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slideQuantify_v2_3_tile_normalizing.sh
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slideQuantify_v2_3_tile_normalizing.sh
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#!/bin/bash
#
# Description: Runs slideNormalize to normalize images 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 "$1" # ERROR MESSAGE
echoerror ""
echoerror "- Argument #1 -- tiles_dir. Directory of tiles to be normalized"
echoerror ""
echoerror "An example command would be: slideQuantify_normalizing [arg1: /path/to/dir]"
echoerror ""
echoerror "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
# The wrong arguments are passed, so we'll exit the script now!
exit 1
}
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold " slideQuantify: Normalization"
echo ""
echoitalic "* Written by : Sander W. van der Laan; Tim Bezemer; Tim van de Kerkhof"
echoitalic " Yipei Song, Tim Peters"
echoitalic "* E-mail : s.w.vanderlaan-2@umcutrecht.nl"
echoitalic "* Last update : 2023-09-01"
echoitalic "* Version : 2.0.3"
echo ""
echoitalic "* Description : This script will start the normalization of images for "
echoitalic " slideToolKit analyses."
echoitalic " This is SLURM based."
echo ""
echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo ""
### REQUIRED | GENERALS
TILESDIR="${1}"
# Reference
# https://stackoverflow.com/questions/8903239/how-to-calculate-time-elapsed-in-bash-script
SECONDS=0
# do some work
# if the list of files to use in CellProfiler exist, we exit this script
if [[ -s $TILESDIR/files2cp.txt ]]
then
echo "..... Normalization was already applied - moving on."
exit
fi
echo $TILESDIR
if [ ! -d $TILESDIR/*tiles ]; then
(>&2 echo "*** ERROR *** No tiles to process. Create tiles first using slideTiles.")
exit;
fi
echo "..... Tiles present, starting normalization."
# moving to the required directory
cd $TILESDIR/*tiles/;
# loading required modules
### Loading the CellProfiler-Anaconda3.8 environment
### You need to also have the conda init lines in your .bash_profile/.bashrc file
echo "..... > loading required anaconda environment containing the CellProfiler installation..."
eval "$(conda shell.bash hook)"
conda activate cp4
echo Loaded conda environment: $CONDA_PREFIX
echo ""
for IMAGE_TILE in *.tile.tissue.png; do
echo "...Processing tile [ $IMAGE_TILE ]"
echo "... - applying normalization ..."
slideNormalize $IMAGE_TILE;
echo "... - removing intermediate [ $IMAGE_TILE ] ..."
rm -v $IMAGE_TILE;
done
# 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 $(pwd)/*tiles/*normalized.tile.tissue.png > files2cp.txt;
echo "..... Normalizing successfully finished."
duration=$SECONDS
echo "[ $(($duration / 60)) minutes and $(($duration % 60)) seconds elapsed ]"
script_copyright_message