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PathologyDataScience / BCSS

Use this to download all elements of the BCSS dataset described in: Amgad M, Elfandy H, ..., Gutman DA, Cooper LAD. Structured crowdsourcing enables convolutional segmentation of histology images. Bioinformatics. 2019. doi: 10.1093/bioinformatics/btz083
MIT License
140 stars 16 forks source link

download whole slides #14

Closed witness97 closed 3 years ago

witness97 commented 3 years ago

I always face this problem when running download_wsis.sh File "/usr/local/bin/girder-client", line 8, in sys.exit(main()) File "/usr/local/lib/python3.7/dist-packages/click/core.py", line 1134, in call return self.main(args, kwargs) File "/usr/local/lib/python3.7/dist-packages/click/core.py", line 1059, in main rv = self.invoke(ctx) File "/usr/local/lib/python3.7/dist-packages/click/core.py", line 1665, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/usr/local/lib/python3.7/dist-packages/click/core.py", line 1401, in invoke return ctx.invoke(self.callback, ctx.params) File "/usr/local/lib/python3.7/dist-packages/click/core.py", line 767, in invoke return __callback(args, *kwargs) File "/usr/local/lib/python3.7/dist-packages/click/decorators.py", line 38, in new_func return f(get_current_context().obj, args, **kwargs) File "/usr/local/lib/python3.7/dist-packages/girder_client/cli.py", line 299, in _download gc.downloadItem(parent_id, local_folder) File "/usr/local/lib/python3.7/dist-packages/girder_client/init.py", line 1262, in downloadItem created=files[0]['created']) File "/usr/local/lib/python3.7/dist-packages/girder_client/init.py", line 1192, in downloadFile length=int(req.headers.get('content-length', 0))) as reporter: File "/usr/local/lib/python3.7/dist-packages/click/_termui_impl.py", line 98, in enter self.render_progress() File "/usr/local/lib/python3.7/dist-packages/click/_termui_impl.py", line 242, in render_progress line = self.format_progress_line() File "/usr/local/lib/python3.7/dist-packages/click/_termui_impl.py", line 193, in format_progress_line info_bits.append(self.format_pos()) File "/usr/local/lib/python3.7/dist-packages/girder_client/cli.py", line 58, in formatPos if _self.length_known: AttributeError: 'ProgressBar' object has no attribute 'length_known' I just wonder why this would happen and how to download the whole slide image?

kheffah commented 3 years ago

@witness97 Actually, the whole-slide images are no longer available for download as there is too much traffic on the Kitware server (each image is 2GB+). The recommended way is to specify the resolution you want and only download the RGB and mask for the region of interest. If you still want the whole-slide image please note that TCGA slides are public, and can be obtained using the instructions shown in this blog post.