new tool to normalize image intensity

[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 fe1784a796492b106e635668058926e5aa118048..3a9bba6b23b01002bb32dd303a9d3259dd787475 100755 (executable)
--- a/cluster_tools/gate_power_merge.sh
+++ b/cluster_tools/gate_power_merge.sh
@@ -299,7 +299,7 @@ function merge_mhd_image {
 
         update_bar ${count} "adding ${partial}"
         ${mhdImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${mhdImageMerger}"
-        if test "$last_character" = "d" 
+        if test "$last_character" = "d" && test "${merged_bin}" != "${merged_bin%.*}.${partial_bin##*.}"
         then
             mv "${merged_bin}" "${merged_bin%.*}.${partial_bin##*.}"
             sed -i "s/$(basename "${merged_bin}")/$(basename "${merged_bin%.*}.${partial_bin##*.}")/" "${merged}"
@@ -444,7 +444,7 @@ function merge_dispatcher_uncertainty {
 
     if [[ "${firstpartialoutputfile}" == *Uncertainty* ]]
     then
-        if test "${firstpartialoutputextension}" == "mhd"
+       if test "${firstpartialoutputextension}" == "mhd" || test "${firstpartialoutputextension}" == "mha"
         then
             echo "${indent}Uncertainty file found: ${firstpartialoutputfile}"
             ## search for sum
@@ -466,7 +466,7 @@ function merge_dispatcher_uncertainty {
             echo "${indent}${squared_merged_file} found"
             ## search for NumberOfEvent
             totalEvents=0;
-            for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
+            for outputfile in $(find "${rundir}" -regextype 'posix-extended' -type f -regex "${rundir}/output.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
             do
                 #echo $outputfile
                 if grep -q 'NumberOfEvent' "${outputdir}/${outputfile}"
@@ -485,6 +485,8 @@ function merge_dispatcher_uncertainty {
                 warning "${totalEvents} not positive. A at least one stat file (SimulationStatisticActor) must be provided. Error, no uncertainty computed"
                 return;
             fi
+       else
+            error "merge_dispatcher_uncertainty does not handle ${firstpartialoutputfile} files"
         fi
     fi
 
@@ -517,7 +519,7 @@ done
 
 echo ""
 echo "Merging done. Special case for statistical uncertainty"
-for outputfile in $(find "${outputdir}" -regextype 'posix-extended' -type f -regex "${outputdir}/output.*\.(hdr|mhd|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
+for outputfile in $(find "${outputdir}" -regextype 'posix-extended' -type f -regex "${outputdir}/.*\.(hdr|mhd|mha|root|txt)" | awk -F '/' '{ print $NF; }' | sort | uniq)
 do
     merge_dispatcher_uncertainty "${outputfile}"
 done