R6289/pipeline2.run
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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`