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choosehappy / HistoQC

HistoQC is an open-source quality control tool for digital pathology slides
BSD 3-Clause Clear License
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countTissuePieces() takes 1 positional argument but 2 were given #315

Closed Himanshunitrr closed 2 months ago

Himanshunitrr commented 3 months ago

I am trying to run HistoQC on a dataset but I am getting:

2024-08-14 18:03:37,380 - WARNING - HS14-29933 1A .ndpi - Mask file '/opt/HistoQC/.histoqc_pkg_data_tmpk_mr7_8v/./pen/1k_version/pen_black_mask.png' is not a binary image. Automatically converting to binary... 2024-08-14 18:09:02,260 - ERROR - /data/HS14-29933 1A .ndpi - Error analyzing file (skipping): <class 'TypeError'> Inappropriate argument type. countTissuePieces() takes 1 positional argument but 2 were given 2024-08-14 18:16:22,410 - ERROR - /data/HS16-26406 2A .ndpi - Error analyzing file (skipping): <class 'TypeError'> Inappropriate argument type. countTissuePieces() takes 1 positional argument but 2 were given 2024-08-14 18:17:11,626 - ERROR - /data/HS12-32993 2A .ndpi - Error analyzing file (skipping): <class 'TypeError'> Inappropriate argument type. countTissuePieces() takes 1 positional argument but 2 were given......

How to resolve this

CielAl commented 3 months ago

I am trying to run HistoQC on a dataset but I am getting:

2024-08-14 18:03:37,380 - WARNING - HS14-29933 1A .ndpi - Mask file '/opt/HistoQC/.histoqc_pkg_data_tmpk_mr7_8v/./pen/1k_version/pen_black_mask.png' is not a binary image. Automatically converting to binary... 2024-08-14 18:09:02,260 - ERROR - /data/HS14-29933 1A .ndpi - Error analyzing file (skipping): <class 'TypeError'> Inappropriate argument type. countTissuePieces() takes 1 positional argument but 2 were given 2024-08-14 18:16:22,410 - ERROR - /data/HS16-26406 2A .ndpi - Error analyzing file (skipping): <class 'TypeError'> Inappropriate argument type. countTissuePieces() takes 1 positional argument but 2 were given 2024-08-14 18:17:11,626 - ERROR - /data/HS12-32993 2A .ndpi - Error analyzing file (skipping): <class 'TypeError'> Inappropriate argument type. countTissuePieces() takes 1 positional argument but 2 were given......

How to resolve this

@choosehappy @jacksonjacobs1 @nanli-emory Seems like the BasicModule.countTissuePieces does not define a params signature following the paradigm of custom modules invoked in pipelines, yet it is invoked as a module in the config files.