##name##X * sin(alpha) + base.f##name##Y * cos(alpha); p[i].f##name##Z = base.f##name##Z; } while(0) - - for (unsigned int i = 0; i < iProjAngles; ++i) { - ROTATE0(Ray, i, pfAngles[i]); - ROTATE0(DetS, i, pfAngles[i]); - ROTATE0(DetU, i, pfAngles[i]); - ROTATE0(DetV, i, pfAngles[i]); - } - -#undef ROTATE0 - - return p; -} - diff --git a/cuda/3d/astra3d.h b/cuda/3d/astra3d.h index 6c3fcfb..2782994 100644 --- a/cuda/3d/astra3d.h +++ b/cuda/3d/astra3d.h @@ -281,6 +281,15 @@ protected: AstraCGLS3d_internal *pData; }; +bool convertAstraGeometry_dims(const CVolumeGeometry3D* pVolGeom, + const CProjectionGeometry3D* pProjGeom, + astraCUDA3d::SDimensions3D& dims); + +bool convertAstraGeometry(const CVolumeGeometry3D* pVolGeom, + const CProjectionGeometry3D* pProjGeom, + SPar3DProjection*& pParProjs, + SConeProjection*& pConeProjs, + float& fOutputScale); _AstraExport bool astraCudaFP(const float* pfVolume, float* pfProjections, const CVolumeGeometry3D* pVolGeom, diff --git a/cuda/3d/mem3d.cu b/cuda/3d/mem3d.cu new file mode 100644 index 0000000..6d81dc0 --- /dev/null +++ b/cuda/3d/mem3d.cu @@ -0,0 +1,270 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the ASTRA Toolbox. + + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see . + +----------------------------------------------------------------------- +$Id$ +*/ + +#include +#include + +#include "util3d.h" + +#include "mem3d.h" + +#include "astra3d.h" +#include "cone_fp.h" +#include "cone_bp.h" +#include "par3d_fp.h" +#include "par3d_bp.h" + +#include "astra/Logging.h" + + +namespace astraCUDA3d { + + +struct SMemHandle3D_internal +{ + cudaPitchedPtr ptr; + unsigned int nx; + unsigned int ny; + unsigned int nz; +}; + +size_t availableGPUMemory() +{ + size_t free, total; + cudaError_t err = cudaMemGetInfo(&free, &total); + if (err != cudaSuccess) + return 0; + return free; +} + +MemHandle3D allocateGPUMemory(unsigned int x, unsigned int y, unsigned int z, Mem3DZeroMode zero) +{ + SMemHandle3D_internal hnd; + hnd.nx = x; + hnd.ny = y; + hnd.nz = z; + + size_t free = availableGPUMemory(); + + cudaError_t err; + err = cudaMalloc3D(&hnd.ptr, make_cudaExtent(sizeof(float)*x, y, z)); + + if (err != cudaSuccess) { + return MemHandle3D(); + } + + size_t free2 = availableGPUMemory(); + + ASTRA_DEBUG("Allocated %d x %d x %d on GPU. (Pre: %lu, post: %lu)", x, y, z, free, free2); + + + + if (zero == INIT_ZERO) { + err = cudaMemset3D(hnd.ptr, 0, make_cudaExtent(sizeof(float)*x, y, z)); + if (err != cudaSuccess) { + cudaFree(hnd.ptr.ptr); + return MemHandle3D(); + } + } + + MemHandle3D ret; + ret.d = boost::shared_ptr(new SMemHandle3D_internal); + *ret.d = hnd; + + return ret; +} + +bool freeGPUMemory(MemHandle3D handle) +{ + size_t free = availableGPUMemory(); + cudaError_t err = cudaFree(handle.d->ptr.ptr); + size_t free2 = availableGPUMemory(); + + ASTRA_DEBUG("Freeing memory. (Pre: %lu, post: %lu)", free, free2); + + return err == cudaSuccess; +} + +bool copyToGPUMemory(const float *src, MemHandle3D dst, const SSubDimensions3D &pos) +{ + ASTRA_DEBUG("Copying %d x %d x %d to GPU", pos.subnx, pos.subny, pos.subnz); + ASTRA_DEBUG("Offset %d,%d,%d", pos.subx, pos.suby, pos.subz); + cudaPitchedPtr s; + s.ptr = (void*)src; // const cast away + s.pitch = pos.pitch * sizeof(float); + s.xsize = pos.nx * sizeof(float); + s.ysize = pos.ny; + ASTRA_DEBUG("Pitch %d, xsize %d, ysize %d", s.pitch, s.xsize, s.ysize); + + cudaMemcpy3DParms p; + p.srcArray = 0; + p.srcPos = make_cudaPos(pos.subx * sizeof(float), pos.suby, pos.subz); + p.srcPtr = s; + + p.dstArray = 0; + p.dstPos = make_cudaPos(0, 0, 0); + p.dstPtr = dst.d->ptr; + + p.extent = make_cudaExtent(pos.subnx * sizeof(float), pos.subny, pos.subnz); + + p.kind = cudaMemcpyHostToDevice; + + cudaError_t err = cudaMemcpy3D(&p); + + return err == cudaSuccess; +} + + +bool copyFromGPUMemory(float *dst, MemHandle3D src, const SSubDimensions3D &pos) +{ + ASTRA_DEBUG("Copying %d x %d x %d from GPU", pos.subnx, pos.subny, pos.subnz); + ASTRA_DEBUG("Offset %d,%d,%d", pos.subx, pos.suby, pos.subz); + cudaPitchedPtr d; + d.ptr = (void*)dst; + d.pitch = pos.pitch * sizeof(float); + d.xsize = pos.nx * sizeof(float); + d.ysize = pos.ny; + ASTRA_DEBUG("Pitch %d, xsize %d, ysize %d", d.pitch, d.xsize, d.ysize); + + cudaMemcpy3DParms p; + p.srcArray = 0; + p.srcPos = make_cudaPos(0, 0, 0); + p.srcPtr = src.d->ptr; + + p.dstArray = 0; + p.dstPos = make_cudaPos(pos.subx * sizeof(float), pos.suby, pos.subz); + p.dstPtr = d; + + p.extent = make_cudaExtent(pos.subnx * sizeof(float), pos.subny, pos.subnz); + + p.kind = cudaMemcpyDeviceToHost; + + cudaError_t err = cudaMemcpy3D(&p); + + return err == cudaSuccess; + +} + + +bool FP(const astra::CProjectionGeometry3D* pProjGeom, MemHandle3D projData, const astra::CVolumeGeometry3D* pVolGeom, MemHandle3D volData, int iDetectorSuperSampling, astra::Cuda3DProjectionKernel projKernel) +{ + SDimensions3D dims; + + bool ok = convertAstraGeometry_dims(pVolGeom, pProjGeom, dims); + if (!ok) + return false; + +#if 1 + dims.iRaysPerDetDim = iDetectorSuperSampling; + if (iDetectorSuperSampling == 0) + return false; +#else + dims.iRaysPerDetDim = 1; + astra::Cuda3DProjectionKernel projKernel = astra::ker3d_default; +#endif + + + SPar3DProjection* pParProjs; + SConeProjection* pConeProjs; + + float outputScale = 1.0f; + + ok = convertAstraGeometry(pVolGeom, pProjGeom, + pParProjs, pConeProjs, + outputScale); + + if (pParProjs) { +#if 0 + for (int i = 0; i < dims.iProjAngles; ++i) { + ASTRA_DEBUG("Vec: %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f %6.3f\n", + pParProjs[i].fRayX, pParProjs[i].fRayY, pParProjs[i].fRayZ, + pParProjs[i].fDetSX, pParProjs[i].fDetSY, pParProjs[i].fDetSZ, + pParProjs[i].fDetUX, pParProjs[i].fDetUY, pParProjs[i].fDetUZ, + pParProjs[i].fDetVX, pParProjs[i].fDetVY, pParProjs[i].fDetVZ); + } +#endif + + switch (projKernel) { + case astra::ker3d_default: + ok &= Par3DFP(volData.d->ptr, projData.d->ptr, dims, pParProjs, outputScale); + break; + case astra::ker3d_sum_square_weights: + ok &= Par3DFP_SumSqW(volData.d->ptr, projData.d->ptr, dims, pParProjs, outputScale*outputScale); + break; + default: + ok = false; + } + } else { + switch (projKernel) { + case astra::ker3d_default: + ok &= ConeFP(volData.d->ptr, projData.d->ptr, dims, pConeProjs, outputScale); + break; + default: + ok = false; + } + } + + return ok; +} + +bool BP(const astra::CProjectionGeometry3D* pProjGeom, MemHandle3D projData, const astra::CVolumeGeometry3D* pVolGeom, MemHandle3D volData, int iVoxelSuperSampling) +{ + SDimensions3D dims; + + bool ok = convertAstraGeometry_dims(pVolGeom, pProjGeom, dims); + if (!ok) + return false; + +#if 1 + dims.iRaysPerVoxelDim = iVoxelSuperSampling; +#else + dims.iRaysPerVoxelDim = 1; +#endif + + SPar3DProjection* pParProjs; + SConeProjection* pConeProjs; + + float outputScale = 1.0f; + + ok = convertAstraGeometry(pVolGeom, pProjGeom, + pParProjs, pConeProjs, + outputScale); + + if (pParProjs) + ok &= Par3DBP(volData.d->ptr, projData.d->ptr, dims, pParProjs, outputScale); + else + ok &= ConeBP(volData.d->ptr, projData.d->ptr, dims, pConeProjs, outputScale); + + return ok; + +} + + + + +} diff --git a/cuda/3d/mem3d.h b/cuda/3d/mem3d.h new file mode 100644 index 0000000..82bad19 --- /dev/null +++ b/cuda/3d/mem3d.h @@ -0,0 +1,99 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the ASTRA Toolbox. + + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see . + +----------------------------------------------------------------------- +*/ + +#ifndef _CUDA_MEM3D_H +#define _CUDA_MEM3D_H + +#include + +#include "astra3d.h" + +namespace astra { +class CVolumeGeometry3D; +class CProjectionGeometry3D; +} + +namespace astraCUDA3d { + +// TODO: Make it possible to delete these handles when they're no longer +// necessary inside the FP/BP +// +// TODO: Add functions for querying capacity + +struct SMemHandle3D_internal; + +struct MemHandle3D { + boost::shared_ptr d; + operator bool() const { return (bool)d; } +}; + +struct SSubDimensions3D { + unsigned int nx; + unsigned int ny; + unsigned int nz; + unsigned int pitch; + unsigned int subnx; + unsigned int subny; + unsigned int subnz; + unsigned int subx; + unsigned int suby; + unsigned int subz; +}; + +/* +// Useful or not? +enum Mem3DCopyMode { + MODE_SET, + MODE_ADD +}; +*/ + +enum Mem3DZeroMode { + INIT_NO, + INIT_ZERO +}; + +size_t availableGPUMemory(); + +MemHandle3D allocateGPUMemory(unsigned int x, unsigned int y, unsigned int z, Mem3DZeroMode zero); + +bool copyToGPUMemory(const float *src, MemHandle3D dst, const SSubDimensions3D &pos); + +bool copyFromGPUMemory(float *dst, MemHandle3D src, const SSubDimensions3D &pos); + +bool freeGPUMemory(MemHandle3D handle); + + +bool FP(const astra::CProjectionGeometry3D* pProjGeom, MemHandle3D projData, const astra::CVolumeGeometry3D* pVolGeom, MemHandle3D volData, int iDetectorSuperSampling, astra::Cuda3DProjectionKernel projKernel); + +bool BP(const astra::CProjectionGeometry3D* pProjGeom, MemHandle3D projData, const astra::CVolumeGeometry3D* pVolGeom, MemHandle3D volData, int iVoxelSuperSampling); + + + +} + +#endif diff --git a/include/astra/CompositeGeometryManager.h b/include/astra/CompositeGeometryManager.h new file mode 100644 index 0000000..a6e57f1 --- /dev/null +++ b/include/astra/CompositeGeometryManager.h @@ -0,0 +1,150 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the ASTRA Toolbox. + + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see . + +----------------------------------------------------------------------- +*/ + +#ifndef _INC_ASTRA_COMPOSITEGEOMETRYMANAGER +#define _INC_ASTRA_COMPOSITEGEOMETRYMANAGER + +#include "Globals.h" + +#ifdef ASTRA_CUDA + +#include +#include +#include +#include + + +namespace astra { + +class CCompositeVolume; +class CCompositeProjections; +class CFloat32Data3DMemory; +class CFloat32ProjectionData3DMemory; +class CFloat32VolumeData3DMemory; +class CVolumeGeometry3D; +class CProjectionGeometry3D; +class CProjector3D; + + + +class _AstraExport CCompositeGeometryManager { +public: + class CPart; + typedef std::list > TPartList; + class CPart { + public: + CPart() { } + CPart(const CPart& other); + virtual ~CPart() { } + + enum { + PART_VOL, PART_PROJ + } eType; + + CFloat32Data3DMemory* pData; + unsigned int subX; + unsigned int subY; + unsigned int subZ; + + bool uploadToGPU(); + bool downloadFromGPU(/*mode?*/); + virtual TPartList split(size_t maxSize, int div) = 0; + virtual CPart* reduce(const CPart *other) = 0; + virtual void getDims(size_t &x, size_t &y, size_t &z) = 0; + size_t getSize(); + }; + + class CVolumePart : public CPart { + public: + CVolumePart() { eType = PART_VOL; } + CVolumePart(const CVolumePart& other); + virtual ~CVolumePart(); + + CVolumeGeometry3D* pGeom; + + virtual TPartList split(size_t maxSize, int div); + virtual CPart* reduce(const CPart *other); + virtual void getDims(size_t &x, size_t &y, size_t &z); + + CVolumePart* clone() const; + }; + class CProjectionPart : public CPart { + public: + CProjectionPart() { eType = PART_PROJ; } + CProjectionPart(const CProjectionPart& other); + virtual ~CProjectionPart(); + + CProjectionGeometry3D* pGeom; + + virtual TPartList split(size_t maxSize, int div); + virtual CPart* reduce(const CPart *other); + virtual void getDims(size_t &x, size_t &y, size_t &z); + + CProjectionPart* clone() const; + }; + + struct SJob { + public: + boost::shared_ptr pInput; + boost::shared_ptr pOutput; + CProjector3D *pProjector; // For a `global' geometry. It will not match + // the geometries of the input and output. + + + enum { + JOB_FP, JOB_BP, JOB_NOP + } eType; + enum { + MODE_ADD, MODE_SET + } eMode; + + }; + + typedef std::list TJobList; + // output part -> list of jobs for that output + typedef std::map TJobSet; + + bool doJobs(TJobList &jobs); + + // Convenience functions for creating and running a single FP or BP job + bool doFP(CProjector3D *pProjector, CFloat32VolumeData3DMemory *pVolData, + CFloat32ProjectionData3DMemory *pProjData); + bool doBP(CProjector3D *pProjector, CFloat32VolumeData3DMemory *pVolData, + CFloat32ProjectionData3DMemory *pProjData); + + +protected: + + bool splitJobs(TJobSet &jobs, size_t maxSize, int div, TJobSet &split); + +}; + +} + +#endif + +#endif diff --git a/include/astra/ConeProjectionGeometry3D.h b/include/astra/ConeProjectionGeometry3D.h index 00e72ce..dede6e1 100644 --- a/include/astra/ConeProjectionGeometry3D.h +++ b/include/astra/ConeProjectionGeometry3D.h @@ -186,9 +186,15 @@ public: */ virtual CVector3D getProjectionDirection(int _iProjectionIndex, int _iDetectorIndex) const; - virtual void projectPoint(float32 fX, float32 fY, float32 fZ, + virtual void projectPoint(double fX, double fY, double fZ, int iAngleIndex, - float32 &fU, float32 &fV) const; + double &fU, double &fV) const; + virtual void backprojectPointX(int iAngleIndex, double fU, double fV, + double fX, double &fY, double &fZ) const; + virtual void backprojectPointY(int iAngleIndex, double fU, double fV, + double fY, double &fX, double &fZ) const; + virtual void backprojectPointZ(int iAngleIndex, double fU, double fV, + double fZ, double &fX, double &fY) const; }; diff --git a/include/astra/ConeVecProjectionGeometry3D.h b/include/astra/ConeVecProjectionGeometry3D.h index 71e8010..f76f9dd 100644 --- a/include/astra/ConeVecProjectionGeometry3D.h +++ b/include/astra/ConeVecProjectionGeometry3D.h @@ -148,9 +148,16 @@ public: const SConeProjection* getProjectionVectors() const { return m_pProjectionAngles; } - virtual void projectPoint(float32 fX, float32 fY, float32 fZ, + virtual void projectPoint(double fX, double fY, double fZ, int iAngleIndex, - float32 &fU, float32 &fV) const; + double &fU, double &fV) const; + virtual void backprojectPointX(int iAngleIndex, double fU, double fV, + double fX, double &fY, double &fZ) const; + virtual void backprojectPointY(int iAngleIndex, double fU, double fV, + double fY, double &fX, double &fZ) const; + virtual void backprojectPointZ(int iAngleIndex, double fU, double fV, + double fZ, double &fX, double &fY) const; + }; } // namespace astra diff --git a/include/astra/GeometryUtil3D.h b/include/astra/GeometryUtil3D.h index 6ceac63..e4d73e4 100644 --- a/include/astra/GeometryUtil3D.h +++ b/include/astra/GeometryUtil3D.h @@ -119,6 +119,23 @@ void computeBP_UV_Coeffs(const SConeProjection& proj, double &fDX, double &fDY, double &fDZ, double &fDC); +SConeProjection* genConeProjections(unsigned int iProjAngles, + unsigned int iProjU, + unsigned int iProjV, + double fOriginSourceDistance, + double fOriginDetectorDistance, + double fDetUSize, + double fDetVSize, + const float *pfAngles); + +SPar3DProjection* genPar3DProjections(unsigned int iProjAngles, + unsigned int iProjU, + unsigned int iProjV, + double fDetUSize, + double fDetVSize, + const float *pfAngles); + + } diff --git a/include/astra/ParallelProjectionGeometry3D.h b/include/astra/ParallelProjectionGeometry3D.h index 72401e5..d95c050 100644 --- a/include/astra/ParallelProjectionGeometry3D.h +++ b/include/astra/ParallelProjectionGeometry3D.h @@ -147,9 +147,16 @@ public: */ virtual CVector3D getProjectionDirection(int _iProjectionIndex, int _iDetectorIndex) const; - virtual void projectPoint(float32 fX, float32 fY, float32 fZ, + virtual void projectPoint(double fX, double fY, double fZ, int iAngleIndex, - float32 &fU, float32 &fV) const; + double &fU, double &fV) const; + virtual void backprojectPointX(int iAngleIndex, double fU, double fV, + double fX, double &fY, double &fZ) const; + virtual void backprojectPointY(int iAngleIndex, double fU, double fV, + double fY, double &fX, double &fZ) const; + virtual void backprojectPointZ(int iAngleIndex, double fU, double fV, + double fZ, double &fX, double &fY) const; + /** * Creates (= allocates) a 2D projection geometry used when projecting one slice using a 2D projector diff --git a/include/astra/ParallelVecProjectionGeometry3D.h b/include/astra/ParallelVecProjectionGeometry3D.h index 59238c8..ec91086 100644 --- a/include/astra/ParallelVecProjectionGeometry3D.h +++ b/include/astra/ParallelVecProjectionGeometry3D.h @@ -149,9 +149,15 @@ public: const SPar3DProjection* getProjectionVectors() const { return m_pProjectionAngles; } - virtual void projectPoint(float32 fX, float32 fY, float32 fZ, + virtual void projectPoint(double fX, double fY, double fZ, int iAngleIndex, - float32 &fU, float32 &fV) const; + double &fU, double &fV) const; + virtual void backprojectPointX(int iAngleIndex, double fU, double fV, + double fX, double &fY, double &fZ) const; + virtual void backprojectPointY(int iAngleIndex, double fU, double fV, + double fY, double &fX, double &fZ) const; + virtual void backprojectPointZ(int iAngleIndex, double fU, double fV, + double fZ, double &fX, double &fY) const; }; } // namespace astra diff --git a/include/astra/ProjectionGeometry3D.h b/include/astra/ProjectionGeometry3D.h index 19ac3ab..0b60287 100644 --- a/include/astra/ProjectionGeometry3D.h +++ b/include/astra/ProjectionGeometry3D.h @@ -317,9 +317,24 @@ public: * @param iAngleIndex the index of the angle to use * @param fU,fV the projected point. */ - virtual void projectPoint(float32 fX, float32 fY, float32 fZ, + virtual void projectPoint(double fX, double fY, double fZ, int iAngleIndex, - float32 &fU, float32 &fV) const = 0; + double &fU, double &fV) const = 0; + + /* Backproject a point onto a plane parallel to a coordinate plane. + * The 2D point coordinates are the (unrounded) indices of the detector + * column and row. The output is in 3D coordinates in units. + * are in units. The output fU,fV are the (unrounded) indices of the + * detector column and row. + * This may fall outside of the actual detector. + */ + virtual void backprojectPointX(int iAngleIndex, double fU, double fV, + double fX, double &fY, double &fZ) const = 0; + virtual void backprojectPointY(int iAngleIndex, double fU, double fV, + double fY, double &fX, double &fZ) const = 0; + virtual void backprojectPointZ(int iAngleIndex, double fU, double fV, + double fZ, double &fX, double &fY) const = 0; + /** Returns true if the type of geometry defined in this class is the one specified in _sType. * diff --git a/src/CompositeGeometryManager.cpp b/src/CompositeGeometryManager.cpp new file mode 100644 index 0000000..fc8bc2e --- /dev/null +++ b/src/CompositeGeometryManager.cpp @@ -0,0 +1,884 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the ASTRA Toolbox. + + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see . + +----------------------------------------------------------------------- +*/ + +#include "astra/CompositeGeometryManager.h" + +#ifdef ASTRA_CUDA + +#include "astra/GeometryUtil3D.h" +#include "astra/VolumeGeometry3D.h" +#include "astra/ConeProjectionGeometry3D.h" +#include "astra/ConeVecProjectionGeometry3D.h" +#include "astra/ParallelProjectionGeometry3D.h" +#include "astra/ParallelVecProjectionGeometry3D.h" +#include "astra/Projector3D.h" +#include "astra/CudaProjector3D.h" +#include "astra/Float32ProjectionData3DMemory.h" +#include "astra/Float32VolumeData3DMemory.h" +#include "astra/Logging.h" + +#include "../cuda/3d/mem3d.h" + +#include + +namespace astra { + +// JOB: +// +// VolumePart +// ProjectionPart +// FP-or-BP +// SET-or-ADD + + +// Running a set of jobs: +// +// [ Assume OUTPUT Parts in a single JobSet don't alias?? ] +// Group jobs by output Part +// One thread per group? + +// Automatically split parts if too large +// Performance model for odd-sized tasks? +// Automatically split parts if not enough tasks to fill available GPUs + + +// Splitting: +// Constraints: +// number of sub-parts divisible by N +// max size of sub-parts + +// For splitting on both input and output side: +// How to divide up memory? (Optimization problem; compute/benchmark) +// (First approach: 0.5/0.5) + + + +bool CCompositeGeometryManager::splitJobs(TJobSet &jobs, size_t maxSize, int div, TJobSet &split) +{ + split.clear(); + + for (TJobSet::const_iterator i = jobs.begin(); i != jobs.end(); ++i) + { + CPart* pOutput = i->first; + const TJobList &L = i->second; + + // 1. Split output part + // 2. Per sub-part: + // a. reduce input part + // b. split input part + // c. create jobs for new (input,output) subparts + + TPartList splitOutput = pOutput->split(maxSize/3, div); + + for (TJobList::const_iterator j = L.begin(); j != L.end(); ++j) + { + const SJob &job = *j; + + for (TPartList::iterator i_out = splitOutput.begin(); + i_out != splitOutput.end(); ++i_out) + { + boost::shared_ptr outputPart = *i_out; + split[outputPart.get()] = TJobList(); + + SJob newjob; + newjob.pOutput = outputPart; + newjob.eType = j->eType; + newjob.eMode = j->eMode; + newjob.pProjector = j->pProjector; + + CPart* input = job.pInput->reduce(outputPart.get()); + + if (input->getSize() == 0) { + ASTRA_DEBUG("Empty input"); + newjob.eType = SJob::JOB_NOP; + split[outputPart.get()].push_back(newjob); + continue; + } + + size_t remainingSize = ( maxSize - outputPart->getSize() ) / 2; + + TPartList splitInput = input->split(remainingSize, 1); + delete input; + ASTRA_DEBUG("Input split into %d parts", splitInput.size()); + + for (TPartList::iterator i_in = splitInput.begin(); + i_in != splitInput.end(); ++i_in) + { + newjob.pInput = *i_in; + + split[outputPart.get()].push_back(newjob); + + // Second and later (input) parts should always be added to + // output of first (input) part. + newjob.eMode = SJob::MODE_ADD; + } + + + } + + } + } + + return true; +} + +CCompositeGeometryManager::CPart::CPart(const CPart& other) +{ + eType = other.eType; + pData = other.pData; + subX = other.subX; + subY = other.subY; + subZ = other.subZ; +} + +CCompositeGeometryManager::CVolumePart::CVolumePart(const CVolumePart& other) + : CPart(other) +{ + pGeom = other.pGeom->clone(); +} + +CCompositeGeometryManager::CVolumePart::~CVolumePart() +{ + delete pGeom; +} + +void CCompositeGeometryManager::CVolumePart::getDims(size_t &x, size_t &y, size_t &z) +{ + if (!pGeom) { + x = y = z = 0; + return; + } + + x = pGeom->getGridColCount(); + y = pGeom->getGridRowCount(); + z = pGeom->getGridSliceCount(); +} + +size_t CCompositeGeometryManager::CPart::getSize() +{ + size_t x, y, z; + getDims(x, y, z); + return x * y * z; +} + + + +CCompositeGeometryManager::CPart* CCompositeGeometryManager::CVolumePart::reduce(const CPart *_other) +{ + const CProjectionPart *other = dynamic_cast(_other); + assert(other); + + // TODO: Is 0.5 sufficient? + double umin = -0.5; + double umax = other->pGeom->getDetectorColCount() + 0.5; + double vmin = -0.5; + double vmax = other->pGeom->getDetectorRowCount() + 0.5; + + double uu[4]; + double vv[4]; + uu[0] = umin; vv[0] = vmin; + uu[1] = umin; vv[1] = vmax; + uu[2] = umax; vv[2] = vmin; + uu[3] = umax; vv[3] = vmax; + + double pixx = pGeom->getPixelLengthX(); + double pixy = pGeom->getPixelLengthY(); + double pixz = pGeom->getPixelLengthZ(); + + double xmin = pGeom->getWindowMinX() - 0.5 * pixx; + double xmax = pGeom->getWindowMaxX() + 0.5 * pixx; + double ymin = pGeom->getWindowMinY() - 0.5 * pixy; + double ymax = pGeom->getWindowMaxY() + 0.5 * pixy; + + // NB: Flipped + double zmax = pGeom->getWindowMinZ() - 2.5 * pixz; + double zmin = pGeom->getWindowMaxZ() + 2.5 * pixz; + + // TODO: This isn't as tight as it could be. + // In particular it won't detect the detector being + // missed entirely on the u side. + + for (int i = 0; i < other->pGeom->getProjectionCount(); ++i) { + for (int j = 0; j < 4; ++j) { + double