@graphty/graph-io 0.3.47 → 0.3.49

package/dist/obo.js

@@ -1,4 +1,4 @@
-import { O, a, b, o, c } from "./chunks/exporter--Mk9gXCJ.js";
+import { O, a, b, o, c } from "./chunks/exporter-BP6otMO6.js";
 export {
   O as OBO_CAPABILITIES,
   a as OBO_ISSUE,

package/dist/pajek.js

@@ -1,4 +1,4 @@
-import { P, a, b, c, p, d } from "./chunks/importer-e6LGpqHB.js";
+import { P, a, b, c, p, d } from "./chunks/importer-vRq4h3j5.js";
 export {
   P as PAJEK_ISSUE,
   a as PAJEK_LOSS,

package/dist/positions.js

@@ -1,5 +1,5 @@
-import { t as toNeutral, m as median } from "./chunks/convert-BcQ8_jMo.js";
-import { f, a, w } from "./chunks/convert-BcQ8_jMo.js";
+import { t as toNeutral, m as median } from "./chunks/convert-Ct2zelbQ.js";
+import { f, a, w } from "./chunks/convert-Ct2zelbQ.js";
 import { t as toolOf } from "./chunks/units-XMZFIFe1.js";
 const POSITION_ISSUE = Object.freeze({
   /** Every placed node sits on one point; the coordinates are dropped and `usable` is false. */
@@ -88,6 +88,11 @@ function extractPositions(importer, snapshot, report, options = {}) {
   const coords = readRows(n, spelling, notes);
   signal?.throwIfAborted();
   const containers = containersOf(snapshot);
+  if (spelling.extra.containersFollowChildren === true) {
+    for (const row of containers) {
+      coords.values.fill(Number.NaN, 3 * row, 3 * row + 3);
+    }
+  }
   const groups = applyGroups(spelling, coords);
   collectGroups(spelling, coords, containers, groups);
   const { placed, total } = countPlaced(coords, containers, notes);
@@ -103,6 +108,7 @@ function extractPositions(importer, snapshot, report, options = {}) {
     },
     units: spelling.extra.units ?? "file",
     ...spelling.extra.pxPerUnit === void 0 ? {} : { pxPerUnit: spelling.extra.pxPerUnit },
+    ...spelling.extra.viewerFit === void 0 ? {} : { viewerFit: spelling.extra.viewerFit },
     medianNodeSize: spelling.medianNodeSize ?? medianSize(spelling.size, n, containers),
     dims: coords.realZ ? 3 : 2,
     coords: coords.values,
@@ -121,11 +127,27 @@ function spellingOf(importer, snapshot, signal) {
   }
   const column = hook?.column === void 0 ? snapshot.nodes.byRole("position") : snapshot.nodes.get(hook.column);
   if (column === null || column.meta.components < 2) {
-    return null;
+    return hook?.unplacedCircle === void 0 ? null : circleSpelling(snapshot, hook);
   }
   const extra = { ...extraOf(column.meta.extra), ...extraOf(hook ?? {}) };
   return { read: vectorReader(column), size: sizeReader(snapshot, extra), extra, ...hookFields(hook) };
 }
+function circleSpelling(snapshot, hook) {
+  const circle = hook.unplacedCircle;
+  const n = snapshot.nodeCount;
+  const read = (row, out) => {
+    if (circle === void 0 || n === 0) {
+      return false;
+    }
+    const a2 = (circle.startDegrees + circle.direction * 360 * row / n) * Math.PI / 180;
+    out[0] = circle.center[0] + circle.radius * Math.cos(a2);
+    out[1] = circle.center[1] + circle.radius * Math.sin(a2);
+    out[2] = 0;
+    return true;
+  };
+  const extra = { ...extraOf(hook), sourceDims: 2 };
+  return { read, size: sizeReader(snapshot, extra), extra, ...hookFields(hook) };
+}
 function plainSpelling(snapshot, hook) {
   const x = snapshot.nodes.get(hook.x ?? "");
   const y = snapshot.nodes.get(hook.y ?? "");
@@ -175,8 +197,15 @@ function extraOf(source) {
   pick("width", (v) => typeof v === "string");
   pick("height", (v) => typeof v === "string");
   pick("pxPerUnit", (v) => typeof v === "number" && Number.isFinite(v) && v > 0);
+  pick("pxPerUnitY", (v) => typeof v === "number" && Number.isFinite(v) && v > 0);
   pick("zOrigin", (v) => typeof v === "number" && Number.isFinite(v));
   pick("zeroUnplaced", (v) => typeof v === "boolean");
+  pick("originUnplaced", (v) => typeof v === "boolean");
+  pick("containersFollowChildren", (v) => typeof v === "boolean");
+  const fit = extra.viewerFit;
+  if (typeof fit?.padding === "number" && Number.isFinite(fit.padding) && fit.padding >= 0) {
+    out.viewerFit = { padding: fit.padding };
+  }
   return out;
 }
 function readRows(n, spelling, notes) {
@@ -195,10 +224,23 @@ function readRows(n, spelling, notes) {
   if (spelling.extra.zeroUnplaced === true) {
     dropZeroPile(values);
   }
+  if (spelling.extra.originUnplaced === true) {
+    placeUnplacedAtOrigin(values);
+  }
   const realZ = spelling.extra.sourceDims === 3 && !constantZ(values);
   convertRows(values, spelling.extra, spelling.size, realZ, notes);
   return { values, realZ };
 }
+function placeUnplacedAtOrigin(values) {
+  if (!values.some((v) => !Number.isNaN(v))) {
+    return;
+  }
+  for (let i = 0; i < values.length; i += 3) {
+    if (Number.isNaN(values[i])) {
+      values.fill(0, i, i + 3);
+    }
+  }
+}
 function convertRows(values, extra, size, realZ, notes) {
   const p = [0, 0, 0];
   for (let i = 0; i < values.length; i += 3) {

package/dist/positions.js.map

@@ -1 +1 @@
-{"version":3,"file":"positions.js","sources":["../src/positions/codes.ts","../src/common/notes.ts","../src/positions/extract.ts"],"sourcesContent":["/**\n * The note codes of `extractPositions()`. Singular `W_POSITION_*` codes are about some nodes,\n * plural `W_POSITIONS_*` codes about the file as a whole. Keys drop the `W_` and `POSITION_` /\n * `POSITIONS_` prefixes.\n */\n\n/**\n * Every code a `PositionNote` carries.\n * @category Positions\n */\nexport const POSITION_ISSUE = Object.freeze({\n    /** Every placed node sits on one point; the coordinates are dropped and `usable` is false. */\n    STACKED: \"W_POSITION_STACKED\",\n    /** Some nodes have no position. */\n    PARTIAL: \"W_POSITION_PARTIAL\",\n    /** Some coordinates are not finite numbers; those nodes count as unplaced. */\n    NON_FINITE: \"W_POSITION_NON_FINITE\",\n    /** The file mixes 2- and 3-coordinate positions. */\n    DIMS_MIXED: \"W_POSITION_DIMS_MIXED\",\n    /** A top-left coordinate has no width or height, so it was not moved to the center. */\n    ANCHOR_NO_SIZE: \"W_POSITION_ANCHOR_NO_SIZE\",\n    /** The file holds more than one view (layout); only the first is used. */\n    OTHER_VIEWS: \"W_POSITION_OTHER_VIEWS\",\n    /** The file has position-like columns this format does not read (plain `x` / `y`). */\n    NOT_READ: \"W_POSITIONS_NOT_READ\",\n} as const);\n\n/**\n * A code of `POSITION_ISSUE`.\n * @category Positions\n */\nexport type PositionNoteCode = (typeof POSITION_ISSUE)[keyof typeof POSITION_ISSUE];\n","/**\n * The note collector file positions use (and file styles, after their rebase): one note per code\n * (and optional property), never one per element, with at most 8 distinct samples of 80\n * characters, a total count and the element indexes the note covers.