/**
 * Image processing pure functions for thresholding, connected component
 * labeling, and other image operations.
 *
 * This module provides pure functions for image processing operations.
 * State management and WebGL operations remain in the Niivue class.
 *
 * @module ImageProcessing
 */

import { mat4, vec3, vec4 } from 'gl-matrix'
import { log } from '@/logger'
import { NiiDataType } from '@/nvimage'

// ============================================================================
// Types and Interfaces
// ============================================================================

/**
 * Parameters for binarizing a volume
 */
export interface BinarizeParams {
    img: ArrayLike<number>
    dims: number[]
}

/**
 * Result of binarizing a volume
 */
export interface BinarizeResult {
    img: Uint8Array
    datatypeCode: number
    cal_min: number
    cal_max: number
}

/**
 * Parameters for finding Otsu thresholds
 */
export interface FindOtsuParams {
    img: ArrayLike<number>
    cal_min: number
    cal_max: number
    scl_inter: number
    scl_slope: number
    mlevel?: number
}

/**
 * Parameters for applying Otsu thresholds to a drawing
 */
export interface ApplyOtsuParams {
    img: ArrayLike<number>
    drawBitmap: Uint8Array
    thresholds: number[]
}

/**
 * Parameters for removing haze from a volume
 */
export interface RemoveHazeParams {
    img: TypedArray
    scl_inter: number
    scl_slope: number
    global_min: number
    threshold: number
}

/**
 * Parameters for determining Otsu level based on removal level
 */
export interface GetOtsuLevelParams {
    level: number
}

/**
 * Parameters for determining threshold from Otsu thresholds based on level
 */
export interface GetHazeThresholdParams {
    level: number
    thresholds: number[]
}

/**
 * TypedArray type for image data
 */
export type TypedArray = Int8Array | Uint8Array | Uint8ClampedArray | Int16Array | Uint16Array | Int32Array | Uint32Array | Float32Array | Float64Array

/**
 * Dimensions object for 3D volumes
 */
export interface Dimensions3D {
    dimX: number
    dimY: number
    dimZ: number
}

/**
 * Parameters for connected component labeling
 */
export interface BwLabelParams {
    img: Uint32Array
    dim: Uint32Array
    conn?: number
    binarize?: boolean
    onlyLargestClusterPerClass?: boolean
}

/**
 * Result of connected component labeling
 */
export interface BwLabelResult {
    clusterCount: number
    labels: Uint32Array
}

/**
 * Internal result from initial labeling pass
 */
export interface InitialLabelingResult {
    labelCount: number
    translationTable: Uint32Array
    initialLabels: Uint32Array
}

/**
 * Internal result from label translation
 */
export interface TranslateLabelResult {
    clusterCount: number
    labels: Uint32Array
}

/**
 * Internal result from largest cluster extraction
 */
export interface LargestClusterResult {
    maxValue: number
    voxels: Uint32Array
}

// ============================================================================
// Binarization Functions
// ============================================================================

/**
 * Binarize a volume by converting all non-zero voxels to 1
 * @param params - Binarization parameters
 * @returns Binarized image data and updated header values
 */
export function binarize(params: BinarizeParams): BinarizeResult {
    const { img, dims } = params
    const vx = dims[1] * dims[2] * dims[3]
    const result = new Uint8Array(vx)

    for (let i = 0; i < vx; i++) {
        if (img[i] !== 0) {
            result[i] = 1
        }
    }

    return {
        img: result,
        datatypeCode: NiiDataType.DT_UINT8,
        cal_min: 0,
        cal_max: 1
    }
}

// ============================================================================
// Otsu Thresholding Functions
// ============================================================================

/**
 * Computes one or more Otsu threshold levels for a volume.
 * Returns raw intensity values corresponding to bin-based thresholds.
 *
 * Based on:
 * - C: https://github.com/rordenlab/niimath
 * - Java: https://github.com/stevenjwest/Multi_OTSU_Segmentation
 *
 * @param params - Otsu threshold parameters
 * @returns Array of threshold values (up to 3 values depending on mlevel)
 */
export function findOtsu(params: FindOtsuParams): number[] {
    const { img, cal_min, cal_max, scl_inter, scl_slope, mlevel = 2 } = params

    const nvox = img.length
    if (nvox < 1) {
        return []
    }

    const nBin = 256
    const maxBin = nBin - 1 // bins indexed from 0: if 256 bins then 0..255
    const h = new Array(nBin).fill(0)

