nirs4all-ui 0.1.16 → 0.2.0

package/dist/qualification/_chart.js

@@ -0,0 +1,30 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+/** Compact display of an engine number: 4 significant digits, exponent only outside [1e-4, 1e5). */
+export function fmt(value) {
+    if (value === null || value === undefined || !Number.isFinite(value))
+        return '—';
+    if (value === 0)
+        return '0';
+    const abs = Math.abs(value);
+    if (abs >= 1e5 || abs < 1e-4)
+        return value.toExponential(2);
+    return String(Number(value.toPrecision(4)));
+}
+export function pct(fraction) {
+    if (!Number.isFinite(fraction))
+        return '—';
+    const p = fraction * 100;
+    return `${p >= 10 || p === 0 ? p.toFixed(0) : p >= 1 ? p.toFixed(1) : p.toPrecision(2)} %`;
+}
+/** HTML tooltip anchored at a point of the SVG viewBox (percent placement, flips near edges). */
+export function ChartTooltip({ x, y, width, height, children }) {
+    const left = (x / width) * 100;
+    const top = (y / height) * 100;
+    const tx = left > 70 ? '-100%' : left < 30 ? '0%' : '-50%';
+    const ty = top < 30 ? '12px' : 'calc(-100% - 12px)';
+    return (_jsx("div", { className: "n4q-tip", role: "presentation", style: { left: `${left}%`, top: `${top}%`, transform: `translate(${tx}, ${ty})` }, children: children }));
+}
+export function TipRow({ color, label, value, line = false }) {
+    return (_jsxs("div", { className: "n4q-tip-row", children: [color ? _jsx("span", { className: line ? 'n4q-key-line' : 'n4q-key-dot', style: { background: color }, "aria-hidden": "true" }) : null, _jsx("strong", { children: value }), _jsx("span", { children: label })] }));
+}
+//# sourceMappingURL=_chart.js.map

package/dist/qualification/_chart.js.map

@@ -0,0 +1 @@
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package/dist/qualification/engineNumber.d.ts

@@ -0,0 +1,26 @@
+import type { Locale } from '../lab/locale.js';
+export declare const SCALED_REPRESENTATION = "significand_times_2_pow_exponent";
+export type EngineNumber = {
+    kind: 'double';
+    value: number;
+} | {
+    kind: 'scaled';
+    significand: number;
+    exponent: number;
+};
+/** Reads a plain finite number or a scaled `significand × 2^exponent` object; anything else is null. */
+export declare function parseEngineNumber(value: unknown): EngineNumber | null;
+/** True when the value is a scaled engine number (whatever its exponent). */
+export declare function isScaledEngineNumber(value: unknown): boolean;
+/** Double value when representable, else null (never ±Infinity, never NaN). */
+export declare function engineNumberToDouble(n: EngineNumber | null): number | null;
+/** Exact text of a scaled number, e.g. `−0,75 × 2¹¹⁰⁰`. */
+export declare function formatEngineNumberExact(n: EngineNumber, locale?: Locale): string;
+/**
+ * Display text: ordinary doubles with `digits` significant digits (exponent form outside
+ * [1e-4, 1e6)) and values beyond the double range as `m × 10^k` rounded from their exact
+ * decimal expansion (the exact `significand × 2^exponent` form is `formatEngineNumberExact`).
+ * Never NaN or Infinity.
+ */
+export declare function formatEngineNumber(value: unknown, locale?: Locale, digits?: number): string | null;
+//# sourceMappingURL=engineNumber.d.ts.map

package/dist/qualification/engineNumber.d.ts.map

@@ -0,0 +1 @@
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package/dist/qualification/engineNumber.js

