Mercurial > repos > imgteam > segmetrics
comparison segmetrics.xml @ 0:0729657d9e4e draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/segmetrics/ commit 3b911df716a7b42115c6cd773f666bc90a2bb10f
author | imgteam |
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date | Fri, 07 Oct 2022 22:05:59 +0000 |
parents | |
children | 3a7310406943 |
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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> |