Update slideflow_fork submodule to include TIFF mpp-detection fix#12
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JurreWeijer wants to merge 234 commits intoSbrussee:mainfrom
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Update slideflow_fork submodule to include TIFF mpp-detection fix#12JurreWeijer wants to merge 234 commits intoSbrussee:mainfrom
JurreWeijer wants to merge 234 commits intoSbrussee:mainfrom
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…raction of tiles/features, added more robust handling of QC hyperparameters, removed double intializations, removed TRANSFORMER_CACHE environment variable
…de benchmarking and optimization applicable to multiple test sets
…dataset locations, removed uninformative warnings
… exceptions during tile extraction
Also, fix invalid balancing strategy in the yaml configuration templates for survival analysis
Also, defend against exception being triggered when empty an dataframe is passed to make_labels in plot_benchmarking_output()
Some bug fixes
…prediction metrics, fixed visualization of survival ROC-AUC curve, addition of (fastai, custom) callbacks
These were undone in 666748f
the loss function retrieval requires ‘loss’ to be passed in kwargs, see _build_fastai_learner() in slideflow/mil/train/_fastai.py
Fixes slide level mode not being applied
Small fixes (and redo earlier fixes)
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@JurreWeijer Thanks for the PR! Could you maybe add this as a PR to the slideflow_fork module itself, that will make merging easier: https://github.com/Sbrussee/slideflow_fork |
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SlideFlow uses some strange logic to get the resolution from tiff files, however in the documentation is says that the xres and yres are always given in pixel per milimeter so the resolution unit does not matter.
"Use xres and yres to override the default horizontal and vertical resolutions. By default these values are taken from the VIPS image header. libvips resolution is always in pixels per millimetre."
source: https://www.libvips.org/API/8.17/method.Image.tiffsave.html?utm_source=chatgpt.com