px, py, pz; + + other->pGeom->backprojectPointX(i, uu[j], vv[j], xmin, py, pz); + //ASTRA_DEBUG("%f %f (%f - %f)", py, pz, ymin, ymax); + if (pz < zmin) zmin = pz; + if (pz > zmax) zmax = pz; + other->pGeom->backprojectPointX(i, uu[j], vv[j], xmax, py, pz); + //ASTRA_DEBUG("%f %f (%f - %f)", py, pz, ymin, ymax); + if (pz < zmin) zmin = pz; + if (pz > zmax) zmax = pz; + + other->pGeom->backprojectPointY(i, uu[j], vv[j], ymin, px, pz); + //ASTRA_DEBUG("%f %f (%f - %f)", px, pz, xmin, xmax); + if (pz < zmin) zmin = pz; + if (pz > zmax) zmax = pz; + other->pGeom->backprojectPointY(i, uu[j], vv[j], ymax, px, pz); + //ASTRA_DEBUG("%f %f (%f - %f)", px, pz, xmin, xmax); + if (pz < zmin) zmin = pz; + if (pz > zmax) zmax = pz; + } + } + + //ASTRA_DEBUG("coord extent: %f - %f", zmin, zmax); + + zmin = (zmin - pixz - pGeom->getWindowMinZ()) / pixz; + zmax = (zmax + pixz - pGeom->getWindowMinZ()) / pixz; + + int _zmin = (int)floor(zmin); + int _zmax = (int)ceil(zmax); + + //ASTRA_DEBUG("index extent: %d - %d", _zmin, _zmax); + + if (_zmin < 0) + _zmin = 0; + if (_zmax > pGeom->getGridSliceCount()) + _zmax = pGeom->getGridSliceCount(); + + if (_zmax <= _zmin) { + _zmin = _zmax = 0; + } + //ASTRA_DEBUG("adjusted extent: %d - %d", _zmin, _zmax); + + CVolumePart *sub = new CVolumePart(); + sub->subX = this->subX; + sub->subY = this->subY; + sub->subZ = this->subZ + _zmin; + sub->pData = pData; + + if (_zmin == _zmax) { + sub->pGeom = 0; + } else { + sub->pGeom = new CVolumeGeometry3D(pGeom->getGridColCount(), + pGeom->getGridRowCount(), + _zmax - _zmin, + pGeom->getWindowMinX(), + pGeom->getWindowMinY(), + pGeom->getWindowMinZ() + _zmin * pixz, + pGeom->getWindowMaxX(), + pGeom->getWindowMaxY(), + pGeom->getWindowMinZ() + _zmax * pixz); + } + + ASTRA_DEBUG("Reduce volume from %d - %d to %d - %d", this->subZ, this->subZ + pGeom->getGridSliceCount(), this->subZ + _zmin, this->subZ + _zmax); + + return sub; +} + + + +static size_t ceildiv(size_t a, size_t b) { + return (a + b - 1) / b; +} + +static size_t computeVerticalSplit(size_t maxBlock, int div, size_t sliceCount) +{ + size_t blockSize = maxBlock; + size_t blockCount = ceildiv(sliceCount, blockSize); + + // Increase number of blocks to be divisible by div + size_t divCount = div * ceildiv(blockCount, div); + + // If divCount is above sqrt(number of slices), then + // we can't guarantee divisibility by div, but let's try anyway + if (ceildiv(sliceCount, ceildiv(sliceCount, divCount)) % div == 0) { + blockCount = divCount; + } else { + // If divisibility isn't achievable, we may want to optimize + // differently. + // TODO: Figure out how to model and optimize this. + } + + // Final adjustment to make blocks more evenly sized + // (This can't make the blocks larger) + blockSize = ceildiv(sliceCount, blockCount); + + ASTRA_DEBUG("%ld %ld -> %ld * %ld\n", sliceCount, maxBlock, blockCount, blockSize); + + assert(blockSize <= maxBlock); + assert((divCount * divCount > sliceCount) || (blockCount % div) == 0); + + return blockSize; +} + +template +static V* getProjectionVectors(const P* geom); + +template<> +SConeProjection* getProjectionVectors(const CConeProjectionGeometry3D* pProjGeom) +{ + return genConeProjections(pProjGeom->getProjectionCount(), + pProjGeom->getDetectorColCount(), + pProjGeom->getDetectorRowCount(), + pProjGeom->getOriginSourceDistance(), + pProjGeom->getOriginDetectorDistance(), + pProjGeom->getDetectorSpacingX(), + pProjGeom->getDetectorSpacingY(), + pProjGeom->getProjectionAngles()); +} + +template<> +SConeProjection* getProjectionVectors(const CConeVecProjectionGeometry3D* pProjGeom) +{ + int nth = pProjGeom->getProjectionCount(); + + SConeProjection* pProjs = new SConeProjection[nth]; + for (int i = 0; i < nth; ++i) + pProjs[i] = pProjGeom->getProjectionVectors()[i]; + + return pProjs; +} + +template<> +SPar3DProjection* getProjectionVectors(const CParallelProjectionGeometry3D* pProjGeom) +{ + return genPar3DProjections(pProjGeom->getProjectionCount(), + pProjGeom->getDetectorColCount(), + pProjGeom->getDetectorRowCount(), + pProjGeom->getDetectorSpacingX(), + pProjGeom->getDetectorSpacingY(), + pProjGeom->getProjectionAngles()); +} + +template<> +SPar3DProjection* getProjectionVectors(const CParallelVecProjectionGeometry3D* pProjGeom) +{ + int nth = pProjGeom->getProjectionCount(); + + SPar3DProjection* pProjs = new SPar3DProjection[nth]; + for (int i = 0; i < nth; ++i) + pProjs[i] = pProjGeom->getProjectionVectors()[i]; + + return pProjs; +} + + +template +static void translateProjectionVectors(V* pProjs, int count, double dv) +{ + for (int i = 0; i < count; ++i) { + pProjs[i].fDetSX += dv * pProjs[i].fDetVX; + pProjs[i].fDetSY += dv * pProjs[i].fDetVY; + pProjs[i].fDetSZ += dv * pProjs[i].fDetVZ; + } +} + + + +static CProjectionGeometry3D* getSubProjectionGeometry(const CProjectionGeometry3D* pProjGeom, int v, int size) +{ + // First convert to vectors, then translate, then convert into new object + + const CConeProjectionGeometry3D* conegeom = dynamic_cast(pProjGeom); + const CParallelProjectionGeometry3D* par3dgeom = dynamic_cast(pProjGeom); + const CParallelVecProjectionGeometry3D* parvec3dgeom = dynamic_cast(pProjGeom); + const CConeVecProjectionGeometry3D* conevec3dgeom = dynamic_cast(pProjGeom); + + if (conegeom || conevec3dgeom) { + SConeProjection* pConeProjs; + if (conegeom) { + pConeProjs = getProjectionVectors(conegeom); + } else { + pConeProjs = getProjectionVectors(conevec3dgeom); + } + + translateProjectionVectors(pConeProjs, pProjGeom->getProjectionCount(), v); + + CProjectionGeometry3D* ret = new CConeVecProjectionGeometry3D(pProjGeom->getProjectionCount(), + size, + pProjGeom->getDetectorColCount(), + pConeProjs); + + + delete[] pConeProjs; + return ret; + } else { + assert(par3dgeom || parvec3dgeom); + SPar3DProjection* pParProjs; + if (par3dgeom) { + pParProjs = getProjectionVectors(par3dgeom); + } else { + pParProjs = getProjectionVectors(parvec3dgeom); + } + + translateProjectionVectors(pParProjs, pProjGeom->getProjectionCount(), v); + + CProjectionGeometry3D* ret = new CParallelVecProjectionGeometry3D(pProjGeom->getProjectionCount(), + size, + pProjGeom->getDetectorColCount(), + pParProjs); + + delete[] pParProjs; + return ret; + } + +} + + + +// split self into sub-parts: +// - each no bigger than maxSize +// - number of sub-parts is divisible by div +// - maybe all approximately the same size? +CCompositeGeometryManager::TPartList CCompositeGeometryManager::CVolumePart::split(size_t maxSize, int div) +{ + TPartList ret; + + if (true) { + // Split in vertical direction only at first, until we figure out + // a model for splitting in other directions + + size_t sliceSize = ((size_t) pGeom->getGridColCount()) * pGeom->getGridRowCount(); + int sliceCount = pGeom->getGridSliceCount(); + size_t blockSize = computeVerticalSplit(maxSize / sliceSize, div, sliceCount); + + int rem = sliceCount % blockSize; + + ASTRA_DEBUG("From %d to %d step %d", -(rem / 2), sliceCount, blockSize); + + for (int z = -(rem / 2); z < sliceCount; z += blockSize) { + int newsubZ = z; + if (newsubZ < 0) newsubZ = 0; + int endZ = z + blockSize; + if (endZ > sliceCount) endZ = sliceCount; + int size = endZ - newsubZ; + + CVolumePart *sub = new CVolumePart(); + sub->subX = this->subX; + sub->subY = this->subY; + sub->subZ = this->subZ + newsubZ; + + ASTRA_DEBUG("VolumePart split %d %d %d -> %p", sub->subX, sub->subY, sub->subZ, (void*)sub); + + double shift = pGeom->getPixelLengthZ() * newsubZ; + + sub->pData = pData; + sub->pGeom = new CVolumeGeometry3D(pGeom->getGridColCount(), + pGeom->getGridRowCount(), + size, + pGeom->getWindowMinX(), + pGeom->getWindowMinY(), + pGeom->getWindowMinZ() + shift, + pGeom->getWindowMaxX(), + pGeom->getWindowMaxY(), + pGeom->getWindowMinZ() + shift + size * pGeom->getPixelLengthZ()); + + ret.push_back(boost::shared_ptr(sub)); + } + } + + return ret; +} + +CCompositeGeometryManager::CVolumePart* CCompositeGeometryManager::CVolumePart::clone() const +{ + return new CVolumePart(*this); +} + +CCompositeGeometryManager::CProjectionPart::CProjectionPart(const CProjectionPart& other) + : CPart(other) +{ + pGeom = other.pGeom->clone(); +} + +CCompositeGeometryManager::CProjectionPart::~CProjectionPart() +{ + delete pGeom; +} + +void CCompositeGeometryManager::CProjectionPart::getDims(size_t &x, size_t &y, size_t &z) +{ + if (!pGeom) { + x = y = z = 0; + return; + } + + x = pGeom->getDetectorColCount(); + y = pGeom->getProjectionCount(); + z = pGeom->getDetectorRowCount(); +} + + +CCompositeGeometryManager::CPart* CCompositeGeometryManager::CProjectionPart::reduce(const CPart *_other) +{ + const CVolumePart *other = dynamic_cast(_other); + assert(other); + + double vmin_g, vmax_g; + + // reduce self to only cover intersection with projection of VolumePart + // (Project corners of volume, take bounding box) + + for (int i = 0; i < pGeom->getProjectionCount(); ++i) { + + double vol_u[8]; + double vol_v[8]; + + double pixx = other->pGeom->getPixelLengthX(); + double pixy = other->pGeom->getPixelLengthY(); + double pixz = other->pGeom->getPixelLengthZ(); + + // TODO: Is 0.5 sufficient? + double xmin = other->pGeom->getWindowMinX() - 0.5 * pixx; + double xmax = other->pGeom->getWindowMaxX() + 0.5 * pixx; + double ymin = other->pGeom->getWindowMinY() - 0.5 * pixy; + double ymax = other->pGeom->getWindowMaxY() + 0.5 * pixy; + double zmin = other->pGeom->getWindowMinZ() - 0.5 * pixz; + double zmax = other->pGeom->getWindowMaxZ() + 0.5 * pixz; + + pGeom->projectPoint(xmin, ymin, zmin, i, vol_u[0], vol_v[0]); + pGeom->projectPoint(xmin, ymin, zmax, i, vol_u[1], vol_v[1]); + pGeom->projectPoint(xmin, ymax, zmin, i, vol_u[2], vol_v[2]); + pGeom->projectPoint(xmin, ymax, zmax, i, vol_u[3], vol_v[3]); + pGeom->projectPoint(xmax, ymin, zmin, i, vol_u[4], vol_v[4]); + pGeom->projectPoint(xmax, ymin, zmax, i, vol_u[5], vol_v[5]); + pGeom->projectPoint(xmax, ymax, zmin, i, vol_u[6], vol_v[6]); + pGeom->projectPoint(xmax, ymax, zmax, i, vol_u[7], vol_v[7]); + + double vmin = vol_v[0]; + double vmax = vol_v[0]; + + for (int j = 1; j < 8; ++j) { + if (vol_v[j] < vmin) + vmin = vol_v[j]; + if (vol_v[j] > vmax) + vmax = vol_v[j]; + } + + if (i == 0 || vmin < vmin_g) + vmin_g = vmin; + if (i == 0 || vmax > vmax_g) + vmax_g = vmax; + } + + // fprintf(stderr, "v extent: %f %f\n", vmin_g, vmax_g); + + int _vmin = (int)floor(vmin_g - 1.0f); + int _vmax = (int)ceil(vmax_g + 1.0f); + if (_vmin < 0) + _vmin = 0; + if (_vmax > pGeom->getDetectorRowCount()) + _vmax = pGeom->getDetectorRowCount(); + + if (_vmin >= _vmax) { + _vmin = _vmax = 0; + } + + CProjectionPart *sub = new CProjectionPart(); + sub->subX = this->subX; + sub->subY = this->subY; + sub->subZ = this->subZ + _vmin; + + sub->pData = pData; + + if (_vmin == _vmax) { + sub->pGeom = 0; + } else { + sub->pGeom = getSubProjectionGeometry(pGeom, _vmin, _vmax - _vmin); + } + + ASTRA_DEBUG("Reduce projection from %d - %d to %d - %d", this->subZ, this->subZ + pGeom->getDetectorRowCount(), this->subZ + _vmin, this->subZ + _vmax); + + return sub; +} + + +CCompositeGeometryManager::TPartList CCompositeGeometryManager::CProjectionPart::split(size_t maxSize, int div) +{ + TPartList ret; + + if (true) { + // Split in vertical direction only at first, until we figure out + // a model for splitting in other directions + + size_t sliceSize = ((size_t) pGeom->getDetectorColCount()) * pGeom->getProjectionCount(); + int sliceCount = pGeom->getDetectorRowCount(); + size_t blockSize = computeVerticalSplit(maxSize / sliceSize, div, sliceCount); + + int rem = sliceCount % blockSize; + + for (int z = -(rem / 2); z < sliceCount; z += blockSize) { + int newsubZ = z; + if (newsubZ < 0) newsubZ = 0; + int endZ = z + blockSize; + if (endZ > sliceCount) endZ = sliceCount; + int size = endZ - newsubZ; + + CProjectionPart *sub = new CProjectionPart(); + sub->subX = this->subX; + sub->subY = this->subY; + sub->subZ = this->subZ + newsubZ; + + ASTRA_DEBUG("ProjectionPart split %d %d %d -> %p", sub->subX, sub->subY, sub->subZ, (void*)sub); + + sub->pData = pData; + + sub->pGeom = getSubProjectionGeometry(pGeom, newsubZ, size); + + ret.push_back(boost::shared_ptr(sub)); + } + } + + return ret; + +} + +CCompositeGeometryManager::CProjectionPart* CCompositeGeometryManager::CProjectionPart::clone() const +{ + return new CProjectionPart(*this); +} + + +bool CCompositeGeometryManager::doFP(CProjector3D *pProjector, CFloat32VolumeData3DMemory *pVolData, + CFloat32ProjectionData3DMemory *pProjData) +{ + ASTRA_DEBUG("CCompositeGeometryManager::doFP"); + // Create single job for FP + // Run result + + CVolumePart *input = new CVolumePart(); + input->pData = pVolData; + input->subX = 0; + input->subY = 0; + input->subZ = 0; + input->pGeom = pVolData->getGeometry()->clone(); + ASTRA_DEBUG("Main FP VolumePart -> %p", (void*)input); + + CProjectionPart *output = new CProjectionPart(); + output->pData = pProjData; + output->subX = 0; + output->subY = 0; + output->subZ = 0; + output->pGeom = pProjData->getGeometry()->clone(); + ASTRA_DEBUG("Main FP ProjectionPart -> %p", (void*)output); + + SJob FP; + FP.pInput = boost::shared_ptr(input); + FP.pOutput = boost::shared_ptr(output); + FP.pProjector = pProjector; + FP.eType = SJob::JOB_FP; + FP.eMode = SJob::MODE_SET; + + TJobList L; + L.push_back(FP); + + return doJobs(L); +} + +bool CCompositeGeometryManager::doBP(CProjector3D *pProjector, CFloat32VolumeData3DMemory *pVolData, + CFloat32ProjectionData3DMemory *pProjData) +{ + ASTRA_DEBUG("CCompositeGeometryManager::doBP"); + // Create single job for BP + // Run result + + CProjectionPart *input = new CProjectionPart(); + input->pData = pProjData; + input->subX = 0; + input->subY = 0; + input->subZ = 0; + input->pGeom = pProjData->getGeometry()->clone(); + + CVolumePart *output = new CVolumePart(); + output->pData = pVolData; + output->subX = 0; + output->subY = 0; + output->subZ = 0; + output->pGeom = pVolData->getGeometry()->clone(); + + SJob BP; + BP.pInput = boost::shared_ptr(input); + BP.pOutput = boost::shared_ptr(output); + BP.pProjector = pProjector; + BP.eType = SJob::JOB_BP; + BP.eMode = SJob::MODE_SET; + + TJobList L; + L.push_back(BP); + + return doJobs(L); +} + + + +bool CCompositeGeometryManager::doJobs(TJobList &jobs) +{ + ASTRA_DEBUG("CCompositeGeometryManager::doJobs"); + + // Sort job list into job set by output part + TJobSet jobset; + + for (TJobList::iterator i = jobs.begin(); i != jobs.end(); ++i) { + jobset[i->pOutput.get()].push_back(*i); + } + + size_t maxSize = astraCUDA3d::availableGPUMemory(); + if (maxSize == 0) { + ASTRA_WARN("Unable to get available GPU memory. Defaulting to 1GB."); + maxSize = 1024 * 1024 * 1024; + } else { + ASTRA_DEBUG("Detected %lu bytes of GPU memory", maxSize); + } + maxSize = (maxSize * 9) / 10; + + maxSize /= sizeof(float); + int div = 1; + + // TODO: Multi-GPU support + + // Split jobs to fit + TJobSet split; + splitJobs(jobset, maxSize, div, split); + jobset.clear(); + + // Run jobs + + for (TJobSet::iterator iter = split.begin(); iter != split.end(); ++iter) { + + CPart* output = iter->first; + TJobList& L = iter->second; + + assert(!L.empty()); + + bool zero = L.begin()->eMode == SJob::MODE_SET; + + size_t outx, outy, outz; + output->getDims(outx, outy, outz); + + if (L.begin()->eType == SJob::JOB_NOP) { + // just zero output? + if (zero) { + for (size_t z = 0; z < outz; ++z) { + for (size_t y = 0; y < outy; ++y) { + float* ptr = output->pData->getData(); + ptr += (z + output->subX) * (size_t)output->pData->getHeight() * (size_t)output->pData->getWidth(); + ptr += (y + output->subY) * (size_t)output->pData->getWidth(); + ptr += output->subX; + memset(ptr, 0, sizeof(float) * outx); + } + } + } + continue; + } + + + astraCUDA3d::SSubDimensions3D dstdims; + dstdims.nx = output->pData->getWidth(); + dstdims.pitch = dstdims.nx; + dstdims.ny = output->pData->getHeight(); + dstdims.nz = output->pData->getDepth(); + dstdims.subnx = outx; + dstdims.subny = outy; + dstdims.subnz = outz; + ASTRA_DEBUG("dstdims: %d,%d,%d in %d,%d,%d", dstdims.subnx, dstdims.subny, dstdims.subnz, dstdims.nx, dstdims.ny, dstdims.nz); + dstdims.subx = output->subX; + dstdims.suby = output->subY; + dstdims.subz = output->subZ; + float *dst = output->pData->getData(); + + astraCUDA3d::MemHandle3D outputMem = astraCUDA3d::allocateGPUMemory(outx, outy, outz, zero ? astraCUDA3d::INIT_ZERO : astraCUDA3d::INIT_NO); + bool ok = outputMem; + + for (TJobList::iterator i = L.begin(); i != L.end(); ++i) { + SJob &j = *i; + + assert(j.pInput); + + CCudaProjector3D *projector = dynamic_cast(j.pProjector); + Cuda3DProjectionKernel projKernel = ker3d_default; + int detectorSuperSampling = 1; + int voxelSuperSampling = 1; + if (projector) { + projKernel = projector->getProjectionKernel(); + detectorSuperSampling = projector->getDetectorSuperSampling(); + voxelSuperSampling = projector->getVoxelSuperSampling(); + } + + size_t inx, iny, inz; + j.pInput->getDims(inx, iny, inz); + astraCUDA3d::MemHandle3D inputMem = astraCUDA3d::allocateGPUMemory(inx, iny, inz, astraCUDA3d::INIT_NO); + + astraCUDA3d::SSubDimensions3D srcdims; + srcdims.nx = j.pInput->pData->getWidth(); + srcdims.pitch = srcdims.nx; + srcdims.ny = j.pInput->pData->getHeight(); + srcdims.nz = j.pInput->pData->getDepth(); + srcdims.subnx = inx; + srcdims.subny = iny; + srcdims.subnz = inz; + srcdims.subx = j.pInput->subX; + srcdims.suby = j.pInput->subY; + srcdims.subz = j.pInput->subZ; + const float *src = j.pInput->pData->getDataConst(); + + ok = astraCUDA3d::copyToGPUMemory(src, inputMem, srcdims); + if (!ok) ASTRA_ERROR("Error copying input data to GPU"); + + if (j.eType == SJob::JOB_FP) { + assert(dynamic_cast(j.pInput.get())); + assert(dynamic_cast(j.pOutput.get())); + + ASTRA_DEBUG("CCompositeGeometryManager::doJobs: doing FP"); + + ok = astraCUDA3d::FP(((CProjectionPart*)j.pOutput.get())->pGeom, outputMem, ((CVolumePart*)j.pInput.get())->pGeom, inputMem, detectorSuperSampling, projKernel); + if (!ok) ASTRA_ERROR("Error performing sub-FP"); + ASTRA_DEBUG("CCompositeGeometryManager::doJobs: FP done"); + } else if (j.eType == SJob::JOB_BP) { + assert(dynamic_cast(j.pOutput.get())); + assert(dynamic_cast(j.pInput.get())); + + ASTRA_DEBUG("CCompositeGeometryManager::doJobs: doing BP"); + + ok = astraCUDA3d::BP(((CProjectionPart*)j.pInput.get())->pGeom, inputMem, ((CVolumePart*)j.pOutput.get())->pGeom, outputMem, voxelSuperSampling); + if (!ok) ASTRA_ERROR("Error performing sub-BP"); + ASTRA_DEBUG("CCompositeGeometryManager::doJobs: BP done"); + } else { + assert(false); + } + + ok = astraCUDA3d::freeGPUMemory(inputMem); + if (!ok) ASTRA_ERROR("Error freeing GPU memory"); + + } + + ok = astraCUDA3d::copyFromGPUMemory(dst, outputMem, dstdims); + if (!ok) ASTRA_ERROR("Error copying output data from GPU"); + + ok = astraCUDA3d::freeGPUMemory(outputMem); + if (!ok) ASTRA_ERROR("Error freeing GPU memory"); + } + + return true; +} + + + +} + +#endif diff --git a/src/ConeProjectionGeometry3D.cpp b/src/ConeProjectionGeometry3D.cpp index dd22eba..18f0f8a 100644 --- a/src/ConeProjectionGeometry3D.cpp +++ b/src/ConeProjectionGeometry3D.cpp @@ -29,6 +29,7 @@ $Id$ #include "astra/ConeProjectionGeometry3D.h" #include "astra/Logging.h" +#include "astra/GeometryUtil3D.h" #include #include @@ -230,14 +231,14 @@ CVector3D CConeProjectionGeometry3D::getProjectionDirection(int _iProjectionInde return ret; } -void CConeProjectionGeometry3D::projectPoint(float32 fX, float32 fY, float32 fZ, - int iAngleIndex, - float32 &fU, float32 &fV) const +void CConeProjectionGeometry3D::projectPoint(double fX, double fY, double fZ, + int iAngleIndex, + double &fU, double &fV) const { ASTRA_ASSERT(iAngleIndex >= 0); ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); - float alpha = m_pfProjectionAngles[iAngleIndex]; + double alpha = m_pfProjectionAngles[iAngleIndex]; // Project point onto optical axis @@ -245,14 +246,14 @@ void CConeProjectionGeometry3D::projectPoint(float32 fX, float32 fY, float32 fZ, // Vector source->origin is (-sin(alpha), cos(alpha)) // Distance from source, projected on optical axis - float fD = -sin(alpha) * fX + cos(alpha) * fY + m_fOriginSourceDistance; + double fD = -sin(alpha) * fX + cos(alpha) * fY + m_fOriginSourceDistance; // Scale fZ to detector plane fV = detectorOffsetYToRowIndexFloat( (fZ * (m_fOriginSourceDistance + m_fOriginDetectorDistance)) / fD ); // Orthogonal distance in XY-plane to optical axis - float fS = cos(alpha) * fX + sin(alpha) * fY; + double fS = cos(alpha) * fX + sin(alpha) * fY; // Scale fS to detector plane fU = detectorOffsetXToColIndexFloat( (fS * (m_fOriginSourceDistance + m_fOriginDetectorDistance)) / fD ); @@ -261,5 +262,84 @@ void CConeProjectionGeometry3D::projectPoint(float32 fX, float32 fY, float32 fZ, } +void CConeProjectionGeometry3D::backprojectPointX(int iAngleIndex, double fU, double fV, + double fX, double &fY, double &fZ) const +{ + ASTRA_ASSERT(iAngleIndex >= 0); + ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); + + SConeProjection *projs = genConeProjections(1, m_iDetectorColCount, m_iDetectorRowCount, + m_fOriginSourceDistance, + m_fOriginDetectorDistance, + m_fDetectorSpacingX, m_fDetectorSpacingY, + &m_pfProjectionAngles[iAngleIndex]); + + SConeProjection &proj = projs[0]; + + double px = proj.fDetSX + fU * proj.fDetUX + fV * proj.fDetVX; + double py = proj.fDetSY + fU * proj.fDetUY + fV * proj.fDetVY; + double pz = proj.fDetSZ + fU * proj.fDetUZ + fV * proj.fDetVZ; + + double a = (fX - proj.fSrcX) / (px - proj.fSrcX); + + fY = proj.fSrcY + a * (py - proj.fSrcY); + fZ = proj.fSrcZ + a * (pz - proj.fSrcZ); + + delete[] projs; +} + +void CConeProjectionGeometry3D::backprojectPointY(int iAngleIndex, double fU, double fV, + double fY, double &fX, double &fZ) const +{ + ASTRA_ASSERT(iAngleIndex >= 0); + ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); + + SConeProjection *projs = genConeProjections(1, m_iDetectorColCount, m_iDetectorRowCount, + m_fOriginSourceDistance, + m_fOriginDetectorDistance, + m_fDetectorSpacingX, m_fDetectorSpacingY, + &m_pfProjectionAngles[iAngleIndex]); + + SConeProjection &proj = projs[0]; + + double px = proj.fDetSX + fU * proj.fDetUX + fV * proj.fDetVX; + double py = proj.fDetSY + fU * proj.fDetUY + fV * proj.fDetVY; + double pz = proj.fDetSZ + fU * proj.fDetUZ + fV * proj.fDetVZ; + + double a = (fY - proj.fSrcY) / (py - proj.fSrcY); + + fX = proj.fSrcX + a * (px - proj.fSrcX); + fZ = proj.fSrcZ + a * (pz - proj.fSrcZ); + + delete[] projs; +} + +void CConeProjectionGeometry3D::backprojectPointZ(int iAngleIndex, double fU, double fV, + double fZ, double &fX, double &fY) const +{ + ASTRA_ASSERT(iAngleIndex >= 0); + ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); + + SConeProjection *projs = genConeProjections(1, m_iDetectorColCount, m_iDetectorRowCount, + m_fOriginSourceDistance, + m_fOriginDetectorDistance, + m_fDetectorSpacingX, m_fDetectorSpacingY, + &m_pfProjectionAngles[iAngleIndex]); + + SConeProjection &proj = projs[0]; + + double px = proj.fDetSX + fU * proj.fDetUX + fV * proj.fDetVX; + double py = proj.fDetSY + fU * proj.fDetUY + fV * proj.fDetVY; + double pz = proj.fDetSZ + fU * proj.fDetUZ + fV * proj.fDetVZ; + + double a = (fZ - proj.fSrcZ) / (pz - proj.fSrcZ); + + fX = proj.fSrcX + a * (px - proj.fSrcX); + fY = proj.fSrcY + a * (py - proj.fSrcY); + + delete[] projs; +} + + } // end namespace astra diff --git a/src/ConeVecProjectionGeometry3D.cpp b/src/ConeVecProjectionGeometry3D.cpp