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Mar 21, 2018 Version 6.0.2
* Add more OpenMP parallelism
* Improve testing script comparing results between OpenMP and non-OpenMP builds
* Fix all remaining compiler warnings
Mar 20, 2018 Version 6.0.0
* Migrate to wxgtk3.0
* Add OpenMP parallelism and use by default
Dec 21, 2012 Version 5.2.1
* tools/phm2helix.cpp: Fix spelling mistake
Nov 7, 2010 Version 5.2.0
* tools/ifexport.cpp: Add Text output option (thanks to
Christian Thibaudeau)
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Makefile deleted 100644 → 0
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Makefile.am
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......@@ -20,7 +20,7 @@ SUBDIRS=man libctsupport libctsim html cgi-bin include $(EXTRA_DIRS1) $(EXTRA_D
EXTRA_DIST=acsite.m4 make.bat msvc/ctsim.dsw msvc/ctsimtext/ctsimtext.dsp msvc/libctsim/libctsim.dsp msvc/ctsim/ctsim.dsp
CLEANFILES=docs/html/\* config.log config.status configure.in config.h stamp-h1
CLEANFILES=docs/html/\* config.log configure.in config.h stamp-h1
clean-local:
rm -rf docs/html
......
Makefile.in
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aclocal.m4
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bootstrap.sh 0 → 100755
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rm -f config.cache aclocal.m4
aclocal
autoconf
autoheader
automake
cgi-bin/Makefile deleted 100644 → 0
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test -z "$(cgibindir)" || $(MKDIR_P) "$(DESTDIR)$(cgibindir)"
@list='$(cgibin_SCRIPTS)'; test -n "$(cgibindir)" || list=; \
if test -n "$$list"; then \
echo " $(MKDIR_P) '$(DESTDIR)$(cgibindir)'"; \
$(MKDIR_P) "$(DESTDIR)$(cgibindir)" || exit 1; \
fi; \
for p in $$list; do \
if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
if test -f "$$d$$p"; then echo "$$d$$p"; echo "$$p"; else :; fi; \
......@@ -264,14 +359,12 @@ uninstall-cgibinSCRIPTS:
@list='$(cgibin_SCRIPTS)'; test -n "$(cgibindir)" || exit 0; \
files=`for p in $$list; do echo "$$p"; done | \
sed -e 's,.*/,,;$(transform)'`; \
test -n "$$list" || exit 0; \
echo " ( cd '$(DESTDIR)$(cgibindir)' && rm -f" $$files ")"; \
cd "$(DESTDIR)$(cgibindir)" && rm -f $$files
tags: TAGS
TAGS:
dir='$(DESTDIR)$(cgibindir)'; $(am__uninstall_files_from_dir)
tags TAGS:
ctags: CTAGS
CTAGS:
ctags CTAGS:
cscope cscopelist:
distdir: $(DISTFILES)
......@@ -321,10 +414,15 @@ install-am: all-am
installcheck: installcheck-am
install-strip:
if test -z '$(STRIP)'; then \
$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
`test -z '$(STRIP)' || \
echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
install; \
else \
$(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
"INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'" install; \
fi
mostlyclean-generic:
clean-generic:
......@@ -404,16 +502,19 @@ uninstall-am: uninstall-cgibinSCRIPTS
.MAKE: install-am install-strip
.PHONY: all all-am check check-am clean clean-generic distclean \
distclean-generic distdir dvi dvi-am html html-am info info-am \
install install-am install-cgibinSCRIPTS install-data \
install-data-am install-dvi install-dvi-am install-exec \
install-exec-am install-html install-html-am install-info \
install-info-am install-man install-pdf install-pdf-am \
install-ps install-ps-am install-strip installcheck \
installcheck-am installdirs maintainer-clean \
.PHONY: all all-am check check-am clean clean-generic cscopelist-am \
ctags-am distclean distclean-generic distdir dvi dvi-am html \
html-am info info-am install install-am install-cgibinSCRIPTS \
install-data install-data-am install-dvi install-dvi-am \
install-exec install-exec-am install-html install-html-am \
install-info install-info-am install-man install-pdf \
install-pdf-am install-ps install-ps-am install-strip \
installcheck installcheck-am installdirs maintainer-clean \
maintainer-clean-generic mostlyclean mostlyclean-generic pdf \
pdf-am ps ps-am uninstall uninstall-am uninstall-cgibinSCRIPTS
pdf-am ps ps-am tags-am uninstall uninstall-am \
uninstall-cgibinSCRIPTS
.PRECIOUS: Makefile
# Tell versions [3.59,3.63) of GNU make to not export all variables.
......
