Mercurial > repos > iuc > imagej2_analyze_skeleton

annotate jython_script.py @ 0:a989ca433027 draft

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planemo upload commit 8f8692e83217a072a3ed928469621f1f606ab28a-dirty
author iuc
date Tue, 04 Aug 2015 11:14:30 -0400
parents
children dd8e4e000d2f
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0
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1 import jython_utils
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2 import math
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3 import sys
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4 from ij import IJ
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5 from ij import ImagePlus
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6 from skeleton_analysis import AnalyzeSkeleton_
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7
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8 BASIC_NAMES = [ 'Branches', 'Junctions', 'End-point Voxels',
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9 'Junction Voxels', 'Slab Voxels', 'Average branch length',
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10 'Triple Points', 'Quadruple Points', 'Maximum Branch Length' ]
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11 DETAIL_NAMES = [ 'Skeleton ID', 'Branch length', 'V1 x', 'V1 y', 'V1 z', 'V2 x',
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12 'V2 y', 'V2 z', 'Euclidean distance' ]
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13 VALID_IMAGE_TYPES = [ ImagePlus.GRAY8 ]
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14
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15 def asbool( val ):
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16 return val == 'yes'
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17
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18 def get_euclidean_distance( vertex1, vertex2 ):
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19 x1, y1, z1 = get_points( vertex1 )
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20 x2, y2, z2 = get_points( vertex2 )
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21 return math.sqrt( math.pow( ( x2 - x1 ), 2 ) +
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22 math.pow( ( y2 - y1 ), 2 ) +
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23 math.pow( ( z2 - z1 ), 2 ) )
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24
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25 def get_graph_length( graph ):
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26 length = 0
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27 for edge in graph.getEdges():
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28 length = length + edge.getLength()
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29 return length
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30
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31 def get_points( vertex ):
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32 # An array of Point, which has attributes x,y,z.
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33 point = vertex.getPoints()[ 0 ]
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34 return point.x, point.y, point.z
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35
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36 def get_sorted_edge_lengths( graph ):
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37 # Return graph edges sorted from longest to shortest.
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38 edges = graph.getEdges()
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39 edges = sorted( edges, key=lambda edge: edge.getLength(), reverse=True )
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40 return edges
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41
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42 def get_sorted_graph_lengths( result ):
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43 # Get the separate graphs (skeletons).
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44 graphs = result.getGraph()
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45 # Sort graphs from longest to shortest.
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46 graphs = sorted( graphs, key=lambda g: get_graph_length( g ), reverse=True )
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47 return graphs
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48
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49 def save( result, output, show_detailed_info, calculate_largest_shortest_path, sep='\t' ):
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50 num_trees = int( result.getNumOfTrees() )
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51 outf = open( output, 'wb' )
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52 outf.write( '# %s\n' % sep.join( BASIC_NAMES ) )
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53 for index in range( num_trees ):
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54 outf.write( '%d%s' % ( result.getBranches()[ index ], sep ) )
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55 outf.write( '%d%s' % ( result.getJunctions()[ index ], sep ) )
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56 outf.write( '%d%s' % ( result.getEndPoints()[ index ], sep ) )
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57 outf.write( '%d%s' % ( result.getJunctionVoxels()[ index ], sep ) )
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58 outf.write( '%d%s' % ( len( result.getListOfSlabVoxels() ), sep ) )
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59 outf.write( '%.3f%s' % ( result.getAverageBranchLength()[ index ], sep ) )
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60 outf.write( '%d%s' % ( result.getTriples()[ index ], sep ) )
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61 outf.write( '%d%s' % ( result.getQuadruples()[ index ], sep ) )
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62 outf.write( '%.3f' % result.getMaximumBranchLength()[ index ] )
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63 if calculate_largest_shortest_path:
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64 outf.write( '%s%.3f%s' % ( sep, result.shortestPathList.get( index ), sep ) )
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65 outf.write( '%d%s' % ( result.spStartPosition[ index ][ 0 ], sep ) )
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66 outf.write( '%d%s' % ( result.spStartPosition[ index ][ 1 ], sep ) )
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67 outf.write( '%d\n' % result.spStartPosition[ index ][ 2 ] )
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68 else:
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69 outf.write( '\n' )
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70 if show_detailed_info:
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71 outf.write( '# %s\n' % sep.join( DETAIL_NAMES ) )
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72 # The following index is a placeholder for the skeleton ID.
