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pipeline_2.run
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Mon, Nov 11, 00:22

pipeline_2.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_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="20 30 40 50 60 70 80 90"
#gs="40"
#ls="1100 1200 1300 1400 1500 1600 1700 1800 1900"
#command="test('$filename',[1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900],[0])"
#ls="4000 5000"
#ls="1000"
#command="test('$filename',[1000, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000, 10000],[20, 30, 40, 50, 60, 70, 80, 90])"
#command="test('$filename',[3000, 6000, 7000, 8000],[50])"
##command="test('$filename',[1000],[20])"
#matlab -nodesktop -nodisplay -r "$command"
#
#command="test('$filename',[9000, 10000],[50])"
#matlab -nodesktop -nodisplay -r "$command"
#
#echo 2 half 1
#command="test('$filename',[100, 200, 300, 400, 500],[2])"
#matlab -nodesktop -nodisplay -r "$command"
#echo 4 half 1
#command="test('$filename',[100, 200, 300, 400, 500],[4])"
#matlab -nodesktop -nodisplay -r "$command"
#echo 6 half 1
#command="test('$filename',[100, 200, 300, 400, 500],[6])"
#matlab -nodesktop -nodisplay -r "$command"
#echo 8 half 1
#command="test('$filename',[100, 200, 300, 400, 500],[8])"
#matlab -nodesktop -nodisplay -r "$command"
#echo 12 half 1
#command="test('$filename',[100, 200, 300, 400, 500],[12])"
#matlab -nodesktop -nodisplay -r "$command"
#echo 14 half 1
#command="test('$filename',[100, 200, 300, 400, 500],[14])"
#matlab -nodesktop -nodisplay -r "$command"
#echo 16 half 1
#command="test('$filename',[100, 200, 300, 400, 500],[16])"
#matlab -nodesktop -nodisplay -r "$command"
#echo 18 half 1
#command="test('$filename',[100, 200, 300, 400, 500],[18])"
#matlab -nodesktop -nodisplay -r "$command"
#
#echo 2 half 2
#command="test('$filename',[600, 700, 800, 900, 1000],[2])"
#matlab -nodesktop -nodisplay -r "$command"
#echo 4 half 2
#command="test('$filename',[600, 700, 800, 900, 1000],[4])"
#matlab -nodesktop -nodisplay -r "$command"
#echo 6 half 2
#command="test('$filename',[600, 700, 800, 900, 1000],[6])"
#matlab -nodesktop -nodisplay -r "$command"
#echo 8 half 2
#command="test('$filename',[600, 700, 800, 900, 1000],[8])"
#matlab -nodesktop -nodisplay -r "$command"
#echo 12 half 2
#command="test('$filename',[600, 700, 800, 900, 1000],[12])"
#matlab -nodesktop -nodisplay -r "$command"
#echo 14 half 2
#command="test('$filename',[600, 700, 800, 900, 1000],[14])"
#matlab -nodesktop -nodisplay -r "$command"
#echo 16 half 2
#command="test('$filename',[600, 700, 800, 900, 1000],[16])"
#matlab -nodesktop -nodisplay -r "$command"
#echo 18 half 2
#command="test('$filename',[600, 700, 800, 900, 1000],[18])"
#matlab -nodesktop -nodisplay -r "$command"
#command="test('$filename',[100, 200, 300, 400, 500, 600, 700, 800, 900, 1000],[2,4,6,8,12,14,16,18])"
#matlab -nodesktop -nodisplay -r "$command"
command="test('$filename',[500],[0])"
matlab -nodesktop -nodisplay -r "$command"
echo FINISHED Matlab at `date`
gs="2 4 6 8 12 14 16 18"
ls="100 200 300 400 500 600 700 800 900 1000"
gs="0"
ls="500"
for g in $gs
do
for l in $ls
do
/home/aymanns/Fiji.app/ImageJ-linux64 --ij2 --headless --console --run /home/aymanns/motion-correction-paper/fiji_script_vertical_combination.py 'parameter_file="files_2_170608_fly1_007.json", lmbd='$l", gamma="$g
done
done
echo FINISHED Fiji at `date`

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