cgi-bin/ctsim.cgi deleted 100644 → 0
View file @ cb6b6b38
#!/usr/bin/perl
# cgi-bin/ctsim.cgi. Generated from ctsim.cgi.in by configure.
use strict;
use CGI;
use File::Basename;
use Fcntl ':flock';
require './ctsim.conf';
my $opt_d = 0;
$ENV{'PATH'} = "$::bindir:$::lamrundir:/bin";
my $fromhost = $ENV{'REMOTE_HOST'};
my $gmt_start = time();
my $gmt_end;
my $execution_time;
my %in;
CGI::ReadParse(\%in);
# Incoming variables
# Phantom_Name, Phantom_Nx, Phantom_Ny, Phantom_NSample
# PJ_NDet, PJ_NRot, PJ_NRay, PJ_RotAngle,
# IR_Nx, IR_Ny, IR_Filter, IR_Filter_Param
my $error = "";
if ($::single_process_only > 0) {
my @processes = `/bin/ps -A`;
my $running = 0;
foreach my $p (@processes) {
if ($p =~ m/ctsimtext/) {
$error .= "Another online simulation is currently running.<br>You may wait a moment and then click your browser's <b>Refresh</b> button to resubmit your simulation<br>";
last;
}
}
}
my $Phantom_Name = FilterMetaChars($in{'Phantom_Name'});
my $Phantom_Nx = FilterToNumber($in{'Phantom_Nx'});
my $Phantom_Ny = FilterToNumber($in{'Phantom_Ny'});
my $Phantom_ViewRatio = FilterToNumber($in{'Phantom_ViewRatio'});
my $Phantom_NSample = FilterToNumber($in{'Phantom_NSample'});
$error .= "Phantom name must not be blank<br>" if ($Phantom_Name eq "");
$error .= "Phantom Size must be between 5 and 512<br>" if ($Phantom_Nx < 5 || $Phantom_Nx > 512 || $Phantom_Ny < 5 || $Phantom_Ny > 512);
$error .= "Phantom NSample must be between 1 and 5<br>" if ($Phantom_NSample < 1 || $Phantom_NSample > 5);
$error .= "View Ratio must be between 0 and 100<br>" if ($Phantom_ViewRatio <= 0 || $Phantom_ViewRatio > 100);
my $PJ_Geometry = FilterMetaChars($in{'PJ_Geometry'});
my $PJ_NDet = FilterToNumber($in{'PJ_NDet'});
my $PJ_NRot = FilterToNumber($in{'PJ_NRot'});
my $PJ_FocalLength = FilterToNumber($in{'PJ_FocalLength'});
my $PJ_NRay = FilterToNumber($in{'PJ_NRay'});
my $PJ_RotAngle = FilterToNumber($in{'PJ_RotAngle'});
my $PJ_ScanRatio = FilterToNumber($in{'PJ_ScanRatio'});
$error .= "Projection NDet must be between 5 and 1000<br>" if ($PJ_NDet < 5 || $PJ_NDet > 1000);
$error .= "Projection NRot must be between 5 and 1000<br>" if ($PJ_NRot < 5 || $PJ_NRot > 1000);
$error .= "Projection NRay must be between 1 and 5<br>" if ($PJ_NRay < 1 || $PJ_NRay > 5);
$error .= "Projection RotAngle must be between 0.1 and 2<br>" if ($PJ_RotAngle < 0.1 || $PJ_RotAngle > 2);
$error .= "Focal length must be between 1.01 and 10<b>" if ($PJ_FocalLength <= 1 || $PJ_FocalLength > 10);
$error .= "Scan Ratio must be between 0 and 10<br>" if ($PJ_ScanRatio <= 0 || $PJ_ScanRatio > 10);
#my $IR_Nx = FilterToNumber($in{'IR_Nx'});
#my $IR_Ny = FilterToNumber($in{'IR_Ny'});
my $IR_Nx = $Phantom_Nx;
my $IR_Ny = $Phantom_Ny;
my $IR_FilterMethod = FilterMetaChars($in{'IR_FilterMethod'});
my $IR_Zeropad = FilterToNumber($in{'IR_Zeropad'});
my $IR_Filter = FilterMetaChars($in{'IR_Filter'});
my $IR_Filter_Param = FilterToNumber($in{'IR_Filter_Param'});
my $IR_Interp = FilterMetaChars($in{'IR_Interp'});
my $IR_Backproj = FilterMetaChars($in{'IR_Backproj'});
my $Disp_Min = "auto";
my $Disp_Max = "auto";
$Disp_Min = FilterToNumber($in{'Disp_Min'}) if ($in{'Disp_Min'} ne "auto" && $in{'Disp_Min'} ne "");
$Disp_Max = FilterToNumber($in{'Disp_Max'}) if ($in{'Disp_Max'} ne "auto" && $in{'Disp_Max'} ne "");
if ($Disp_Min ne 'auto' && ! ($Disp_Min =~ /^[\d\.\-]+$/)) {
$error .= "Display Minimum must be 'auto' or numeric (received $Disp_Min) <br>";
}
if ($Disp_Max ne 'auto' && ! ($Disp_Max =~ /^[\d\.\-]+$/)) {
