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comparison segmetrics.xml @ 0:0729657d9e4e draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
author imgteam
date Fri, 07 Oct 2022 22:05:59 +0000
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-1:000000000000 0:0729657d9e4e
1 <tool id="ip_segmetrics" name="SegMetrics" version="0.11.3" profile="20.05">
2 <description>image segmentation and object detection performance measures</description>
3 <requirements>
4 <requirement type="package" version="0.11.3">segmetrics</requirement>
5 <requirement type="package" version="0.18.1">scikit-image</requirement>
6 </requirements>
7 <command detect_errors="aggressive">
8 <![CDATA[
9 python '$__tool_directory__/run-segmetrics.py'
10 '$input_seg'
11 '$input_gt'
12 ./results.csv
13 $unzip
14 $is_seg_unique
15 $is_gt_unique
16 $measures.dice
17 $measures.seg
18 $measures.jc
19 $measures.ji
20 $measures.ri
21 $measures.ari
22 $measures.hsd_sym
23 $measures.hsd_e2a
24 $measures.hsd_a2e
25 $measures.nsd
26 $measures.o_hsd_sym
27 $measures.o_hsd_e2a
28 $measures.o_hsd_a2e
29 $measures.o_nsd
30 $measures.fs
31 $measures.fm
32 $measures.fp
33 $measures.fn
34 ]]>
35 </command>
36 <inputs>
37
38 <param name="input_seg" type="data" format="tiff,png,zip" label="Segmented images" />
39 <param name="input_gt" type="data" format="tiff,png,zip" label="Ground truth images" />
40
41 <param name="unzip" type="boolean" checked="false" truevalue="-unzip" falsevalue="" label="Unzip" />
42
43 <param name="is_seg_unique" type="boolean" checked="false" truevalue="-seg_unique" falsevalue="" label="Segmentation is uniquely labeled" />
44 <param name="is_gt_unique" type="boolean" checked="false" truevalue="-gt_unique" falsevalue="" label="Ground truth is uniquely labeled" />
45
46 <section name="measures" title="Performance measures" >
47 <param name="dice" type="boolean" checked="true" truevalue="-measure-dice" falsevalue="" label="Dice" />
48 <param name="seg" type="boolean" checked="true" truevalue="-measure-seg" falsevalue="" label="SEG" />
49 <param name="jc" type="boolean" checked="false" truevalue="-measure-jc" falsevalue="" label="Jaccard coefficient" />
50 <param name="ji" type="boolean" checked="true" truevalue="-measure-ji" falsevalue="" label="Jaccard index" />
51 <param name="ri" type="boolean" checked="false" truevalue="-measure-ri" falsevalue="" label="Rand index" />
52 <param name="ari" type="boolean" checked="false" truevalue="-measure-ari" falsevalue="" label="Adjusted Rand index" />
53 <param name="hsd_sym" type="boolean" checked="false" truevalue="-measure-hsd_sym" falsevalue="" label="Hausdorff distance (symmetric)" />
54 <param name="hsd_e2a" type="boolean" checked="false" truevalue="-measure-hsd_e2a" falsevalue="" label="Hausdorff distance (ground truth to segmented)" />
55 <param name="hsd_a2e" type="boolean" checked="false" truevalue="-measure-hsd_a2e" falsevalue="" label="Hausdorff distance (segmented to ground truth)" />
56 <param name="nsd" type="boolean" checked="false" truevalue="-measure-nsd" falsevalue="" label="Normalized sum of distances" />
57 <param name="o_hsd_sym" type="boolean" checked="true" truevalue="-measure-o_hsd_sym" falsevalue="" label="Object-based Hausdorff distance (symmetric)" />
58 <param name="o_hsd_e2a" type="boolean" checked="false" truevalue="-measure-o_hsd_e2a" falsevalue="" label="Object-based Hausdorff distance (ground truth to segmented)" />
59 <param name="o_hsd_a2e" type="boolean" checked="false" truevalue="-measure-o_hsd_a2e" falsevalue="" label="Object-based Hausdorff distance (segmented to ground truth)" />
60 <param name="o_nsd" type="boolean" checked="true" truevalue="-measure-o_nsd" falsevalue="" label="Object-based normalized sum of distances" />
61 <param name="fs" type="boolean" checked="true" truevalue="-measure-fs" falsevalue="" label="Falsely split objects per image" />
62 <param name="fm" type="boolean" checked="true" truevalue="-measure-fm" falsevalue="" label="Falsely merged objects per image" />
63 <param name="fp" type="boolean" checked="true" truevalue="-measure-fp" falsevalue="" label="Spurious objects per image" />
64 <param name="fn" type="boolean" checked="true" truevalue="-measure-fn" falsevalue="" label="Missing objects per image" />
65 </section>
66
67 </inputs>
68 <outputs>
69 <data format="csv" name="results" from_work_dir="results.csv" />
70 </outputs>
71 <tests>
72 <test>
73 <param name="input_seg" value="input2.png"/>
74 <param name="input_gt" value="input1.png"/>
75 <output name="results" value="results1.csv" ftype="csv" compare="diff"/>
76 <param name="is_seg_unique" value="True"/>
77 <param name="is_gt_unique" value="True"/>
78 </test>
79 <test>
80 <param name="input_seg" value="input1.zip"/>
81 <param name="input_gt" value="input2.zip"/>
82 <output name="results" value="results2.csv" ftype="csv" compare="diff"/>
83 <param name="is_seg_unique" value="True"/>
84 <param name="is_gt_unique" value="True"/>
85 <param name="unzip" value="True"/>
86 </test>
87 </tests>
88 <help>
89 Image segmentation and object detection performance measures for 2-D image data.
90 </help>
91 <citations>
92 <citation type="doi">10.1093/bioinformatics/btu080</citation>
93 <citation type="doi">10.1109/ISBI.2009.5193098</citation>
94 <citation type="doi">10.1109/ICIP.2003.1246871</citation>
95 </citations>
96 </tool>