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Draft: Refactor pipelines

Pierre Paleo requested to merge refactor_pipelines into master

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This MR is a refactoring of full-field pipelines (Chunked and Grouped).

Close #292 (closed)

To do

  • Proper inheritance scheme (close #288 (closed)) - use a base class
  • Simplify the implementation logic to be fairly understandable. For example callbacks might be obscure and should not be used by default (but can be used later for a plugin mechanism)
  • When using a "margin" mechanism, add an explicit "crop_radios" in the pipeline. Rename "margin" to "overlap" ?
  • Get rid of CudaChunkedPipelineLimitedMemory (close #262 (closed))
    • Adapt ChunkedReconstructor
  • GroupedPipeline should be able to do everything in-memory (don't dump to disk if it can be avoided)
  • Fix radios.get() for dumping data in GroupedPipeline
  • Adapt app.reconstruct
  • End-to-end reconstruction tests
Edited by Pierre Paleo

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