Mercurial > repos > imgteam > orientationpy

comparison orientationpy.xml @ 0:214f548481eb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
author imgteam
date Tue, 12 Mar 2024 10:54:40 +0000
parents
children df211f6b5cf2
comparison
equal deleted inserted replaced
-1:000000000000 0:214f548481eb
1 <tool id="orientationpy" name="Compute image orientation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
2 <description>with OrientationPy</description>
3 <macros>
4 <token name="@TOOL_VERSION@">0.2.0.4</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <edam_operations>
8 <edam_operation>operation_3443</edam_operation>
9 </edam_operations>
10 <xrefs>
11 <xref type="biii">orientationj</xref>
12 </xrefs>
13 <requirements>
14 <requirement type="package" version="0.2.0.4">orientationpy</requirement>
15 <requirement type="package" version="0.22.0">scikit-image</requirement>
16 </requirements>
17 <command><![CDATA[
18
19 ## Inputs
20
21 python '$__tool_directory__/orientationpy-cli.py' '$image'
22 --mode $mode
23 --sigma $sigma
24 --min_energy $min_energy
25 --min_coherency $min_coherency
26 --max_precision $max_precision
27
28 ## Outputs
29
30 --output_angle_tsv '$output_angle_tsv'
31
32 ]]>
33 </command>
34 <inputs>
35 <param name="image" type="data" format="png,tiff" label="Input image" />
36 <param argument="--mode" type="select" label="Gradient computation">
37 <option value="finite_difference" selected="True">Finite differences</option>
38 <option value="gaussian">Gaussian</option>
39 <option value="splines">Splines</option>
40 </param>
41 <param argument="--sigma" type="float" label="Spatial scale (in pixels)" value="2" />
42 <param argument="--min_energy" type="float" label="Minimum energy" value="0.1" min="0" max="1" />
43 <param argument="--min_coherency" type="float" label="Minimum coherency" value="0.2" min="0" max="1" />
44 <param argument="--max_precision" type="integer" label="Maximum possible precision (in decimals)" value="3" min="0" max="8" help="Governs the histogram bin size (increasing maximum possible precision leads to smaller bin sizes). Note that increasing the maximum possible precision too far may actually decrease the actual precision, because the bin size becomes too small." />
45 </inputs>
46 <outputs>
47 <data format="tabular" name="output_angle_tsv" from_work_dir="output_angle.tsv" />
48 </outputs>
49 <tests>
50 <!-- Test negative angle -->
51 <test>
52 <param name="image" value="input1.tif" />
53 <param name="mode" value="finite_difference" />
54 <param name="sigma" value="2" />
55 <param name="min_energy" value="0.1" />
56 <param name="min_coherency" value="0.2" />
57 <param name="max_precision" value="1" />
58 <output name="output_angle_tsv">
59 <assert_contents>
60 <has_line line="Angle" />
61 <has_line line="-45.0" />
62 <has_n_lines n="2" />
63 <has_n_columns n="1" />
64 </assert_contents>
65 </output>
66 </test>
67 <!-- Test positive angle -->
68 <test>
69 <param name="image" value="input2.tif" />
70 <param name="mode" value="finite_difference" />
71 <param name="sigma" value="2" />
72 <param name="min_energy" value="0.1" />
73 <param name="min_coherency" value="0.2" />
74 <param name="max_precision" value="1" />
75 <output name="output_angle_tsv">
76 <assert_contents>
77 <has_line line="Angle" />
78 <has_line line="45.0" />
79 <has_n_lines n="2" />
80 <has_n_columns n="1" />
81 </assert_contents>
82 </output>
83 </test>
84 </tests>
85 <help>
86 Compute the orientation of 2-D images in degrees using OrientationPy.
87
88 OrientationPy is the pythonic successor to the well-loved OrientationJ Fiji Plugin.
89 It is a library that takes in images and computes the orientation of the greylevels.
90 A key step is the computation of image gradients, for a number of different techniques is supported.
91
92 For more information on ``--min_energy`` and ``--min_coherency`` see: https://epfl-center-for-imaging.gitlab.io/orientationpy/orientationpy_examples/plot_fibres_2d.html#plot-hsv-composition
93 </help>
94 <citations>
95 <citation type="doi">10.1007/s10237-011-0325-z</citation>
96 </citations>
97 </tool>