    // Build 1D histogram
    const mn = cal_min
    const mx = cal_max
    if (mx <= mn) {
        return []
    }

    const scale2raw = (mx - mn) / nBin
    function bin2raw(bin: number): number {
        return bin * scale2raw + mn
    }

    const scale2bin = (nBin - 1) / Math.abs(mx - mn)

    for (let v = 0; v < nvox; v++) {
        let val = img[v] * scl_slope + scl_inter
        val = Math.min(Math.max(val, mn), mx)
        val = Math.round((val - mn) * scale2bin)
        h[val]++
    }

    // Build lookup tables P and S
    const P = Array(nBin)
        .fill(0)
        .map(() => Array(nBin).fill(0))
    const S = Array(nBin)
        .fill(0)
        .map(() => Array(nBin).fill(0))

    // Diagonal
    for (let i = 1; i < nBin; ++i) {
        P[i][i] = h[i]
        S[i][i] = i * h[i]
    }

    // Calculate first row (row 0 is all zero)
    for (let i = 1; i < nBin - 1; ++i) {
        P[1][i + 1] = P[1][i] + h[i + 1]
        S[1][i + 1] = S[1][i] + (i + 1) * h[i + 1]
    }

    // Using row 1 to calculate others
    for (let i = 2; i < nBin; i++) {
        for (let j = i + 1; j < nBin; j++) {
            P[i][j] = P[1][j] - P[1][i - 1]
            S[i][j] = S[1][j] - S[1][i - 1]
        }
    }

    // Now calculate H[i][j]
    for (let i = 1; i < nBin; ++i) {
        for (let j = i + 1; j < nBin; j++) {
            if (P[i][j] !== 0) {
                P[i][j] = (S[i][j] * S[i][j]) / P[i][j]
            }
        }
    }

    let max = 0
    const t = [Infinity, Infinity, Infinity]

    if (mlevel > 3) {
        for (let l = 0; l < nBin - 3; l++) {
            for (let m = l + 1; m < nBin - 2; m++) {
                for (let hIdx = m + 1; hIdx < nBin - 1; hIdx++) {
                    const v = P[0][l] + P[l + 1][m] + P[m + 1][hIdx] + P[hIdx + 1][maxBin]
                    if (v > max) {
                        t[0] = l
                        t[1] = m
                        t[2] = hIdx
                        max = v
                    }
                }
            }
        }
    } else if (mlevel === 3) {
        for (let l = 0; l < nBin - 2; l++) {
            for (let hIdx = l + 1; hIdx < nBin - 1; hIdx++) {
                const v = P[0][l] + P[l + 1][hIdx] + P[hIdx + 1][maxBin]
                if (v > max) {
                    t[0] = l
                    t[1] = hIdx
                    max = v
                }
            }
        }
    } else {
        for (let i = 0; i < nBin - 1; i++) {
            const v = P[0][i] + P[i + 1][maxBin]
            if (v > max) {
                t[0] = i
                max = v
            }
        }
    }

    return [bin2raw(t[0]), bin2raw(t[1]), bin2raw(t[2])]
}

/**
 * Apply Otsu thresholds to a drawing bitmap.
 * Voxels that are already marked in the drawing are preserved.
 *
 * @param params - Apply Otsu parameters
 * @returns Modified drawing bitmap
 */
export function applyOtsuToDrawing(params: ApplyOtsuParams): Uint8Array {
    const { img, drawBitmap, thresholds } = params
    const nvox = img.length
    const result = new Uint8Array(drawBitmap)

    for (let i = 0; i < nvox; i++) {
        if (result[i] !== 0) {
            continue
        }
        const v = img[i]
        if (v > thresholds[0]) {
            result[i] = 1
        }
        if (v > thresholds[1]) {
            result[i] = 2
        }
        if (v > thresholds[2]) {
            result[i] = 3
        }
    }

    return result
}

// ============================================================================
// Haze Removal Functions
// ============================================================================

/**
 * Determine the Otsu level based on the removal level
 * @param params - Parameters containing the level
 * @returns The Otsu level to use (2, 3, or 4)
 */
export function getOtsuLevelForHaze(params: GetOtsuLevelParams): number {
    const { level } = params
    if (level === 5 || level === 1) {
        return 4
    }
    if (level === 4 || level === 2) {
        return 3
    }
    return 2
}

