From 67f982146fd2a8affb3a61d470ba50a93d046a9a Mon Sep 17 00:00:00 2001
From: Tim Behrens <behrens@fmrib.ox.ac.uk>
Date: Wed, 25 Aug 2004 15:19:14 +0000
Subject: [PATCH] *** empty log message ***
---
eddy_correct | 2 +-
old_bedpost | 27 +++++++++++++++++++--------
old_bedpost_cleanup | 12 ++++++++++++
old_bedpost_kill_all | 9 +++++++++
old_bedpost_kill_pid | 16 ++++++++++++++++
5 files changed, 57 insertions(+), 9 deletions(-)
create mode 100755 old_bedpost_cleanup
create mode 100755 old_bedpost_kill_all
create mode 100755 old_bedpost_kill_pid
diff --git a/eddy_correct b/eddy_correct
index db9c0da..1f03db6 100644
--- a/eddy_correct
+++ b/eddy_correct
@@ -13,7 +13,7 @@ input=`${FSLDIR}/bin/remove_ext ${1}`
output=`${FSLDIR}/bin/remove_ext ${2}`
ref=${3}
-if [ ! `${FSLDIR}/bin/imtest $input` ];then
+if [ `${FSLDIR}/bin/imtest $input` -eq 0 ];then
echo "Input does not exist or is not in analyze format"
exit
fi
diff --git a/old_bedpost b/old_bedpost
index 5451982..7c79372 100755
--- a/old_bedpost
+++ b/old_bedpost
@@ -18,9 +18,11 @@ Clean_Exit(){
if [ -d ${subjdir}.bedpost/logs/pid_${$} ];then
i=`ls ${subjdir}.bedpost/logs/pid_${$}`
for j in ${i};do
- host=`echo $j | awk --field-separator=_fdt_ '{print $1}'`
- pid=`echo $j | awk --field-separator=_fdt_ '{print $2}'`
- ${FSL_REMOTE_CALL} $host "kill -KILL $pid" #this leaves one child process per processor - what can you do?
+ host=`echo $j | awk -F _fdt_ '{print $1}'`
+ pid=`echo $j | awk -F _fdt_ '{print $2}'`
+# ${FSL_REMOTE_CALL} $host "kill -KILL $pid" #this leaves one child process per processor - what can you do?
+ $FSL_REMOTE_CALL $host "if [ -r /etc/fslconf/fsl.sh ];then . /etc/fslconf/fsl.sh; elif [ -r /usr/local/etc/fslconf/fsl.sh ];then . /usr/local/etc/fslconf/fsl.sh; elif [ -r \${HOME}/.fslconf/fsl.sh ]; then . \${HOME}/.fslconf/fsl.sh; fi; if [ x\${FSLDIR} != "x" ];then \${FSLDIR}/bin/bedpost_kill_pid ${pid} >/dev/null 2>&1; else echo FSLDIR not set in any default location on machine `hostname`;fi" >/dev/null 2>&1 &
+ rm ${subjdir}.bedpost/logs/pid_${$}/${j}
done
fi
@@ -127,29 +129,38 @@ mkdir -p ${subjdir}.bedpost/logs/pid_${$}
nslices=`avwval ${subjdir}/data dim3`
-#${FSLDIR}/bin/avwslice ${subjdir}/data
-#${FSLDIR}/bin/avwslice ${subjdir}/nodif_brain_mask
+${FSLDIR}/bin/avwslice ${subjdir}/data
+${FSLDIR}/bin/avwslice ${subjdir}/nodif_brain_mask
#following need to be setup elsewhere
-#FSL_MACHINE_LIST="cayenne0 cayenne0 cayenne2 cayenne3"
-#FSL_REMOTE_CALL="ssh"
+#FSL_MACHINE_LIST="list of machines (can be duplicated for two processors etc. )"
+#FSL_REMOTE_CALL="ssh (or rsh or whatever you want to use)"
if [ "$FSL_MACHINE_LIST" = "" ] ; then
+ echo "processing data on local host"
