Mercurial > repos > imgteam > imagej2_adjust_threshold_binary

annotate imagej2_analyze_skeleton_jython_script.py @ 2:da29019170f1 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author imgteam
date Sun, 05 Nov 2023 10:52:33 +0000
parents 29a4d422f32a
children 2b007b1e6c1b
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f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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1 import math
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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2 import sys
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29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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4 from ij import IJ
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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5 from sc.fiji.analyzeSkeleton import AnalyzeSkeleton_
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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6
2
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7 BASIC_NAMES = [
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8 "Branches",
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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9 "Junctions",
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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10 "End-point Voxels",
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11 "Junction Voxels",
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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12 "Slab Voxels",
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13 "Average branch length",
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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14 "Triple Points",
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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15 "Quadruple Points",
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16 "Maximum Branch Length",
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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17 ]
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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18 DETAIL_NAMES = [
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19 "Skeleton ID",
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20 "Branch length",
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21 "V1 x",
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22 "V1 y",
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23 "V1 z",
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24 "V2 x",
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25 "V2 y",
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26 "V2 z",
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27 "Euclidean distance",
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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28 ]
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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29 OPTIONS = ["edm=Overwrite", "iterations=1", "count=1"]
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30
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31
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32 def get_euclidean_distance(vertex1, vertex2):
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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33 x1, y1, z1 = get_points(vertex1)
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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34 x2, y2, z2 = get_points(vertex2)
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35 return math.sqrt(
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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36 math.pow((x2 - x1), 2) + math.pow((y2 - y1), 2) + math.pow((z2 - z1), 2)
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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37 )
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38
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40 def get_graph_length(graph):
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41 length = 0
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42 for edge in graph.getEdges():
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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43 length = length + edge.getLength()
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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44 return length
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45
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47 def get_points(vertex):
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48 # An array of Point, which has attributes x,y,z.
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49 point = vertex.getPoints()[0]
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50 return point.x, point.y, point.z
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53 def get_sorted_edge_lengths(graph):
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54 # Return graph edges sorted from longest to shortest.
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55 edges = graph.getEdges()
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56 edges = sorted(edges, key=lambda edge: edge.getLength(), reverse=True)
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57 return edges
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58
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60 def get_sorted_graph_lengths(result):
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61 # Get the separate graphs (skeletons).
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62 graphs = result.getGraph()
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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63 # Sort graphs from longest to shortest.
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64 graphs = sorted(graphs, key=lambda g: get_graph_length(g), reverse=True)
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65 return graphs
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66
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67
2
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68 def save(result, output, show_detailed_info, calculate_largest_shortest_path, sep="\t"):
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69 num_trees = int(result.getNumOfTrees())
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70 outf = open(output, "wb")
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71 outf.write("# %s\n" % sep.join(BASIC_NAMES))
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72 for index in range(num_trees):
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73 outf.write("%d%s" % (result.getBranches()[index], sep))
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74 outf.write("%d%s" % (result.getJunctions()[index], sep))
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75 outf.write("%d%s" % (result.getEndPoints()[index], sep))
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76 outf.write("%d%s" % (result.getJunctionVoxels()[index], sep))
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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77 outf.write("%d%s" % (result.getSlabs()[index], sep))
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78 outf.write("%.3f%s" % (result.getAverageBranchLength()[index], sep))
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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79 outf.write("%d%s" % (result.getTriples()[index], sep))
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80 outf.write("%d%s" % (result.getQuadruples()[index], sep))
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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81 outf.write("%.3f" % result.getMaximumBranchLength()[index])
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f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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82 if calculate_largest_shortest_path:
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83 outf.write("%s%.3f%s" % (sep, result.shortestPathList.get(index), sep))
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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84 outf.write("%d%s" % (result.spStartPosition[index][0], sep))
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85 outf.write("%d%s" % (result.spStartPosition[index][1], sep))
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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86 outf.write("%d\n" % result.spStartPosition[index][2])
0
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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87 else:
2
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88 outf.write("\n")
0
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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89 if show_detailed_info:
2
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90 outf.write("# %s\n" % sep.join(DETAIL_NAMES))
0
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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91 # The following index is a placeholder for the skeleton ID.
