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Add exporting ellipsoids to file #45

Merged
merged 28 commits into from
Sep 26, 2023
Merged

Add exporting ellipsoids to file #45

merged 28 commits into from
Sep 26, 2023

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stefanhahmann
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Resolves #40

@stefanhahmann stefanhahmann self-assigned this Sep 19, 2023
@stefanhahmann stefanhahmann requested review from maarzt and removed request for maarzt September 19, 2023 15:00
@stefanhahmann
Add Image Segmentation using ellipsoids of Spots
22af0d0 
* 2 options:
* Show segmentation in BDV
* Save segmentation to file
* Spot Ids and BranchSpot Ids may be used as labels
@stefanhahmann
Move LabelOptions and SegmentationTask to separate package config
946c85d
@stefanhahmann
Replace usage of Shared BDV data by timepoints and source
f566ee7
@stefanhahmann
Add human readable plugin name
b9d2168
@stefanhahmann
Add unit tests
24313f4
@stefanhahmann
Add more unit tests in LabelOptionsTest and SegmentationTaskTest
ca70996
@stefanhahmann
Move SegmentUsingEllipsoidsView to UI package
11a00cb
@stefanhahmann
Extend LabelOptions by Track Id
0c9834a
@stefanhahmann
Remove implements Initializable from SegmentUsingEllipsoidsView
0f7ca13 
* Implementation is not need, since the view is not initialized
@stefanhahmann
Add track id as option in SegmentUsingEllipsoidsView
71e0533
@stefanhahmann
Change label for show result option
8ceaf22
@stefanhahmann
Add methods to get SpotTrackIdFeatureProjection to SegmentUsingEllips…
080c69e 
…oidsController
@stefanhahmann
Remove ImgSaver instance as class variable and add context instead
7aa38e6 
* context can be used to generate an ImgSaver object where needed
* trackIdProjection is also added as class variable
@stefanhahmann
Add separate method addBackground()
adbb2a4 
* the method takes care of adding the background to the exported images, if the respective option is active
@stefanhahmann
Add Write Lock to ModelGraph/ModelBranchGraph
2f68192 
* The intention is to prevent modifications while the segmentation is generated
@stefanhahmann
Rename variable labelOptions to labelOption
d216f16 
* Singular makes more sense here, since it as a specific option of the existing options
@stefanhahmann
Add the track id option to the getLabelId() method
c4420c2
@stefanhahmann
Add track id segmentation to unit test
e8be6cb
maarzt
maarzt previously approved these changes Sep 25, 2023
View reviewed changes
src/main/java/org/mastodon/mamut/segment/SegmentUsingEllipsoidsController.java Outdated Show resolved Hide resolved
src/main/java/org/mastodon/mamut/segment/SegmentUsingEllipsoidsController.java Outdated Show resolved Hide resolved
src/main/java/org/mastodon/mamut/segment/SegmentUsingEllipsoidsController.java Outdated Show resolved Hide resolved
src/main/java/org/mastodon/mamut/segment/SegmentUsingEllipsoidsController.java Outdated Show resolved Hide resolved
src/main/java/org/mastodon/mamut/segment/SegmentUsingEllipsoidsController.java Outdated Show resolved Hide resolved
src/main/java/org/mastodon/mamut/segment/SegmentUsingEllipsoidsController.java Outdated Show resolved Hide resolved
src/main/java/org/mastodon/mamut/segment/SegmentUsingEllipsoidsController.java Outdated Show resolved Hide resolved
src/main/java/org/mastodon/mamut/segment/SegmentByEllipsoidsPlugin.java Outdated Show resolved Hide resolved
@stefanhahmann
Rename slice to frame in saveEllipsoidSegmentationToFile() method
ff74605 
* the name "frame" is correct here, since a temporal "slice" is produced, not a spatial
@stefanhahmann
Remove unrequired cast.unchecked() call
67a40ab
@stefanhahmann
Use read lock instead of write lock while saving ellipsoid segmentati…
1890979 
…on to file

* A read lock is sufficient here, since this method does not write to the graph, but only reads it
@stefanhahmann
Rename getDimensionsSpimSource() to getDimensionsOfSource()
5a140f5 
* The new name would be more precise, since there is a generic source in the SegmentUsingEllipsoidsController, not a spim source
@stefanhahmann
Change debug message
ac6feb4
@stefanhahmann
Use only MamutAppModel and Context in public constructor of SegmentUs…
e2a46b2 
…ingEllipsoidsController
@stefanhahmann
Remove option to show segmentation in BDV
3636768
@stefanhahmann
Remove option to include intensity in the segmentation
28c08b4
@sonarcloud
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sonarcloud bot commented Sep 26, 2023

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

80.1% 80.1% Coverage
0.0% 0.0% Duplication

warning The version of Java (11.0.20) you have used to run this analysis is deprecated and we will stop accepting it soon. Please update to at least Java 17.
Read more here

@stefanhahmann stefanhahmann merged commit 8b4e871 into master Sep 26, 2023
4 checks passed
@stefanhahmann stefanhahmann deleted the segmentation branch September 28, 2023 16:10
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Export Label Image Using Spot Ellipsoids
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@stefanhahmann @maarzt