\n */\n\n/** At most this many samples per note. */\nconst MAX_SAMPLES = 8;\n/** A sample is cut to this many characters. */\nconst MAX_SAMPLE_LENGTH = 80;\n\n/** One occurrence (or `count` occurrences) of a condition. */\ninterface NoteReport {\n    /** An example of the offending value. */\n    readonly sample?: unknown;\n    /** The element the report is about, by index. */\n    readonly element?: number;\n    /** How many occurrences the report stands for; defaults to 1. */\n    readonly count?: number;\n}\n\n/** A collected note, before a module shapes it into its own note type. */\ninterface CollectedNote<C extends string> {\n    readonly code: C;\n    readonly property: string | null;\n    readonly count: number;\n    readonly samples: readonly string[];\n    readonly elements: readonly number[] | { readonly count: number };\n}\n\ninterface Collecting<C extends string> {\n    readonly code: C;\n    readonly property: string | null;\n    count: number;\n    readonly samples: string[];\n    readonly elements: Set<number>;\n    unindexed: boolean;\n}\n\n/** Collects notes, aggregated per (code, property), in the order their conditions first occur. */\nexport class NoteCollector<C extends string> {\n    readonly #notes = new Map<string, Collecting<C>>();\n\n    /**\n     * Record a condition.\n     * @param code - the condition\n     * @param report - a sample, the element index and a count\n     * @param property - what the note is about, or null\n     */\n    add(code: C, report: NoteReport = {}, property: string | null = null): void {\n        const key = `${code}\\u0000${property ?? \"\"}`;\n        let note = this.#notes.get(key);\n        if (note === undefined) {\n            note = { code, property, count: 0, samples: [], elements: new Set(), unindexed: false };\n            this.#notes.set(key, note);\n        }\n        note.count += report.count ?? 1;\n        if (report.element === undefined) {\n            note.unindexed = true;\n        } else {\n            note.elements.add(report.element);\n        }\n        if (report.sample !== undefined && note.samples.length < MAX_SAMPLES) {\n            const sample = sampleText(report.sample);\n            if (!note.samples.includes(sample)) {\n                note.samples.push(sample);\n            }\n        }\n    }\n\n    /**\n     * The collected notes.\n     * @returns one note per (code, property)\n     */\n    list(): CollectedNote<C>[] {\n        return Array.from(this.#notes.values(), (n) => ({\n            code: n.code,\n            property: n.property,\n            count: n.count,\n            samples: [...n.samples],\n            elements: n.unindexed ? { count: n.count } : Array.from(n.elements).sort((a, b) => a - b),\n        }));\n    }\n}\n\n/**\n * A sample as at most 80 characters of text.\n * @param value - the sample\n * @returns the text\n */\nfunction sampleText(value: unknown): string {\n    const text = typeof value === \"string\" ? value : (JSON.stringify(value) ?? String(value));\n    return text.length > MAX_SAMPLE_LENGTH ? `${text.slice(0, MAX_SAMPLE_LENGTH - 3)}...` : text;\n}\n","/**\n * `extractPositions()`: any format's stored node coordinates in the neutral convention (center,\n * y up, the file's unit, 3 components). The snapshot's role-`position` column keeps the values the\n * file wrote; this reads them through the spelling the column's `meta.extra` (or the importer's\n * `positions()` hook) declares.\n */\n\nimport type { Column, GraphSnapshot } from \"@graphty/graph-format\";\n\nimport { NoteCollector } from \"../common/notes.js\";\nimport { type GraphTool, toolOf } from \"../common/units.js\";\nimport type { GraphImporter, ImportReport } from \"../types.js\";\nimport { POSITION_ISSUE, type PositionNoteCode } from \"./codes.js\";\nimport { median, toNeutral } from \"./convert.js\";\nimport type {\n    ExtractPositionsOptions,\n    FilePositionGroup,\n    FilePositions,\n    ImporterGroupBox,\n    ImporterPositions,\n    PositionColumnExtra,\n    PositionNote,\n} from \"./types.js\";\n\ntype Point = [number, number, number];\n\n/** Reads one row's raw coordinates into `out`; false when the row has none. */\ntype RowReader = (row: number, out: Point) => boolean;\n\n/** Reads one row's width and height; null when the row has no size. */\ntype SizeReader = (row: number) => readonly [number, number] | null;\n\n/** Where a file's coordinates are and how they are spelled. */\ninterface Spelling {\n    readonly read: RowReader;\n    /** Reads a row's width and height from the size columns the spelling names; null without both. */\n    readonly size: SizeReader;\n    readonly extra: PositionColumnExtra;\n    readonly groups: readonly ImporterGroupBox[];\n    readonly medianNodeSize: number | null | undefined;\n    readonly tool: GraphTool | null | undefined;\n}\n\n/** Report codes of format readers that mean the file mixes 2- and 3-coordinate positions. */\nconst DIMS_MIXED_CODES: ReadonlySet<string> = new Set([\"W_PAJEK_COORD_DIMS\", \"W_DOT_POS_DIMS\"]);\n\n/** graph-io's English for each note, for its own logs only. */\nconst PHRASES: Readonly<Record<PositionNoteCode, string>> = {\n    W_POSITION_STACKED: \"every placed node is on one point; the positions were dropped\",\n    W_POSITION_PARTIAL: \"nodes have no position\",\n    W_POSITION_NON_FINITE: \"positions are not finite numbers\",\n    W_POSITION_DIMS_MIXED: \"positions mix 2 and 3 coordinates\",\n    W_POSITION_ANCHOR_NO_SIZE: \"top-left positions have no size and were not moved to the center\",\n    W_POSITION_OTHER_VIEWS: \"other views were not used\",\n    W_POSITIONS_NOT_READ: \"position-like columns this format does not read\",\n};\n\n/**\n * A file's stored node coordinates in the neutral convention: each node's center, y up, in the\n * file's own unit. Call it with the importer that read the snapshot and the report it returned.\n * @example\n * ```ts\n * const { snapshot, report } = await importGraph(text, { format: \"gml\" });\n * const positions = extractPositions(gmlImporter, snapshot, report);\n * if (positions?.usable) console.log(positions.coords.subarray(0, 3)); // node 0's x, y, z\n * ```\n * @param importer - the importer that read the snapshot (its `positions()` hook, when it has one, says how the coordinates are spelled)\n * @param snapshot - the imported graph\n * @param report - the import's report\n * @param options - `signal` to abort\n * @returns the positions, or null when the file stores none and has no position-like columns\n * @category Positions\n */\nexport function extractPositions(\n    importer: GraphImporter,\n    snapshot: GraphSnapshot,\n    report: ImportReport,\n    options: ExtractPositionsOptions = {},\n): FilePositions | null {\n    const signal = options.signal ?? null;\n    signal?.throwIfAborted();\n    const notes = new NoteCollector<PositionNoteCode>();\n    const spelling = spellingOf(importer, snapshot, signal);\n    if (spelling === null) {\n        noteUnread(snapshot, notes);\n        return notes.list().length === 0 ? null : emptyPositions(importer, snapshot, notes);\n    }\n    const n = snapshot.nodeCount;\n    const coords = readRows(n, spelling, notes);\n    signal?.throwIfAborted();\n    const containers = containersOf(snapshot);\n    const groups = applyGroups(spelling, coords);\n    collectGroups(spelling, coords, containers, groups);\n    const { placed, total } = countPlaced(coords, containers, notes);\n    const stacked = dropStacked(coords, placed, notes);\n    noteReport(report, notes);\n    noteOtherViews(snapshot, notes);\n    return {\n        version: 1,\n        source: {\n            format: importer.format,\n            tool: spelling.tool ?? toolOf(snapshot.meta.creator),\n            yAxis: spelling.extra.yAxis ?? \"up\",\n        },\n        units: spelling.extra.units ?? \"file\",\n        ...