Mercurial > repos > imgteam > imagej2_bunwarpj_convert_to_raw
view imagej2_analyze_particles_binary_jython_script.py @ 0:95fb6fa70c2f draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author | imgteam |
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date | Tue, 17 Sep 2019 17:06:56 -0400 |
parents | |
children | 7f9840d3b7e7 |
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import jython_utils import sys from ij import IJ from ij.plugin.filter import Analyzer # Fiji Jython interpreter implements Python 2.5 which does not # provide support for argparse. error_log = sys.argv[ -14 ] input = sys.argv[ -13 ] black_background = jython_utils.asbool( sys.argv[ -12 ] ) size = sys.argv[ -11 ] circularity_min = float( sys.argv[ -10 ] ) circularity_max = float( sys.argv[ -9 ] ) show = sys.argv[ -8 ] display_results = jython_utils.asbool( sys.argv[ -7 ] ) all_results = jython_utils.asbool( sys.argv[ -6 ] ) exclude_edges = jython_utils.asbool( sys.argv[ -5 ] ) include_holes = jython_utils.asbool( sys.argv[ -4 ] ) tmp_output_path = sys.argv[ -3 ] output_datatype = sys.argv[ -2 ] results_path = sys.argv[ -1 ] # Open the input image file. input_image_plus = IJ.openImage( input ) # Create a copy of the image. input_image_plus_copy = input_image_plus.duplicate() image_processor_copy = input_image_plus_copy.getProcessor() analyzer = Analyzer( input_image_plus_copy ) try: # Set binary options. options = jython_utils.get_binary_options( black_background=black_background ) IJ.run( input_image_plus_copy, "Options...", options ) # Convert image to binary if necessary. if not image_processor_copy.isBinary(): # Convert the image to binary grayscale. IJ.run( input_image_plus_copy, "Make Binary", "" ) # Set the options. options = [ 'size=%s' % size ] circularity_str = '%.3f-%.3f' % ( circularity_min, circularity_max ) options.append( 'circularity=%s' % circularity_str ) if show.find( '_' ) >= 0: show_str = '[%s]' % show.replace( '_', ' ' ) else: show_str = show options.append( 'show=%s' % show_str ) if display_results: options.append( 'display' ) if not all_results: options.append( 'summarize' ) if exclude_edges: options.append( 'exclude' ) if include_holes: options.append( 'include' ) # Always run "in_situ". options.append( 'in_situ' ) # Run the command. IJ.run( input_image_plus_copy, "Analyze Particles...", " ".join( options ) ) # Save outputs. if tmp_output_path not in [ None, 'None' ]: # Save the ImagePlus object as a new image. IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path ) if display_results and results_path not in [ None, 'None' ]: results_table = analyzer.getResultsTable() results_table.saveAs( results_path ) except Exception, e: jython_utils.handle_error( error_log, str( e ) )