Duplicate Code: Shared Setup Logic in coordinates.ts Utility Functions

[github-actions]

Analysis of commit 846ffc9

Assignee: @copilot

Summary

Two duplication patterns were found in fidnii/src/utils/coordinates.ts:

1. normalizedToWorld / worldToNormalized share ~18 identical lines of axis-index setup and error-handling code.
2. clampPixelCoord / roundPixelCoord / floorPixelCoord / ceilPixelCoord all apply a single Math.* function element-wise to a [number, number, number] triple — 4 structurally identical functions totalling ~37 lines.

---

Duplication Details

Pattern 1 — Shared Axis-Index Setup in normalizedToWorld / worldToNormalized

• Severity: Medium
• Occurrences: 2
• Locations:
  • fidnii/src/utils/coordinates.ts lines 131–163 (normalizedToWorld)
  • fidnii/src/utils/coordinates.ts lines 173–207 (worldToNormalized)
• Duplicated block (~18 lines, identical in both functions):

const shape = ngffImage.data.shape
const dims = ngffImage.dims

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")
const dimZ = zIdx !== -1 ? shape[zIdx] : 1
const dimY = shape[yIdx]
const dimX = shape[xIdx]

Refactoring suggestion: Extract to a private helper, e.g.:

function getSpatialDims(ngffImage: NgffImage): {
  dimX: number; dimY: number; dimZ: number
} { ... }

Both normalizedToWorld and worldToNormalized call this helper and use the returned values.

---

Pattern 2 — Four Identical Element-Wise Pixel-Coordinate Mappers

• Severity: Low-Medium
• Occurrences: 4
• Locations:
  • fidnii/src/utils/coordinates.ts lines 216–225 (clampPixelCoord)
  • fidnii/src/utils/coordinates.ts lines 233–241 (roundPixelCoord)
  • fidnii/src/utils/coordinates.ts lines 249–257 (floorPixelCoord)
  • fidnii/src/utils/coordinates.ts lines 265–273 (ceilPixelCoord)
• Structural template (same for every function except the Math.* call):

export function (name)PixelCoord(
  pixelCoord: [number, number, number],
  // (clampPixelCoord also takes `shape` as a second param)
): [number, number, number] {
  return [
    Math.(op)(pixelCoord[0], ...),
    Math.(op)(pixelCoord[1], ...),
    Math.(op)(pixelCoord[2], ...),
  ]
}

Refactoring suggestion: Extract a generic helper:

function mapPixelCoord(
  pixelCoord: [number, number, number],
  fn: (v: number, i: number) => number,
): [number, number, number] {
  return [fn(pixelCoord[0], 0), fn(pixelCoord[1], 1), fn(pixelCoord[2], 2)]
}

Then each public function becomes a one-liner wrapper.

---

Impact Analysis

• Maintainability: Both patterns require parallel edits whenever the logic changes — for Pattern 1, any update to the axis-validation error message or default-z handling must be copied to both functions.
• Bug Risk: Inconsistent fixes are likely; a bug fix applied to one function may be missed in the other.
• Code Bloat: ~55 lines can be reduced to ~20 after refactoring.

---

Implementation Checklist

• Review duplication findings
• Extract getSpatialDims helper for normalizedToWorld / worldToNormalized
• Extract mapPixelCoord helper (or inline Array.from map) for the four element-wise functions
• Verify no behaviour change (existing Playwright tests cover these paths)
• Run bun run check to confirm linting passes

---

Analysis Metadata

• Analyzed Files: fidnii/src/utils/coordinates.ts (primary), fidnii/src/OMEZarrNVImage.ts, fidnii/src/ClipPlanes.ts, fidnii/src/utils/orientation.ts
• Detection Method: Serena semantic code analysis + pattern search
• Commit: 846ffc9ba09295d0427772a86fddb822b9d7d307
• Analysis Date: 2026-04-16

Generated by Duplicate Code Detector

To install this agentic workflow, run

gh aw add github/gh-aw/.github/workflows/duplicate-code-detector.md@33cd6c7f1fee588654ef19def2e6a4174be66197