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cellorganizer-demo3D12 public CI script #ubuntu #macosx #matlab #cellorganizer
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########################################### | |
# REMEMBER TO SET UP THE VARIABLE $OPTION # | |
########################################### | |
find . -name "*lock*" -exec rm -f {} \; | |
OPTION=$1 | |
echo "help demo3D12; | |
TRAIN = true; | |
SYNTHESIS = true; | |
POSTPROCESSING = true; | |
option = $OPTION; | |
patterns = {'LAM','Mit','Nuc','TfR'}; | |
model_filenames = {'./lam.mat', './mit.mat', './nuc.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 = 'all'; | |
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 = 5; | |
param.compression = 'lzw'; | |
param.microscope = 'none'; | |
param.synthesis = 'all'; | |
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 | |
if [ -n $OPTION ]; then | |
$MATLAB $MATLAB_OPTS -r "script;" | |
else | |
echo "Variable OPTION not set. Not running demo." | |
fi | |
DEMO='demo3D12' | |
DIRECTORY='demos/3D/demo3D12' | |
for FILE in $DIRECTORY/*.tgz | |
do | |
rm -fv '$FILE' | |
end | |
if | |
PATTERNS=( 'LAM' 'TfR' 'Nuc' 'Mit' ) | |
for PATTERN in "${PATTERNS[@]}" | |
do | |
if [ -d $DIRECTORY/$PATTERN ]; then | |
rm -fvr $DIRECTORY/$PATTERN | |
fi | |
done | |
echo "" | |
if [ -n "$SAVED_RESULTS" ]; then | |
DATE=`date +%F-%H%M%S` | |
if [ ! -d "$SAVED_RESULTS"/"$DEMO" ]; then | |
mkdir -v "$SAVED_RESULTS"/"$DEMO" | |
fi | |
cp -r "$DIRECTORY" "$SAVED_RESULTS"/"$DEMO"/"$DATE" | |
fi |
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