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comparison imagej2_skeletonize3d.xml @ 1:269923244cc8 draft

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planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
author iuc
date Wed, 26 Aug 2015 14:38:34 -0400
parents 8b787f641b9c
children 99f75b64cdf3
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1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="imagej2_skeletonize3d" name="Skeletonize images" version="1.0.0"> 2 <tool id="imagej2_skeletonize3d" name="Skeletonize images" version="@WRAPPER_VERSION@.0">
3 <description>with ImageJ2</description> 3 <description>with ImageJ2</description>
4 <macros> 4 <macros>
5 <import>imagej2_macros.xml</import> 5 <import>imagej2_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="fiji_20141125_requirements" /> 7 <expand macro="fiji_requirements" />
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 python $__tool_directory__/imagej2_skeletonize3d.py 10 python $__tool_directory__/imagej2_skeletonize3d.py
11 --input "$input" 11 --input "$input"
12 --input_datatype $input.ext 12 --input_datatype $input.ext
13 @max_heap_size_args@ 13 --black_background $black_background
14 --jython_script $__tool_directory__/jython_script.py 14 --jython_script $__tool_directory__/jython_script.py
15 --output "$output" 15 --output "$output"
16 --output_datatype $output_datatype 16 --output_datatype $output.ext
17 ]]> 17 ]]>
18 </command> 18 </command>
19 <inputs> 19 <inputs>
20 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select grayscale image"/> 20 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select grayscale image"/>
21 <param name="output_datatype" type="select" label="Save as format"> 21 <expand macro="black_background_param" />
22 <expand macro="image_datatypes" />
23 </param>
24 <expand macro="max_heap_size_type_conditional" />
25 </inputs> 22 </inputs>
26 <outputs> 23 <outputs>
27 <data name="output" format_source="input" label="${tool.name} on ${on_string}"> 24 <data name="output" format_source="input" label="${tool.name} on ${on_string}"/>
28 <actions>
29 <action type="format">
30 <option type="from_param" name="output_datatype" />
31 </action>
32 </actions>
33 </data>
34 </outputs> 25 </outputs>
35 <tests> 26 <tests>
36 <test> 27 <test>
37 <param name="input" value="blobs.gif" /> 28 <param name="input" value="blobs.gif" />
38 <param name="input_datatype" value="gif" /> 29 <param name="input_datatype" value="gif" />
48 </tests> 39 </tests>
49 <help> 40 <help>
50 41
51 .. class:: warningmark 42 .. class:: warningmark
52 43
53 The underlying AnalyzeSkeleton Fiji plugin works on binary images, so other image types will 44 @requires_binary_input@
54 automatically be converted to binary before they are analyzed. This step is performed using the
55 ImageJ2 **Make Binary** command with the following settings: **Iterations:** 1, **Count:** 1,
56 **Black background:** No, **Pad edges when eroding:** No. If these settings are not appropriate,
57 first manually convert the image to binary using the **Convert to binary (black and white) with
58 ImageJ2** tool, which allows you to change them.
59 45
60 **What it does** 46 **What it does**
61 47
62 <![CDATA[ 48 <![CDATA[
63 Skeletonizes a 2D or 3D binary (8-bit) image. As Hanno Homman explains in his paper, binary thinning is 49 Skeletonizes a 2D or 3D binary (8-bit) image. As Hanno Homman explains in his paper, binary thinning is