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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92 # The terms "graph" and "skeleton" refer to the same thing.
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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93 # Also, the SkeletonResult.java code states that the
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94 # private Graph[] graph object is an array of graphs (one
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95 # per tree).
1
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96 for index, graph in enumerate(get_sorted_graph_lengths(result)):
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97 for edge in get_sorted_edge_lengths(graph):
0
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98 vertex1 = edge.getV1()
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99 x1, y1, z1 = get_points(vertex1)
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100 vertex2 = edge.getV2()
1
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101 x2, y2, z2 = get_points(vertex2)
2
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102 outf.write("%d%s" % (index + 1, sep))
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103 outf.write("%.3f%s" % (edge.getLength(), sep))
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104 outf.write("%d%s" % (x1, sep))
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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105 outf.write("%d%s" % (y1, sep))
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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106 outf.write("%d%s" % (z1, sep))
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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107 outf.write("%d%s" % (x2, sep))
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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108 outf.write("%d%s" % (y2, sep))
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109 outf.write("%d%s" % (z2, sep))
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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110 outf.write("%.3f" % get_euclidean_distance(vertex1, vertex2))
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f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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111 if calculate_largest_shortest_path:
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112 # Keep number of separated items the same for each line.
2
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113 outf.write("%s %s" % (sep, sep))
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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114 outf.write(" %s" % sep)
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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115 outf.write(" %s" % sep)
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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116 outf.write(" \n")
0
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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117 else:
2
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118 outf.write("\n")
0
f1ba33cd9edf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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119 outf.close()
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120
1
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121
0
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122 # Fiji Jython interpreter implements Python 2.5 which does not
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123 # provide support for argparse.
1
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124 error_log = sys.argv[-8]
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125 input = sys.argv[-7]
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126 black_background = sys.argv[-6] == "yes"
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127 prune_cycle_method = sys.argv[-5]
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128 prune_ends = sys.argv[-4] == "yes"
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129 calculate_largest_shortest_path = sys.argv[-3] == "yes"
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130 if calculate_largest_shortest_path:
2
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131 BASIC_NAMES.extend(["Longest Shortest Path", "spx", "spy", "spz"])
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132 DETAIL_NAMES.extend([" ", " ", " ", " "])
1
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133 show_detailed_info = sys.argv[-2] == "yes"
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134 output = sys.argv[-1]
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135
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136 # Open the input image file.
1
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137 input_image_plus = IJ.openImage(input)
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138
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139 # Create a copy of the image.
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140 input_image_plus_copy = input_image_plus.duplicate()
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141 image_processor_copy = input_image_plus_copy.getProcessor()
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142
1
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143 # Set binary options.
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144 options_list = OPTIONS
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145 if black_background:
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146 options_list.append("black")
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147 options = " ".join(options_list)
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148 IJ.run(input_image_plus_copy, "Options...", options)
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149
1
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150 # Convert image to binary if necessary.
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151 if not image_processor_copy.isBinary():
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152 IJ.run(input_image_plus_copy, "Make Binary", "")
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153
1
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154 # Run AnalyzeSkeleton
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155 analyze_skeleton = AnalyzeSkeleton_()
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156 analyze_skeleton.setup("", input_image_plus_copy)
2
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157 if prune_cycle_method == "none":
1
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158 prune_index = analyze_skeleton.NONE
2
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159 elif prune_cycle_method == "shortest_branch":
1
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160 prune_index = analyze_skeleton.SHORTEST_BRANCH
2
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161 elif prune_cycle_method == "lowest_intensity_voxel":
1
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162 prune_index = analyze_skeleton.LOWEST_INTENSITY_VOXEL
2
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163 elif prune_cycle_method == "lowest_intensity_branch":
1
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164 prune_index = analyze_skeleton.LOWEST_INTENSITY_BRANCH
2
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165 result = analyze_skeleton.run(
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166 prune_index,
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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167 prune_ends,
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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168 calculate_largest_shortest_path,
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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169 input_image_plus_copy,
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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170 True,
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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171 True,
da29019170f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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172 )
1
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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173 # Save the results.
29a4d422f32a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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174 save(result, output, show_detailed_info, calculate_largest_shortest_path)