/**
 * Determine the threshold value from Otsu thresholds based on level
 * @param params - Parameters containing level and thresholds
 * @returns The threshold value to use
 */
export function getHazeThreshold(params: GetHazeThresholdParams): number {
    const { level, thresholds } = params
    if (level === 1) {
        return thresholds[2]
    }
    if (level === 2) {
        return thresholds[1]
    }
    return thresholds[0]
}

/**
 * Apply haze removal to image data.
 * Voxels below the threshold are set to the global minimum value.
 *
 * @param params - Haze removal parameters
 */
export function applyHazeRemoval(params: RemoveHazeParams): void {
    const { img, scl_inter, scl_slope, global_min, threshold } = params
    const nvox = img.length

    for (let v = 0; v < nvox; v++) {
        const val = img[v] * scl_slope + scl_inter
        if (val < threshold) {
            img[v] = global_min
        }
    }
}

// ============================================================================
// Connected Component Labeling Functions
// ============================================================================

/**
 * Computes the linear voxel index from 3D coordinates using image dimensions.
 * @param a - X coordinate
 * @param b - Y coordinate
 * @param c - Z coordinate (slice)
 * @param dim - Dimensions array [dimX, dimY, dimZ]
 * @returns Linear index
 */
export function idx(a: number, b: number, c: number, dim: Uint32Array): number {
    return c * dim[0] * dim[1] + b * dim[0] + a
}

/**
 * Merges multiple provisional labels into a unified class using a translation table.
 * @param tt - Translation table
 * @param nabo - Neighbor labels array
 * @param nr_set - Number of neighbor labels
 */
export function fillTranslationTable(tt: Uint32Array, nabo: Uint32Array, nr_set: number): void {
    let cntr = 0
    const tn = new Uint32Array(nr_set + 5).fill(0)
    const INT_MAX = 2147483647
    let ltn = INT_MAX

    for (let i = 0; i < nr_set; i++) {
        let j = nabo[i]
        cntr = 0
        while (tt[j - 1] !== j) {
            j = tt[j - 1]
            cntr++
            if (cntr > 100) {
                log.info('\nOoh no!!')
                break
            }
        }
        tn[i] = j
        ltn = Math.min(ltn, j)
    }

    for (let i = 0; i < nr_set; i++) {
        tt[tn[i] - 1] = ltn
    }
}

/**
 * Checks if voxels below the given voxel have labels matching its value.
 * Returns the first matching label or 0.
 *
 * @param bw - Binary/label image
 * @param il - Initial labels image
 * @param r - Row (X coordinate)
 * @param c - Column (Y coordinate)
 * @param sl - Slice (Z coordinate)
 * @param dim - Dimensions array
 * @param conn - Connectivity (6, 18, or 26)
 * @param tt - Translation table
 * @returns First matching label or 0
 */
export function checkPreviousSlice(bw: Uint32Array, il: Uint32Array, r: number, c: number, sl: number, dim: Uint32Array, conn: number, tt: Uint32Array): number {
    const nabo = new Uint32Array(27)
    let nr_set = 0

    if (!sl) {
        return 0
    }

    const val = bw[idx(r, c, sl, dim)]

    if (conn >= 6) {
        const i = idx(r, c, sl - 1, dim)
        if (val === bw[i]) {
            nabo[nr_set++] = il[i]
        }
    }

    if (conn >= 18) {
        if (r) {
            const i = idx(r - 1, c, sl - 1, dim)
            if (val === bw[i]) {
                nabo[nr_set++] = il[i]
            }
        }
        if (c) {
            const i = idx(r, c - 1, sl - 1, dim)
            if (val === bw[i]) {
                nabo[nr_set++] = il[i]
            }
        }
        if (r < dim[0] - 1) {
            const i = idx(r + 1, c, sl - 1, dim)
            if (val === bw[i]) {
                nabo[nr_set++] = il[i]
            }
        }
        if (c < dim[1] - 1) {
            const i = idx(r, c + 1, sl - 1, dim)
            if (val === bw[i]) {
                nabo[nr_set++] = il[i]
            }
        }
    }

    if (conn === 26) {
        if (r && c) {
            const i = idx(r - 1, c - 1, sl - 1, dim)
            if (val === bw[i]) {
                nabo[nr_set++] = il[i]
            }
        }
        if (r < dim[0] - 1 && c) {
            const i = idx(r + 1, c - 1, sl - 1, dim)
            if (val === bw[i]) {
                nabo[nr_set++] = il[i]
            }
        }
        if (r && c < dim[1] - 1) {
            const i = idx(r - 1, c + 1, sl - 1, dim)
            if (val === bw[i]) {
                nabo[nr_set++] = il[i]
            }
        }
        if (r < dim[0] - 1 && c < dim[1] - 1) {
            const i = idx(r + 1, c + 1, sl - 1, dim)
            if (val === bw[i]) {
                nabo[nr_set++] = il[i]
            }
        }
    }

    if (nr_set) {
        fillTranslationTable(tt, nabo, nr_set)
        return nabo[0]
    } else {
        return 0
    }
}

