just cp when all txt files are identical

[clitk.git] / cluster_tools / gate_power_merge.sh

diff --git a/cluster_tools/gate_power_merge.sh b/cluster_tools/gate_power_merge.sh
index 590fcd6c3df87903962099e8b4d698d4c939a2b2..8949b35b0be6afd05f474c5ea107419531868976 100755 (executable)
--- a/cluster_tools/gate_power_merge.sh
+++ b/cluster_tools/gate_power_merge.sh
@@ -163,6 +163,40 @@ end_bar
 echo "  ${indent}merged ${count} files"
 }
 
+mhdImageMerger="clitkImageArithm"
+test -x "./clitkImageArithm" && mhdImageMerger="./clitkImageArithm"
+
+function merge_mhd_image {
+local merged="$1"
+local merged_bin="${merged%.*}.raw"
+shift
+echo "  ${indent}entering mhd image merger"
+echo "  ${indent}merger is ${mhdImageMerger}"
+echo "  ${indent}creating ${merged}"
+local count=0
+start_bar $#
+while test $# -gt 0
+do
+    local partial="$1"
+    local partial_bin="${partial%.*}.raw"
+    shift
+    let count++
+
+    if test ! -f "${merged}"
+    then
+        update_bar ${count} "copying first partial result ${partial}"
+        cp "${partial}" "${merged}"
+        cp "${partial_bin}" "${merged_bin}"
+        continue
+    fi
+
+    update_bar ${count} "adding ${partial}"
+    ${mhdImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${mhdImageMerger}"
+done
+end_bar
+echo "  ${indent}merged ${count} files"
+}
+
 function merge_dispatcher {
     local indent="  ** "
     local outputfile="${1:?"provide output filename"}"
@@ -188,6 +222,14 @@ function merge_dispatcher {
         return
     fi
 
+    if test "${firstpartialoutputextension}" == "mhd"
+    then
+        echo "${indent}this is a mhd image"
+        local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+        merge_mhd_image "${mergedfile}" ${partialoutputfiles} || error "error while merging"
+        return
+    fi
+
     if test "${firstpartialoutputextension}" == "root"
     then
         echo "${indent}this is a root file"
@@ -230,17 +272,27 @@ function merge_dispatcher {
     then
         echo "${indent}this is a non specific txt output"
         local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
-        echo "  ${indent}catting ${mergedfile}"
-        cat ${partialoutputfiles} > "${mergedfile}" || error "error while merging"
-        return
+        local nbdifferent="$(md5sum ${partialoutputfiles} | awk '{ print $1; }' | sort | uniq | wc -l)"
+        echo "  ${indent}${nbdifferent} different files"
+        if test ${nbdifferent} -gt 1
+        then
+            echo "  ${indent}catting to ${mergedfile}"
+            cat ${partialoutputfiles} > "${mergedfile}" || error "error while merging"
+            return
+        else
+            echo "  ${indent}moving to ${mergedfile}"
+            cp "${firstpartialoutputfile}" "${mergedfile}" || error "error while merging"
+            return
+        fi
     fi
 
-    warning "unknown file type"
+    error "unknown file type"
 }
 
-echo "!!!! this is $0 v0.3g !!!!"
+echo "!!!! this is $0 v0.3i !!!!"
 
 rundir="${1?"provide run dir"}"
+rundir="$(echo "${rundir}" | sed 's|/*$||')"
 nboutputdirs="$(find "${rundir}" -mindepth 1 -type d -name 'output*' | wc -l)"
 
 test ${nboutputdirs} -gt 0 || error "no output dir found"
@@ -256,7 +308,7 @@ echo "output dir is ${outputdir}"
 test -d "${outputdir}" && rm -r "${outputdir}"
 mkdir "${outputdir}"
 
-for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
+for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
 do
     merge_dispatcher "${outputfile}"
 done