indent

diff --git a/cluster_tools/gate_power_merge.sh b/cluster_tools/gate_power_merge.sh
index fc0e6aa3233fe032bf9713b1038e27315f4c9e67..2733e406a823958069c7ab1f8f9aba6ed64a677a 100755 (executable)
--- a/cluster_tools/gate_power_merge.sh
+++ b/cluster_tools/gate_power_merge.sh
@@ -1,41 +1,41 @@
 #!/usr/bin/env bash
 
-set -u 
+set -u
 
 function error {
-echo "ERROR: $1"
-exit 1
+    echo "ERROR: $1"
+    exit 1
 }
 
 warning_count=0
 function warning {
-let "warning_count++"
-echo "MERGE_WARNING: $1"
+    let "warning_count++"
+    echo "MERGE_WARNING: $1"
 }
 
 function start_bar {
-count_max="${1:?"provide count max"}"
+    count_max="${1:?"provide count max"}"
 }
 
 function update_bar {
-local count="${1:?"provide count"}"
-local message="${2:?"provide message"}"
-local percent=$(echo "100*${count}/${count_max}" | bc)
-#printf "[%03d/%03d] %3d%% %-80.80s\r" ${count} ${count_max} ${percent} "${message}"
-printf "[%03d/%03d] %3d%% %-80.80s\n" ${count} ${count_max} ${percent} "${message}"
+    local count="${1:?"provide count"}"
+    local message="${2:?"provide message"}"
+    local percent=$(echo "100*${count}/${count_max}" | bc)
+    #printf "[%03d/%03d] %3d%% %-80.80s\r" ${count} ${count_max} ${percent} "${message}"
+    printf "[%03d/%03d] %3d%% %-80.80s\n" ${count} ${count_max} ${percent} "${message}"
 }
 
 function end_bar {
-unset count_max
-#echo -ne '\n'
+    unset count_max
+    #echo -ne '\n'
 }
 
 function check_interfile {
-local input_interfile="${1:?"provide input interfile"}"
+    local input_interfile="${1:?"provide input interfile"}"
 
-grep -qs '!INTERFILE :=' "${input_interfile}" || return 1
+    grep -qs '!INTERFILE :=' "${input_interfile}" || return 1
 
-local header_byte_size=$(awk -F' ' '
+    local header_byte_size=$(awk -F' ' '
 BEGIN { zsize = 0; }
 /matrix size/ && $3 == "[1]" { xsize = $5; }
 /matrix size/ && $3 == "[2]" { ysize = $5; }
@@ -43,19 +43,19 @@ BEGIN { zsize = 0; }
 /number of bytes per pixel/ { byte_per_pixel = $7; }
 END { print xsize * ysize * zsize * byte_per_pixel; }' "${input_interfile}")
 
-local raw_interfile="$(dirname "${input_interfile}")/$(awk -F' := ' '/name of data file/ { print $2; }' "${input_interfile}")"
+    local raw_interfile="$(dirname "${input_interfile}")/$(awk -F' := ' '/name of data file/ { print $2; }' "${input_interfile}")"
 
-test -f "${raw_interfile}" || return 1
-test $(stat -c%s "${raw_interfile}") -eq ${header_byte_size} || return 1
+    test -f "${raw_interfile}" || return 1
+    test $(stat -c%s "${raw_interfile}") -eq ${header_byte_size} || return 1
 }
 
 function write_mhd_header {
-local input_interfile="${1:?"provide input interfile"}"
-local output_mhd="$(dirname "${input_interfile}")/$(basename "${input_interfile}" ".hdr").mhd"
+    local input_interfile="${1:?"provide input interfile"}"
+    local output_mhd="$(dirname "${input_interfile}")/$(basename "${input_interfile}" ".hdr").mhd"
 
-check_interfile "${input_interfile}" || error "${input_interfile} isn't an interfile image"
+    check_interfile "${input_interfile}" || error "${input_interfile} isn't an interfile image"
 
-local header_start='ObjectType = Image
+    local header_start='ObjectType = Image
 NDims = 3
 AcquisitionDate = none
 BinaryData = True
@@ -67,21 +67,21 @@ CenterOfRotation = 0 0 0
 DistanceUnits = mm
 AnatomicalOrientation = RIP'
 
-echo "${header_start}" > "${output_mhd}"
+    echo "${header_start}" > "${output_mhd}"
 
-awk -F' ' '
+    awk -F' ' '
 /scaling factor/ && $4 == "[1]" { xspacing = $6; }
 /scaling factor/ && $4 == "[2]" { yspacing = $6; }
 END { print "ElementSpacing = " xspacing " " yspacing " 1"; }' "${input_interfile}" >> "${output_mhd}"
 
-awk -F' ' '
+    awk -F' ' '
 BEGIN { zsize = 0; }
 /matrix size/ && $3 == "[1]" { xsize = $5; }
 /matrix size/ && $3 == "[2]" { ysize = $5; }
 /number of projections/ { zsize += $5; }
 END { print "DimSize = " xsize " " ysize " " zsize; }' "${input_interfile}" >> "${output_mhd}"
 
