slideQuantifyOSX

#!/bin/bash
#
# Description: slideQuantify for local (macOS) use to debug and test workflows and
#              CellProfiler pipelines, or simply to analyze (small) batches of 
#              slides locally.
# 
# 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.
# 

### Creating display functions
### Setting colouring
NONE='\033[00m'
BOLD='\033[1m'
ITALIC='\033[3m'
OPAQUE='\033[2m'
FLASHING='\033[5m'
UNDERLINE='\033[4m'

RED='\033[01;31m'
GREEN='\033[01;32m'
YELLOW='\033[01;33m'
PURPLE='\033[01;35m'
CYAN='\033[01;36m'
WHITE='\033[01;37m'
### Regarding changing the 'type' of the things printed with 'echo'
### Refer to: 
### - http://askubuntu.com/questions/528928/how-to-do-underline-bold-italic-strikethrough-color-background-and-size-i
### - http://misc.flogisoft.com/bash/tip_colors_and_formatting
### - http://unix.stackexchange.com/questions/37260/change-font-in-echo-command

### echo -e "\033[1mbold\033[0m"
### echo -e "\033[3mitalic\033[0m" ### THIS DOESN'T WORK ON MAC!
### echo -e "\033[4munderline\033[0m"
### echo -e "\033[9mstrikethrough\033[0m"
### echo -e "\033[31mHello World\033[0m"
### echo -e "\x1B[31mHello World\033[0m"

function echobold { #'echobold' is the function name
    echo -e "${BOLD}${1}${NONE}" # this is whatever the function needs to execute, note ${1} is the text for echo
}
function echoitalic { 
    echo -e "${ITALIC}${1}${NONE}" 
}
function echocyan { 
    echo -e "${CYAN}${1}${NONE}" 
}

function echonooption { 
    echo -e "${OPAQUE}${RED}${1}${NONE}"
}

# errors
function echoerrorflash { 
    echo -e "${RED}${BOLD}${FLASHING}${1}${NONE}" 
}
function echoerror { 
    echo -e "${RED}${1}${NONE}"
}

# errors no option
function echoerrornooption { 
    echo -e "${YELLOW}${1}${NONE}"
}
function echoerrorflashnooption { 
    echo -e "${YELLOW}${BOLD}${FLASHING}${1}${NONE}"
}

### MESSAGE FUNCTIONS
script_copyright_message() {
	echo ""
	THISYEAR=$(date +'%Y')
	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
	echo "+ The MIT License (MIT)                                                                                 +"
	echo "+ Copyright (c) 2016-${THISYEAR} Sander W. van der Laan                                                        +"
	echo "+                                                                                                       +"
	echo "+ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and     +"
	echo "+ associated documentation files (the \"Software\"), to deal in the Software without restriction,         +"
	echo "+ including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, +"
	echo "+ and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, +"
	echo "+ subject to the following conditions:                                                                  +"
	echo "+                                                                                                       +"
	echo "+ The above copyright notice and this permission notice shall be included in all copies or substantial  +"
	echo "+ portions of the Software.                                                                             +"
	echo "+                                                                                                       +"
	echo "+ THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT     +"
	echo "+ NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND                +"
	echo "+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES  +"
	echo "+ OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN   +"
	echo "+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.                            +"
	echo "+                                                                                                       +"
	echo "+ Reference: http://opensource.org.                                                                     +"
	echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
}
script_arguments_error() {
	echoerror "$1" # ERROR MESSAGE
	echoerror "- Argument #1  -- name of the stain as it appears in the filenames, e.g. FIBRIN."
	echoerror "- Argument #2  -- path_to CellProfiler pipeline, e.g. FIBRIN.cppipe."
	echoerror "- Argument #3  -- path_to working directory, i.e. where all the image-subdirectories are."
	echoerror "- Argument #4  -- starting letters/characters of the image-subdirectories, e.g. IMG or AE or AAA."
	echoerror "- Argument #5  -- output filename where the CellProfiler results are stored, e.g. Image.csv (delimiter is assumed '_')."
	echoerror "- Argument #6  -- eMask threshold. A smaller number is less stringent, best results are obtained using, e.g. '210'."
	echoerror "- Argument #7  -- Unique label. A string-number combination (no spaces) for reference to the analysis run. [OPTIONAL]"
	echoerror "- Argument #8  -- Batch size. A number to indicate the batch size, e.g. '5000'. [OPTIONAL]"
	echoerror "- Argument #9  -- Random sample. A number to indicate the number of overlay-images after analysis to keep, e.g. '20'. [OPTIONAL]"
	echoerror ""
	echoerror "An example command would be: slideQuantifyOSX [arg1: STAIN] [arg2: path_to_cellprofiler_pipeline] [arg3: path_to_working_directory] [arg4: IMG or AE or AAA] [arg5: Image.txt] [arg6: 210]"
	echoerror ""
	echoerror "Please note that this command should be run within the working directory (Argument #3)."