(spelling.extra.pxPerUnit === undefined ? {} : { pxPerUnit: spelling.extra.pxPerUnit }),\n        medianNodeSize: spelling.medianNodeSize ?? medianSize(spelling.size, n, containers),\n        dims: coords.realZ ? 3 : 2,\n        coords: coords.values,\n        placed: stacked ? 0 : placed,\n        total,\n        usable: !stacked && placed > 0,\n        bounds: stacked ? null : boundsOf(coords.values),\n        groups,\n        notes: noteList(notes),\n    };\n}\n\n// ------------------------------------------------------------ spelling\n\n/**\n * Where the coordinates are: the importer's hook wins over the column's `meta.extra`.\n * @param importer - the importer\n * @param snapshot - the graph\n * @param signal - the abort signal\n * @returns the spelling, or null when the file stores no coordinates\n */\nfunction spellingOf(importer: GraphImporter, snapshot: GraphSnapshot, signal: AbortSignal | null): Spelling | null {\n    const hook = importer.positions?.(snapshot, { signal }) ?? null;\n    if (hook?.x !== undefined && hook.y !== undefined) {\n        return plainSpelling(snapshot, hook);\n    }\n    const column = hook?.column === undefined ? snapshot.nodes.byRole(\"position\") : snapshot.nodes.get(hook.column);\n    if (column === null || column.meta.components < 2) {\n        return null;\n    }\n    const extra = { ...extraOf(column.meta.extra), ...extraOf(hook ?? {}) };\n    return { read: vectorReader(column), size: sizeReader(snapshot, extra), extra, ...hookFields(hook) };\n}\n\n/**\n * The spelling of the simple hook form: plain x / y (/ z) columns.\n * @param snapshot - the graph\n * @param hook - the hook's answer\n * @returns the spelling, or null when a named column is missing\n */\nfunction plainSpelling(snapshot: GraphSnapshot, hook: ImporterPositions): Spelling | null {\n    const x = snapshot.nodes.get(hook.x ?? \"\");\n    const y = snapshot.nodes.get(hook.y ?? \"\");\n    const z = hook.z === undefined ? null : snapshot.nodes.get(hook.z);\n    if (x === null || y === null) {\n        return null;\n    }\n    const read: RowReader = (row, out) => {\n        if (!x.isSet(row) || !y.isSet(row)) {\n            return false;\n        }\n        out[0] = Number(x.value(row));\n        out[1] = Number(y.value(row));\n        out[2] = z?.isSet(row) === true ? Number(z.value(row)) : 0;\n        return true;\n    };\n    const extra = { ...extraOf(hook), sourceDims: z === null ? 2 : 3 } as const;\n    return { read, size: sizeReader(snapshot, extra), extra, ...hookFields(hook) };\n}\n\n/**\n * The hook's fields beside the spelling.\n * @param hook - the hook's answer, or null\n * @returns groups, median node size and tool\n */\nfunction hookFields(hook: ImporterPositions | null): Pick<Spelling, \"groups\" | \"medianNodeSize\" | \"tool\"> {\n    return { groups: hook?.groups ?? [], medianNodeSize: hook?.medianNodeSize, tool: hook?.tool };\n}\n\n/**\n * A reader over a 2- or 3-component column.\n * @param column - the column\n * @returns the reader\n */\nfunction vectorReader(column: Column): RowReader {\n    return (row, out) => {\n        if (!column.isSet(row)) {\n            return false;\n        }\n        const v = column.value(row) as ArrayLike<number>;\n        out[0] = v[0];\n        out[1] = v[1];\n        out[2] = v.length > 2 ? v[2] : 0;\n        return true;\n    };\n}\n\n/**\n * The spelling fields of an extra (or a hook's answer), each kept only when well formed.\n * @param source - a column's meta.extra or a hook's answer\n * @returns the fields\n */\nfunction extraOf(source: object): PositionColumnExtra {\n    const extra = source as Readonly<Record<string, unknown>>;\n    const out: Record<string, unknown> = {};\n    const pick = (key: keyof PositionColumnExtra, ok: (v: unknown) => boolean): void => {\n        if (ok(extra[key])) {\n            out[key] = extra[key];\n        }\n    };\n    pick(\"units\", (v) => v === \"px\" || v === \"file\");\n    pick(\"sourceDims\", (v) => v === 2 || v === 3);\n    pick(\"yAxis\", (v) => v === \"up\" || v === \"down\");\n    pick(\"anchor\", (v) => v === \"center\" || v === \"top-left\");\n    pick(\"width\", (v) => typeof v === \"string\");\n    pick(\"height\", (v) => typeof v === \"string\");\n    pick(\"pxPerUnit\", (v) => typeof v === \"number\" && Number.isFinite(v) && v > 0);\n    pick(\"zOrigin\", (v) => typeof v === \"number\" && Number.isFinite(v));\n    pick(\"zeroUnplaced\", (v) => typeof v === \"boolean\");\n    return out;\n}\n\n// ------------------------------------------------------------ rows\n\n/** Coordinates by node index, with whether the file has a z that differs between nodes. */\ninterface Rows {\n    readonly values: Float64Array;\n    readonly realZ: boolean;\n}\n\n/**\n * Read every row and convert it to the neutral convention.\n * @param n - the node count\n * @param spelling - how the coordinates are spelled\n * @param notes - receives non-finite and anchor notes\n * @returns the coordinates (NaN rows have none)\n */\nfunction readRows(n: number, spelling: Spelling, notes: NoteCollector<PositionNoteCode>): Rows {\n    const values = new Float64Array(3 * n).fill(Number.NaN);\n    const p: Point = [0, 0, 0];\n    for (let row = 0; row < n; row++) {\n        if (!spelling.read(row, p)) {\n            continue;\n        }\n        if (Number.isFinite(p[0]) && Number.isFinite(p[1]) && Number.isFinite(p[2])) {\n            values.set(p, 3 * row);\n        } else {\n            notes.add(POSITION_ISSUE.NON_FINITE, { element: row, sample: p.join(\",\") });\n        }\n    }\n    if (spelling.extra.zeroUnplaced === true) {\n        dropZeroPile(values);\n    }\n    const realZ = spelling.extra.sourceDims === 3 && !constantZ(values);\n    convertRows(values, spelling.extra, spelling.size, realZ, notes);\n    return { values, realZ };\n}\n\n/**\n * Convert every placed row in place.