Mercurial > repos > iuc > imagej2_make_binary
diff imagej2_macros.xml @ 1:d26f11339f08 draft
planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
| author | iuc |
|---|---|
| date | Wed, 26 Aug 2015 14:37:41 -0400 |
| parents | 66d9e595dff2 |
| children | c026d0eddc3e |
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--- a/imagej2_macros.xml Tue Aug 04 13:20:29 2015 -0400 +++ b/imagej2_macros.xml Wed Aug 26 14:37:41 2015 -0400 @@ -1,11 +1,12 @@ <?xml version='1.0' encoding='UTF-8'?> <macros> - <xml name="fiji_20141125_requirements"> + <token name="@WRAPPER_VERSION@">1.0</token> + <xml name="fiji_requirements"> <requirements> <requirement type="package" version="20141125">fiji</requirement> </requirements> </xml> - <xml name="python_bioformats_104_requirements"> + <xml name="python_bioformats_requirements"> <requirements> <requirement type="package" version="20141125">fiji</requirement> <requirement type="package" version="1.0.11">javabridge</requirement> @@ -53,33 +54,27 @@ <option value="yes">Yes</option> </param> </xml> + <xml name="black_background_param"> + <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)."> + <option value="no" selected="True">No</option> + <option value="yes">Yes</option> + </param> + </xml> <token name="@make_binary_args@"> --iterations $iterations --count $count --black_background $black_background --pad_edges_when_eroding $pad_edges_when_eroding </token> - <xml name="max_heap_size_type_conditional"> - <conditional name="set_max_heap_size"> - <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."> - <option value="default" selected="True">Do not set</option> - <option value="megabytes">Set in megabytes</option> - <option value="gigabytes">Set in gigabytes</option> - </param> - <when value="default" > - <param name="max_heap_size" type="integer" value="0" hidden="true" label="Do not set" help="Use system default"/> - </when> - <when value="megabytes"> - <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."/> - </when> - <when value="gigabytes"> - <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."/> - </when> - </conditional> - </xml> - <token name="@max_heap_size_args@"> - --max_heap_size_type $set_max_heap_size.max_heap_size_type - --max_heap_size $set_max_heap_size.max_heap_size + <token name="@requires_binary_input@"> +.. class:: warningmark + +This tool works on binary images, so other image types will automatically be converted to binary +before they are analyzed. This step is performed using the ImageJ2 **Make Binary** command with +the following settings: **Iterations:** 1, **Count:** 1, **Pad edges when eroding:** No. The tool +allows you to choose the **Black background** setting. If these settings are not appropriate, +first manually convert the image to binary using the **Convert to binary (black and white) with ImageJ2** +tool, which allows you to change them. </token> <xml name="image_datatypes"> <option value="bmp">bmp</option>
