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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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worker() got an unexpected keyword argument 'debug' #302

Closed zhaolei4383 closed 2 weeks ago

zhaolei4383 commented 1 month ago

2024-05-27 02:34:28,044 - WARNING - Configuration file v2.1 assuming to be a template...checking. 2024-05-27 02:34:28,316 - INFO - the pipeline will use these steps: 2024-05-27 02:34:28,316 - INFO - BasicModule getBasicStats 2024-05-27 02:34:28,316 - INFO - LightDarkModule saveEqualisedImage 2024-05-27 02:34:28,317 - INFO - LightDarkModule minimumPixelIntensityNeighborhoodFiltering 2024-05-27 02:34:28,318 - INFO - LightDarkModule getIntensityThresholdPercent:darktissue 2024-05-27 02:34:28,318 - INFO - BubbleRegionByRegion detectSmoothness 2024-05-27 02:34:28,320 - INFO - MorphologyModule removeFatlikeTissue 2024-05-27 02:34:28,329 - INFO - MorphologyModule fillSmallHoles 2024-05-27 02:34:28,329 - INFO - MorphologyModule removeSmallObjects 2024-05-27 02:34:28,329 - INFO - LocalTextureEstimationModule estimateGreyComatrixFeatures:background 2024-05-27 02:34:28,330 - INFO - BrightContrastModule getContrast:background 2024-05-27 02:34:28,330 - INFO - BrightContrastModule getBrightnessGray:background 2024-05-27 02:34:28,330 - INFO - BrightContrastModule getBrightnessByChannelinColorSpace:RGB_background 2024-05-27 02:34:28,330 - INFO - BlurDetectionModule identifyBlurryRegions 2024-05-27 02:34:28,330 - INFO - BasicModule finalProcessingSpur 2024-05-27 02:34:28,330 - INFO - BasicModule finalProcessingArea 2024-05-27 02:34:28,330 - INFO - HistogramModule compareToTemplates 2024-05-27 02:34:28,330 - INFO - HistogramModule getHistogram 2024-05-27 02:34:28,330 - INFO - LocalTextureEstimationModule estimateGreyComatrixFeatures:final 2024-05-27 02:34:28,330 - INFO - BrightContrastModule getContrast 2024-05-27 02:34:28,330 - INFO - BrightContrastModule getBrightnessGray 2024-05-27 02:34:28,330 - INFO - BrightContrastModule getBrightnessByChannelinColorSpace:RGB 2024-05-27 02:34:28,330 - INFO - BrightContrastModule getBrightnessByChannelinColorSpace:YUV 2024-05-27 02:34:28,330 - INFO - DeconvolutionModule separateStains 2024-05-27 02:34:28,330 - INFO - SaveModule saveFinalMask 2024-05-27 02:34:28,330 - INFO - SaveModule saveMacro 2024-05-27 02:34:28,330 - INFO - SaveModule saveThumbnails 2024-05-27 02:34:28,330 - INFO - BasicModule finalComputations 2024-05-27 02:34:33,579 - INFO - moving fileHandler '/nasdata/private/lzhao/workspace/projects/HER2/libs/HistoQC/error.log' to './histoqc_output_20240527-023428/error.log' 2024-05-27 02:34:33,666 - INFO - -------------------------------------------------------------------------------- 2024-05-27 02:34:33,666 - INFO - Number of files detected by pattern: 32 8 2024-05-27 02:34:34,386 - INFO - ----------Done-----------

2024-05-27 02:34:34,387 - INFO - There are 32 explicitly failed images (available also in error.log), warnings are listed in warnings column in output 2024-05-27 02:34:34,393 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,394 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,394 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,394 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,394 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,394 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,394 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,394 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,395 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,395 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,395 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,395 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,395 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,395 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,395 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,396 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,396 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,396 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,396 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,396 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,396 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,396 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,396 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,397 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,397 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,397 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,397 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,397 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,397 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,397 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,398 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None 2024-05-27 02:34:34,398 - INFO - N/A error outside of pipeline TypeError("worker() got an unexpected keyword argument 'debug'") None

Hello, could anyone help me with this error? I can't find out how does it happen. I created my conda environments with follows:

  1. conda create -n histoqc python=3.9
  2. pip install -r requirements.txt
  3. pip install .
  4. python -m histoqc -c v2.1 -n 8 /data/2024-05-22/*.tiff
jacksonjacobs1 commented 1 month ago

Hi @zhaolei4383 ,

Thank you for catching this bug which was introduced in the most recent commit to histoqc (8aec6060ab38d2af3021b20f1ae16943e279f562). I have just pushed a fix in 14c49e346ccd78fe90e7cf3d8513ec509841d559

Please reinstall histoqc using either of the installation options and try again.

If you have any further issues, I'll be happy to help.

zhaolei4383 commented 1 month ago

Hi @zhaolei4383 ,

Thank you for catching this bug which was introduced in the most recent commit to histoqc (8aec606). I have just pushed a fix in 14c49e3

Please reinstall histoqc using either of the installation options and try again.

If you have any further issues, I'll be happy to help.

Very helpful, thanks!