	echoerror "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
  	# The wrong arguments are passed, so we'll exit the script now!
  	exit 1
}

echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold "                               slideQuantifyOSX"
echo ""
echoitalic "* Written by  : Sander W. van der Laan; Tim Bezemer; Tim van de Kerkhof"
echoitalic "                Yipei Song"
echoitalic "* E-mail      : s.w.vanderlaan-2@umcutrecht.nl"
echoitalic "* Last update : 2024-01-10"
echoitalic "* Version     : 2.0.7"
echo ""
echoitalic "* Description : This script will start the quantification for a given stain"
echoitalic "                in a given project directory on macOS, for instance"
echoitalic "                your iMac, mac mini or MacBook"
echo ""
echocyan "NOTE: this *only* works on macOS (10.14.5+) with Anaconda 3.8 and brew."
echo ""
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"

echo ""
### REQUIRED | GENERALS	
STAIN="$1" # Depends on arg1
PIPELINE="$2" # Depends on arg2
PROJECTDIR="$3" # Depends on arg3
FILESTART="$4" # Depends on arg4
OUTPUTFILENAME="$5" # Depends on arg5
EMASKTHRESHOLD="$6" # Depends on arg6

### OPTIONAL | GENERALS	 
### https://stackoverflow.com/questions/9332802/how-to-write-a-bash-script-that-takes-optional-input-arguments
UNIQUE_LABEL=${7-V1} # Depends on arg7
BATCH_SIZE=${8-5000} # Depends on arg8
RANDOM_SAMPLE=${9-50} # Depends on arg9

### Set slideToolKit DIRECTORY
SLIDETOOLKITDIR="$HOME/git/swvanderlaan/slideToolKit"

### START of if-else statement for the number of command-line arguments passed ###
if [[ $# -lt 6 ]]; then 
	echo "Oh, computer says no! Number of arguments found "$#"."
	script_arguments_error "You must supply correct (number of) arguments when running *** slideQuantifyOSX ***!"
		
else
	echobold "Cleaning up house, first."
	rm -rfv "$FILESTART*"/magick-tmp

	echobold "Starting up the virtual environment."
	
	source activate cp4
	
	### FOR DEBUG
	### echobold "Testing the virtual environment."
	### 
	### python $SLIDETOOLKITDIR/slideToolKitTest.py
	
	echobold "Alright. All is set."
	ENTROPY_THRESHOLD="$EMASKTHRESHOLD" 
# 	HOLD_JIDS=()
	INDEX=0
	#BATCH_SIZE=5000 # should be argument, but how exactly does this work?
	#UNIQUE_LABEL="V3" # should be argument

