Mercurial > repos > imgteam > 2d_filter_segmentation_by_features
changeset 2:8f76184ca03f draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_filter_segmentation_by_features/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
| author | imgteam |
|---|---|
| date | Thu, 04 Apr 2024 15:23:28 +0000 |
| parents | 6ad1d3cfdea1 |
| children | 9d47aabda459 |
| files | 2d_filter_segmentation_by_features.xml creators.xml tests.xml |
| diffstat | 3 files changed, 176 insertions(+), 13 deletions(-) [+] |
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--- a/2d_filter_segmentation_by_features.xml Mon Nov 13 22:10:21 2023 +0000 +++ b/2d_filter_segmentation_by_features.xml Thu Apr 04 15:23:28 2024 +0000 @@ -1,5 +1,12 @@ -<tool id="ip_2d_filter_segmentation_by_features" name="Filter label map by rules" version="0.0.1-2"> - <description></description> +<tool id="ip_2d_filter_segmentation_by_features" name="Filter label map by rules" version="0.0.1-3" profile="20.05"> + <description></description> + <macros> + <import>creators.xml</import> + <import>tests.xml</import> + </macros> + <creator> + <expand macro="creators/bmcv" /> + </creator> <edam_operations> <edam_operation>operation_3443</edam_operation> </edam_operations> @@ -12,15 +19,20 @@ <requirement type="package" version="0.23.4">pandas</requirement> <requirement type="package" version="0.15.1">tifffile</requirement> </requirements> - <command detect_errors="aggressive"> - <![CDATA[ - python '$__tool_directory__/2d_filter_segmentation_by_features.py' '$input' '$output' '$feature_file' '$rule_file' - ]]> - </command> + <command detect_errors="aggressive"><![CDATA[ + + python '$__tool_directory__/2d_filter_segmentation_by_features.py' + + '$input' + '$output' + '$feature_file' + '$rule_file' + + ]]></command> <inputs> - <param name="input" type="data" format="tiff" label="Source file" /> - <param name="feature_file" type="data" format="tabular" label="Feature file" /> - <param name="rule_file" type="data" format="tabular" label="Rules file" /> + <param name="input" type="data" format="tiff" label="Label map" /> + <param name="feature_file" type="data" format="tabular" label="Features" /> + <param name="rule_file" type="data" format="tabular" label="Rules" /> </inputs> <outputs> <data format="tiff" name="output" /> @@ -30,12 +42,45 @@ <param name="input" value="in.tif"/> <param name="feature_file" value="features.tabular"/> <param name="rule_file" value="rules.tabular"/> - <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/> + <expand macro="tests/label_image_diff" name="output" value="out.tif" ftype="tiff"/> </test> </tests> <help> - Filter label image by rules (e.g., remove large or deformed objects). - Rules file has a specific format (cols: ,f1,2, rows: feature_name, min, max). The features have to be also profived in a specific format (cols: label, f1, f2). + + **Filters a label map by rules (e.g., remove large or deformed objects).** + + The properties of the labeled image regions (features) must be provided in a specific tabular format + (columns: ``label``, ``feature1``, ``feature2``, and so on, where ``feature1`` and ``feature2`` can be arbitrary strings). + Each row corresponds to a labeled image region. + An example is given below. + + +-------+-------+---------------------+ + | label | area | eccentricity | + +-------+-------+---------------------+ + | 1 | 344 | 0.42521053699241596 | + +-------+-------+---------------------+ + | 2 | 434 | 0.47679001553231926 | + +-------+-------+---------------------+ + | 3 | 907 | 0.9973539531125177 | + +-------+-------+---------------------+ + | 4 | 14320 | 0.17131009631035327 | + +-------+-------+---------------------+ + + The rules also must be supplied in a specific tabular format with three rows. + The top-left cell is empty, and the rest of the first row corresponds to the feature names (such as ``feature1`` or ``feature2``, see above). + The rest of the first column corresponds to the two values ``min`` and ``max``. + Each of the rows defines the minimum and maximum values for the corresponding features. + A labeled image region is retrained if and only if it passes all checks with repsect to the given ``min`` and ``max`` values. + An example is given below. + + +-----+--------+--------------+ + | | area | eccentricity | + +-----+--------+--------------+ + | min | 500 | 0. | + +-----+--------+--------------+ + | max | 100000 | 0.5 | + +-----+--------+--------------+ + </help> <citations> <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/creators.xml Thu Apr 04 15:23:28 2024 +0000 @@ -0,0 +1,23 @@ +<macros> + + <xml name="creators/bmcv"> + <organization name="Biomedical Computer Vision Group, Heidelberg Universtiy" alternateName="BMCV" url="http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html" /> + <yield /> + </xml> + + <xml name="creators/alliecreason"> + <person givenName="Allison" familyName="Creason"/> + <yield/> + </xml> + + <xml name="creators/bugraoezdemir"> + <person givenName="Bugra" familyName="Oezdemir"/> + <yield/> + </xml> + + <xml name="creators/thawn"> + <person givenName="Till" familyName="Korten"/> + <yield/> + </xml> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests.xml Thu Apr 04 15:23:28 2024 +0000 @@ -0,0 +1,95 @@ +<macros> + + <!-- Macros for verification of image outputs --> + + <xml + name="tests/binary_image_diff" + tokens="name,value,ftype,metric,eps" + token_metric="mae" + token_eps="0.01"> + + <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="0"> + <assert_contents> + <has_image_n_labels n="2"/> + <yield/> + </assert_contents> + </output> + + </xml> + + <xml + name="tests/label_image_diff" + tokens="name,value,ftype,metric,eps,pin_labels" + token_metric="iou" + token_eps="0.01" + token_pin_labels="0"> + + <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="@PIN_LABELS@"> + <assert_contents> + <yield/> + </assert_contents> + </output> + + </xml> + + <xml + name="tests/intensity_image_diff" + tokens="name,value,ftype,metric,eps" + token_metric="rms" + token_eps="0.01"> + + <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@"> + <assert_contents> + <yield/> + </assert_contents> + </output> + + </xml> + + <!-- Variants of the above for verification of collection elements --> + + <xml + name="tests/binary_image_diff/element" + tokens="name,value,ftype,metric,eps" + token_metric="mae" + token_eps="0.01"> + + <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="0"> + <assert_contents> + <has_image_n_labels n="2"/> + <yield/> + </assert_contents> + </element> + + </xml> + + <xml + name="tests/label_image_diff/element" + tokens="name,value,ftype,metric,eps" + token_metric="iou" + token_eps="0.01" + token_pin_labels="0"> + + <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="@PIN_LABELS@"> + <assert_contents> + <yield/> + </assert_contents> + </element> + + </xml> + + <xml + name="tests/intensity_image_diff/element" + tokens="name,value,ftype,metric,eps" + token_metric="rms" + token_eps="0.01"> + + <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@"> + <assert_contents> + <yield/> + </assert_contents> + </element> + + </xml> + +</macros>