diff imagej2_analyze_particles_binary_jython_script.py @ 0:1bffabc15695 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_analyze_particles_binary_jython_script.py	Tue Sep 17 16:55:25 2019 -0400
@@ -0,0 +1,72 @@
+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 ) )