@fideus-labs/fidnii 0.1.0 → 0.2.0

package/src/utils/affine.ts

@@ -1,8 +1,8 @@
 // SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
 // SPDX-License-Identifier: MIT
 
-import { mat4 } from "gl-matrix";
-import type { NgffImage } from "@fideus-labs/ngff-zarr";
+import type { NgffImage } from "@fideus-labs/ngff-zarr"
+import { mat4 } from "gl-matrix"
 
 /**
  * Create a 4x4 affine transformation matrix from OME-Zarr scale and translation.
@@ -27,50 +27,50 @@ export function createAffineFromOMEZarr(
   scale: Record<string, number>,
   translation: Record<string, number>,
 ): mat4 {
-  const affine = mat4.create();
+  const affine = mat4.create()
 
   // NIfTI expects the matrix in a specific orientation
   // The affine maps from (i, j, k) voxel indices to (x, y, z) world coordinates
   // For OME-Zarr with [z, y, x] ordering, we need to handle the axis mapping
 
   // Extract scale and translation for each axis
-  const sx = scale.x ?? scale.X ?? 1;
-  const sy = scale.y ?? scale.Y ?? 1;
-  const sz = scale.z ?? scale.Z ?? 1;
+  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;
+  const tx = translation.x ?? translation.X ?? 0
+  const ty = translation.y ?? translation.Y ?? 0
+  const tz = translation.z ?? translation.Z ?? 0
 
   // Build affine matrix
   // NIfTI convention: first index (i) -> x, second (j) -> y, third (k) -> z
   // OME-Zarr stores data as [z, y, x], so we need to account for this
 
   // Column 0: x direction (from third array index in [z,y,x])
-  affine[0] = sx;
-  affine[1] = 0;
-  affine[2] = 0;
-  affine[3] = 0;
+  affine[0] = sx
+  affine[1] = 0
+  affine[2] = 0
+  affine[3] = 0
 
   // Column 1: y direction (from second array index in [z,y,x])
-  affine[4] = 0;
-  affine[5] = sy;
-  affine[6] = 0;
-  affine[7] = 0;
+  affine[4] = 0
+  affine[5] = sy
+  affine[6] = 0
+  affine[7] = 0
 
   // Column 2: z direction (from first array index in [z,y,x])
-  affine[8] = 0;
-  affine[9] = 0;
-  affine[10] = sz;
-  affine[11] = 0;
+  affine[8] = 0
+  affine[9] = 0
+  affine[10] = sz
+  affine[11] = 0
 
   // Column 3: translation
-  affine[12] = tx;
-  affine[13] = ty;
-  affine[14] = tz;
-  affine[15] = 1;
+  affine[12] = tx
+  affine[13] = ty
+  affine[14] = tz
+  affine[15] = 1
 
-  return affine;
+  return affine
 }
 
 /**
@@ -80,7 +80,7 @@ export function createAffineFromOMEZarr(
  * @returns 4x4 affine matrix
  */
 export function createAffineFromNgffImage(ngffImage: NgffImage): mat4 {
-  return createAffineFromOMEZarr(ngffImage.scale, ngffImage.translation);
+  return createAffineFromOMEZarr(ngffImage.scale, ngffImage.translation)
 }
 
 /**
@@ -91,9 +91,9 @@ export function createAffineFromNgffImage(ngffImage: NgffImage): mat4 {
  * @returns Object with srow_x, srow_y, srow_z arrays
  */
 export function affineToNiftiSrows(affine: mat4): {
-  srow_x: [number, number, number, number];
-  srow_y: [number, number, number, number];
-  srow_z: [number, number, number, number];
+  srow_x: [number, number, number, number]
+  srow_y: [number, number, number, number]
+  srow_z: [number, number, number, number]
 } {
   // gl-matrix uses column-major order
   // Row 0 (srow_x): elements 0, 4, 8, 12
@@ -103,7 +103,7 @@ export function affineToNiftiSrows(affine: mat4): {
     srow_x: [affine[0], affine[4], affine[8], affine[12]],
     srow_y: [affine[1], affine[5], affine[9], affine[13]],
     srow_z: [affine[2], affine[6], affine[10], affine[14]],
-  };
+  }
 }
 
 /**
@@ -114,11 +114,11 @@ export function affineToNiftiSrows(affine: mat4): {
  */
 export function getPixelDimensions(affine: mat4): [number, number, number] {
   // The pixel dimensions are the lengths of the column vectors
-  const dx = Math.sqrt(affine[0] ** 2 + affine[1] ** 2 + affine[2] ** 2);
-  const dy = Math.sqrt(affine[4] ** 2 + affine[5] ** 2 + affine[6] ** 2);
-  const dz = Math.sqrt(affine[8] ** 2 + affine[9] ** 2 + affine[10] ** 2);
+  const dx = Math.sqrt(affine[0] ** 2 + affine[1] ** 2 + affine[2] ** 2)
+  const dy = Math.sqrt(affine[4] ** 2 + affine[5] ** 2 + affine[6] ** 2)
+  const dz = Math.sqrt(affine[8] ** 2 + affine[9] ** 2 + affine[10] ** 2)
 