$error .= "Display Maximum must be 'auto' or numeric (received $Disp_Max) <br>";
}
my $MPI_Str = FilterMetaChars($in{'MPI'});
my $MPI = 0;
$MPI = 1 if ($MPI_Str eq "yes" && $::mpi_enable ne "");
$error .= "IR Nx and Ny must be between 5 and 1024<br>" if ($IR_Nx < 5 || $IR_Nx > 1024 || $IR_Ny < 5 || $IR_Ny > 1024);
$error .= "IR Filter Parameter must be between 0 and 1<br>" if ($IR_Filter_Param < 0 || $IR_Filter_Param > 1);
my $tmpid = $$;
my $auto_window_img = "std0.1";
my $auto_window_diff = "std1";
my $auto_window_pj = "full";
my $logfile = "$::jobdir/ctsim.log";
my $result_fname = "$::datadir/result-$tmpid.html";
my $phantom_fname = "$::datadir/phantom-$tmpid.if";
my $pj_fname = "$::datadir/pj-$tmpid.pj";
my $ir_fname = "$::datadir/ir-$tmpid.if";
my $pj_if_fname = "$::datadir/pj-$tmpid.if";
my $sub_fname = "$::datadir/sub-$tmpid.if";
my $phantom_png = "$::datadir/phantom-$tmpid.png";
my $ir_png = "$::datadir/ir-$tmpid.png";
my $pj_png = "$::datadir/pj-$tmpid.png";
my $sub_png = "$::datadir/sub-$tmpid.png";
my $result_url = "$::url_datadir/result-$tmpid.html";
my $phantom_png_url = "$::url_datadir/phantom-$tmpid.png";
my $ir_png_url = "$::url_datadir/ir-$tmpid.png";
my $pj_png_url = "$::url_datadir/pj-$tmpid.png";
my $sub_png_url = "$::url_datadir/sub-$tmpid.png";
my $pjrec_ver = "$::bindir/ctsimtext pjrec";
my $phm2pj_ver = "$::bindir/ctsimtext phm2pj";
my $phm2if_ver = "$::bindir/ctsimtext phm2if";
my $diff_ver = "$::bindir/ctsimtext if2";
$pjrec_ver = "/opt/lam/bin/mpirun N N $::lamrundir/pjrec-lam" if $MPI;
$phm2pj_ver = "/opt/lam/bin/mpirun N N $::lamrundir/phm2pj-lam" if $MPI;
$phm2if_ver = "/opt/lam/bin/mpirun N N $::lamrundir/phm2if-lam" if $MPI;
my $gp_cmd = "$phm2if_ver $phantom_fname $Phantom_Nx $Phantom_Ny --phantom $Phantom_Name --nsample $Phantom_NSample --view-ratio $Phantom_ViewRatio";
my $pj_cmd = "$phm2pj_ver $pj_fname $PJ_NDet $PJ_NRot --phantom $Phantom_Name --nray $PJ_NRay --rotangle $PJ_RotAngle --geometry $PJ_Geometry --focal-length $PJ_FocalLength --view-ratio $Phantom_ViewRatio --scan-ratio $PJ_ScanRatio";
my $pj_if_cmd = "$::bindir/pj2if $pj_fname $pj_if_fname";
my $pjrec_cmd = "$pjrec_ver $pj_fname $ir_fname $IR_Nx $IR_Ny --filter $IR_Filter --filter-param $IR_Filter_Param --interp $IR_Interp --backproj $IR_Backproj --filter-method $IR_FilterMethod --zeropad $IR_Zeropad";
my $sub_cmd = "$diff_ver $phantom_fname $ir_fname $sub_fname --sub";
my $diff_cmd = "$diff_ver $phantom_fname $ir_fname --comp";
my $window_options = "--auto $auto_window_img";
if ($Disp_Min ne 'auto') {
$window_options .= " --min $Disp_Min";
}
if ($Disp_Max ne 'auto') {
$window_options .= " --max $Disp_Max";
}
my $png1_cmd = "$::bindir/ifexport $phantom_fname $phantom_png $window_options --stats --format png --center mode";
my $png2_cmd = "$::bindir/ifexport $ir_fname $ir_png $window_options --stats --format png --center mode";
my $png3_cmd = "$::bindir/ifexport $pj_if_fname $pj_png --auto $auto_window_pj --stats --format png --center mode";
my $png4_cmd = "$::bindir/ifexport $sub_fname $sub_png --auto $auto_window_diff --stats --format png --center mode";
my $title = "CTSim Results";
my $out = head();
$out .= "<HTML> <HEAD><TITLE> $title </TITLE><LINK rel=\"stylesheet\" href=\"http://www.ctsim.org/main.css\" type=\"text/css\">
</HEAD>\n";
$out .= "<BODY BGCOLOR=\"#FFFFFF\" TEXT=\"#000000\" VLINK=\"#800020\" LINK=\"#0000FF\">\n";
$out .= "<H1>$title</H1><HR>\n";
if ($opt_d) {
$out .= "<H2>Commands</H2>\n";
$out .= "$gp_cmd<br>\n$pj_cmd<br>\n$pj_if_cmd<br>\n$pjrec_cmd<br>\n$diff_cmd<br>\n$png1_cmd<br>\n$png2_cmd<br>\n" .
