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slideQuantify_v2
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slideQuantify_v2
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#!/bin/bash
### 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 -- Path to file containing the study numbers to process"
echoerror "- Argument #5 -- output filename where the CellProfiler results are stored, e.g. Image.csv (delimiter is assumed '_')."
echoerror "- Argument #6 -- email address to send aborted/error jobs too, e.g. y.name@umcutrecht.nl."
echoerror "- Argument #7 -- by default emails are send when jobs are aborted/error, you can change that here, e.g. you can choose: BEGIN=begin of job; END=end of job; FAIL=abort of job; ALL=all message job; NONE=no mail is send."
echoerror "- Argument #8 -- Patch size. Size of the tiles in pixels, e.g. 512 indicates a tile of 512x512; slideToolKit was tested using patches of 2000x2000. [default: 2000]"
echoerror "- Argument #9 -- Down-sampling. Down-sampling number, to indicate the magnification to use, e.g. with a maximum magnification of 40x, a 1 indicates a downsample to 20x. [default: 1]"
echoerror "- Argument #10 -- Mask directory. Path to optional masks directory of given images. [OPTIONAL]"
echoerror ""
echoerror "An example command would be: slideQuantify [arg1: STAIN] [arg2: path_to_cellprofiler_pipeline] [arg3: path_to_working_directory] [arg4: path_to_procces_file] [arg5: Image.csv] [arg6: y.name@umcutrecht.nl] [arg7: FAIL] [arg8: 2000] [arg9: 2] [args10: path/to/dir]"
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 " slideQuantify V2"
echo ""
echoitalic "* Written by : Sander W. van der Laan; Tim Bezemer; Tim van de Kerkhof;"
echoitalic " Yipei Song; Tim Peters"
echoitalic "* E-mail : s.w.vanderlaan-2@umcutrecht.nl"
echoitalic "* Last update : 2024-01-04"
echoitalic "* Version : 2.1.3"
echo ""
echoitalic "* Description : This script will start the quantification for a given stain"
echoitalic " in a given project directory. "
echoitalic " This is SLURM based."
echo ""
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
### REQUIRED | GENERALS
STAIN="${1}" # Depends on arg1
PIPELINE="${2}" # Depends on arg2
PROJECTDIR="${3}" # Depends on arg3
PROCESSFILE="${4}" # Depends on arg4
OUTPUTFILENAME="${5}" # Depends on arg5
EMAIL="${6}" # Depends on arg5
MAILSETTING="${7}" # Depends on arg6
PATCHSIZE="${8}" # Depends on arg7
OUTPUTDOWN="${9}" # Depends on arg8
MASKSDIR="${10:-slideToolkit/masks}"
### Set slideToolKit DIRECTORY
SLIDETOOLKITDIR="/hpc/local/Rocky8/dhl_ec/software/slideToolKit"
QJOB_MEM_SLIDEMASK="8G"
QJOB_TIME_SLIDEMASK="00:15:00"
QJOB_MEM_SLIDETILES="128G"
QJOB_TIME_SLIDETILES="00:30:00" # emperical evidence shows ±20 minutes
QJOB_MEM_SLIDENORM="8G"
QJOB_TIME_SLIDENORM="00:25:00"
QJOB_MEM_CP="24G"
QJOB_TIME_CP="13:00:00"
QJOB_MEM_WRAP="8G"
QJOB_TIME_WRAP="00:15:00"
### START of if-else statement for the number of command-line arguments passed ###
if [[ $# -lt 8 ]]; then
echo "Oh, computer says no! Number of arguments found \"$#\"."
script_arguments_error "You must supply correct (number of) arguments when running *** slideQuantify ***!"
else
echobold "Cleaning up house, first."
mkdir -pv "$PROJECTDIR"/slideToolkit/logs
mkdir -pv "$PROJECTDIR"/slideToolkit/errors
PROCESSFILELINES=$(cat $PROCESSFILE)
cd $PROJECTDIR
for SNR in $PROCESSFILELINES; do
sleep 0.2
echobold "Processing images of file [ ${SNR} ] in directory [ ${PROJECTDIR}/slideToolkit/ ] for staining [ ${STAIN} ]."