\n * @param values - the raw coordinates\n * @param extra - the spelling\n * @param size - reads a row's width and height\n * @param realZ - whether z differs between nodes\n * @param notes - receives the anchor note\n */\nfunction convertRows(\n    values: Float64Array,\n    extra: PositionColumnExtra,\n    size: SizeReader,\n    realZ: boolean,\n    notes: NoteCollector<PositionNoteCode>,\n): void {\n    const p: Point = [0, 0, 0];\n    for (let i = 0; i < values.length; i += 3) {\n        if (Number.isNaN(values[i])) {\n            continue;\n        }\n        const s = extra.anchor === \"top-left\" ? size(i / 3) : null;\n        if (extra.anchor === \"top-left\" && s === null) {\n            notes.add(POSITION_ISSUE.ANCHOR_NO_SIZE, { element: i / 3 });\n        }\n        p[0] = values[i];\n        p[1] = values[i + 1];\n        p[2] = values[i + 2];\n        toNeutral(p, extra, s, realZ);\n        values.set(p, i);\n    }\n}\n\n/**\n * Reads a row's width and height from the size columns a spelling names.\n * @param snapshot - the graph\n * @param extra - the spelling\n * @returns the reader; it answers null for a row without both, or when the columns are missing\n */\nfunction sizeReader(snapshot: GraphSnapshot, extra: PositionColumnExtra): SizeReader {\n    const w = extra.width === undefined ? null : snapshot.nodes.get(extra.width);\n    const h = extra.height === undefined ? null : snapshot.nodes.get(extra.height);\n    if (w === null || h === null) {\n        return () => null;\n    }\n    return (row) => {\n        if (!w.isSet(row) || !h.isSet(row)) {\n            return null;\n        }\n        const size: [number, number] = [Number(w.value(row)), Number(h.value(row))];\n        return Number.isFinite(size[0]) && Number.isFinite(size[1]) ? size : null;\n    };\n}\n\n/**\n * NetworkX writes (0, 0) for a node with no position: when other rows are placed, an exact (0, 0)\n * shared by two or more rows counts as unplaced.\n * @param values - the raw coordinates, changed in place\n */\nfunction dropZeroPile(values: Float64Array): void {\n    const zeros: number[] = [];\n    let others = 0;\n    for (let i = 0; i < values.length; i += 3) {\n        if (values[i] === 0 && values[i + 1] === 0) {\n            zeros.push(i);\n        } else if (!Number.isNaN(values[i])) {\n            others++;\n        }\n    }\n    if (zeros.length >= 2 && others > 0) {\n        for (const i of zeros) {\n            values.fill(Number.NaN, i, i + 3);\n        }\n    }\n}\n\n/**\n * Whether every placed row has the same z (Pajek writes z = 0.5 on 2D drawings).\n * @param values - the raw coordinates\n * @returns true when z never differs\n */\nfunction constantZ(values: Float64Array): boolean {\n    let z = Number.NaN;\n    for (let i = 0; i < values.length; i += 3) {\n        if (Number.isNaN(values[i])) {\n            continue;\n        }\n        if (Number.isNaN(z)) {\n            z = values[i + 2];\n        } else if (values[i + 2] !== z) {\n            return false;\n        }\n    }\n    return true;\n}\n\n// ------------------------------------------------------------ groups\n\n/**\n * The nodes another node names as its parent: group containers.\n * @param snapshot - the graph\n * @returns the container indexes\n */\nfunction containersOf(snapshot: GraphSnapshot): Set<number> {\n    const out = new Set<number>();\n    const parent = snapshot.nodes.byRole(\"parent\");\n    if (parent === null) {\n        return out;\n    }\n    for (let row = 0; row < parent.length; row++) {\n        const v = parent.isSet(row) ? parent.value(row) : undefined;\n        if (typeof v === \"number\") {\n            out.add(v);\n        }\n    }\n    return out;\n}\n\n/**\n * The hook's group boxes in the neutral convention; a container with no coordinate of its own is\n * placed at its box's center.\n * @param spelling - the spelling and the hook's boxes\n * @param rows - the coordinates, changed in place\n * @returns the boxes\n */\nfunction applyGroups(spelling: Spelling, rows: Rows): FilePositionGroup[] {\n    const out: FilePositionGroup[] = [];\n    for (const { node, box } of spelling.groups) {\n        const p: Point = [box.x, box.y, 0];\n        toNeutral(p, spelling.extra, [box.width, box.height], false);\n        if (Number.isNaN(rows.values[3 * node])) {\n            rows.values.set(p, 3 * node);\n        }\n        if (!out.some((g) => g.node === node)) {\n            out.push({ node, box: { x: p[0], y: p[1], width: box.width, height: box.height } });\n        }\n    }\n    return out;\n}\n\n/**\n * Boxes for the containers the file gives a coordinate and a size (yEd groups).\n * @param spelling - the size reader\n * @param rows - the coordinates\n * @param containers - the container indexes\n * @param groups - receives the boxes\n */\nfunction collectGroups(\n    spelling: Spelling,\n    rows: Rows,\n    containers: ReadonlySet<number>,\n    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Keys drop the `W_` and `POSITION_` /\n * `POSITIONS_` prefixes.\n */\n\n/**\n * Every code a `PositionNote` carries.\n * @category Positions\n */\nexport const POSITION_ISSUE = Object.freeze({\n    /** Every placed node sits on one point; the coordinates are dropped and `usable` is false. */\n    STACKED: \"W_POSITION_STACKED\",\n    /** Some nodes have no position. */\n    PARTIAL: \"W_POSITION_PARTIAL\",\n    /** Some coordinates are not finite numbers; those nodes count as unplaced. */\n    NON_FINITE: \"W_POSITION_NON_FINITE\",\n    /** The file mixes 2- and 3-coordinate positions. */\n    DIMS_MIXED: \"W_POSITION_DIMS_MIXED\",\n    /** A top-left coordinate has no width or height, so it was not moved to the center. */\n    ANCHOR_NO_SIZE: \"W_POSITION_ANCHOR_NO_SIZE\",\n    /** The file holds more than one view (layout); only the first is used. */\n    OTHER_VIEWS: \"W_POSITION_OTHER_VIEWS\",\n    /** The file has position-like columns this format does not read (plain `x` / `y`). */\n    NOT_READ: \"W_POSITIONS_NOT_READ\",\n} as const);\n\n/**\n * A code of `POSITION_ISSUE`.\n * @category Positions\n */\nexport type PositionNoteCode = (typeof POSITION_ISSUE)[keyof typeof POSITION_ISSUE];\n","/**\n * The note collector file positions use (and file styles, after their rebase): one note per code\n * (and optional property), never one per element, with at most 8 distinct samples of 80\n * characters, a total count and the element indexes the note covers.\n */\n\n/** At most this many samples per note. */\nconst MAX_SAMPLES = 8;\n/** A sample is cut to this many characters. */\nconst MAX_SAMPLE_LENGTH = 80;\n\n/** One occurrence (or `count` occurrences) of a condition. */\ninterface NoteReport {\n    /** An example of the offending value. */\n    readonly sample?: unknown;\n    /** The element the report is about, by index. */\n    readonly element?: number;\n    /** How many occurrences the report stands for; defaults to 1. */\n    readonly count?: number;\n}\n\n/** A collected note, before a module shapes it into its own note type. */\ninterface CollectedNote<C extends string> {\n    readonly code: C;\n    readonly property: string | null;\n    readonly count: number;\n    readonly samples: readonly string[];\n    readonly elements: readonly number[] | { readonly count: number };\n}\n\ninterface Collecting<C extends string> {\n    readonly code: C;\n    readonly property: string | null;\n    count: number;\n    readonly samples: string[];\n    readonly elements: Set<number>;\n    unindexed: boolean;\n}\n\n/** Collects notes, aggregated per (code, property), in the order their conditions first occur. */\nexport class NoteCollector<C extends string> {\n    readonly #notes = new Map<string, Collecting<C>>();\n\n    /**\n     * Record a condition.