"$png3_cmd<br>\n$png4_cmd<br>\n";
}
my $cmdout = "";
if ($error ne "") {
$out .= "<FONT COLOR=\"#FF0000\">The following errors were present in your request.<br>\n";
$out .= "Please correct them and try submitting your request again.</FONT><br>\n";
$out .= "<i>$error</i>";
} else {
my $gp_out;
my $pj_out;
my $pj_if_out;
my $pjrec_out;
my $sub_out;
my $diff_out;
my $png_gp_out;
my $png_pjrec_out;
my $png_pj_out;
my $png_sub_out;
$gp_out = `$gp_cmd`;
if (-s $phantom_fname) {
$pj_out .= `$pj_cmd`;
$png_gp_out .= `$png1_cmd`;
if (-s $pj_fname) {
$pj_if_out .= `$pj_if_cmd`;
$png_pj_out .= `$png3_cmd`;
$pjrec_out .= `$pjrec_cmd`;
if (-s $ir_fname) {
$png_pjrec_out .= `$png2_cmd`;
$sub_out .= `$sub_cmd`;
$diff_out .= `$diff_cmd`;
$png_sub_out .= `$png4_cmd`;
}
}
}
# Delete image files and projection files
unlink($phantom_fname);
unlink($ir_fname);
unlink($pj_fname);
unlink($pj_if_fname);
unlink($sub_fname);
$cmdout = "$gp_cmd\n $gp_out $pj_cmd\n $pj_out $pj_if_cmd\n $pj_if_out $pjrec_cmd\n $pjrec_out $diff_cmd\n $diff_out $png1_cmd\n $png_gp_out $png2_cmd\n $png_pjrec_out $png3_cmd\n $png_pj_out $png4_cmd\n $png_sub_out";
if (open(LOGFILE,">> $logfile")) {
flock(LOGFILE,LOCK_EX);
seek(LOGFILE, 0, 2);
print LOGFILE "Client Address: $ENV{'REMOTE_ADDR'}\n";
print LOGFILE "Job $tmpid\n";
print LOGFILE $cmdout;
print LOGFILE "----------------------------------------------------\n";
flock(LOGFILE,LOCK_UN);
close(LOGFILE);
}
$gmt_end = time();
$execution_time = $gmt_end - $gmt_start;
if ($opt_d) {
$out .= "<H3>Command Output</H3>$cmdout<HR>\n";
}
my $png_gp_out_html = $png_gp_out;
my $png_pjrec_out_html = $png_pjrec_out;
my $png_pj_out_html = $png_pj_out;
my $png_sub_out_html = $png_sub_out;
$png_gp_out_html =~ s/\n/<br>/gms;
$png_pjrec_out_html =~ s/\n/<br>/gms;
$png_pj_out_html =~ s/\n/<br>/gms;
$png_sub_out_html =~ s/\n/<br>/gms;
$out .= "<TABLE><TR><TD><b>Phantom Image</b></TD><TD><b>Reconstructed Image</b></TD></TR>\n";
$out .= "<TR><TD><IMG SRC=\"$phantom_png_url\"><br><FONT SIZE=1>$png_gp_out</FONT></TD>\n";
$out .= "<TD><IMG SRC=\"$ir_png_url\"><br><FONT SIZE=1>$png_pjrec_out</FONT></TD></TR>\n";
$out .= "<TR><TD><b>Projection Sinogram</b></TD><TD><b>Reconstruction Error</b></TD></TR>\n";
$out .= "<TR><TD><IMG SRC=\"$pj_png_url\"><br><FONT SIZE=1>$png_pj_out</FONT></TD>\n";
$out .= "<TD><IMG SRC=\"$sub_png_url\"><br><FONT SIZE=2>$sub_out</FONT><br><FONT SIZE=1>$png_sub_out</FONT></TD></TR>\n";
$out .= "</TABLE>";
$out .= "<p><b>Error Measurements</b><br>";
$out .= "$diff_out";
$out .= "<p>Execution time: $execution_time seconds\n";
}
$out .= "<HR>\n";
$out .= "Specify another <a href=\"http://www.ctsim.org/simulate.shtml\">simulation</a>.<br>";
$out .= "Return to CTSim's <A HREF=\"http://www.ctsim.org\">home</a>.<br>\n";
$out .= "</BODY> </HTML>";
$out .= "\n";
if (open(OUTFILE,"> $result_fname"))
{
flock(OUTFILE,LOCK_EX);
print OUTFILE $out;
flock(OUTFILE,LOCK_UN);
close OUTFILE;
print "Location: $result_url\n\n";
}
else
{
print "Content-type: text/plain\n\n";
print "The simulator was unable to create an result file.\n";
}
if (open(JOBFILES,"> $::jobdir/$tmpid"))
{
flock(JOBFILES,LOCK_EX);
print JOBFILES "execution_time=$execution_time\n";
print JOBFILES "Phantom_Name=$Phantom_Name\n";
print JOBFILES "Phantom_Nx=$Phantom_Nx\n";
print JOBFILES "Phantom_Ny=$Phantom_Nx\n";
print JOBFILES "Phantom_NSample=$Phantom_NSample\n";
print JOBFILES "PJ_NDet=$PJ_NDet\n";
print JOBFILES "PJ_NRot=$PJ_NRot\n";
print JOBFILES "PJ_NRay=$PJ_NRay\n";
print JOBFILES "PJ_RotAngle=$PJ_RotAngle\n";
print JOBFILES "IR_Nx=$IR_Nx\n";
print JOBFILES "IR_Ny=$IR_Ny\n";
print JOBFILES "IR_Interp=$IR_Interp\n";
print JOBFILES "IR_Filter=$IR_Filter\n";
print JOBFILES "IR_Filter_Param=$IR_Filter_Param\n";
print JOBFILES "IR_Backproj=$IR_Backproj\n";
print JOBFILES "Disp_Min=$Disp_Min\n";
print JOBFILES "Disp_Max=$Disp_Max\n";
print JOBFILES "MPI=$MPI\n";
print JOBFILES "Files=$result_fname,$phantom_fname,$pj_fname,$ir_fname,$phantom_png,$ir_png,$pj_if_fname,$pj_png\n" if ($error eq "");
printf JOBFILES "cmdout=$cmdout\n";
flock(JOBFILES,LOCK_UN);
close JOBFILES;
}
exit;
sub internal_error
{
my $out = head();
$out .= "<H1>Internal error</H1>
Please notify <A HREF=mailto:webmaster\@med-info.com>webmaster\@med-info.com</A>
</BODY>";
print $out;
exit;
}
sub head
{
# "Content: text/html\n\n";
}
sub FilterMetaChars
{
my $var = pop(@_);
$var =~ /^([-\w]+)$/;
$1;
}
sub FilterToNumber
{
my $var = pop(@_);
$var =~ /^(\-*\d*\.*\d*)$/;
$1;
