Mercurial > repos > thomaswollmann > wsi_extract_top_view
changeset 0:9f01fd145af4 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/wsi_extract_top_view/ commit 42d972afdd700fccae1017c06efbfd06b9c96791
| author | thomaswollmann |
|---|---|
| date | Mon, 07 Jan 2019 08:38:08 -0500 |
| parents | |
| children | 257397c40c25 |
| files | test-data/CMU-1-Small-Region.svs test-data/out.tif wsi_extract_top_view.py wsi_extract_top_view.xml |
| diffstat | 4 files changed, 52 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/wsi_extract_top_view.py Mon Jan 07 08:38:08 2019 -0500 @@ -0,0 +1,22 @@ +import argparse +import openslide +import os +import fnmatch +import skimage.io +import numpy as np + +def wsi_extract_top_view(input_path, out_path): + img_raw = openslide.OpenSlide(input_path) + top_size = img_raw.level_dimensions[len(img_raw.level_dimensions)-1] + img_area = img_raw.read_region((0,0), len(img_raw.level_dimensions)-1, top_size) + img_area = np.asarray(img_area, dtype=np.uint8) + skimage.io.imsave(out_path, img_area, plugin="tifffile") + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument('input_file', type=argparse.FileType('r'), help='input file') + parser.add_argument('out_file', help='out file') + args = parser.parse_args() + + wsi_extract_top_view(args.input_file.name, args.out_file)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/wsi_extract_top_view.xml Mon Jan 07 08:38:08 2019 -0500 @@ -0,0 +1,30 @@ +<tool id="wsi_extract_top_view" name="Extract Top View from WSI" version="0.1"> + <description>Extracts top view from WSI</description> + <requirements> + <requirement type="package" version="0.14.0" >scikit-image</requirement> + <requirement type="package" version="1.15.4">numpy</requirement> + <requirement type="package" version="1.1.1">openslide-python</requirement> + <requirement type="package" version="0.5">glob2</requirement> + </requirements> + <command> + <![CDATA[ + python "$__tool_directory__/wsi_extract_top_view.py" '$input' '$output' + ]]> + </command> + <inputs> + <param name="input" type="data" format="svs,tif,ndpi,vms,vmu,scn,mrxs,tiff,svslide,bif" label="Whole Slice Image"/><!--formats taken as listed on https://openslide.org/api/python/--> + </inputs> + <outputs> + <data name="output" format="tiff"/> + </outputs> + <tests> + <test> + <param name="input" value="CMU-1-Small-Region.svs"/> + <output name="output" value="out.tif" ftype="tiff" compare="sim_size"/> + </test> + </tests> + <help>Extracts the top view from a whole-slice image, also known as virtual slide, which are high-resolution images used in digital pathology.</help> + <citations> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + </citations> +</tool>