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Merge dev into master#278

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constantinpape merged 53 commits intomastercomputational-cell-analytics/micro-sam:masterfrom devcomputational-cell-analytics/micro-sam:devCopy head branch name to clipboardNov 18, 2023

+1,021-378

Commits

Commits on Oct 17, 2023

• Start on embedding widget

  GenevieveBuckley

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• Add missing typing import in visualization.py file

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• Fix npe2 napari manifest validation

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Commits on Oct 19, 2023

• Graceful error handling for torch device backend selection

  GenevieveBuckley

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• Embedding widget for napari plugin

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• Merge branch 'dev' into embedding-widget

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• Fix _available_devices utility function

  GenevieveBuckley

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• Merge branch 'embedding-widget' of github.com:GenevieveBuckley/micro-sam into embedding-widget

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• More clear variable names

  GenevieveBuckley

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• Add GUI test for embedding widget

  GenevieveBuckley

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• Thread worker function doesn't actually return object the same way single-threaded code works

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• Fix rgb ndim calculation

  GenevieveBuckley

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• Move location where global IMAGE_EMBEDDINGS is defined

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Commits on Oct 23, 2023

• Order of output files does not matter for test

  GenevieveBuckley

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• Fix ndim for rgb images in embedding_widget

  GenevieveBuckley

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• Let's be careful since now the prgress bar is an unnamed argument to this function

  GenevieveBuckley

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• Match progress bar with thread worker example from napari/examples

  GenevieveBuckley

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• Implement singleton state and use it in the 2d annotator

  constantinpape

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Commits on Oct 24, 2023

• Use singleton state in all annotator tools

  constantinpape

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• Sanitize user string input to _get_device()

  GenevieveBuckley

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Commits on Oct 25, 2023

• Fixes for test_training.py failures

  GenevieveBuckley

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• Merge pull request #245 from GenevieveBuckley/fix-training-test-errors

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Commits on Oct 29, 2023

• Add support for batched inference with prompts

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• Merge pull request #252 from computational-cell-analytics/master

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• Merge pull request #253 from computational-cell-analytics/inference

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Commits on Oct 30, 2023

• Add unittests for the state

  constantinpape

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• Fix instance segmentation on the GPU

  constantinpape

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• Merge pull request #240 from computational-cell-analytics/singleton

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• Fix instance segmentation on GPU and CPU

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Commits on Nov 1, 2023

• Refactor Iterative Prompting Evaluation (#254)

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  constantinpape

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Commits on Nov 2, 2023

• Add 3d segmentation functionality (#255)

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Commits on Nov 3, 2023

• Merge branch 'dev' into embedding-widget-singleton

  GenevieveBuckley

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• Workaround for issue 246

  GenevieveBuckley

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• Image embedding widget now uses singleton AnnotatorState

  GenevieveBuckley

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• Embedding widget, ensure save directory exists and is empty

  GenevieveBuckley

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• Update Evaluation - Iterative Prompting (#260)

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  constantinpape

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Commits on Nov 4, 2023

• Don't set a device for custom checkpoint export

  constantinpape

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Commits on Nov 5, 2023

• More consise code with os.makedirs exist_ok

  GenevieveBuckley

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• Merge branch 'embedding-widget' of github.com:GenevieveBuckley/micro-sam into embedding-widget

  GenevieveBuckley

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Commits on Nov 7, 2023

• Upgrade invalid embeddings path from user warning to runtime error (so napari users will see error popup)

  GenevieveBuckley

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• Move all computation into thread worker, allow previously computed embeddings to exist

  GenevieveBuckley

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• Add reset_state method to clear all attributes held in state

  GenevieveBuckley

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• Remove data_signature attribute from AnnotatorState attributes

  GenevieveBuckley

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• Embedding widget, image_shape in annotator state

  GenevieveBuckley

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Commits on Nov 8, 2023

• Use a consistent cache directory

  GenevieveBuckley

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• Make module docstring a raw string, to cope with backslash characters

  GenevieveBuckley

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• Merge pull request #235 from GenevieveBuckley/embedding-widget

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• Merge pull request #268 from GenevieveBuckley/consistent-cache-dir

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Commits on Nov 9, 2023

• Fix typo in function name _segment_slice_widget

  GenevieveBuckley

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• Merge pull request #273 from GenevieveBuckley/fix-typo

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Commits on Nov 13, 2023

• Use qtpy instead of PyQt5

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• Merge pull request #275 from computational-cell-analytics/qtpy

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Commits on Nov 15, 2023

• Experiments with Mask Inputs Probability (#265)

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