}
cgi-bin/ctsim.conf deleted 100644 → 0
View file @ cb6b6b38
# cgi-bin/ctsim.conf. Generated from ctsim.conf.in by configure.
$::bindir = "/usr/local/bin";
$::lamrundir = "/usr/local/bin";
$::jobdir = "";
$::datadir = "";
$::url_datadir = "";
$::mpi_enable = "";
$::single_process_only = 1;
1;
config.h.in
View file @ 81160e42
......@@ -6,12 +6,64 @@
/* turn on debugging */
#undef DEBUG
/* Define to 1 to support Advanced Bit Manipulation */
#undef HAVE_ABM
/* Define to 1 to support Multi-Precision Add-Carry Instruction Extensions */
#undef HAVE_ADX
/* Define to 1 to support Advanced Encryption Standard New Instruction Set
(AES-NI) */
#undef HAVE_AES
/* Support Altivec instructions */
#undef HAVE_ALTIVEC
/* Define to 1 if you have the <assert.h> header file. */
#undef HAVE_ASSERT_H
/* Define to 1 to support Advanced Vector Extensions */
#undef HAVE_AVX
/* Define to 1 to support Advanced Vector Extensions 2 */
#undef HAVE_AVX2
/* Define to 1 to support AVX-512 Byte and Word Instructions */
#undef HAVE_AVX512_BW
/* Define to 1 to support AVX-512 Conflict Detection Instructions */
#undef HAVE_AVX512_CD
/* Define to 1 to support AVX-512 Doubleword and Quadword Instructions */
#undef HAVE_AVX512_DQ
/* Define to 1 to support AVX-512 Exponential & Reciprocal Instructions */
#undef HAVE_AVX512_ER
/* Define to 1 to support AVX-512 Foundation Extensions */
#undef HAVE_AVX512_F
/* Define to 1 to support AVX-512 Integer Fused Multiply Add Instructions */
#undef HAVE_AVX512_IFMA
/* Define to 1 to support AVX-512 Conflict Prefetch Instructions */
#undef HAVE_AVX512_PF
/* Define to 1 to support AVX-512 Vector Byte Manipulation Instructions */
#undef HAVE_AVX512_VBMI
/* Define to 1 to support AVX-512 Vector Length Extensions */
#undef HAVE_AVX512_VL
/* Define to 1 if you have the `basename' function. */
#undef HAVE_BASENAME
/* Define to 1 to support Bit Manipulation Instruction Set 1 */
#undef HAVE_BMI1
/* Define to 1 to support Bit Manipulation Instruction Set 2 */
#undef HAVE_BMI2
/* ctn dicom library */
#undef HAVE_CTN_DICOM
......@@ -33,6 +85,12 @@
/* FFTW library */
#undef HAVE_FFTW
/* Define to 1 to support Fused Multiply-Add Extensions 3 */
#undef HAVE_FMA3
/* Define to 1 to support Fused Multiply-Add Extensions 4 */
#undef HAVE_FMA4
/* Define to 1 if you have the `getenv' function. */
#undef HAVE_GETENV
......@@ -60,12 +118,27 @@
/* Define to 1 if you have the <memory.h> header file. */
#undef HAVE_MEMORY_H
/* Define to 1 to support Multimedia Extensions */
#undef HAVE_MMX
/* Define to 1 to support Memory Protection Extensions */
#undef HAVE_MPX
/* Define to 1 if you have the <netinet/in.h> header file. */
#undef HAVE_NETINET_IN_H
/* Define if OpenMP is enabled */
#undef HAVE_OPENMP
/* PNG library */
#undef HAVE_PNG
/* Define to 1 to support Prefetch Vector Data Into Caches WT1 */
#undef HAVE_PREFETCHWT1
/* Define to 1 to support Digital Random Number Generator */
#undef HAVE_RDRND
/* Readline library */
#undef HAVE_READLINE
......@@ -87,9 +160,33 @@
/* use sgp library */
#undef HAVE_SGP
/* Define to 1 to support Secure Hash Algorithm Extension */
#undef HAVE_SHA
/* Define to 1 if you have the `snprintf' function. */
#undef HAVE_SNPRINTF
/* Define to 1 to support Streaming SIMD Extensions */
#undef HAVE_SSE
/* Define to 1 to support Streaming SIMD Extensions */
#undef HAVE_SSE2
/* Define to 1 to support Streaming SIMD Extensions 3 */
#undef HAVE_SSE3
/* Define to 1 to support Streaming SIMD Extensions 4.1 */
#undef HAVE_SSE4_1
/* Define to 1 to support Streaming SIMD Extensions 4.2 */
#undef HAVE_SSE4_2
/* Define to 1 to support AMD Streaming SIMD Extensions 4a */
#undef HAVE_SSE4a
/* Define to 1 to support Supplemental Streaming SIMD Extensions 3 */
#undef HAVE_SSSE3
/* sstream header */
#undef HAVE_SSTREAM
......@@ -156,6 +253,9 @@
/* Define to 1 if you have the `vsprintf' function. */
#undef HAVE_VSPRINTF
/* Support VSX instructions */
#undef HAVE_VSX
/* have wxthreads library */
#undef HAVE_WXTHREADS
......@@ -165,6 +265,9 @@
/* X11 system */
#undef HAVE_X11
/* Define to 1 to support eXtended Operations Extensions */
#undef HAVE_XOP
/* no debugging */
#undef NDEBUG
......
configure
View file @ 81160e42
This diff is collapsed.
configure.ac
View file @ 81160e42
......@@ -27,8 +27,13 @@ dnl Process this file with autoconf to produce a configure script.
