Merge pull request #16 from magnostherobot/trh/utility-scripts

Implement scripts for mass-processing

bin/mass-czinspect.sh

@@ -0,0 +1,126 @@
+#!/bin/bash
+
+set -e
+
+CZINSPECT="czinspect"
+JXRCONVERT="mass-jxr-convert.sh -P1"
+
+usage () {
+    cat<<EOF
+Usage: mass-czinspect.sh [operation] <in_folder>
+
+This a wrapper script around a czi manipulation tool, and will pass most options
+directly to said tool.
+
+mass-czinspect's options:
+    -d          <dir> Output directory for output(s) of czinspect.
+    -P          Number of maximum concurrent czinspect processes; passed
+                directly to xargs if used
+    -v          Verbosity of output (default is 0 - silent)
+    -x          Remove .czi files after extraction (caution!)
+    -t <suffix> Specify output image type (default is '.jxr')
+    -v          Verbosity of output (default is 0 - silent)
+
+czi manipulation tool in use: '$CZINSPECT'
+jxr conversion tool in use: '$JXRCONVERT'
+
+czi extraction tool's help text:
+---
+$($CZINSPECT $opts -h $*)
+---
+
+If -t is specified to be anything other than '.jxr', an image conversion tool is
+used, limited to one process to allow the concurrency of many mass-czinspect
+jobs. In this case, -v and -x are passed to it. Make sure the conversion tool
+can convert to the image type you're specifying!
+
+jxr conversion tool's help text:
+---
+$($JXRCONVERT -h $*)
+---
+EOF
+}
+
+error () {
+    echo "$@" >&2
+    exit 1
+}
+
+outdir=""
+opts=""
+xargargs=""
+destroy=""
+suffix=".jxr"
+verbosity=0
+
+while getopts "xv:P:EShd:f:gaes:t:" opt; do
+    case $opt in
+    d)
+        outdir="$OPTARG"
+        ;;
+    h)
+        usage
+        exit 0
+        ;;
+    E|S|a|e|g)
+        opts="$opts -$opt"
+        ;;
+    s|f)
+        opts="$opts -$opt $OPTARG"
+        ;;
+    v)
+        verbosity="$OPTARG"
+        ;;
+    P)
+        xargargs="$xargargs -$opt $OPTARG"
+        ;;
+    x)
+        destroy="1"
+        ;;
+    t)
+        suffix="$OPTARG"
+        ;;
+    esac
+done
+
+shift $((OPTIND - 1))
+
+if (( $# == 0 )); then
+    error "Missing input directory"
+fi
+
+if [[ -z "$outdir" ]]; then
+    error "Missing output directory"
+fi
+
+INDIR="$1"
+indirsafe="$(echo $INDIR | sed 's/[[\.*^$,]/\\&/g')"
+
+EXEC="out=\"\$(echo '{}' | sed 's,$indirsafe/*\(.*\).czi\$,$outdir/\1,g')\""
+
+if [[ -n "$verbosity" ]] ; then
+    EXEC="$EXEC && echo extracting '{}'"
+fi
+
+EXEC="$EXEC && mkdir -p \"\$out\""
+EXEC="$EXEC && '$CZINSPECT' $opts -d\"\$out\" '{}'"
+
+if [[ -n "$destroy" ]] ; then
+    EXEC="$EXEC && rm -f '{}'"
+fi
+
+if [[ "$suffix" != ".jxr" ]] ; then
+    jxrcflags="-v \"$verbosity\" -t \"$suffix\""
+
+    if [[ -n "$destroy" ]] ; then
+        jxrcflags="$jxrcflags -x"
+    fi
+
+    if [[ -n "$verbose" ]] ; then
+        EXEC="$EXEC && echo converting tiles for '{}'"
+    fi
+
+    EXEC="$EXEC && $JXRCONVERT $jxrcflags \"\$out\""
+fi
+
+find $INDIR -maxdepth 1 -name '*.czi' | xargs $xargargs -I'{}' sh -c "$EXEC"

bin/mass-jxr-convert.sh

@@ -0,0 +1,114 @@
+#!/bin/bash
+
+set -e
+
+JXRDECAPP="JxrDecApp"
+CONVERT="vips --vips-concurrency=1 copy"
+
+JXRFMT="-i %s -o %s"
+
+usage () {
+    cat <<EOF
+Usage: deczi.sh [options] <input_dir>
+
+mass-jxr-convert's options:
+    -d <dir>    Output directory (defaults to input directory)
+    -x          Destructive: remove old images after making new ones
+    -t <suffix> Specify output image type (default is '.tif')
+    -P <procs>  Number of processes to run simultaneously;
+                passed to xargs if used
+    -v          Verbosity of output (default is 0 - silent)
+    -h          Print this help message
+
+jxr conversion tool in use: '$JXRDECAPP'
+general image converter in use: '$CONVERT'
+
+jxr conversion tool's help text:
+===
+$($JXRDECAPP -h $*)
+===
+
+If -t is specified to be anything other than '.tif', a general image conversion
+tool is used, limited to one process. MAke sure this converter can convert to
+the image type you're specifying!
+
+general image converter's help text:
+===
+$($CONVERT --help)
+===
+EOF
+}
+
+error () {
+    echo "$@" >& 2
+    exit 1
+}
+
+OUTDIR=""
+DESTROY=""
+SUFFIX=".tif"
+XARGSARGS=""
+VERBOSITY=0
+
+while getopts "d:hxt:P:v:" opt; do
+    case $opt in
+        d)
+            OUTDIR="$OPTARG"
+            ;;
+        h)
+            usage
+            exit 0
+            ;;
+        x)
+            DESTROY="1"
+            ;;
+        t)
+            SUFFIX="$OPTARG"
+            ;;
+        P)
+            XARGSARGS="$XARGSARGS -$opt$OPTARG"
+            ;;
+        v)
+            VERBOSITY="$OPTARG"
+            ;;
+    esac
+done
+
+shift $((OPTIND - 1))
+
+if (( $# == 0 )); then
+    error "Missing input folder"
+fi
+
+INDIR=$1
+INDIRSAFE="$(echo $INDIR | sed 's/[[\.*^$,]/\\&/g')"
+
+if [[ -z "$OUTDIR" ]]; then
+    OUTDIR="$INDIR"
+fi
+
+EXEC="mid=\"\$(echo '{}' | sed 's,$INDIRSAFE/*\(.*\)\.jxr\$,$OUTDIR/\1,g')\""
+
+if [[ -n "$VERBOSITY" ]]; then
+    EXEC="$EXEC && echo \"\$mid\"\"{.jxr->.tif}\""
+fi
+
+EXEC="$EXEC && $JXRDECAPP \$(printf -- '$JXRFMT' '{}' \"\$mid\"\".tif\")"
+
+if [[ -n "$DESTROY" ]] ; then
+    EXEC="$EXEC && rm -f '{}'"
+fi
+
+if [ "$SUFFIX" != ".tif" ] ; then
+    if [[ -n "$VERBOSITY" ]] ; then
+        EXEC="$EXEC && echo \"\$mid\"\"{.tif->$SUFFIX}\""
+    fi
+
+    EXEC="$EXEC && $CONVERT \"\$mid\".tif \"\$mid\"\"$SUFFIX\""
+
+    if [[ -n "$DESTROY" ]] ; then
+        EXEC="$EXEC && rm -f \"\$mid\".tif"
+    fi
+fi
+
+find $INDIR -maxdepth 1 -name '*.jxr' | xargs $XARGSARGS -I'{}' sh -c "$EXEC"