Mercurial > repos > imgteam > imagej2_noise

comparison imagej2_analyze_skeleton_jython_script.py @ 0:3f6599ec7d30 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author imgteam
date Tue, 17 Sep 2019 16:58:28 -0400
parents
children 7a44772cc89f
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-1:000000000000 0:3f6599ec7d30
1 import jython_utils
2 import math
3 import sys
4 from ij import IJ
5 from sc.fiji.analyzeSkeleton import AnalyzeSkeleton_
6
7 BASIC_NAMES = [ 'Branches', 'Junctions', 'End-point Voxels',
8 'Junction Voxels', 'Slab Voxels', 'Average branch length',
9 'Triple Points', 'Quadruple Points', 'Maximum Branch Length' ]
10 DETAIL_NAMES = [ 'Skeleton ID', 'Branch length', 'V1 x', 'V1 y', 'V1 z', 'V2 x',
11 'V2 y', 'V2 z', 'Euclidean distance' ]
12
13 def get_euclidean_distance( vertex1, vertex2 ):
14 x1, y1, z1 = get_points( vertex1 )
15 x2, y2, z2 = get_points( vertex2 )
16 return math.sqrt( math.pow( ( x2 - x1 ), 2 ) +
17 math.pow( ( y2 - y1 ), 2 ) +
18 math.pow( ( z2 - z1 ), 2 ) )
19
20 def get_graph_length( graph ):
21 length = 0
22 for edge in graph.getEdges():
23 length = length + edge.getLength()
24 return length
25
26 def get_points( vertex ):
27 # An array of Point, which has attributes x,y,z.
28 point = vertex.getPoints()[ 0 ]
29 return point.x, point.y, point.z
30
31 def get_sorted_edge_lengths( graph ):
32 # Return graph edges sorted from longest to shortest.
33 edges = graph.getEdges()
34 edges = sorted( edges, key=lambda edge: edge.getLength(), reverse=True )
35 return edges
36
37 def get_sorted_graph_lengths( result ):
38 # Get the separate graphs (skeletons).
39 graphs = result.getGraph()
40 # Sort graphs from longest to shortest.
41 graphs = sorted( graphs, key=lambda g: get_graph_length( g ), reverse=True )
42 return graphs
43
44 def save( result, output, show_detailed_info, calculate_largest_shortest_path, sep='\t' ):
45 num_trees = int( result.getNumOfTrees() )
46 outf = open( output, 'wb' )
47 outf.write( '# %s\n' % sep.join( BASIC_NAMES ) )
48 for index in range( num_trees ):
49 outf.write( '%d%s' % ( result.getBranches()[ index ], sep ) )
50 outf.write( '%d%s' % ( result.getJunctions()[ index ], sep ) )
51 outf.write( '%d%s' % ( result.getEndPoints()[ index ], sep ) )
52 outf.write( '%d%s' % ( result.getJunctionVoxels()[ index ], sep ) )
53 outf.write( '%d%s' % ( result.getSlabs()[ index ], sep ) )
54 outf.write( '%.3f%s' % ( result.getAverageBranchLength()[ index ], sep ) )
55 outf.write( '%d%s' % ( result.getTriples()[ index ], sep ) )
56 outf.write( '%d%s' % ( result.getQuadruples()[ index ], sep ) )
57 outf.write( '%.3f' % result.getMaximumBranchLength()[ index ] )
58 if calculate_largest_shortest_path:
59 outf.write( '%s%.3f%s' % ( sep, result.shortestPathList.get( index ), sep ) )
60 outf.write( '%d%s' % ( result.spStartPosition[ index ][ 0 ], sep ) )
61 outf.write( '%d%s' % ( result.spStartPosition[ index ][ 1 ], sep ) )
62 outf.write( '%d\n' % result.spStartPosition[ index ][ 2 ] )
63 else:
64 outf.write( '\n' )
65 if show_detailed_info:
66 outf.write( '# %s\n' % sep.join( DETAIL_NAMES ) )
67 # The following index is a placeholder for the skeleton ID.
