[CellOrganizer] demo3D12 generic test skeleton

script.sh

echo "help demo3D12;

TRAIN = false;
SYNTHESIS = false;
POSTPROCESSING = true;

option = 1;
patterns = {'LAM','Nuc','Mit','TfR'};
model_filenames = {'./lam.mat', './nuc.mat', './mit.mat', './tfr.mat'};
downsampling_scale = 5;

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