slideRename

#!/bin/bash
#
# Description: Batch rename slides
# 
# The MIT License (MIT)
# Copyright (c) 2014-2021, Bas G.L. Nelissen, Sander W. van der Laan, 
# UMC Utrecht, Utrecht, the Netherlands.
# 
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation the rights to use, copy, modify, merge, publish,
# distribute, sublicense, and/or sell copies of the Software, and to
# permit persons to whom the Software is furnished to do so, subject to
# the following conditions:
# 
# The above copyright notice and this permission notice shall be included
# in all copies or substantial portions of the Software.
# 
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
# IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
# CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
# TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
# SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
# 

# Variables
SCRIPTNAME=$(basename $0)
DESCRIPTIONSHORT="Batch rename slides"
DEPENDENCIES=("awk" "convert" "dmtxread" "grep" "identify" "display" "perl" "tiffinfo" "wmctrl" "zbarimg")
SUPPORTED_FORMATS=("Generic-TIFF" "Aperio" "Hamamatsu" "iScan" "iScanHT" "Leica")
DEFAULT_RESIZE="512x1024"
DEFAULT_OUTPUT_PREFIX="" # empty by default
DEFAULT_OUTPUT_SUFFIX="" # empty by default
DEFAULT_IM_ARGS="" # imagemagick arguments # +dither -colors 2 -colorspace gray
DEFAULT_WMCTRL_TIMEOUT="0.1" # timeout for window switching when using im-display
DEFAULT_DMTXREAD_ARGS="--stop-after 1 --milliseconds 1000 --shrink 2 --square-deviation 10" # options for dmtxread. See man dmtxread for details
DEFAULT_ZBARIMG_ARGS="--quiet " # options for zbarimg. --quiet for barcode only. See man dmtxread for details


# sort arrays
DEPENDENCIES=( $( for el in "${DEPENDENCIES[@]}"; do echo "$el"; done | sort) )
SUPPORTED_FORMATS=( $( for el in "${SUPPORTED_FORMATS[@]}"; do echo "$el"; done | sort) )

# Cleanup stage
set -e
function cleanup {
  # kill display like a real man if alive
  if [[ $IM_DISPLAY_PID > 0 ]]; then
    kill $IM_DISPLAY_PID
  fi
  # quit Preview like a polite man if it is still alive.
  if [[ "$PREVIEW" == "osx" ]];then # did we use preview at all?
    if [[ $(ps ux | grep -i [P]review | wc -l) != 0 ]]; then
      osascript -e "ignoring application responses" -e "tell application \"Preview\"" -e "if it is running then" -e "quit with saving" -e "end if" -e "end tell" -e "end ignoring"
    fi
  fi
  
  # remove temp files
  rm -rf "$PREVIEW_TMPFILE"
}
trap cleanup EXIT

# Errors go to stderr
err() {
  echo "${SCRIPTNAME} ERROR: $@" >&2
}

# usage message
usage() {
cat <<- EOF
$SCRIPTNAME --help for more information.
EOF
}

# version info
version() {
cat << EOF
slideToolKit v1.2
($SCRIPTNAME is part of the slideToolKit)

The MIT License (MIT) <http://opensource.org/licenses/MIT>
Copyright (c) 2014-2016, Bas G.L. Nelissen, UMC Utrecht, the Netherlands.

Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:

The above copyright notice and this permission notice shall be included
in all copies or substantial portions of the Software.

There is NO WARRANTY, to the extent permitted by law.

Written by Bas G.L. Nelissen | https://github.com/bglnelissen.
Edits by Sander W. van der Laan | https://github.com/swvanderlaan.

EOF
}


# help message
helpMessage() {
cat <<- EOF
${SCRIPTNAME}: ${DESCRIPTIONSHORT}

usage:
  $SCRIPTNAME [options] -f <filename>

options:
  -f, --file <filename>           virtual slide to rename

  [-l, --layer] <integer>         force specific layer by layer id
  [--prefix] <text>               filename prefix
  [--suffix] <text>               filename suffix
  [--to-lower]                    filename output is transformed to lower cases
  [--to-upper]                    filename output is transformed to upper cases
  [--barcode dmtx|zbar]           find barcode (by library) and rename accordingly. 
  [--resize] <widthxheight>       preview dimentions ["$DEFAULT_RESIZE"]
  [--convert-args]='<arguments>'  convert arguments ('=' sign and 'quotes' required)
  [--preview im|osx|none]         display preview miniature (imageMagick, OS X Preview.app, none)
  [--wmctrl-timeout] <seconds>    window switching timeout ["$DEFAULT_WMCTRL_TIMEOUT"](see description)
  [--ignore-dependencies]         ignores all dependencies, but gives warning

