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slideQuantify_v2_5_wrapup.sh
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slideQuantify_v2_5_wrapup.sh
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#!/bin/bash
#
# Description: Wraps up a slideToolKit-CellProfiler analysis for a given slide as part
# of a slideQuantify job-session.
#
# 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 -- Study number of slide being processed, e.g. AE21."
echoerror "- Argument #2 -- name of the stain as it appears in the filenames, e.g. FIBRIN."
echoerror "- Argument #3 -- output filename where the CellProfiler results are stored, e.g. Image.csv (delimiter is assumed '_')."
echoerror "- Argument #4 -- SlideToolkit directory."
echoerror "- Argument # -- Tiles directory."
echoerror ""
echoerror "An example command would be: slideQuantify_wrapup [args: AE21] [arg2: STAIN] [arg3: Image.csv] [arg4: /path/to/dir] [arg5: /path/to/dir] "
echoerror ""
echoerror "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
# The wrong arguments are passed, so we'll exit the script now!
exit 1
}
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold " slideQuantify: Wrap Up"
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 : 2023-02-09"
echoitalic "* Version : 2.2.0"
echo ""
echoitalic "* Description : This script will start the wrap up of a slideToolKit analysis."
echoitalic " This is SLURM based."
echo ""
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo ""
### REQUIRED | GENERALS
STUDY_NUM="$1" # Depends on arg1
STAIN="$2" # Depends on arg2
OUTPUTFILENAME="$3" # Depends on arg3
SLIDETOOLKITDIR="$4" # Depends on arg5
TILESDIR="$5" # Depends on arg6
### Loading the CellProfiler-Anaconda3.8 environment
### You need to also have the conda init lines in your .bash_profile/.bashrc file
echo "..... > loading required anaconda environment containing the CellProfiler installation..."
eval "$(conda shell.bash hook)"
conda activate cp4
echo Loaded conda environment: $CONDA_PREFIX
echo ""
cd ./slideToolkit
### START of if-else statement for the number of command-line arguments passed ###
if [[ $# -lt 5 ]]; then
echo "Oh, computer says no! Number of arguments found \"$#\"."
script_arguments_error "You must supply correct (number of) arguments when running *** slideQuantify_wrapup ***!"
else
# Reference
# https://stackoverflow.com/questions/8903239/how-to-calculate-time-elapsed-in-bash-script
SECONDS=0
# do some work
# Collecting all the data
echo "..... Creating [ results.txt ] and collecting data."
if [ ! -f ./results.csv ]
then
# echo ${STAIN}
# echo "test: CD68"
if [ ${STAIN} == HE ]; then
tee results.csv <<< 'Study_number, Stain, STAIN_count_or_area_per_Total_Tissue_area, STAIN_count_or_area, Total_Tissue_area'
elif [ ${STAIN} == SMA ]; then
tee results.csv <<< 'Study_number, Stain, STAIN_area_per_Total_Tissue_area, Total_DAB_object_area, Total_Tissue_area, Total_DAB_nuclei_object_area'
elif [ ${STAIN} == CD68 ]; then
tee results.csv <<< 'Study_number, Stain, Total_DAB_object_area, Total_DAB_nuclei_area, Total_HE_object_area, Total_HE_nuclei_area, Total_Tissue_area'
elif [ ${STAIN} == CD66b ]; then
tee results.csv <<< 'Study_number, Stain, Total_Filtered_Objects, Total_Tissue_area'
elif [ ${STAIN} == CD34_DAB ]; then
tee results.csv <<< 'Study_number, Stain, Total_DAB_object_area, Total_DAB_nuclei_area, Total_HE_object_area, Total_HE_nuclei_area, Total_Tissue_area'
else
tee results.csv <<< 'Study_number, Stain, STAIN_count_or_area_per_Total_Tissue_area, STAIN_count_or_area, Total_Tissue_area'
fi
fi
# Moving into the cellprofiler output directory for the given $SLIDE_NUM
cd ./cp_output/${STUDY_NUM}/
### DEBUG
echo "Original study number: $STUDY_NUM"
SCRIPT_NAME="Colsums_${STAIN}.R"
# echo $STUDY_NUM, $STAIN, $(Rscript ${SLIDETOOLKITDIR}/utilities/$SCRIPT_NAME $STAIN $OUTPUTFILENAME) >> ../../results.csv
tee -a ../../results.csv <<< "$STUDY_NUM, $STAIN, $(Rscript ${SLIDETOOLKITDIR}/utilities/$SCRIPT_NAME $STAIN $OUTPUTFILENAME)"
# cat ../../results.txt | wc -l
# moving up to the PROJECT directory again
cd ../../
### OLD - we may want to keep tiles as these are most time consuming to create
### echo "..... Removing overlay images:"
### echo "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 -v;
###
### echo "..... Removing tiling directory and its contents."
### echo "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 -v;
###
### if [ -f *.ndpi ]; then
### echo "..... Removing intermediate tif- & png-files converted from NDPI-files.";
### ### We used to work at 40x
### ### rm -v *x40*.tif;
### ### rm -v *x40*.png;
### ### Remember - we work at 20x
### ### rm -v *x20*.tif;
### ### rm -v *x20*.png;
### fi;
### OLD - These files are each a couple KB big, so gzipping doesnt really make sense
echo "..... Gzipping list of files to process.";
gzip -v $TILESDIR/${STUDY_NUM}.*/files2cp.txt;
# gzip -d $TILESDIR/${STUDY_NUM}*/files2cp.txt.gz;
echo "..... Gzipping result files.";
gzip -vf cp_output/${STUDY_NUM}/$STAIN*.gct;
# gzip -d cp_output/${STUDY_NUM}*/$STAIN*.gct.gz;
gzip -vf cp_output/${STUDY_NUM}/$STAIN*.csv;
# gzip -d cp_output/${STUDY_NUM}*/$STAIN*.csv.gz;
echo "..... Wrapping up this slideToolKit run successfully finished."
duration=$SECONDS
echo "[ $(($duration / 60)) minutes and $(($duration % 60)) seconds elapsed ]"
### END of if-else statement for the number of command-line arguments passed ###
fi
script_copyright_message