-awk -F' := ' '
+    awk -F' := ' '
 /number format/ { format = $2; }
 /number of bytes per pixel/ { byte_per_pixel = $2 }
 END {
@@ -98,7 +98,7 @@ if (format == "float" && byte_per_pixel == 4) { print "ElementType = MET_DOUBLE"
 print "ElementType = MET_INT";
 }' "${input_interfile}" >> "${output_mhd}"
 
-awk -F' := ' '
+    awk -F' := ' '
 /name of data file/ { print "ElementDataFile = " $2; }' "${input_interfile}" >> "${output_mhd}"
 }
 
@@ -106,200 +106,200 @@ rootMerger="clitkMergeRootFiles"
 test -x "./clitkMergeRootFiles" && rootMerger="./clitkMergeRootFiles"
 
 function merge_root {
-local merged="$1"
-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
-do
-    local partial="$1"
+    local merged="$1"
     shift
-    let count++
-    local arguments=" -i ${partial} ${arguments}"
-done
-${rootMerger} ${arguments} > /dev/null || error "error while calling ${rootMerger}"
-echo "  ${indent}merged ${count} files"
+    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
+    do
+        local partial="$1"
+        shift
+        let count++
+        local arguments=" -i ${partial} ${arguments}"
+    done
+    ${rootMerger} ${arguments} > /dev/null || error "error while calling ${rootMerger}"
+    echo "  ${indent}merged ${count} files"
 }
 
 statMerger="mergeStatFile.py"
 test -x "./mergeStatFile.sh" && statMerger="./mergeStatFile.sh"
 
 function merge_stat {
-local merged="$1"
-shift
-echo "  ${indent}entering stat merger"
-echo "  ${indent}merger is ${statMerger}"
-echo "  ${indent}creating ${merged}"
-local count=0
-start_bar $#
-while test $# -gt 0
-do
-    local partial="$1"
+    local merged="$1"
     shift
-    let count++
-
-    if test ! -f "${merged}"
-    then
-        update_bar ${count} "copying first partial result ${partial}"
-        cp "${partial}" "${merged}"
-        continue
-    fi
+    echo "  ${indent}entering stat merger"
+    echo "  ${indent}merger is ${statMerger}"
+    echo "  ${indent}creating ${merged}"
+    local count=0
+    start_bar $#
+    while test $# -gt 0
+    do
+        local partial="$1"
+        shift
+        let count++
+
+        if test ! -f "${merged}"
+        then
+            update_bar ${count} "copying first partial result ${partial}"
+            cp "${partial}" "${merged}"
+            continue
+        fi
 
-    update_bar ${count} "adding ${partial}"
-    ${statMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${statMerger}"
-done
-end_bar
-echo "  ${indent}merged ${count} files"
+        update_bar ${count} "adding ${partial}"
+        ${statMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${statMerger}"
+    done
+    end_bar
+    echo "  ${indent}merged ${count} files"
 }
 
 doseMerger="mergeDosePerEnegryFile.sh"
 test -x "./mergeDosePerEnergyFile.sh" && doseMerger="./mergeDosePerEnergyFile.sh"
 
 function merge_dose {
-local merged="$1"
-shift
-echo "  ${indent}entering dose merger"
-echo "  ${indent}merger is ${doseMerger}"
-echo "  ${indent}creating ${merged}"
-local count=0
-start_bar $#
-while test $# -gt 0
-do
-    local partial="$1"
+    local merged="$1"
     shift
-    let count++
-
-    if test ! -f "${merged}"
-    then
-        update_bar ${count} "copying first partial result ${partial}"
-        cp "${partial}" "${merged}"
-        continue
-    fi
+    echo "  ${indent}entering dose merger"
+    echo "  ${indent}merger is ${doseMerger}"
+    echo "  ${indent}creating ${merged}"
+    local count=0
+    start_bar $#
+    while test $# -gt 0
+    do
+        local partial="$1"
+        shift
+        let count++
+
+        if test ! -f "${merged}"
+        then
+            update_bar ${count} "copying first partial result ${partial}"
+            cp "${partial}" "${merged}"
+            continue
+        fi
 