  --help                          display this help
  --version                       display version and license information


examples:
  $SCRIPTNAME "file.tif"
  $SCRIPTNAME --prefix="AE" --suffix=".CD68.\${RANDOM}" --file="file.tif"
  $SCRIPTNAME  --layer=5 --convert-args="-rotate 90" -f "file.tif"

print a job list -- for automatic renaming:
  find "\$(pwd)" -iname "*.tif" \\
      -exec "$(command -v "${SCRIPTNAME}")" \\
      --barcode="dmtx" --to-upper --preview="none" -f="{}" \;

print a job list -- for manual renaming:
  find "\$(pwd)" -iname "*.tif" \\
      -exec "$(command -v "${SCRIPTNAME}")" \\
      --to-upper --preview="osx" -f="{}" \;


dependencies: ${DEPENDENCIES[@]}
supported formats: ${SUPPORTED_FORMATS[@]}

This script displays a miniture of the whole slide and asks for a  new
name. The --convert-args overrides all other convert arguments that are
already set (like --resize). For some slides, the virtual slide format
is not known. For these instances you need to run slideInfo to find the
correct layer manually. When the layer containing the label is
identified, use the --layer flag. Using a slow system can cause the
focus switching to fail, if so, set the '--wmctrl-timeout' to a higher
number (e.g. 1.0). On OS X, by default, Preview.app is used for thumb
previews. The '--preview' option only works properly from an X11
terminal (on a Mac use '/Applications/Utilities/XQuartz.app'). Using the
--barcode flag, different libraries can be used to rename slides using
barcodes, dmtx (for Data Matrix 2D barcodes), and zlib (for
EAN-13/UPC-A, UPC-E, EAN-8, Code 128, Code 39, Interleaved 2 of 5 and QR
Code). Image manipulation can be done befor previewing the slide using
the --convert-args flag, the equal sign ('=') and surrounding quotes "'"
are required.

The slideToolKit and all its tools are released under the terms of the MIT license.
The slideToolKit (C) 2014-2021, Bas G.L. Nelissen, UMC Utrecht, the Netherlands;
Sander W. van der Laan | s.w.vanderlaan-2 [at] gmail [dot] com, UMC Utrecht, 
the Netherlands.