\n     * @param code - the condition\n     * @param report - a sample, the element index and a count\n     * @param property - what the note is about, or null\n     */\n    add(code: C, report: NoteReport = {}, property: string | null = null): void {\n        const key = `${code}\\u0000${property ?? \"\"}`;\n        let note = this.#notes.get(key);\n        if (note === undefined) {\n            note = { code, property, count: 0, samples: [], elements: new Set(), unindexed: false };\n            this.#notes.set(key, note);\n        }\n        note.count += report.count ?? 1;\n        if (report.element === undefined) {\n            note.unindexed = true;\n        } else {\n            note.elements.add(report.element);\n        }\n        if (report.sample !== undefined && note.samples.length < MAX_SAMPLES) {\n            const sample = sampleText(report.sample);\n            if (!note.samples.includes(sample)) {\n                note.samples.push(sample);\n            }\n        }\n    }\n\n    /**\n     * The collected notes.\n     * @returns one note per (code, property)\n     */\n    list(): CollectedNote<C>[] {\n        return Array.from(this.#notes.values(), (n) => ({\n            code: n.code,\n            property: n.property,\n            count: n.count,\n            samples: [...n.samples],\n            elements: n.unindexed ? { count: n.count } : Array.from(n.elements).sort((a, b) => a - b),\n        }));\n    }\n}\n\n/**\n * A sample as at most 80 characters of text.\n * @param value - the sample\n * @returns the text\n */\nfunction sampleText(value: unknown): string {\n    const text = typeof value === \"string\" ? value : (JSON.stringify(value) ?? String(value));\n    return text.length > MAX_SAMPLE_LENGTH ? `${text.slice(0, MAX_SAMPLE_LENGTH - 3)}...` : text;\n}\n","/**\n * `extractPositions()`: any format's stored node coordinates in the neutral convention (center,\n * y up, the file's unit, 3 components). The snapshot's role-`position` column keeps the values the\n * file wrote; this reads them through the spelling the column's `meta.extra` (or the importer's\n * `positions()` hook) declares.\n */\n\nimport type { Column, GraphSnapshot } from \"@graphty/graph-format\";\n\nimport { NoteCollector } from \"../common/notes.js\";\nimport { type GraphTool, toolOf } from \"../common/units.js\";\nimport type { GraphImporter, ImportReport } from \"../types.js\";\nimport { POSITION_ISSUE, type PositionNoteCode } from \"./codes.js\";\nimport { median, toNeutral } from \"./convert.js\";\nimport type {\n    ExtractPositionsOptions,\n    FilePositionGroup,\n    FilePositions,\n    ImporterGroupBox,\n    ImporterPositions,\n    PositionColumnExtra,\n    PositionNote,\n} from \"./types.js\";\n\ntype Point = [number, number, number];\n\n/** Reads one row's raw coordinates into `out`; false when the row has none. */\ntype RowReader = (row: number, out: Point) => boolean;\n\n/** Reads one row's width and height; null when the row has no size. */\ntype SizeReader = (row: number) => readonly [number, number] | null;\n\n/** Where a file's coordinates are and how they are spelled. */\ninterface Spelling {\n    readonly read: RowReader;\n    /** Reads a row's width and height from the size columns the spelling names; null without both. */\n    readonly size: SizeReader;\n    readonly extra: PositionColumnExtra;\n    readonly groups: readonly ImporterGroupBox[];\n    readonly medianNodeSize: number | null | undefined;\n    readonly tool: GraphTool | null | undefined;\n}\n\n/** Report codes of format readers that mean the file mixes 2- and 3-coordinate positions. */\nconst DIMS_MIXED_CODES: ReadonlySet<string> = new Set([\"W_PAJEK_COORD_DIMS\", \"W_DOT_POS_DIMS\"]);\n\n/** graph-io's English for each note, for its own logs only. */\nconst PHRASES: Readonly<Record<PositionNoteCode, string>> = {\n    W_POSITION_STACKED: \"every placed node is on one point; the positions were dropped\",\n    W_POSITION_PARTIAL: \"nodes have no position\",\n    W_POSITION_NON_FINITE: \"positions are not finite numbers\",\n    W_POSITION_DIMS_MIXED: \"positions mix 2 and 3 coordinates\",\n    W_POSITION_ANCHOR_NO_SIZE: \"top-left positions have no size and were not moved to the center\",\n    W_POSITION_OTHER_VIEWS: \"other views were not used\",\n    W_POSITIONS_NOT_READ: \"position-like columns this format does not read\",\n};\n\n/**\n * A file's stored node coordinates in the neutral convention: each node's center, y up, in the\n * file's own unit. Call it with the importer that read the snapshot and the report it returned.\n * @example\n * ```ts\n * const { snapshot, report } = await importGraph(text, { format: \"gml\" });\n * const positions = extractPositions(gmlImporter, snapshot, report);\n * if (positions?.usable) console.log(positions.coords.subarray(0, 3)); // node 0's x, y, z\n * ```\n * @param importer - the importer that read the snapshot (its `positions()` hook, when it has one, says how the coordinates are spelled)\n * @param snapshot - the imported graph\n * @param report - the import's report\n * @param options - `signal` to abort\n * @returns the positions, or null when the file stores none and has no position-like columns\n * @category Positions\n */\nexport function extractPositions(\n    importer: GraphImporter,\n    snapshot: GraphSnapshot,\n    report: ImportReport,\n    options: ExtractPositionsOptions = {},\n): FilePositions | null {\n    const signal = options.signal ?? null;\n    signal?.throwIfAborted();\n    const notes = new NoteCollector<PositionNoteCode>();\n    const spelling = spellingOf(importer, snapshot, signal);\n    if (spelling === null) {\n        noteUnread(snapshot, notes);\n        return notes.list().length === 0 ? null : emptyPositions(importer, snapshot, notes);\n    }\n    const n = snapshot.nodeCount;\n    const coords = readRows(n, spelling, notes);\n    signal?.throwIfAborted();\n    const containers = containersOf(snapshot);\n    if (spelling.extra.containersFollowChildren === true) {\n        for (const row of containers) {\n            coords.values.fill(Number.NaN, 3 * row, 3 * row + 3);\n        }\n    }\n    const groups = applyGroups(spelling, coords);\n    collectGroups(spelling, coords, containers, groups);\n    const { placed, total } = countPlaced(coords, containers, notes);\n    const stacked = dropStacked(coords, placed, notes);\n    noteReport(report, notes);\n    noteOtherViews(snapshot, notes);\n    return {\n        version: 1,\n        source: {\n            format: importer.format,\n            tool: spelling.tool ?? toolOf(snapshot.meta.creator),\n            yAxis: spelling.extra.yAxis ?? \"up\",\n        },\n        units: spelling.extra.units ?? \"file\",\n        ...