/**
 * Performs provisional labeling of connected voxels in a volume using specified connectivity.
 *
 * @param bw - Binary/label image
 * @param dim - Dimensions array [dimX, dimY, dimZ]
 * @param conn - Connectivity (6, 18, or 26)
 * @returns Initial labeling result
 */
export function doInitialLabeling(bw: Uint32Array, dim: Uint32Array, conn: number): InitialLabelingResult {
    let label = 1
    const kGrowArrayBy = 8192
    let ttn = kGrowArrayBy
    let tt = new Uint32Array(ttn).fill(0)
    const il = new Uint32Array(dim[0] * dim[1] * dim[2]).fill(0)
    const nabo = new Uint32Array(27)

    for (let sl = 0; sl < dim[2]; sl++) {
        for (let c = 0; c < dim[1]; c++) {
            for (let r = 0; r < dim[0]; r++) {
                let nr_set = 0
                const val = bw[idx(r, c, sl, dim)]
                if (val === 0) {
                    continue
                }

                nabo[0] = checkPreviousSlice(bw, il, r, c, sl, dim, conn, tt)
                if (nabo[0]) {
                    nr_set += 1
                }

                if (conn >= 6) {
                    if (r) {
                        const i = idx(r - 1, c, sl, dim)
                        if (val === bw[i]) {
                            nabo[nr_set++] = il[i]
                        }
                    }
                    if (c) {
                        const i = idx(r, c - 1, sl, dim)
                        if (val === bw[i]) {
                            nabo[nr_set++] = il[i]
                        }
                    }
                }

                if (conn >= 18) {
                    if (c && r) {
                        const i = idx(r - 1, c - 1, sl, dim)
                        if (val === bw[i]) {
                            nabo[nr_set++] = il[i]
                        }
                    }
                    if (c && r < dim[0] - 1) {
                        const i = idx(r + 1, c - 1, sl, dim)
                        if (val === bw[i]) {
                            nabo[nr_set++] = il[i]
                        }
                    }
                }

                if (nr_set) {
                    il[idx(r, c, sl, dim)] = nabo[0]
                    fillTranslationTable(tt, nabo, nr_set)
                } else {
                    il[idx(r, c, sl, dim)] = label
                    if (label >= ttn) {
                        ttn += kGrowArrayBy
                        const ext = new Uint32Array(ttn)
                        ext.set(tt)
                        tt = ext
                    }
                    tt[label - 1] = label
                    label++
                }
            }
        }
    }

    // Flatten the translation table
    for (let i = 0; i < label - 1; i++) {
        let j = i
        while (tt[j] !== j + 1) {
            j = tt[j] - 1
        }
        tt[i] = j + 1
    }

    return {
        labelCount: label - 1,
        translationTable: tt,
        initialLabels: il
    }
}

/**
 * Removes gaps in label indices to produce a dense labeling.
 *
 * @param il - Initial labels image
 * @param dim - Dimensions array
 * @param tt - Translation table
 * @param ttn - Number of labels in translation table
 * @returns Translated labels result
 */
export function translateLabels(il: Uint32Array, dim: Uint32Array, tt: Uint32Array, ttn: number): TranslateLabelResult {
    const nvox = dim[0] * dim[1] * dim[2]
    let ml = 0
    const l = new Uint32Array(nvox).fill(0)

    for (let i = 0; i < ttn; i++) {
        ml = Math.max(ml, tt[i])
    }

    const fl = new Uint32Array(ml).fill(0)
    let cl = 0

    for (let i = 0; i < nvox; i++) {
        if (il[i]) {
            if (!fl[tt[il[i] - 1] - 1]) {
                cl += 1
                fl[tt[il[i] - 1] - 1] = cl
            }
            l[i] = fl[tt[il[i] - 1] - 1]
        }
    }