Report issues at https://github.com/swvanderlaan/slideToolKit/issues.
EOF
}

# Menu
# Empty variables
FILE=""
LAYER=""
OUTPUT_PREFIX=""
OUTPUT_SUFFIX=""
RESIZE=""
IM_DISPLAY=""
WMCTRL_TIMEOUT=""
BARCODE=""
PREVIEW=""
# illegal option
illegalOption() {
cat <<- EOF
$SCRIPTNAME: illegal option $1
$(usage)
EOF
exit 1
}
# loop through options
while :
do
  case $1 in
    -h)
    usage
    exit 0 ;;
    --help | -\?)
      helpMessage
      exit 0 ;;
    --version )
      version
      exit 0 ;;
    -f | --file)
      FILE=$2
      shift 2 ;;
    -f=* | --file=*)
      FILE=${1#*=}
      shift ;;
    -l | --layer)
      LAYER=$2
      shift 2 ;;
    --layer=*)
      LAYER=${1#*=}
      shift ;;
    --file=*)
      FILE=${1#*=}
      shift ;;
    --prefix=*)
      OUTPUT_PREFIX=${1#*=}
      shift ;;
    --prefix)
      OUTPUT_PREFIX=$2
      shift 2 ;;
    --suffix=*)
      OUTPUT_SUFFIX=${1#*=}
      shift ;;
    --suffix)
      OUTPUT_SUFFIX=$2
      shift 2 ;;
    --resize=*)
      RESIZE=${1#*=}
      shift ;;
    --resize)
      RESIZE=$2
      shift 2 ;;
    --to-upper)
      CASE="CASE_UPPER"
      shift ;;
    --to-lower)
      CASE="CASE_LOWER"
      shift ;;
    --preview=*)
      PREVIEW=${1#*=}
      shift ;;
    --preview)
      PREVIEW=$2
      shift 2 ;;
    --convert-args=*) # Equal sign and quotes are required for this option. If not, the convert arguments are seen as slideRename options.
      IM_ARGS=${1#*=}
      shift ;;
    --wmctrl-timeout)
      WMCTRL_TIMEOUT=$2
      shift 2 ;;
    --wmctrl-timeout=*)
      WMCTRL_TIMEOUT=${1#*=}
      shift ;;
    --extension=*)
      OUTPUT_EXTENSION=${1#*=}
      shift ;;
    --barcode=*)
      BARCODE=${1#*=}
      shift ;;
    --barcode)
      BARCODE=$2
      shift 2 ;;
     --ignore-dependencies)
      IGNOREDEPENDENCIES=TRUE
      shift ;;
    --) # End of all options
      shift
      break ;;
    -*)
      illegalOption "$1"
      shift ;;
    *)  # no more options. Stop while loop
      break ;;
  esac
done
# DEFAULTS
# set FILE default
if [ "$FILE" != "" ]; then
  FILE="$FILE"
else
  FILE="$1"
fi
# set OUTPUT_PREFIX default
if [ "$OUTPUT_PREFIX" != "" ]; then
  OUTPUT_PREFIX="$OUTPUT_PREFIX"
else
  OUTPUT_PREFIX="$DEFAULT_OUTPUT_PREFIX"
fi
# set OUTPUT_SUFFIX default
if [ "$OUTPUT_SUFFIX" != "" ]; then
  OUTPUT_SUFFIX="$OUTPUT_SUFFIX"
else
  OUTPUT_SUFFIX="$DEFAULT_OUTPUT_SUFFIX"
fi
# set RESIZE default
if [ "$RESIZE" != "" ]; then
  RESIZE="$RESIZE"
else
  RESIZE="$DEFAULT_RESIZE"
fi
# set IM_ARGS default
if [ "$IM_ARGS" != "" ]; then
  IM_ARGS="$IM_ARGS"
else
  IM_ARGS="$DEFAULT_IM_ARGS"
fi
# set WMCTRL_TIMEOUT default
if [ "$WMCTRL_TIMEOUT" != "" ]; then
  WMCTRL_TIMEOUT="$WMCTRL_TIMEOUT"
else
  WMCTRL_TIMEOUT="$DEFAULT_WMCTRL_TIMEOUT"
fi
# set IGNOREDEPENDENCIES
if [[ "$IGNOREDEPENDENCIES" =~ (true|TRUE|YES|yes) ]] ; then
  IGNOREDEPENDENCIES=true
else
  IGNOREDEPENDENCIES=false
fi

# requirements
checkRequirements() {
  if ! [[ -f "$FILE" ]] ; then
    err "No such file: $FILE"
    usage
    exit 1
  fi
  regexresize='^[0-9]*x[0-9]*$' # 1234x4321, but x4132 or 234x must also be possible
  if ! [[ "$RESIZE" =~ $regexresize ]] ; then
    err "This is not a valid --resize value: $RESIZE"
    usage
    exit 1
  fi
  timeoutnr='^[0-9]+[.]*[0-9]*$' # 0.1
  if ! [[ "$WMCTRL_TIMEOUT" =~ $timeoutnr ]] ; then
    err "This is not a valid --wmctrl-timeout value: $WMCTRL_TIMEOUT"
    usage
    exit 1
  fi
  if [[ -n "$PREVIEW" ]]; then
    if ! [[ "$PREVIEW" =~ (im|osx|none) ]]; then
      err "This is not a valid --preview value: $PREVIEW"
      usage
      exit 1
    fi
  fi
  if [[ -n "$BARCODE" ]]; then
    if ! [[ "$BARCODE" =~ (dmtx|zbar) ]]; then
      err "This is not a valid --barcode value: $BARCODE"
      usage
      exit 1
    fi
  fi
}

