Feature/v2 enhanced analysis

[ezhil384]

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[eraser-labs]

fibermorph-architecture

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Updated as of commit: 69f15d48925b303c5c7ec8ea124f3bf4d3122eb1

Changed Files

Relevant Files

• fibermorph/main.py
• fibermorph/cli.py
• fibermorph/fibermorph.py
• fibermorph/workflows.py
• fibermorph/analysis/section_pipeline.py
• fibermorph/analysis/curvature_pipeline.py
• fibermorph/analysis/parallel.py
• fibermorph/io/readers.py
• fibermorph/io/writers.py
• fibermorph/io/converters.py
• fibermorph/core/section.py
• fibermorph/core/curvature.py
• fibermorph/core/filters.py
• fibermorph/processing/section_sam2.py
• fibermorph/core/shape_analysis.py
• fibermorph/pipeline/batch.py
• fibermorph/processing/binary.py
• fibermorph/processing/morphology.py
• fibermorph/processing/geometry.py
• fibermorph/utils/filesystem.py
• fibermorph/utils/metadata.py

Diagram Syntax

title CI Pipeline Workflow

// Define actors in order
Developer [icon: user, color: blue]
GitHub [icon: github]
CI Runner [icon: server, color: green]
Cache Service [icon: database, color: orange]
Test Environment [icon: tool, color: purple]
Artifact Storage [icon: archive, color: orange]

// Workflow begins
Developer > GitHub: Push code changes
activate Developer
GitHub > CI Runner: Trigger workflow

activate CI Runner
CI Runner > CI Runner: Checkout repository

// Setup phase
CI Runner > Cache Service: Check for cached dependencies
alt [label: cache exists, icon: check] {
  Cache Service > CI Runner: Return cached dependencies
}
else [label: cache miss, icon: x] {
  CI Runner > CI Runner: Install dependencies
  CI Runner > Cache Service: Store dependencies in cache
}

// Testing phase
par [label: run tests in parallel, icon: layers] {
  CI Runner > Test Environment: Run unit tests
  Test Environment --> CI Runner: Unit test results
}
and {
  CI Runner > Test Environment: Run integration tests
  Test Environment --> CI Runner: Integration test results
}

// Handle test results
alt [label: all tests pass, icon: check] {
  CI Runner > Artifact Storage: Upload build artifacts
  Artifact Storage --> CI Runner: Confirm upload
  CI Runner > GitHub: Report success status
  GitHub --> Developer: Notify success
}
else [label: tests fail, icon: x] {
  CI Runner > GitHub: Report failure status
  GitHub --> Developer: Notify failure
}

deactivate CI Runner
deactivate Developer

[ezhil384]

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