THIS_SLIDEMASK=${SNR}_slideMask
THIS_SLIDETILES=${SNR}_slideTiles
THIS_SLIDENORMALIZE=${SNR}_slideNormalize
THIS_CELLPROFILER=${SNR}_CellProfiler
THIS_WRAPUP=${SNR}_WrapUp
echo ""
pwd
## 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 with StudyNumber ${SNR}. Submitting jobs for: "
rm -rfv "$PROJECTDIR"/slideToolkit/logs/"$SNR"_*
rm -rfv "$PROJECTDIR"/slideToolkit/errors/"$SNR"_*
## Check if masks directory is given
if [ -z "$9" ]
then
### TODO: Make mask of file
echo ""
echoitalic "* slideMask for creating mask from image. [$THIS_SLIDEMASK]"
echo "Removing log files from previous runs... "
rm -rfv "$PROJECTDIR"/slideToolkit/logs/${THIS_SLIDEMASK}.log
rm -rfv "$PROJECTDIR"/slideToolkit/errors/${THIS_SLIDEMASK}.errors
JOB_ID_THIS_SLIDEMASK=$(sbatch -J ${THIS_SLIDEMASK} -e ${PROJECTDIR}/slideToolkit/errors/${THIS_SLIDEMASK}.errors -o ${PROJECTDIR}/slideToolkit/logs/${THIS_SLIDEMASK}.log --mem=${QJOB_MEM_SLIDEMASK} --time=${QJOB_TIME_SLIDEMASK} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --parsable ${SLIDETOOLKITDIR}/slideQuantify_v2_1_entropy_segmentation.sh ${PROJECTDIR} ${MASKSDIR} ${SNR} )
else
echo ""
echoitalic "* Path to masks directory given. Masking step skipped."
fi
### slideTiles
echo ""
echoitalic "* slideTiles for extracting tiles. [ $THIS_SLIDETILES ]"
echo "Removing log files from previous runs... "
rm -rfv "$PROJECTDIR"/slideToolkit/logs/${THIS_SLIDETILES}.log
rm -rfv "$PROJECTDIR"/slideToolkit/errors/${THIS_SLIDETILES}.errors
### Check if masks directory is given
if [ -z "$9" ]
then
### run slideTiles with dependency on masking step
JOB_ID_THIS_SLIDETILES=$(sbatch -J ${THIS_SLIDETILES} -e ${PROJECTDIR}/slideToolkit/errors/${THIS_SLIDETILES}.errors -o ${PROJECTDIR}/slideToolkit/logs/${THIS_SLIDETILES}.log --mem=${QJOB_MEM_SLIDETILES} --time=${QJOB_TIME_SLIDETILES} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --depend=afterany:$JOB_ID_THIS_SLIDEMASK --parsable ${SLIDETOOLKITDIR}/slideQuantify_v2_2_extract_tiles.sh ${PROJECTDIR} ${MASKSDIR} ${OUTPUTDOWN} ${PATCHSIZE} ${SNR} )
else
# echo "sbatch -J ${THIS_SLIDETILES} -e ${PROJECTDIR}/slideToolkit/errors/${THIS_SLIDETILES}.errors -o ${PROJECTDIR}/slideToolkit/logs/${THIS_SLIDETILES}.log --mem=${QJOB_MEM_SLIDETILES} --time=${QJOB_TIME_SLIDETILES} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --parsable ${SLIDETOOLKITDIR}/slideQuantify_v2_2_extract_tiles.sh ${PROJECTDIR} ${MASKSDIR} ${OUTPUTDOWN} ${PATCHSIZE} ${SNR}"
JOB_ID_THIS_SLIDETILES=$(sbatch -J ${THIS_SLIDETILES} -e ${PROJECTDIR}/slideToolkit/errors/${THIS_SLIDETILES}.errors -o ${PROJECTDIR}/slideToolkit/logs/${THIS_SLIDETILES}.log --mem=${QJOB_MEM_SLIDETILES} --time=${QJOB_TIME_SLIDETILES} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --parsable ${SLIDETOOLKITDIR}/slideQuantify_v2_2_extract_tiles.sh ${PROJECTDIR} ${MASKSDIR} ${OUTPUTDOWN} ${PATCHSIZE} ${SNR} )
fi
### slideNormalize
echo ""
echoitalic "* slideNormalize for normalization of tiles. [ $THIS_SLIDENORMALIZE ]"
echo "Removing log files from previous runs... "
rm -rfv "$PROJECTDIR"/slideToolkit/logs/${THIS_SLIDENORMALIZE}.log
rm -rfv "$PROJECTDIR"/slideToolkit/errors/${THIS_SLIDENORMALIZE}.errors
