From fa93944386ff066765f476d41c037945d96d6152 Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Mon, 11 Jun 2007 09:58:04 +0000
Subject: [PATCH] whirlgif
---
fslanimate | 8 ++++----
fslstats.cc | 17 +++++++++++++++--
sliceanimate | 12 ++++++------
3 files changed, 25 insertions(+), 12 deletions(-)
diff --git a/fslanimate b/fslanimate
index e20827e..2af213a 100755
--- a/fslanimate
+++ b/fslanimate
@@ -56,12 +56,12 @@ $FSLDIR/bin/avwsplit $im
for fnm in `$FSLDIR/bin/imglob vol*` ; do
num=`$FSLDIR/bin/remove_ext $fnm | sed 's/vol//'`; export num;
echo $num;
- $FSLDIR/bin/slicer $fnm -s 2 -a ${iout}_$num.pgm
- ${FSLCONVERT} ${iout}_$num.pgm ${iout}_$num.gif
- rm -f ${iout}_$num.pgm
+ $FSLDIR/bin/slicer $fnm -s 2 -a ${iout}_$num.png
+ ${FSLDIR}/bin/pngappend ${iout}_$num.png ${iout}_$num.gif
+ rm -f ${iout}_$num.png
done
-$FSLDIR/bin/gifmerge -15 -l0 ${iout}_*.gif > ${iout}.gif
+$FSLDIR/bin/whirlgif -o ${iout}.gif -time 15 -loop 0 ${iout}_*.gif
mv $tmpdir/${iout}.gif ${imoutdir}/${iout}.gif
diff --git a/fslstats.cc b/fslstats.cc
index dc25d87..d8cc418 100644
--- a/fslstats.cc
+++ b/fslstats.cc
@@ -20,6 +20,12 @@ bool masks_used=false;
bool lthr_used=false;
bool uthr_used=false;
+#if defined ( __CYGWIN__ ) || defined (__sun)
+extern "C" {
+#include <ieeefp.h> //for finite
+}
+#endif
+
void print_usage(const string& progname) {
cout << "Usage: avwstats++ <input> [options]" << endl << endl;
cout << endl;
@@ -43,6 +49,7 @@ void print_usage(const string& progname) {
cout << "-p <n> : output nth percentile (n between 0 and 100)" << endl;
cout << "-P <n> : output nth percentile (for nonzero voxels)" << endl;
cout << "-a : use absolute values of all image intensities"<< endl;
+ cout << "-n : treat NaN or Inf as zero for subsequent stats" << endl;
cout << "-k <mask> : use the specified image (filename) for masking - overrides lower and upper thresholds" << endl;
cout << "-h <nbins> : output a histogram (for the thresholded/masked voxels only) with nbins" << endl;
cout << "-H <nbins> <min> <max> : output a histogram (for the thresholded/masked voxels only) with nbins and histogram limits of min and max" << endl;
@@ -160,8 +167,14 @@ int fmrib_main_float(int argc, char* argv[])
while (narg<argc) {
sarg=argv[narg];
-
- if (sarg=="-m") {
+ if (sarg=="-n") {
+ for (int t=vol.mint(); t<=vol.maxt(); t++)
+ for (int z=vol.minz(); z<=vol.maxz(); z++)
+ for (int y=vol.miny(); y<=vol.maxy(); y++)
+ for (int x=vol.minx(); x<=vol.maxx(); x++)
+ if (!finite((double)vol(x,y,z,t)))
+ vol(x,y,z,t)=0;
+ } else if (sarg=="-m") {
if (masks_used) cout << vol.mean(mask) << " ";
else cout << vol.mean() << " ";
} else if (sarg=="-M") {
diff --git a/sliceanimate b/sliceanimate
index 3d14a4f..269b13d 100755
--- a/sliceanimate
+++ b/sliceanimate
@@ -2,9 +2,9 @@
# sliceanimate - make animated gif of a volume, slice at a time
#
-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+# Stephen Smith, Mark Jenkinson and Matthew Webster FMRIB Image Analysis Group
#
-# Copyright (C) 1999-2004 University of Oxford
+# Copyright (C) 1999-2007 University of Oxford
#
# SHCOPYRIGHT
@@ -25,16 +25,16 @@ tmpdir=/tmp
while [ $n -lt $nn ] ; do
# echo $FSLDIR/bin/slicer $volname $@ -z -$n $tmpdir/${tmpnam}
- $FSLDIR/bin/slicer $volname $@ -z -$n $tmpdir/${tmpnam}
+ $FSLDIR/bin/slicer $volname $@ -z -$n $tmpdir/${tmpnam}.png
snum=`echo "0000${n}" | sed 's/^.*\(....\)$/\1/'`;
echo slice $snum
- ${FSLCONVERT} $tmpdir/$tmpnam $tmpdir/${bnm}_slice${snum}.gif
+ ${FSLDIR}/bin/pngappend $tmpdir/${tmpnam}.png $tmpdir/${bnm}_slice${snum}.gif
n=`echo $n + 1 | bc`;
done
-rm -f $tmpdir/${tmpnam}
+rm -f $tmpdir/${tmpnam}.png
-$FSLDIR/bin/gifmerge -l1000 -35 $tmpdir/${bnm}_slice*.gif > ${volname}_sliceanim.gif
+$FSLDIR/bin/whirlgif -o ${volname}_sliceanim.gif -time 35 -loop 0 $tmpdir/${bnm}_slice*.gif
rm -f $tmpdir/${bnm}_slice*.gif
--
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