-    update_bar ${count} "adding ${partial}"
-    ${doseMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
-done
-end_bar
-echo "  ${indent}merged ${count} files"
+        update_bar ${count} "adding ${partial}"
+        ${doseMerger} -i "${merged}" -j "${partial}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${doseMerger}"
+    done
+    end_bar
+    echo "  ${indent}merged ${count} files"
 }
 
 txtImageMerger="clitkMergeAsciiDoseActor"
 test -f "./clitkMergeAsciiDoseActor" && txtImageMerger="./clitkMergeAsciiDoseActor"
 
 function merge_txt_image {
-local merged="$1"
-shift
-echo "  ${indent}entering text image merger"
-echo "  ${indent}merger is ${txtImageMerger}"
-echo "  ${indent}creating ${merged}"
-local count=0
-start_bar $#
-while test $# -gt 0
-do
-    local partial="$1"
+    local merged="$1"
     shift
-    let count++
-
-    if test ! -f "${merged}"
-    then
-        update_bar ${count} "copying first partial result ${partial}"
-        cp "${partial}" "${merged}"
-        continue
-    fi
+    echo "  ${indent}entering text image merger"
+    echo "  ${indent}merger is ${txtImageMerger}"
+    echo "  ${indent}creating ${merged}"
+    local count=0
+    start_bar $#
+    while test $# -gt 0
+    do
+        local partial="$1"
+        shift
+        let count++
+
+        if test ! -f "${merged}"
+        then
+            update_bar ${count} "copying first partial result ${partial}"
+            cp "${partial}" "${merged}"
+            continue
+        fi
 
-    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 ${txtImageMerger}"
-    echo "${header}" > "${merged}"
-    grep -v '## Merge' "${tmp}" >> "${merged}"
-    rm "${tmp}"
-done
-end_bar
-echo "  ${indent}merged ${count} files"
+        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 ${txtImageMerger}"
+        echo "${header}" > "${merged}"
+        grep -v '## Merge' "${tmp}" >> "${merged}"
+        rm "${tmp}"
+    done
+    end_bar
+    echo "  ${indent}merged ${count} files"
 }
 
 hdrImageMerger="clitkImageArithm"
 test -x "./clitkImageArithm" && hdrImageMerger="./clitkImageArithm"
 
 function merge_hdr_image {
-local merged="$1"
-local merged_bin="${merged%.*}.img"
-shift
-echo "  ${indent}entering hdr image merger"
-echo "  ${indent}merger is ${hdrImageMerger}"
-echo "  ${indent}creating ${merged}"
-local count=0
-start_bar $#
-while test $# -gt 0
-do
-    local partial="$1"
-    local partial_bin="${partial%.*}.img"
+    local merged="$1"
+    local merged_bin="${merged%.*}.img"
     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
+    echo "  ${indent}entering hdr image merger"
+    echo "  ${indent}merger is ${hdrImageMerger}"
+    echo "  ${indent}creating ${merged}"
+    local count=0
+    start_bar $#
+    while test $# -gt 0
+    do
+        local partial="$1"
+        local partial_bin="${partial%.*}.img"
+        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}"
-    ${hdrImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${hdrImageMerger}"
-done
-end_bar
-echo "  ${indent}merged ${count} files"
+        update_bar ${count} "adding ${partial}"
+        ${hdrImageMerger} -t 0 -i "${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="$1"
-    local partial_bin="$(dirname "${partial}")/$(awk -F' = ' '/ElementDataFile/ { print $2; }' "${partial}")"
+    local merged="$1"
+    local merged_bin="${merged%.*}.raw"
     shift
-    let count++
-
-    if test ! -f "${merged}"
-    then
-        update_bar ${count} "copying first partial result ${partial}"
-        cp "${partial}" "${merged}"
-        cp "${partial_bin}" "${merged_bin%.*}.${partial_bin##*.}"
-        continue
-    fi
+    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="$1"
+        local partial_bin="$(dirname "${partial}")/$(awk -F' = ' '/ElementDataFile/ { print $2; }' "${partial}")"
+        shift
+        let count++
+
+        if test ! -f "${merged}"
+        then
+            update_bar ${count} "copying first partial result ${partial}"
+            cp "${partial}" "${merged}"
+            cp "${partial_bin}" "${merged_bin%.*}.${partial_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 ${mhdImageMerger}"
-    mv "${merged_bin}" "${merged_bin%.*}.${partial_bin##*.}"
-    sed -i "s/$(basename "${merged_bin}")/$(basename "${merged_bin%.*}.${partial_bin##*.}")/" "${merged}"
-done
-end_bar
-echo "  ${indent}merged ${count} files"
+        update_bar ${count} "adding ${partial}"
+        ${mhdImageMerger} -t 0 -i "${partial}" -j "${merged}" -o "${merged}" 2> /dev/null > /dev/null || warning "error while calling ${mhdImageMerger}"
+        mv "${merged_bin}" "${merged_bin%.*}.${partial_bin##*.}"
+        sed -i "s/$(basename "${merged_bin}")/$(basename "${merged_bin%.*}.${partial_bin##*.}")/" "${merged}"
+    done
+    end_bar
+    echo "  ${indent}merged ${count} files"
 }
 
 function merge_dispatcher {
@@ -446,8 +446,8 @@ done
 
 if [ -f "${rundir}/params.txt" ]
 then
-       echo "copying params file"
-       cp "${rundir}/params.txt" "${outputdir}/params.txt"
+    echo "copying params file"
+    cp "${rundir}/params.txt" "${outputdir}/params.txt"
 fi
 
 echo "these was ${warning_count} warning(s)"