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baidu-research / NCRF

Cancer metastasis detection with neural conditional random field (NCRF)
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About how to generater Normal_*.json #26

Closed wilmerwang closed 5 years ago

wilmerwang commented 5 years ago

Hi,

I was wondering how to generater Normal_*. json files?

And if it was generatered by the normal tissue mask? can you share the process detail. Thank you!

Kind regards,

yil8 commented 5 years ago

@ilikewind yes, for Normal_*.json files they were generated by random sampling coordinates from the normal tissue mask at some higher level, e.g. level 6.

wilmerwang commented 5 years ago

@yil8 I think the Normal_*.json should include all normal tissue, e.g. Normal_001.json represent the tissue area of Normal_001.tif. so I was confused about random sampling... thanks.

yil8 commented 5 years ago

@ilikewind It's always impossible to enumerate all the tissue regions of a normal samples, so you have to do subsampling.

wilmerwang commented 5 years ago

@yil8 In order to check what Normal_.json are, I translate Normal_001.json to Normal001.xml, so I can visualiize it. but it is obvious that normal.json include all normal tissue. It is a intersting to use normal*.json than normal tissue mask images. _20181207221528

and I also want to know more detail you employ for the normal_.json generated. thank you .

yil8 commented 5 years ago

@ilikewind I'm not quite sure how you generated this figure, it seems the blue dots are concentrated about boundary regions. This might due to the effect of hard negative mining.

wilmerwang commented 5 years ago

@yil8 the figure was generated by your file Normal-001.json at NCRF/jsons/train/. And I am not sure if you mistake the json file for coordinates/normal_train.txt . It seems we are discuss different issues. Best wish.

yil8 commented 5 years ago

@ilikewind I am so sorry, I was completely wrong about your question, and indeed I confused between Normal_001.json with coordinates/normal_train.txt. Normal001.json was not really used through out this code base. Honestly, I forgot how Normal*.json were generated, but they were probably not generated base on tissue mask

wilmerwang commented 5 years ago

@yil8 Ok, thanks for your patient. I will do something about it.