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Update testing dataset for new loader #5

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mariehbourget opened this issue Dec 8, 2020 · 2 comments
Open
3 of 7 tasks

Update testing dataset for new loader #5

mariehbourget opened this issue Dec 8, 2020 · 2 comments

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@mariehbourget
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mariehbourget commented Dec 8, 2020

To test the new loader, we want to add those modalities to the data-testing dataset:

  • microscopy PNG
  • microscopy OMETIFF
  • anat (2D single-slice nifti)
  • dwi (4D nifti)
  • eeg (files TBD)
  • sessions.tsv architectures and files
  • scans.tsv architectures and files
@mariehbourget
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microscopy PNG, sessions.tsv and scans.tsv are added in PR #6.

@mariehbourget
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mariehbourget commented Mar 15, 2021

Updates to do to the datasets following new loader first integration (ivadomed/ivadomed#699) for test_loader.py:

  • add participant_id column in df_ref.csv
  • add participant_id and sample_id in microscopy_png/df_ref.csv
  • a df_ref.csv for multiple folders in path_data
  • update df_ref.csv for test when roi_suffix is not None
  • add CT-scan data

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