(spelling.extra.pxPerUnit === undefined ? {} : { pxPerUnit: spelling.extra.pxPerUnit }),\n        ...(spelling.extra.viewerFit === undefined ? {} : { viewerFit: spelling.extra.viewerFit }),\n        medianNodeSize: spelling.medianNodeSize ?? medianSize(spelling.size, n, containers),\n        dims: coords.realZ ? 3 : 2,\n        coords: coords.values,\n        placed: stacked ? 0 : placed,\n        total,\n        usable: !stacked && placed > 0,\n        bounds: stacked ? null : boundsOf(coords.values),\n        groups,\n        notes: noteList(notes),\n    };\n}\n\n// ------------------------------------------------------------ spelling\n\n/**\n * Where the coordinates are: the importer's hook wins over the column's `meta.extra`.\n * @param importer - the importer\n * @param snapshot - the graph\n * @param signal - the abort signal\n * @returns the spelling, or null when the file stores no coordinates\n */\nfunction spellingOf(importer: GraphImporter, snapshot: GraphSnapshot, signal: AbortSignal | null): Spelling | null {\n    const hook = importer.positions?.(snapshot, { signal }) ?? null;\n    if (hook?.x !== undefined && hook.y !== undefined) {\n        return plainSpelling(snapshot, hook);\n    }\n    const column = hook?.column === undefined ? snapshot.nodes.byRole(\"position\") : snapshot.nodes.get(hook.column);\n    if (column === null || column.meta.components < 2) {\n        return hook?.unplacedCircle === undefined ? null : circleSpelling(snapshot, hook);\n    }\n    const extra = { ...extraOf(column.meta.extra), ...extraOf(hook ?? {}) };\n    return { read: vectorReader(column), size: sizeReader(snapshot, extra), extra, ...hookFields(hook) };\n}\n\n/**\n * The spelling of a file that places no node, whose program puts them round a circle (`unplacedCircle`).\n * @param snapshot - the graph\n * @param hook - the hook's answer, with its circle\n * @returns the spelling\n */\nfunction circleSpelling(snapshot: GraphSnapshot, hook: ImporterPositions): Spelling {\n    const circle = hook.unplacedCircle;\n    const n = snapshot.nodeCount;\n    const read: RowReader = (row, out) => {\n        if (circle === undefined || n === 0) {\n            return false;\n        }\n        const a = ((circle.startDegrees + (circle.direction * 360 * row) / n) * Math.PI) / 180;\n        out[0] = circle.center[0] + circle.radius * Math.cos(a);\n        out[1] = circle.center[1] + circle.radius * Math.sin(a);\n        out[2] = 0;\n        return true;\n    };\n    const extra = { ...extraOf(hook), sourceDims: 2 } as const;\n    return { read, size: sizeReader(snapshot, extra), extra, ...hookFields(hook) };\n}\n\n/**\n * The spelling of the simple hook form: plain x / y (/ z) columns.\n * @param snapshot - the graph\n * @param hook - the hook's answer\n * @returns the spelling, or null when a named column is missing\n */\nfunction plainSpelling(snapshot: GraphSnapshot, hook: ImporterPositions): Spelling | null {\n    const x = snapshot.nodes.get(hook.x ?? \"\");\n    const y = snapshot.nodes.get(hook.y ?? \"\");\n    const z = hook.z === undefined ? null : snapshot.nodes.get(hook.z);\n    if (x === null || y === null) {\n        return null;\n    }\n    const read: RowReader = (row, out) => {\n        if (!x.isSet(row) || !y.isSet(row)) {\n            return false;\n        }\n        out[0] = Number(x.value(row));\n        out[1] = Number(y.value(row));\n        out[2] = z?.isSet(row) === true ? Number(z.value(row)) : 0;\n        return true;\n    };\n    const extra = { ...extraOf(hook), sourceDims: z === null ? 2 : 3 } as const;\n    return { read, size: sizeReader(snapshot, extra), extra, ...hookFields(hook) };\n}\n\n/**\n * The hook's fields beside the spelling.\n * @param hook - the hook's answer, or null\n * @returns groups, median node size and tool\n */\nfunction hookFields(hook: ImporterPositions | null): Pick<Spelling, \"groups\" | \"medianNodeSize\" | \"tool\"> {\n    return { groups: hook?.groups ?? [], medianNodeSize: hook?.medianNodeSize, tool: hook?.tool };\n}\n\n/**\n * A reader over a 2- or 3-component column.\n * @param column - the column\n * @returns the reader\n */\nfunction vectorReader(column: Column): RowReader {\n    return (row, out) => {\n        if (!column.isSet(row)) {\n            return false;\n        }\n        const v = column.value(row) as ArrayLike<number>;\n        out[0] = v[0];\n        out[1] = v[1];\n        out[2] = v.length > 2 ? v[2] : 0;\n        return true;\n    };\n}\n\n/**\n * The spelling fields of an extra (or a hook's answer), each kept only when well formed.\n * @param source - a column's meta.extra or a hook's answer\n * @returns the fields\n */\nfunction extraOf(source: object): PositionColumnExtra {\n    const extra = source as Readonly<Record<string, unknown>>;\n    const out: Record<string, unknown> = {};\n    const pick = (key: keyof PositionColumnExtra, ok: (v: unknown) => boolean): void => {\n        if (ok(extra[key])) {\n            out[key] = extra[key];\n        }\n    };\n    pick(\"units\", (v) => v === \"px\" || v === \"file\");\n    pick(\"sourceDims\", (v) => v === 2 || v === 3);\n    pick(\"yAxis\", (v) => v === \"up\" || v === \"down\");\n    pick(\"anchor\", (v) => v === \"center\" || v === \"top-left\");\n    pick(\"width\", (v) => typeof v === \"string\");\n    pick(\"height\", (v) => typeof v === \"string\");\n    pick(\"pxPerUnit\", (v) => typeof v === \"number\" && Number.isFinite(v) && v > 0);\n    pick(\"pxPerUnitY\", (v) => typeof v === \"number\" && Number.isFinite(v) && v > 0);\n    pick(\"zOrigin\", (v) => typeof v === \"number\" && Number.isFinite(v));\n    pick(\"zeroUnplaced\", (v) => typeof v === \"boolean\");\n    pick(\"originUnplaced\", (v) => typeof v === \"boolean\");\n    pick(\"containersFollowChildren\", (v) => typeof v === \"boolean\");\n    const fit = extra.viewerFit as Readonly<Record<string, unknown>> | null | undefined;\n    if (typeof fit?.padding === \"number\" && Number.isFinite(fit.padding) && fit.padding >= 0) {\n        out.viewerFit = { padding: fit.padding };\n    }\n    return out;\n}\n\n// ------------------------------------------------------------ rows\n\n/** Coordinates by node index, with whether the file has a z that differs between nodes. */\ninterface Rows {\n    readonly values: Float64Array;\n    readonly realZ: boolean;\n}\n\n/**\n * Read every row and convert it to the neutral convention.