Mercurial > repos > iuc > imagej2_analyze_skeleton

comparison jython_script.py @ 2:9631aab7da53 draft

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planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
author iuc
date Wed, 26 Aug 2015 14:36:10 -0400
parents dd8e4e000d2f
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1:dd8e4e000d2f 2:9631aab7da53
1 import jython_utils 1 import jython_utils
2 import math 2 import math
3 import sys 3 import sys
4 from ij import IJ 4 from ij import IJ
5 from ij import ImagePlus
6 from skeleton_analysis import AnalyzeSkeleton_ 5 from skeleton_analysis import AnalyzeSkeleton_
7 6
8 BASIC_NAMES = [ 'Branches', 'Junctions', 'End-point Voxels', 7 BASIC_NAMES = [ 'Branches', 'Junctions', 'End-point Voxels',
9 'Junction Voxels', 'Slab Voxels', 'Average branch length', 8 'Junction Voxels', 'Slab Voxels', 'Average branch length',
10 'Triple Points', 'Quadruple Points', 'Maximum Branch Length' ] 9 'Triple Points', 'Quadruple Points', 'Maximum Branch Length' ]
11 DETAIL_NAMES = [ 'Skeleton ID', 'Branch length', 'V1 x', 'V1 y', 'V1 z', 'V2 x', 10 DETAIL_NAMES = [ 'Skeleton ID', 'Branch length', 'V1 x', 'V1 y', 'V1 z', 'V2 x',
12 'V2 y', 'V2 z', 'Euclidean distance' ] 11 'V2 y', 'V2 z', 'Euclidean distance' ]
13 VALID_IMAGE_TYPES = [ ImagePlus.GRAY8 ]
14
15 def asbool( val ):
16 return val == 'yes'
17 12
18 def get_euclidean_distance( vertex1, vertex2 ): 13 def get_euclidean_distance( vertex1, vertex2 ):
19 x1, y1, z1 = get_points( vertex1 ) 14 x1, y1, z1 = get_points( vertex1 )
20 x2, y2, z2 = get_points( vertex2 ) 15 x2, y2, z2 = get_points( vertex2 )
21 return math.sqrt( math.pow( ( x2 - x1 ), 2 ) + 16 return math.sqrt( math.pow( ( x2 - x1 ), 2 ) +
53 for index in range( num_trees ): 48 for index in range( num_trees ):
54 outf.write( '%d%s' % ( result.getBranches()[ index ], sep ) ) 49 outf.write( '%d%s' % ( result.getBranches()[ index ], sep ) )
55 outf.write( '%d%s' % ( result.getJunctions()[ index ], sep ) ) 50 outf.write( '%d%s' % ( result.getJunctions()[ index ], sep ) )
56 outf.write( '%d%s' % ( result.getEndPoints()[ index ], sep ) ) 51 outf.write( '%d%s' % ( result.getEndPoints()[ index ], sep ) )
57 outf.write( '%d%s' % ( result.getJunctionVoxels()[ index ], sep ) ) 52 outf.write( '%d%s' % ( result.getJunctionVoxels()[ index ], sep ) )
58 outf.write( '%d%s' % ( len( result.getListOfSlabVoxels() ), sep ) ) 53 outf.write( '%d%s' % ( result.getSlabs()[ index ], sep ) )
59 outf.write( '%.3f%s' % ( result.getAverageBranchLength()[ index ], sep ) ) 54 outf.write( '%.3f%s' % ( result.getAverageBranchLength()[ index ], sep ) )
60 outf.write( '%d%s' % ( result.getTriples()[ index ], sep ) ) 55 outf.write( '%d%s' % ( result.getTriples()[ index ], sep ) )
61 outf.write( '%d%s' % ( result.getQuadruples()[ index ], sep ) ) 56 outf.write( '%d%s' % ( result.getQuadruples()[ index ], sep ) )
62 outf.write( '%.3f' % result.getMaximumBranchLength()[ index ] ) 57 outf.write( '%.3f' % result.getMaximumBranchLength()[ index ] )
63 if calculate_largest_shortest_path: 58 if calculate_largest_shortest_path:
99 outf.write( '\n' ) 94 outf.write( '\n' )
100 outf.close() 95 outf.close()
101 96
102 # Fiji Jython interpreter implements Python 2.5 which does not 97 # Fiji Jython interpreter implements Python 2.5 which does not
103 # provide support for argparse. 98 # provide support for argparse.
104 error_log = sys.argv[ -7 ] 99 error_log = sys.argv[ -8 ]
105 input = sys.argv[ -6 ] 100 input = sys.argv[ -7 ]
101 black_background = jython_utils.asbool( sys.argv[ -6 ] )
106 prune_cycle_method = sys.argv[ -5 ] 102 prune_cycle_method = sys.argv[ -5 ]
107 prune_ends = asbool( sys.argv[ -4 ] ) 103 prune_ends = jython_utils.asbool( sys.argv[ -4 ] )
108 calculate_largest_shortest_path = asbool( sys.argv[ -3 ] ) 104 calculate_largest_shortest_path = jython_utils.asbool( sys.argv[ -3 ] )
109 if calculate_largest_shortest_path: 105 if calculate_largest_shortest_path:
110 BASIC_NAMES.extend( [ 'Longest Shortest Path', 'spx', 'spy', 'spz' ] ) 106 BASIC_NAMES.extend( [ 'Longest Shortest Path', 'spx', 'spy', 'spz' ] )
111 DETAIL_NAMES.extend( [ ' ', ' ', ' ', ' ' ] ) 107 DETAIL_NAMES.extend( [ ' ', ' ', ' ', ' ' ] )
112 show_detailed_info = asbool( sys.argv[ -2 ] ) 108 show_detailed_info = jython_utils.asbool( sys.argv[ -2 ] )
113 output = sys.argv[ -1 ] 109 output = sys.argv[ -1 ]
114 110
115 # Open the input image file. 111 # Open the input image file.
116 input_image_plus = IJ.openImage( input ) 112 input_image_plus = IJ.openImage( input )
117 bit_depth = input_image_plus.getBitDepth()
118 image_type = input_image_plus.getType()
119 113
120 # Create a copy of the image. 114 # Create a copy of the image.
121 input_image_plus_copy = input_image_plus.createImagePlus() 115 input_image_plus_copy = input_image_plus.duplicate()
122 image_processor_copy = input_image_plus.getProcessor().duplicate() 116 image_processor_copy = input_image_plus_copy.getProcessor()
123 input_image_plus_copy.setProcessor( "iCopy", image_processor_copy )
124 117
125 try: 118 try:
126 if image_type not in VALID_IMAGE_TYPES: 119 # Set binary options.
127 # Convert the image to binary grayscale. 120 options = jython_utils.get_binary_options( black_background=black_background )
128 IJ.run( input_image_plus_copy, "Make Binary","iterations=1 count=1 edm=Overwrite do=Nothing" ) 121 IJ.run( input_image_plus_copy, "Options...", options )
122
123 # Convert image to binary if necessary.
124 if not image_processor_copy.isBinary():
125 IJ.run( input_image_plus_copy, "Make Binary", "" )
126
129 # Run AnalyzeSkeleton 127 # Run AnalyzeSkeleton
130 analyze_skeleton = AnalyzeSkeleton_() 128 analyze_skeleton = AnalyzeSkeleton_()
131 analyze_skeleton.setup( "", input_image_plus_copy ) 129 analyze_skeleton.setup( "", input_image_plus_copy )
132 if prune_cycle_method == 'none': 130 if prune_cycle_method == 'none':
133 prune_index = analyze_skeleton.NONE 131 prune_index = analyze_skeleton.NONE