    return {
        clusterCount: cl,
        labels: l
    }
}

/**
 * Retains only the largest cluster for each region in a labeled volume.
 *
 * @param bw - Binary/label image
 * @param cl - Number of clusters
 * @param ls - Labels image
 * @returns Largest cluster result
 */
export function largestOriginalClusterLabels(bw: Uint32Array, cl: number, ls: Uint32Array): LargestClusterResult {
    const nvox = bw.length
    const ls2bw = new Uint32Array(cl + 1).fill(0)
    const sumls = new Uint32Array(cl + 1).fill(0)

    for (let i = 0; i < nvox; i++) {
        const bwVal = bw[i]
        const lsVal = ls[i]
        ls2bw[lsVal] = bwVal
        sumls[lsVal]++
    }

    let mxbw = 0
    for (let i = 0; i < cl + 1; i++) {
        const bwVal = ls2bw[i]
        mxbw = Math.max(mxbw, bwVal)
        // See if this is largest cluster of this bw-value
        for (let j = 0; j < cl + 1; j++) {
            if (j === i) {
                continue
            }
            if (bwVal !== ls2bw[j]) {
                continue
            }
            if (sumls[i] < sumls[j]) {
                ls2bw[i] = 0
            } else if (sumls[i] === sumls[j] && i < j) {
                ls2bw[i] = 0
            } // ties: arbitrary winner
        }
    }

    const vxs = new Uint32Array(nvox).fill(0)
    for (let i = 0; i < nvox; i++) {
        vxs[i] = ls2bw[ls[i]]
    }

    return {
        maxValue: mxbw,
        voxels: vxs
    }
}

/**
 * Computes connected components labeling on a 3D image.
 *
 * Port of https://github.com/rordenlab/niimath/blob/master/src/bwlabel.c
 *
 * @param params - Connected component labeling parameters
 * @returns Labeling result with cluster count and labels
 */
export function bwlabel(params: BwLabelParams): BwLabelResult {
    const { img, dim, conn = 26, binarize: shouldBinarize = false, onlyLargestClusterPerClass = false } = params

    const start = Date.now()
    const nvox = dim[0] * dim[1] * dim[2]
    const bw = new Uint32Array(nvox).fill(0)

    if (![6, 18, 26].includes(conn)) {
        log.info('bwlabel: conn must be 6, 18 or 26.')
        return { clusterCount: 0, labels: bw }
    }

    if (dim[0] < 2 || dim[1] < 2 || dim[2] < 1) {
        log.info('bwlabel: img must be 2 or 3-dimensional')
        return { clusterCount: 0, labels: bw }
    }

    if (shouldBinarize) {
        for (let i = 0; i < nvox; i++) {
            if (img[i] !== 0.0) {
                bw[i] = 1
            }
        }
    } else {
        bw.set(img)
    }

    let { labelCount: ttn, translationTable: tt, initialLabels: il } = doInitialLabeling(bw, dim, conn)
    if (tt === undefined) {
        tt = new Uint32Array()
    }

    const { clusterCount: cl, labels: ls } = translateLabels(il, dim, tt, ttn)
    log.info(conn + ' neighbor clustering into ' + cl + ' regions in ' + (Date.now() - start) + 'ms')

    if (onlyLargestClusterPerClass) {
        const { maxValue: nbw, voxels: bwMx } = largestOriginalClusterLabels(bw, cl, ls)
        return { clusterCount: nbw, labels: bwMx }
    }

    return { clusterCount: cl, labels: ls }
}

/**
 * Check if connectivity value is valid
 * @param conn - Connectivity value
 * @returns True if valid (6, 18, or 26)
 */
export function isValidConnectivity(conn: number): boolean {
    return [6, 18, 26].includes(conn)
}

/**
 * Check if dimensions are valid for bwlabel
 * @param dim - Dimensions array
 * @returns True if valid
 */
export function isValidDimensions(dim: Uint32Array): boolean {
    return dim[0] >= 2 && dim[1] >= 2 && dim[2] >= 1
}

// ============================================================================
// Conform Functions (FreeSurfer-style resampling)
// ============================================================================

/**
 * Parameters for computing intensity scale factors
 */
export interface GetScaleParams {
    img: ArrayLike<number>
    dims: number[]
    global_min: number
    global_max: number
    datatypeCode: number
    scl_slope: number
    scl_inter: number
    cal_min?: number
    cal_max?: number
    dst_min?: number
    dst_max?: number
    f_low?: number
    f_high?: number
}