dnl Must reset CDPATH so that bash's cd does not print to stdout
dnl CDPATH=
AC_INIT([CTSim], [5.2.0], [ctsim-users@b9.com], [ctsim], [http://www.ctsim.org/])
AC_INIT([CTSim], [6.0.0], [ctsim-users@kpe.io], [ctsim], [http://www.ctsim.org/])
AC_CONFIG_SRCDIR([src/ctsim.cpp])
AC_CONFIG_MACRO_DIR([scripts])
dnl permit auxiliary scripts directory (e.g. config.sub, config.guess, install-sh)
AC_CONFIG_AUX_DIR(scripts/)
AC_CANONICAL_TARGET
AM_MAINTAINER_MODE
AM_INIT_AUTOMAKE
AM_CONFIG_HEADER(config.h)
......@@ -41,6 +46,9 @@ AC_PROG_RANLIB
AC_PROG_CC
AC_PROG_CXX
CFLAGS=""
CXXFLAGS=""
AC_C_BIGENDIAN
AC_PATH_PROG(wxconfig,wx-config)
......@@ -54,7 +62,6 @@ AC_CHECK_SIZEOF(long, 4)
AC_CHECK_SIZEOF(float, 4)
AC_CHECK_SIZEOF(double, 8)
dnl Add define templates
dnl Checks for libraries.
AC_CHECK_LIB(z, deflate, [ zlib="true" ], [ zlib="false" ; AC_MSG_WARN([zlib missing. Will need zlib for PNG support])])
......@@ -77,8 +84,8 @@ if test "$hasx11gtk2" = "true" ; then
CFLAGS="${CFLAGS} ${g76GTK_CFLAGS} ${GLIB_CFLAGS}"
fi
AC_CHECK_LIB(wx_gtk2u_core-2.8, main, [wxwin=true; wx_gtk=true; AC_DEFINE(HAVE_WXWINDOWS,1,[wxwindows library])], [], [-L/usr/lib64 -L/usr/lib ${GTK_LIBS} ${GLIB_LIBS} ])
AC_CHECK_LIB(wx_mac_core-2.8, main, [wxwin=true; wx_mac=true; AC_DEFINE(HAVE_WXWINDOWS,1,[wxwindows library])])
AC_CHECK_LIB(wx_gtk2u_core-3.0, main, [wxwin=true; wx_gtk=true; AC_DEFINE(HAVE_WXWINDOWS,1,[wxwindows library])], [], [-L/usr/lib64 -L/usr/lib ${GTK_LIBS} ${GLIB_LIBS} ])
AC_CHECK_LIB(wx_mac_core-3.0, main, [wxwin=true; wx_mac=true; AC_DEFINE(HAVE_WXWINDOWS,1,[wxwindows library])])
AC_CHECK_LIB(fftw3, fftw_malloc, [fftw=true; AC_DEFINE(HAVE_FFTW,1,[FFTW library])], [fftw=false], [-L/usr/lib64 -L/usr/lib])
AC_CHECK_LIB(GL, main, [libgl=true], [libgl=false], [-L/usr/X11R6/lib -L/usr/X11R6/lib64])
AC_CHECK_LIB(pthread, main, [pthread=true], [pthread=false])
......@@ -122,6 +129,26 @@ if test "${getopt_long}" = "false" ; then
fi
AM_CONDITIONAL(INCLUDED_GETOPT_LONG, test "$GETOPTLONG"="1")
ARCH_OPTION=""
case $target_cpu in
i386|i486|i586|i686|x86|x86_64)
AX_EXT
CFLAGS="$CFLAGS $CPUEXT_FLAGS $SIMD_FLAGS"
CXXFLAGS="$CXXFLAGS $CPUEXT_FLAGS $SIMD_FLAGS"
;;
powerpc*)
ARCH_OPTION="-fno-common -faltivec";;
armv1*|armv2*|armv3*|armv4*|armv5*|armv6*)
ARCH_OPTION="-ffast-math";;
armv7*|armv8*)
ARCH_OPTION="-ffast-math -mcpu=cortex-a7 -mfloat-abi=hard -mfpu=neon-vfpv4";;
*)
# unknown architecture : use portable C version
ARCH_OPTION="";;
esac
CPPFLAGS="$CPPFLAGS $ARCH_OPTION"
CXXFLAGS="$CPPFLAGS $ARCH_OPTION"
if test "${readline}" = "true" ; then
ctlibs_base="$ctlibs_base -lreadline"
if test "${ncurses}" = "true"; then
......@@ -158,7 +185,7 @@ if test "$debug" = "true" ; then
CFLAGS="$CFLAGS -g -O0 -DDEBUG"
AC_DEFINE(DEBUG,1,[turn on debugging])
else
CFLAGS="$CFLAGS -O2 -DNDEBUG -fomit-frame-pointer"
CFLAGS="$CFLAGS -g -O4 -DNDEBUG -fomit-frame-pointer"
AC_DEFINE(NDEBUG,1,[no debugging])
fi
......@@ -180,9 +207,7 @@ AC_MSG_CHECKING(sstream)
CFLAGS="$CFLAGS -Wall"
AC_MSG_CHECKING(whether to enable verbose warnings)
AC_ARG_ENABLE(verbose-warnings,
[ --enable-verbose-warnings
Enable verbose compiler warnings.],
AC_ARG_ENABLE(verbose-warnings,AS_HELP_STRING([--enable-verbose-warnings],[Enable verbose compiler warnings.]),
[ case "$enableval" in
yes)
AC_MSG_RESULT(yes)
......@@ -195,9 +220,7 @@ AC_ARG_ENABLE(verbose-warnings,
)
AC_MSG_CHECKING(static executables)
AC_ARG_ENABLE(static,
[ --enable-static
Enable static executables.],
AC_ARG_ENABLE(static,AS_HELP_STRING([--enable-static],[Enable static executables]),
[ case "$enableval" in
yes)
AC_MSG_RESULT(yes)
......@@ -209,9 +232,16 @@ AC_ARG_ENABLE(static,
esac ], AC_MSG_RESULT(no)
)
dnl Checking if use OpenMP
AC_ARG_ENABLE([openmp], AS_HELP_STRING([--disable-openmp],[Disable use of OpenMP]))
AS_IF([test "x$enable_openmp" != "xno"], [
AX_OPENMP
CFLAGS="$CFLAGS $OPENMP_CFLAGS"
CXXFLAGS="$CXXFLAGS $OPENMP_CXXFLAGS"
])
dnl Set LAM path
AC_ARG_WITH(lam,
[ --with-lam[=PATH] Set path of LAM MPI ],
AC_ARG_WITH(lam,AS_HELP_STRING([--with-lam[=PATH]],[Set path of LAM MPI ]),
[ if test "$withval" != "no" ; then
trylamdir=$withval
fi ]
......@@ -354,7 +384,6 @@ dnl whether X should be supported.