68 # The terms "graph" and "skeleton" refer to the same thing.
69 # Also, the SkeletonResult.java code states that the
70 # private Graph[] graph object is an array of graphs (one
71 # per tree).
72 for index, graph in enumerate( get_sorted_graph_lengths( result ) ):
73 for edge in get_sorted_edge_lengths( graph ):
74 vertex1 = edge.getV1()
75 x1, y1, z1 = get_points( vertex1 )
76 vertex2 = edge.getV2()
77 x2, y2, z2 = get_points( vertex2 )
78 outf.write( '%d%s' % ( index+1, sep ) )
79 outf.write( '%.3f%s' % ( edge.getLength(), sep ) )
80 outf.write( '%d%s' % ( x1, sep ) )
81 outf.write( '%d%s' % ( y1, sep ) )
82 outf.write( '%d%s' % ( z1, sep ) )
83 outf.write( '%d%s' % ( x2, sep ) )
84 outf.write( '%d%s' % ( y2, sep ) )
85 outf.write( '%d%s' % ( z2, sep ) )
86 outf.write( '%.3f' % get_euclidean_distance( vertex1, vertex2 ) )
87 if calculate_largest_shortest_path:
88 # Keep number of separated items the same for each line.
89 outf.write( '%s %s' % ( sep, sep ) )
90 outf.write( ' %s' % sep )
91 outf.write( ' %s' % sep )
92 outf.write( ' \n' )
93 else:
94 outf.write( '\n' )
95 outf.close()
96
97 # Fiji Jython interpreter implements Python 2.5 which does not
98 # provide support for argparse.
99 error_log = sys.argv[ -8 ]
100 input = sys.argv[ -7 ]
101 black_background = jython_utils.asbool( sys.argv[ -6 ] )
102 prune_cycle_method = sys.argv[ -5 ]
103 prune_ends = jython_utils.asbool( sys.argv[ -4 ] )
104 calculate_largest_shortest_path = jython_utils.asbool( sys.argv[ -3 ] )
105 if calculate_largest_shortest_path:
106 BASIC_NAMES.extend( [ 'Longest Shortest Path', 'spx', 'spy', 'spz' ] )
107 DETAIL_NAMES.extend( [ ' ', ' ', ' ', ' ' ] )
108 show_detailed_info = jython_utils.asbool( sys.argv[ -2 ] )
109 output = sys.argv[ -1 ]
110
111 # Open the input image file.
112 input_image_plus = IJ.openImage( input )
113
114 # Create a copy of the image.
115 input_image_plus_copy = input_image_plus.duplicate()
116 image_processor_copy = input_image_plus_copy.getProcessor()
117
118 try:
119 # Set binary options.
120 options = jython_utils.get_binary_options( black_background=black_background )
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
127 # Run AnalyzeSkeleton
128 analyze_skeleton = AnalyzeSkeleton_()
129 analyze_skeleton.setup( "", input_image_plus_copy )
130 if prune_cycle_method == 'none':
131 prune_index = analyze_skeleton.NONE
132 elif prune_cycle_method == 'shortest_branch':
133 prune_index = analyze_skeleton.SHORTEST_BRANCH
134 elif prune_cycle_method == 'lowest_intensity_voxel':
135 prune_index = analyze_skeleton.LOWEST_INTENSITY_VOXEL
136 elif prune_cycle_method == 'lowest_intensity_branch':
137 prune_index = analyze_skeleton.LOWEST_INTENSITY_BRANCH
138 result = analyze_skeleton.run( prune_index,
139 prune_ends,
140 calculate_largest_shortest_path,
141 input_image_plus_copy,
142 True,
143 True )
144 # Save the results.
145 save( result, output, show_detailed_info, calculate_largest_shortest_path )
146 except Exception, e:
147 jython_utils.handle_error( error_log, str( e ) )