-  return [dx, dy, dz];
+  return [dx, dy, dz]
 }
 
 /**
@@ -137,33 +137,33 @@ export function updateAffineForRegion(
   regionStart: [number, number, number],
   scaleFactor: [number, number, number],
 ): mat4 {
-  const result = mat4.clone(originalAffine);
+  const result = mat4.clone(originalAffine)
 
   // Scale the voxel dimensions
   // Column 0 (x direction)
-  result[0] *= scaleFactor[2]; // x scale factor
-  result[1] *= scaleFactor[2];
-  result[2] *= scaleFactor[2];
+  result[0] *= scaleFactor[2] // x scale factor
+  result[1] *= scaleFactor[2]
+  result[2] *= scaleFactor[2]
 
   // Column 1 (y direction)
-  result[4] *= scaleFactor[1]; // y scale factor
-  result[5] *= scaleFactor[1];
-  result[6] *= scaleFactor[1];
+  result[4] *= scaleFactor[1] // y scale factor
+  result[5] *= scaleFactor[1]
+  result[6] *= scaleFactor[1]
 
   // Column 2 (z direction)
-  result[8] *= scaleFactor[0]; // z scale factor
-  result[9] *= scaleFactor[0];
-  result[10] *= scaleFactor[0];
+  result[8] *= scaleFactor[0] // z scale factor
+  result[9] *= scaleFactor[0]
+  result[10] *= scaleFactor[0]
 
   // Update translation for region offset
   // New origin = original_origin + regionStart * original_voxel_size
-  const originalPixelDims = getPixelDimensions(originalAffine);
+  const originalPixelDims = getPixelDimensions(originalAffine)
 
-  result[12] += regionStart[2] * originalPixelDims[0]; // x offset
-  result[13] += regionStart[1] * originalPixelDims[1]; // y offset
-  result[14] += regionStart[0] * originalPixelDims[2]; // z offset
+  result[12] += regionStart[2] * originalPixelDims[0] // x offset
+  result[13] += regionStart[1] * originalPixelDims[1] // y offset
+  result[14] += regionStart[0] * originalPixelDims[2] // z offset
 
-  return result;
+  return result
 }
 
 /**
@@ -178,7 +178,7 @@ export function calculateWorldBounds(
   dimensions: [number, number, number],
 ): { min: [number, number, number]; max: [number, number, number] } {
   // Calculate all 8 corners of the volume in world space
-  const [dimZ, dimY, dimX] = dimensions;
+  const [dimZ, dimY, dimX] = dimensions
   const corners = [
     [0, 0, 0],
     [dimX, 0, 0],
@@ -188,31 +188,31 @@ export function calculateWorldBounds(
     [dimX, 0, dimZ],
     [0, dimY, dimZ],
     [dimX, dimY, dimZ],
-  ];
+  ]
 
   let minX = Infinity,
     minY = Infinity,
-    minZ = Infinity;
+    minZ = Infinity
   let maxX = -Infinity,
     maxY = -Infinity,
-    maxZ = -Infinity;
+    maxZ = -Infinity
 
   for (const [i, j, k] of corners) {
     // Apply affine: world = affine * [i, j, k, 1]^T
-    const wx = affine[0] * i + affine[4] * j + affine[8] * k + affine[12];
-    const wy = affine[1] * i + affine[5] * j + affine[9] * k + affine[13];
-    const wz = affine[2] * i + affine[6] * j + affine[10] * k + affine[14];
-
-    minX = Math.min(minX, wx);
-    minY = Math.min(minY, wy);
-    minZ = Math.min(minZ, wz);
-    maxX = Math.max(maxX, wx);
-    maxY = Math.max(maxY, wy);
-    maxZ = Math.max(maxZ, wz);
+    const wx = affine[0] * i + affine[4] * j + affine[8] * k + affine[12]
+    const wy = affine[1] * i + affine[5] * j + affine[9] * k + affine[13]
+    const wz = affine[2] * i + affine[6] * j + affine[10] * k + affine[14]
+
+    minX = Math.min(minX, wx)
+    minY = Math.min(minY, wy)
+    minZ = Math.min(minZ, wz)
+    maxX = Math.max(maxX, wx)
+    maxY = Math.max(maxY, wy)
+    maxZ = Math.max(maxZ, wz)
   }
 
   return {
     min: [minX, minY, minZ],
     max: [maxX, maxY, maxZ],
-  };
+  }
 }

package/src/utils/coordinates.ts

@@ -1,8 +1,8 @@
 // SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
 // SPDX-License-Identifier: MIT
 
