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Inference Updates #405

Merged
merged 11 commits into from
Jul 19, 2024
Merged

Inference Updates #405

merged 11 commits into from
Jul 19, 2024

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benjijamorris
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@benjijamorris benjijamorris commented Jul 10, 2024 •
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What does this PR do?

  • add callback template for saving model features as a csv
  • rework czi dataloader to work for multidim images (timelapse, multiscene, etc.)
  • Add option to pass dict to multidim dataset instead of a csv
  • add feature-only inference option for MAE models

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  • Did you make sure title is self-explanatory and the description concisely explains the PR?
  • Did you make sure your PR does only one thing, instead of bundling different changes together?
  • Did you list all the breaking changes introduced by this pull request?
  • Did you test your PR locally with pytest command?
  • Did you run pre-commit hooks with pre-commit run -a command?

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Make sure you had fun coding 🙃

ritvikvasan
ritvikvasan previously approved these changes Jul 16, 2024
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sweet!

cyto_dl/datamodules/multidim_image.py Outdated
"""Function to create a CZI Dataset. Currently, this dataset is only useful during prediction
and cannot be used for training or testing.
) -> DataLoader:
"""Function to create a MultiDimImage Dataset. Currently, this dataset is only useful during
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create a data loader?

cyto_dl/nn/vits/mae.py
@@ -290,5 +295,7 @@ def __init__(

def forward(self, img):
features, mask, forward_indexes, backward_indexes = self.encoder(img, self.mask_ratio)
if self.features_only:
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if features_only mask_ratio must be 0?

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I don't want to enforce that in case we want to pass in a mask and just look at features from that subset of tokens (wishful thinking for now, but that's the reason behind that choice)

@benjijamorris benjijamorris merged commit c65dbbf into main Jul 19, 2024
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@benjijamorris benjijamorris deleted the feature/timelapse_inference_dataloader branch July 19, 2024 18:59
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@ritvikvasan ritvikvasan ritvikvasan approved these changes

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@benjijamorris @ritvikvasan