	cd $PROJECTDIR
	
	### FOR DEBUG
	### echocyan "Debug mode - processing debug-images."
	### DEBUGLIST="AE1088.UMC.CD3_CD56_NKT"
	### DEBUGLIST="AE1088.UMC.CD3_CD56_NKT AE2292.UMC.CD3_CD56_NKT AE861.UMC.CD3_CD56_NKT AE3892.UMC.CD3_CD56_NKT"
	### for SLIDE_NUM in $DEBUGLIST; do
	### for SLIDE_NUM in AE1088.UMC.CD3_CD56_NKT; do
	### AE1088.UMC.CD3_CD56_NKT AE1165.UMC.CD3_CD56_NKT AE1249.UMC.CD3_CD56_NKT AE1462.UMC.CD3_CD56_NKT AE1468.UMC.CD3_CD56_NKT AE1495.UMC.CD3_CD56_NKT AE1548.UMC.CD3_CD56_NKT AE1550.UMC.CD3_CD56_NKT AE1701.UMC.CD3_CD56_NKT AE1707.CD3_CD56_NKT.v2 AE1710.UMC.CD3_CD56_NKT AE1713.UMC.CD3_CD56_NKT AE1722.UMC.CD3_CD56_NKT AE1731.UMC.CD3_CD56_NKT AE1732.UMC.CD3_CD56_NKT AE1737.UMC.CD3_CD56_NKT AE1750.UMC.CD3_CD56_NKT AE1771.UMC.CD3_CD56_NKT AE1780.UMC.CD3_CD56_NKT AE1781.UMC.CD3_CD56_NKT AE1857.UMC.CD3_CD56_NKT.2 AE1858.UMC.CD3_CD56_NKT AE1872.UMC.CD3_CD56_NKT AE1878.UMC.CD3_CD56_NKT AE1897.UMC.CD3_CD56_NKT AE1969.UMC.CD3_CD56_NKT AE2107.UMC.CD3_CD56_NKT AE2131.UMC.CD3_CD56_NKT AE2138.CD45CD3.v2goed AE2139.UMC.CD3_CD56_NKT.2 AE2157.CD3_CD56_NKT.v2 AE2160.UMC.CD3_CD56_NKT AE2163.UMC.CD3_CD56_NKT.2 AE2170.UMC.CD3_CD56_NKT AE2176.UMC.CD3_CD56_NKT AE2183.UMC.CD3_CD56_NKT AE2188.UMC.CD3_CD56_NKT AE2197.CD3_CD56_NKT.v2 AE21A.UMC.CD3_CD56_NKT.2 AE21B.UMC.CD3_CD56_NKT.2 AE2200.CD3_CD56_NKT.v2 AE2211.UMC.CD3_CD56_NKT AE2227.UMC.CD3_CD56_NKT AE2254.UMC.CD3_CD56_NKT AE2255.UMC.CD3_CD56_NKT AE2259.UMC.CD3_CD56_NKT AE2270.UMC.CD3_CD56_NKT.2 AE2281.UMC.CD3_CD56_NKT AE2292.UMC.CD3_CD56_NKT AE2293.UMC.CD3_CD56_NKT AE2295.UMC.CD3_CD56_NKT AE2296.CD3_CD56_NKT.v2 AE2296.UMC.CD3_CD56_NKT.2 AE2364.UMC.CD3_CD56_NKT AE2376.UMC.CD3_CD56_NKT AE2385.UMC.CD3_CD56_NKT AE2427.UMC.CD3_CD56_NKT.2 AE2433.UMC.CD3_CD56_NKT.2 AE2539.UMC.CD3_CD56_NKT AE2601.CD3_CD56_NKT.v2 AE2601.UMC.CD3_CD56_NKT.2 AE2613.UMC.CD3_CD56_NKT AE2637.UMC.CD3_CD56_NKT AE2649.UMC.CD3_CD56_NKT.2 AE2658.UMC.CD3_CD56_NKT AE2659.UMC.CD3_CD56_NKT AE2682.UMC.CD3_CD56_NKT AE2684.UMC.CD3_CD56_NKT