JOB_ID_THIS_SLIDENORMALIZE=$(sbatch -J ${THIS_SLIDENORMALIZE} -e ${PROJECTDIR}/slideToolkit/errors/${THIS_SLIDENORMALIZE}.errors -o ${PROJECTDIR}/slideToolkit/logs/${THIS_SLIDENORMALIZE}.log --mem=${QJOB_MEM_SLIDENORM} --time=${QJOB_TIME_SLIDENORM} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --depend=afterany:$JOB_ID_THIS_SLIDETILES --parsable ${SLIDETOOLKITDIR}/slideQuantify_v2_3_tile_normalizing.sh ${PROJECTDIR}/slideToolkit/_tiles_layer${OUTPUTDOWN}/${SNR}.* )
### FOR DEBUG
# JOB_ID_THIS_SLIDENORMALIZE=$(sbatch -J ${THIS_SLIDENORMALIZE} -e ${PROJECTDIR}/slideToolkit/errors/${THIS_SLIDENORMALIZE}.errors -o ${PROJECTDIR}/slideToolkit/logs/${THIS_SLIDENORMALIZE}.log --mem=${QJOB_MEM_SLIDENORM} --time=${QJOB_TIME_SLIDENORM} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --parsable ${SLIDETOOLKITDIR}/slideQuantify_v2_3_tile_normalizing.sh ${PROJECTDIR}/slideToolkit/_tiles_layer${OUTPUTDOWN}/${SNR}.* )
### CellProfiler
# echo ""
# echoitalic "* CellProfiler to analyze images. [ $THIS_CELLPROFILER ]"
# echo "Removing log files from previous runs... "
# rm -rfv "$PROJECTDIR"/slideToolkit/logs/${THIS_CELLPROFILER}.log
# rm -rfv "$PROJECTDIR"/slideToolkit/errors/${THIS_CELLPROFILER}.errors
# JOB_ID_THIS_CELLPROFILER=$(sbatch -J ${THIS_CELLPROFILER} -e ${PROJECTDIR}/slideToolkit/errors/${THIS_CELLPROFILER}.errors -o ${PROJECTDIR}/slideToolkit/logs/${THIS_CELLPROFILER}.log --mem=${QJOB_MEM_CP} --time=${QJOB_TIME_CP} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --depend=afterany:$JOB_ID_THIS_SLIDENORMALIZE --parsable ${SLIDETOOLKITDIR}/slideQuantify_v2_4_cellprofiler.sh ${PROJECTDIR}/slideToolkit/ ${PIPELINE} ${STAIN} ${SNR} ${PROJECTDIR}/slideToolkit/_tiles_layer${OUTPUTDOWN}/${SNR}.* )
# ### FOR DEBUG
# # JOB_ID_THIS_CELLPROFILER=$(sbatch -J ${THIS_CELLPROFILER} -e ${PROJECTDIR}/slideToolkit/errors/${THIS_CELLPROFILER}.errors -o ${PROJECTDIR}/slideToolkit/logs/${THIS_CELLPROFILER}.log --mem=${QJOB_MEM_CP} --time=${QJOB_TIME_CP} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --parsable ${SLIDETOOLKITDIR}/slideQuantify_v2_4_cellprofiler.sh ${PROJECTDIR}/slideToolkit/ ${PIPELINE} ${STAIN} ${SNR} ${PROJECTDIR}/slideToolkit/_tiles_layer${OUTPUTDOWN}/${SNR}.* )
### Wrap Up
# echo ""
# echoitalic "* WrapUp the work we have done, and clean house. [ $THIS_WRAPUP ]"
# echo "Removing log files from previous runs... "
# rm -rfv "$PROJECTDIR"/slideToolkit/logs/${THIS_WRAPUP}.log
# rm -rfv "$PROJECTDIR"/slideToolkit/errors/${THIS_WRAPUP}.errors
# JOB_ID_THIS_WRAPUP=$(sbatch -J ${THIS_WRAPUP} -e ${PROJECTDIR}/slideToolkit/errors/${THIS_WRAPUP}.errors -o ${PROJECTDIR}/slideToolkit/logs/${THIS_WRAPUP}.log --mem=${QJOB_MEM_WRAP} --time=${QJOB_TIME_WRAP} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --parsable --depend=afterany:$JOB_ID_THIS_CELLPROFILER ${SLIDETOOLKITDIR}/slideQuantify_v2_5_wrapup.sh ${SNR} ${STAIN} ${OUTPUTFILENAME} ${SLIDETOOLKITDIR} _tiles_layer${OUTPUTDOWN} )
# ### FOR DEBUG
# # JOB_ID_THIS_WRAPUP=$(sbatch -J ${THIS_WRAPUP} -e ${PROJECTDIR}/slideToolkit/errors/${THIS_WRAPUP}.errors -o ${PROJECTDIR}/slideToolkit/logs/${THIS_WRAPUP}.log --mem=${QJOB_MEM_WRAP} --time=${QJOB_TIME_WRAP} --mail-type=${MAILSETTING} --mail-user=${EMAIL} --parsable ${SLIDETOOLKITDIR}/slideQuantify_v2_5_wrapup.sh ${SNR} ${STAIN} ${OUTPUTFILENAME} ${SLIDETOOLKITDIR} _tiles_layer${OUTPUTDOWN} )
### END OF for-loop
done
### END of if-else statement for the number of command-line arguments passed ###
fi
script_copyright_message