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Improve the predict output file options

See original GitHub issue

Issue description

Currently, predict/deepreg_predict saves input images/labels for different label pairs, with both png and nifti file formats. This leads to sizable written files.

1 - Add options that can turn off the following for space-saving/speed:

  • Save input images/labels (useful for debugging or research);
  • Save png files
  • Save nifti files (is this useful to be able to turn off?)

2 - Avoid saving the same input files multiple times.

Type of Issue

  • New feature request
  • Documentation update
  • Test request

What’s the expected result?

What’s the actual result?

Additional details / screenshot


Issue Analytics

  • State:closed
  • Created 3 years ago
  • Comments:6 (6 by maintainers)

github_iconTop GitHub Comments

NMontanaBrowncommented, Aug 6, 2020

Also, I was reviewing this for the edu challenge and at this line we call:

# predict
 # (batch, f_dim1, f_dim2, f_dim3)
        pred_fixed_label = outputs_dict.get("pred_fixed_label", None)
        pred_fixed_image = (
            layer_util.resample(vol=moving_image, loc=fixed_grid_ref + ddf)
            if ddf is not None
            else None

Which I found quite confusing: the warped image is called pred_fixed_image, which I associated to the fixed image. I would suggest renaming this and the save file for clarity to warped_moving_image, or something along the lines?

@YipengHu @mathpluscode @s-sd

mathpluscodecommented, Aug 2, 2020

so ideally, the output should be like following (this has been discussed before lol)

  • one folder per image pair (not related to label)
    • input images
    • one subfolder per label
      • input label
      • outputs

then for the following items we can choose to save or not

  • input images/labels, default false
  • png, default false
  • nifti, default true

@YipengHu what do you think?

Read more comments on GitHub >

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