/**
 * Parameters for conform voxel-to-voxel transform computation
 */
export interface ConformVox2VoxParams {
    inDims: number[]
    inAffine: number[]
    /** @deprecated Use outDims instead */
    outDim?: number
    /** Output dimensions [x, y, z]. If not specified, uses outDim for cubic output. */
    outDims?: [number, number, number]
    outMM?: number
    toRAS?: boolean
}

/**
 * Result of conform voxel-to-voxel transform computation
 */
export interface ConformVox2VoxResult {
    outAffine: mat4
    vox2vox: mat4
    invVox2vox: mat4
}

/**
 * Parameters for resampling a volume
 */
export interface ResampleVolumeParams {
    inImg: Float32Array
    inDims: number[]
    /** @deprecated Use outDims instead */
    outDim?: number
    /** Output dimensions [x, y, z]. If not specified, uses outDim for cubic output. */
    outDims?: [number, number, number]
    invVox2vox: mat4
    isLinear: boolean
}

/**
 * Scales and crops a Float32 image to Uint8 range.
 * @param img32 - Input Float32 image
 * @param dst_min - Destination minimum value (default 0)
 * @param dst_max - Destination maximum value (default 255)
 * @param src_min - Source minimum value for scaling
 * @param scale - Scale factor
 * @returns Scaled Uint8 image
 */
export function scalecropUint8(img32: Float32Array, dst_min: number = 0, dst_max: number = 255, src_min: number, scale: number): Uint8Array {
    const voxnum = img32.length
    const img8 = new Uint8Array(voxnum)
    for (let i = 0; i < voxnum; i++) {
        let val = img32[i]
        val = dst_min + scale * (val - src_min)
        val = Math.max(val, dst_min)
        val = Math.min(val, dst_max)
        img8[i] = val
    }
    return img8
}

/**
 * Scales and crops a Float32 image to a specified range.
 * @param img32 - Input Float32 image
 * @param dst_min - Destination minimum value (default 0)
 * @param dst_max - Destination maximum value (default 1)
 * @param src_min - Source minimum value for scaling
 * @param scale - Scale factor
 * @returns Scaled Float32 image
 */
export function scalecropFloat32(img32: Float32Array, dst_min: number = 0, dst_max: number = 1, src_min: number, scale: number): Float32Array {
    const voxnum = img32.length
    const img = new Float32Array(voxnum)
    for (let i = 0; i < voxnum; i++) {
        let val = img32[i]
        val = dst_min + scale * (val - src_min)
        val = Math.max(val, dst_min)
        val = Math.min(val, dst_max)
        img[i] = val
    }
    return img
}

/**
 * Computes offset and scale to robustly rescale image intensities to a target range.
 * Translation of FastSurfer conform.py (Apache License).
 * @param params - Scale computation parameters
 * @returns Tuple of [src_min, scale]
 */
export function getScale(params: GetScaleParams): [number, number] {
    const { img, dims, global_min, global_max, datatypeCode, scl_slope, scl_inter, cal_min, cal_max, dst_min = 0, dst_max = 255, f_low = 0.0, f_high = 0.999 } = params

    let src_min = global_min
    let src_max = global_max

    // For compatibility with conform.py: uint8 is not transformed
    if (datatypeCode === NiiDataType.DT_UINT8) {
        return [src_min, 1.0]
    }

    if (!isFinite(f_low) || !isFinite(f_high)) {
        if (isFinite(cal_min!) && isFinite(cal_max!) && cal_max! > cal_min!) {
            src_min = cal_min!
            src_max = cal_max!
            const scale = (dst_max - dst_min) / (src_max - src_min)
            log.info(' Robust Rescale:  min: ' + src_min + '  max: ' + src_max + ' scale: ' + scale)
            return [src_min, scale]
        }
    }

    const voxnum = dims[1] * dims[2] * dims[3]
    let scaledImg: Float32Array | ArrayLike<number> = img

    if (scl_slope !== 1.0 || scl_inter !== 0.0) {
        const newImg = new Float32Array(voxnum)
        for (let i = 0; i < voxnum; i++) {
            newImg[i] = img[i] * scl_slope + scl_inter
        }
        scaledImg = newImg
    }

    if (src_min < 0.0) {
        log.warn('WARNING: Input image has value(s) below 0.0 !')
    }

    log.info(' Input:    min: ' + src_min + '  max: ' + src_max)

    if (f_low === 0.0 && f_high === 1.0) {
        return [src_min, 1.0]
    }

    // Compute non-zeros and total vox num
    let nz = 0
    for (let i = 0; i < voxnum; i++) {
        if (Math.abs(scaledImg[i]) >= 1e-15) {
            nz++
        }
    }

