Source Repository - anchor | Anchor Image Analysis

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Introduction

A Java (Maven) source repository on GitHub containing the main libraries used by Anchor.

What belongs?

Tip: It should include: frequently used utility classes, and key abstract base classes for plugins.

Warning: It should not include: plugins, pipeline BeanXML, entry-point applications.

Supporting libraries and tooling

A SonarCloud project performs static code analysis.
Project Lombok reduces boiler-plate source code. Please see key libraries for relevant libraries and tooling.
Coding style specifies the applicable style-guide.
GitHub Actions and Maven for CI/CD.

Modules

Module	Java Package Root & Description	Classes	Lines‑of‑Code
anchor-annotation	`org.anchoranalysis.annotation` Annotating images with shapes / labels.	5	160
anchor-annotation-io	`org.anchoranalysis.annotation.io` Reading / writing related to anchor-annotation	30	1,158
anchor-bean	`org.anchoranalysis.bean` Dependency injection framework and object-model.	99	3,153
anchor-beans-shared	`org.anchoranalysis.bean.shared` Generic reusable utility beans.	30	645
anchor-core	`org.anchoranalysis.core` Fundamental core library objects.	166	4,181
anchor-experiment	`org.anchoranalysis.experiment` Defines an experiment and how to execute it.	63	2,300
anchor-feature	`org.anchoranalysis.feature` Defines a feature generically and related utilities.	72	2,351
anchor-feature-io	`org.anchoranalysis.feature.io` Reading / writing related to anchor-feature	18	717
anchor-feature-session	`org.anchoranalysis.feature.session` Sessions to calculate many features optimally.	35	1,479
anchor-inference	`org.anchoranalysis.inference` High-level classes for performing machine learning model inference.	9	222
anchor-image-bean	`org.anchoranalysis.image.bean` Core (bean) data objects for images.	80	1,932
anchor-image-core	`org.anchoranalysis.image.core` Core (non-bean) data objects for images.	117	5,508
anchor-image-experiment	`org.anchoranalysis.image.experiment` Base classes for general tasks that involve images.	4	152
anchor-image-feature	`org.anchoranalysis.image.feature` Feature calculation on images or parts of images.	48	1,445
anchor-image-inference	`org.anchoranalysis.image.inference` Machine learning model inference on images.	18	775
anchor-image-io	`org.anchoranalysis.image.io` Reading / writing related to anchor-image	86	3,716
anchor-image-voxel	`org.anchoranalysis.image.voxel` Data objects for per-voxel manipulation of images.	230	10,195
anchor-imagej	`org.anchoranalysis.io.ij` Converters and IO that uses ImageJ.	11	656
anchor-inference	`org.anchoranalysis.inference` Performing machine learning model inference.	6	143
anchor-io-bioformats	`org.anchoranalysis.io.bioformats` Input / output that uses Bioformats.	37	1,510
anchor-io-generator	`org.anchoranalysis.io.generator` Generators for producing output.	35	1,325
anchor-io-input	`org.anchoranalysis.io.input` Collecting inputs (not image specific) for tasks/experiments.	46	1,372
anchor-io-output	`org.anchoranalysis.io.output` Output-manager and utilities for outputting.	72	2,042
anchor-math	`org.anchoranalysis.math` Mathematical algorithms or utility functions.	11	855
anchor-mpp	`org.anchoranalysis.mpp` Core data classes for Marked Point Processes	133	5,431
anchor-mpp-feature	`org.anchoranalysis.mpp.feature` Feature calculation on objects in anchor-mpp	46	2,247
anchor-mpp-io	`org.anchoranalysis.mpp.io` Input / output related to objects in anchor-mpp	29	1,5152
anchor-mpp-segment	`org.anchoranalysis.mpp.segment` Segmentation involving objects in anchor-mpp	64	1,867
anchor-overlay	`org.anchoranalysis.anchor.overlay` Graphics output of entities on top of a raster.	17	710
anchor-spatial	`org.anchoranalysis.spatial` Core geometry and spatial manipulation.	27	1,178
anchor-test	`org.anchoranalysis.test` Reusable test fixtures/utilities (at highest generality).	4	212
anchor-test-feature	`org.anchoranalysis.test.feature` Reusable test fixtures related to features.	1	60
anchor-test-image	`org.anchoranalysis.test.image` Reusable test fixtures related to images.	34	1,697
anchor-test-io-output	`org.anchoranalysis.test.io-output` Test fixtures related to non-image outputs.	1	33

Number of classes/code is as per SonarQube, October 18th, 2020. Lines-of-code excludes whitespace and comments.