AE2753.UMC.CD3_CD56_NKT AE2754.CD3_CD56_NKT.v2 AE2754.UMC.CD3_CD56_NKT.2 AE2757.UMC.CD3_CD56_NKT AE2759.UMC.CD3_CD56_NKT AE276.UMC.CD3_CD56_NKT AE285.UMC.CD3_CD56_NKT AE2953.CD3_CD56_NKT.v2 AE2953.UMC.CD3_CD56_NKT.2 AE2963.CD3_CD56_NKT.v2 AE2963.UMC.CD3_CD56_NKT.2 AE296.UMC.CD3_CD56_NKT AE2973.UMC.CD3_CD56_NKT.2 AE2990.UMC.CD3_CD56_NKT.2 AE3023.CD3_CD56_NKT.v2 AE3023.UMC.CD3_CD56_NKT.2 AE3136.UMC.CD3_CD56_NKT.2 AE3148.CD3_CD56_NKT.v2 AE3148.UMC.CD3_CD56_NKT.2 AE3251.CD3_CD56_NKT.v2 AE3251.UMC.CD3_CD56_NKT.2 AE3255.CD3_CD56_NKT.v2 AE3255.UMC.CD3_CD56_NKT.2 AE3305.UMC.CD3_CD56_NKT AE3348.UMC.CD3_CD56_NKT.2 AE3350.UMC.CD3_CD56_NKT.2 AE3680.UMC.CD3_CD56_NKT AE3690.UMC.CD3_CD56_NKT.2 AE3691.UMC.CD3_CD56_NKT.2 AE3762.UMC.CD3_CD56_NKT.2 AE3763.UMC.CD3_CD56_NKT.2 AE3764.UMC.CD3_CD56_NKT.2 AE3769.UMC.CD3_CD56_NKT.2 AE3777.UMC.CD3_CD56_NKT AE3795.UMC.CD3_CD56_NKT AE3796.UMC.CD3_CD56_NKT AE3886.UMC.CD3_CD56_NKT AE3892.UMC.CD3_CD56_NKT AE410.UMC.CD3_CD56_NKT AE424.UMC.CD3_CD56_NKT AE460.UMC.CD3_CD56_NKT AE488.UMC.CD3_CD56_NKT AE737.UMC.CD3_CD56_NKT AE815.UMC.CD3_CD56_NKT AE826.UMC.CD3_CD56_NKT AE838.UMC.CD3_CD56_NKT AE861.UMC.CD3_CD56_NKT
	### for SLIDE_NUM in AE1088.UMC.CD3 AE1165.UMC.CD3_CD56_NKT AE1249.UMC.CD3_CD56_NKT AE1462.UMC.CD3_CD56_NKT AE1468.UMC.CD3_CD56_NKT AE1495.UMC.CD3_CD56_NKT AE1548.UMC.CD3_CD56_NKT AE1550.UMC.CD3_CD56_NKT AE1701.UMC.CD3_CD56_NKT AE1707.CD3_CD56_NKT.v2 AE1710.UMC.CD3_CD56_NKT AE1713.UMC.CD3_CD56_NKT AE1722.UMC.CD3_CD56_NKT AE1731.UMC.CD3_CD56_NKT AE1732.UMC.CD3_CD56_NKT AE1737.UMC.CD3_CD56_NKT AE1750.UMC.CD3_CD56_NKT AE1771.UMC.CD3_CD56_NKT AE1780.UMC.CD3_CD56_NKT AE1781.UMC.CD3_CD56_NKT AE1857.UMC.CD3_CD56_NKT.2 AE1858.UMC.CD3_CD56_NKT AE1872.UMC.CD3_CD56_NKT AE1878.UMC.CD3_CD56_NKT AE1897.UMC.CD3_CD56_NKT AE1969.UMC.CD3_CD56_NKT AE2107.UMC.CD3_CD56_NKT AE2131.UMC.CD3_CD56_NKT AE2138.CD45CD3.v2goed AE2139.UMC.CD3_CD56_NKT.2 AE2157.CD3_CD56_NKT.v2 AE2160.UMC.CD3_CD56_NKT AE2163.UMC.CD3_CD56_NKT.2 AE2170.UMC.CD3_CD56_NKT