Duplicate Code: Repeated Extraction Patterns in coordinates.ts

[github-actions]

Analysis of recent commits on main

Assignee: @copilot

Summary

Two structurally duplicated code blocks were found in fidnii/src/utils/coordinates.ts. Each block is copied verbatim into two functions, inflating the file and creating a risk of inconsistent edits.

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Duplication Details

Pattern 1 — Scale/Translation Extraction

• Severity: Low-Medium
• Occurrences: 2
• Locations:
  • fidnii/src/utils/coordinates.ts (lines 24–30, inside worldToPixel)
  • fidnii/src/utils/coordinates.ts (lines 56–62, inside pixelToWorld)

Duplicated block (identical in both functions):

const sx = scale.x ?? scale.X ?? 1
const sy = scale.y ?? scale.Y ?? 1
const sz = scale.z ?? scale.Z ?? 1

const tx = translation.x ?? translation.X ?? 0
const ty = translation.y ?? translation.Y ?? 0
const tz = translation.z ?? translation.Z ?? 0

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Pattern 2 — Spatial Dimension Index Lookup & Validation

• Severity: Medium
• Occurrences: 2
• Locations:
  • fidnii/src/utils/coordinates.ts (lines 138–154, inside normalizedToWorld)
  • fidnii/src/utils/coordinates.ts (lines 180–196, inside worldToNormalized)

Duplicated block (identical in both functions):

const yIdx = dims.indexOf("y")
const xIdx = dims.indexOf("x")

if (yIdx === -1 || xIdx === -1) {
  const missingAxes = [xIdx === -1 ? "x" : null, yIdx === -1 ? "y" : null]
    .filter((axis): axis is string => axis !== null)
    .join(", ")
  throw new Error(
    `NgffImage is missing required spatial dimension(s): \$\{missingAxes}`,
  )
}

// Look up spatial dimensions by name; default z to 1 for 2D images
const zIdx = dims.indexOf("z")
const dimZ = zIdx !== -1 ? shape[zIdx] : 1
const dimY = shape[yIdx]
const dimX = shape[xIdx]

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Impact Analysis

• Maintainability: Adding support for a new axis key convention (e.g. capitalised Z) in pattern 1 would require edits in two places. Changing the error message or 2D-fallback logic in pattern 2 similarly requires two edits.
• Bug Risk: Divergence between the two copies could silently produce inconsistent behaviour (e.g. different fallback values or missing axis names in error messages).
• Code Bloat: ~25 lines of redundant code in a 273-line file.

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Refactoring Recommendations

1. Extract getScaleTranslation(ngffImage) helper

function getScaleTranslation(ngffImage: NgffImage): {
  sx: number; sy: number; sz: number
  tx: number; ty: number; tz: number
} {
  const { scale, translation } = ngffImage
  return {
    sx: scale.x ?? scale.X ?? 1,
    sy: scale.y ?? scale.Y ?? 1,
    sz: scale.z ?? scale.Z ?? 1,
    tx: translation.x ?? translation.X ?? 0,
    ty: translation.y ?? translation.Y ?? 0,
    tz: translation.z ?? translation.Z ?? 0,
  }
}

Replace the duplicated blocks in worldToPixel and pixelToWorld with a single call to this helper.

2. Extract getSpatialDimensions(ngffImage) helper

function getSpatialDimensions(ngffImage: NgffImage): {
  dimX: number; dimY: number; dimZ: number
} {
  const { data: { shape }, dims } = ngffImage
  const yIdx = dims.indexOf("y")
  const xIdx = dims.indexOf("x")
  if (yIdx === -1 || xIdx === -1) {
    const missingAxes = [xIdx === -1 ? "x" : null, yIdx === -1 ? "y" : null]
      .filter((axis): axis is string => axis !== null)
      .join(", ")
    throw new Error(
      `NgffImage is missing required spatial dimension(s): \$\{missingAxes}`,
    )
  }
  const zIdx = dims.indexOf("z")
  return {
    dimZ: zIdx !== -1 ? shape[zIdx] : 1,
    dimY: shape[yIdx],
    dimX: shape[xIdx],
  }
}

Replace the duplicated blocks in normalizedToWorld and worldToNormalized with a single call to this helper.

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Implementation Checklist

• Review duplication findings
• Extract getScaleTranslation helper and update worldToPixel / pixelToWorld
• Extract getSpatialDimensions helper and update normalizedToWorld / worldToNormalized
• Verify TypeScript strict-mode compliance (noUnusedLocals, noUnusedParameters)
• Run bunx tsc --noEmit and bun run check to confirm no regressions
• Update/run existing Playwright tests to verify no behaviour change

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Analysis Metadata

• Analyzed Files: 14 TypeScript source files in fidnii/src/ and fidnii/src/utils/
• Detection Method: Serena semantic code analysis + pattern search
• Analysis Date: 2026-03-26

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