index 47ed630..86e3bd6 100644 --- a/src/ConeVecProjectionGeometry3D.cpp +++ b/src/ConeVecProjectionGeometry3D.cpp @@ -241,9 +241,9 @@ CVector3D CConeVecProjectionGeometry3D::getProjectionDirection(int _iProjectionI return CVector3D(p.fDetSX + (u+0.5)*p.fDetUX + (v+0.5)*p.fDetVX - p.fSrcX, p.fDetSY + (u+0.5)*p.fDetUY + (v+0.5)*p.fDetVY - p.fSrcY, p.fDetSZ + (u+0.5)*p.fDetUZ + (v+0.5)*p.fDetVZ - p.fSrcZ); } -void CConeVecProjectionGeometry3D::projectPoint(float32 fX, float32 fY, float32 fZ, +void CConeVecProjectionGeometry3D::projectPoint(double fX, double fY, double fZ, int iAngleIndex, - float32 &fU, float32 &fV) const + double &fU, double &fV) const { ASTRA_ASSERT(iAngleIndex >= 0); ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); @@ -262,6 +262,60 @@ void CConeVecProjectionGeometry3D::projectPoint(float32 fX, float32 fY, float32 } +void CConeVecProjectionGeometry3D::backprojectPointX(int iAngleIndex, double fU, double fV, + double fX, double &fY, double &fZ) const +{ + ASTRA_ASSERT(iAngleIndex >= 0); + ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); + + SConeProjection &proj = m_pProjectionAngles[iAngleIndex]; + + double px = proj.fDetSX + fU * proj.fDetUX + fV * proj.fDetVX; + double py = proj.fDetSY + fU * proj.fDetUY + fV * proj.fDetVY; + double pz = proj.fDetSZ + fU * proj.fDetUZ + fV * proj.fDetVZ; + + double a = (fX - proj.fSrcX) / (px - proj.fSrcX); + + fY = proj.fSrcY + a * (py - proj.fSrcY); + fZ = proj.fSrcZ + a * (pz - proj.fSrcZ); +} + +void CConeVecProjectionGeometry3D::backprojectPointY(int iAngleIndex, double fU, double fV, + double fY, double &fX, double &fZ) const +{ + ASTRA_ASSERT(iAngleIndex >= 0); + ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); + + SConeProjection &proj = m_pProjectionAngles[iAngleIndex]; + + double px = proj.fDetSX + fU * proj.fDetUX + fV * proj.fDetVX; + double py = proj.fDetSY + fU * proj.fDetUY + fV * proj.fDetVY; + double pz = proj.fDetSZ + fU * proj.fDetUZ + fV * proj.fDetVZ; + + double a = (fY - proj.fSrcY) / (py - proj.fSrcY); + + fX = proj.fSrcX + a * (px - proj.fSrcX); + fZ = proj.fSrcZ + a * (pz - proj.fSrcZ); +} + +void CConeVecProjectionGeometry3D::backprojectPointZ(int iAngleIndex, double fU, double fV, + double fZ, double &fX, double &fY) const +{ + ASTRA_ASSERT(iAngleIndex >= 0); + ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); + + SConeProjection &proj = m_pProjectionAngles[iAngleIndex]; + + double px = proj.fDetSX + fU * proj.fDetUX + fV * proj.fDetVX; + double py = proj.fDetSY + fU * proj.fDetUY + fV * proj.fDetVY; + double pz = proj.fDetSZ + fU * proj.fDetUZ + fV * proj.fDetVZ; + + double a = (fZ - proj.fSrcZ) / (pz - proj.fSrcZ); + + fX = proj.fSrcX + a * (px - proj.fSrcX); + fY = proj.fSrcY + a * (py - proj.fSrcY); +} + //---------------------------------------------------------------------------------------- bool CConeVecProjectionGeometry3D::_check() diff --git a/src/CudaBackProjectionAlgorithm3D.cpp b/src/CudaBackProjectionAlgorithm3D.cpp index 8cf4c3b..ce8e111 100644 --- a/src/CudaBackProjectionAlgorithm3D.cpp +++ b/src/CudaBackProjectionAlgorithm3D.cpp @@ -37,6 +37,7 @@ $Id$ #include "astra/ParallelProjectionGeometry3D.h" #include "astra/ParallelVecProjectionGeometry3D.h" #include "astra/ConeVecProjectionGeometry3D.h" +#include "astra/CompositeGeometryManager.h" #include "astra/Logging.h" @@ -203,9 +204,16 @@ void CCudaBackProjectionAlgorithm3D::run(int _iNrIterations) &volgeom, projgeom, m_iGPUIndex, m_iVoxelSuperSampling); } else { + +#if 1 + CCompositeGeometryManager cgm; + + cgm.doBP(m_pProjector, pReconMem, pSinoMem); +#else astraCudaBP(pReconMem->getData(), pSinoMem->getDataConst(), &volgeom, projgeom, m_iGPUIndex, m_iVoxelSuperSampling); +#endif } } diff --git a/src/CudaForwardProjectionAlgorithm3D.cpp b/src/CudaForwardProjectionAlgorithm3D.cpp index e57e077..209f5a5 100644 --- a/src/CudaForwardProjectionAlgorithm3D.cpp +++ b/src/CudaForwardProjectionAlgorithm3D.cpp @@ -40,6 +40,8 @@ $Id$ #include "astra/ParallelVecProjectionGeometry3D.h" #include "astra/ConeVecProjectionGeometry3D.h" +#include "astra/CompositeGeometryManager.h" + #include "astra/Logging.h" #include "../cuda/3d/astra3d.h" @@ -263,6 +265,12 @@ void CCudaForwardProjectionAlgorithm3D::run(int) // check initialized assert(m_bIsInitialized); +#if 1 + CCompositeGeometryManager cgm; + + cgm.doFP(m_pProjector, m_pVolume, m_pProjections); + +#else const CProjectionGeometry3D* projgeom = m_pProjections->getGeometry(); const CVolumeGeometry3D& volgeom = *m_pVolume->getGeometry(); @@ -294,6 +302,7 @@ void CCudaForwardProjectionAlgorithm3D::run(int) astraCudaFP(m_pVolume->getDataConst(), m_pProjections->getData(), &volgeom, projgeom, m_iGPUIndex, m_iDetectorSuperSampling, projKernel); +#endif } diff --git a/src/GeometryUtil3D.cpp b/src/GeometryUtil3D.cpp index 52dd5a9..c6bfd8b 100644 --- a/src/GeometryUtil3D.cpp +++ b/src/GeometryUtil3D.cpp @@ -28,8 +28,96 @@ $Id$ #include "astra/GeometryUtil3D.h" +#include + namespace astra { + +SConeProjection* genConeProjections(unsigned int iProjAngles, + unsigned int iProjU, + unsigned int iProjV, + double fOriginSourceDistance, + double fOriginDetectorDistance, + double fDetUSize, + double fDetVSize, + const float *pfAngles) +{ + SConeProjection base; + base.fSrcX = 0.0f; + base.fSrcY = -fOriginSourceDistance; + base.fSrcZ = 0.0f; + + base.fDetSX = iProjU * fDetUSize * -0.5f; + base.fDetSY = fOriginDetectorDistance; + base.fDetSZ = iProjV * fDetVSize * -0.5f; + + base.fDetUX = fDetUSize; + base.fDetUY = 0.0f; + base.fDetUZ = 0.0f; + + base.fDetVX = 0.0f; + base.fDetVY = 0.0f; + base.fDetVZ = fDetVSize; + + SConeProjection* p = new SConeProjection[iProjAngles]; + +#define ROTATE0(name,i,alpha) do { p[i].f##name##X = base.f##name##X * cos(alpha) - base.f##name##Y * sin(alpha); p[i].f##name##Y = base.f##name##X * sin(alpha) + base.f##name##Y * cos(alpha); p[i].f##name##Z = base.f##name##Z; } while(0) + + for (unsigned int i = 0; i < iProjAngles; ++i) { + ROTATE0(Src, i, pfAngles[i]); + ROTATE0(DetS, i, pfAngles[i]); + ROTATE0(DetU, i, pfAngles[i]); + ROTATE0(DetV, i, pfAngles[i]); + } + +#undef ROTATE0 + + return p; +} + +SPar3DProjection* genPar3DProjections(unsigned int iProjAngles, + unsigned int iProjU, + unsigned int iProjV, + double fDetUSize, + double fDetVSize, + const float *pfAngles) +{ + SPar3DProjection base; + base.fRayX = 0.0f; + base.fRayY = 1.0f; + base.fRayZ = 0.0f; + + base.fDetSX = iProjU * fDetUSize * -0.5f; + base.fDetSY = 0.0f; + base.fDetSZ = iProjV * fDetVSize * -0.5f; + + base.fDetUX = fDetUSize; + base.fDetUY = 0.0f; + base.fDetUZ = 0.0f; + + base.fDetVX = 0.0f; + base.fDetVY = 0.0f; + base.fDetVZ = fDetVSize; + + SPar3DProjection* p = new SPar3DProjection[iProjAngles]; + +#define ROTATE0(name,i,alpha) do { p[i].f##name##X = base.f##name##X * cos(alpha) - base.f##name##Y * sin(alpha); p[i].f##name##Y = base.f##name##X * sin(alpha) + base.f##name##Y * cos(alpha); p[i].f##name##Z = base.f##name##Z; } while(0) + + for (unsigned int i = 0; i < iProjAngles; ++i) { + ROTATE0(Ray, i, pfAngles[i]); + ROTATE0(DetS, i, pfAngles[i]); + ROTATE0(DetU, i, pfAngles[i]); + ROTATE0(DetV, i, pfAngles[i]); + } + +#undef ROTATE0 + + return p; +} + + + + // (See declaration in header for (mathematical) description of these functions) @@ -72,4 +160,88 @@ void computeBP_UV_Coeffs(const SConeProjection& proj, double &fUX, double &fUY, } +// TODO: Handle cases of rays parallel to coordinate planes + +void backprojectPointX(const SPar3DProjection& proj, double fU, double fV, + double fX, double &fY, double &fZ) +{ + double px = proj.fDetSX + fU * proj.fDetUX + fV * proj.fDetVX; + double py = proj.fDetSY + fU * proj.fDetUY + fV * proj.fDetVY; + double pz = proj.fDetSZ + fU * proj.fDetUZ + fV * proj.fDetVZ; + + double a = (fX - px) / proj.fRayX; + + fY = py + a * proj.fRayY; + fZ = pz + a * proj.fRayZ; +} + +void backprojectPointY(const SPar3DProjection& proj, double fU, double fV, + double fY, double &fX, double &fZ) +{ + double px = proj.fDetSX + fU * proj.fDetUX + fV * proj.fDetVX; + double py = proj.fDetSY + fU * proj.fDetUY + fV * proj.fDetVY; + double pz = proj.fDetSZ + fU * proj.fDetUZ + fV * proj.fDetVZ; + + double a = (fY - py) / proj.fRayY; + + fX = px + a * proj.fRayX; + fZ = pz + a * proj.fRayZ; + +} + +void backprojectPointZ(const SPar3DProjection& proj, double fU, double fV, + double fZ, double &fX, double &fY) +{ + double px = proj.fDetSX + fU * proj.fDetUX + fV * proj.fDetVX; + double py = proj.fDetSY + fU * proj.fDetUY + fV * proj.fDetVY; + double pz = proj.fDetSZ + fU * proj.fDetUZ + fV * proj.fDetVZ; + + double a = (fZ - pz) / proj.fRayZ; + + fX = px + a * proj.fRayX; + fY = py + a * proj.fRayY; +} + + + +void backprojectPointX(const SConeProjection& proj, double fU, double fV, + double fX, double &fY, double &fZ) +{ + double px = proj.fDetSX + fU * proj.fDetUX + fV * proj.fDetVX; + double py = proj.fDetSY + fU * proj.fDetUY + fV * proj.fDetVY; + double pz = proj.fDetSZ + fU * proj.fDetUZ + fV * proj.fDetVZ; + + double a = (fX - proj.fSrcX) / (px - proj.fSrcX); + + fY = proj.fSrcY + a * (py - proj.fSrcY); + fZ = proj.fSrcZ + a * (pz - proj.fSrcZ); +} + +void backprojectPointY(const SConeProjection& proj, double fU, double fV, + double fY, double &fX, double &fZ) +{ + double px = proj.fDetSX + fU * proj.fDetUX + fV * proj.fDetVX; + double py = proj.fDetSY + fU * proj.fDetUY + fV * proj.fDetVY; + double pz = proj.fDetSZ + fU * proj.fDetUZ + fV * proj.fDetVZ; + + double a = (fY - proj.fSrcY) / (py - proj.fSrcY); + + fX = proj.fSrcX + a * (px - proj.fSrcX); + fZ = proj.fSrcZ + a * (pz - proj.fSrcZ); +} + +void backprojectPointZ(const SConeProjection& proj, double fU, double fV, + double fZ, double &fX, double &fY) +{ + double px = proj.fDetSX + fU * proj.fDetUX + fV * proj.fDetVX; + double py = proj.fDetSY + fU * proj.fDetUY + fV * proj.fDetVY; + double pz = proj.fDetSZ + fU * proj.fDetUZ + fV * proj.fDetVZ; + + double a = (fZ - proj.fSrcZ) / (pz - proj.fSrcZ); + + fX = proj.fSrcX + a * (px - proj.fSrcX); + fY = proj.fSrcY + a * (py - proj.fSrcY); +} + + } diff --git a/src/ParallelProjectionGeometry3D.cpp b/src/ParallelProjectionGeometry3D.cpp index 1c87157..7b64fd9 100644 --- a/src/ParallelProjectionGeometry3D.cpp +++ b/src/ParallelProjectionGeometry3D.cpp @@ -27,8 +27,10 @@ $Id$ */ #include "astra/ParallelProjectionGeometry3D.h" -#include +#include "astra/GeometryUtil3D.h" + +#include #include using namespace std; @@ -185,9 +187,9 @@ CVector3D CParallelProjectionGeometry3D::getProjectionDirection(int _iProjection return CVector3D(fDirX, fDirY, fDirZ); } -void CParallelProjectionGeometry3D::projectPoint(float32 fX, float32 fY, float32 fZ, +void CParallelProjectionGeometry3D::projectPoint(double fX, double fY, double fZ, int iAngleIndex, - float32 &fU, float32 &fV) const + double &fU, double &fV) const { ASTRA_ASSERT(iAngleIndex >= 0); ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); @@ -214,6 +216,79 @@ CParallelProjectionGeometry2D * CParallelProjectionGeometry3D::createProjectionG return pOutput; } +void CParallelProjectionGeometry3D::backprojectPointX(int iAngleIndex, double fU, double fV, + double fX, double &fY, double &fZ) const +{ + ASTRA_ASSERT(iAngleIndex >= 0); + ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); + + SPar3DProjection *projs = genPar3DProjections(1, m_iDetectorColCount, m_iDetectorRowCount, + m_fDetectorSpacingX, m_fDetectorSpacingY, + &m_pfProjectionAngles[iAngleIndex]); + + SPar3DProjection &proj = projs[0]; + + double px = proj.fDetSX + fU * proj.fDetUX + fV * proj.fDetVX; + double py = proj.fDetSY + fU * proj.fDetUY + fV * proj.fDetVY; + double pz = proj.fDetSZ + fU * proj.fDetUZ + fV * proj.fDetVZ; + + double a = (fX - px) / proj.fRayX; + + fY = py + a * proj.fRayY; + fZ = pz + a * proj.fRayZ; + + delete[] projs; +} + +void CParallelProjectionGeometry3D::backprojectPointY(int iAngleIndex, double fU, double fV, + double fY, double &fX, double &fZ) const +{ + ASTRA_ASSERT(iAngleIndex >= 0); + ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); + + SPar3DProjection *projs = genPar3DProjections(1, m_iDetectorColCount, m_iDetectorRowCount, + m_fDetectorSpacingX, m_fDetectorSpacingY, + &m_pfProjectionAngles[iAngleIndex]); + + SPar3DProjection &proj = projs[0]; + + double px = proj.fDetSX + fU * proj.fDetUX + fV * proj.fDetVX; + double py = proj.fDetSY + fU * proj.fDetUY + fV * proj.fDetVY; + double pz = proj.fDetSZ + fU * proj.fDetUZ + fV * proj.fDetVZ; + + double a = (fY - py) / proj.fRayY; + + fX = px + a * proj.fRayX; + fZ = pz + a * proj.fRayZ; + + delete[] projs; +} + +void CParallelProjectionGeometry3D::backprojectPointZ(int iAngleIndex, double fU, double fV, + double fZ, double &fX, double &fY) const +{ + ASTRA_ASSERT(iAngleIndex >= 0); + ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); + + SPar3DProjection *projs = genPar3DProjections(1, m_iDetectorColCount, m_iDetectorRowCount, + m_fDetectorSpacingX, m_fDetectorSpacingY, + &m_pfProjectionAngles[iAngleIndex]); + + SPar3DProjection &proj = projs[0]; + + double px = proj.fDetSX + fU * proj.fDetUX + fV * proj.fDetVX; + double py = proj.fDetSY + fU * proj.fDetUY + fV * proj.fDetVY; + double pz = proj.fDetSZ + fU * proj.fDetUZ + fV * proj.fDetVZ; + + double a = (fZ - pz) / proj.fRayZ; + + fX = px + a * proj.fRayX; + fY = py + a * proj.fRayY; + + delete[] projs; +} + + //---------------------------------------------------------------------------------------- } // end namespace astra diff --git a/src/ParallelVecProjectionGeometry3D.cpp b/src/ParallelVecProjectionGeometry3D.cpp index ffad6d0..d04400b 100644 --- a/src/ParallelVecProjectionGeometry3D.cpp +++ b/src/ParallelVecProjectionGeometry3D.cpp @@ -239,9 +239,9 @@ CVector3D CParallelVecProjectionGeometry3D::getProjectionDirection(int _iProject return CVector3D(p.fRayX, p.fRayY, p.fRayZ); } -void CParallelVecProjectionGeometry3D::projectPoint(float32 fX, float32 fY, float32 fZ, - int iAngleIndex, - float32 &fU, float32 &fV) const +void CParallelVecProjectionGeometry3D::projectPoint(double fX, double fY, double fZ, + int iAngleIndex, + double &fU, double &fV) const { ASTRA_ASSERT(iAngleIndex >= 0); ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); @@ -258,6 +258,61 @@ void CParallelVecProjectionGeometry3D::projectPoint(float32 fX, float32 fY, floa } +void CParallelVecProjectionGeometry3D::backprojectPointX(int iAngleIndex, double fU, double fV, + double fX, double &fY, double &fZ) const +{ + ASTRA_ASSERT(iAngleIndex >= 0); + ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); + + SPar3DProjection &proj = m_pProjectionAngles[iAngleIndex]; + + double px = proj.fDetSX + fU * proj.fDetUX + fV * proj.fDetVX; + double py = proj.fDetSY + fU * proj.fDetUY + fV * proj.fDetVY; + double pz = proj.fDetSZ + fU * proj.fDetUZ + fV * proj.fDetVZ; + + double a = (fX - px) / proj.fRayX; + + fY = py + a * proj.fRayY; + fZ = pz + a * proj.fRayZ; +} + +void CParallelVecProjectionGeometry3D::backprojectPointY(int iAngleIndex, double fU, double fV, + double fY, double &fX, double &fZ) const +{ + ASTRA_ASSERT(iAngleIndex >= 0); + ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); + + SPar3DProjection &proj = m_pProjectionAngles[iAngleIndex]; + + double px = proj.fDetSX + fU * proj.fDetUX + fV * proj.fDetVX; + double py = proj.fDetSY + fU * proj.fDetUY + fV * proj.fDetVY; + double pz = proj.fDetSZ + fU * proj.fDetUZ + fV * proj.fDetVZ; + + double a = (fY - py) / proj.fRayY; + + fX = px + a * proj.fRayX; + fZ = pz + a * proj.fRayZ; +} + +void CParallelVecProjectionGeometry3D::backprojectPointZ(int iAngleIndex, double fU, double fV, + double fZ, double &fX, double &fY) const +{ + ASTRA_ASSERT(iAngleIndex >= 0); + ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); + + SPar3DProjection &proj = m_pProjectionAngles[iAngleIndex]; + + double px = proj.fDetSX + fU * proj.fDetUX + fV * proj.fDetVX; + double py = proj.fDetSY + fU * proj.fDetUY + fV * proj.fDetVY; + double pz = proj.fDetSZ + fU * proj.fDetUZ + fV * proj.fDetVZ; + + double a = (fZ - pz) / proj.fRayZ; + + fX = px + a * proj.fRayX; + fY = py + a * proj.fRayY; +} + + //---------------------------------------------------------------------------------------- bool CParallelVecProjectionGeometry3D::_check() -- cgit v1.2.3 From b7c5deba2182514ffd6af61bac65ec9e0c0ebfd7 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Wed, 10 Jun 2015 12:45:52 -0500 Subject: Add conda build scripts --- build/linux/Makefile.in | 4 ++++ python/conda/build.sh | 16 ++++++++++++++++ python/conda/meta.yaml | 40 ++++++++++++++++++++++++++++++++++++++++ 3 files changed, 60 insertions(+) create mode 100644 python/conda/build.sh create mode 100644 python/conda/meta.yaml (limited to 'build') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 0361e97..8eb5ffe 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -266,6 +266,10 @@ py: libastra.la cd ../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py install \ --install-base=./finalbuild --install-headers=./finalbuild --install-purelib=./finalbuild \ --install-platlib=./finalbuild --install-scripts=./finalbuild --install-data=./finalbuild + +python-root-install: libastra.la + cd ../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py install + endif diff --git a/python/conda/build.sh b/python/conda/build.sh new file mode 100644 index 0000000..814ea7e --- /dev/null +++ b/python/conda/build.sh @@ -0,0 +1,16 @@ +cd build/linux +./autogen.sh +./configure --with-python --with-cuda=$CUDA_ROOT --prefix=$PREFIX +if [ $MAKEOPTS == '' ] + then + MAKEOPTS="" +fi +make $MAKEOPTS install-libraries +make $MAKEOPTS python-root-install +LIBPATH=lib +if [ $ARCH == 64 ] + then + LIBPATH+=64 +fi +cp -P $CUDA_ROOT/$LIBPATH/libcudart.so.* $PREFIX/lib +cp -P $CUDA_ROOT/$LIBPATH/libcufft.so.* $PREFIX/lib diff --git a/python/conda/meta.yaml b/python/conda/meta.yaml new file mode 100644 index 0000000..45ea812 --- /dev/null +++ b/python/conda/meta.yaml @@ -0,0 +1,40 @@ +package: + name: astra-toolbox + version: '1.6' + +source: + git_url: https://github.com/astra-toolbox/astra-toolbox.git + git_tag: v1.6 + +build: + number: 0 + script_env: + - CUDA_ROOT + - MAKEOPTS + +test: + imports: + - astra + +requirements: + build: + - python + - cython >=0.13 + - numpy + - six + + run: + - python + - numpy + - scipy + - six + + +about: + home: http://sourceforge.net/p/astra-toolbox/wiki/Home/ + license: GPLv3 + summary: 'The ASTRA Toolbox is a Python toolbox of high-performance GPU primitives for 2D and 3D tomography.' + +# See +# http://docs.continuum.io/conda/build.html for +# more information about meta.yaml -- cgit v1.2.3 From 8603f9a768c99b18eb74aff13a015fc60fa57ea6 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Fri, 4 Dec 2015 16:20:35 +0100 Subject: Update version to 1.7 --- build/linux/configure.ac | 2 +- include/astra/Globals.h | 4 ++-- python/builder.py | 2 +- python/conda/meta.yaml | 4 ++-- python/docSRC/conf.py | 4 ++-- 5 files changed, 8 insertions(+), 8 deletions(-) (limited to 'build') diff --git a/build/linux/configure.ac b/build/linux/configure.ac index 7c314f3..38c2946 100644 --- a/build/linux/configure.ac +++ b/build/linux/configure.ac @@ -24,7 +24,7 @@ dnl dnl ----------------------------------------------------------------------- dnl $Id$ -AC_INIT(astra_toolbox, 1.6.0) +AC_INIT(astra_toolbox, 1.7.0) AC_CONFIG_SRCDIR([Makefile.in]) LT_INIT([disable-static]) diff --git a/include/astra/Globals.h b/include/astra/Globals.h index f70c3a9..31f1371 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 6 +#define ASTRA_TOOLBOXVERSION_MINOR 7 #define ASTRA_TOOLBOXVERSION ((ASTRA_TOOLBOXVERSION_MAJOR)*100 + (ASTRA_TOOLBOXVERSION_MINOR)) -#define ASTRA_TOOLBOXVERSION_STRING "1.6" +#define ASTRA_TOOLBOXVERSION_STRING "1.7" #define ASTRA_ASSERT(a) assert(a) diff --git a/python/builder.py b/python/builder.py index 44d9c3b..5322182 100644 --- a/python/builder.py +++ b/python/builder.py @@ -71,7 +71,7 @@ ext_modules = cythonize("astra/*.pyx", language_level=2) cmdclass = { 'build_ext': build_ext } setup (name = 'PyASTRAToolbox', - version = '1.6', + version = '1.7', description = 'Python interface to the ASTRA-Toolbox', author='D.M. Pelt', author_email='D.M.Pelt@cwi.nl', diff --git a/python/conda/meta.yaml b/python/conda/meta.yaml index 45ea812..e1adc83 100644 --- a/python/conda/meta.yaml +++ b/python/conda/meta.yaml @@ -1,10 +1,10 @@ package: name: astra-toolbox - version: '1.6' + version: '1.7' source: git_url: https://github.com/astra-toolbox/astra-toolbox.git - git_tag: v1.6 + git_tag: v1.7 build: number: 0 diff --git a/python/docSRC/conf.py b/python/docSRC/conf.py index e54bbb8..cc95a80 100644 --- a/python/docSRC/conf.py +++ b/python/docSRC/conf.py @@ -48,9 +48,9 @@ copyright = u'2013, Centrum Wiskunde & Informatica, Amsterdam' # built documents. # # The short X.Y version. -version = '1.6' +version = '1.7' # The full version, including alpha/beta/rc tags. -release = '1.6' +release = '1.7' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. -- cgit v1.2.3 From 0d015b1c91581ee5ef3e936f03e4c62fbc7ea362 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Fri, 4 Dec 2015 16:34:44 +0100 Subject: Update Windows build files --- astra_vc09.vcproj | 8 ++++++++ astra_vc11.vcxproj | 2 ++ astra_vc11.vcxproj.filters | 6 ++++++ build/msvc/gen.py | 2 ++ 4 files changed, 18 insertions(+) (limited to 'build') diff --git a/astra_vc09.vcproj b/astra_vc09.vcproj index b928662..f2cf62a 100644 --- a/astra_vc09.vcproj +++ b/astra_vc09.vcproj @@ -748,6 +748,10 @@ RelativePath=".\include\astra\ForwardProjectionAlgorithm.h" > + + @@ -796,6 +800,10 @@ RelativePath=".