AE2176.UMC.CD3_CD56_NKT AE2183.UMC.CD3_CD56_NKT AE2188.UMC.CD3_CD56_NKT AE2197.CD3_CD56_NKT.v2 AE21A.UMC.CD3_CD56_NKT.2 AE21B.UMC.CD3_CD56_NKT.2 AE2200.CD3_CD56_NKT.v2 AE2211.UMC.CD3_CD56_NKT AE2227.UMC.CD3_CD56_NKT AE2254.UMC.CD3_CD56_NKT AE2255.UMC.CD3_CD56_NKT AE2259.UMC.CD3_CD56_NKT AE2270.UMC.CD3_CD56_NKT.2 AE2281.UMC.CD3_CD56_NKT AE2292.UMC.CD3_CD56_NKT AE2293.UMC.CD3_CD56_NKT AE2295.UMC.CD3_CD56_NKT AE2296.CD3_CD56_NKT.v2 AE2296.UMC.CD3_CD56_NKT.2 AE2364.UMC.CD3_CD56_NKT AE2376.UMC.CD3_CD56_NKT AE2385.UMC.CD3_CD56_NKT AE2427.UMC.CD3_CD56_NKT.2 AE2433.UMC.CD3_CD56_NKT.2 AE2539.UMC.CD3_CD56_NKT AE2601.CD3_CD56_NKT.v2 AE2601.UMC.CD3_CD56_NKT.2 AE2613.UMC.CD3_CD56_NKT AE2637.UMC.CD3_CD56_NKT AE2649.UMC.CD3_CD56_NKT.2 AE2658.UMC.CD3_CD56_NKT AE2659.UMC.CD3_CD56_NKT AE2682.UMC.CD3_CD56_NKT AE2684.UMC.CD3_CD56_NKT AE2753.UMC.CD3_CD56_NKT AE2754.CD3_CD56_NKT.v2 AE2754.UMC.CD3_CD56_NKT.2 AE2757.UMC.CD3_CD56_NKT AE2759.UMC.CD3_CD56_NKT AE276.UMC.CD3_CD56_NKT AE285.UMC.CD3_CD56_NKT AE2953.CD3_CD56_NKT.v2 AE2953.UMC.CD3_CD56_NKT.2 AE2963.CD3_CD56_NKT.v2 AE2963.UMC.CD3_CD56_NKT.2 AE296.UMC.CD3_CD56_NKT AE2973.UMC.CD3_CD56_NKT.2 AE2990.UMC.CD3_CD56_NKT.2 AE3023.CD3_CD56_NKT.v2 AE3023.UMC.CD3_CD56_NKT.2 AE3136.UMC.CD3_CD56_NKT.2 AE3148.CD3_CD56_NKT.v2 AE3148.UMC.CD3_CD56_NKT.2 AE3251.CD3_CD56_NKT.v2 AE3251.UMC.CD3_CD56_NKT.2 AE3255.CD3_CD56_NKT.v2 AE3255.UMC.CD3_CD56_NKT.2 AE3305.UMC.CD3_CD56_NKT AE3348.UMC.CD3_CD56_NKT.2 AE3350.UMC.CD3_CD56_NKT.2 AE3680.UMC.CD3_CD56_NKT AE3690.UMC.CD3_CD56_NKT.2 AE3691.UMC.CD3_CD56_NKT.2 AE3762.UMC.CD3_CD56_NKT.2 AE3763.UMC.CD3_CD56_NKT.2 AE3764.UMC.CD3_CD56_NKT.2 AE3769.UMC.CD3_CD56_NKT.2 AE3777.UMC.CD3_CD56_NKT AE3795.UMC.CD3_CD56_NKT AE3796.UMC.CD3_CD56_NKT AE3886.UMC.CD3_CD56_NKT AE3892.UMC.CD3_CD56_NKT AE410.UMC.CD3_CD56_NKT AE424.UMC.CD3_CD56_NKT AE460.UMC.CD3_CD56_NKT AE488.UMC.CD3_CD56_NKT AE737.UMC.CD3_CD56_NKT AE815.UMC.CD3_CD56_NKT AE826.UMC.CD3_CD56_NKT AE838.UMC.CD3_CD56_NKT AE861.UMC.CD3_CD56_NKT; do