AM_CONDITIONAL(NO_X, test "x$with_x" = "xno")
my_includes="$my_includes -I../include -I.. -I/usr/local/include"
AC_SUBST(my_includes)
LDFLAGS="$LDFLAGS -L/usr/local/lib"
......@@ -362,12 +391,13 @@ AC_MSG_CHECKING([for X])
if test "$with_x" != "no" && test "$wxwin" = "true"; then
AC_DEFINE(HAVE_X11,1,[X11 system])
LDFLAGS="$LDFLAGS -L../libctgraphics -L/usr/X11R6/lib -L/usr/X11R6/lib64"
my_includes="$my_includes -I/usr/X11R6/include"
my_includes="$my_includes -I/usr/X11R6/include -I/usr/include/X11"
ctlib_graphics="$ctlibs_base -lctgraphics"
AC_MSG_RESULT(yes)
ctlib_graphics="$ctlib_graphics $X_BASIC_LIBS $X_TOOLKIT_LIBS"
wx_cppflags="`$wxconfig --cppflags`"
if test "$libgl" = "true" ; then
# Removed "-lglut" for Mac OS X compilation
dnl Removed "-lglut" for Mac OS X compilation
ctlib_graphics="$ctlib_graphics -lGL -lGLU"
if test "$wxwin" = "true" ; then
wxdebug=""
......@@ -375,9 +405,10 @@ if test "$with_x" != "no" && test "$wxwin" = "true"; then
wxdebug="--debug"
fi
if test "x$wx_gtk" != "x" ; then
ctlib_graphics="$ctlib_graphics `$wxconfig $wxdebug --version=2.8 --libs std,gl` ${GTK_LIBS} ${GLIB_LIBS}"
ctlib_graphics="$ctlib_graphics `$wxconfig $wxdebug --version=3.0 --libs std,gl` ${GTK_LIBS} ${GLIB_LIBS}"
elif test "x$wx_mac" != "x" ; then
ctlib_graphics="$ctlib_graphics `$wxconfig $wxdebug --version=2.8 --libs std,gl`"
ctlib_graphics="$ctlib_graphics `$wxconfig $wxdebug --version=3.0 --libs std,gl`"
fi
fi
fi
......@@ -430,7 +461,7 @@ dnl Check for efence
AC_CHECK_LIB(efence, main, [efence=true], [efence=false])
AC_MSG_CHECKING([for enable-efence])
AC_ARG_ENABLE(efence,
[ --enable-efence Use ElectricFence memory allocation],
[--enable-efence],[Use ElectricFence memory allocation],
[case "${enableval}" in
yes) useefence=true
AC_MSG_RESULT(yes)
......@@ -451,7 +482,7 @@ fi
if test "$wxwin" = "true" ; then
if test "$wx_gtk" = "true" -o "$wx_mac" = "true" ; then
wxcflags=`$wxconfig $wxdebug --cxxflags --version=2.8`
wxcflags=`$wxconfig $wxdebug --cxxflags --version=3.0`
#wxlibs=`$wxconfig --libs`
else
wxcflags="-D__WXMSW__ -D__WIN32__ -D__GNUWIN32__"
......@@ -478,6 +509,9 @@ fi
CXXFLAGS="$CFLAGS"
AC_SUBST(my_includes)
AC_SUBST(wx_cppflags)
AC_CONFIG_FILES([Makefile libctgraphics/Makefile libctsupport/Makefile libctsim/Makefile man/Makefile cgi-bin/ctsim.cgi cgi-bin/Makefile html/simulate.html html/Makefile include/Makefile getopt/Makefile tools/sample-ctsim.sh cgi-bin/ctsim.conf tools/Makefile src/Makefile helical/Makefile helical/sample-helical.sh])
AC_OUTPUT
debian/changelog
View file @ 81160e42
ctsim (6.0.2-1) unstable; urgency=low
* New upstream
* debian/tests/control: Start of test suite
-- Kevin M. Rosenberg <kmr@debian.org> Wed, 21 Mar 2018 12:50:20 -0600
ctsim (6.0.1-1) unstable; urgency=low
* Add missing autoconf file in scripts/.