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73 # The terms "graph" and "skeleton" refer to the same thing.
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74 # Also, the SkeletonResult.java code states that the
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75 # private Graph[] graph object is an array of graphs (one
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76 # per tree).
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77 for index, graph in enumerate( get_sorted_graph_lengths( result ) ):
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78 for edge in get_sorted_edge_lengths( graph ):
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79 vertex1 = edge.getV1()
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80 x1, y1, z1 = get_points( vertex1 )
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81 vertex2 = edge.getV2()
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82 x2, y2, z2 = get_points( vertex2 )
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83 outf.write( '%d%s' % ( index+1, sep ) )
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84 outf.write( '%.3f%s' % ( edge.getLength(), sep ) )
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85 outf.write( '%d%s' % ( x1, sep ) )
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86 outf.write( '%d%s' % ( y1, sep ) )
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87 outf.write( '%d%s' % ( z1, sep ) )
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88 outf.write( '%d%s' % ( x2, sep ) )
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89 outf.write( '%d%s' % ( y2, sep ) )
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90 outf.write( '%d%s' % ( z2, sep ) )
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91 outf.write( '%.3f' % get_euclidean_distance( vertex1, vertex2 ) )
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92 if calculate_largest_shortest_path:
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93 # Keep number of separated items the same for each line.
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94 outf.write( '%s %s' % ( sep, sep ) )
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95 outf.write( ' %s' % sep )
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96 outf.write( ' %s' % sep )
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97 outf.write( ' \n' )
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98 else:
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99 outf.write( '\n' )
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100 outf.close()
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101
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102 # Fiji Jython interpreter implements Python 2.5 which does not
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103 # provide support for argparse.
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104 error_log = sys.argv[ -7 ]
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105 input = sys.argv[ -6 ]
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106 prune_cycle_method = sys.argv[ -5 ]
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107 prune_ends = asbool( sys.argv[ -4 ] )
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108 calculate_largest_shortest_path = asbool( sys.argv[ -3 ] )
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109 if calculate_largest_shortest_path:
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110 BASIC_NAMES.extend( [ 'Longest Shortest Path', 'spx', 'spy', 'spz' ] )
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111 DETAIL_NAMES.extend( [ ' ', ' ', ' ', ' ' ] )
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112 show_detailed_info = asbool( sys.argv[ -2 ] )
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113 output = sys.argv[ -1 ]
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114
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115 # Open the input image file.
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116 input_image_plus = IJ.openImage( input )
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117 bit_depth = input_image_plus.getBitDepth()
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118 image_type = input_image_plus.getType()
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119
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120 # Create a copy of the image.
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121 input_image_plus_copy = input_image_plus.createImagePlus()
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122 image_processor_copy = input_image_plus.getProcessor().duplicate()
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123 input_image_plus_copy.setProcessor( "iCopy", image_processor_copy )
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124
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125 try:
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126 if image_type not in VALID_IMAGE_TYPES:
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127 # Convert the image to binary grayscale.
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128 IJ.run( input_image_plus_copy, "Make Binary","" )
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129 # Run AnalyzeSkeleton
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130 analyze_skeleton = AnalyzeSkeleton_()
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131 analyze_skeleton.setup( "", input_image_plus_copy )
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132 if prune_cycle_method == 'none':
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133 prune_index = analyze_skeleton.NONE
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134 elif prune_cycle_method == 'shortest_branch':
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135 prune_index = analyze_skeleton.SHORTEST_BRANCH
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136 elif prune_cycle_method == 'lowest_intensity_voxel':
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137 prune_index = analyze_skeleton.LOWEST_INTENSITY_VOXEL
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138 elif prune_cycle_method == 'lowest_intensity_branch':
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139 prune_index = analyze_skeleton.LOWEST_INTENSITY_BRANCH
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140 result = analyze_skeleton.run( prune_index,
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141 prune_ends,
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142 calculate_largest_shortest_path,
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143 input_image_plus_copy,
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144 True,
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145 True )
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146 # Save the results.
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147 save( result, output, show_detailed_info, calculate_largest_shortest_path )
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148 except Exception, e:
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149 jython_utils.handle_error( error_log, str( e ) )