-import { mat4, vec4 } from "gl-matrix";
-import type { NgffImage } from "@fideus-labs/ngff-zarr";
+import type { NgffImage } from "@fideus-labs/ngff-zarr"
+import { mat4, vec4 } from "gl-matrix"
 
 /**
  * Convert a world coordinate to pixel indices.
@@ -15,26 +15,26 @@ export function worldToPixel(
   worldCoord: [number, number, number],
   ngffImage: NgffImage,
 ): [number, number, number] {
-  const scale = ngffImage.scale;
-  const translation = ngffImage.translation;
+  const scale = ngffImage.scale
+  const translation = ngffImage.translation
 
   // world = scale * pixel + translation
   // pixel = (world - translation) / scale
 
-  const sx = scale.x ?? scale.X ?? 1;
-  const sy = scale.y ?? scale.Y ?? 1;
-  const sz = scale.z ?? scale.Z ?? 1;
+  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;
+  const tx = translation.x ?? translation.X ?? 0
+  const ty = translation.y ?? translation.Y ?? 0
+  const tz = translation.z ?? translation.Z ?? 0
 
-  const px = (worldCoord[0] - tx) / sx;
-  const py = (worldCoord[1] - ty) / sy;
-  const pz = (worldCoord[2] - tz) / sz;
+  const px = (worldCoord[0] - tx) / sx
+  const py = (worldCoord[1] - ty) / sy
+  const pz = (worldCoord[2] - tz) / sz
 
   // Return in [z, y, x] order to match OME-Zarr array indexing
-  return [pz, py, px];
+  return [pz, py, px]
 }
 
 /**
@@ -48,25 +48,25 @@ export function pixelToWorld(
   pixelCoord: [number, number, number],
   ngffImage: NgffImage,
 ): [number, number, number] {
-  const scale = ngffImage.scale;
-  const translation = ngffImage.translation;
+  const scale = ngffImage.scale
+  const translation = ngffImage.translation
 
   // world = scale * pixel + translation
 
-  const sx = scale.x ?? scale.X ?? 1;
-  const sy = scale.y ?? scale.Y ?? 1;
-  const sz = scale.z ?? scale.Z ?? 1;
+  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;
+  const tx = translation.x ?? translation.X ?? 0
+  const ty = translation.y ?? translation.Y ?? 0
+  const tz = translation.z ?? translation.Z ?? 0
 
   // pixelCoord is [z, y, x]
-  const wx = sx * pixelCoord[2] + tx;
-  const wy = sy * pixelCoord[1] + ty;
-  const wz = sz * pixelCoord[0] + tz;
+  const wx = sx * pixelCoord[2] + tx
+  const wy = sy * pixelCoord[1] + ty
+  const wz = sz * pixelCoord[0] + tz
 
-  return [wx, wy, wz];
+  return [wx, wy, wz]
 }
 
 /**
@@ -81,20 +81,20 @@ export function worldToPixelAffine(
   affine: mat4,
 ): [number, number, number] {
   // Invert the affine to go from world to pixel
-  const inverseAffine = mat4.create();
-  mat4.invert(inverseAffine, affine);
+  const inverseAffine = mat4.create()
+  mat4.invert(inverseAffine, affine)
 
   const worldVec = vec4.fromValues(
     worldCoord[0],
     worldCoord[1],
     worldCoord[2],
     1,
-  );
-  const pixelVec = vec4.create();
-  vec4.transformMat4(pixelVec, worldVec, inverseAffine);
+  )
+  const pixelVec = vec4.create()
+  vec4.transformMat4(pixelVec, worldVec, inverseAffine)
 
   // Return in [z, y, x] order
-  return [pixelVec[2], pixelVec[1], pixelVec[0]];
+  return [pixelVec[2], pixelVec[1], pixelVec[0]]
 }
 
 /**
@@ -114,11 +114,11 @@ export function pixelToWorldAffine(
     pixelCoord[1], // y
     pixelCoord[0], // z
     1,
-  );
-  const worldVec = vec4.create();
-  vec4.transformMat4(worldVec, pixelVec, affine);
+  )
+  const worldVec = vec4.create()
+  vec4.transformMat4(worldVec, pixelVec, affine)
 
-  return [worldVec[0], worldVec[1], worldVec[2]];
+  return [worldVec[0], worldVec[1], worldVec[2]]
 }
 
