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comparison imagej2_macros.xml @ 0:91d82f24657a draft

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planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
author iuc
date Wed, 26 Aug 2015 14:37:25 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <macros>
3 <token name="@WRAPPER_VERSION@">1.0</token>
4 <xml name="fiji_requirements">
5 <requirements>
6 <requirement type="package" version="20141125">fiji</requirement>
7 </requirements>
8 </xml>
9 <xml name="python_bioformats_requirements">
10 <requirements>
11 <requirement type="package" version="20141125">fiji</requirement>
12 <requirement type="package" version="1.0.11">javabridge</requirement>
13 <requirement type="package" version="1.9">numpy</requirement>
14 <requirement type="package" version="1.0.4">python_bioformats</requirement>
15 </requirements>
16 </xml>
17 <xml name="stdio">
18 <stdio>
19 <exit_code range="1:"/>
20 <exit_code range=":-1"/>
21 <regex match="Error:"/>
22 <regex match="Exception:"/>
23 </stdio>
24 </xml>
25 <xml name="image_type">
26 <param name="image_type" type="select" label="Image type">
27 <option value="8-bit_white" selected="True">8-bit white</option>
28 <option value="8-bit_black">8-bit black</option>
29 <option value="8-bit_random">8-bit random</option>
30 <option value="8-bit_ramp">8-bit ramp</option>
31 <option value="16-bit_white">16-bit white</option>
32 <option value="16-bit_black">16-bit black</option>
33 <option value="16-bit_random">16-bit random</option>
34 <option value="16-bit_ramp">16-bit ramp</option>
35 <option value="32-bit_white">32-bit white</option>
36 <option value="32-bit_black">32-bit black</option>
37 <option value="32-bit_random">32-bit random</option>
38 <option value="32-bit_ramp">32-bit ramp</option>
39 <option value="RGB_white">RGB white</option>
40 <option value="RGB_black">RGB black</option>
41 <option value="RGB_random">RGB random</option>
42 <option value="RGB_ramp">RGB ramp</option>
43 </param>
44 </xml>
45 <xml name="make_binary_params">
46 <param name="iterations" type="integer" value="1" min="1" max="100" label="Iterations" help="The number of times (1-100) erosion, dilation, opening, and closing are performed."/>
47 <param name="count" type="integer" value="1" min="1" max="8" label="Count" help="The number of adjacent background pixels necessary (1-8) for erosion or dilation."/>
48 <param name="black_background" type="select" label="Black background" help="If Yes, the background is black and the foreground is white (no implies the opposite).">
49 <option value="no" selected="True">No</option>
50 <option value="yes">Yes</option>
51 </param>
52 <param name="pad_edges_when_eroding" type="select" label="Pad edges when eroding" help="If Yes, eroding does not erode from the edges of the image.">
53 <option value="no" selected="True">No</option>
54 <option value="yes">Yes</option>
55 </param>
56 </xml>
57 <xml name="black_background_param">
58 <param name="black_background" type="select" label="Black background" help="If Yes, the background is black and the foreground is white (no implies the opposite).">
59 <option value="no" selected="True">No</option>
60 <option value="yes">Yes</option>
61 </param>
62 </xml>
63 <token name="@make_binary_args@">
64 --iterations $iterations
65 --count $count
66 --black_background $black_background
67 --pad_edges_when_eroding $pad_edges_when_eroding
68 </token>
69 <token name="@requires_binary_input@">
70 .. class:: warningmark
71
72 This tool works on binary images, so other image types will automatically be converted to binary
73 before they are analyzed. This step is performed using the ImageJ2 **Make Binary** command with
74 the following settings: **Iterations:** 1, **Count:** 1, **Pad edges when eroding:** No. The tool
75 allows you to choose the **Black background** setting. If these settings are not appropriate,
76 first manually convert the image to binary using the **Convert to binary (black and white) with ImageJ2**
77 tool, which allows you to change them.
78 </token>
79 <xml name="image_datatypes">
80 <option value="bmp">bmp</option>
81 <option value="gif">gif</option>
82 <option value="jpg">jpg</option>
83 <option value="png" selected="true">png</option>
84 <option value="tiff">tiff</option>
85 </xml>
86 <xml name="bunwarpj_citations">
87 <citations>
88 <citation type="bibtex">
89 @InProceedings(Arganda-Carreras2006,
90 author = "Ignacio Arganda-Carreras and
91 Carlos Oscar S{\'a}nchez Sorzano and
92 Roberto Marabini and
93 Jos{\'e} Mar\'{\i}a Carazo and
94 Carlos Ortiz-de-Solorzano and
95 Jan Kybic",
96 title = "Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization",
97 publisher = "Springer Berlin / Heidelberg",
98 booktitle = "Computer Vision Approaches to Medical Image Analysis",
99 series = "Lecture Notes in Computer Science",
100 year = "2006",
101 volume = "4241",
102 pages = "85-95",
103 month = "May",
104 city = "Graz, Austria")
105 </citation>
106 <citation type="doi">10.1038/nmeth.2019</citation>
107 </citations>
108 </xml>
109 <xml name="fiji_headless_citations">
110 <citations>
111 <citation type="doi">10.1038/nmeth.2102</citation>
112 </citations>
113 </xml>
114 <xml name="bioformats_fiji_javabridge_citations">
115 <citations>
116 <citation type="doi">10.1038/nmeth.2102</citation>
117 <citation type="doi">10.1038/nmeth.2019</citation>
118 <citation type="doi">10.1083/jcb.201004104</citation>
119 </citations>
120 </xml>
121 </macros>