@@ -0,0 +1,88 @@
+export const SCALED_REPRESENTATION = 'significand_times_2_pow_exponent';
+const isRecord = (v) => typeof v === 'object' && v !== null && !Array.isArray(v);
+/** Reads a plain finite number or a scaled `significand × 2^exponent` object; anything else is null. */
+export function parseEngineNumber(value) {
+    if (typeof value === 'number')
+        return Number.isFinite(value) ? { kind: 'double', value } : null;
+    if (!isRecord(value) || value.representation !== SCALED_REPRESENTATION)
+        return null;
+    const { significand, exponent } = value;
+    if (typeof significand !== 'number' || !Number.isFinite(significand) || typeof exponent !== 'number' || !Number.isInteger(exponent))
+        return null;
+    return exponent === 0 ? { kind: 'double', value: significand } : { kind: 'scaled', significand, exponent };
+}
+/** True when the value is a scaled engine number (whatever its exponent). */
+export function isScaledEngineNumber(value) {
+    return isRecord(value) && value.representation === SCALED_REPRESENTATION;
+}
+/** Double value when representable, else null (never ±Infinity, never NaN). */
+export function engineNumberToDouble(n) {
+    if (!n)
+        return null;
+    if (n.kind === 'double')
+        return n.value;
+    // Two steps so an exponent near the limits does not overflow before the significand scales it.
+    const half = Math.trunc(n.exponent / 2);
+    const v = n.significand * 2 ** half * 2 ** (n.exponent - half);
+    return Number.isFinite(v) && (v !== 0 || n.significand === 0) ? v : null;
+}
+const SUPERSCRIPT = { '-': '⁻', '0': '⁰', '1': '¹', '2': '²', '3': '³', '4': '⁴', '5': '⁵', '6': '⁶', '7': '⁷', '8': '⁸', '9': '⁹' };
+const sup = (k) => String(k).split('').map((c) => SUPERSCRIPT[c] ?? c).join('');
+const MINUS = '−';
+function decimal(m, digits, locale) {
+    return Number(m.toPrecision(digits)).toLocaleString(locale, { maximumSignificantDigits: digits });
+}
+/** Exact text of a scaled number, e.g. `−0,75 × 2¹¹⁰⁰`. */
+export function formatEngineNumberExact(n, locale = 'fr') {
+    if (n.kind === 'double')
+        return n.value.toLocaleString(locale, { maximumSignificantDigits: 17 });
+    const sign = n.significand < 0 ? MINUS : '';
+    return `${sign}${Math.abs(n.significand).toLocaleString(locale, { maximumSignificantDigits: 17 })} × 2${sup(n.exponent)}`;
+}
+/**
+ * Display text: ordinary doubles with `digits` significant digits (exponent form outside
+ * [1e-4, 1e6)) and values beyond the double range as `m × 10^k` rounded from their exact
+ * decimal expansion (the exact `significand × 2^exponent` form is `formatEngineNumberExact`).
+ * Never NaN or Infinity.
+ */
+export function formatEngineNumber(value, locale = 'fr', digits = 4) {
+    const n = parseEngineNumber(value);
+    if (!n)
+        return null;
+    const v = engineNumberToDouble(n);
+    if (v !== null) {
+        if (v === 0)
+            return '0';
+        const abs = Math.abs(v);
+        if (abs >= 1e-4 && abs < 1e6)
+            return decimal(v, digits, locale).replace('-', MINUS);
+        const k = Math.floor(Math.log10(abs));
+        const m = v / 10 ** k;
+        return `${decimal(m, digits, locale).replace('-', MINUS)} × 10${sup(k)}`;
+    }
+    // Out of the double range: |s| < 1 so s·2^53 is an exact integer and the decimal
+    // expansion of s·2^e = (s·2^53)·2^(e−53) is exact with BigInt (never s * 2**e, which overflows).
+    if (n.kind !== 'scaled' || n.significand === 0)
+        return '0';
+    return scientificFromDigits(exactDigits(n), n.significand < 0, digits, locale);
+}
+/** Decimal digits of |significand × 2^exponent| for exponent ≥ 53 (exact). */
+function exactDigits(n) {
+    const scaled = BigInt(Math.abs(n.significand) * 2 ** 53);
+    return (n.exponent >= 53 ? scaled * 2n ** BigInt(n.exponent - 53) : scaled >> BigInt(53 - n.exponent)).toString();
+}
+/** `m × 10^k` from an exact digit string, rounded half up to `digits` significant digits. */
+function scientificFromDigits(d, negative, digits, locale) {
+    let k = d.length - 1;
+    let head = d.slice(0, digits).padEnd(digits, '0');
+    if ((d[digits] ?? '0') >= '5') {
+        head = (BigInt(head) + 1n).toString();
+        if (head.length > digits) {
+            head = head.slice(0, digits);
+            k += 1;
+        }
+    }
+    const m = Number(`${head[0]}.${head.slice(1)}`);
+    return `${negative ? MINUS : ''}${m.toLocaleString(locale, { maximumSignificantDigits: digits })} × 10${sup(k)}`;
+}
+//# sourceMappingURL=engineNumber.js.map

package/dist/qualification/engineNumber.js.map

@@ -0,0 +1 @@
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package/dist/qualification/extract.d.ts

