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comparison slice_image.xml @ 3:1faa7e3c94ff draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:26:38 +0000
parents f312d414f234
children a72590196440
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2:f312d414f234 3:1faa7e3c94ff
1 <tool id="ip_slice_image" name="Slice image" version="0.3-2"> 1 <tool id="ip_slice_image" name="Slice image into patches" version="0.3-3">
2 <description></description> 2 <description></description>
3 <macros>
4 <import>creators.xml</import>
5 <import>tests.xml</import>
6 </macros>
7 <creator>
8 <expand macro="creators/bmcv" />
9 </creator>
3 <edam_operations> 10 <edam_operations>
4 <edam_operation>operation_3443</edam_operation> 11 <edam_operation>operation_3443</edam_operation>
5 </edam_operations> 12 </edam_operations>
6 <xrefs> 13 <xrefs>
7 <xref type="bio.tools">galaxy_image_analysis</xref> 14 <xref type="bio.tools">galaxy_image_analysis</xref>
10 <requirement type="package" version="0.14.2">scikit-image</requirement> 17 <requirement type="package" version="0.14.2">scikit-image</requirement>
11 <requirement type="package" version="1.15.4">numpy</requirement> 18 <requirement type="package" version="1.15.4">numpy</requirement>
12 <requirement type="package" version="1.1.0">scipy</requirement> 19 <requirement type="package" version="1.1.0">scipy</requirement>
13 <requirement type="package" version="0.15.1">tifffile</requirement> 20 <requirement type="package" version="0.15.1">tifffile</requirement>
14 </requirements> 21 </requirements>
15 <command detect_errors="aggressive"> 22 <command detect_errors="aggressive"><![CDATA[
16 <![CDATA[ 23
17 mkdir ./out && 24 mkdir ./out &&
25
18 python '$__tool_directory__/slice_image.py' 26 python '$__tool_directory__/slice_image.py'
19 '$input_file' ./out 27 '$input_file' ./out
20 --stride $stride --window_size $patch_size --bg_thresh $bg_thresh 28
21 --limit_slices $limit_slices 29 --stride '$stride'
22 #if $limit_slices: 30 --window_size '$patch_size'
23 --n_thresh $n_thresh 31 --bg_thresh '$bg_thresh'
32
33 #if $n_thresh > 0:
34 --n_thresh '$n_thresh'
24 #end if 35 #end if
25 #if $control_rng: 36
26 --seed $seed 37 #if len('$seed') > 0:
38 --seed '$seed'
27 #end if 39 #end if
40
28 && ls -l ./out 41 && ls -l ./out
29 ]]> 42
30 </command> 43 ]]></command>
31 <inputs> 44 <inputs>
32 <param name="input_file" type="data" format="tiff,png,jpg,bmp" label="Input image"/> 45 <param name="input_file" type="data" format="tiff,png" label="Input image"/>
33 <!--<param name="out_folder" type="text" label="Output folder for image slices"/> 46 <param name="stride" type="integer" optional="true" value="16" min="1" label="Stride" help="Minimum offset between any two patches in pixels."/>
34 <param name="label_file" type="data" format="tiff,png,jpg,bmp" label="Auxiliary label file to split in the same way"/>--> 47 <param name="patch_size" type="integer" optional="true" value="64" label="Patch size" help="Width of the patches in pixels (the height is identical)."/>
35 <param name="stride" type="integer" optional="true" value="16"/> 48 <param name="bg_thresh" type="float" optional="true" value="0" min="0" label="Maximum patch homogeneity" help="If larger than 0, patches with a homogeneity above this threshold will be considered as purely background and discarded."/>
36 <param name="patch_size" type="integer" optional="true" value="64" label="Size of resulting (quadratic-shaped) slices"/> 49 <param name="n_thresh" type="integer" optional="true" label="Maximum number of patches" value="0" min="0" help="If larger than 0, only the specified number of patches will be retained (or less). Those will be selected randomly."/>
37 <param name="bg_thresh" type="float" optional="true" value="0" label="Threshold to not be considered background"/> 50 <param name="seed" type="hidden" value=""/>
