newsolver alignment pipeline v2 #167
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minnerbe
reviewed
Jan 8, 2024
...ark-client/src/main/java/org/janelia/render/client/spark/pipeline/AlignmentPipelineStep.java
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...k-client/src/main/java/org/janelia/render/client/spark/pipeline/AlignmentPipelineStepId.java
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...ient/src/main/java/org/janelia/render/client/spark/pipeline/AlignmentPipelineParameters.java
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...ient/src/main/java/org/janelia/render/client/spark/pipeline/AlignmentPipelineParameters.java
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.../src/test/java/org/janelia/render/client/spark/pipeline/AlignmentPipelineParametersTest.java
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.../src/test/java/org/janelia/render/client/spark/pipeline/AlignmentPipelineParametersTest.java
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...-ws-spark-client/src/main/java/org/janelia/render/client/spark/match/ClusterCountClient.java
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render-ws-spark-client/src/main/java/org/janelia/render/client/spark/match/CopyMatchClient.java
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...ient/src/main/java/org/janelia/render/client/spark/pipeline/AlignmentPipelineParameters.java
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...ient/src/main/java/org/janelia/render/client/spark/multisem/MFOVMontageMatchPatchClient.java
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I had a look at the latest commits (and your comments), they look very good to me. From my side, I think we can go ahead and merge this. |
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I started refactoring the spark alignment pipeline components to simplify future development. The first draft of the pipeline utilized a JSON configuration file in conjunction with a hard-coded ordering of components. This draft introduces an AlignmentPipelineStep interface that clarifies what a pipeline step must support and allows step ordering to be specified in the JSON configuration file.
If/when we are happy with this draft, the plan is to add intensity correction and thickness correction steps to the pipeline.
For review, I recommend starting by looking first at the AlignmentPipelineStep interface and how use of it simplifies the AlignmentPipelineClient. There is also an test/example JSON file that might be useful.