\n * @param n - the node count\n * @param spelling - how the coordinates are spelled\n * @param notes - receives non-finite and anchor notes\n * @returns the coordinates (NaN rows have none)\n */\nfunction readRows(n: number, spelling: Spelling, notes: NoteCollector<PositionNoteCode>): Rows {\n    const values = new Float64Array(3 * n).fill(Number.NaN);\n    const p: Point = [0, 0, 0];\n    for (let row = 0; row < n; row++) {\n        if (!spelling.read(row, p)) {\n            continue;\n        }\n        if (Number.isFinite(p[0]) && Number.isFinite(p[1]) && Number.isFinite(p[2])) {\n            values.set(p, 3 * row);\n        } else {\n            notes.add(POSITION_ISSUE.NON_FINITE, { element: row, sample: p.join(\",\") });\n        }\n    }\n    if (spelling.extra.zeroUnplaced === true) {\n        dropZeroPile(values);\n    }\n    if (spelling.extra.originUnplaced === true) {\n        placeUnplacedAtOrigin(values);\n    }\n    const realZ = spelling.extra.sourceDims === 3 && !constantZ(values);\n    convertRows(values, spelling.extra, spelling.size, realZ, notes);\n    return { values, realZ };\n}\n\n/**\n * Put every unplaced row at the origin, when at least one row is placed.\n * @param values - the coordinates, three per row; NaN rows are unplaced\n */\nfunction placeUnplacedAtOrigin(values: Float64Array): void {\n    if (!values.some((v) => !Number.isNaN(v))) {\n        return;\n    }\n    for (let i = 0; i < values.length; i += 3) {\n        if (Number.isNaN(values[i])) {\n            values.fill(0, i, i + 3);\n        }\n    }\n}\n\n/**\n * Convert every placed row in place.\n * @param values - the raw coordinates\n * @param extra - the spelling\n * @param size - reads a row's width and height\n * @param realZ - whether z differs between nodes\n * @param notes - receives the anchor note\n */\nfunction convertRows(\n    values: Float64Array,\n    extra: PositionColumnExtra,\n    size: SizeReader,\n    realZ: boolean,\n    notes: NoteCollector<PositionNoteCode>,\n): void {\n    const p: Point = [0, 0, 0];\n    for (let i = 0; i < values.length; i += 3) {\n        if (Number.isNaN(values[i])) {\n            continue;\n        }\n        const s = extra.anchor === \"top-left\" ? size(i / 3) : null;\n        if (extra.anchor === \"top-left\" && s === null) {\n            notes.add(POSITION_ISSUE.ANCHOR_NO_SIZE, { element: i / 3 });\n        }\n        p[0] = values[i];\n        p[1] = values[i + 1];\n        p[2] = values[i + 2];\n        toNeutral(p, extra, s, realZ);\n        values.set(p, i);\n    }\n}\n\n/**\n * Reads a row's width and height from the size columns a spelling names.\n * @param snapshot - the graph\n * @param extra - the spelling\n * @returns the reader; it answers null for a row without both, or when the columns are missing\n */\nfunction sizeReader(snapshot: GraphSnapshot, extra: PositionColumnExtra): SizeReader {\n    const w = extra.width === undefined ? null : snapshot.nodes.get(extra.width);\n    const h = extra.height === undefined ? null : snapshot.nodes.get(extra.height);\n    if (w === null || h === null) {\n        return () => null;\n    }\n    return (row) => {\n        if (!w.isSet(row) || !h.isSet(row)) {\n            return null;\n        }\n        const size: [number, number] = [Number(w.value(row)), Number(h.value(row))];\n        return Number.isFinite(size[0]) && Number.isFinite(size[1]) ? size : null;\n    };\n}\n\n/**\n * NetworkX writes (0, 0) for a node with no position: when other rows are placed, an exact (0, 0)\n * shared by two or more rows counts as unplaced.\n * @param values - the raw coordinates, changed in place\n */\nfunction dropZeroPile(values: Float64Array): void {\n    const zeros: number[] = [];\n    let others = 0;\n    for (let i = 0; i < values.length; i += 3) {\n        if (values[i] === 0 && values[i + 1] === 0) {\n            zeros.push(i);\n        } else if (!Number.isNaN(values[i])) {\n            others++;\n        }\n    }\n    if (zeros.length >= 2 && others > 0) {\n        for (const i of zeros) {\n            values.fill(Number.NaN, i, i + 3);\n        }\n    }\n}\n\n/**\n * Whether every placed row has the same z (Pajek writes z = 0.5 on 2D drawings).\n * @param values - the raw coordinates\n * @returns true when z never differs\n */\nfunction constantZ(values: Float64Array): boolean {\n    let z = Number.NaN;\n    for (let i = 0; i < values.length; i += 3) {\n        if (Number.isNaN(values[i])) {\n            continue;\n        }\n        if (Number.isNaN(z)) {\n            z = values[i + 2];\n        } else if (values[i + 2] !== z) {\n            return false;\n        }\n    }\n    return true;\n}\n\n// ------------------------------------------------------------ groups\n\n/**\n * The nodes another node names as its parent: group containers.\n * @param snapshot - the graph\n * @returns the container indexes\n */\nfunction containersOf(snapshot: GraphSnapshot): Set<number> {\n    const out = new Set<number>();\n    const parent = snapshot.nodes.byRole(\"parent\");\n    if (parent === null) {\n        return out;\n    }\n    for (let row = 0; row < parent.length; row++) {\n        const v = parent.isSet(row) ? parent.value(row) : undefined;\n        if (typeof v === \"number\") {\n            out.add(v);\n        }\n    }\n    return out;\n}\n\n/**\n * The hook's group boxes in the neutral convention; a container with no coordinate of its own is\n * placed at its box's center.\n * @param spelling - the spelling and the hook's boxes\n * @param rows - the coordinates, changed in place\n * @returns the boxes\n */\nfunction applyGroups(spelling: Spelling, rows: Rows): FilePositionGroup[] {\n    const out: FilePositionGroup[] = [];\n    for (const { node, box } of spelling.groups) {\n        const p: Point = [box.x, box.y, 0];\n        toNeutral(p, spelling.extra, [box.width, box.height], false);\n        if (Number.isNaN(rows.values[3 * node])) {\n            rows.values.set(p, 3 * node);\n        }\n        if (!out.some((g) => g.node === node)) {\n            out.push({ node, box: { x: p[0], y: p[1], width: box.width, height: box.height } });\n        }\n    }\n    return out;\n}\n\n/**\n * Boxes for the containers the file gives a coordinate and a size (yEd groups).\n * @param spelling - the size reader\n * @param rows - the coordinates\n * @param containers - the container indexes\n * @param groups - receives the boxes\n */\nfunction collectGroups(\n    spelling: Spelling,\n    rows: Rows,\n    containers: ReadonlySet<number>,\n    groups: FilePositionGroup[],\n): void {\n    for (const node of containers) {\n        const size = spelling.size(node);\n        const i = 3 * node;\n        if (size !== null && !Number.isNaN(rows.values[i]) && !groups.some((g) => g.node === node)) {\n            groups.push({ node, box: { x: rows.values[i], y: rows.values[i + 1], width: size[0], height: size[1] } });\n        }\n    }\n}\n\n// ------------------------------------------------------------ counts and notes\n\n/**\n * Count the placed rows and the rows that need a position; note the unplaced ones.