${FSLDIR}/bin/bedpost_proc $subjdir $nslices
else
+ echo "processing data on hosts: $FSL_MACHINE_LIST"
for machine in $FSL_MACHINE_LIST; do
$FSL_REMOTE_CALL $machine "if [ -r /etc/fslconf/fsl.sh ];then . /etc/fslconf/fsl.sh; elif [ -r /usr/local/etc/fslconf/fsl.sh ];then . /usr/local/etc/fslconf/fsl.sh; elif [ -r \${HOME}/.fslconf/fsl.sh ]; then . \${HOME}/.fslconf/fsl.sh; fi; if [ x\${FSLDIR} != "x" ];then \${FSLDIR}/bin/bedpost_proc $subjdir $nslices ${subjdir}.bedpost/logs/pid_${$}; else echo FSLDIR not set in any default location on machine `hostname`;fi" &
done
fi
+
+b=0
finished=0;
while [ $finished -eq 0 ];do
+ b=`expr $b + 1 `
sleep 60;
- nfin=`ls ${subjdir}.bedpost/logs/.*_finished |wc -w` #fix this (see Bedpost)
+ nfin=`echo ${subjdir}.bedpost/logs/.*_finished | grep -v ".\*" |wc -w`
if [ $nfin -eq $nslices ];then
finished=1;
fi
+ if [ $b -eq 10 ]; then
+ echo "$nfin slices processed"
+ b=0
+ fi
done
#postprocessing
diff --git a/old_bedpost_cleanup b/old_bedpost_cleanup
new file mode 100755
index 0000000..1243fef
--- /dev/null
+++ b/old_bedpost_cleanup
@@ -0,0 +1,12 @@
+#!/bin/sh
+
+if [ "$FSL_MACHINE_LIST" = "" ] ; then
+ ${FSLDIR}/bin/bedpost_kill_all
+else
+ unique_machines=`echo $FSL_MACHINE_LIST |tr " " \\\n |sort -u`
+ echo $unique_machines;
+ for machine in $unique_machines; do
+ $FSL_REMOTE_CALL $machine "if [ -r /etc/fslconf/fsl.sh ];then . /etc/fslconf/fsl.sh; elif [ -r /usr/local/etc/fslconf/fsl.sh ];then . /usr/local/etc/fslconf/fsl.sh; elif [ -r \${HOME}/.fslconf/fsl.sh ]; then . \${HOME}/.fslconf/fsl.sh; fi; if [ x\${FSLDIR} != "x" ];then \${FSLDIR}/bin/bedpost_kill_all; else echo FSLDIR not set in any default location on machine `hostname`;fi" &
+ done
+fi
+
diff --git a/old_bedpost_kill_all b/old_bedpost_kill_all
new file mode 100755
index 0000000..a524252
--- /dev/null
+++ b/old_bedpost_kill_all
@@ -0,0 +1,9 @@
+#!/bin/sh
+j=`ps -U $USER |grep -v grep | grep bedpost|grep -v bedpost_kill | awk '{print $1}'`
+if [ "x${j}" != "x" ];then
+ kill -KILL $j
+fi
+i=`ps -U $USER |grep -v grep | grep diff_pvm| awk '{print $1}'`
+if [ "x${i}" != "x" ];then
+ kill -KILL $i
+fi
diff --git a/old_bedpost_kill_pid b/old_bedpost_kill_pid
new file mode 100755
index 0000000..e319f1e
--- /dev/null
+++ b/old_bedpost_kill_pid
@@ -0,0 +1,16 @@
+#!/bin/sh
+Usage(){
+ echo "bedpost_kill_pid <pid>"
+ echo ""
+ echo "<pid> is the pid of the bedpost_proc"
+ echo "kills this process + all diff_pvm children"
+ echo ""
+ exit
+}
+
+[ "$1" = "" ] && Usage
+pid=$1
+
+i=`ps -fU $USER |grep -v grep | grep diff_pvm |grep ${pid}| awk '{print $2}'`
+kill -KILL $pid $i
+
--
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