cellorganizer-demo3D12-lamp2-framework-downsampling8 Jenkins script

script.sh

#!/bin/bash
#
#$ -j y
#$ -S /bin/bash
#$ -cwd
#PBS -q model1
#PBS -M icaoberg@andrew.cmu.edu

cd $PBS_O_WORKDIR

git checkout dev
git pull origin dev

echo "help demo3D12;
 
TRAIN = true;
SYNTHESIS = true;
POSTPROCESSING = true;
 
%LAMP2
option = 1;
patterns = {'LAM','Mit','Nuc','TfR'};
model_filenames = {'./lam.mat', './mit.mat', './nuc.mat', './tfr.mat'};
downsampling_scale = 8;
 
pattern = patterns{option};
model_filename = model_filenames{option};
 
cd( './demos/3D/demo3D12' );
if TRAIN
	%run demo and make profile
	profile on
 
	param.model.downsampling = [ downsampling_scale, downsampling_scale, 1];
	param.proteinUpsampleZ = 5;
  	param.train.flag = 'framework';
 
	demo3D12( option, false, param );
	profile off
	movefile( model_filename, './model.mat' );
	profsave( profile('info'), 'profile' );
	zip( 'profile.zip', 'profile' )
	rmdir( 'profile', 's' );
end
 
if SYNTHESIS
	%try to synthesize images from model
	try
	 state = rng(3);
	catch
	 state = RandStream.create('mt19937ar','seed', 11);
	 RandStream.setDefaultStream(state);
	end
 
	outputDirectory = pwd;
	param = [];
	param.targetDirectory = [ outputDirectory ];
	param.prefix = 'synthesizedImages';
	param.numberOfSynthesizedImages = 50;
	param.compression = 'lzw';
	param.microscope = 'none';
	param.synthesis = 'framework';
	param.verbose = true;
	param.debug = true;
 
	slml2img( {'./model.mat'}, param );
end
 
if POSTPROCESSING
    input_images_directory = [ pwd filesep pattern ];
	output_images_directory = [ pwd filesep 'temp' filesep 'raw' ];
	answer = ...
	    raw_images_gallery_wrapper( ...
	    	input_images_directory, output_images_directory );
 
	input_images_directory = [ pwd filesep 'intermediate_results' ];
	output_images_directory = [ pwd filesep 'temp' filesep 'intermediate' ];
	answer = ...
	    intermediate_results_image_gallery_wrapper( ...
	    	input_images_directory, output_images_directory );
 
	input_images_directory = [ pwd filesep 'temp' filesep 'preprocessing' ];
	output_images_directory =  [ pwd filesep 'temp' filesep 'preprocessing' ];
	answer = ...
	    preprocessed_images_gallery_wrapper( ...
	    	input_images_directory, output_images_directory );
 
	input_images_directory = [ pwd filesep 'synthesizedImages' ];
	output_images_directory = [ pwd filesep 'temp' filesep 'synthetic' ];
	synthesized_images_gallery_wrapper( ...
		input_images_directory, output_images_directory );
 
	input_images_directory = [ pwd filesep 'temp' filesep 'cell_shape_eigen' ]
	output_images_directory = [ pwd filesep 'temp' filesep 'cellcodes' ];
	cellcodes_images_gallery_wrapper( ...
		input_images_directory, output_images_directory );
end
 
exit;" > script.m

#erase all results
#rm -rf demos/3D/demo3D12/temp

#erase preprocessed images
rm -rf demos/3D/demo3D12/temp/preprocessing

#erase temporary models/parameters
rm -f demos/3D/demo3D12/temp/*.mat

#erase cell codes
DIRECTORY=demos/3D/demo3D12/temp/cellcodes
if [ -d "$DIRECTORY"]; then
	rm -rf $DIRECTORY
fi

#erase compartment statistics
DIRECTORY=demos/3D/demo3D12/temp/compartment_stats
if [ -d "$DIRECTORY"]; then
	rm -rf $DIRECTORY
fi

#erase nuclear features
DIRECTORY=demos/3D/demo3D12/temp/nuclearfeats
if [ -d "$DIRECTORY"]; then
	rm -rf $DIRECTORY
fi

#erase protein objects foldero
DIRECTORY=demos/3D/demo3D12/temp/nuclearfeats/protein_objects_gaussian/
if [ -d "$DIRECTORY"]; then
	rm -rf $DIRECTORY
fi

/usr/local/bin/matlab_7.13 -nodesktop -nosplash -r "script;"