Mercurial > repos > iuc > imagej2_make_binary

comparison imagej2_macros.xml @ 1:d26f11339f08 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
author iuc
date Wed, 26 Aug 2015 14:37:41 -0400
parents 66d9e595dff2
children c026d0eddc3e
comparison
equal deleted inserted replaced
0:66d9e595dff2 1:d26f11339f08
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <macros> 2 <macros>
3 <xml name="fiji_20141125_requirements"> 3 <token name="@WRAPPER_VERSION@">1.0</token>
4 <xml name="fiji_requirements">
4 <requirements> 5 <requirements>
5 <requirement type="package" version="20141125">fiji</requirement> 6 <requirement type="package" version="20141125">fiji</requirement>
6 </requirements> 7 </requirements>
7 </xml> 8 </xml>
8 <xml name="python_bioformats_104_requirements"> 9 <xml name="python_bioformats_requirements">
9 <requirements> 10 <requirements>
10 <requirement type="package" version="20141125">fiji</requirement> 11 <requirement type="package" version="20141125">fiji</requirement>
11 <requirement type="package" version="1.0.11">javabridge</requirement> 12 <requirement type="package" version="1.0.11">javabridge</requirement>
12 <requirement type="package" version="1.9">numpy</requirement> 13 <requirement type="package" version="1.9">numpy</requirement>
13 <requirement type="package" version="1.0.4">python_bioformats</requirement> 14 <requirement type="package" version="1.0.4">python_bioformats</requirement>
51 <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."> 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.">
52 <option value="no" selected="True">No</option> 53 <option value="no" selected="True">No</option>
53 <option value="yes">Yes</option> 54 <option value="yes">Yes</option>
54 </param> 55 </param>
55 </xml> 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>
56 <token name="@make_binary_args@"> 63 <token name="@make_binary_args@">
57 --iterations $iterations 64 --iterations $iterations
58 --count $count 65 --count $count
59 --black_background $black_background 66 --black_background $black_background
60 --pad_edges_when_eroding $pad_edges_when_eroding 67 --pad_edges_when_eroding $pad_edges_when_eroding
61 </token> 68 </token>
62 <xml name="max_heap_size_type_conditional"> 69 <token name="@requires_binary_input@">
63 <conditional name="set_max_heap_size"> 70 .. class:: warningmark
64 <param name="max_heap_size_type" type="select" label="Maximum size of the memory allocation pool used by the JVM" help="This value must be a multiple of 1024 or it will be ignored and the system default will be used."> 71
65 <option value="default" selected="True">Do not set</option> 72 This tool works on binary images, so other image types will automatically be converted to binary
66 <option value="megabytes">Set in megabytes</option> 73 before they are analyzed. This step is performed using the ImageJ2 **Make Binary** command with
67 <option value="gigabytes">Set in gigabytes</option> 74 the following settings: **Iterations:** 1, **Count:** 1, **Pad edges when eroding:** No. The tool
68 </param> 75 allows you to choose the **Black background** setting. If these settings are not appropriate,
69 <when value="default" > 76 first manually convert the image to binary using the **Convert to binary (black and white) with ImageJ2**
70 <param name="max_heap_size" type="integer" value="0" hidden="true" label="Do not set" help="Use system default"/> 77 tool, which allows you to change them.
71 </when>
72 <when value="megabytes">
73 <param name="max_heap_size" type="integer" value="512" min="256" label="Maximum size, in megabytes, of the memory allocation pool" help="Examples: 256, 512, etc."/>
74 </when>
75 <when value="gigabytes">
76 <param name="max_heap_size" type="integer" value="1" min="1" label="Maximum size, in gigabytes, of the memory allocation pool" help="Examples: 1, 2, etc."/>
77 </when>
78 </conditional>
79 </xml>
80 <token name="@max_heap_size_args@">
81 --max_heap_size_type $set_max_heap_size.max_heap_size_type
82 --max_heap_size $set_max_heap_size.max_heap_size
83 </token> 78 </token>
84 <xml name="image_datatypes"> 79 <xml name="image_datatypes">
85 <option value="bmp">bmp</option> 80 <option value="bmp">bmp</option>
86 <option value="gif">gif</option> 81 <option value="gif">gif</option>
87 <option value="jpg">jpg</option> 82 <option value="jpg">jpg</option>