# Dependencies
checkDependencies(){
  DEPS=""
  DEPS_FAIL="0"
  for DEP in ${DEPENDENCIES[@]}; do
    if [[ 0 != "$(command -v "$DEP" >/dev/null ;echo "$?")" ]]; then
       err "Missing dependency: $DEP"
       DEPS_FAIL=$(($DEPS_FAIL + 1))
    fi
  done
  if [[ "$DEPS_FAIL" > 0 ]]; then
    # only warning when --ignore-dependencies is set.
    if [[ "$IGNOREDEPENDENCIES" == "true" ]]; then
      err "Ignoring missing dependencies (${DEPS_FAIL}), continue..."
    else
      err "Fix missing dependencies (${DEPS_FAIL}), exit."
      usage
      exit 1
    fi
  fi
}
# show thumbs per scanner type (-filter box is best for resizing and text)
# layer information can be determined using example files (http://openslide.cs.cmu.edu/download/openslide-testdata/)
getThumb(){
  # get thumb by layer id
  LAYER="$LAYER"
  convert "$FILEFULL[$LAYER]" -filter box -resize "$RESIZE" $IM_ARGS  "$PREVIEW_TMPFILE"
}
getThumbiScanHT(){
  LAYER=0
  convert "$FILEFULL[$LAYER]" -filter box -resize "$RESIZE" $IM_ARGS  "$PREVIEW_TMPFILE"
}
getThumbAperio(){
  NR_LAYERS=`identify "$FILE" | wc -l`
  LAYER="$(($NR_LAYERS - 2))"   # the last 2 layers contain thumb and the tissue (couning starts at 0)
  convert "$FILEFULL[$LAYER]" -filter box -resize "$RESIZE" $IM_ARGS  "$PREVIEW_TMPFILE"
}
getThumbLeica(){
  LAYER=1 # determined from example file (http://openslide.cs.cmu.edu/download/openslide-testdata/)
  convert "$FILEFULL[$LAYER]" -rotate 180 -filter box -resize "$RESIZE" $IM_ARGS  "$PREVIEW_TMPFILE"
}
getThumbHamamatsu(){
  LAYER=7 # determined from example file from our in-house (UMC Utrecht) Hamamatsu scanner 
  convert "$FILEFULL[$LAYER]" -rotate 90 -filter box -resize "$RESIZE" $IM_ARGS  "$PREVIEW_TMPFILE"
}
getThumbiScan(){
  LAYER=0 # determined from example file (http://openslide.cs.cmu.edu/download/openslide-testdata/)
  convert "$FILEFULL[$LAYER]" -filter box -resize "$RESIZE" -filter box -resize "$RESIZE" $IM_ARGS  "$PREVIEW_TMPFILE"
}

programOutput(){
  # set variables
  FILE="$FILE"
  # path variables
  FILEFULL="$(echo "$(cd "$(dirname "$FILE")"; pwd)"/"$(basename "$FILE")")" # full path $FULL
  BASENAME="$(basename "$FILEFULL")"    # basename
  DIRNAME="$(dirname "$FILEFULL")"      # dirname
  EXTENSION="${BASENAME##*.}"           # extension
  FILEPATH="${FILEFULL%.*}"             # full path, no extension
  FILENAME="${BASENAME%.*}"             # filename, no extension"
  # create tmp working file
  PREVIEW_TMPFILE="$(mktemp -q /tmp/${SCRIPTNAME}.XXXXXX)".png
  if [ $? -ne 0 ]; then
       err "$SCRIPTNAME: Can't create temp file, exiting..."
       exit 1
  fi  
  
  # check metadata for scanner data
  if [ "$LAYER" != "" ]; then
    getThumb # layer is set, do it the easy way
  elif [[ "0" < "$(tiffinfo  "$FILEFULL" 2>&1 | strings | grep -i "iScanHT" | wc -l | awk '{print $1}' )" ]]; then
    getThumbiScanHT # iScanHT found
  elif [[ "0" < "$(tiffinfo  "$FILEFULL" 2>&1 | strings | grep -i "Aperio" | wc -l | awk '{print $1}')" ]]; then
    getThumbAperio  # Aperio found
  elif [[ "0" < "$(tiffinfo  "$FILEFULL" 2>&1 | strings | grep -i "Leica" | wc -l | awk '{print $1}')" ]]; then
    getThumbLeica  # Leica found
  elif [[ "0" < "$(tiffinfo  "$FILEFULL" 2>&1 | strings | grep -i "Hamamatsu" | wc -l | awk '{print $1}')" ]]; then
    getThumbHamamatsu  # Hamamatsu found
  elif [[ "0" < "$(tiffinfo  "$FILEFULL" 2>&1 | strings | grep -i "iScan" | wc -l | awk '{print $1}')" ]]; then
    getThumbiScan  # iScan found
  else
    err "Unknown virtual slide format: $FILE"
    err "You probably want to set --layer manually."
    err "Run slideInfo for layer information."
    usage
    exit 1
  fi

