enclosed fn within dquotes

JaneliaSciComp · Nov 23, 2021 · 1b47aa3 · 1b47aa3
1 parent 1ec0fdb
commit 1b47aa3
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Showing 3 changed files with 18 additions and 36 deletions.
diff --git a/colormipsearch-tools/src/main/scripts/pad-all.sh b/colormipsearch-tools/src/main/scripts/pad-all.sh
@@ -27,22 +27,6 @@ NEURON_P2_PARTITIONS=(
 90 91 92 93 94 95 96 97 98 99
 )
 
-NEURON_P1_PARTITIONS=(
-10
-)
-
-NEURON_P2_PARTITIONS=(
-06
-09
-10
-22
-31
-57
-58
-70
-93
-)
-
 SRCDIR=/nrs/neuronbridge/ppp_imagery/v2.3.0-pre/FlyEM_VNC_v0.6
 RESDIR=/nrs/neuronbridge/ppp_imagery/v2.3.0-pre-resized/FlyEM_VNC_v0.6
 NCORES=32
@@ -73,7 +57,7 @@ function runLocal {
     createInputParams $p1
 
     for ((jobIndex=${p2From}; jobIndex<=${p2To} && jobIndex<=$((maxJobIndex)); jobIndex++)) ; do
-	${DIR}/pad-neuron-dirs.sh < ${DIR}/inputs/RESIZE_${p1}_$((jobIndex+1)) > ${DIR}/logs/output_${jobIndex}.out
+	${DIR}/pad-neuron-dirs.sh < ${DIR}/inputs/RESIZE_${p1}_$((jobIndex+1)) > ${DIR}/logs/output_${p1}_$((jobIndex+1)).out
     done
 }
 

diff --git a/colormipsearch-tools/src/main/scripts/pad-neuron-dirs.sh b/colormipsearch-tools/src/main/scripts/pad-neuron-dirs.sh
@@ -22,8 +22,8 @@ function process_neuron_dir {
 
     local nfiles=0
     for fn in ${neuronDir}/* ; do
-	echo ${DIR}/pad-single-pppimage.sh ${fn} ${RESDIR}/${neuronPartition}/${neuronName}
-	${DIR}/pad-single-pppimage.sh ${fn} ${RESDIR}/${neuronPartition}/${neuronName} &
+	echo ${DIR}/pad-single-pppimage.sh "${fn}" ${RESDIR}/${neuronPartition}/${neuronName}
+	${DIR}/pad-single-pppimage.sh "${fn}" ${RESDIR}/${neuronPartition}/${neuronName} &
 	pid=$!
 	pids=("${pids[@]}" $pid)
 	npids=${#pids[@]}

diff --git a/colormipsearch-tools/src/main/scripts/pad-single-pppimage.sh b/colormipsearch-tools/src/main/scripts/pad-single-pppimage.sh
@@ -4,64 +4,62 @@ function process_raw {
     fullfn=$1
     resdir=$2
 
-    fn=`basename ${fullfn}`
+    fn=`basename "${fullfn}"`
     echo "Process raw $fullfn -> $resdir/$fn"
 
-    fn=`basename ${fullfn}`
-    convert $fullfn -background black -splice 0x90 -gravity North ${resdir}/${fn}
+    convert "$fullfn" -background black -splice 0x90 -gravity North "${resdir}/${fn}"
 }
 
 function process_ch {
     fullfn=$1
     resdir=$2
 
-    fn=`basename ${fullfn}`
+    fn=`basename "${fullfn}"`
     echo "Process ch $fullfn -> $resdir/$fn"
 
-    convert $fullfn -background black -splice 0x90 -gravity North ${resdir}/${fn}
+    convert "$fullfn" -background black -splice 0x90 -gravity North "${resdir}/${fn}"
 }
 
 
 function process_skel {
     fullfn=$1
     resdir=$2
 
-    fn=`basename ${fullfn}`
+    fn=`basename "${fullfn}"`
     echo "Process skel $fullfn -> $resdir/$fn"
 
-    convert $fullfn -background "rgb(100,100,100)" -splice 0x90 -gravity North ${resdir}/${fn}
+    convert "$fullfn" -background "rgb(100,100,100)" -splice 0x90 -gravity North "${resdir}/${fn}"
 }
 
 
 function process_ppp_image {
     fullfn=$1
     resdir=$2
 
-    case ${fullfn} in
+    case "${fullfn}" in
 	*-ch.png)
-	    process_ch ${fullfn} ${resdir}
+	    process_ch "${fullfn}" ${resdir}
 	    ;;
 	*-ch_skel.png)
-	    process_ch ${fullfn} ${resdir}
+	    process_ch "${fullfn}" ${resdir}
 	    ;;
 	*-masked_raw.png)
-	    process_skel ${fullfn} ${resdir}
+	    process_skel "${fullfn}" ${resdir}
 	    ;;
 	*-skel.png)
-	    process_skel ${fullfn} ${resdir}
+	    process_skel "${fullfn}" ${resdir}
 	    ;;
 	*-raw.png)
-	    process_raw ${fullfn} ${resdir}
+	    process_raw "${fullfn}" ${resdir}
 	    ;;
 	*)
-	    echo "Unsupported file type"
+	    echo "Unsupported file type: ${fullfn}"
 	    exit 1
-	    ;;			   
+	    ;;
     esac
 }
 
 input="$1"
 outputdir="$2"
 
-process_ppp_image $input $outputdir
-
+process_ppp_image "$input" $outputdir