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Make Import Spots handling single pixels and planar pixels properly #105

Merged
merged 16 commits into from
Jun 6, 2024
Merged

Make Import Spots handling single pixels and planar pixels properly #105

merged 16 commits into from
Jun 6, 2024

Commits on May 31, 2024

  1. Handle the case of single pixel values and covariances that are only … 

    …in one plane and thus have zero values on the diagonal

* The goal that resulting ellipoids are at least 1pixel wide in each dimension
    @stefanhahmann
    stefanhahmann committed May 31, 2024
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  2. Add a SphereRenderer and a Demo for small labels to ellipsoid conversion

    @stefanhahmann
    stefanhahmann committed May 31, 2024
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  3. Extend Small Label Demo with some Circle and a line example

    @stefanhahmann
    stefanhahmann committed May 31, 2024
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Commits on Jun 6, 2024

  1. Change some code formatting in LabelImageUtilsTest

    @stefanhahmann
    stefanhahmann committed Jun 6, 2024
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  2. Change assertion in testCreateSpotFromNonLabelImage() 

    * Since single pixels are not filtered anymore, they are now all converted to a spot in the graph
    @stefanhahmann
    stefanhahmann committed Jun 6, 2024
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  3. Replace test testImportSpotsFromBdvChannel() by multiple tests 

    * test importing a sphere
* test importing a circle in only one plane
* test importing a single pixel
* test importing a line
    @stefanhahmann
    stefanhahmann committed Jun 6, 2024
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  4. Remove obsolete LegacyInjector.preinit(); from some test im LabelImag… 

    …eUtilsTest
    @stefanhahmann
    stefanhahmann committed Jun 6, 2024
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  5. Increase JVM max ram to 2GB also for sonar cloud job 

    * Build job had 2GB before
* Now both jobs have more consistently the same setting
    @stefanhahmann
    stefanhahmann committed Jun 6, 2024
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  6. Checking internal pool index removed, since it adds no value to the u… 

    …nit test
    @stefanhahmann
    stefanhahmann committed Jun 6, 2024
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  7. Bounding sphere radius check removed from unit test

    @stefanhahmann
    stefanhahmann committed Jun 6, 2024
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  8. Use arrayEquals for coordinate check in unit test.

    @stefanhahmann
    stefanhahmann committed Jun 6, 2024
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  9. Introduce a new method getSemiAxesOfSpot() in LabelImageUtilsTest 

    * Reduces code duplication
    @stefanhahmann
    stefanhahmann committed Jun 6, 2024
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  10. Transform ellipsoid center and ellipsoid axes to mastodon coordinate … 

    …system

* Replaces scaling the center with voxel dimensions
* Replaces scaling the covariance matrix with voxel dimensions
* Required, since besides scaling, also rotation, translation and shearing may exist in the images
    @stefanhahmann
    stefanhahmann committed Jun 6, 2024
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  11. Let the user decide, which source has been used for the segmentation

    @stefanhahmann
    stefanhahmann committed Jun 6, 2024
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  12. Move generation of Image in SmallLabelDemo

    @stefanhahmann
    stefanhahmann committed Jun 6, 2024
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  13. Add new class SpotRenderer

    @stefanhahmann
    stefanhahmann committed Jun 6, 2024
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