@@ -0,0 +1,107 @@
+import type { QualificationMetricView, QualificationReportView } from './types.js';
+/** First computed metric matching id (and source/target when given). */
+export declare function findComputed(view: QualificationReportView, id: string, where?: {
+    sourceId?: string | null;
+    targetId?: string | null;
+}): QualificationMetricView | null;
+/** Numeric engine value of a computed metric, or null. */
+export declare function computedNumber(view: QualificationReportView, id: string, where?: {
+    sourceId?: string | null;
+    targetId?: string | null;
+}): number | null;
+/** Distinct source / target ids that appear in metrics, in report order. */
+export declare function reportSourceIds(view: QualificationReportView): string[];
+export declare function reportTargetIds(view: QualificationReportView): string[];
+export interface SamplePopulations {
+    developmentReal: number | null;
+    retainedTest: number | null;
+    augmentedExcluded: number | null;
+}
+export declare function extractSamplePopulations(view: QualificationReportView): SamplePopulations;
+/** Observation accounting of one source, from integrity + structure denominators. */
+export interface ObservationFlow {
+    sourceId: string;
+    sourceObservations: number;
+    developmentObservations: number;
+    excludedAmbiguousRepeat: number;
+    excludedIncomplete: number;
+    excludedMulticontext: number;
+    /** aggregated structure units (null when the structure eligibility metric is absent) */
+    structureUnits: number | null;
+}
+export declare function extractObservationFlow(view: QualificationReportView, sourceId: string): ObservationFlow | null;
+export interface IntegritySummary {
+    missingCells: number | null;
+    totalCells: number | null;
+    axisOrder: string | null;
+    physicalDuplicatePairs: number | null;
+    partitionDuplicatePairs: number | null;
+}
+export declare function extractIntegrity(view: QualificationReportView, sourceId: string): IntegritySummary;
+/** One repeatability context (repeat type × instrument × campaign) with its paired ICC. */
+export interface RepeatabilityContext {
+    id: string;
+    repeatType: string | null;
+    instrument: string | null;
+    campaign: string | null;
+    unit: string | null;
+    pooledSd: (number | null)[];
+    icc: (number | null)[] | null;
+    /** engine band status: 0 computed, 1 insufficient, 2 unbalanced, 3 zero total variance */
+    bandStatus: number[];
+    observations: number | null;
+    physicalGroups: number | null;
+    /** engine interval bands of the SD / ICC (see `withRepeatabilityUncertainty`) */
+    sdInterval?: {
+        lower: readonly (number | null)[];
+        upper: readonly (number | null)[];
+    } | null;
+    iccInterval?: {
+        lower: readonly (number | null)[];
+        upper: readonly (number | null)[];
+    } | null;
+    /** which ICC the `icc` series is: balanced ICC(1,1) (default) or REML ICC(1) */
+    iccKind?: 'icc_1_1' | 'icc_1_reml';
+}
+/** Computed repeatability contexts of a source; each ICC metric is emitted right after its SD metric. */
+export declare function extractRepeatability(view: QualificationReportView, sourceId: string): RepeatabilityContext[];
+export interface PcaStructure {
+    sourceId: string;
+    viewId: string;
+    sampleIds: string[];
+    aggregationKeys: string[];
+    scores: number[][];
+    eigenvalues: number[] | null;
+    /** trace of the full centered covariance (sum of all eigenvalues), when reported */
+    totalVariance: number | null;
+    retainedFraction: number | null;
+    effectiveDimension: number | null;
+}
+export declare function extractPca(view: QualificationReportView, sourceId: string): PcaStructure | null;
+/** Engine (Methods) summary of a continuous target. */
+export interface ContinuousSummary {
+    count: number;
+    min: number;
+    q25: number;
+    median: number;
+    q75: number;
+    max: number;
+    mean: number;
+    sampleSd: number | null;
+}
+export interface TargetOverview {
+    targetId: string;
+    unit: string | null;
+    eligible: number | null;
+    denominators: Readonly<Record<string, number>>;
+    summary: ContinuousSummary | null;
+    classCounts: Record<string, number> | null;
+    /** local X→Y contrast per source, when computed */
+    localContrast: {
+        sourceId: string | null;
+        value: number;
+        k: number | null;
+    }[];
+}
+export declare function extractTarget(view: QualificationReportView, targetId: string): TargetOverview;
+//# sourceMappingURL=extract.d.ts.map