 /**
@@ -132,24 +132,24 @@ export function normalizedToWorld(
   normalizedCoord: [number, number, number],
   ngffImage: NgffImage,
 ): [number, number, number] {
-  const shape = ngffImage.data.shape;
-  const dims = ngffImage.dims;
+  const shape = ngffImage.data.shape
+  const dims = ngffImage.dims
 
   // Find z, y, x indices in dims
-  const zIdx = dims.indexOf("z");
-  const yIdx = dims.indexOf("y");
-  const xIdx = dims.indexOf("x");
+  const zIdx = dims.indexOf("z")
+  const yIdx = dims.indexOf("y")
+  const xIdx = dims.indexOf("x")
 
-  let dimX: number, dimY: number, dimZ: number;
+  let dimX: number, dimY: number, dimZ: number
   if (zIdx === -1 || yIdx === -1 || xIdx === -1) {
-    const n = shape.length;
-    dimZ = shape[n - 3] || 1;
-    dimY = shape[n - 2] || 1;
-    dimX = shape[n - 1] || 1;
+    const n = shape.length
+    dimZ = shape[n - 3] || 1
+    dimY = shape[n - 2] || 1
+    dimX = shape[n - 1] || 1
   } else {
-    dimZ = shape[zIdx];
-    dimY = shape[yIdx];
-    dimX = shape[xIdx];
+    dimZ = shape[zIdx]
+    dimY = shape[yIdx]
+    dimX = shape[xIdx]
   }
 
   // Convert normalized to pixel
@@ -157,9 +157,9 @@ export function normalizedToWorld(
     normalizedCoord[2] * dimZ, // z
     normalizedCoord[1] * dimY, // y
     normalizedCoord[0] * dimX, // x
-  ];
+  ]
 
-  return pixelToWorld(pixelCoord, ngffImage);
+  return pixelToWorld(pixelCoord, ngffImage)
 }
 
 /**
@@ -173,35 +173,35 @@ export function worldToNormalized(
   worldCoord: [number, number, number],
   ngffImage: NgffImage,
 ): [number, number, number] {
-  const shape = ngffImage.data.shape;
-  const dims = ngffImage.dims;
+  const shape = ngffImage.data.shape
+  const dims = ngffImage.dims
 
   // Find z, y, x indices in dims
-  const zIdx = dims.indexOf("z");
-  const yIdx = dims.indexOf("y");
-  const xIdx = dims.indexOf("x");
+  const zIdx = dims.indexOf("z")
+  const yIdx = dims.indexOf("y")
+  const xIdx = dims.indexOf("x")
 
-  let dimX: number, dimY: number, dimZ: number;
+  let dimX: number, dimY: number, dimZ: number
   if (zIdx === -1 || yIdx === -1 || xIdx === -1) {
-    const n = shape.length;
-    dimZ = shape[n - 3] || 1;
-    dimY = shape[n - 2] || 1;
-    dimX = shape[n - 1] || 1;
+    const n = shape.length
+    dimZ = shape[n - 3] || 1
+    dimY = shape[n - 2] || 1
+    dimX = shape[n - 1] || 1
   } else {
-    dimZ = shape[zIdx];
-    dimY = shape[yIdx];
-    dimX = shape[xIdx];
+    dimZ = shape[zIdx]
+    dimY = shape[yIdx]
+    dimX = shape[xIdx]
   }
 
   // Convert world to pixel
-  const pixelCoord = worldToPixel(worldCoord, ngffImage);
+  const pixelCoord = worldToPixel(worldCoord, ngffImage)
 
   // Convert pixel to normalized
   return [
     pixelCoord[2] / dimX, // x normalized
     pixelCoord[1] / dimY, // y normalized
     pixelCoord[0] / dimZ, // z normalized
-  ];
+  ]
 }
 
 /**
@@ -219,7 +219,7 @@ export function clampPixelCoord(
     Math.max(0, Math.min(pixelCoord[0], shape[0] - 1)),
     Math.max(0, Math.min(pixelCoord[1], shape[1] - 1)),
     Math.max(0, Math.min(pixelCoord[2], shape[2] - 1)),
-  ];
+  ]
 }
 
 /**
@@ -235,7 +235,7 @@ export function roundPixelCoord(
     Math.round(pixelCoord[0]),
     Math.round(pixelCoord[1]),
     Math.round(pixelCoord[2]),
-  ];
+  ]
 }
 
 /**
@@ -251,7 +251,7 @@ export function floorPixelCoord(
     Math.floor(pixelCoord[0]),
     Math.floor(pixelCoord[1]),
     Math.floor(pixelCoord[2]),
-  ];
+  ]
 }
 
 /**
@@ -267,5 +267,5 @@ export function ceilPixelCoord(
     Math.ceil(pixelCoord[0]),
     Math.ceil(pixelCoord[1]),
     Math.ceil(pixelCoord[2]),
-  ];
+  ]
 }