Mercurial > repos > galaxyp > qupath_roi_splitter
changeset 1:064b53fd3131 draft
planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit e08a178a7c35c0673f6bfc163614a8fc730ffc6c
| author | galaxyp |
|---|---|
| date | Wed, 14 Jun 2023 16:37:01 +0000 |
| parents | b5e9cebb27e3 |
| children | 7bee859bbd11 |
| files | qupath_roi_splitter.py qupath_roi_splitter.xml |
| diffstat | 2 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/qupath_roi_splitter.py Tue Apr 25 09:30:06 2023 +0000 +++ b/qupath_roi_splitter.py Wed Jun 14 16:37:01 2023 +0000 @@ -22,11 +22,11 @@ tma_name = qupath_roi["name"] cell_types = [ct.rsplit(" - ", 1)[-1] for ct in qupath_roi["featureNames"]] - # create numpy array with white background - img = np.zeros((dim_plt[1], dim_plt[0], 3), dtype="uint8") - img.fill(255) + for cell_type in cell_types: + # create numpy array with white background + img = np.zeros((dim_plt[1], dim_plt[0], 3), dtype="uint8") + img.fill(255) - for cell_type in cell_types: for i, roi in enumerate(qupath_roi["features"]): if roi["properties"]["classification"]["name"] == cell_type: if len(roi["geometry"]["coordinates"]) == 1:
--- a/qupath_roi_splitter.xml Tue Apr 25 09:30:06 2023 +0000 +++ b/qupath_roi_splitter.xml Wed Jun 14 16:37:01 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="qupath_roi_splitter" name="QuPath ROI Splitter" version="0.1.0"> +<tool id="qupath_roi_splitter" name="QuPath ROI Splitter" version="0.1.0+galaxy1"> <description>Split ROI coordinates of QuPath TMA annotation by cell type (classification)</description> <requirements> <requirement type="package" version="3.0.1">geojson</requirement> @@ -34,8 +34,8 @@ <assert_contents> <has_text text="x"/> <has_text text="y"/> - <has_text text="14240"/> - <has_text text="21008"/> + <has_text text="15561"/> + <has_text text="21160"/> </assert_contents> </element> </output_collection>