38 <param name="limit_slices" type="boolean" checked="true" label="Should the number of slices be limited?"/>
39 <param name="n_thresh" type="integer" optional="true" label="Maximum amount of slices; only needed if limit_slices is selected"/>
40 <param name="control_rng" type="boolean" checked="false" label="Boolean that controls if a certain seed should be selected for the random number generator"/>
41 <param name="seed" type="integer" value="1"
42 label="Seed chosen for the random number generator of the random choice of limited slices. Only required if cotrol_rng is selected"/>
43 </inputs> 51 </inputs>
44 <outputs> 52 <outputs>
45 <collection name="slices" type="list" label="Slices obtained from input"> 53 <collection name="slices" type="list" label="Slices obtained from input">
46 <discover_datasets directory="out" format="tiff" pattern="__name__"/> 54 <discover_datasets directory="out" format="tiff" pattern="__name__"/>
47 </collection> 55 </collection>
48 </outputs> 56 </outputs>
49 <tests> 57 <tests>
58 <!-- Tests for TIFF input -->
50 <test> 59 <test>
51 <param name="input_file" value="input.tiff"/> 60 <param name="input_file" value="input.tiff"/>
52 <param name="limit_slices" value="true"/>
53 <param name="n_thresh" value="5"/> 61 <param name="n_thresh" value="5"/>
54 <param name="control_rng" value="true"/>
55 <param name="seed" value="17"/> 62 <param name="seed" value="17"/>
56 <output_collection name="slices" type="list"> 63 <output_collection name="slices" type="list">
57 <element name="148.tiff" file="input_148.tiff" ftype="tiff" compare="sim_size"/> 64 <expand macro="tests/intensity_image_diff/element" name="148.tiff" value="input_148.tiff" ftype="tiff"/>
58 <element name="155.tiff" file="input_155.tiff" ftype="tiff" compare="sim_size"/> 65 <expand macro="tests/intensity_image_diff/element" name="155.tiff" value="input_155.tiff" ftype="tiff"/>
59 <element name="187.tiff" file="input_187.tiff" ftype="tiff" compare="sim_size"/> 66 <expand macro="tests/intensity_image_diff/element" name="187.tiff" value="input_187.tiff" ftype="tiff"/>
60 <element name="212.tiff" file="input_212.tiff" ftype="tiff" compare="sim_size"/> 67 <expand macro="tests/intensity_image_diff/element" name="212.tiff" value="input_212.tiff" ftype="tiff"/>
61 <element name="267.tiff" file="input_267.tiff" ftype="tiff" compare="sim_size"/> 68 <expand macro="tests/intensity_image_diff/element" name="267.tiff" value="input_267.tiff" ftype="tiff"/>
62 </output_collection> 69 </output_collection>
63 </test> 70 </test>
71 <!-- TODO: Add tests for PNG input -->
64 </tests> 72 </tests>
65 <help> 73 <help>
66 **What it does**
67 74
68 Slices image into multiple smaller patches. 75 **Slices an image into multiple smaller, square-shaped patches.**
76
77 For overlapping patches, set the stride to a value smaller than the patch size.
78 For non-overlapping patches, set the stride to a value identical to the patch size (or larger).
79 If the stride is set to a value larger than the patch size, parts of the original image will be skipped.
80
81 Optionally, patches entirely corresponding to image background are discarded.
82 To decide whether a patch corresponds to image background, the `homogeneity`_ of its `gray-level co-occurrence matrix`_ is considered.
83
84 .. _homogeneity: https://scikit-image.org/docs/stable/api/skimage.feature.html#skimage.feature.graycoprops
85 .. _gray-level co-occurrence matrix: https://scikit-image.org/docs/stable/api/skimage.feature.html#skimage.feature.graycomatrix
86
87 In addition, the number of the remaining patches can be reduced by specifying a maximum number of patches to retain.
88 Those will be selected randomly.
89
69 </help> 90 </help>
70 <citations> 91 <citations>
71 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 92 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
72 </citations> 93 </citations>
73 </tool> 94 </tool>