Mercurial > repos > imgteam > imagej2_bunwarpj_compose_raw_elastic
view imagej2_noise.py @ 0:1bf7e70e67f9 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author | imgteam |
---|---|
date | Tue, 17 Sep 2019 16:56:02 -0400 |
parents | |
children |
line wrap: on
line source
#!/usr/bin/env python import argparse import os import shutil import subprocess import tempfile import imagej2_base_utils if __name__=="__main__": # Parse Command Line. parser = argparse.ArgumentParser() parser.add_argument( '--input', dest='input', help='Path to the input file' ) parser.add_argument( '--input_datatype', dest='input_datatype', help='Datatype of the input image' ) parser.add_argument( '--noise', dest='noise', help='Specified noise to add to or remove from the image' ) parser.add_argument( '--standard_deviation', dest='standard_deviation', type=float, default=None, help='Standard deviation' ) parser.add_argument( '--radius', dest='radius', type=float, default=None, help='Radius' ) parser.add_argument( '--threshold', dest='threshold', type=float, default=None, help='Threshold' ) parser.add_argument( '--which_outliers', dest='which_outliers', default=None, help='Which outliers' ) parser.add_argument( '--randomj', dest='randomj', default=None, help='RandomJ' ) parser.add_argument( '--trials', dest='trials', type=float, default=None, help='Trials' ) parser.add_argument( '--probability', dest='probability', type=float, default=None, help='Probability' ) parser.add_argument( '--lammbda', dest='lammbda', type=float, default=None, help='Lambda' ) parser.add_argument( '--order', dest='order', type=int, default=None, help='Order' ) parser.add_argument( '--mean', dest='mean', type=float, default=None, help='Mean' ) parser.add_argument( '--sigma', dest='sigma', type=float, default=None, help='Sigma' ) parser.add_argument( '--min', dest='min', type=float, default=None, help='Min' ) parser.add_argument( '--max', dest='max', type=float, default=None, help='Max' ) parser.add_argument( '--insertion', dest='insertion', default=None, help='Insertion' ) parser.add_argument( '--jython_script', dest='jython_script', help='Path to the Jython script' ) parser.add_argument( '--output', dest='output', help='Path to the output file' ) args = parser.parse_args() tmp_dir = imagej2_base_utils.get_temp_dir() # ImageJ expects valid image file extensions, so the Galaxy .dat extension does not # work for some features. The following creates a symlink with an appropriate file # extension that points to the Galaxy dataset. This symlink is used by ImageJ. tmp_input_path = imagej2_base_utils.get_input_image_path( tmp_dir, args.input, args.input_datatype ) tmp_output_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, args.input_datatype ) # Define command response buffers. tmp_out = tempfile.NamedTemporaryFile().name tmp_stdout = open( tmp_out, 'wb' ) tmp_err = tempfile.NamedTemporaryFile().name tmp_stderr = open( tmp_err, 'wb' ) # Java writes a lot of stuff to stderr, so we'll specify a file for handling actual errors. error_log = tempfile.NamedTemporaryFile( delete=False ).name # Build the command line. cmd = imagej2_base_utils.get_base_command_imagej2( None, jython_script=args.jython_script ) if cmd is None: imagej2_base_utils.stop_err( "ImageJ not found!" ) cmd += ' %s' % error_log cmd += ' %s' % tmp_input_path cmd += ' %s' % args.input_datatype cmd += ' %s ' % args.noise cmd += imagej2_base_utils.handle_none_type( args.standard_deviation ) cmd += imagej2_base_utils.handle_none_type( args.radius ) cmd += imagej2_base_utils.handle_none_type( args.threshold ) cmd += ' %s' % args.which_outliers cmd += ' %s' % args.randomj cmd += imagej2_base_utils.handle_none_type( args.trials ) cmd += imagej2_base_utils.handle_none_type( args.probability ) cmd += imagej2_base_utils.handle_none_type( args.lammbda ) cmd += imagej2_base_utils.handle_none_type( args.order, val_type='int' ) cmd += imagej2_base_utils.handle_none_type( args.mean ) cmd += imagej2_base_utils.handle_none_type( args.sigma ) cmd += imagej2_base_utils.handle_none_type( args.min ) cmd += imagej2_base_utils.handle_none_type( args.max ) cmd += ' %s' % args.insertion cmd += ' %s' % tmp_output_path proc = subprocess.Popen( args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True ) rc = proc.wait() # Handle execution errors. if rc != 0: error_message = imagej2_base_utils.get_stderr_exception( tmp_err, tmp_stderr, tmp_out, tmp_stdout ) imagej2_base_utils.stop_err( error_message ) # Handle processing errors. if os.path.getsize( error_log ) > 0: error_message = open( error_log, 'r' ).read() imagej2_base_utils.stop_err( error_message ) # Save the output image. shutil.move( tmp_output_path, args.output ) imagej2_base_utils.cleanup_before_exit( tmp_dir )