  # display preview, im by default or Preview.app if it exists
  if [[ -z "$PREVIEW" ]]; then
    PREVIEW="im"
    if [[ -f "/Applications/Preview.app/Contents/MacOS/Preview" ]]; then
      PREVIEW="osx" # OS X Preview.app is available, use it.
    fi
  fi

  # now the PREVIEW is set with im|osx|none
  if [[ "$PREVIEW" == "im" ]];then
    # wmctrl makes sure the terminal stays active, and 'display' will open in the background.
    wmctrl -T master$$ -r :ACTIVE: ; display "$PREVIEW_TMPFILE" & sleep "$WMCTRL_TIMEOUT" ; wmctrl -a master$$
    IM_DISPLAY_PID=$(ps ax | grep [d]isplay | grep "$(basename "$PREVIEW_TMPFILE")" | awk '{print $1}')
  elif [[ "$PREVIEW" == "osx" ]];then
    # close preview gently using applescript
    open -g -a Preview "$PREVIEW_TMPFILE"
  elif [[ "$PREVIEW" == "none" ]];then
    PREVIEW="none" # do nothing really.
    # echo "Preview is set to none." # tell user/log files what is going on.
  fi

  # check barcodes
  if [[ "$BARCODE" == "dmtx" ]] ; then
    # automatically rename file using datamatrix barcode?
    SLIDENAME_BARCODE="$(dmtxread $DEFAULT_DMTXREAD_ARGS $PREVIEW_TMPFILE)" >/dev/null 2>&1 || err "Cancel slide, no barcode found :"$FILEFULL""
    if [[ -z "$SLIDENAME_BARCODE" ]]; then
      exit 1 # No barcode found. Exit (Message is already printed)
    else
      SLIDENAME_UNSAVE="$SLIDENAME_BARCODE" # barcode found, rename
    fi
  fi
  if [[ "$BARCODE" == "zbar" ]] ; then
    # automatically rename file using zbar's barcodes?
    SLIDENAME_BARCODE="$(zbarimg $DEFAULT_ZBARIMG_ARGS $PREVIEW_TMPFILE)" >/dev/null 2>&1 || err "Cancel slide, no barcode found :"$FILEFULL""
    if [[ -z "$SLIDENAME_BARCODE" ]]; then
      exit 1 # No barcode found. Exit (Message is already printed)
    else
      SLIDENAME_UNSAVE="$SLIDENAME_BARCODE" # barcode found, rename
    fi
  fi
  # ask for filename if non is existing (by typing or by barcode)
  while [ "$SLIDENAME_UNSAVE" == "" ]; do
    read -p "Enter slide name:" SLIDENAME_UNSAVE
    if [[ -z "$SLIDENAME_UNSAVE" ]] ; then
      err "Cancel slide..."
      exit 1
    fi
  done

#  fix this line.
#  SLIDENAME_UNSAVE="$(printf "$SLIDENAME_UNSAVE" | strings | perl -p -e 's/^\[B//g')"  # fix strange hand-scanner output 
  SLIDENAME=$(printf "${OUTPUT_PREFIX}${SLIDENAME_UNSAVE}${OUTPUT_SUFFIX}" | perl -p -e 's/[^A-Za-z0-9._-]/_/g') # Only OS save characters. printf keeps it all on one line
  SLIDEFILE="${SLIDENAME}.${EXTENSION}"
  # change case if needed
  if [[ "CASE_LOWER" = "$CASE" ]]; then
    # change case to lower case
    SLIDEFILE=$(echo "$SLIDEFILE" | tr [:upper:] [:lower:])
  elif  [[ "CASE_UPPER" = "$CASE" ]]; then
    # change case to upper case
    SLIDEFILE=$(echo "$SLIDEFILE" | tr [:lower:] [:upper:])
  fi
  OUTPUTFILE="${DIRNAME}/${SLIDEFILE}"
  #   rename the file
  if [[ -n "$OUTPUTFILE" ]]; then
    if [[ ! -a "$OUTPUTFILE" ]]; then
      # verbose rename file
      mv -v "$FILEFULL" "$OUTPUTFILE"
    else
      err "Filename exists: $OUTPUTFILE"
      exit 1
    fi
  else
    err "No new filename given."
    usage
    exit 1
  fi
}

# all check?
checkRequirements
checkDependencies

# lets go!
programOutput