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Import spots from labels#47

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stefanhahmann wants to merge 23 commits intomastermastodon-sc/mastodon-deep-lineage:masterfrom import_spots_from_labelsmastodon-sc/mastodon-deep-lineage:import_spots_from_labelsCopy head branch name to clipboard

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Commits on Feb 29, 2024

• Import spots from labels (unfinished)

  stefanhahmann

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• Set channel to min 0

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• implemented proper algorithm for finding the spots efficiently from all label IDs.

  

  Noam-Dori

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• Fixed a bunch of bugs relating to data size incompatibility during summation (might need more robust fix later), anisotropic dimensions, finding minimum and max pixel value to account for unsigned …

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  Noam-Dori

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• Fixed accuracy via order of division and fixed overflow bug by introducing BigInteger. We have no way to avoid this as we needed a 128bit integer to truly solve the problem.

  

  Noam-Dori

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• Apply project code formatter to ImportSpots classes

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• Remove jetbrains annotations from ImportSpotsFromLabelImageController

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• Remove blocks from 1 line if conditions

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• Suppress warning re final for parameter with default value

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• Initialize mixedSum with zero on first use to avoid NullPointerException

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• Add final modifier to param VoxelDimensions

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• Modified ImportSpotsFromLabelImageControllerTest to contain a mathematically trivial example that can easily be tested.

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• Increase code coverage of test by providing a non empty context in the unit test

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• Rename timepoint variables to frame

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• Add javadoc to createSpotsFromLabels() method

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• Rename bg to background

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• A possible human-caused error can occur by choosing the incorrect channel to convert labels into ellipsoids (using the raw image instead of the label image)

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• Use ProjectModel instead of MamutAppModel

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• Move import spots from label image plugin to org.mastodon.mamut.io.importer.labelimage

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• Rename classes to ImportSpotsFromLabelImage*

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• Move Plugin in menu to Plugins > Imports

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• Fix javadoc related errors

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• Change variable name to projectModel when calling ImportSpotsFromLabelImageView via the CommandService

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