    // Compute histogram
    const histosize = 1000
    const bin_size = (src_max - src_min) / histosize
    const hist = new Array(histosize).fill(0)
    for (let i = 0; i < voxnum; i++) {
        const val = scaledImg[i]
        let bin = Math.floor((val - src_min) / bin_size)
        bin = Math.min(bin, histosize - 1)
        hist[bin]++
    }

    // Compute cumulative sum
    const cs = new Array(histosize).fill(0)
    cs[0] = hist[0]
    for (let i = 1; i < histosize; i++) {
        cs[i] = cs[i - 1] + hist[i]
    }

    // Get lower limit
    let nth = Math.floor(f_low * voxnum)
    let idx = 0
    while (idx < histosize) {
        if (cs[idx] >= nth) {
            break
        }
        idx++
    }
    const global_min_saved = src_min
    src_min = idx * bin_size + global_min_saved

    // Get upper limit
    nth = voxnum - Math.floor((1.0 - f_high) * nz)
    idx = 0
    while (idx < histosize - 1) {
        if (cs[idx + 1] >= nth) {
            break
        }
        idx++
    }
    src_max = idx * bin_size + global_min_saved

    // Scale
    let scale = 1
    if (src_min !== src_max) {
        scale = (dst_max - dst_min) / (src_max - src_min)
    }

    log.info(' Rescale:  min: ' + src_min + '  max: ' + src_max + ' scale: ' + scale)
    return [src_min, scale]
}

/**
 * Computes output affine, voxel-to-voxel transform, and its inverse for resampling.
 * Translation of nibabel mghformat.py (MIT License) and FastSurfer conform.py (Apache License).
 * @param params - Voxel-to-voxel transform parameters
 * @returns Transform matrices
 */
export function conformVox2Vox(params: ConformVox2VoxParams): ConformVox2VoxResult {
    const { inDims, inAffine, outDim = 256, outDims, outMM = 1, toRAS = false } = params

    // Support both outDim (cubic) and outDims (non-cubic)
    const [outDimX, outDimY, outDimZ] = outDims ?? [outDim, outDim, outDim]

    const a = inAffine.flat()
    const affine = mat4.fromValues(a[0], a[1], a[2], a[3], a[4], a[5], a[6], a[7], a[8], a[9], a[10], a[11], a[12], a[13], a[14], a[15])
    const half = vec4.fromValues(inDims[1] / 2, inDims[2] / 2, inDims[3] / 2, 1)
    const Pxyz_c4 = vec4.create()
    const affineT = mat4.create()
    mat4.transpose(affineT, affine)
    vec4.transformMat4(Pxyz_c4, half, affineT)
    const Pxyz_c = vec3.fromValues(Pxyz_c4[0], Pxyz_c4[1], Pxyz_c4[2])

    // MGH format doesn't store the transform directly. Instead it's gleaned
    // from the zooms (delta), direction cosines (Mdc), RAS centers
    const delta = vec3.fromValues(outMM, outMM, outMM)
    let Mdc = mat4.fromValues(-1, 0, 0, 0, 0, 0, 1, 0, 0, -1, 0, 0, 0, 0, 0, 1)
    if (toRAS) {
        Mdc = mat4.fromValues(1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1)
    }
    mat4.transpose(Mdc, Mdc)

    const dims = vec4.fromValues(outDimX, outDimY, outDimZ, 1)
    const MdcD = mat4.create()
    mat4.scale(MdcD, Mdc, delta)

    const vol_center = vec4.fromValues(dims[0], dims[1], dims[2], 1)
    vec4.transformMat4(vol_center, vol_center, MdcD)
    vec4.scale(vol_center, vol_center, 0.5)

    const translate = vec3.create()
    vec3.subtract(translate, Pxyz_c, vec3.fromValues(vol_center[0], vol_center[1], vol_center[2]))

    const outAffine = mat4.create()
    mat4.transpose(outAffine, MdcD)
    outAffine[3] = translate[0]
    outAffine[7] = translate[1]
    outAffine[11] = translate[2]

    const invOutAffine = mat4.create()
    mat4.invert(invOutAffine, outAffine)

    const vox2vox = mat4.create()
    // Compute vox2vox from src to trg
    mat4.mul(vox2vox, affine, invOutAffine)