\src\ForwardProjectionAlgorithm.cpp" > + + diff --git a/astra_vc11.vcxproj b/astra_vc11.vcxproj index fc8b9ce..d050b96 100644 --- a/astra_vc11.vcxproj +++ b/astra_vc11.vcxproj @@ -540,6 +540,7 @@ + @@ -652,6 +653,7 @@ + diff --git a/astra_vc11.vcxproj.filters b/astra_vc11.vcxproj.filters index af8ca39..dd7f574 100644 --- a/astra_vc11.vcxproj.filters +++ b/astra_vc11.vcxproj.filters @@ -105,6 +105,9 @@ Algorithms\source + + Algorithms\source + Algorithms\source @@ -350,6 +353,9 @@ Algorithms\headers + + Algorithms\headers + Algorithms\headers diff --git a/build/msvc/gen.py b/build/msvc/gen.py index c18c1e8..999710f 100644 --- a/build/msvc/gen.py +++ b/build/msvc/gen.py @@ -183,6 +183,7 @@ P_astra["filters"]["Algorithms\\source"] = [ "src\\CglsAlgorithm.cpp", "src\\FilteredBackProjectionAlgorithm.cpp", "src\\ForwardProjectionAlgorithm.cpp", +"src\\PluginAlgorithm.cpp", "src\\ReconstructionAlgorithm2D.cpp", "src\\ReconstructionAlgorithm3D.cpp", "src\\SartAlgorithm.cpp", @@ -315,6 +316,7 @@ P_astra["filters"]["Algorithms\\headers"] = [ "include\\astra\\CudaBackProjectionAlgorithm3D.h", "include\\astra\\FilteredBackProjectionAlgorithm.h", "include\\astra\\ForwardProjectionAlgorithm.h", +"include\\astra\\PluginAlgorithm.h", "include\\astra\\ReconstructionAlgorithm2D.h", "include\\astra\\ReconstructionAlgorithm3D.h", "include\\astra\\SartAlgorithm.h", -- cgit v1.2.3 From 3aabe41914a93d4c9afbc1a6cc498156924cbf18 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 23 Dec 2015 10:47:37 +0100 Subject: Update version to 1.7.1 --- build/linux/configure.ac | 2 +- include/astra/Globals.h | 2 +- python/builder.py | 2 +- python/conda/meta.yaml | 4 ++-- python/docSRC/conf.py | 4 ++-- 5 files changed, 7 insertions(+), 7 deletions(-) (limited to 'build') diff --git a/build/linux/configure.ac b/build/linux/configure.ac index 38c2946..85e4324 100644 --- a/build/linux/configure.ac +++ b/build/linux/configure.ac @@ -24,7 +24,7 @@ dnl dnl ----------------------------------------------------------------------- dnl $Id$ -AC_INIT(astra_toolbox, 1.7.0) +AC_INIT(astra_toolbox, 1.7.1) AC_CONFIG_SRCDIR([Makefile.in]) LT_INIT([disable-static]) diff --git a/include/astra/Globals.h b/include/astra/Globals.h index 31f1371..5dbac83 100644 --- a/include/astra/Globals.h +++ b/include/astra/Globals.h @@ -63,7 +63,7 @@ $Id$ #define ASTRA_TOOLBOXVERSION_MAJOR 1 #define ASTRA_TOOLBOXVERSION_MINOR 7 #define ASTRA_TOOLBOXVERSION ((ASTRA_TOOLBOXVERSION_MAJOR)*100 + (ASTRA_TOOLBOXVERSION_MINOR)) -#define ASTRA_TOOLBOXVERSION_STRING "1.7" +#define ASTRA_TOOLBOXVERSION_STRING "1.7.1" #define ASTRA_ASSERT(a) assert(a) diff --git a/python/builder.py b/python/builder.py index 5322182..018b26b 100644 --- a/python/builder.py +++ b/python/builder.py @@ -71,7 +71,7 @@ ext_modules = cythonize("astra/*.pyx", language_level=2) cmdclass = { 'build_ext': build_ext } setup (name = 'PyASTRAToolbox', - version = '1.7', + version = '1.7.1', description = 'Python interface to the ASTRA-Toolbox', author='D.M. Pelt', author_email='D.M.Pelt@cwi.nl', diff --git a/python/conda/meta.yaml b/python/conda/meta.yaml index e1adc83..41250dc 100644 --- a/python/conda/meta.yaml +++ b/python/conda/meta.yaml @@ -1,10 +1,10 @@ package: name: astra-toolbox - version: '1.7' + version: '1.7.1' source: git_url: https://github.com/astra-toolbox/astra-toolbox.git - git_tag: v1.7 + git_tag: v1.7.1 build: number: 0 diff --git a/python/docSRC/conf.py b/python/docSRC/conf.py index cc95a80..78f7d42 100644 --- a/python/docSRC/conf.py +++ b/python/docSRC/conf.py @@ -48,9 +48,9 @@ copyright = u'2013, Centrum Wiskunde & Informatica, Amsterdam' # built documents. # # The short X.Y version. -version = '1.7' +version = '1.7.1' # The full version, including alpha/beta/rc tags. -release = '1.7' +release = '1.7.1' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. -- cgit v1.2.3 From fc86917da1a175c04e9bd2e5f0bedb0a48a81c26 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Thu, 17 Dec 2015 14:37:41 +0100 Subject: Replace boost::lexical_cast by stringstreams This is to avoid the dependence of lexical_cast on the current locale. The stringstreams used for the new string parsing/output functions are explicitly imbued with the C/classic locale. --- build/linux/configure.ac | 1 - include/astra/Utilities.h | 51 ++++++++++++++++ include/astra/XMLNode.h | 8 +++ matlab/mex/mexHelpFunctions.cpp | 8 +-- matlab/mex/mexHelpFunctions.h | 1 - src/ArtAlgorithm.cpp | 2 - src/BackProjectionAlgorithm.cpp | 2 - src/CglsAlgorithm.cpp | 2 - src/ConeProjectionGeometry3D.cpp | 5 +- src/ConeVecProjectionGeometry3D.cpp | 30 ++++----- src/CudaBackProjectionAlgorithm3D.cpp | 2 - src/CudaCglsAlgorithm3D.cpp | 2 - src/CudaDartMaskAlgorithm.cpp | 5 +- src/CudaDartMaskAlgorithm3D.cpp | 5 +- src/CudaDartSmoothingAlgorithm.cpp | 5 +- src/CudaDartSmoothingAlgorithm3D.cpp | 5 +- src/CudaDataOperationAlgorithm.cpp | 5 +- src/CudaFDKAlgorithm3D.cpp | 2 - src/CudaFilteredBackProjectionAlgorithm.cpp | 13 ++-- src/CudaForwardProjectionAlgorithm.cpp | 8 +-- src/CudaForwardProjectionAlgorithm3D.cpp | 8 +-- src/CudaReconstructionAlgorithm2D.cpp | 2 - src/CudaRoiSelectAlgorithm.cpp | 3 +- src/CudaSirtAlgorithm.cpp | 5 +- src/CudaSirtAlgorithm3D.cpp | 2 - src/FanFlatBeamLineKernelProjector2D.cpp | 1 - src/FanFlatBeamStripKernelProjector2D.cpp | 1 - src/FanFlatProjectionGeometry2D.cpp | 5 +- src/FanFlatVecProjectionGeometry2D.cpp | 15 +++-- src/FilteredBackProjectionAlgorithm.cpp | 8 +-- src/ForwardProjectionAlgorithm.cpp | 12 ++-- src/ParallelBeamBlobKernelProjector2D.cpp | 7 +-- src/ParallelBeamLineKernelProjector2D.cpp | 1 - src/ParallelBeamLinearKernelProjector2D.cpp | 1 - src/ParallelBeamStripKernelProjector2D.cpp | 1 - src/ParallelProjectionGeometry2D.cpp | 1 - src/ParallelProjectionGeometry3D.cpp | 1 - src/ParallelVecProjectionGeometry3D.cpp | 30 ++++----- src/PluginAlgorithm.cpp | 14 ++--- src/ProjectionGeometry2D.cpp | 6 +- src/ProjectionGeometry3D.cpp | 10 ++- src/ReconstructionAlgorithm2D.cpp | 12 ++-- src/ReconstructionAlgorithm3D.cpp | 12 ++-- src/ReconstructionAlgorithmMultiSlice2D.cpp | 8 +-- src/SartAlgorithm.cpp | 2 - src/SirtAlgorithm.cpp | 2 - src/SparseMatrixProjectionGeometry2D.cpp | 3 +- src/SparseMatrixProjector2D.cpp | 1 - src/Utilities.cpp | 95 +++++++++++++++++++++++++++++ src/VolumeGeometry2D.cpp | 5 +- src/VolumeGeometry3D.cpp | 8 +-- src/XMLNode.cpp | 77 +++++++++-------------- 52 files changed, 297 insertions(+), 224 deletions(-) (limited to 'build') diff --git a/build/linux/configure.ac b/build/linux/configure.ac index 85e4324..9b6f7ab 100644 --- a/build/linux/configure.ac +++ b/build/linux/configure.ac @@ -73,7 +73,6 @@ AC_SUBST(HAVEBOOSTUTF) AC_SUBST(LIBS_BOOSTUTF) BOOSTok=yes -AC_CHECK_HEADER([boost/lexical_cast.hpp],[],[BOOSTok=no],[]) AC_CHECK_HEADER([boost/any.hpp],[],[BOOSTok=no],[]) dnl AC_CHECK_HEADER([boost/thread.hpp],[],[BOOSTok=no],[]) dnl AC_CHECK_HEADER([boost/bind.hpp],[],[BOOSTok=no],[]) diff --git a/include/astra/Utilities.h b/include/astra/Utilities.h index a3655a8..3ae0e6c 100644 --- a/include/astra/Utilities.h +++ b/include/astra/Utilities.h @@ -39,6 +39,57 @@ namespace astra { +namespace StringUtil { + +// Exception thrown by functions below +class bad_cast : public std::exception { +public: + bad_cast() { } +}; + + +//< Parse string as int. +//< Throw exception on failure. +int stringToInt(const std::string& s); + +//< Parse string as float. +//< Throw exception on failure. +float stringToFloat(const std::string& s); + +//< Parse string as double. +//< Throw exception on failure. +double stringToDouble(const std::string& s); + +template +T stringTo(const std::string& s); + +//< Parse comma/semicolon-separated string as float vector. +//< Throw exception on failure. +std::vector stringToFloatVector(const std::string& s); + +//< Parse comma/semicolon-separated string as double vector. +//< Throw exception on failure. +std::vector stringToDoubleVector(const std::string& s); + +template +std::vector stringToVector(const std::string& s); + + + +//< Generate string from float. +std::string floatToString(float f); + +//< Generate string from double. +std::string doubleToString(double f); + +template +std::string toString(T f); + +} + + + + template std::map mergeMap(std::map _mMap1, std::map _mMap2) { diff --git a/include/astra/XMLNode.h b/include/astra/XMLNode.h index 4d29d5c..7d1edf5 100644 --- a/include/astra/XMLNode.h +++ b/include/astra/XMLNode.h @@ -101,6 +101,12 @@ public: */ string getContent() const; + /** Get the content of the XML node as an integer + * + * @return node content + */ + int getContentInt() const; + /** Get the content of the XML node as a numerical. * * @return node content @@ -152,6 +158,7 @@ public: */ float32 getAttributeNumerical(string _sName, float32 _fDefaultValue = 0) const; double getAttributeNumericalDouble(string _sName, double _fDefaultValue = 0) const; + int getAttributeInt(string _sName, int _fDefaultValue = 0) const; /** Get the value of a boolean attribute. * @@ -186,6 +193,7 @@ public: * @return option value, _fDefaultValue if the option doesn't exist */ float32 getOptionNumerical(string _sKey, float32 _fDefaultValue = 0) const; + int getOptionInt(string _sKey, int _fDefaultValue = 0) const; /** Get the value of an option within this XML Node * diff --git a/matlab/mex/mexHelpFunctions.cpp b/matlab/mex/mexHelpFunctions.cpp index 58e84d2..13c4ade 100644 --- a/matlab/mex/mexHelpFunctions.cpp +++ b/matlab/mex/mexHelpFunctions.cpp @@ -31,9 +31,9 @@ $Id$ * \brief Contains some functions for interfacing matlab with c data structures */ #include "mexHelpFunctions.h" +#include "astra/Utilities.h" #include -#include #include #include #include @@ -58,7 +58,7 @@ string mexToString(const mxArray* pInput) // is scalar? if (mxIsNumeric(pInput) && mxGetM(pInput)*mxGetN(pInput) == 1) { - return boost::lexical_cast(mxGetScalar(pInput)); + return StringUtil::doubleToString(mxGetScalar(pInput)); } return ""; @@ -378,7 +378,7 @@ mxArray* stringToMxArray(std::string input) boost::split(col_strings, row_strings[row], boost::is_any_of(",")); // check size for (unsigned int col = 0; col < col_strings.size(); col++) { - out[col*rows + row] = boost::lexical_cast(col_strings[col]); + out[col*rows + row] = StringUtil::stringToFloat(col_strings[col]); } } return pMatrix; @@ -397,7 +397,7 @@ mxArray* stringToMxArray(std::string input) // loop elements for (unsigned int i = 0; i < items.size(); i++) { - out[i] = boost::lexical_cast(items[i]); + out[i] = StringUtil::stringToFloat(items[i]); } return pVector; } diff --git a/matlab/mex/mexHelpFunctions.h b/matlab/mex/mexHelpFunctions.h index 3ac5bd8..07edc64 100644 --- a/matlab/mex/mexHelpFunctions.h +++ b/matlab/mex/mexHelpFunctions.h @@ -37,7 +37,6 @@ $Id$ #include #include -#include #include #include "astra/Globals.h" diff --git a/src/ArtAlgorithm.cpp b/src/ArtAlgorithm.cpp index 6a699ec..b59bd93 100644 --- a/src/ArtAlgorithm.cpp +++ b/src/ArtAlgorithm.cpp @@ -28,8 +28,6 @@ $Id$ #include "astra/ArtAlgorithm.h" -#include - #include "astra/AstraObjectManager.h" using namespace std; diff --git a/src/BackProjectionAlgorithm.cpp b/src/BackProjectionAlgorithm.cpp index f561a90..c9beee1 100644 --- a/src/BackProjectionAlgorithm.cpp +++ b/src/BackProjectionAlgorithm.cpp @@ -28,8 +28,6 @@ $Id$ #include "astra/BackProjectionAlgorithm.h" -#include - #include "astra/AstraObjectManager.h" #include "astra/DataProjectorPolicies.h" diff --git a/src/CglsAlgorithm.cpp b/src/CglsAlgorithm.cpp index b9031e3..1ca2549 100644 --- a/src/CglsAlgorithm.cpp +++ b/src/CglsAlgorithm.cpp @@ -28,8 +28,6 @@ $Id$ #include "astra/CglsAlgorithm.h" -#include - #include "astra/AstraObjectManager.h" using namespace std; diff --git a/src/ConeProjectionGeometry3D.cpp b/src/ConeProjectionGeometry3D.cpp index 18f0f8a..99b4bf4 100644 --- a/src/ConeProjectionGeometry3D.cpp +++ b/src/ConeProjectionGeometry3D.cpp @@ -31,7 +31,6 @@ $Id$ #include "astra/Logging.h" #include "astra/GeometryUtil3D.h" -#include #include using namespace std; @@ -90,13 +89,13 @@ bool CConeProjectionGeometry3D::initialize(const Config& _cfg) // Required: DistanceOriginDetector XMLNode node = _cfg.self.getSingleNode("DistanceOriginDetector"); ASTRA_CONFIG_CHECK(node, "ConeProjectionGeometry3D", "No DistanceOriginDetector tag specified."); - m_fOriginDetectorDistance = boost::lexical_cast(node.getContent()); + m_fOriginDetectorDistance = node.getContentNumerical(); CC.markNodeParsed("DistanceOriginDetector"); // Required: DetectorOriginSource node = _cfg.self.getSingleNode("DistanceOriginSource"); ASTRA_CONFIG_CHECK(node, "ConeProjectionGeometry3D", "No DistanceOriginSource tag specified."); - m_fOriginSourceDistance = boost::lexical_cast(node.getContent()); + m_fOriginSourceDistance = node.getContentNumerical(); CC.markNodeParsed("DistanceOriginSource"); // success diff --git a/src/ConeVecProjectionGeometry3D.cpp b/src/ConeVecProjectionGeometry3D.cpp index 86e3bd6..f4f900d 100644 --- a/src/ConeVecProjectionGeometry3D.cpp +++ b/src/ConeVecProjectionGeometry3D.cpp @@ -27,9 +27,9 @@ $Id$ */ #include "astra/ConeVecProjectionGeometry3D.h" +#include "astra/Utilities.h" #include -#include using namespace std; @@ -82,13 +82,13 @@ bool CConeVecProjectionGeometry3D::initialize(const Config& _cfg) // Required: DetectorRowCount node = _cfg.self.getSingleNode("DetectorRowCount"); ASTRA_CONFIG_CHECK(node, "ConeVecProjectionGeometry3D", "No DetectorRowCount tag specified."); - m_iDetectorRowCount = boost::lexical_cast(node.getContent()); + m_iDetectorRowCount = node.getContentInt(); CC.markNodeParsed("DetectorRowCount"); // Required: DetectorColCount node = _cfg.self.getSingleNode("DetectorColCount"); ASTRA_CONFIG_CHECK(node, "ConeVecProjectionGeometry3D", "No DetectorColCount tag specified."); - m_iDetectorColCount = boost::lexical_cast(node.getContent()); + m_iDetectorColCount = node.getContentInt(); m_iDetectorTotCount = m_iDetectorRowCount * m_iDetectorColCount; CC.markNodeParsed("DetectorColCount"); @@ -212,18 +212,18 @@ Config* CConeVecProjectionGeometry3D::getConfiguration() const std::string vectors = ""; for (int i = 0; i < m_iProjectionAngleCount; ++i) { SConeProjection& p = m_pProjectionAngles[i]; - vectors += boost::lexical_cast(p.fSrcX) + ","; - vectors += boost::lexical_cast(p.fSrcY) + ","; - vectors += boost::lexical_cast(p.fSrcZ) + ","; - vectors += boost::lexical_cast(p.fDetSX + 0.5f*m_iDetectorRowCount*p.fDetVX + 0.5f*m_iDetectorColCount*p.fDetUX) + ","; - vectors += boost::lexical_cast(p.fDetSY + 0.5f*m_iDetectorRowCount*p.fDetVY + 0.5f*m_iDetectorColCount*p.fDetUY) + ","; - vectors += boost::lexical_cast(p.fDetSZ + 0.5f*m_iDetectorRowCount*p.fDetVZ + 0.5f*m_iDetectorColCount*p.fDetUZ) + ","; - vectors += boost::lexical_cast(p.fDetUX) + ","; - vectors += boost::lexical_cast(p.fDetUY) + ","; - vectors += boost::lexical_cast(p.fDetUZ) + ","; - vectors += boost::lexical_cast(p.fDetVX) + ","; - vectors += boost::lexical_cast(p.fDetVY) + ","; - vectors += boost::lexical_cast(p.fDetVZ); + vectors += StringUtil::toString(p.fSrcX) + ","; + vectors += StringUtil::toString(p.fSrcY) + ","; + vectors += StringUtil::toString(p.fSrcZ) + ","; + vectors += StringUtil::toString(p.fDetSX + 0.5f*m_iDetectorRowCount*p.fDetVX + 0.5f*m_iDetectorColCount*p.fDetUX) + ","; + vectors += StringUtil::toString(p.fDetSY + 0.5f*m_iDetectorRowCount*p.fDetVY + 0.5f*m_iDetectorColCount*p.fDetUY) + ","; + vectors += StringUtil::toString(p.fDetSZ + 0.5f*m_iDetectorRowCount*p.fDetVZ + 0.5f*m_iDetectorColCount*p.fDetUZ) + ","; + vectors += StringUtil::toString(p.fDetUX) + ","; + vectors += StringUtil::toString(p.fDetUY) + ","; + vectors += StringUtil::toString(p.fDetUZ) + ","; + vectors += StringUtil::toString(p.fDetVX) + ","; + vectors += StringUtil::toString(p.fDetVY) + ","; + vectors += StringUtil::toString(p.fDetVZ); if (i < m_iProjectionAngleCount-1) vectors += ';'; } cfg->self.addChildNode("Vectors", vectors); diff --git a/src/CudaBackProjectionAlgorithm3D.cpp b/src/CudaBackProjectionAlgorithm3D.cpp index ce8e111..76d7b35 100644 --- a/src/CudaBackProjectionAlgorithm3D.cpp +++ b/src/CudaBackProjectionAlgorithm3D.cpp @@ -28,8 +28,6 @@ $Id$ #include "astra/CudaBackProjectionAlgorithm3D.h" -#include - #include "astra/AstraObjectManager.h" #include "astra/CudaProjector3D.h" diff --git a/src/CudaCglsAlgorithm3D.cpp b/src/CudaCglsAlgorithm3D.cpp index abc18d1..930a71e 100644 --- a/src/CudaCglsAlgorithm3D.cpp +++ b/src/CudaCglsAlgorithm3D.cpp @@ -28,8 +28,6 @@ $Id$ #include "astra/CudaCglsAlgorithm3D.h" -#include - #include "astra/AstraObjectManager.h" #include "astra/CudaProjector3D.h" diff --git a/src/CudaDartMaskAlgorithm.cpp b/src/CudaDartMaskAlgorithm.cpp index 950b428..c2a4cca 100644 --- a/src/CudaDartMaskAlgorithm.cpp +++ b/src/CudaDartMaskAlgorithm.cpp @@ -34,7 +34,6 @@ $Id$ #include "../cuda/2d/algo.h" #include "astra/AstraObjectManager.h" -#include using namespace std; @@ -67,14 +66,14 @@ bool CCudaDartMaskAlgorithm::initialize(const Config& _cfg) // reconstruction data XMLNode node = _cfg.self.getSingleNode("SegmentationDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No SegmentationDataId tag specified."); - int id = boost::lexical_cast(node.getContent()); + int id = node.getContentInt(); m_pSegmentation = dynamic_cast(CData2DManager::getSingleton().get(id)); CC.markNodeParsed("SegmentationDataId"); // reconstruction data node = _cfg.self.getSingleNode("MaskDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No MaskDataId tag specified."); - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); m_pMask = dynamic_cast(CData2DManager::getSingleton().get(id)); CC.markNodeParsed("MaskDataId"); diff --git a/src/CudaDartMaskAlgorithm3D.cpp b/src/CudaDartMaskAlgorithm3D.cpp index b0dfc5b..dd12c58 100644 --- a/src/CudaDartMaskAlgorithm3D.cpp +++ b/src/CudaDartMaskAlgorithm3D.cpp @@ -34,7 +34,6 @@ $Id$ #include "../cuda/3d/dims3d.h" #include "astra/AstraObjectManager.h" -#include using namespace std; @@ -67,14 +66,14 @@ bool CCudaDartMaskAlgorithm3D::initialize(const Config& _cfg) // reconstruction data XMLNode node = _cfg.self.getSingleNode("SegmentationDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No SegmentationDataId tag specified."); - int id = boost::lexical_cast(node.getContent()); + int id = node.getContentInt(); m_pSegmentation = dynamic_cast(CData3DManager::getSingleton().get(id)); CC.markNodeParsed("SegmentationDataId"); // reconstruction data node = _cfg.self.getSingleNode("MaskDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No MaskDataId tag specified."); - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); m_pMask = dynamic_cast(CData3DManager::getSingleton().get(id)); CC.markNodeParsed("MaskDataId"); diff --git a/src/CudaDartSmoothingAlgorithm.cpp b/src/CudaDartSmoothingAlgorithm.cpp index 7e22809..425f0a3 100644 --- a/src/CudaDartSmoothingAlgorithm.cpp +++ b/src/CudaDartSmoothingAlgorithm.cpp @@ -34,7 +34,6 @@ $Id$ #include "../cuda/2d/algo.h" #include "astra/AstraObjectManager.h" -#include using namespace std; @@ -67,14 +66,14 @@ bool CCudaDartSmoothingAlgorithm::initialize(const Config& _cfg) // reconstruction data XMLNode node = _cfg.self.getSingleNode("InDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No InDataId tag specified."); - int id = boost::lexical_cast(node.getContent()); + int id = node.getContentInt(); m_pIn = dynamic_cast(CData2DManager::getSingleton().get(id)); CC.markNodeParsed("InDataId"); // reconstruction data node = _cfg.self.getSingleNode("OutDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No OutDataId tag specified."); - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); m_pOut = dynamic_cast(CData2DManager::getSingleton().get(id)); CC.markNodeParsed("OutDataId"); diff --git a/src/CudaDartSmoothingAlgorithm3D.cpp b/src/CudaDartSmoothingAlgorithm3D.cpp index 9c4437a..df7e0df 100644 --- a/src/CudaDartSmoothingAlgorithm3D.cpp +++ b/src/CudaDartSmoothingAlgorithm3D.cpp @@ -34,7 +34,6 @@ $Id$ #include "../cuda/3d/dims3d.h" #include "astra/AstraObjectManager.h" -#include using namespace std; @@ -67,14 +66,14 @@ bool CCudaDartSmoothingAlgorithm3D::initialize(const Config& _cfg) // reconstruction data XMLNode node = _cfg.self.getSingleNode("InDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No InDataId tag specified."); - int id = boost::lexical_cast(node.getContent()); + int id = node.getContentInt(); m_pIn = dynamic_cast(CData3DManager::getSingleton().get(id)); CC.markNodeParsed("InDataId"); // reconstruction data node = _cfg.self.getSingleNode("OutDataId"); ASTRA_CONFIG_CHECK(node, "CudaDartMask", "No OutDataId tag specified."); - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); m_pOut = dynamic_cast(CData3DManager::getSingleton().get(id)); CC.markNodeParsed("OutDataId"); diff --git a/src/CudaDataOperationAlgorithm.cpp b/src/CudaDataOperationAlgorithm.cpp index ae133c2..15886a4 100644 --- a/src/CudaDataOperationAlgorithm.cpp +++ b/src/CudaDataOperationAlgorithm.cpp @@ -35,7 +35,6 @@ $Id$ #include "../cuda/2d/arith.h" #include "astra/AstraObjectManager.h" -#include using namespace std; @@ -78,7 +77,7 @@ bool CCudaDataOperationAlgorithm::initialize(const Config& _cfg) ASTRA_CONFIG_CHECK(node, "CCudaDataOperationAlgorithm", "No DataId tag specified."); vector data = node.getContentArray(); for (vector::iterator it = data.begin(); it != data.end(); it++){ - int id = boost::lexical_cast(*it); + int id = StringUtil::stringToInt(*it); m_pData.push_back(dynamic_cast(CData2DManager::getSingleton().get(id))); } CC.markNodeParsed("DataId"); @@ -97,7 +96,7 @@ bool CCudaDataOperationAlgorithm::initialize(const Config& _cfg) CC.markOptionParsed("GPUIndex"); if (_cfg.self.hasOption("MaskId")) { - int id = boost::lexical_cast(_cfg.self.getOption("MaskId")); + int id = _cfg.self.getOptionInt("MaskId"); m_pMask = dynamic_cast(CData2DManager::getSingleton().get(id)); } CC.markOptionParsed("MaskId"); diff --git a/src/CudaFDKAlgorithm3D.cpp b/src/CudaFDKAlgorithm3D.cpp index 1316daa..b5ce545 100644 --- a/src/CudaFDKAlgorithm3D.cpp +++ b/src/CudaFDKAlgorithm3D.cpp @@ -28,8 +28,6 @@ $Id$ #include "astra/CudaFDKAlgorithm3D.h" -#include - #include "astra/AstraObjectManager.h" #include "astra/CudaProjector3D.h" diff --git a/src/CudaFilteredBackProjectionAlgorithm.cpp b/src/CudaFilteredBackProjectionAlgorithm.cpp index bcd70c4..aa97eec 100644 --- a/src/CudaFilteredBackProjectionAlgorithm.cpp +++ b/src/CudaFilteredBackProjectionAlgorithm.cpp @@ -28,7 +28,6 @@ $Id$ #include #include -#include #include #include "astra/AstraObjectManager.h" @@ -100,7 +99,7 @@ bool CCudaFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) XMLNode node = _cfg.self.getSingleNode("ProjectorId"); CCudaProjector2D* pCudaProjector = 0; if (node) { - int id = boost::lexical_cast(node.getContent()); + int id = node.getContentInt(); CProjector2D *projector = CProjector2DManager::getSingleton().get(id); pCudaProjector = dynamic_cast(projector); if (!pCudaProjector) { @@ -113,14 +112,14 @@ bool CCudaFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) // sinogram data node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "CudaFBP", "No ProjectionDataId tag specified."); - int id = boost::lexical_cast(node.getContent()); + int id = node.getContentInt(); m_pSinogram = dynamic_cast(CData2DManager::getSingleton().get(id)); CC.markNodeParsed("ProjectionDataId"); // reconstruction data node = _cfg.self.getSingleNode("ReconstructionDataId"); ASTRA_CONFIG_CHECK(node, "CudaFBP", "No ReconstructionDataId tag specified."); - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); m_pReconstruction = dynamic_cast(CData2DManager::getSingleton().get(id)); CC.markNodeParsed("ReconstructionDataId"); @@ -140,7 +139,7 @@ bool CCudaFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) node = _cfg.self.getSingleNode("FilterSinogramId"); if (node) { - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); const CFloat32ProjectionData2D * pFilterData = dynamic_cast(CData2DManager::getSingleton().get(id)); m_iFilterWidth = pFilterData->getGeometry()->getDetectorCount(); int iFilterProjectionCount = pFilterData->getGeometry()->getProjectionAngleCount(); @@ -159,7 +158,7 @@ bool CCudaFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) node = _cfg.self.getSingleNode("FilterParameter"); if (node) { - float fParameter = boost::lexical_cast(node.getContent()); + float fParameter = node.getContentNumerical(); m_fFilterParameter = fParameter; } else @@ -172,7 +171,7 @@ bool CCudaFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) node = _cfg.self.getSingleNode("FilterD"); if (node) { - float fD = boost::lexical_cast(node.getContent()); + float fD = node.getContentNumerical(); m_fFilterD = fD; } else diff --git a/src/CudaForwardProjectionAlgorithm.cpp b/src/CudaForwardProjectionAlgorithm.cpp index d38469c..80f2e02 100644 --- a/src/CudaForwardProjectionAlgorithm.cpp +++ b/src/CudaForwardProjectionAlgorithm.cpp @@ -35,8 +35,6 @@ $Id$ #include #include -#include - #include "astra/AstraObjectManager.h" #include "astra/ParallelProjectionGeometry2D.h" #include "astra/FanFlatProjectionGeometry2D.h" @@ -97,7 +95,7 @@ bool CCudaForwardProjectionAlgorithm::initialize(const Config& _cfg) m_pProjector = 0; XMLNode node = _cfg.self.getSingleNode("ProjectorId"); if (node) { - int id = boost::lexical_cast(node.getContent()); + int id = node.getContentInt(); m_pProjector = CProjector2DManager::getSingleton().get(id); } CC.markNodeParsed("ProjectorId"); @@ -107,14 +105,14 @@ bool CCudaForwardProjectionAlgorithm::initialize(const Config& _cfg) // sinogram data node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "FP_CUDA", "No ProjectionDataId tag specified."); - int id = boost::lexical_cast(node.getContent()); + int id = node.getContentInt(); m_pSinogram = dynamic_cast(CData2DManager::getSingleton().get(id)); CC.markNodeParsed("ProjectionDataId"); // volume data node = _cfg.self.getSingleNode("VolumeDataId"); ASTRA_CONFIG_CHECK(node, "FP_CUDA", "No VolumeDataId tag specified."); - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); m_pVolume = dynamic_cast(CData2DManager::getSingleton().get(id)); CC.markNodeParsed("VolumeDataId"); diff --git a/src/CudaForwardProjectionAlgorithm3D.cpp b/src/CudaForwardProjectionAlgorithm3D.cpp index 209f5a5..f709e34 100644 --- a/src/CudaForwardProjectionAlgorithm3D.cpp +++ b/src/CudaForwardProjectionAlgorithm3D.cpp @@ -30,8 +30,6 @@ $Id$ #ifdef ASTRA_CUDA -#include - #include "astra/AstraObjectManager.h" #include "astra/CudaProjector3D.h" @@ -103,14 +101,14 @@ bool CCudaForwardProjectionAlgorithm3D::initialize(const Config& _cfg) // sinogram data node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "CudaForwardProjection3D", "No ProjectionDataId tag specified."); - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); m_pProjections = dynamic_cast(CData3DManager::getSingleton().get(id)); CC.markNodeParsed("ProjectionDataId"); // reconstruction data node = _cfg.self.getSingleNode("VolumeDataId"); ASTRA_CONFIG_CHECK(node, "CudaForwardProjection3D", "No VolumeDataId tag specified."); - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); m_pVolume = dynamic_cast(CData3DManager::getSingleton().get(id)); CC.markNodeParsed("VolumeDataId"); @@ -118,7 +116,7 @@ bool CCudaForwardProjectionAlgorithm3D::initialize(const Config& _cfg) node = _cfg.self.getSingleNode("ProjectorId"); m_pProjector = 0; if (node) { - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); m_pProjector = CProjector3DManager::getSingleton().get(id); } CC.markNodeParsed("ProjectorId"); diff --git a/src/CudaReconstructionAlgorithm2D.cpp b/src/CudaReconstructionAlgorithm2D.cpp index 71dddf7..5a1910c 100644 --- a/src/CudaReconstructionAlgorithm2D.cpp +++ b/src/CudaReconstructionAlgorithm2D.cpp @@ -30,8 +30,6 @@ $Id$ #include "astra/CudaReconstructionAlgorithm2D.h" -#include - #include "astra/AstraObjectManager.h" #include "astra/FanFlatProjectionGeometry2D.h" #include "astra/FanFlatVecProjectionGeometry2D.h" diff --git a/src/CudaRoiSelectAlgorithm.cpp b/src/CudaRoiSelectAlgorithm.cpp index 7635c69..dfb8056 100644 --- a/src/CudaRoiSelectAlgorithm.cpp +++ b/src/CudaRoiSelectAlgorithm.cpp @@ -34,7 +34,6 @@ $Id$ #include "../cuda/2d/algo.h" #include "astra/AstraObjectManager.h" -#include using namespace std; @@ -68,7 +67,7 @@ bool CCudaRoiSelectAlgorithm::initialize(const Config& _cfg) // reconstruction data XMLNode node = _cfg.self.getSingleNode("DataId"); ASTRA_CONFIG_CHECK(node, "CudaRoiSelect", "No DataId tag specified."); - int id = boost::lexical_cast(node.getContent()); + int id = node.getContentInt(); m_pData = dynamic_cast(CData2DManager::getSingleton().get(id)); CC.markNodeParsed("DataId"); diff --git a/src/CudaSirtAlgorithm.cpp b/src/CudaSirtAlgorithm.cpp index ab0a418..33e381a 100644 --- a/src/CudaSirtAlgorithm.cpp +++ b/src/CudaSirtAlgorithm.cpp @@ -30,7 +30,6 @@ $Id$ #include "astra/CudaSirtAlgorithm.h" -#include #include "astra/AstraObjectManager.h" #include "../cuda/2d/sirt.h" @@ -77,12 +76,12 @@ bool CCudaSirtAlgorithm::initialize(const Config& _cfg) // min/max masks if (_cfg.self.hasOption("MinMaskId")) { - int id = boost::lexical_cast(_cfg.self.getOption("MinMaskId")); + int id = _cfg.self.getOptionInt("MinMaskId"); m_pMinMask = dynamic_cast(CData2DManager::getSingleton().get(id)); } CC.markOptionParsed("MinMaskId"); if (_cfg.self.hasOption("MaxMaskId")) { - int id = boost::lexical_cast(_cfg.self.getOption("MaxMaskId")); + int id = _cfg.self.getOptionInt("MaxMaskId"); m_pMaxMask = dynamic_cast(CData2DManager::getSingleton().get(id)); } CC.markOptionParsed("MaxMaskId"); diff --git a/src/CudaSirtAlgorithm3D.cpp b/src/CudaSirtAlgorithm3D.cpp index 1fa0da2..605c470 100644 --- a/src/CudaSirtAlgorithm3D.cpp +++ b/src/CudaSirtAlgorithm3D.cpp @@ -28,8 +28,6 @@ $Id$ #include "astra/CudaSirtAlgorithm3D.h" -#include - #include "astra/AstraObjectManager.h" #include "astra/ConeProjectionGeometry3D.h" diff --git a/src/FanFlatBeamLineKernelProjector2D.cpp b/src/FanFlatBeamLineKernelProjector2D.cpp index 0681715..fd4195b 100644 --- a/src/FanFlatBeamLineKernelProjector2D.cpp +++ b/src/FanFlatBeamLineKernelProjector2D.cpp @@ -30,7 +30,6 @@ $Id$ #include #include -#include #include "astra/DataProjectorPolicies.h" diff --git a/src/FanFlatBeamStripKernelProjector2D.cpp b/src/FanFlatBeamStripKernelProjector2D.cpp index e94d3da..b48beab 100644 --- a/src/FanFlatBeamStripKernelProjector2D.cpp +++ b/src/FanFlatBeamStripKernelProjector2D.cpp @@ -29,7 +29,6 @@ $Id$ #include "astra/FanFlatBeamStripKernelProjector2D.h" #include -#include #include "astra/DataProjectorPolicies.h" diff --git a/src/FanFlatProjectionGeometry2D.cpp b/src/FanFlatProjectionGeometry2D.cpp index 32a19bc..8bee0d6 100644 --- a/src/FanFlatProjectionGeometry2D.cpp +++ b/src/FanFlatProjectionGeometry2D.cpp @@ -30,7 +30,6 @@ $Id$ #include #include -#include using namespace std; @@ -136,13 +135,13 @@ bool CFanFlatProjectionGeometry2D::initialize(const Config& _cfg) // Required: DistanceOriginDetector XMLNode node = _cfg.self.getSingleNode("DistanceOriginDetector"); ASTRA_CONFIG_CHECK(node, "FanFlatProjectionGeometry2D", "No DistanceOriginDetector tag specified."); - m_fOriginDetectorDistance = boost::lexical_cast(node.getContent()); + m_fOriginDetectorDistance = node.getContentNumerical(); CC.markNodeParsed("DistanceOriginDetector"); // Required: DetectorOriginSource node = _cfg.self.getSingleNode("DistanceOriginSource"); ASTRA_CONFIG_CHECK(node, "FanFlatProjectionGeometry2D", "No DistanceOriginSource tag specified."); - m_fOriginSourceDistance = boost::lexical_cast(node.getContent()); + m_fOriginSourceDistance = node.getContentNumerical(); CC.markNodeParsed("DistanceOriginSource"); // success diff --git a/src/FanFlatVecProjectionGeometry2D.cpp b/src/FanFlatVecProjectionGeometry2D.cpp index 4104379..0b76fc5 100644 --- a/src/FanFlatVecProjectionGeometry2D.cpp +++ b/src/FanFlatVecProjectionGeometry2D.cpp @@ -30,7 +30,6 @@ $Id$ #include #include -#include using namespace std; @@ -125,7 +124,7 @@ bool CFanFlatVecProjectionGeometry2D::initialize(const Config& _cfg) // Required: DetectorCount node = _cfg.self.getSingleNode("DetectorCount"); ASTRA_CONFIG_CHECK(node, "FanFlatVecProjectionGeometry3D", "No DetectorRowCount tag specified."); - m_iDetectorCount = boost::lexical_cast(node.getContent()); + m_iDetectorCount = node.getContentInt(); CC.markNodeParsed("DetectorCount"); // Required: Vectors @@ -235,12 +234,12 @@ Config* CFanFlatVecProjectionGeometry2D::getConfiguration() const std::string vectors = ""; for (int i = 0; i < m_iProjectionAngleCount; ++i) { SFanProjection& p = m_pProjectionAngles[i]; - vectors += boost::lexical_cast(p.fSrcX) + ","; - vectors += boost::lexical_cast(p.fSrcY) + ","; - vectors += boost::lexical_cast(p.fDetSX + 0.5f * m_iDetectorCount * p.fDetUX) + ","; - vectors += boost::lexical_cast(p.fDetSY + 0.5f * m_iDetectorCount * p.fDetUY) + ","; - vectors += boost::lexical_cast(p.fDetUX) + ","; - vectors += boost::lexical_cast(p.fDetUY); + vectors += StringUtil::toString(p.fSrcX) + ","; + vectors += StringUtil::toString(p.fSrcY) + ","; + vectors += StringUtil::toString(p.fDetSX + 0.5f * m_iDetectorCount * p.fDetUX) + ","; + vectors += StringUtil::toString(p.fDetSY + 0.5f * m_iDetectorCount * p.fDetUY) + ","; + vectors += StringUtil::toString(p.fDetUX) + ","; + vectors += StringUtil::toString(p.fDetUY); if (i < m_iProjectionAngleCount-1) vectors += ';'; } cfg->self.addChildNode("Vectors", vectors); diff --git a/src/FilteredBackProjectionAlgorithm.cpp b/src/FilteredBackProjectionAlgorithm.cpp index f494d22..c195578 100644 --- a/src/FilteredBackProjectionAlgorithm.cpp +++ b/src/FilteredBackProjectionAlgorithm.cpp @@ -28,8 +28,6 @@ $Id$ #include "astra/FilteredBackProjectionAlgorithm.h" -#include - #include #include #include @@ -96,19 +94,19 @@ bool CFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) // projector XMLNode node = _cfg.self.getSingleNode("ProjectorId"); ASTRA_CONFIG_CHECK(node, "FilteredBackProjection", "No ProjectorId tag specified."); - int id = boost::lexical_cast(node.getContent()); + int id = node.getContentInt(); m_pProjector = CProjector2DManager::getSingleton().get(id); // sinogram data node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "FilteredBackProjection", "No ProjectionDataId tag specified."); - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); m_pSinogram = dynamic_cast(CData2DManager::getSingleton().get(id)); // volume data node = _cfg.self.getSingleNode("ReconstructionDataId"); ASTRA_CONFIG_CHECK(node, "FilteredBackProjection", "No ReconstructionDataId tag specified."); - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); m_pReconstruction = dynamic_cast(CData2DManager::getSingleton().get(id)); node = _cfg.self.getSingleNode("ProjectionIndex"); diff --git a/src/ForwardProjectionAlgorithm.cpp b/src/ForwardProjectionAlgorithm.cpp index f356824..dcf5790 100644 --- a/src/ForwardProjectionAlgorithm.cpp +++ b/src/ForwardProjectionAlgorithm.cpp @@ -28,8 +28,6 @@ $Id$ #include "astra/ForwardProjectionAlgorithm.h" -#include - #include "astra/AstraObjectManager.h" #include "astra/DataProjectorPolicies.h" @@ -128,32 +126,32 @@ bool CForwardProjectionAlgorithm::initialize(const Config& _cfg) // projector XMLNode node = _cfg.self.getSingleNode("ProjectorId"); ASTRA_CONFIG_CHECK(node, "ForwardProjection", "No ProjectorId tag specified."); - int id = boost::lexical_cast(node.getContent()); + int id = node.getContentInt(); m_pProjector = CProjector2DManager::getSingleton().get(id); // sinogram data node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "ForwardProjection", "No ProjectionDataId tag specified."); - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); m_pSinogram = dynamic_cast(CData2DManager::getSingleton().get(id)); // volume data node = _cfg.self.getSingleNode("VolumeDataId"); ASTRA_CONFIG_CHECK(node, "ForwardProjection", "No VolumeDataId tag specified."); - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); m_pVolume = dynamic_cast(CData2DManager::getSingleton().get(id)); // volume mask if (_cfg.self.hasOption("VolumeMaskId")) { m_bUseVolumeMask = true; - id = boost::lexical_cast(_cfg.self.getOption("VolumeMaskId")); + id = _cfg.self.getOptionInt("VolumeMaskId"); m_pVolumeMask = dynamic_cast(CData2DManager::getSingleton().get(id)); } // sino mask if (_cfg.self.hasOption("SinogramMaskId")) { m_bUseSinogramMask = true; - id = boost::lexical_cast(_cfg.self.getOption("SinogramMaskId")); + id = _cfg.self.getOptionInt("SinogramMaskId"); m_pSinogramMask = dynamic_cast(CData2DManager::getSingleton().get(id)); } diff --git a/src/ParallelBeamBlobKernelProjector2D.cpp b/src/ParallelBeamBlobKernelProjector2D.cpp index 4559a48..679d5c6 100644 --- a/src/ParallelBeamBlobKernelProjector2D.cpp +++ b/src/ParallelBeamBlobKernelProjector2D.cpp @@ -29,7 +29,6 @@ $Id$ #include "astra/ParallelBeamBlobKernelProjector2D.h" #include -#include #include "astra/DataProjectorPolicies.h" @@ -134,17 +133,17 @@ bool CParallelBeamBlobKernelProjector2D::initialize(const Config& _cfg) // Required: KernelSize XMLNode node2 = node.getSingleNode("KernelSize"); ASTRA_CONFIG_CHECK(node2, "BlobProjector", "No Kernel/KernelSize tag specified."); - m_fBlobSize = boost::lexical_cast(node2.getContent()); + m_fBlobSize = node2.getContentNumerical(); // Required: SampleRate node2 = node.getSingleNode("SampleRate"); ASTRA_CONFIG_CHECK(node2, "BlobProjector", "No Kernel/SampleRate tag specified."); - m_fBlobSampleRate = boost::lexical_cast(node2.getContent()); + m_fBlobSampleRate = node2.getContentNumerical(); // Required: SampleCount node2 = node.getSingleNode("SampleCount"); ASTRA_CONFIG_CHECK(node2, "BlobProjector", "No Kernel/SampleCount tag specified."); - m_iBlobSampleCount = boost::lexical_cast(node2.getContent()); + m_iBlobSampleCount = node2.getContentInt(); // Required: KernelValues node2 = node.getSingleNode("KernelValues"); diff --git a/src/ParallelBeamLineKernelProjector2D.cpp b/src/ParallelBeamLineKernelProjector2D.cpp index 5a23413..e4a1bff 100644 --- a/src/ParallelBeamLineKernelProjector2D.cpp +++ b/src/ParallelBeamLineKernelProjector2D.cpp @@ -29,7 +29,6 @@ $Id$ #include "astra/ParallelBeamLineKernelProjector2D.h" #include -#include #include "astra/DataProjectorPolicies.h" diff --git a/src/ParallelBeamLinearKernelProjector2D.cpp b/src/ParallelBeamLinearKernelProjector2D.cpp index a710664..27aa168 100644 --- a/src/ParallelBeamLinearKernelProjector2D.cpp +++ b/src/ParallelBeamLinearKernelProjector2D.cpp @@ -29,7 +29,6 @@ $Id$ #include "astra/ParallelBeamLinearKernelProjector2D.h" #include -#include #include "astra/DataProjectorPolicies.h" diff --git a/src/ParallelBeamStripKernelProjector2D.cpp b/src/ParallelBeamStripKernelProjector2D.cpp index 44c6fec..3f4e7f3 100644 --- a/src/ParallelBeamStripKernelProjector2D.cpp +++ b/src/ParallelBeamStripKernelProjector2D.cpp @@ -29,7 +29,6 @@ $Id$ #include "astra/ParallelBeamStripKernelProjector2D.h" #include -#include #include "astra/DataProjectorPolicies.h" diff --git a/src/ParallelProjectionGeometry2D.cpp b/src/ParallelProjectionGeometry2D.cpp index 7260b83..cc2a129 100644 --- a/src/ParallelProjectionGeometry2D.cpp +++ b/src/ParallelProjectionGeometry2D.cpp @@ -27,7 +27,6 @@ $Id$ */ #include "astra/ParallelProjectionGeometry2D.h" -#include #include diff --git a/src/ParallelProjectionGeometry3D.cpp b/src/ParallelProjectionGeometry3D.cpp index 7b64fd9..2f80883 100644 --- a/src/ParallelProjectionGeometry3D.cpp +++ b/src/ParallelProjectionGeometry3D.cpp @@ -30,7 +30,6 @@ $Id$ #include "astra/GeometryUtil3D.h" -#include #include using namespace std; diff --git a/src/ParallelVecProjectionGeometry3D.cpp b/src/ParallelVecProjectionGeometry3D.cpp index d04400b..3172818 100644 --- a/src/ParallelVecProjectionGeometry3D.cpp +++ b/src/ParallelVecProjectionGeometry3D.cpp @@ -27,9 +27,9 @@ $Id$ */ #include "astra/ParallelVecProjectionGeometry3D.h" +#include "astra/Utilities.h" #include -#include using namespace std; @@ -82,13 +82,13 @@ bool CParallelVecProjectionGeometry3D::initialize(const Config& _cfg) // Required: DetectorRowCount node = _cfg.self.getSingleNode("DetectorRowCount"); ASTRA_CONFIG_CHECK(node, "ParallelVecProjectionGeometry3D", "No DetectorRowCount tag specified."); - m_iDetectorRowCount = boost::lexical_cast(node.getContent()); + m_iDetectorRowCount = node.getContentInt(); CC.markNodeParsed("DetectorRowCount"); // Required: DetectorCount node = _cfg.self.getSingleNode("DetectorColCount"); ASTRA_CONFIG_CHECK(node, "", "No DetectorColCount tag specified."); - m_iDetectorColCount = boost::lexical_cast(node.getContent()); + m_iDetectorColCount = node.getContentInt(); m_iDetectorTotCount = m_iDetectorRowCount * m_iDetectorColCount; CC.markNodeParsed("DetectorColCount"); @@ -212,18 +212,18 @@ Config* CParallelVecProjectionGeometry3D::getConfiguration() const std::string vectors = ""; for (int i = 0; i < m_iProjectionAngleCount; ++i) { SPar3DProjection& p = m_pProjectionAngles[i]; - vectors += boost::lexical_cast(p.fRayX) + ","; - vectors += boost::lexical_cast(p.fRayY) + ","; - vectors += boost::lexical_cast(p.fRayZ) + ","; - vectors += boost::lexical_cast(p.fDetSX + 0.5f*m_iDetectorRowCount*p.fDetVX + 0.5f*m_iDetectorColCount*p.fDetUX) + ","; - vectors += boost::lexical_cast(p.fDetSY + 0.5f*m_iDetectorRowCount*p.fDetVY + 0.5f*m_iDetectorColCount*p.fDetUY) + ","; - vectors += boost::lexical_cast(p.fDetSZ + 0.5f*m_iDetectorRowCount*p.fDetVZ + 0.5f*m_iDetectorColCount*p.fDetUZ) + ","; - vectors += boost::lexical_cast(p.fDetUX) + ","; - vectors += boost::lexical_cast(p.fDetUY) + ","; - vectors += boost::lexical_cast(p.fDetUZ) + ","; - vectors += boost::lexical_cast(p.fDetVX) + ","; - vectors += boost::lexical_cast(p.fDetVY) + ","; - vectors += boost::lexical_cast(p.fDetVZ); + vectors += StringUtil::toString(p.fRayX) + ","; + vectors += StringUtil::toString(p.fRayY) + ","; + vectors += StringUtil::toString(p.fRayZ) + ","; + vectors += StringUtil::toString(p.fDetSX + 0.5f*m_iDetectorRowCount*p.fDetVX + 0.5f*m_iDetectorColCount*p.fDetUX) + ","; + vectors += StringUtil::toString(p.fDetSY + 0.5f*m_iDetectorRowCount*p.fDetVY + 0.5f*m_iDetectorColCount*p.fDetUY) + ","; + vectors += StringUtil::toString(p.fDetSZ + 0.5f*m_iDetectorRowCount*p.fDetVZ + 0.5f*m_iDetectorColCount*p.fDetUZ) + ","; + vectors += StringUtil::toString(p.fDetUX) + ","; + vectors += StringUtil::toString(p.fDetUY) + ","; + vectors += StringUtil::toString(p.fDetUZ) + ","; + vectors += StringUtil::toString(p.fDetVX) + ","; + vectors += StringUtil::toString(p.fDetVY) + ","; + vectors += StringUtil::toString(p.fDetVZ); if (i < m_iProjectionAngleCount-1) vectors += ';'; } cfg->self.addChildNode("Vectors", vectors); diff --git a/src/PluginAlgorithm.cpp b/src/PluginAlgorithm.cpp index 8f7dfc5..9fc511a 100644 --- a/src/PluginAlgorithm.cpp +++ b/src/PluginAlgorithm.cpp @@ -30,9 +30,9 @@ $Id$ #include "astra/PluginAlgorithm.h" #include "astra/Logging.h" +#include "astra/Utilities.h" #include #include -#include #include #include #include @@ -338,7 +338,7 @@ PyObject* stringToPythonValue(std::string str){ boost::split(row, rows[i], boost::is_any_of(",")); PyObject *rowlist = PyList_New(row.size()); for(unsigned int j=0;j(row[j]))); + PyList_SetItem(rowlist, j, PyFloat_FromDouble(StringUtil::stringToDouble(row[j]))); } PyList_SetItem(mat, i, rowlist); } @@ -349,16 +349,16 @@ PyObject* stringToPythonValue(std::string str){ boost::split(vec, str, boost::is_any_of(",")); PyObject *veclist = PyList_New(vec.size()); for(unsigned int i=0;i(vec[i]))); + PyList_SetItem(veclist, i, PyFloat_FromDouble(StringUtil::stringToDouble(vec[i]))); } return veclist; } try{ - return PyLong_FromLong(boost::lexical_cast(str)); - }catch(const boost::bad_lexical_cast &){ + return PyLong_FromLong(StringUtil::stringToInt(str)); + }catch(const StringUtil::bad_cast &){ try{ - return PyFloat_FromDouble(boost::lexical_cast(str)); - }catch(const boost::bad_lexical_cast &){ + return PyFloat_FromDouble(StringUtil::stringToDouble(str)); + }catch(const StringUtil::bad_cast &){ return pyStringFromString(str); } } diff --git a/src/ProjectionGeometry2D.cpp b/src/ProjectionGeometry2D.cpp index b89605b..8ce06dc 100644 --- a/src/ProjectionGeometry2D.cpp +++ b/src/ProjectionGeometry2D.cpp @@ -28,8 +28,6 @@ $Id$ #include "astra/ProjectionGeometry2D.h" -#include - using namespace std; namespace astra @@ -126,13 +124,13 @@ bool CProjectionGeometry2D::initialize(const Config& _cfg) // Required: DetectorWidth XMLNode node = _cfg.self.getSingleNode("DetectorWidth"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry2D", "No DetectorWidth tag specified."); - m_fDetectorWidth = boost::lexical_cast(node.getContent()); + m_fDetectorWidth = node.getContentNumerical(); CC.markNodeParsed("DetectorWidth"); // Required: DetectorCount node = _cfg.self.getSingleNode("DetectorCount"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry2D", "No DetectorCount tag specified."); - m_iDetectorCount = boost::lexical_cast(node.getContent()); + m_iDetectorCount = node.getContentInt(); CC.markNodeParsed("DetectorCount"); // Required: ProjectionAngles diff --git a/src/ProjectionGeometry3D.cpp b/src/ProjectionGeometry3D.cpp index ef0246c..281db7c 100644 --- a/src/ProjectionGeometry3D.cpp +++ b/src/ProjectionGeometry3D.cpp @@ -28,8 +28,6 @@ $Id$ #include "astra/ProjectionGeometry3D.h" -#include - using namespace std; namespace astra @@ -151,25 +149,25 @@ bool CProjectionGeometry3D::initialize(const Config& _cfg) // Required: DetectorWidth XMLNode node = _cfg.self.getSingleNode("DetectorSpacingX"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry3D", "No DetectorSpacingX tag specified."); - m_fDetectorSpacingX = boost::lexical_cast(node.getContent()); + m_fDetectorSpacingX = node.getContentNumerical(); CC.markNodeParsed("DetectorSpacingX"); // Required: DetectorHeight node = _cfg.self.getSingleNode("DetectorSpacingY"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry3D", "No DetectorSpacingY tag specified."); - m_fDetectorSpacingY = boost::lexical_cast(node.getContent()); + m_fDetectorSpacingY = node.getContentNumerical(); CC.markNodeParsed("DetectorSpacingY"); // Required: DetectorRowCount node = _cfg.self.getSingleNode("DetectorRowCount"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry3D", "No DetectorRowCount tag specified."); - m_iDetectorRowCount = boost::lexical_cast(node.getContent()); + m_iDetectorRowCount = node.getContentInt(); CC.markNodeParsed("DetectorRowCount"); // Required: DetectorCount node = _cfg.self.getSingleNode("DetectorColCount"); ASTRA_CONFIG_CHECK(node, "ProjectionGeometry3D", "No DetectorColCount tag specified."); - m_iDetectorColCount = boost::lexical_cast(node.getContent()); + m_iDetectorColCount = node.getContentInt(); m_iDetectorTotCount = m_iDetectorRowCount * m_iDetectorColCount; CC.markNodeParsed("DetectorColCount"); diff --git a/src/ReconstructionAlgorithm2D.cpp b/src/ReconstructionAlgorithm2D.cpp index 4575ff7..1c6d855 100644 --- a/src/ReconstructionAlgorithm2D.cpp +++ b/src/ReconstructionAlgorithm2D.cpp @@ -28,8 +28,6 @@ $Id$ #include "astra/ReconstructionAlgorithm2D.h" -#include - #include "astra/AstraObjectManager.h" using namespace std; @@ -90,7 +88,7 @@ bool CReconstructionAlgorithm2D::initialize(const Config& _cfg) } int id; if (node) { - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); m_pProjector = CProjector2DManager::getSingleton().get(id); } else { m_pProjector = 0; @@ -100,21 +98,21 @@ bool CReconstructionAlgorithm2D::initialize(const Config& _cfg) // sinogram data node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "Reconstruction2D", "No ProjectionDataId tag specified."); - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); m_pSinogram = dynamic_cast(CData2DManager::getSingleton().get(id)); CC.markNodeParsed("ProjectionDataId"); // reconstruction data node = _cfg.self.getSingleNode("ReconstructionDataId"); ASTRA_CONFIG_CHECK(node, "Reconstruction2D", "No ReconstructionDataId tag specified."); - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); m_pReconstruction = dynamic_cast(CData2DManager::getSingleton().get(id)); CC.markNodeParsed("ReconstructionDataId"); // fixed mask if (_cfg.self.hasOption("ReconstructionMaskId")) { m_bUseReconstructionMask = true; - id = boost::lexical_cast(_cfg.self.getOption("ReconstructionMaskId")); + id = _cfg.self.getOptionInt("ReconstructionMaskId"); m_pReconstructionMask = dynamic_cast(CData2DManager::getSingleton().get(id)); ASTRA_CONFIG_CHECK(m_pReconstructionMask, "Reconstruction2D", "Invalid ReconstructionMaskId."); } @@ -123,7 +121,7 @@ bool CReconstructionAlgorithm2D::initialize(const Config& _cfg) // fixed mask if (_cfg.self.hasOption("SinogramMaskId")) { m_bUseSinogramMask = true; - id = boost::lexical_cast(_cfg.self.getOption("SinogramMaskId")); + id = _cfg.self.getOptionInt("SinogramMaskId"); m_pSinogramMask = dynamic_cast(CData2DManager::getSingleton().get(id)); ASTRA_CONFIG_CHECK(m_pSinogramMask, "Reconstruction2D", "Invalid SinogramMaskId."); } diff --git a/src/ReconstructionAlgorithm3D.cpp b/src/ReconstructionAlgorithm3D.cpp index 13d4b07..55f1031 100644 --- a/src/ReconstructionAlgorithm3D.cpp +++ b/src/ReconstructionAlgorithm3D.cpp @@ -28,8 +28,6 @@ $Id$ #include "astra/ReconstructionAlgorithm3D.h" -#include - #include "astra/AstraObjectManager.h" using namespace std; @@ -111,7 +109,7 @@ bool CReconstructionAlgorithm3D::initialize(const Config& _cfg) node = _cfg.self.getSingleNode("ProjectorId"); m_pProjector = 0; if (node) { - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); m_pProjector = CProjector3DManager::getSingleton().get(id); if (!m_pProjector) { // TODO: Report @@ -122,21 +120,21 @@ bool CReconstructionAlgorithm3D::initialize(const Config& _cfg) // sinogram data node = _cfg.self.getSingleNode("ProjectionDataId"); ASTRA_CONFIG_CHECK(node, "Reconstruction3D", "No ProjectionDataId tag specified."); - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); m_pSinogram = dynamic_cast(CData3DManager::getSingleton().get(id)); CC.markNodeParsed("ProjectionDataId"); // reconstruction data node = _cfg.self.getSingleNode("ReconstructionDataId"); ASTRA_CONFIG_CHECK(node, "Reconstruction3D", "No ReconstructionDataId tag specified."); - id = boost::lexical_cast(node.getContent()); + id = node.getContentInt(); m_pReconstruction = dynamic_cast(CData3DManager::getSingleton().get(id)); CC.markNodeParsed("ReconstructionDataId"); // fixed mask if (_cfg.self.hasOption("ReconstructionMaskId")) { m_bUseReconstructionMask = true; - id = boost::lexical_cast(_cfg.self.getOption("ReconstructionMaskId")); + id = _cfg.self.getOptionInt("ReconstructionMaskId"); m_pReconstructionMask = dynamic_cast(CData3DManager::getSingleton().get(id)); } CC.markOptionParsed("ReconstructionMaskId"); @@ -144,7 +142,7 @@ bool CReconstructionAlgorithm3D::initialize(const Config& _cfg) // fixed mask if (_cfg.self.hasOption("SinogramMaskId")) { m_bUseSinogramMask = true; - id = boost::lexical_cast(_cfg.self.getOption("SinogramMaskId")); + id = _cfg.self.getOptionInt("SinogramMaskId"); m_pSinogramMask = dynamic_cast(CData3DManager::getSingleton().get(id)); } CC.markOptionParsed("SinogramMaskId"); diff --git a/src/ReconstructionAlgorithmMultiSlice2D.cpp b/src/ReconstructionAlgorithmMultiSlice2D.cpp index fe64c86..39c337f 100644 --- a/src/ReconstructionAlgorithmMultiSlice2D.cpp +++ b/src/ReconstructionAlgorithmMultiSlice2D.cpp @@ -28,8 +28,6 @@ $Id$ #include "astra/ReconstructionAlgorithmMultiSlice2D.h" -#include - #include "astra/AstraObjectManager.h" using namespace std; @@ -96,7 +94,7 @@ bool CReconstructionAlgorithmMultiSlice2D::initialize(const Config& _cfg) // projector XMLNode* node = _cfg.self->getSingleNode("ProjectorId"); ASTRA_CONFIG_CHECK(node, "Reconstruction2D", "No ProjectorId tag specified."); - int id = boost::lexical_cast(node->getContent()); + int id = node->getContentInt(); m_pProjector = CProjector2DManager::getSingleton().get(id); ASTRA_DELETE(node); CC.markNodeParsed("ProjectorId"); @@ -125,7 +123,7 @@ bool CReconstructionAlgorithmMultiSlice2D::initialize(const Config& _cfg) // reconstruction masks if (_cfg.self->hasOption("ReconstructionMaskId")) { m_bUseReconstructionMask = true; - id = boost::lexical_cast(_cfg.self->getOption("ReconstructionMaskId")); + id = _cfg.self->getOptionInt("ReconstructionMaskId"); m_pReconstructionMask = dynamic_cast(CData2DManager::getSingleton().get(id)); } CC.markOptionParsed("ReconstructionMaskId"); @@ -133,7 +131,7 @@ bool CReconstructionAlgorithmMultiSlice2D::initialize(const Config& _cfg) // sinogram masks if (_cfg.self->hasOption("SinogramMaskId")) { m_bUseSinogramMask = true; - id = boost::lexical_cast(_cfg.self->getOption("SinogramMaskId")); + id = _cfg.self->getOptionInt("SinogramMaskId"); m_pSinogramMask = dynamic_cast(CData2DManager::getSingleton().get(id)); } CC.markOptionParsed("SinogramMaskId"); diff --git a/src/SartAlgorithm.cpp b/src/SartAlgorithm.cpp index e4dc5c7..9346160 100644 --- a/src/SartAlgorithm.cpp +++ b/src/SartAlgorithm.cpp @@ -28,8 +28,6 @@ $Id$ #include "astra/SartAlgorithm.h" -#include - #include "astra/AstraObjectManager.h" #include "astra/DataProjectorPolicies.h" diff --git a/src/SirtAlgorithm.cpp b/src/SirtAlgorithm.cpp index ae3b3bc..d9f3a65 100644 --- a/src/SirtAlgorithm.cpp +++ b/src/SirtAlgorithm.cpp @@ -28,8 +28,6 @@ $Id$ #include "astra/SirtAlgorithm.h" -#include - #include "astra/AstraObjectManager.h" #include "astra/DataProjectorPolicies.h" diff --git a/src/SparseMatrixProjectionGeometry2D.cpp b/src/SparseMatrixProjectionGeometry2D.cpp index 073720f..358c992 100644 --- a/src/SparseMatrixProjectionGeometry2D.cpp +++ b/src/SparseMatrixProjectionGeometry2D.cpp @@ -28,7 +28,6 @@ $Id$ #include "astra/SparseMatrixProjectionGeometry2D.h" -#include #include "astra/AstraObjectManager.h" @@ -100,7 +99,7 @@ bool CSparseMatrixProjectionGeometry2D::initialize(const Config& _cfg) // get matrix XMLNode node = _cfg.self.getSingleNode("MatrixID"); ASTRA_CONFIG_CHECK(node, "SparseMatrixProjectionGeometry2D", "No MatrixID tag specified."); - int id = boost::lexical_cast(node.getContent()); + int id = node.getContentInt(); m_pMatrix = CMatrixManager::getSingleton().get(id); CC.markNodeParsed("MatrixID"); diff --git a/src/SparseMatrixProjector2D.cpp b/src/SparseMatrixProjector2D.cpp index bc2e974..be7e069 100644 --- a/src/SparseMatrixProjector2D.cpp +++ b/src/SparseMatrixProjector2D.cpp @@ -29,7 +29,6 @@ $Id$ #include "astra/SparseMatrixProjector2D.h" #include -#include #include "astra/DataProjectorPolicies.h" diff --git a/src/Utilities.cpp b/src/Utilities.cpp index cb54e93..4b80503 100644 --- a/src/Utilities.cpp +++ b/src/Utilities.cpp @@ -28,4 +28,99 @@ $Id$ #include "astra/Utilities.h" +#include +#include +#include +#include +#include +#include + +namespace astra { + +namespace StringUtil { + +int stringToInt(const std::string& s) +{ + double i; + std::istringstream iss(s); + iss.imbue(std::locale::classic()); + iss >> i; + if (iss.fail() || !iss.eof()) + throw bad_cast(); + return i; + +} + +float stringToFloat(const std::string& s) +{ + return (float)stringToDouble(s); +} + +double stringToDouble(const std::string& s) +{ + double f; + std::istringstream iss(s); + iss.imbue(std::locale::classic()); + iss >> f; + if (iss.fail() || !iss.eof()) + throw bad_cast(); + return f; +} + +template<> float stringTo(const std::string& s) { return stringToFloat(s); } +template<> double stringTo(const std::string& s) { return stringToDouble(s); } + +std::vector stringToFloatVector(const std::string &s) +{ + return stringToVector(s); +} + +std::vector stringToDoubleVector(const std::string &s) +{ + return stringToVector(s); +} + +template +std::vector stringToVector(const std::string& s) +{ + // split + std::vector items; + boost::split(items, s, boost::is_any_of(",;")); + + // init list + std::vector out; + out.resize(items.size()); + + // loop elements + for (unsigned int i = 0; i < items.size(); i++) { + out[i] = stringTo(items[i]); + } + return out; +} + + +std::string floatToString(float f) +{ + std::ostringstream s; + s.imbue(std::locale::classic()); + s << std::setprecision(9) << f; + return s.str(); +} + +std::string doubleToString(double f) +{ + std::ostringstream s; + s.imbue(std::locale::classic()); + s << std::setprecision(17) << f; + return s.str(); +} + + +template<> std::string toString(float f) { return floatToString(f); } +template<> std::string toString(double f) { return doubleToString(f); } + + +} + +} diff --git a/src/VolumeGeometry2D.cpp b/src/VolumeGeometry2D.cpp index 6eea1b2..9d74e47 100644 --- a/src/VolumeGeometry2D.cpp +++ b/src/VolumeGeometry2D.cpp @@ -28,7 +28,6 @@ $Id$ #include "astra/VolumeGeometry2D.h" -#include #include namespace astra @@ -166,13 +165,13 @@ bool CVolumeGeometry2D::initialize(const Config& _cfg) // Required: GridColCount XMLNode node = _cfg.self.getSingleNode("GridColCount"); ASTRA_CONFIG_CHECK(node, "ReconstructionGeometry2D", "No GridColCount tag specified."); - m_iGridColCount = boost::lexical_cast(node.getContent()); + m_iGridColCount = node.getContentInt(); CC.markNodeParsed("GridColCount"); // Required: GridRowCount node = _cfg.self.getSingleNode("GridRowCount"); ASTRA_CONFIG_CHECK(node, "ReconstructionGeometry2D", "No GridRowCount tag specified."); - m_iGridRowCount = boost::lexical_cast(node.getContent()); + m_iGridRowCount = node.getContentInt(); CC.markNodeParsed("GridRowCount"); // Optional: Window minima and maxima diff --git a/src/VolumeGeometry3D.cpp b/src/VolumeGeometry3D.cpp index 3de146f..5d72c24 100644 --- a/src/VolumeGeometry3D.cpp +++ b/src/VolumeGeometry3D.cpp @@ -28,8 +28,6 @@ $Id$ #include "astra/VolumeGeometry3D.h" -#include - namespace astra { @@ -196,19 +194,19 @@ bool CVolumeGeometry3D::initialize(const Config& _cfg) // Required: GridColCount XMLNode node = _cfg.self.getSingleNode("GridColCount"); ASTRA_CONFIG_CHECK(node, "ReconstructionGeometry2D", "No GridColCount tag specified."); - m_iGridColCount = boost::lexical_cast(node.getContent()); + m_iGridColCount = node.getContentInt(); CC.markNodeParsed("GridColCount"); // Required: GridRowCount node = _cfg.self.getSingleNode("GridRowCount"); ASTRA_CONFIG_CHECK(node, "ReconstructionGeometry2D", "No GridRowCount tag specified."); - m_iGridRowCount = boost::lexical_cast(node.getContent()); + m_iGridRowCount = node.getContentInt(); CC.markNodeParsed("GridRowCount"); // Required: GridRowCount node = _cfg.self.getSingleNode("GridSliceCount"); ASTRA_CONFIG_CHECK(node, "ReconstructionGeometry2D", "No GridSliceCount tag specified."); - m_iGridSliceCount = boost::lexical_cast(node.getContent()); + m_iGridSliceCount = node.getContentInt(); CC.markNodeParsed("GridSliceCount"); // Optional: Window minima and maxima diff --git a/src/XMLNode.cpp b/src/XMLNode.cpp index 0ec701f..40a9b22 100644 --- a/src/XMLNode.cpp +++ b/src/XMLNode.cpp @@ -31,12 +31,6 @@ $Id$ #include "rapidxml/rapidxml.hpp" #include "rapidxml/rapidxml_print.hpp" -#include -#include -#include -#include - - using namespace rapidxml; using namespace astra; @@ -138,8 +132,13 @@ string XMLNode::getContent() const // Get node content - NUMERICAL float32 XMLNode::getContentNumerical() const { - return boost::lexical_cast(getContent()); + return StringUtil::stringToFloat(getContent()); } +int XMLNode::getContentInt() const +{ + return StringUtil::stringToInt(getContent()); +} + //----------------------------------------------------------------------------- // Get node content - BOOLEAN @@ -154,7 +153,7 @@ bool XMLNode::getContentBool() const vector XMLNode::getContentArray() const { // get listsize - int iSize = boost::lexical_cast(getAttribute("listsize")); + int iSize = StringUtil::stringToInt(getAttribute("listsize")); // create result array vector res(iSize); // loop all list item nodes @@ -175,40 +174,12 @@ vector XMLNode::getContentArray() const // NB: A 2D matrix is returned as a linear list vector XMLNode::getContentNumericalArray() const { - string input = getContent(); - - // split - std::vector items; - boost::split(items, input, boost::is_any_of(",;")); - - // init list - vector out; - out.resize(items.size()); - - // loop elements - for (unsigned int i = 0; i < items.size(); i++) { - out[i] = boost::lexical_cast(items[i]); - } - return out; + return StringUtil::stringToFloatVector(getContent()); } vector XMLNode::getContentNumericalArrayDouble() const { - string input = getContent(); - - // split - std::vector items; - boost::split(items, input, boost::is_any_of(",;")); - - // init list - vector out; - out.resize(items.size()); - - // loop elements - for (unsigned int i = 0; i < items.size(); i++) { - out[i] = boost::lexical_cast(items[i]); - } - return out; + return StringUtil::stringToDoubleVector(getContent()); } //----------------------------------------------------------------------------- @@ -235,14 +206,20 @@ string XMLNode::getAttribute(string _sName, string _sDefaultValue) const float32 XMLNode::getAttributeNumerical(string _sName, float32 _fDefaultValue) const { if (!hasAttribute(_sName)) return _fDefaultValue; - return boost::lexical_cast(getAttribute(_sName)); + return StringUtil::stringToFloat(getAttribute(_sName)); } double XMLNode::getAttributeNumericalDouble(string _sName, double _fDefaultValue) const { if (!hasAttribute(_sName)) return _fDefaultValue; - return boost::lexical_cast(getAttribute(_sName)); + return StringUtil::stringToDouble(getAttribute(_sName)); +} +int XMLNode::getAttributeInt(string _sName, int _iDefaultValue) const +{ + if (!hasAttribute(_sName)) return _iDefaultValue; + return StringUtil::stringToInt(getAttribute(_sName)); } + //----------------------------------------------------------------------------- // Get attribute - BOOLEAN bool XMLNode::getAttributeBool(string _sName, bool _bDefaultValue) const @@ -287,9 +264,15 @@ string XMLNode::getOption(string _sKey, string _sDefaultValue) const float32 XMLNode::getOptionNumerical(string _sKey, float32 _fDefaultValue) const { if (!hasOption(_sKey)) return _fDefaultValue; - return boost::lexical_cast(getOption(_sKey)); + return StringUtil::stringToFloat(getOption(_sKey)); +} +int XMLNode::getOptionInt(string _sKey, int _iDefaultValue) const +{ + if (!hasOption(_sKey)) return _iDefaultValue; + return StringUtil::stringToInt(getOption(_sKey)); } + //----------------------------------------------------------------------------- // Get option - BOOL bool XMLNode::getOptionBool(string _sKey, bool _bDefaultValue) const @@ -386,7 +369,7 @@ void XMLNode::setContent(string _sText) // Set content - FLOAT void XMLNode::setContent(float32 _fValue) { - setContent(boost::lexical_cast(_fValue)); + setContent(StringUtil::floatToString(_fValue)); } //----------------------------------------------------------------------------- @@ -394,9 +377,9 @@ void XMLNode::setContent(float32 _fValue) template static std::string setContentList_internal(T* pfList, int _iSize) { - std::string str = (_iSize > 0) ? boost::lexical_cast(pfList[0]) : ""; + std::string str = (_iSize > 0) ? StringUtil::toString(pfList[0]) : ""; for (int i = 1; i < _iSize; i++) { - str += "," + boost::lexical_cast(pfList[i]); + str += "," + StringUtil::toString(pfList[i]); } return str; } @@ -431,9 +414,9 @@ static std::string setContentMatrix_internal(T* _pfMatrix, int _iWidth, int _iHe for (int y = 0; y < _iHeight; ++y) { if (_iWidth > 0) - str += boost::lexical_cast(_pfMatrix[0*s1 + y*s2]); + str += StringUtil::toString(_pfMatrix[0*s1 + y*s2]); for (int x = 1; x < _iWidth; x++) - str += "," + boost::lexical_cast(_pfMatrix[x*s1 + y*s2]); + str += "," + StringUtil::toString(_pfMatrix[x*s1 + y*s2]); if (y != _iHeight-1) str += ";"; @@ -468,7 +451,7 @@ void XMLNode::addAttribute(string _sName, string _sText) // Add attribute - FLOAT void XMLNode::addAttribute(string _sName, float32 _fValue) { - addAttribute(_sName, boost::lexical_cast(_fValue)); + addAttribute(_sName, StringUtil::floatToString(_fValue)); } //----------------------------------------------------------------------------- -- cgit v1.2.3 From 34bab2b0caa6ee955d5d2f7882a6cd36cf142536 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Mon, 18 Jan 2016 17:29:58 +0100 Subject: Allow user to pass NVCCFLAGS to configure --- build/linux/Makefile.in | 3 ++- build/linux/acinclude.m4 | 6 +++--- build/linux/configure.ac | 9 +++++---- 3 files changed, 10 insertions(+), 8 deletions(-) (limited to 'build') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 8eb5ffe..01ef527 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -25,6 +25,7 @@ VPATH=../.. CPPFLAGS=@SAVED_CPPFLAGS@ CXXFLAGS=@SAVED_CXXFLAGS@ +NVCCFLAGS=@SAVED_NVCCFLAGS@ LDFLAGS=@SAVED_LDFLAGS@ LIBS=@SAVED_LIBS@ @@ -37,7 +38,7 @@ CPPFLAGS+=@CPPFLAGS_OS@ ifeq ($(cuda),yes) CPPFLAGS += @CPPFLAGS_CUDA@ -DASTRA_CUDA -NVCCFLAGS = @NVCCFLAGS@ @CPPFLAGS_CUDA@ -I../.. -I../../include -DASTRA_CUDA +NVCCFLAGS += @NVCCFLAGS_EXTRA@ @CPPFLAGS_CUDA@ -I../.. -I../../include -DASTRA_CUDA LDFLAGS += @LDFLAGS_CUDA@ LIBS += -lcudart -lcufft NVCC = @NVCC@ diff --git a/build/linux/acinclude.m4 b/build/linux/acinclude.m4 index e4b6de7..d6866c3 100644 --- a/build/linux/acinclude.m4 +++ b/build/linux/acinclude.m4 @@ -93,13 +93,13 @@ int main() { } _ACEOF $1="yes" -ASTRA_RUN_STOREOUTPUT([$NVCC -c -o conftest.o conftest.cu $$2],conftest.nvcc.out) || { +ASTRA_RUN_STOREOUTPUT([$NVCC -c -o conftest.o conftest.cu $NVCCFLAGS $$2],conftest.nvcc.out) || { $1="no" # Check if hack for gcc 4.4 helps if grep -q __builtin_stdarg_start conftest.nvcc.out; then AS_ECHO(["$as_me:${as_lineno-$LINENO}: Trying CUDA hack for gcc 4.4"]) >&AS_MESSAGE_LOG_FD NVCC_OPT="-Xcompiler -D__builtin_stdarg_start=__builtin_va_start" - ASTRA_RUN_LOGOUTPUT([$NVCC -c -o conftest.o conftest.cu $$2 $NVCC_OPT]) && { + ASTRA_RUN_LOGOUTPUT([$NVCC -c -o conftest.o conftest.cu $NVCCFLAGS $$2 $NVCC_OPT]) && { $1="yes" $2="$$2 $NVCC_OPT" } @@ -133,7 +133,7 @@ IFS=, for arch in $1; do IFS=$astra_save_IFS NVCC_opt="-gencode=arch=compute_$arch,code=sm_$arch" - $NVCC -c -o conftest.o conftest.cu $$2 $NVCC_opt >conftest.nvcc.out 2>&1 && { + $NVCC -c -o conftest.o conftest.cu $NVCCFLAGS $$2 $NVCC_opt >conftest.nvcc.out 2>&1 && { NVCC_lastarch=$arch NVCC_extra="$NVCC_extra $NVCC_opt" NVCC_list="${NVCC_list:+$NVCC_list, }$arch" diff --git a/build/linux/configure.ac b/build/linux/configure.ac index 85e4324..487a8cc 100644 --- a/build/linux/configure.ac +++ b/build/linux/configure.ac @@ -30,6 +30,7 @@ LT_INIT([disable-static]) SAVED_CPPFLAGS="$CPPFLAGS" SAVED_CXXFLAGS="$CXXFLAGS" +SAVED_NVCCFLAGS="$NVCCFLAGS" SAVED_LDFLAGS="$LDFLAGS" SAVED_LIBS="$LIBS" @@ -124,10 +125,9 @@ if test x"$NVCC" != xno; then AC_SUBST(NVCC) fi -NVCCFLAGS="" if test x"$HAVECUDA" = xyes; then AC_MSG_CHECKING([if nvcc works]) - ASTRA_CHECK_NVCC(HAVECUDA,NVCCFLAGS) + ASTRA_CHECK_NVCC(HAVECUDA,NVCCFLAGS_EXTRA) AC_MSG_RESULT($HAVECUDA) fi @@ -138,7 +138,7 @@ if test x"$HAVECUDA" = xyes; then if test x"$with_cuda_compute" = x; then with_cuda_compute="10,12,20,30,35,50" fi - ASTRA_FIND_NVCC_ARCHS([$with_cuda_compute],NVCCFLAGS,NVCCARCHS) + ASTRA_FIND_NVCC_ARCHS([$with_cuda_compute],NVCCFLAGS_EXTRA,NVCCARCHS) AC_MSG_RESULT([$NVCCARCHS]) fi @@ -146,7 +146,7 @@ fi AC_SUBST(HAVECUDA) AC_SUBST(LDFLAGS_CUDA) AC_SUBST(CPPFLAGS_CUDA) -AC_SUBST(NVCCFLAGS) +AC_SUBST(NVCCFLAGS_EXTRA) # mex, matlab @@ -249,6 +249,7 @@ AC_SUBST(CPPFLAGS_OS) AC_SUBST(SAVED_CPPFLAGS) AC_SUBST(SAVED_CXXFLAGS) +AC_SUBST(SAVED_NVCCFLAGS) AC_SUBST(SAVED_LDFLAGS) AC_SUBST(SAVED_LIBS) AC_CONFIG_FILES([Makefile]) -- cgit v1.2.3 From eee5fe536591e96af67ad4bcd417d6c8b89e26bb Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Tue, 19 Jan 2016 14:25:03 +0100 Subject: Allow out-of-tree builds --- build/linux/Makefile.in | 67 +++++++++++++++++++++++++++---------------------- 1 file changed, 37 insertions(+), 30 deletions(-) (limited to 'build') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 01ef527..90f8801 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -21,7 +21,10 @@ all: $(TARGETS) prefix=@prefix@ exec_prefix=@exec_prefix@ -VPATH=../.. +srcdir=@srcdir@ +abs_top_builddir=@abs_top_builddir@ + +VPATH=$(srcdir)/../.. CPPFLAGS=@SAVED_CPPFLAGS@ CXXFLAGS=@SAVED_CXXFLAGS@ @@ -29,7 +32,7 @@ NVCCFLAGS=@SAVED_NVCCFLAGS@ LDFLAGS=@SAVED_LDFLAGS@ LIBS=@SAVED_LIBS@ -CPPFLAGS+=-I../.. -I../../include -I../../lib/include +CPPFLAGS+=-I$(srcdir)/../.. -I$(srcdir)/../../include -I$(srcdir)/../../lib/include CXXFLAGS+=-g -O3 -Wall -Wshadow LIBS+=-lpthread LDFLAGS+=-g @@ -38,7 +41,7 @@ CPPFLAGS+=@CPPFLAGS_OS@ ifeq ($(cuda),yes) CPPFLAGS += @CPPFLAGS_CUDA@ -DASTRA_CUDA -NVCCFLAGS += @NVCCFLAGS_EXTRA@ @CPPFLAGS_CUDA@ -I../.. -I../../include -DASTRA_CUDA +NVCCFLAGS += @NVCCFLAGS_EXTRA@ @CPPFLAGS_CUDA@ -I$(srcdir)/../.. -I$(srcdir)/../../include -DASTRA_CUDA LDFLAGS += @LDFLAGS_CUDA@ LIBS += -lcudart -lcufft NVCC = @NVCC@ @@ -59,7 +62,7 @@ CPPFLAGS += -DASTRA_PYTHON -I$(PYINCDIR) PYCPPFLAGS = $(CPPFLAGS) PYCPPFLAGS += -I../include PYLDFLAGS = $(LDFLAGS) -PYLDFLAGS += -L../build/linux/.libs +PYLDFLAGS += -L$(abs_top_builddir)/.libs LIBS += -l$(PYLIBVER) LDFLAGS += -L$(PYLIBDIR) endif @@ -78,6 +81,7 @@ MKDIR=mkdir -p CXX=@CXX@ LD=@CXX@ SHELL=@SHELL@ +INSTALL_SH=$(SHELL) $(srcdir)/install-sh ifeq ($(matlab),yes) MEXFLAGS = -cxx @@ -264,12 +268,12 @@ endif ifeq ($(python),yes) py: libastra.la - cd ../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py install \ + cd $(srcdir)/../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py install \ --install-base=./finalbuild --install-headers=./finalbuild --install-purelib=./finalbuild \ --install-platlib=./finalbuild --install-scripts=./finalbuild --install-data=./finalbuild python-root-install: libastra.la - cd ../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py install + cd $(srcdir)/../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py install endif @@ -331,33 +335,33 @@ clean: rm -f $(addsuffix /*.d,$(DEPDIRS)) rm -f $(addsuffix /*,$(LIBDIRS)) rm -f $(TEST_OBJECTS) test.bin - rm -fr ../../python/finalbuild/ - rm -fr ../../python/build/ - rm -f ../../python/astra/*.cpp - rm -f ../../python/astra/*.c + rm -fr $(srcdir)/../../python/finalbuild/ + rm -fr $(srcdir)/../../python/build/ + rm -f $(srcdir)/../../python/astra/*.cpp + rm -f $(srcdir)/../../python/astra/*.c distclean: clean - rm -f config.guess config.sub ltmain.sh libtool install-sh + rm -f $(srcdir)/config.guess $(srcdir)/config.sub $(srcdir)/ltmain.sh libtool $(srcdir)/install-sh rm -f config.log config.status - rm -f aclocal.m4 - rm -rf autom4te.cache - rm -f configure Makefile + rm -f $(srcdir)/aclocal.m4 + rm -rf $(srcdir)/autom4te.cache + rm -f $(srcdir)/configure Makefile install: install-libraries install-matlab install-python install-libraries: libastra.la - ./install-sh -m 755 -d @libdir@ - ./libtool --mode=install ./install-sh -m 644 libastra.la @libdir@ + $(INSTALL_SH) -m 755 -d @libdir@ + ./libtool --mode=install $(INSTALL_SH) -m 644 libastra.la @libdir@ ./libtool --mode=finish @libdir@ ifeq ($(matlab),yes) # TODO: This install location doesn't work well for /usr or /usr/local install-matlab: $(MATLAB_MEX) - ./install-sh -m 755 -d @prefix@/matlab - ./install-sh -m 755 -d @prefix@/matlab/mex - ./install-sh -m 755 -d @prefix@/matlab/tools - ./install-sh -m 644 $(MATLAB_MEX) @prefix@/matlab/mex - ./install-sh -m 644 ../../matlab/tools/*.m @prefix@/matlab/tools + $(INSTALL_SH) -m 755 -d @prefix@/matlab + $(INSTALL_SH) -m 755 -d @prefix@/matlab/mex + $(INSTALL_SH) -m 755 -d @prefix@/matlab/tools + $(INSTALL_SH) -m 644 $(MATLAB_MEX) @prefix@/matlab/mex + $(INSTALL_SH) -m 644 $(srcdir)/../../matlab/tools/*.m @prefix@/matlab/tools # TODO: docs else install-matlab: @@ -366,11 +370,11 @@ endif ifeq ($(python),yes) # TODO: This install location doesn't work well for /usr or /usr/local install-python: py - ./install-sh -m 755 -d @prefix@/python - ./install-sh -m 755 -d @prefix@/python/astra - ./install-sh -m 644 ../../python/finalbuild/astra/*.so @prefix@/python/astra - ./install-sh -m 644 ../../python/finalbuild/astra/*.py @prefix@/python/astra - ./install-sh -m 644 ../../python/finalbuild/*.egg-info @prefix@/python/ + $(INSTALL_SH) -m 755 -d @prefix@/python + $(INSTALL_SH) -m 755 -d @prefix@/python/astra + $(INSTALL_SH) -m 644 $(srcdir)/../../python/finalbuild/astra/*.so @prefix@/python/astra + $(INSTALL_SH) -m 644 $(srcdir)/../../python/finalbuild/astra/*.py @prefix@/python/astra + $(INSTALL_SH) -m 644 $(srcdir)/../../python/finalbuild/*.egg-info @prefix@/python/ @echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++" @echo "To use ASTRA in Python, add @prefix@/python/ to your PYTHONPATH" @echo "and @libdir@ to your LD_LIBRARY_PATH." @@ -381,18 +385,21 @@ install-python: endif -Makefile: Makefile.in config.status +Makefile: $(srcdir)/Makefile.in config.status CONFIG_HEADERS= CONFIG_LINKS= CONFIG_FILES=$@ $(SHELL) ./config.status -config.status: configure +config.status: $(srcdir)/configure @echo "configure script has changed. Re-running it with last parameters" $(SHELL) ./config.status --recheck -configure: configure.ac +$(srcdir)/configure: $(srcdir)/configure.ac @echo "configure.ac has been changed. Regenerating configure script" - $(SHELL) ./autogen.sh + cd $(srcdir) && $(SHELL) ./autogen.sh .PHONY: all mex test clean distclean install install-libraries # don't remove intermediate files: .SECONDARY: + +# disable all implicit built-in rules +.SUFFIXES: -- cgit v1.2.3 From 61d95e4d4cabcc1da959ccf68588895862ec64c5 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Tue, 19 Jan 2016 15:54:08 +0100 Subject: Place Python build/temporary files in build directory This also allows out-of-tree builds for Python. --- build/linux/Makefile.in | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) (limited to 'build') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 90f8801..4f99db2 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -268,12 +268,15 @@ endif ifeq ($(python),yes) py: libastra.la - cd $(srcdir)/../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py install \ - --install-base=./finalbuild --install-headers=./finalbuild --install-purelib=./finalbuild \ - --install-platlib=./finalbuild --install-scripts=./finalbuild --install-data=./finalbuild + $(MKDIR) python/build + $(MKDIR) python/finalbuild + cd $(srcdir)/../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build install \ + --install-base=$(abs_top_builddir)/python/finalbuild --install-headers=$(abs_top_builddir)/python/finalbuild --install-purelib=$(abs_top_builddir)/python/finalbuild \ + --install-platlib=$(abs_top_builddir)/python/finalbuild --install-scripts=$(abs_top_builddir)/python/finalbuild --install-data=$(abs_top_builddir)/python/finalbuild python-root-install: libastra.la - cd $(srcdir)/../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py install + $(MKDIR) python/build + cd $(srcdir)/../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build install endif @@ -335,8 +338,8 @@ clean: rm -f $(addsuffix /*.d,$(DEPDIRS)) rm -f $(addsuffix /*,$(LIBDIRS)) rm -f $(TEST_OBJECTS) test.bin - rm -fr $(srcdir)/../../python/finalbuild/ - rm -fr $(srcdir)/../../python/build/ + rm -fr python/finalbuild/ + rm -fr python/build/ rm -f $(srcdir)/../../python/astra/*.cpp rm -f $(srcdir)/../../python/astra/*.c @@ -372,9 +375,9 @@ ifeq ($(python),yes) install-python: py $(INSTALL_SH) -m 755 -d @prefix@/python $(INSTALL_SH) -m 755 -d @prefix@/python/astra - $(INSTALL_SH) -m 644 $(srcdir)/../../python/finalbuild/astra/*.so @prefix@/python/astra - $(INSTALL_SH) -m 644 $(srcdir)/../../python/finalbuild/astra/*.py @prefix@/python/astra - $(INSTALL_SH) -m 644 $(srcdir)/../../python/finalbuild/*.egg-info @prefix@/python/ + $(INSTALL_SH) -m 644 python/finalbuild/astra/*.so @prefix@/python/astra + $(INSTALL_SH) -m 644 python/finalbuild/astra/*.py @prefix@/python/astra + $(INSTALL_SH) -m 644 python/finalbuild/*.egg-info @prefix@/python/ @echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++" @echo "To use ASTRA in Python, add @prefix@/python/ to your PYTHONPATH" @echo "and @libdir@ to your LD_LIBRARY_PATH." -- cgit v1.2.3 From 2d2be13aa9dcfc77afed1dbe52c78e5dce5a04fa Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Tue, 19 Jan 2016 17:06:57 +0100 Subject: Fail when python six module is not found --- build/linux/configure.ac | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'build') diff --git a/build/linux/configure.ac b/build/linux/configure.ac index 684a4c5..354bccc 100644 --- a/build/linux/configure.ac +++ b/build/linux/configure.ac @@ -213,7 +213,7 @@ assert(LooseVersion(Cython.__version__)>=LooseVersion("0.13")) fi AC_MSG_RESULT(yes) AC_MSG_CHECKING(for six module) - ASTRA_TRY_PYTHON([import six]) + ASTRA_TRY_PYTHON([import six],,HAVEPYTHON=no) if test x$HAVEPYTHON = xno; then AC_MSG_RESULT(no) AC_MSG_ERROR(You need the six module to use the ASTRA toolbox in Python) -- cgit v1.2.3 From 5c33826855a8d88889cdbbfc78b27c86549715d5 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 20 Jan 2016 13:02:36 +0100 Subject: Add check for scipy The module matrix_c.pyx uses it. --- build/linux/configure.ac | 7 +++++++ python/conda/meta.yaml | 1 + 2 files changed, 8 insertions(+) (limited to 'build') diff --git a/build/linux/configure.ac b/build/linux/configure.ac index 354bccc..5a04509 100644 --- a/build/linux/configure.ac +++ b/build/linux/configure.ac @@ -219,6 +219,13 @@ assert(LooseVersion(Cython.__version__)>=LooseVersion("0.13")) AC_MSG_ERROR(You need the six module to use the ASTRA toolbox in Python) fi AC_MSG_RESULT(yes) + AC_MSG_CHECKING(for scipy module) + ASTRA_TRY_PYTHON([import scipy],,HAVEPYTHON=no) + if test x$HAVEPYTHON = xno; then + AC_MSG_RESULT(no) + AC_MSG_ERROR(You need the scipy module to use the ASTRA toolbox in Python) + fi + AC_MSG_RESULT(yes) fi AC_SUBST(HAVEPYTHON) diff --git a/python/conda/meta.yaml b/python/conda/meta.yaml index 41250dc..7e4679b 100644 --- a/python/conda/meta.yaml +++ b/python/conda/meta.yaml @@ -21,6 +21,7 @@ requirements: - python - cython >=0.13 - numpy + - scipy - six run: -- cgit v1.2.3 From 5e3bcf20be6188331c856d9d8854fb931b2abba7 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 20 Jan 2016 14:34:00 +0100 Subject: Avoid incorrect include dirs when building python modules --- build/linux/Makefile.in | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) (limited to 'build') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 4f99db2..c165d37 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -32,7 +32,6 @@ NVCCFLAGS=@SAVED_NVCCFLAGS@ LDFLAGS=@SAVED_LDFLAGS@ LIBS=@SAVED_LIBS@ -CPPFLAGS+=-I$(srcdir)/../.. -I$(srcdir)/../../include -I$(srcdir)/../../lib/include CXXFLAGS+=-g -O3 -Wall -Wshadow LIBS+=-lpthread LDFLAGS+=-g @@ -59,7 +58,7 @@ PYLIBDIR = $(shell $(PYTHON) -c 'from distutils.sysconfig import get_config_var; PYINCDIR = $(shell $(PYTHON) -c 'from distutils.sysconfig import get_python_inc; import six; six.print_(get_python_inc())') PYLIBVER = `basename $(PYINCDIR)` CPPFLAGS += -DASTRA_PYTHON -I$(PYINCDIR) -PYCPPFLAGS = $(CPPFLAGS) +PYCPPFLAGS := $(CPPFLAGS) PYCPPFLAGS += -I../include PYLDFLAGS = $(LDFLAGS) PYLDFLAGS += -L$(abs_top_builddir)/.libs @@ -67,6 +66,10 @@ LIBS += -l$(PYLIBVER) LDFLAGS += -L$(PYLIBDIR) endif +# This is below where PYCPPFLAGS copies CPPFLAGS. The python code is built +# from a different directory, so these relative includes would be wrong. +CPPFLAGS+=-I$(srcdir)/../.. -I$(srcdir)/../../include -I$(srcdir)/../../lib/include + BOOST_CPPFLAGS= BOOST_LDFLAGS= -- cgit v1.2.3 From 29c5c86e56697286a92031aaa9fdd903b3bcc426 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 20 Jan 2016 16:18:05 +0100 Subject: Use nvcc's -MT option --- build/linux/Makefile.in | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) (limited to 'build') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index c165d37..12c9e2b 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -303,10 +303,8 @@ ifeq ($(cuda),yes) @$(MKDIR) $(*D)/.libs @$(MKDIR) $(*D)/$(DEPDIR) @$(NVCC) $(NVCCFLAGS) -c $(<) -Xcompiler -fPIC -DPIC -o $(*D)/.libs/$(*F).o >/dev/null 2>&1 - @# Generate a .d file, and change the target name in it from .o to .lo - @$(NVCC) $(NVCCFLAGS) -M $(<) -odir $(*D) -o $(*D)/$(DEPDIR)/$(*F).d2 - @sed '1s/\.o :/.lo :/' < $(*D)/$(DEPDIR)/$(*F).d2 > $(*D)/$(DEPDIR)/$(*F).d - @rm -f $(*D)/$(DEPDIR)/$(*F).d2 + @# Generate a .d file, with target name $*.lo + @$(NVCC) $(NVCCFLAGS) -M $(<) -MT $(*F).lo -odir $(*D) -o $(*D)/$(DEPDIR)/$(*F).d @# Generate a fake libtool .lo file @echo "# $*.lo - a libtool object file" > $*.lo @echo "# Generated by" `./libtool --version | head -n 1` >> $*.lo -- cgit v1.2.3 From b428366389ecdad457fb04e13857902e11585881 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 20 Jan 2016 16:18:08 +0100 Subject: Try to improve nvcc dependency file generation We now append empty targets for all dependencies listed in the .d file generated by nvcc. This mimics the behaviour of gcc's -MP option, and prevents deleted header files from breaking the build. --- build/linux/Makefile.in | 3 +++ 1 file changed, 3 insertions(+) (limited to 'build') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 12c9e2b..f556066 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -305,6 +305,9 @@ ifeq ($(cuda),yes) @$(NVCC) $(NVCCFLAGS) -c $(<) -Xcompiler -fPIC -DPIC -o $(*D)/.libs/$(*F).o >/dev/null 2>&1 @# Generate a .d file, with target name $*.lo @$(NVCC) $(NVCCFLAGS) -M $(<) -MT $(*F).lo -odir $(*D) -o $(*D)/$(DEPDIR)/$(*F).d + @# Generate empty targets for all dependencies listed in the .d file. + @# This mimics gcc's -MP option. + @for x in `cat $(*D)/$(DEPDIR)/$(*F).d`; do if test a$$x != a: -a a$$x != a\\; then echo -e "\n$$x:\n" >> $(*D)/$(DEPDIR)/$(*F).d; fi; done @# Generate a fake libtool .lo file @echo "# $*.lo - a libtool object file" > $*.lo @echo "# Generated by" `./libtool --version | head -n 1` >> $*.lo -- cgit v1.2.3 From 8fecf27e5eba5e89d9212c2235e957a64e58ec22 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 20 Jan 2016 16:38:01 +0100 Subject: Don't build cuda non-PIC object if static libs are disabled This significantly speeds up builds since we usually pass disable-static to libtool. --- build/linux/Makefile.in | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) (limited to 'build') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index f556066..8398e35 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -295,14 +295,18 @@ libastra.la: $(ALL_OBJECTS) $(MKDIR) $(*D)/$(DEPDIR) ./libtool --mode=compile --tag=CXX $(CXX) -Wp,-MMD,"$(*D)/$(DEPDIR)/$(*F).d",-MQ,"$@",-MP $(CXXFLAGS) $(CPPFLAGS) -c $(<) -o $*.o +gen_static_libs := `./libtool --features | grep -q 'disable static' && echo no || echo yes` + ifeq ($(cuda),yes) %.lo: %.cu @# Behave like libtool: compile both a PIC and a non-PIC object file @$(MKDIR) $(*D) - $(NVCC) $(NVCCFLAGS) -c $(<) -o $*.o @$(MKDIR) $(*D)/.libs @$(MKDIR) $(*D)/$(DEPDIR) - @$(NVCC) $(NVCCFLAGS) -c $(<) -Xcompiler -fPIC -DPIC -o $(*D)/.libs/$(*F).o >/dev/null 2>&1 + $(NVCC) $(NVCCFLAGS) -c $(<) -Xcompiler -fPIC -DPIC -o $(*D)/.libs/$(*F).o +ifeq ($(gen_static_libs),yes) + @$(NVCC) $(NVCCFLAGS) -c $(<) -o $*.o >/dev/null 2>&1 +endif @# Generate a .d file, with target name $*.lo @$(NVCC) $(NVCCFLAGS) -M $(<) -MT $(*F).lo -odir $(*D) -o $(*D)/$(DEPDIR)/$(*F).d @# Generate empty targets for all dependencies listed in the .d file. @@ -319,7 +323,11 @@ ifeq ($(cuda),yes) @echo "pic_object='.libs/$(*F).o'" >> $*.lo @echo >> $*.lo @echo "# Name of the non-PIC object." >> $*.lo +ifeq ($(gen_static_libs),yes) @echo "non_pic_object='$(*F).o'" >> $*.lo +else + @echo "non_pic_object=none" >> $*.lo +endif @# Remove generated .linkinfo file @rm -f $(*F).linkinfo endif -- cgit v1.2.3 From 6a7eaf9c8fee52e01e7a48cd7e4630453c033655 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Thu, 21 Jan 2016 11:29:53 +0100 Subject: Fix VPATH problem with older autoconf versions --- build/linux/Makefile.in | 2 +- build/linux/configure.ac | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) (limited to 'build') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 8398e35..3018674 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -24,7 +24,7 @@ exec_prefix=@exec_prefix@ srcdir=@srcdir@ abs_top_builddir=@abs_top_builddir@ -VPATH=$(srcdir)/../.. +VPATH=@VPATH_SRCDIR@/../.. CPPFLAGS=@SAVED_CPPFLAGS@ CXXFLAGS=@SAVED_CXXFLAGS@ diff --git a/build/linux/configure.ac b/build/linux/configure.ac index 5a04509..630b08d 100644 --- a/build/linux/configure.ac +++ b/build/linux/configure.ac @@ -243,6 +243,12 @@ esac AC_SUBST(CPPFLAGS_OS) +# For some reason, some older versions of autoconf produce a config.status +# that disables all lines looking like VPATH=@srcdir@ +# (More recent autoconf fixes the too broad matching there.) +# We use a different variable name as a workaround. +VPATH_SRCDIR="$srcdir" +AC_SUBST(VPATH_SRCDIR) # TODO: -- cgit v1.2.3 From 56809b0359af7e9108adeb1fd21823a225edf6fa Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 20 Jan 2016 18:08:59 +0100 Subject: Remove dependency of libastra on libpython by refactoring PluginAlgorithm --- build/linux/Makefile.in | 2 - include/astra/AstraObjectFactory.h | 7 +- include/astra/PluginAlgorithm.h | 57 ++-- matlab/mex/astra_mex_plugin_c.cpp | 18 +- python/astra/plugin_c.pyx | 17 +- python/astra/src/PythonPluginAlgorithm.cpp | 402 +++++++++++++++++++++++++++++ python/astra/src/PythonPluginAlgorithm.h | 89 +++++++ python/builder.py | 4 + src/PluginAlgorithm.cpp | 367 +------------------------- 9 files changed, 544 insertions(+), 419 deletions(-) create mode 100644 python/astra/src/PythonPluginAlgorithm.cpp create mode 100644 python/astra/src/PythonPluginAlgorithm.h (limited to 'build') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 3018674..d5644bc 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -62,8 +62,6 @@ PYCPPFLAGS := $(CPPFLAGS) PYCPPFLAGS += -I../include PYLDFLAGS = $(LDFLAGS) PYLDFLAGS += -L$(abs_top_builddir)/.libs -LIBS += -l$(PYLIBVER) -LDFLAGS += -L$(PYLIBDIR) endif # This is below where PYCPPFLAGS copies CPPFLAGS. The python code is built diff --git a/include/astra/AstraObjectFactory.h b/include/astra/AstraObjectFactory.h index 325989e..6af9cd8 100644 --- a/include/astra/AstraObjectFactory.h +++ b/include/astra/AstraObjectFactory.h @@ -155,8 +155,11 @@ class _AstraExport CAlgorithmFactory : public CAstraObjectFactory inline CAlgorithm* CAstraObjectFactory::findPlugin(std::string _sType) { - CPluginAlgorithmFactory *fac = CPluginAlgorithmFactory::getSingletonPtr(); - return fac->getPlugin(_sType); + CPluginAlgorithmFactory *fac = CPluginAlgorithmFactory::getFactory(); + if (fac) + return fac->getPlugin(_sType); + else + return 0; } #endif diff --git a/include/astra/PluginAlgorithm.h b/include/astra/PluginAlgorithm.h index 667e813..cbd80fc 100644 --- a/include/astra/PluginAlgorithm.h +++ b/include/astra/PluginAlgorithm.h @@ -29,62 +29,37 @@ $Id$ #ifndef _INC_ASTRA_PLUGINALGORITHM #define _INC_ASTRA_PLUGINALGORITHM -#ifdef ASTRA_PYTHON - -#include "astra/Algorithm.h" -#include "astra/Singleton.h" -#include "astra/XMLDocument.h" -#include "astra/XMLNode.h" - -// Slightly hackish forward declaration of PyObject -struct _object; -typedef _object PyObject; +#include "astra/Globals.h" +#include +#include namespace astra { -class _AstraExport CPluginAlgorithm : public CAlgorithm { - -public: - - CPluginAlgorithm(PyObject* pyclass); - ~CPluginAlgorithm(); - - bool initialize(const Config& _cfg); - void run(int _iNrIterations); - -private: - PyObject * instance; -}; +class CAlgorithm; -class _AstraExport CPluginAlgorithmFactory : public Singleton { +class _AstraExport CPluginAlgorithmFactory { public: + CPluginAlgorithmFactory() { } + virtual ~CPluginAlgorithmFactory() { } - CPluginAlgorithmFactory(); - ~CPluginAlgorithmFactory(); + virtual CAlgorithm * getPlugin(const std::string &name) = 0; - CPluginAlgorithm * getPlugin(std::string name); + virtual bool registerPlugin(std::string name, std::string className) = 0; + virtual bool registerPlugin(std::string className) = 0; - bool registerPlugin(std::string name, std::string className); - bool registerPlugin(std::string className); - bool registerPluginClass(std::string name, PyObject * className); - bool registerPluginClass(PyObject * className); + virtual std::map getRegisteredMap() = 0; - PyObject * getRegistered(); - std::map getRegisteredMap(); - - std::string getHelp(std::string name); + virtual std::string getHelp(const std::string &name) = 0; + + static void registerFactory(CPluginAlgorithmFactory *factory) { m_factory = factory; } + static CPluginAlgorithmFactory* getFactory() { return m_factory; } private: - PyObject * pluginDict; - PyObject *inspect, *six; + static CPluginAlgorithmFactory *m_factory; }; -PyObject* XMLNode2dict(XMLNode node); - } #endif - -#endif diff --git a/matlab/mex/astra_mex_plugin_c.cpp b/matlab/mex/astra_mex_plugin_c.cpp index 177fcf4..0dc0edf 100644 --- a/matlab/mex/astra_mex_plugin_c.cpp +++ b/matlab/mex/astra_mex_plugin_c.cpp @@ -48,7 +48,11 @@ using namespace astra; */ void astra_mex_plugin_get_registered(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) { - astra::CPluginAlgorithmFactory *fact = astra::CPluginAlgorithmFactory::getSingletonPtr(); + astra::CPluginAlgorithmFactory *fact = astra::CPluginAlgorithmFactory::getFactory(); + if (!fact) { + mexPrintf("Plugin support not initialized."); + return; + } std::map mp = fact->getRegisteredMap(); for(std::map::iterator it=mp.begin();it!=mp.end();it++){ mexPrintf("%s: %s\n",it->first.c_str(), it->second.c_str()); @@ -62,9 +66,13 @@ void astra_mex_plugin_get_registered(int nlhs, mxArray* plhs[], int nrhs, const */ void astra_mex_plugin_register(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) { + astra::CPluginAlgorithmFactory *fact = astra::CPluginAlgorithmFactory::getFactory(); + if (!fact) { + mexPrintf("Plugin support not initialized."); + return; + } if (2 <= nrhs) { string class_name = mexToString(prhs[1]); - astra::CPluginAlgorithmFactory *fact = astra::CPluginAlgorithmFactory::getSingletonPtr(); fact->registerPlugin(class_name); }else{ mexPrintf("astra_mex_plugin('register', class_name);\n"); @@ -78,9 +86,13 @@ void astra_mex_plugin_register(int nlhs, mxArray* plhs[], int nrhs, const mxArra */ void astra_mex_plugin_get_help(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) { + astra::CPluginAlgorithmFactory *fact = astra::CPluginAlgorithmFactory::getFactory(); + if (!fact) { + mexPrintf("Plugin support not initialized."); + return; + } if (2 <= nrhs) { string name = mexToString(prhs[1]); - astra::CPluginAlgorithmFactory *fact = astra::CPluginAlgorithmFactory::getSingletonPtr(); mexPrintf((fact->getHelp(name)+"\n").c_str()); }else{ mexPrintf("astra_mex_plugin('get_help', name);\n"); diff --git a/python/astra/plugin_c.pyx b/python/astra/plugin_c.pyx index 8d6816b..775ccd4 100644 --- a/python/astra/plugin_c.pyx +++ b/python/astra/plugin_c.pyx @@ -32,21 +32,25 @@ import inspect from libcpp.string cimport string from libcpp cimport bool -cdef CPluginAlgorithmFactory *fact = getSingletonPtr() +cdef CPythonPluginAlgorithmFactory *fact = getSingletonPtr() from . import utils -cdef extern from "astra/PluginAlgorithm.h" namespace "astra": - cdef cppclass CPluginAlgorithmFactory: +cdef extern from "src/PythonPluginAlgorithm.h" namespace "astra": + cdef cppclass CPythonPluginAlgorithmFactory: bool registerPlugin(string className) bool registerPlugin(string name, string className) bool registerPluginClass(object className) bool registerPluginClass(string name, object className) object getRegistered() - string getHelp(string name) + string getHelp(string &name) + +cdef extern from "src/PythonPluginAlgorithm.h" namespace "astra::CPythonPluginAlgorithmFactory": + cdef CPythonPluginAlgorithmFactory* getSingletonPtr() cdef extern from "astra/PluginAlgorithm.h" namespace "astra::CPluginAlgorithmFactory": - cdef CPluginAlgorithmFactory* getSingletonPtr() + # NB: Using wrong pointer type here for convenience + cdef void registerFactory(CPythonPluginAlgorithmFactory *) def register(className, name=None): if inspect.isclass(className): @@ -65,3 +69,6 @@ def get_registered(): def get_help(name): return utils.wrap_from_bytes(fact.getHelp(six.b(name))) + +# Register python plugin factory with astra +registerFactory(fact) diff --git a/python/astra/src/PythonPluginAlgorithm.cpp b/python/astra/src/PythonPluginAlgorithm.cpp new file mode 100644 index 0000000..1ea858d --- /dev/null +++ b/python/astra/src/PythonPluginAlgorithm.cpp @@ -0,0 +1,402 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the ASTRA Toolbox. + + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see . + +----------------------------------------------------------------------- +$Id$ +*/ + +#ifdef ASTRA_PYTHON + +#include "PythonPluginAlgorithm.h" + +#include "astra/Logging.h" +#include "astra/Utilities.h" +#include +#include +#include +#include +#include + +#include +#include "bytesobject.h" + +namespace astra { + + + +void logPythonError(){ + if(PyErr_Occurred()){ + PyObject *ptype, *pvalue, *ptraceback; + PyErr_Fetch(&ptype, &pvalue, &ptraceback); + PyErr_NormalizeException(&ptype, &pvalue, &ptraceback); + PyObject *traceback = PyImport_ImportModule("traceback"); + if(traceback!=NULL){ + PyObject *exc; + if(ptraceback==NULL){ + exc = PyObject_CallMethod(traceback,"format_exception_only","OO",ptype, pvalue); + }else{ + exc = PyObject_CallMethod(traceback,"format_exception","OOO",ptype, pvalue, ptraceback); + } + if(exc!=NULL){ + PyObject *six = PyImport_ImportModule("six"); + if(six!=NULL){ + PyObject *iter = PyObject_GetIter(exc); + if(iter!=NULL){ + PyObject *line; + std::string errStr = ""; + while(line = PyIter_Next(iter)){ + PyObject *retb = PyObject_CallMethod(six,"b","O",line); + if(retb!=NULL){ + errStr += std::string(PyBytes_AsString(retb)); + Py_DECREF(retb); + } + Py_DECREF(line); + } + ASTRA_ERROR("%s",errStr.c_str()); + Py_DECREF(iter); + } + Py_DECREF(six); + } + Py_DECREF(exc); + } + Py_DECREF(traceback); + } + if(ptype!=NULL) Py_DECREF(ptype); + if(pvalue!=NULL) Py_DECREF(pvalue); + if(ptraceback!=NULL) Py_DECREF(ptraceback); + } +} + + +CPluginAlgorithm::CPluginAlgorithm(PyObject* pyclass){ + instance = PyObject_CallObject(pyclass, NULL); + if(instance==NULL) logPythonError(); +} + +CPluginAlgorithm::~CPluginAlgorithm(){ + if(instance!=NULL){ + Py_DECREF(instance); + instance = NULL; + } +} + +bool CPluginAlgorithm::initialize(const Config& _cfg){ + if(instance==NULL) return false; + PyObject *cfgDict = XMLNode2dict(_cfg.self); + PyObject *retVal = PyObject_CallMethod(instance, "astra_init", "O",cfgDict); + Py_DECREF(cfgDict); + if(retVal==NULL){ + logPythonError(); + return false; + } + m_bIsInitialized = true; + Py_DECREF(retVal); + return m_bIsInitialized; +} + +void CPluginAlgorithm::run(int _iNrIterations){ + if(instance==NULL) return; + PyGILState_STATE state = PyGILState_Ensure(); + PyObject *retVal = PyObject_CallMethod(instance, "run", "i",_iNrIterations); + if(retVal==NULL){ + logPythonError(); + }else{ + Py_DECREF(retVal); + } + PyGILState_Release(state); +} + +void fixLapackLoading(){ + // When running in Matlab, we need to force numpy + // to use its internal lapack library instead of + // Matlab's MKL library to avoid errors. To do this, + // we set Python's dlopen flags to RTLD_NOW|RTLD_DEEPBIND + // and import 'numpy.linalg.lapack_lite' here. We reset + // Python's dlopen flags afterwards. + PyObject *sys = PyImport_ImportModule("sys"); + if(sys!=NULL){ + PyObject *curFlags = PyObject_CallMethod(sys,"getdlopenflags",NULL); + if(curFlags!=NULL){ + PyObject *retVal = PyObject_CallMethod(sys, "setdlopenflags", "i",10); + if(retVal!=NULL){ + PyObject *lapack = PyImport_ImportModule("numpy.linalg.lapack_lite"); + if(lapack!