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WIP - Instance Segmentation Experiments #187

Merged
merged 10 commits into from
Dec 20, 2023
Merged

WIP - Instance Segmentation Experiments #187

merged 10 commits into from
Dec 20, 2023

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anwai98
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@anwai98 anwai98 commented Dec 12, 2023

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@anwai98 anwai98 marked this pull request as ready for review December 14, 2023 14:31
anwai98 and others added 6 commits December 14, 2023 15:46
@anwai98
Restore unetr
c6bc2db
@anwai98
Restore unetr2
8779e79
@anwai98
Update freezing unetr
741366f
@anwai98
UNETR - Make skip connections optional (#9)
41bab4a 
Update UNETR model to optionally use skip connections or not
@anwai98
Add encoder flexibility in UNETR (#10)
7f06c97 
* Update distance transform (#11 - Getting instance segmentations from the distance transform)

* Making the encoder argument flexible (to either pytorch modules or model name as str)
@anwai98
Fix checkpoint path argument
8c6648f
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anwai98 commented Dec 20, 2023 •
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@constantinpape This PR makes the following updates and fixes:

  • Updates the postprocessing parameters (subjected to grid search) for distance-based experiments
  • Adds train_by_parts.py, to check for joint and disjoint training experiments
  • Adds a script to check UNETR initialization using different setups
  • Makes the encoder argument in UNETR modular - to accept pytorch modules or model type as str
  • Also makes the use of skip connections flexible.
  • Updates the distance transform, to return instances as well (when expected)

@constantinpape constantinpape merged commit 1409c56 into constantinpape:dev Dec 20, 2023
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@anwai98 @constantinpape