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R6289/pipeline_1.run
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pipeline_1.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 12:00:00
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_1_170426_fly1_013.json"'
echo FINISHED preprocessing at `date`
filename="files_1_170426_fly1_013.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])"
#ls="1100 1200 1300 1400 1500 1600 1700 1800 1900"
#command="test('$filename',[1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900],[0])"
gs="0 10 20 30 40 50 60 70 80 90 100"
ls="1000 2000 3000 4000 5000 6000 7000 8000 9000 10000"
command="test('$filename',[1000, 2000, 3000, 4000, 5000],[0])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[1000, 2000, 3000, 4000, 5000],[10])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[1000, 2000, 3000, 4000, 5000],[20])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[1000, 2000, 3000, 4000, 5000],[30])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[1000, 2000, 3000, 4000, 5000],[40])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[1000, 2000, 3000, 4000, 5000],[50])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[1000, 2000, 3000, 4000, 5000],[60])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[1000, 2000, 3000, 4000, 5000],[70])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[1000, 2000, 3000, 4000, 5000],[80])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[1000, 2000, 3000, 4000, 5000],[90])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[1000, 2000, 3000, 4000, 5000],[100])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[6000, 7000, 8000, 9000, 10000],[0])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[6000, 7000, 8000, 9000, 10000],[10])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[6000, 7000, 8000, 9000, 10000],[20])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[6000, 7000, 8000, 9000, 10000],[30])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[6000, 7000, 8000, 9000, 10000],[40])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[6000, 7000, 8000, 9000, 10000],[50])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[6000, 7000, 8000, 9000, 10000],[60])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[6000, 7000, 8000, 9000, 10000],[70])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[6000, 7000, 8000, 9000, 10000],[80])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[6000, 7000, 8000, 9000, 10000],[90])"
matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[6000, 7000, 8000, 9000, 10000],[100])"
matlab -nodesktop -nodisplay -r "$command"
echo FINISHED Matlab at `date`
for g in $gs
do
for l in $ls
do
/home/aymanns/Fiji.app/ImageJ-linux64 --ij2 --headless --console --run /home/aymanns/motion-correction-paper/fiji_script_vertical_combination.py 'parameter_file="files_1_170426_fly1_013.json", lmbd='$l", gamma="$g
done
done
echo FINISHED Fiji at `date`
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