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wyli avatar wyli commented on August 22, 2024

HI @Kyuuki93 The classification application has been implemented recently but the documentation is still work in progress, it'll be available in the next release (v0.3).

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Kyuuki93 avatar Kyuuki93 commented on August 22, 2024

Great work, which format should label data saved in?

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eligibson avatar eligibson commented on August 22, 2024

Currently, you can load labels by making them 1x1x1 images, but set interp_order to -1 in the config file. We are still working out what formats to support for labels, so if you have preferences, please let us know.

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Kyuuki93 avatar Kyuuki93 commented on August 22, 2024

@wyli @eligibson
I finished the training according to your suggestion,the dataset include some MR images download from OASIS.
There are two flaws in INFERENCE stage:

  1. the prediction result will be saved in a .nii file, it's not so convenient to evaluate the accuracy, like this
    INFO:niftynet: Inference iter 2, (0.045657s) ...... (1, 1) Saved /home/*/NiftyNet/models/tstnet/output/tstnet/S007_niftynet_out.nii.gz INFO:niftynet: Inference iter 3, (0.040947s) ...... (1, 1) Saved /home/*/NiftyNet/models/tstnet/output/tstnet/S020_niftynet_out.nii.gz
  2. the output_prob parameter in [CLASSIFICATION] section must be False, otherwise will throw ValueError: cannot reshape array of size 2 into shape (1,1,1,1,1), (num_class=2 in my task) the error should come from the label format

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eligibson avatar eligibson commented on August 22, 2024

@Kyuuki93

  1. I agree that output as nii files is not ideal. We are working on that in two ways. First, we are adding built in tools for evaluation. Second, we are planning to revamp the IO to allow other ways to specify labels and get the outputs. Some of this will be ready for the next release.

Until then, it is fairly straightforward to write a short python script to go through the nii files and add the output to a csv file:

import nibabel, glob
with open('output.csv','w') as f:
  for fn in glob.glob('*_niftynet_out.nii.gz'):
    f.write('%s,%i\n'%(fn.replace('_niftynet_out.nii.gz',''), nibabel.load(fn).get_data()[0,0,0,0,0]))
  1. This looks like a bug. I'll add an issue and get it fixed.

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eligibson avatar eligibson commented on August 22, 2024

These should both be resolved by commit 0f4ac84
Classification now outputs a csv file in addition to the nii files.

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andys0975 avatar andys0975 commented on August 22, 2024

So... I wonder now we still need to use 1x1x1 images as label's format ?
Is there a method to use pandas to read the labels for Classification & Regression task ?

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koriavinash1 avatar koriavinash1 commented on August 22, 2024

@Kyuuki93 can you share your config file?

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