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Error on faas pyramid (after zarr groups normalization) #23

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Yu-AnChen opened this issue Jul 17, 2021 · 0 comments
Open

Error on faas pyramid (after zarr groups normalization) #23

Yu-AnChen opened this issue Jul 17, 2021 · 0 comments

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@Yu-AnChen
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Ran into an error when trying to run the save_exhibit_pyramid.py script on a faas pyramid generated by ashlar at the latest commit (c32f018). Checked out a previous commit (aaefbdd), and the same command ran through. It seems to me this commit (cf32a1e) introduced the issue

(minerva-author) $ python src\save_exhibit_pyramid.py "Y:\sorger\data\IN_Cell_Analyzer_6000\Danae\201911_Quiescence_CyCIF_Her2-3x\FullOmeTiffs\HER2_1_WS.ome.tif" "Y:\sorger\data\minerva\gaglia-2020-PCQ\minerva-overviews\story-json\HER2_1_WS.ome.tif.json" Y:\sorger\data\minerva\gaglia-2020-PCQ\minerva-overviews\HER2_1_WS --force
330
OME  5
RGB  False
RGB type  None
2021-07-17 02:42:57,142 - app - WARNING - Writing to existing output directory Y:\sorger\data\minerva\gaglia-2020-PCQ\minerva-overviews\HER2_1_WS
2021-07-17 02:42:57,142 - app - WARNING - Writing to existing output directory Y:\sorger\data\minerva\gaglia-2020-PCQ\minerva-overviews\HER2_1_WS
Processing: Y:\sorger\data\IN_Cell_Analyzer_6000\Danae\201911_Quiescence_CyCIF_Her2-3x\FullOmeTiffs\HER2_1_WS.ome.tif
    level 0 (26 x 53)
Traceback (most recent call last):
  File "src\save_exhibit_pyramid.py", line 162, in <module>
    main(ome_tiff, author_json, output_dir, root_url, vis_dir, force)
  File "src\save_exhibit_pyramid.py", line 125, in main
    render(opener, saved, output_dir, logger)
  File "src\save_exhibit_pyramid.py", line 19, in render
    render_color_tiles(opener, output_dir, 1024, config_rows, logger, None, False)
  File "C:\Users\Public\Downloads\minerva-author\src\render_jpg.py", line 101, in render_color_tiles
    opener.save_tile(output_file, settings, tile_size, level, tx, ty)
  File "C:\Users\Public\Downloads\minerva-author\src\app.py", line 502, in save_tile
    img = self.return_tile(output_file, settings, tile_size, level, tx, ty)
  File "C:\Users\Public\Downloads\minerva-author\src\app.py", line 489, in return_tile
    target, tile, colors.to_rgb(color), float(start), float(end)
  File "C:\Users\Public\Downloads\minerva-author\src\render_jpg.py", line 23, in composite_channel
    target[:, :, i] += f_image * component
ValueError: operands could not be broadcast together with shapes (48,1024,3) (48,1024,53552) (48,1024,3)
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