	for SLIDE_NUM in $FILESTART*; do
	
		sleep 1
		THIS_SLIDE=${SLIDE_NUM/\//}
		THIS_SLIDEMASK=${THIS_SLIDE}_slideMask_${UNIQUE_LABEL}
		THIS_SLIDE2TILES=${THIS_SLIDE}_slide2Tiles_${UNIQUE_LABEL}
		THIS_SLIDENORMALIZE=${THIS_SLIDE}_slideNormalize_${UNIQUE_LABEL}
		THIS_CELLPROFILER=${THIS_SLIDE}_CellProfiler_${UNIQUE_LABEL}
		THIS_WRAPUP=${THIS_SLIDE}_WrapUp_${UNIQUE_LABEL}

		echobold "Processing images of file [ ${SLIDE_NUM} ] in directory [ ${PROJECTDIR} ] for staining [ ${STAIN} ] -- at index [ ${INDEX} ] with total batch size [ ${BATCH_SIZE} ]."	

		cd "$SLIDE_NUM" || exit
		echo ""
	
		# Checking if an analysis was done before
		if [[ -s cp_output/"$STAIN"_Image.csv.gz ]]; then 
			echoitalic "Checking if this file was processed before; cp_output/${STAIN}_Image.csv.gz should be present ....."
			ls -lh cp_output/*.gz
			cd .. ; 
			INDEX=$((INDEX+1)); 
			echo "..... Analysis was already done!"; 
			continue; 
		fi
		
		echo "..... Processing file for the first time."
		echo "..... Removing previous logs."
		rm -rfv "$PROJECTDIR"/logs/"$SLIDE_NUM"*
		rm -rfv "$PROJECTDIR"/errors/"$SLIDE_NUM"*

		### slideEMask for macro, and NDPISplit when necessary
		echo ""
		echoitalic "* slideEMask, which will mask, create a macro, and do NDPISplit when necessary."

		# checking if masks exist - if so, skip this script
		if [ -f *.emask.png ] || [ -f *.mask.png ]; then 
			echo "..... Masked images already exists - moving on."

		else

			mkdir -pv magick-tmp
			export MAGICK_TMPDIR=$(pwd)/magick-tmp
			export TMPDIR=$(pwd)/magick-tmp

			# Note that slideMask automatically determines what the layer of the macro is
			if [ -f *.ndpi ]; then
				echo "The image-file is a NDPI and will be converted to .tif before masking."
				if [ -f *.ndpi ]; then  
					ndpisplit -x20 -z0 *.ndpi; 
				fi

				# level should be an argument (easiest), or automatically determined (harder)
				# slideMacro.py -i *.ndpi -l 5 -o $(pwd)
				slideMask --layer 0 -f *x20*.tif;

			elif [ -f *.tif ]; then 
				echo "The image-file is a (NDPI-converted) .tif."
				# level should be an argument (easiest), or automatically determined (harder)
				# slideMacro.py -i *.tif -l 0 -o $(pwd)
				slideMask --layer 0 -f *x20*.tif;

			elif [ -f *.TIF ]; then 
				echo "The image-file is a .TIF."
				# level should be an argument (easiest), or automatically determined (harder)
				# slideMacro.py -i *.TIF -l 3 -o $(pwd)
				slideMask -f *.TIF;

			else
				echoerrorflash "*** ERROR *** Something is rotten in the City of Gotham; most likely a typo. Double back, please. 
				[image-extension not recognized, should be 'ndpi', 'tif' or 'TIF']"
				exit 1 
			fi
		
