pipeline2.run
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	#!/bin/bash
	#SBATCH -p debug
	#SBATCH --workdir /home/aymanns/motion-correction-paper
	#SBATCH --nodes 1
	#SBATCH --ntasks 1
	#SBATCH --cpus-per-task 1
	#SBATCH --mem 128000
	#SBATCH --time 01:00:00
	module load matlab
	module load jdk
	module load gcc
	module load openblas/0.2.19-openmp
	echo STARTING at `date`
	/home/aymanns/Fiji.app/ImageJ-linux64 --ij2 --headless --console --run /home/aymanns/motion-correction-paper/preprocessing.py 'parameter_file="files_2_170608_fly1_007_all.json"'
	echo FINISHED preprocessing at `date`
	filename="files_2_170608_fly1_007_all.json"
	# filename="files_4_170609_fly1_001.json"
	# gs=""
	# ls=""
	# for g in 0 10 100
	# do
	# for l in 5000 # 1000 5000 10000
	# do
	# # matlab -nodesktop -nodisplay -r "test('$filename',$l,$g);"
	# command="${command}test('$filename',$l,$g);clear all;"
	# gs="$gs $g"
	# ls="$ls $l"
	# done
	# done
	# command="test('$filename',[1000,5000,10000],[0,10,100])"
	#gs="0 10 100"
	gs="0"
	#ls="1100 1200 1300 1400 1500 1600 1700 1800 1900"
	#command="test('$filename',[1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900],[0])"
	ls="1000"
	command="test('$filename',[1000],[0])"
	matlab -nodesktop -nodisplay -r "$command"
	echo FINISHED Matlab at `date`

	for g in $gs
	do
	for l in $ls
	do
	/home/aymanns/Fiji.app/ImageJ-linux64 --ij2 --headless --console --run /home/aymanns/motion-correction-paper/fiji_script_vertical_combination.py 'parameter_file="files_2_170608_fly1_007_all.json", lmbd='$l", gamma="$g
	done
	done

	echo FINISHED Fiji at `date`