Multi project classification #107

stefanhahmann · 2024-06-21T15:21:59Z

Resolves #101

maarzt

Awesome test coverage! Also very well implemented user feedback in the Classify Lineages dialog.

The PR adds new functionality to allow lineage classification for multiple mastodon projects. The new functionality is not trivial. Unfortunately this also leads to growing classes and methods. Which makes the PR hard to review, and very likely complicate code maintenance in the future. If possible please try to keep classes and methods small.

src/main/java/org/mastodon/mamut/classification/ClassifyLineagesPlugin.java

src/main/java/org/mastodon/mamut/classification/ClassifyLineagesController.java

src/main/java/org/mastodon/mamut/classification/util/Classification.java

src/test/java/org/mastodon/mamut/classification/ClassifyLineagesControllerTest.java

maarzt · 2024-07-04T21:28:07Z

src/main/java/org/mastodon/mamut/classification/ClassifyLineagesController.java

@@ -291,6 +419,73 @@ public void setVisualisationParams( final boolean showDendrogram )
 		this.showDendrogram = showDendrogram;
 	}

+	public void setExternalProjects( final File[] projects, final boolean addTagSetToExternalProjects )


I would recommend remove the ProjectSession, MastodonProjectService classes. They don't bring any advantage for the code. Instead I would recommend to add a class ExternalProjects which has this setExternalProjects(File[]) method, a close() method and probably some getter methods....

…nstead of a 2D array * By this in other parts of the code generics can be used better

…and updateFeedback()

…Controller

…Command

… classifyLineageTrees to method getDistanceMatrix()

…ller * This allows that this method can be called with any project model in the future * For backwards compatibility a getRoots() method with the project model of the controller is introduced

…odel in ClassifyLineagesController

* Allows passing different kinds of distance matrices to classify lineage trees

…eter

…eter annotation in the ClassifyLineagesPlugin

* Instead use temp copies of pre generated test models that are stored in files

…sifyLineagesController

…ableProject

sonarqubecloud · 2024-07-24T11:01:13Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
82.4% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

stefanhahmann self-assigned this Jun 21, 2024

stefanhahmann force-pushed the multi_project_classification branch 11 times, most recently from 1226a51 to 070bab3 Compare June 24, 2024 14:29

stefanhahmann requested a review from maarzt June 24, 2024 14:56

stefanhahmann force-pushed the multi_project_classification branch 2 times, most recently from 094e34f to 1b4eb25 Compare June 27, 2024 16:21

maarzt previously approved these changes Jul 4, 2024

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stefanhahmann dismissed maarzt’s stale review via 65344cc July 18, 2024 09:25

stefanhahmann added 6 commits July 18, 2024 12:10

Rename method getDistanceMatrix to getAverageDistanceMatrix

eabf5f8

Add a unit test to getAverageDistanceMatrix

e8d4e84

Make ClassificationUtils getAverageDistanceMatrix use List of Lists i…

65e45df

…nstead of a 2D array * By this in other parts of the code generics can be used better

Add some logging to getAverageDistanceMatrix method

0b6eced

Make methods getDistanceMatrix and getAverageDistanceMatrix more generic

26c66f9

Extract 2 new methods in the ClassifyLineagesCommand: updateParams() …

ecd5854

…and updateFeedback()

stefanhahmann force-pushed the multi_project_classification branch from 6275b5a to 217689b Compare July 18, 2024 10:10

stefanhahmann added 6 commits July 18, 2024 12:10

Add some missing final modifiers to method params in ClassifyLineages…

ac621e5

…Controller

Add the possibility to specify a list of projects to ClassifyLineages…

34b6460

…Command

Move time measurements logs for computing distance matrix from method…

84ac31c

… classifyLineageTrees to method getDistanceMatrix()

Add param ProjectModel to getRoots() method in ClassifyLineagesContro…

a783e50

…ller * This allows that this method can be called with any project model in the future * For backwards compatibility a getRoots() method with the project model of the controller is introduced

Rename model and projectModel to referenceModel and referenceProjectM…

add2091

…odel in ClassifyLineagesController

Pass distance matrix as param to method classifyLineageTrees()

114a200

* Allows passing different kinds of distance matrices to classify lineage trees

stefanhahmann added 4 commits July 18, 2024 12:10

Update scijava-common version to 2.99.1-SNAPSHOT

c2a7415

Override scijava-ui-swing version to 1.0.2

3faf6b1

Update heap size for tests to 3gb

217689b

Set log level to INFO in general and to DEBUG for org.mastodon.mamut

34887fc

stefanhahmann force-pushed the multi_project_classification branch from a0eedf3 to 34887fc Compare July 18, 2024 15:07

stefanhahmann added 3 commits July 18, 2024 17:18

Declare prefService and projectService as a private field with @param…

381dd82

…eter annotation in the ClassifyLineagesPlugin

Extract new method classifyUsingExternalProjects()

cceb23d

Rename method setVisualisationParams to setShowDendrogram

01eda6a

stefanhahmann force-pushed the multi_project_classification branch from 8287d82 to d26d428 Compare July 18, 2024 15:40

stefanhahmann added 3 commits July 18, 2024 17:40

Add hierarchical to the class javadoc of the classification class

d26d428

Refactor variable from expectedClassCount to expectedSpotsPerClass

8c0b872

Remove generation of test dataset from ClassifyLineagesControllerTest

e51b3a8

* Instead use temp copies of pre generated test models that are stored in files

stefanhahmann force-pushed the multi_project_classification branch from 7989e81 to e51b3a8 Compare July 19, 2024 13:53

stefanhahmann added 4 commits July 22, 2024 10:25

Refactor method openProjectSessionsCount to activeSessions()

ee9476a

Introduce new class ExternalProjects

193db41

Make constructor of ProjectSession package protected

cbcafba

Change methods runClassification and classifyExternalProjects in Clas…

83e35ca

…sifyLineagesController

stefanhahmann force-pushed the multi_project_classification branch from 9a1e8d3 to 83e35ca Compare July 23, 2024 07:19

Replace ProjectSession and MastodonProjectService by simpler Classifi…

eefe2fe

…ableProject

stefanhahmann force-pushed the multi_project_classification branch from 2df93d4 to ff76f59 Compare July 24, 2024 09:46

stefanhahmann added 7 commits July 24, 2024 11:46

Remove Dendrogram test from ClassifyLineagesControllerTest

ff76f59

Add name of current project to ClassifyLineagesCommand

de2a8dd

Change label of further projects parameter

180c3f6

Fix messages for crop start and end

52a4292

Ensure that only distinct projects are part of the analysis

4a3a94b

Ensure that current project is not added again as further project

96b09e5

Fix unit test bug

cdaf1f7

stefanhahmann merged commit 3b8a4b1 into master Jul 24, 2024
3 checks passed

stefanhahmann deleted the multi_project_classification branch September 2, 2024 10:13

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Multi project classification #107

Multi project classification #107

stefanhahmann commented Jun 21, 2024

maarzt left a comment •

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maarzt Jul 4, 2024

sonarqubecloud bot commented Jul 24, 2024

Multi project classification #107

Multi project classification #107

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stefanhahmann commented Jun 21, 2024

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maarzt Jul 4, 2024

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sonarqubecloud bot commented Jul 24, 2024

Quality Gate passed

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