			# running slideEMask on the macro
			for MACRO in $(ls *.macro.png); do 
				echo "Running slideEMask on the macro-images."
				slideEMask -f $MACRO -t $EMASKTHRESHOLD; 

			done

			# removing temporary files
			echo "..... Removing temporary directory."
			rm -rfv magick-tmp
		
		fi
		
	
		### slide2Tiles
		echo ""
		echoitalic "* slide2Tiles to create tiles from images. [ $THIS_SLIDE2TILES ]"
		
		### NOTE: this does not work locally on macOS
		if [ -d *.tiles ]; then 
			echo "..... Tiles directory already exists - moving on."
		
		else

			mkdir -pv magick-tmp
			export MAGICK_TMPDIR=$(pwd)/magick-tmp
			export TMPDIR=$(pwd)/magick-tmp

			if [ -f *.ndpi ]; then
				echo "The image-file is a NDPI and should first be converted to .tif before tiling."
				# getting the x20 magnification
				ndpisplit -x20 -z0 *.ndpi
				slide2Tiles --layer 0 -f *x20*.tif -m *.emask.png --verbose;
	
			elif [ -f *.tif ]; then
				echo "The image-file is a (NDPI-converted) .tif."
				slide2Tiles --layer 0 -f *x20*.tif -m *.emask.png --verbose;
	
			elif [ -f *.TIF ]; then
				echo "The image-file is a .TIF."
				### old layer selection - it should fit the above mask-creation layer-selection
				### slide2Tiles --layer 8 -f *.TIF -m *.emask.png --verbose;
				slide2Tiles -f *.TIF -m *.emask.png --verbose;
	
			else
				echoerrorflash "*** ERROR *** Something is rotten in the City of Gotham; most likely a typo. Double back, please. 
				[image-extension not recognized, should be 'ndpi', 'tif' or 'TIF']"
				exit 1 
			fi
		
			echo "..... Removing temporary directory."
			rm -rfv magick-tmp
		fi
		

		### slideNormalize
		echo ""
		echoitalic "* slideNormalize for normalization of images. [ $THIS_SLIDENORMALIZE ]."
		
		### NOTE: this does not work locally on macOS
		if [ -f files2cp.txt ]; then 
			echo "..... Normalization was already applied - moving on."
		
		else
			echo "..... Checking existence of tiles."
			### DEBUG
			### ls $PROJECTDIR/$SLIDE_NUM/*.tiles/;

			if [ ! -d *.tiles ]; then
				(>&2 echo "*** ERROR *** No tiles to process. Create tiles first using slide2Tiles.")
				exit; 
		
			else
				echo "..... Tiles present, starting normalization."
				# moving to appropriate directory
				cd *.tiles

				mkdir -pv magick-tmp
				export MAGICK_TMPDIR=$(pwd)/magick-tmp
				export TMPDIR=$(pwd)/magick-tmp
		
				for IMAGE_TILE in *.png; do
					echo "...Processing tile [ $IMAGE_TILE ]"
					echo "... - applying normalization ..."
					slideNormalize $IMAGE_TILE
		
					echo "... - masking the normalized image ..."
					slideEMask -c -f $IMAGE_TILE -t $ENTROPY_THRESHOLD
					
					echo "... - removing intermediate $IMAGE_TILE ..."
# 					rm -v $IMAGE_TILE;
		
				done
				echo "..... Removing temporary directory."
				rm -rfv magick-tmp
			
				# moving back to the root of the $SLIDE_NUM directory
				cd ..
			
				echo "..... Collecting all normalized and masked tiles in a file for CellProfiler."
# 				ls -d -1 $(pwd)/*tiles/
				ls -d -1 $(pwd)/*tiles/*normalized* > files2cp.txt
				ls -d -1 $(pwd)/*tiles/ENTROPY* >> files2cp.txt
				
			fi

		fi

		### CellProfiler
		### This does not work on macOS Mojave 10.14.5 because we need vigra.
		### However installing this comes with issues: https://github.com/ukoethe/vigra/issues/468
		### There is no issue running it on macOS Big Sur 11.5.1+.
		
