Mercurial > repos > iuc > imagej2_analyze_particles_binary

annotate jython_script.py @ 1:dd9041dc3c27 draft

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planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
author iuc
date Sun, 11 Oct 2015 13:29:46 -0400
parents d065ec177dcd
children
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1 import jython_utils
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2 import sys
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3 from ij import IJ
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4 from ij.plugin.filter import Analyzer
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5
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6 # Fiji Jython interpreter implements Python 2.5 which does not
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7 # provide support for argparse.
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8 error_log = sys.argv[ -14 ]
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9 input = sys.argv[ -13 ]
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10 black_background = jython_utils.asbool( sys.argv[ -12 ] )
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11 size = sys.argv[ -11 ]
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12 circularity_min = float( sys.argv[ -10 ] )
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13 circularity_max = float( sys.argv[ -9 ] )
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14 show = sys.argv[ -8 ]
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15 display_results = jython_utils.asbool( sys.argv[ -7 ] )
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16 all_results = jython_utils.asbool( sys.argv[ -6 ] )
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17 exclude_edges = jython_utils.asbool( sys.argv[ -5 ] )
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18 include_holes = jython_utils.asbool( sys.argv[ -4 ] )
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19 tmp_output_path = sys.argv[ -3 ]
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20 output_datatype = sys.argv[ -2 ]
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21 results_path = sys.argv[ -1 ]
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22
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23 # Open the input image file.
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24 input_image_plus = IJ.openImage( input )
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25
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26 # Create a copy of the image.
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27 input_image_plus_copy = input_image_plus.duplicate()
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28 image_processor_copy = input_image_plus_copy.getProcessor()
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29 analyzer = Analyzer( input_image_plus_copy )
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30
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31 try:
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32 # Set binary options.
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33 options = jython_utils.get_binary_options( black_background=black_background )
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34 IJ.run( input_image_plus_copy, "Options...", options )
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35
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36 # Convert image to binary if necessary.
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37 if not image_processor_copy.isBinary():
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38 # Convert the image to binary grayscale.
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39 IJ.run( input_image_plus_copy, "Make Binary", "" )
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40
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41 # Set the options.
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42 options = [ 'size=%s' % size ]
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43 circularity_str = '%.3f-%.3f' % ( circularity_min, circularity_max )
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44 options.append( 'circularity=%s' % circularity_str )
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45 if show.find( '_' ) >= 0:
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46 show_str = '[%s]' % show.replace( '_', ' ' )
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47 else:
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48 show_str = show
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49 options.append( 'show=%s' % show_str )
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50 if display_results:
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51 options.append( 'display' )
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52 if not all_results:
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53 options.append( 'summarize' )
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54 if exclude_edges:
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55 options.append( 'exclude' )
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56 if include_holes:
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57 options.append( 'include' )
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58 # Always run "in_situ".
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59 options.append( 'in_situ' )
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60
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61 # Run the command.
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62 IJ.run( input_image_plus_copy, "Analyze Particles...", " ".join( options ) )
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63
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64 # Save outputs.
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65 if tmp_output_path not in [ None, 'None' ]:
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66 # Save the ImagePlus object as a new image.
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67 IJ.saveAs( input_image_plus_copy, output_datatype, tmp_output_path )
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68 if display_results and results_path not in [ None, 'None' ]:
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69 results_table = analyzer.getResultsTable()
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70 results_table.saveAs( results_path )
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71 except Exception, e:
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72 jython_utils.handle_error( error_log, str( e ) )