    // Compute inverse
    const invVox2vox = mat4.create()
    mat4.invert(invVox2vox, vox2vox)

    return { outAffine, vox2vox, invVox2vox }
}

/**
 * Resamples a volume using the given inverse voxel-to-voxel transform.
 * Supports both linear and nearest neighbor interpolation.
 * @param params - Resampling parameters
 * @returns Resampled volume as Float32Array
 */
export function resampleVolume(params: ResampleVolumeParams): Float32Array {
    const { inImg, inDims, outDim, outDims, invVox2vox, isLinear } = params

    // Support both outDim (cubic) and outDims (non-cubic)
    const [outDimX, outDimY, outDimZ] = outDims ?? [outDim ?? 256, outDim ?? 256, outDim ?? 256]

    const outNvox = outDimX * outDimY * outDimZ
    const outImg = new Float32Array(outNvox)

    const dimX = inDims[1]
    const dimY = inDims[2]
    const dimZ = inDims[3]
    const dimXY = dimX * dimY

    function voxidx(vx: number, vy: number, vz: number): number {
        return vx + vy * dimX + vz * dimXY
    }

    const inv0 = invVox2vox[0]
    const inv4 = invVox2vox[4]
    const inv8 = invVox2vox[8]

    let i = -1

    if (isLinear) {
        for (let z = 0; z < outDimZ; z++) {
            for (let y = 0; y < outDimY; y++) {
                // Loop hoisting
                const ixYZ = y * invVox2vox[1] + z * invVox2vox[2] + invVox2vox[3]
                const iyYZ = y * invVox2vox[5] + z * invVox2vox[6] + invVox2vox[7]
                const izYZ = y * invVox2vox[9] + z * invVox2vox[10] + invVox2vox[11]

                for (let x = 0; x < outDimX; x++) {
                    const ix = x * inv0 + ixYZ
                    const iy = x * inv4 + iyYZ
                    const iz = x * inv8 + izYZ

                    const fx = Math.floor(ix)
                    const fy = Math.floor(iy)
                    const fz = Math.floor(iz)

                    i++

                    if (fx < 0 || fy < 0 || fz < 0) {
                        continue
                    }

                    const cx = Math.ceil(ix)
                    const cy = Math.ceil(iy)
                    const cz = Math.ceil(iz)

                    if (cx >= dimX || cy >= dimY || cz >= dimZ) {
                        continue
                    }

                    // Residuals
                    const rcx = ix - fx
                    const rcy = iy - fy
                    const rcz = iz - fz
                    const rfx = 1 - rcx
                    const rfy = 1 - rcy
                    const rfz = 1 - rcz

                    const fff = voxidx(fx, fy, fz)
                    let vx = 0
                    vx += inImg[fff] * rfx * rfy * rfz
                    vx += inImg[fff + dimXY] * rfx * rfy * rcz
                    vx += inImg[fff + dimX] * rfx * rcy * rfz
                    vx += inImg[fff + dimX + dimXY] * rfx * rcy * rcz
                    vx += inImg[fff + 1] * rcx * rfy * rfz
                    vx += inImg[fff + 1 + dimXY] * rcx * rfy * rcz
                    vx += inImg[fff + 1 + dimX] * rcx * rcy * rfz
                    vx += inImg[fff + 1 + dimX + dimXY] * rcx * rcy * rcz
                    outImg[i] = vx
                }
            }
        }
    } else {
        // Nearest neighbor interpolation
        for (let z = 0; z < outDimZ; z++) {
            for (let y = 0; y < outDimY; y++) {
                // Loop hoisting
                const ixYZ = y * invVox2vox[1] + z * invVox2vox[2] + invVox2vox[3]
                const iyYZ = y * invVox2vox[5] + z * invVox2vox[6] + invVox2vox[7]
                const izYZ = y * invVox2vox[9] + z * invVox2vox[10] + invVox2vox[11]

                for (let x = 0; x < outDimX; x++) {
                    const ix = Math.round(x * inv0 + ixYZ)
                    const iy = Math.round(x * inv4 + iyYZ)
                    const iz = Math.round(x * inv8 + izYZ)

                    i++

                    if (ix < 0 || iy < 0 || iz < 0) {
                        continue
                    }

                    if (ix >= dimX || iy >= dimY || iz >= dimZ) {
                        continue
                    }

                    outImg[i] = inImg[voxidx(ix, iy, iz)]
                }
            }
        }
    }

    return outImg
}