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package/dist/qualification/extract.js

@@ -0,0 +1,139 @@
+const isNumber = (v) => typeof v === 'number' && Number.isFinite(v);
+const isNullableNumberArray = (v) => Array.isArray(v) && v.every((x) => x === null || isNumber(x));
+const isNumberArray = (v) => Array.isArray(v) && v.every(isNumber);
+const isRecord = (v) => typeof v === 'object' && v !== null && !Array.isArray(v);
+/** First computed metric matching id (and source/target when given). */
+export function findComputed(view, id, where = {}) {
+    return view.metrics.find((m) => m.id === id
+        && m.status === 'computed'
+        && (where.sourceId === undefined || m.sourceId === where.sourceId)
+        && (where.targetId === undefined || m.targetId === where.targetId)) ?? null;
+}
+/** Numeric engine value of a computed metric, or null. */
+export function computedNumber(view, id, where = {}) {
+    const value = findComputed(view, id, where)?.value;
+    return isNumber(value) ? value : null;
+}
+/** Distinct source / target ids that appear in metrics, in report order. */
+export function reportSourceIds(view) {
+    return [...new Set(view.metrics.flatMap((m) => (m.sourceId === null ? [] : [m.sourceId])))];
+}
+export function reportTargetIds(view) {
+    return [...new Set(view.metrics.flatMap((m) => (m.targetId === null ? [] : [m.targetId])))];
+}
+export function extractSamplePopulations(view) {
+    return {
+        developmentReal: computedNumber(view, 'population.development_real_samples'),
+        retainedTest: computedNumber(view, 'population.retained_test_samples'),
+        augmentedExcluded: computedNumber(view, 'population.augmented_samples_excluded'),
+    };
+}
+export function extractObservationFlow(view, sourceId) {
+    const dev = findComputed(view, 'integrity.development_observations', { sourceId });
+    const total = dev?.denominators.n_observations_source;
+    if (!dev || !isNumber(dev.value) || !isNumber(total))
+        return null;
+    const eligible = findComputed(view, 'structure.eligible_samples', { sourceId });
+    const d = eligible?.denominators ?? {};
+    return {
+        sourceId,
+        sourceObservations: total,
+        developmentObservations: dev.value,
+        excludedAmbiguousRepeat: d.n_excluded_ambiguous_repeat_observations ?? 0,
+        excludedIncomplete: d.n_excluded_incomplete_observations ?? 0,
+        excludedMulticontext: d.n_excluded_multicontext_observations ?? 0,
+        structureUnits: eligible && isNumber(eligible.value) ? eligible.value : null,
+    };
+}
+export function extractIntegrity(view, sourceId) {
+    const missing = findComputed(view, 'integrity.missing_cells', { sourceId });
+    const axis = findComputed(view, 'integrity.axis_order', { sourceId })?.value;
+    return {
+        missingCells: missing && isNumber(missing.value) ? missing.value : null,
+        totalCells: missing?.denominators.n_cells ?? null,
+        axisOrder: typeof axis === 'string' ? axis : null,
+        physicalDuplicatePairs: computedNumber(view, 'integrity.cross_physical_exact_duplicate_pairs', { sourceId }),
+        partitionDuplicatePairs: computedNumber(view, 'integrity.cross_partition_exact_duplicate_pairs', { sourceId }),
+    };
+}
+const BAND_STATUS_KEY = 'band_status_0_icc_1_insufficient_2_unbalanced_3_zero_total';
+const str = (v) => (typeof v === 'string' ? v : null);
+/** Computed repeatability contexts of a source; each ICC metric is emitted right after its SD metric. */
+export function extractRepeatability(view, sourceId) {
+    const out = [];
+    const metrics = view.metrics;
+    metrics.forEach((m, i) => {
+        if (m.id !== 'measurement.repeatability_sd' || m.sourceId !== sourceId || m.status !== 'computed' || !isNullableNumberArray(m.value))