\n * @param rows - the coordinates\n * @param containers - containers without a coordinate do not need one\n * @param notes - receives the partial note\n * @returns placed and total\n */\nfunction countPlaced(\n    rows: Rows,\n    containers: ReadonlySet<number>,\n    notes: NoteCollector<PositionNoteCode>,\n): { placed: number; total: number } {\n    const { values } = rows;\n    const unplaced: number[] = [];\n    let placed = 0;\n    let total = 0;\n    for (let row = 0; 3 * row < values.length; row++) {\n        const has = !Number.isNaN(values[3 * row]);\n        if (has) {\n            placed++;\n        } else if (!containers.has(row)) {\n            unplaced.push(row);\n        }\n        total += has || !containers.has(row) ? 1 : 0;\n    }\n    if (placed > 0 && unplaced.length > 0) {\n        for (const element of unplaced) {\n            notes.add(POSITION_ISSUE.PARTIAL, { element });\n        }\n    }\n    return { placed, total };\n}\n\n/**\n * Drop the coordinates when every placed node sits on one point.\n * @param rows - the coordinates, cleared in place when stacked\n * @param placed - the placed count\n * @param notes - receives the stacked note\n * @returns whether they were stacked\n */\nfunction dropStacked(rows: Rows, placed: number, notes: NoteCollector<PositionNoteCode>): boolean {\n    if (placed < 2) {\n        return false;\n    }\n    const { values } = rows;\n    let first = -1;\n    for (let i = 0; i < values.length; i += 3) {\n        if (Number.isNaN(values[i])) {\n            continue;\n        }\n        if (first < 0) {\n            first = i;\n        } else if (\n            values[i] !== values[first] ||\n            values[i + 1] !== values[first + 1] ||\n            values[i + 2] !== values[first + 2]\n        ) {\n            return false;\n        }\n    }\n    notes.add(POSITION_ISSUE.STACKED, {\n        count: placed,\n        sample: Array.from(values.subarray(first, first + 3)).join(\",\"),\n    });\n    values.fill(Number.NaN);\n    return true;\n}\n\n/**\n * Lift the format readers' mixed-dimension warnings into the shared code.\n * @param report - the import report\n * @param notes - receives the note\n */\nfunction noteReport(report: ImportReport, notes: NoteCollector<PositionNoteCode>): void {\n    for (const issue of report.issues) {\n        if (DIMS_MIXED_CODES.has(issue.code)) {\n            notes.add(POSITION_ISSUE.DIMS_MIXED, { sample: issue.code });\n        }\n    }\n}\n\n/**\n * Note the extra view columns of a CX file (`position@2`, ...): only the first view is used.\n * @param snapshot - the graph\n * @param notes - receives the note\n */\nfunction noteOtherViews(snapshot: GraphSnapshot, notes: NoteCollector<PositionNoteCode>): void {\n    for (const column of snapshot.nodes) {\n        if (/^position@\\d+$/.test(column.meta.name) && column.meta.role === null) {\n            notes.add(POSITION_ISSUE.OTHER_VIEWS, { sample: column.meta.name });\n        }\n    }\n}\n\n/**\n * Note plain numeric `x` and `y` node columns a format does not read as positions.\n * @param snapshot - the graph\n * @param notes - receives the note\n */\nfunction noteUnread(snapshot: GraphSnapshot, notes: NoteCollector<PositionNoteCode>): void {\n    const numeric = (name: string): Column | undefined =>\n        [...snapshot.nodes].find(\n            (c) => c.meta.name.toLowerCase() === name && c.meta.components === 1 && isNumeric(c.dtype),\n        );\n    const x = numeric(\"x\");\n    const y = numeric(\"y\");\n    if (x !== undefined && y !== undefined) {\n        notes.add(POSITION_ISSUE.NOT_READ, { sample: x.meta.name });\n        notes.add(POSITION_ISSUE.NOT_READ, { sample: y.meta.name });\n    }\n}\n\n/**\n * Whether a dtype holds numbers.\n * @param dtype - the dtype\n * @returns true for the numeric dtypes\n */\nfunction isNumeric(dtype: string): boolean {\n    return dtype === \"f64\" || dtype === \"f32\" || dtype === \"i32\" || dtype === \"u32\" || dtype === \"u8\";\n}\n\n/**\n * The notes with graph-io's English.\n * @param notes - the collector\n * @returns the notes\n */\nfunction noteList(notes: NoteCollector<PositionNoteCode>): PositionNote[] {\n    return notes.list().map((n) => ({\n        code: n.code,\n        params: { count: n.count, samples: n.samples },\n        elements: n.elements,\n        message: `${PHRASES[n.code]} (${n.count})`,\n    }));\n}\n\n/**\n * The answer for a file with no readable positions but position-like columns.\n * @param importer - the importer\n * @param snapshot - the graph\n * @param notes - the notes\n * @returns positions with nothing placed\n */\nfunction emptyPositions(\n    importer: GraphImporter,\n    snapshot: GraphSnapshot,\n    notes: NoteCollector<PositionNoteCode>,\n): FilePositions {\n    return {\n        version: 1,\n        source: { format: importer.format, tool: toolOf(snapshot.meta.creator), yAxis: \"up\" },\n        units: \"file\",\n        medianNodeSize: null,\n        dims: 2,\n        coords: new Float64Array(3 * snapshot.nodeCount).fill(Number.NaN),\n        placed: 0,\n        total: snapshot.nodeCount,\n        usable: false,\n        bounds: null,\n        groups: [],\n        notes: noteList(notes),\n    };\n}\n\n// ------------------------------------------------------------ sizes and bounds\n\n/**\n * The median node diameter from the size columns the spelling names.\n * @param size - the size reader\n * @param n - the node count\n * @param containers - group containers, left out\n * @returns the median of each node's mean of width and height, or null when no node has a size\n */\nfunction medianSize(size: SizeReader, n: number, containers: ReadonlySet<number>): number | null {\n    const sizes: number[] = [];\n    for (let row = 0; row < n; row++) {\n        const s = containers.has(row) ? null : size(row);\n        if (s !== null) {\n            sizes.push((s[0] + s[1]) / 2);\n        }\n    }\n    return median(sizes);\n}\n\n/**\n * The box around every placed row.\n * @param values - the coordinates\n * @returns min and max, or null when none is placed\n */\nfunction boundsOf(values: Float64Array): FilePositions[\"bounds\"] {\n    const min: Point = [Infinity, Infinity, Infinity];\n    const max: Point = [-Infinity, -Infinity, -Infinity];\n    for (let i = 0; i < values.length; i += 3) {\n        if (Number.isNaN(values[i])) {\n            continue;\n        }\n        for (let k = 0; k < 3; k++) {\n            min[k] = Math.min(min[k], values[i + k]);\n            max[k] = Math.max(max[k], values[i + k]);\n        }\n    }\n    return min[0] === Infinity ? null : { min, max 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package/dist/sources-cypher.d.ts

@@ -0,0 +1 @@
+export * from "./src/sources/cypher/index.js";