Mercurial > repos > bgruening > imagej2_crop
diff imagej2_macros.xml @ 0:018144807556 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
| author | bgruening |
|---|---|
| date | Tue, 24 Sep 2024 17:12:52 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagej2_macros.xml Tue Sep 24 17:12:52 2024 +0000 @@ -0,0 +1,124 @@ +<macros> + <token name="@TOOL_VERSION@">20240614</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="fiji_requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">fiji</requirement> + <requirement type="package" version="3.11">grep</requirement> + </requirements> + </xml> + <xml name="image_type"> + <param name="image_type" type="select" label="Image type"> + <option value="8-bit_white" selected="true">8-bit white</option> + <option value="8-bit_black">8-bit black</option> + <option value="8-bit_random">8-bit random</option> + <option value="8-bit_ramp">8-bit ramp</option> + <option value="16-bit_white">16-bit white</option> + <option value="16-bit_black">16-bit black</option> + <option value="16-bit_random">16-bit random</option> + <option value="16-bit_ramp">16-bit ramp</option> + <option value="32-bit_white">32-bit white</option> + <option value="32-bit_black">32-bit black</option> + <option value="32-bit_random">32-bit random</option> + <option value="32-bit_ramp">32-bit ramp</option> + <option value="RGB_white">RGB white</option> + <option value="RGB_black">RGB black</option> + <option value="RGB_random">RGB random</option> + <option value="RGB_ramp">RGB ramp</option> + </param> + </xml> + <xml name="make_binary_params"> + <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."/> + <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."/> + <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> + <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."> + <option value="no" selected="true">No</option> + <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> + <xml name="param_input"> + <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/> + </xml> + <xml name="param_source_image"> + <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_image" type="data" label="Source image"/> + </xml> + <xml name="param_source_mask"> + <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="source_mask" type="data" label="Source mask"/> + </xml> + <xml name="param_target_image"> + <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_image" type="data" label="Target image"/> + </xml> + <xml name="param_target_mask"> + <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="target_mask" type="data" label="Target mask"/> + </xml> + <xml name="test_bunwarpj_raw_transform"> + <param name="target_image" value="dotblot.jpg"/> + <param name="source_image" value="blobs.gif"/> + <param name="target_raw_transformation" value="target_raw_transformation.txt"/> + <param name="source_raw_transformation" value="source_raw_transformation.txt"/> + </xml> + <xml name="test_target_source_images"> + <param name="target_image" value="dotblot.jpg"/> + <param name="source_image" value="blobs.gif"/> + </xml> + <token name="@make_binary_args@"> + --iterations $iterations + --count $count + --black_background $black_background + --pad_edges_when_eroding $pad_edges_when_eroding + </token> + <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)** +tool, which allows you to change them. + </token> + <xml name="image_datatypes"> + <option value="bmp">bmp</option> + <option value="gif">gif</option> + <option value="jpg">jpg</option> + <option value="png" selected="true">png</option> + <option value="tiff">tiff</option> + </xml> + <xml name="bunwarpj_citations"> + <citations> + <citation type="bibtex"> + @InProceedings(Arganda-Carreras2006, + author = "Ignacio Arganda-Carreras and + Carlos Oscar S{\'a}nchez Sorzano and + Roberto Marabini and + Jos{\'e} Mar\'{\i}a Carazo and + Carlos Ortiz-de-Solorzano and + Jan Kybic", + title = "Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization", + publisher = "Springer Berlin / Heidelberg", + booktitle = "Computer Vision Approaches to Medical Image Analysis", + series = "Lecture Notes in Computer Science", + year = "2006", + volume = "4241", + pages = "85-95", + month = "May", + city = "Graz, Austria") + </citation> + <citation type="doi">10.1038/nmeth.2019</citation> + </citations> + </xml> + <xml name="fiji_headless_citations"> + <citations> + <citation type="doi">10.1038/nmeth.2102</citation> + </citations> + </xml> +</macros>