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volume.from_pointset needs revision #528

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1 of 2 tasks
dickscheid opened this issue Jan 9, 2024 · 1 comment
Open
1 of 2 tasks

volume.from_pointset needs revision #528

dickscheid opened this issue Jan 9, 2024 · 1 comment
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@dickscheid
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dickscheid commented Jan 9, 2024

In the current implementation c72ece9, the siibra.volumes.from_pointset method seems to have two issues:

  • It sets a label value to the pixels before gaussian smoothing, but the intended operation is a KDE which assumed to smooth a peak with value 1 (Smoothing of labels is not a proper operation anyways). So independent of the selected label, the smoothing should be based on setting pixels to 1.
  • The function states that the kernel bandwidth is in millimeter, but applies it to voxels irrespective of the physical resolution. A translation form millimeter to voxels should be added so the bandwidth unit applies also for image resolutions that differ from 1mm.
@AhmetNSimsek AhmetNSimsek self-assigned this Jan 9, 2024
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AhmetNSimsek commented Jan 15, 2024

#529 fixes the first task

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