-- Kevin M. Rosenberg <kmr@debian.org> Wed, 21 Mar 2018 01:27:19 -0600
ctsim (6.0.0-2) unstable; urgency=low
* Merge patches and packaging changes kindly make by Debian Med Team
-- Kevin M. Rosenberg <kmr@debian.org> Wed, 21 Mar 2018 00:55:11 -0600
ctsim (6.0.0-1) unstable; urgency=low
* New upstream, supports OpenMP parallelism and migrated to wxgtk3.0 and libpng1.6
* debian/control: Update for wxgtk3
-- Kevin M. Rosenberg <kmr@debian.org> Tue, 20 Mar 2018 22:40:50 -0600
ctsim (5.2.0-4) unstable; urgency=medium
* Fix watch file
......
debian/control
View file @ 81160e42
......@@ -11,14 +11,8 @@ Build-Depends: debhelper (>= 10),
libglu1-mesa-dev,
libwxgtk3.0-dev,
ctn-dev,
libpng-dev,
libglib2.0-dev,
libgtk2.0-dev,
autotools-dev,
dh-autoreconf
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/ctsim.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/ctsim.git
libpng-dev
Standards-Version: 4.1.3
Homepage: http://www.ctsim.org
Package: ctsim
......
debian/ctsim.desktop
View file @ 81160e42
......@@ -3,7 +3,9 @@ Version=1.0
Name=CTSim Computed Tomography Simulator
GenericName=Computed Tomography Simulator
Comment=Simulate the process of X-ray Computed Tomography
Keywords=medicine;imaging;simulation
Type=Application
Exec=ctsim
Icon=ctsim
Categories=Education;Science;MedicalSoftware
debian/patches/cope_with_existing_makefile.patch deleted 100644 → 0
View file @ cb6b6b38
This diff is collapsed.
debian/patches/libpng16.patch deleted 100644 → 0
View file @ cb6b6b38
Author: Tobias Frost <tobi@debian.org>
Last-Update: Sun, 24 Jan 2016 12:59:10 +0100
Bug-Debian: https://bugs.debian.org/809897
Description: Porting to with libpng16
--- a/libctsim/imagefile.cpp
+++ b/libctsim/imagefile.cpp
@@ -1565,7 +1565,7 @@
return false;
}
- if (setjmp(png_ptr->jmpbuf)) {
+ if (setjmp(png_jmpbuf(png_ptr))) {
png_destroy_read_struct(&png_ptr, &info_ptr, &end_info);
fclose(fp);
return false;
@@ -1815,7 +1815,7 @@
return false;
}
- if (setjmp (png_ptr->jmpbuf)) {
+ if (setjmp (png_jmpbuf(png_ptr))) {
png_destroy_write_struct (&png_ptr, &info_ptr);
fclose (fp);
return false;
debian/patches/prevent_symlinking_on_build_host_dir.patch deleted 100644 → 0
View file @ cb6b6b38
Author: Andreas Tille <tille@debian.org>
Last-Update: Mon, 11 Aug 2014 10:05:01 +0200
Description: Upstream install target tries to do some symlinking
on the Build host ...
--- a/tools/Makefile.am
+++ b/tools/Makefile.am
@@ -9,18 +9,18 @@ SOURCE_DEPEND=../include/ct.h ../libctsi
endif
install-exec-hook:
- ln -sf ctsimtext $(bindir)/if1
- ln -sf ctsimtext $(bindir)/if2
- ln -sf ctsimtext $(bindir)/ifexport
- ln -sf ctsimtext $(bindir)/ifinfo
- ln -sf ctsimtext $(bindir)/phm2if
- ln -sf ctsimtext $(bindir)/phm2pj
- ln -sf ctsimtext $(bindir)/phm2helix
- ln -sf ctsimtext $(bindir)/pj2if
- ln -sf ctsimtext $(bindir)/pjinfo
- ln -sf ctsimtext $(bindir)/pjrec
- ln -sf ctsimtext $(bindir)/pjHinterp
- ln -sf ctsimtext $(bindir)/linogram
+ ln -sf ctsimtext $(DESTDIR)$(bindir)/if1
+ ln -sf ctsimtext $(DESTDIR)$(bindir)/if2
+ ln -sf ctsimtext $(DESTDIR)$(bindir)/ifexport
+ ln -sf ctsimtext $(DESTDIR)$(bindir)/ifinfo
+ ln -sf ctsimtext $(DESTDIR)$(bindir)/phm2if
+ ln -sf ctsimtext $(DESTDIR)$(bindir)/phm2pj
+ ln -sf ctsimtext $(DESTDIR)$(bindir)/phm2helix
+ ln -sf ctsimtext $(DESTDIR)$(bindir)/pj2if
+ ln -sf ctsimtext $(DESTDIR)$(bindir)/pjinfo
+ ln -sf ctsimtext $(DESTDIR)$(bindir)/pjrec
+ ln -sf ctsimtext $(DESTDIR)$(bindir)/pjHinterp
+ ln -sf ctsimtext $(DESTDIR)$(bindir)/linogram
ctsimtext_SOURCES = ctsimtext.cpp if1.cpp if2.cpp ifinfo.cpp ifexport.cpp phm2if.cpp phm2pj.cpp pj2if.cpp pjinfo.cpp pjrec.cpp nographics.cpp phm2helix.cpp pjHinterp.cpp linogram.cpp
ctsimtext_LDADD=@ctlibs@
debian/patches/series deleted 100644 → 0
View file @ cb6b6b38
wx3.0-compat.patch
cope_with_existing_makefile.patch
prevent_symlinking_on_build_host_dir.patch
spelling.patch
libpng16.patch