=NULL){ + Py_DECREF(lapack); + } + PyObject_CallMethod(sys, "setdlopenflags", "O",curFlags); + Py_DECREF(retVal); + } + Py_DECREF(curFlags); + } + Py_DECREF(sys); + } +} + +CPythonPluginAlgorithmFactory::CPythonPluginAlgorithmFactory(){ + if(!Py_IsInitialized()){ + Py_Initialize(); + PyEval_InitThreads(); + } +#ifndef _MSC_VER + if(astra::running_in_matlab) fixLapackLoading(); +#endif + pluginDict = PyDict_New(); + inspect = PyImport_ImportModule("inspect"); + six = PyImport_ImportModule("six"); +} + +CPythonPluginAlgorithmFactory::~CPythonPluginAlgorithmFactory(){ + if(pluginDict!=NULL){ + Py_DECREF(pluginDict); + } + if(inspect!=NULL) Py_DECREF(inspect); + if(six!=NULL) Py_DECREF(six); +} + +PyObject * getClassFromString(std::string str){ + std::vector items; + boost::split(items, str, boost::is_any_of(".")); + PyObject *pyclass = PyImport_ImportModule(items[0].c_str()); + if(pyclass==NULL){ + logPythonError(); + return NULL; + } + PyObject *submod = pyclass; + for(unsigned int i=1;i CPythonPluginAlgorithmFactory::getRegisteredMap(){ + std::map ret; + PyObject *key, *value; + Py_ssize_t pos = 0; + while (PyDict_Next(pluginDict, &pos, &key, &value)) { + PyObject *keystr = PyObject_Str(key); + if(keystr!=NULL){ + PyObject *valstr = PyObject_Str(value); + if(valstr!=NULL){ + PyObject * keyb = PyObject_CallMethod(six,"b","O",keystr); + if(keyb!=NULL){ + PyObject * valb = PyObject_CallMethod(six,"b","O",valstr); + if(valb!=NULL){ + ret[PyBytes_AsString(keyb)] = PyBytes_AsString(valb); + Py_DECREF(valb); + } + Py_DECREF(keyb); + } + Py_DECREF(valstr); + } + Py_DECREF(keystr); + } + logPythonError(); + } + return ret; +} + +std::string CPythonPluginAlgorithmFactory::getHelp(const std::string &name){ + PyObject *className = PyDict_GetItemString(pluginDict, name.c_str()); + if(className==NULL){ + ASTRA_ERROR("Plugin %s not found!",name.c_str()); + PyErr_Clear(); + return ""; + } + std::string ret = ""; + PyObject *pyclass; + if(PyBytes_Check(className)){ + std::string str = std::string(PyBytes_AsString(className)); + pyclass = getClassFromString(str); + }else{ + pyclass = className; + } + if(pyclass==NULL) return ""; + if(inspect!=NULL && six!=NULL){ + PyObject *retVal = PyObject_CallMethod(inspect,"getdoc","O",pyclass); + if(retVal!=NULL){ + if(retVal!=Py_None){ + PyObject *retb = PyObject_CallMethod(six,"b","O",retVal); + if(retb!=NULL){ + ret = std::string(PyBytes_AsString(retb)); + Py_DECREF(retb); + } + } + Py_DECREF(retVal); + }else{ + logPythonError(); + } + } + if(PyBytes_Check(className)){ + Py_DECREF(pyclass); + } + return ret; +} + +DEFINE_SINGLETON(CPythonPluginAlgorithmFactory); + +#if PY_MAJOR_VERSION >= 3 +PyObject * pyStringFromString(std::string str){ + return PyUnicode_FromString(str.c_str()); +} +#else +PyObject * pyStringFromString(std::string str){ + return PyBytes_FromString(str.c_str()); +} +#endif + +PyObject* stringToPythonValue(std::string str){ + if(str.find(";")!=std::string::npos){ + std::vector rows, row; + boost::split(rows, str, boost::is_any_of(";")); + PyObject *mat = PyList_New(rows.size()); + for(unsigned int i=0; i vec; + boost::split(vec, str, boost::is_any_of(",")); + PyObject *veclist = PyList_New(vec.size()); + for(unsigned int i=0;i nodes = node.getNodes(); + std::list::iterator it = nodes.begin(); + while(it!=nodes.end()){ + XMLNode subnode = *it; + if(subnode.getName()=="Option"){ + PyObject *obj; + if(subnode.hasAttribute("value")){ + obj = stringToPythonValue(subnode.getAttribute("value")); + }else{ + obj = stringToPythonValue(subnode.getContent()); + } + PyDict_SetItemString(opts, subnode.getAttribute("key").c_str(), obj); + Py_DECREF(obj); + }else{ + PyObject *obj = stringToPythonValue(subnode.getContent()); + PyDict_SetItemString(dct, subnode.getName().c_str(), obj); + Py_DECREF(obj); + } + ++it; + } + PyDict_SetItemString(dct, "options", opts); + Py_DECREF(opts); + return dct; +} + +} +#endif diff --git a/python/astra/src/PythonPluginAlgorithm.h b/python/astra/src/PythonPluginAlgorithm.h new file mode 100644 index 0000000..0b1309e --- /dev/null +++ b/python/astra/src/PythonPluginAlgorithm.h @@ -0,0 +1,89 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the ASTRA Toolbox. + + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see . + +----------------------------------------------------------------------- +$Id$ +*/ + +#ifndef _INC_PYTHONPLUGINALGORITHM +#define _INC_PYTHONPLUGINALGORITHM + +#ifdef ASTRA_PYTHON + +#include "astra/Algorithm.h" +#include "astra/Singleton.h" +#include "astra/XMLDocument.h" +#include "astra/XMLNode.h" +#include "astra/PluginAlgorithm.h" + +#include + +namespace astra { +class CPluginAlgorithm : public CAlgorithm { + +public: + + CPluginAlgorithm(PyObject* pyclass); + ~CPluginAlgorithm(); + + bool initialize(const Config& _cfg); + void run(int _iNrIterations); + +private: + PyObject * instance; + +}; + +class CPythonPluginAlgorithmFactory : public CPluginAlgorithmFactory, public Singleton { + +public: + + CPythonPluginAlgorithmFactory(); + virtual ~CPythonPluginAlgorithmFactory(); + + virtual CAlgorithm * getPlugin(const std::string &name); + + virtual bool registerPlugin(std::string name, std::string className); + virtual bool registerPlugin(std::string className); + bool registerPluginClass(std::string name, PyObject * className); + bool registerPluginClass(PyObject * className); + + PyObject * getRegistered(); + virtual std::map getRegisteredMap(); + + virtual std::string getHelp(const std::string &name); + +private: + PyObject * pluginDict; + PyObject *inspect, *six; +}; + +PyObject* XMLNode2dict(XMLNode node); + +} + + +#endif + +#endif diff --git a/python/builder.py b/python/builder.py index 018b26b..9a77ecc 100644 --- a/python/builder.py +++ b/python/builder.py @@ -70,6 +70,10 @@ ext_modules = [ ] ext_modules = cythonize("astra/*.pyx", language_level=2) cmdclass = { 'build_ext': build_ext } +for m in ext_modules: + if m.name == 'astra.plugin_c': + m.sources.append('astra/src/PythonPluginAlgorithm.cpp') + setup (name = 'PyASTRAToolbox', version = '1.7.1', description = 'Python interface to the ASTRA-Toolbox', diff --git a/src/PluginAlgorithm.cpp b/src/PluginAlgorithm.cpp index 9fc511a..1bcfbdb 100644 --- a/src/PluginAlgorithm.cpp +++ b/src/PluginAlgorithm.cpp @@ -26,376 +26,11 @@ along with the ASTRA Toolbox. If not, see . $Id$ */ -#ifdef ASTRA_PYTHON - #include "astra/PluginAlgorithm.h" -#include "astra/Logging.h" -#include "astra/Utilities.h" -#include -#include -#include -#include -#include - -#include -#include "bytesobject.h" namespace astra { +CPluginAlgorithmFactory *CPluginAlgorithmFactory::m_factory = 0; - -void logPythonError(){ - if(PyErr_Occurred()){ - PyObject *ptype, *pvalue, *ptraceback; - PyErr_Fetch(&ptype, &pvalue, &ptraceback); - PyErr_NormalizeException(&ptype, &pvalue, &ptraceback); - PyObject *traceback = PyImport_ImportModule("traceback"); - if(traceback!=NULL){ - PyObject *exc; - if(ptraceback==NULL){ - exc = PyObject_CallMethod(traceback,"format_exception_only","OO",ptype, pvalue); - }else{ - exc = PyObject_CallMethod(traceback,"format_exception","OOO",ptype, pvalue, ptraceback); - } - if(exc!=NULL){ - PyObject *six = PyImport_ImportModule("six"); - if(six!=NULL){ - PyObject *iter = PyObject_GetIter(exc); - if(iter!=NULL){ - PyObject *line; - std::string errStr = ""; - while(line = PyIter_Next(iter)){ - PyObject *retb = PyObject_CallMethod(six,"b","O",line); - if(retb!=NULL){ - errStr += std::string(PyBytes_AsString(retb)); - Py_DECREF(retb); - } - Py_DECREF(line); - } - ASTRA_ERROR("%s",errStr.c_str()); - Py_DECREF(iter); - } - Py_DECREF(six); - } - Py_DECREF(exc); - } - Py_DECREF(traceback); - } - if(ptype!=NULL) Py_DECREF(ptype); - if(pvalue!=NULL) Py_DECREF(pvalue); - if(ptraceback!=NULL) Py_DECREF(ptraceback); - } -} - - -CPluginAlgorithm::CPluginAlgorithm(PyObject* pyclass){ - instance = PyObject_CallObject(pyclass, NULL); - if(instance==NULL) logPythonError(); -} - -CPluginAlgorithm::~CPluginAlgorithm(){ - if(instance!=NULL){ - Py_DECREF(instance); - instance = NULL; - } -} - -bool CPluginAlgorithm::initialize(const Config& _cfg){ - if(instance==NULL) return false; - PyObject *cfgDict = XMLNode2dict(_cfg.self); - PyObject *retVal = PyObject_CallMethod(instance, "astra_init", "O",cfgDict); - Py_DECREF(cfgDict); - if(retVal==NULL){ - logPythonError(); - return false; - } - m_bIsInitialized = true; - Py_DECREF(retVal); - return m_bIsInitialized; -} - -void CPluginAlgorithm::run(int _iNrIterations){ - if(instance==NULL) return; - PyGILState_STATE state = PyGILState_Ensure(); - PyObject *retVal = PyObject_CallMethod(instance, "run", "i",_iNrIterations); - if(retVal==NULL){ - logPythonError(); - }else{ - Py_DECREF(retVal); - } - PyGILState_Release(state); } -void fixLapackLoading(){ - // When running in Matlab, we need to force numpy - // to use its internal lapack library instead of - // Matlab's MKL library to avoid errors. To do this, - // we set Python's dlopen flags to RTLD_NOW|RTLD_DEEPBIND - // and import 'numpy.linalg.lapack_lite' here. We reset - // Python's dlopen flags afterwards. - PyObject *sys = PyImport_ImportModule("sys"); - if(sys!=NULL){ - PyObject *curFlags = PyObject_CallMethod(sys,"getdlopenflags",NULL); - if(curFlags!=NULL){ - PyObject *retVal = PyObject_CallMethod(sys, "setdlopenflags", "i",10); - if(retVal!=NULL){ - PyObject *lapack = PyImport_ImportModule("numpy.linalg.lapack_lite"); - if(lapack!=NULL){ - Py_DECREF(lapack); - } - PyObject_CallMethod(sys, "setdlopenflags", "O",curFlags); - Py_DECREF(retVal); - } - Py_DECREF(curFlags); - } - Py_DECREF(sys); - } -} - -CPluginAlgorithmFactory::CPluginAlgorithmFactory(){ - if(!Py_IsInitialized()){ - Py_Initialize(); - PyEval_InitThreads(); - } -#ifndef _MSC_VER - if(astra::running_in_matlab) fixLapackLoading(); -#endif - pluginDict = PyDict_New(); - inspect = PyImport_ImportModule("inspect"); - six = PyImport_ImportModule("six"); -} - -CPluginAlgorithmFactory::~CPluginAlgorithmFactory(){ - if(pluginDict!=NULL){ - Py_DECREF(pluginDict); - } - if(inspect!=NULL) Py_DECREF(inspect); - if(six!=NULL) Py_DECREF(six); -} - -PyObject * getClassFromString(std::string str){ - std::vector items; - boost::split(items, str, boost::is_any_of(".")); - PyObject *pyclass = PyImport_ImportModule(items[0].c_str()); - if(pyclass==NULL){ - logPythonError(); - return NULL; - } - PyObject *submod = pyclass; - for(unsigned int i=1;i CPluginAlgorithmFactory::getRegisteredMap(){ - std::map ret; - PyObject *key, *value; - Py_ssize_t pos = 0; - while (PyDict_Next(pluginDict, &pos, &key, &value)) { - PyObject *keystr = PyObject_Str(key); - if(keystr!=NULL){ - PyObject *valstr = PyObject_Str(value); - if(valstr!=NULL){ - PyObject * keyb = PyObject_CallMethod(six,"b","O",keystr); - if(keyb!=NULL){ - PyObject * valb = PyObject_CallMethod(six,"b","O",valstr); - if(valb!=NULL){ - ret[PyBytes_AsString(keyb)] = PyBytes_AsString(valb); - Py_DECREF(valb); - } - Py_DECREF(keyb); - } - Py_DECREF(valstr); - } - Py_DECREF(keystr); - } - logPythonError(); - } - return ret; -} - -std::string CPluginAlgorithmFactory::getHelp(std::string name){ - PyObject *className = PyDict_GetItemString(pluginDict, name.c_str()); - if(className==NULL){ - ASTRA_ERROR("Plugin %s not found!",name.c_str()); - PyErr_Clear(); - return ""; - } - std::string ret = ""; - PyObject *pyclass; - if(PyBytes_Check(className)){ - std::string str = std::string(PyBytes_AsString(className)); - pyclass = getClassFromString(str); - }else{ - pyclass = className; - } - if(pyclass==NULL) return ""; - if(inspect!=NULL && six!=NULL){ - PyObject *retVal = PyObject_CallMethod(inspect,"getdoc","O",pyclass); - if(retVal!=NULL){ - if(retVal!=Py_None){ - PyObject *retb = PyObject_CallMethod(six,"b","O",retVal); - if(retb!=NULL){ - ret = std::string(PyBytes_AsString(retb)); - Py_DECREF(retb); - } - } - Py_DECREF(retVal); - }else{ - logPythonError(); - } - } - if(PyBytes_Check(className)){ - Py_DECREF(pyclass); - } - return ret; -} - -DEFINE_SINGLETON(CPluginAlgorithmFactory); - -#if PY_MAJOR_VERSION >= 3 -PyObject * pyStringFromString(std::string str){ - return PyUnicode_FromString(str.c_str()); -} -#else -PyObject * pyStringFromString(std::string str){ - return PyBytes_FromString(str.c_str()); -} -#endif - -PyObject* stringToPythonValue(std::string str){ - if(str.find(";")!=std::string::npos){ - std::vector rows, row; - boost::split(rows, str, boost::is_any_of(";")); - PyObject *mat = PyList_New(rows.size()); - for(unsigned int i=0; i vec; - boost::split(vec, str, boost::is_any_of(",")); - PyObject *veclist = PyList_New(vec.size()); - for(unsigned int i=0;i nodes = node.getNodes(); - std::list::iterator it = nodes.begin(); - while(it!=nodes.end()){ - XMLNode subnode = *it; - if(subnode.getName()=="Option"){ - PyObject *obj; - if(subnode.hasAttribute("value")){ - obj = stringToPythonValue(subnode.getAttribute("value")); - }else{ - obj = stringToPythonValue(subnode.getContent()); - } - PyDict_SetItemString(opts, subnode.getAttribute("key").c_str(), obj); - Py_DECREF(obj); - }else{ - PyObject *obj = stringToPythonValue(subnode.getContent()); - PyDict_SetItemString(dct, subnode.getName().c_str(), obj); - Py_DECREF(obj); - } - ++it; - } - PyDict_SetItemString(dct, "options", opts); - Py_DECREF(opts); - return dct; -} - -} -#endif -- cgit v1.2.3 From 96fa285132bf88462c33c5b24cc1b241fb3d4d73 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Thu, 21 Jan 2016 14:30:32 +0100 Subject: Initialize Python plugins when available in Matlab --- build/linux/Makefile.in | 10 ++++++++++ matlab/mex/astra_mex_plugin_c.cpp | 25 ++++++++++++++++++++++++- matlab/mex/mexInitFunctions.cpp | 8 ++++++++ 3 files changed, 42 insertions(+), 1 deletion(-) (limited to 'build') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index d5644bc..57ed8f8 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -95,6 +95,11 @@ ifeq ($(cuda),yes) MEXFLAGS += -DASTRA_CUDA endif +ifeq ($(python),yes) +MEXPYLDFLAGS='$$LDFLAGS $(LDFLAGS) -L$(PYLIBDIR)' +MEXPYLIBS=$(MEXLIBS) -l$(PYLIBVER) +endif + endif LIBDIR=/usr/local/lib @@ -265,6 +270,11 @@ mex: $(MATLAB_MEX) %.$(MEXSUFFIX): %.o $(MATLAB_CXX_OBJECTS) libastra.la $(MEX) LDFLAGS=$(MEXLDFLAGS) $(MEXFLAGS) $(LIBS) $(MEXLIBS) -lastra -output $* $*.o $(MATLAB_CXX_OBJECTS) + +ifeq ($(python),yes) +matlab/mex/astra_mex_plugin_c.$(MEXSUFFIX): matlab/mex/astra_mex_plugin_c.o $(MATLAB_CXX_OBJECTS) libastra.la + $(MEX) LDFLAGS=$(MEXPYLDFLAGS) $(MEXFLAGS) $(LIBS) $(MEXPYLIBS) -lastra -output matlab/mex/astra_mex_plugin_c $< $(MATLAB_CXX_OBJECTS) +endif endif ifeq ($(python),yes) diff --git a/matlab/mex/astra_mex_plugin_c.cpp b/matlab/mex/astra_mex_plugin_c.cpp index 627e34a..9bd4446 100644 --- a/matlab/mex/astra_mex_plugin_c.cpp +++ b/matlab/mex/astra_mex_plugin_c.cpp @@ -37,10 +37,31 @@ $Id$ #include "astra/PluginAlgorithm.h" +#include + using namespace std; using namespace astra; +//----------------------------------------------------------------------------------------- +/** astra_mex_plugin('init'); + * + * Initialize plugin support by initializing python and importing astra + */ +void astra_mex_plugin_init() +{ + if(!Py_IsInitialized()){ + Py_Initialize(); + PyEval_InitThreads(); + } + + // Importing astra may be overkill, since we only need to initialize + // PythonPluginAlgorithmFactory from astra.plugin_c. + PyObject *mod = PyImport_ImportModule("astra"); + Py_DECREF(mod); +} + + //----------------------------------------------------------------------------------------- /** astra_mex_plugin('get_registered'); * @@ -128,7 +149,9 @@ void mexFunction(int nlhs, mxArray* plhs[], initASTRAMex(); // SWITCH (MODE) - if (sMode == std::string("get_registered")) { + if (sMode == "init") { + astra_mex_plugin_init(); + } else if (sMode == std::string("get_registered")) { astra_mex_plugin_get_registered(nlhs, plhs, nrhs, prhs); }else if (sMode == std::string("get_help")) { astra_mex_plugin_get_help(nlhs, plhs, nrhs, prhs); diff --git a/matlab/mex/mexInitFunctions.cpp b/matlab/mex/mexInitFunctions.cpp index bd3df2c..7245af2 100644 --- a/matlab/mex/mexInitFunctions.cpp +++ b/matlab/mex/mexInitFunctions.cpp @@ -23,5 +23,13 @@ void initASTRAMex(){ if(!astra::CLogger::setCallbackScreen(&logCallBack)){ mexErrMsgTxt("Error initializing mex functions."); } + mexIsInitialized=true; + + + // If we have support for plugins, initialize them. + // (NB: Call this after setting mexIsInitialized, to avoid recursively + // calling initASTRAMex) + mexEvalString("if exist('astra_mex_plugin_c') == 3; astra_mex_plugin_c('init'); end"); + } -- cgit v1.2.3 From 3c194763acb879f0d51b7d4c90c3aad667223214 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Thu, 21 Jan 2016 14:37:07 +0100 Subject: Add missing .PHONY targets --- build/linux/Makefile.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'build') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 57ed8f8..9535b4c 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -419,7 +419,7 @@ $(srcdir)/configure: $(srcdir)/configure.ac @echo "configure.ac has been changed. Regenerating configure script" cd $(srcdir) && $(SHELL) ./autogen.sh -.PHONY: all mex test clean distclean install install-libraries +.PHONY: all mex test clean distclean install install-libraries py python-root-install install-python # don't remove intermediate files: .SECONDARY: -- cgit v1.2.3 From 46836ee3195fdc8d09a0f03cee13b475b4ff9fc1 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Wed, 10 Feb 2016 17:14:54 +0100 Subject: Update gen.py to work on more python versions --- build/msvc/gen.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) (limited to 'build') diff --git a/build/msvc/gen.py b/build/msvc/gen.py index 999710f..cc69a62 100644 --- a/build/msvc/gen.py +++ b/build/msvc/gen.py @@ -1,6 +1,8 @@ from __future__ import print_function import sys import os +import codecs +import six vcppguid = "8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942" # C++ project siguid = "2150E333-8FDC-42A3-9474-1A3956D46DE8" # project group @@ -428,7 +430,10 @@ P_astra["files"].sort() projects = [ P_astra, F_astra_mex, P0, P1, P2, P3, P4, P5, P6, P7, P8 ] -bom = "\xef\xbb\xbf" +if six.PY2: + bom = "\xef\xbb\xbf" +else: + bom = codecs.BOM_UTF8.decode("utf-8") class Configuration: def __init__(self, debug, cuda, x64): -- cgit v1.2.3 From 2206dba14d1830af0e22a3fd06f301da01398c0e Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Thu, 3 Mar 2016 13:01:00 +0100 Subject: Include PluginAlgorithm in non-Python builds as well --- build/linux/Makefile.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'build') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 9535b4c..5d3f677 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -150,6 +150,7 @@ BASE_OBJECTS=\ src/ParallelProjectionGeometry3D.lo \ src/ParallelVecProjectionGeometry3D.lo \ src/PlatformDepSystemCode.lo \ + src/PluginAlgorithm.lo \ src/ProjectionGeometry2D.lo \ src/ProjectionGeometry3D.lo \ src/Projector2D.lo \ @@ -255,7 +256,6 @@ MATLAB_MEX=\ matlab/mex/astra_mex_direct_c.$(MEXSUFFIX) ifeq ($(python),yes) -ALL_OBJECTS+=src/PluginAlgorithm.lo MATLAB_MEX+=matlab/mex/astra_mex_plugin_c.$(MEXSUFFIX) endif -- cgit v1.2.3 From ac5d33197f5e1e07327ba1f7eee8b1c91fad2fe6 Mon Sep 17 00:00:00 2001 From: Willem Jan Palenstijn Date: Tue, 1 Mar 2016 17:24:33 +0100 Subject: Revert "Use nvcc's -MT option" This reverts commit 29c5c86e56697286a92031aaa9fdd903b3bcc426. This fixes building with CUDA 5.5. --- build/linux/Makefile.in | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'build') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 9535b4c..951e9f0 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -315,8 +315,10 @@ ifeq ($(cuda),yes) ifeq ($(gen_static_libs),yes) @$(NVCC) $(NVCCFLAGS) -c $(<) -o $*.o >/dev/null 2>&1 endif - @# Generate a .d file, with target name $*.lo - @$(NVCC) $(NVCCFLAGS) -M $(<) -MT $(*F).lo -odir $(*D) -o $(*D)/$(DEPDIR)/$(*F).d + @# Generate a .d file, and change the target name in it from .o to .lo + @$(NVCC) $(NVCCFLAGS) -M $(<) -odir $(*D) -o $(*D)/$(DEPDIR)/$(*F).d2 + @sed '1s/\.o :/.lo :/' < $(*D)/$(DEPDIR)/$(*F).d2 > $(*D)/$(DEPDIR)/$(*F).d + @rm -f $(*D)/$(DEPDIR)/$(*F).d2 @# Generate empty targets for all dependencies listed in the .d file. @# This mimics gcc's -MP option. @for x in `cat $(*D)/$(DEPDIR)/$(*F).d`; do if test a$$x != a: -a a$$x != a\\; then echo -e "\n$$x:\n" >> $(*D)/$(DEPDIR)/$(*F).d; fi; done -- cgit v1.2.3 From c58929ca7d0201335b5036773b26f82361793f25 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Tue, 19 Apr 2016 16:40:14 +0200 Subject: Use CXX for Python compilation as well --- build/linux/Makefile.in | 4 ++-- python/astra/extrautils.pyx | 2 ++ 2 files changed, 4 insertions(+), 2 deletions(-) (limited to 'build') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index a199bf6..2214734 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -281,13 +281,13 @@ ifeq ($(python),yes) py: libastra.la $(MKDIR) python/build $(MKDIR) python/finalbuild - cd $(srcdir)/../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build install \ + cd $(srcdir)/../../python; CXX="${CXX}" CC="${CXX}" CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build install \ --install-base=$(abs_top_builddir)/python/finalbuild --install-headers=$(abs_top_builddir)/python/finalbuild --install-purelib=$(abs_top_builddir)/python/finalbuild \ --install-platlib=$(abs_top_builddir)/python/finalbuild --install-scripts=$(abs_top_builddir)/python/finalbuild --install-data=$(abs_top_builddir)/python/finalbuild python-root-install: libastra.la $(MKDIR) python/build - cd $(srcdir)/../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build install + cd $(srcdir)/../../python; CXX="${CXX}" CC="${CXX}" CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build install endif diff --git a/python/astra/extrautils.pyx b/python/astra/extrautils.pyx index 5bc315f..2c7771e 100644 --- a/python/astra/extrautils.pyx +++ b/python/astra/extrautils.pyx @@ -22,6 +22,8 @@ # along with the ASTRA Toolbox. If not, see . # # ----------------------------------------------------------------------- +# distutils: language = c++ + def clipCircle(img): cdef int i,j -- cgit v1.2.3 From 93eacadc5b94f8e1241dc6836be27d16881a2826 Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Tue, 19 Apr 2016 17:12:58 +0200 Subject: Add comment about setting CC to CXX --- build/linux/Makefile.in | 2 ++ 1 file changed, 2 insertions(+) (limited to 'build') diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index 2214734..f10f482 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -281,12 +281,14 @@ ifeq ($(python),yes) py: libastra.la $(MKDIR) python/build $(MKDIR) python/finalbuild + # Note: setting CC to CXX is intentional. Python uses CC for compilation even if input is C++. cd $(srcdir)/../../python; CXX="${CXX}" CC="${CXX}" CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build install \ --install-base=$(abs_top_builddir)/python/finalbuild --install-headers=$(abs_top_builddir)/python/finalbuild --install-purelib=$(abs_top_builddir)/python/finalbuild \ --install-platlib=$(abs_top_builddir)/python/finalbuild --install-scripts=$(abs_top_builddir)/python/finalbuild --install-data=$(abs_top_builddir)/python/finalbuild python-root-install: libastra.la $(MKDIR) python/build + # Note: setting CC to CXX is intentional. Python uses CC for compilation even if input is C++. cd $(srcdir)/../../python; CXX="${CXX}" CC="${CXX}" CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py build --build-base=$(abs_top_builddir)/python/build install endif -- cgit v1.2.3