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pipeline.run
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Created
Mon, Jul 29, 10:32
Size
1 KB
Mime Type
text/x-shellscript
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Wed, Jul 31, 10:32 (1 d, 23 h)
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blob
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19431132
Attached To
R6289 Motion correction paper
pipeline.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.json"'
echo FINISHED preprocessing at `date`
filename="files_2_170608_fly1_007.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])"
command="test('$filename',[10000],[0, 10, 100])"
matlab -nodesktop -nodisplay -r "$command"
echo FINISHED Matlab at `date`
for g in $gs
do
for l in $ls
do
/home/aymanns/Fiji.app/ImageJ-linux64 --ij2 --headless --console --run /home/aymanns/motion-correction-paper/fiji_script_vertical_combination.py 'parameter_file="files_2_170608_fly1_007.json", lmbd='$l", gamma="$g
done
done
echo FINISHED Fiji at `date`
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