Mercurial > repos > galaxyp > qupath_roi_splitter
comparison qupath_roi_splitter.py @ 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 |
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| 0:b5e9cebb27e3 | 1:064b53fd3131 |
|---|---|
| 20 dim_plt = [qupath_roi["dim"]["width"], qupath_roi["dim"]["height"]] | 20 dim_plt = [qupath_roi["dim"]["width"], qupath_roi["dim"]["height"]] |
| 21 | 21 |
| 22 tma_name = qupath_roi["name"] | 22 tma_name = qupath_roi["name"] |
| 23 cell_types = [ct.rsplit(" - ", 1)[-1] for ct in qupath_roi["featureNames"]] | 23 cell_types = [ct.rsplit(" - ", 1)[-1] for ct in qupath_roi["featureNames"]] |
| 24 | 24 |
| 25 # create numpy array with white background | 25 for cell_type in cell_types: |
| 26 img = np.zeros((dim_plt[1], dim_plt[0], 3), dtype="uint8") | 26 # create numpy array with white background |
| 27 img.fill(255) | 27 img = np.zeros((dim_plt[1], dim_plt[0], 3), dtype="uint8") |
| 28 img.fill(255) | |
| 28 | 29 |
| 29 for cell_type in cell_types: | |
| 30 for i, roi in enumerate(qupath_roi["features"]): | 30 for i, roi in enumerate(qupath_roi["features"]): |
| 31 if roi["properties"]["classification"]["name"] == cell_type: | 31 if roi["properties"]["classification"]["name"] == cell_type: |
| 32 if len(roi["geometry"]["coordinates"]) == 1: | 32 if len(roi["geometry"]["coordinates"]) == 1: |
| 33 # Polygon w/o holes | 33 # Polygon w/o holes |
| 34 img = draw_poly(roi["geometry"]["coordinates"][0], img) | 34 img = draw_poly(roi["geometry"]["coordinates"][0], img) |