+            return;
+        const next = metrics[i + 1];
+        const icc = next && next.id === 'measurement.icc_1_1' && next.sourceId === sourceId && next.status === 'computed' && isNullableNumberArray(next.value) ? next.value : null;
+        const p = m.parameters;
+        const status = p[BAND_STATUS_KEY];
+        const parts = [str(p.repeat_type), str(p.instrument), str(p.campaign)].filter((x) => x !== null);
+        out.push({
+            id: parts.join(' · ') || `${sourceId}#${out.length + 1}`,
+            repeatType: str(p.repeat_type),
+            instrument: str(p.instrument),
+            campaign: str(p.campaign),
+            unit: m.unit,
+            pooledSd: m.value,
+            icc,
+            bandStatus: isNumberArray(status) ? status : m.value.map((v) => (v === null ? 1 : 0)),
+            observations: m.denominators.n_observations ?? null,
+            physicalGroups: m.denominators.n_physical_groups ?? null,
+        });
+    });
+    return out;
+}
+export function extractPca(view, sourceId) {
+    const scores = findComputed(view, 'structure.pca_scores', { sourceId });
+    const v = scores?.value;
+    if (!scores || !isRecord(v) || !Array.isArray(v.sample_ids) || !Array.isArray(v.scores))
+        return null;
+    const rows = v.scores.filter(isNumberArray);
+    if (rows.length !== v.sample_ids.length)
+        return null;
+    const eig = findComputed(view, 'structure.pca_eigenvalues', { sourceId })?.value;
+    const moments = findComputed(view, 'structure.full_variance_moments', { sourceId })?.value;
+    return {
+        sourceId,
+        viewId: scores.viewId,
+        sampleIds: v.sample_ids.map(String),
+        aggregationKeys: Array.isArray(v.aggregation_keys) ? v.aggregation_keys.map(String) : [],
+        scores: rows,
+        eigenvalues: isNumberArray(eig) ? eig : null,
+        totalVariance: isRecord(moments) && isNumber(moments.sum_eigenvalues) ? moments.sum_eigenvalues : null,
+        retainedFraction: computedNumber(view, 'structure.explained_variance_retained', { sourceId }),
+        effectiveDimension: computedNumber(view, 'structure.effective_dimension', { sourceId }),
+    };
+}
+export function extractTarget(view, targetId) {
+    const eligible = findComputed(view, 'target.exact_eligible_samples', { targetId });
+    const dist = findComputed(view, 'target.continuous_distribution', { targetId });
+    const classes = findComputed(view, 'target.class_counts', { targetId })?.value;
+    const s = dist?.value;
+    const summary = isRecord(s) && ['count', 'min', 'q25', 'median', 'q75', 'max', 'mean'].every((k) => isNumber(s[k]))
+        ? {
+            count: s.count,
+            min: s.min,
+            q25: s.q25,
+            median: s.median,
+            q75: s.q75,
+            max: s.max,
+            mean: s.mean,
+            sampleSd: isNumber(s.sample_sd) ? s.sample_sd : null,
+        }
+        : null;
+    return {
+        targetId,
+        unit: dist?.unit ?? null,
+        eligible: eligible && isNumber(eligible.value) ? eligible.value : null,
+        denominators: eligible?.denominators ?? {},
+        summary,
+        classCounts: isRecord(classes) && Object.values(classes).every(isNumber) ? classes : null,
+        localContrast: view.metrics
+            .filter((m) => m.id === 'local.global_contrast' && m.targetId === targetId && m.status === 'computed' && isNumber(m.value))
+            .map((m) => ({ sourceId: m.sourceId, value: m.value, k: isNumber(m.parameters.k) ? m.parameters.k : null })),
+    };
+}
+//# sourceMappingURL=extract.js.map

package/dist/qualification/extract.js.map

@@ -0,0 +1 @@
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