diff imagej2_analyze_particles_binary_jython_script.py @ 1:53fb6f4afcc8 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"

--- a/imagej2_analyze_particles_binary_jython_script.py	Tue Sep 17 17:04:21 2019 -0400
+++ b/imagej2_analyze_particles_binary_jython_script.py	Mon Sep 28 16:42:12 2020 +0000
@@ -1,72 +1,74 @@
-import jython_utils
 import sys
+
 from ij import IJ
 from ij.plugin.filter import Analyzer
 
+
+OPTIONS = ['edm=Overwrite', 'iterations=1', 'count=1']
+
 # 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 ]
+error_log = sys.argv[-14]
+input_file = sys.argv[-13]
+black_background = sys.argv[-12] == "yes"
+size = sys.argv[-11]
+circularity_min = float(sys.argv[-10])
+circularity_max = float(sys.argv[-9])
+show = sys.argv[-8]
+display_results = sys.argv[-7] == "yes"
+all_results = sys.argv[-6] == "yes"
+exclude_edges = sys.argv[-5] == "yes"
+include_holes = sys.argv[-4] == "yes"
+output_filename = sys.argv[-3]
+output_datatype = sys.argv[-2]
+results_path = sys.argv[-1]
 
 # Open the input image file.
-input_image_plus = IJ.openImage( input )
+input_image_plus = IJ.openImage(input_file)
 
 # 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 )
+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 )
+# Set binary options.
+options_list = OPTIONS
+if black_background:
+    options_list.append("black")
+options = " ".join(options_list)
+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", "" )
+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' )
+# 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 ) )
+# 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 ) )
+# Save outputs.
+if len(output_filename) > 0:
+    # Save the ImagePlus object as a new image.
+    IJ.saveAs(input_image_plus_copy, output_datatype, output_filename)
+if display_results and len(results_path) > 0:
+    results_table = analyzer.getResultsTable()
+    results_table.saveAs(results_path)