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 2e9776dc7559c5e940be7b3bd58a24cad4b45fcb..8949b35b0be6afd05f474c5ea107419531868976 100755 (executable)
--- a/cluster_tools/gate_power_merge.sh
+++ b/cluster_tools/gate_power_merge.sh
@@ -10,7 +10,7 @@ exit 1
 warning_count=0
 function warning {
 let "warning_count++"
-echo "WARNING: $1"
+echo "MERGE_WARNING: $1"
 }
 
 function start_bar {
@@ -39,6 +39,16 @@ shift
 echo "  ${indent}entering root merger"
 echo "  ${indent}merger is ${rootMerger}"
 echo "  ${indent}creating ${merged}"
+#echo "######## $#"
+#echo "######## $*"
+
+if test $# -eq 1
+then
+    echo "  ${indent}just one partial file => just copy it"
+    cp "$1" "${merged}"
+    return
+fi
+
 local count=0
 local arguments=" -o ${merged}"
 while test $# -gt 0
@@ -48,13 +58,12 @@ do
     let count++
     local arguments=" -i ${partial} ${arguments}"
 done
-${rootMerger} ${arguments} > /dev/null || { warning "error while calling ${rootMerger}" && return; }
+${rootMerger} ${arguments} > /dev/null || warning "error while calling ${rootMerger}"
 echo "  ${indent}merged ${count} files"
 }
 
 statMerger="mergeStatFile.py"
 test -x "./mergeStatFile.sh" && statMerger="./mergeStatFile.sh"
-test -x "./mergeStatFile.py" && statMerger="./mergeStatFile.py"
 
 function merge_stat {
 local merged="$1"
@@ -78,7 +87,7 @@ do
     fi
 
     update_bar ${count} "adding ${partial}"
-    ${statMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || { warning "error while calling ${statMerger}" && return; }
+    ${statMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${statMerger}"
 done
 end_bar
 echo "  ${indent}merged ${count} files"
@@ -111,7 +120,7 @@ do
     update_bar ${count} "adding ${partial}"
     local header="$(cat "${merged}" | head -n 6)"
     local tmp="$(mktemp)"
-    ${txtImageMerger} -i "${partial}" -j "${merged}" -o "${tmp}" 2> /dev/null > /dev/null || { warning "error while calling ${txtImageMerger}" && return; }
+    ${txtImageMerger} -i "${partial}" -j "${merged}" -o "${tmp}" 2> /dev/null > /dev/null || warning "error while calling ${txtImageMerger}"
     echo "${header}" > "${merged}"
     grep -v '## Merge' "${tmp}" >> "${merged}"
     rm "${tmp}"
@@ -148,7 +157,41 @@ do
     fi
 
     update_bar ${count} "adding ${partial}"
-    ${hdrImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || { warning "error while calling ${hdrImageMerger}" && return; }
+    ${hdrImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${hdrImageMerger}"
+done
+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"
@@ -179,6 +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"
@@ -217,10 +268,31 @@ function merge_dispatcher {
         fi
     fi
 
-    warning "unknown file type"
+    if test "${firstpartialoutputextension}" == "txt"
+    then
+        echo "${indent}this is a non specific txt output"
+        local mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}")"
+        local nbdifferent="$(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
+
+    error "unknown file type"
 }
 
+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"
@@ -236,9 +308,15 @@ echo "output dir is ${outputdir}"
 test -d "${outputdir}" && rm -r "${outputdir}"
 mkdir "${outputdir}"
 
-for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex '.*\.(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}"
+    merge_dispatcher "${outputfile}"
 done
 
+if [ -f "${rundir}/params.txt" ]
+then
+       echo "copying params file"
+       cp "${rundir}/params.txt" "${outputdir}/params.txt"
+fi
+
 echo "these was ${warning_count} warning(s)"