		echo ""
		echoitalic "* CellProfiler to analyze images. [ $THIS_CELLPROFILER ]"
		
		if [ -z "$(ls -A cp_output)" ]; then 
			echo "..... > checking CellProfiler version..."
			cellprofiler --version
			
			echo "..... > making output directory..."
			mkdir -pv cp_output
			
			echo "..... Running CellProfiler using $PIPELINE for [ $SLIDE_NUM ] samples stained with [ $STAIN ]."
			cellprofiler -c -r -p $PIPELINE --file-list files2cp.txt -o cp_output/;

		else
			echo "..... CellProfiler was already run, or at least there is a 'cp_output'-directory."
			
		fi
		

		### Wrap Up
		### 1. we randomly grap 10 masked & tiled PNG-files to keep for post-analysis check >> OUT-COMMENTED
		### 2. we get the data (in STAIN_Image.txt) for each study number (SLIDE_NUM) in 'cp_output' using >> OUT-COMMENTED
		###    Colsums.R
		### 3. we remove tiles, and other files we don't need
		echo ""
		echoitalic "* WrapUp the work we have done, and clean house. [ $THIS_WRAPUP ] "

		# Randomly grab x (50) overlay images, and remove the rest
		ls cp_output/*.png | shuf -n $(expr $(ls cp_output/*.png | wc -l) - $RANDOM_SAMPLE) | xargs rm;

		# Collecting all the data
		echo "..... Creating [ results.txt ] and collecting data."
		echo 'SampleID Slide_number Stain Counts_per_Tissue_area' > results.txt;
		
		# Moving into the cellprofiler output directory for the given $SLIDE_NUM
		cd cp_output;
		
		# parsing SLIDE_NUM "$PWD"
		# cut on . (period), output is 1
		SAMPLE_NUM=$(echo $SLIDE_NUM | cut -d'.' -f1)
		### DEBUG
		### echo "Original slide number: $SLIDE_NUM"
		### echo "Sample number: $SAMPLE_NUM"
		SCRIPT_NAME="Colsums_${STAIN}.R"
		echo $SAMPLE_NUM $SLIDE_NUM $STAIN $(Rscript $SLIDETOOLKITDIR/utilities/$SCRIPT_NAME $STAIN $OUTPUTFILENAME ) >> ../results.txt;
		### we used to Gzip
		### gzip -v ../results.txt;
		head ../results.txt
		cat ../results.txt | wc -l
		# moving up to the $SLIDE_NUM directory again
		cd ..
		
		echo "..... Removing tiling directory and its contents.";
		# Randomly grab x (50) overlay images, and remove the rest
		ls *tiles/*.png | shuf -n $(expr $(ls *tiles/*.png | wc -l) - $RANDOM_SAMPLE) | xargs rm;
		rm -rfv *tiles/;
		if [ -f *.ndpi ]; then 
			echo "..... Removing intermediate tif- & png-files converted from NDPI-files.";
			rm -v *x40*.tif; 
			rm -v *x40*.png; 
		fi;
		
		echo "..... Removing list of files to process.";
		rm -v files2cp.txt;

		echo "..... Gzipping result files.";
		gzip -vf cp_output/${STAIN}*.gct;
		gzip -vf cp_output/${STAIN}*.csv;

		echo ""
		echo "* Moving back to the project directory [$PROJECTDIR]"
		cd $PROJECTDIR
		
		### REMOVE THIS BREAK FOR PRODUCTION!
		### When this break is active, only the first item 
		### in the list of items to be processed will be processed.
		###
		### OLD CODE
		### INDEX=$((INDEX+1))
		### break;	
		
		### NEW CODE
		INDEX=$((INDEX+1))
		if [ "$INDEX" -eq "$BATCH_SIZE" ]; then 
			break; 
		fi

	# END OF for-loop
	done


### END of if-else statement for the number of command-line arguments passed ###
fi

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