@holoscript/radio-astronomy-plugin 2.0.3 → 2.0.4

package/src/fits/FITSParser.ts

@@ -1,312 +0,0 @@
-/**
- * FITSParser — Pure JavaScript parser for FITS (Flexible Image Transport System) files.
- *
- * FITS is the standard data format in astronomy. Structure:
- *   - Header: 2880-byte blocks of 80-character ASCII "cards" (key=value pairs)
- *   - Data: big-endian binary arrays, padded to 2880-byte boundary
- *   - Extensions: additional HDUs (Header Data Units) with same structure
- *
- * Supports: BITPIX 8 (uint8), 16 (int16), 32 (int32), -32 (float32), -64 (float64)
- * Handles: BSCALE/BZERO physical value scaling, WCS coordinate metadata
- *
- * @see https://fits.gsfc.nasa.gov/fits_standard.html
- */
-
-// ── Types ────────────────────────────────────────────────────────────────────
-
-export interface WCSInfo {
-  /** Reference pixel (1-indexed, per FITS convention) */
-  crpix: number[];
-  /** Reference value (world coordinate at reference pixel) */
-  crval: number[];
-  /** Pixel scale (coordinate increment per pixel) */
-  cdelt: number[];
-  /** Axis types (e.g., 'RA---TAN', 'DEC--TAN', 'FREQ') */
-  ctype: string[];
-  /** Axis units */
-  cunit: string[];
-}
-
-export interface FITSFile {
-  /** All header cards as key→value */
-  headers: Map<string, string | number | boolean>;
-  /** Data array (physical values after BSCALE/BZERO) */
-  data: Float32Array;
-  /** Axis dimensions [NAXIS1, NAXIS2, ...] */
-  shape: number[];
-  /** World Coordinate System info (if present) */
-  wcs: WCSInfo | null;
-  /** BITPIX from header */
-  bitpix: number;
-  /** Object name (OBJECT card) */
-  object: string;
-  /** Telescope name (TELESCOP card) */
-  telescope: string;
-  /** Observation date (DATE-OBS card) */
-  dateObs: string;
-}
-
-// ── Constants ────────────────────────────────────────────────────────────────
-
-const BLOCK_SIZE = 2880;
-const CARD_SIZE = 80;
-const CARDS_PER_BLOCK = BLOCK_SIZE / CARD_SIZE; // 36
-
-// ── Parser ───────────────────────────────────────────────────────────────────
-
-/**
- * Parse a FITS file from an ArrayBuffer.
- * Returns the primary HDU (first header + data unit).
- */
-export function parseFITS(buffer: ArrayBuffer): FITSFile {
-  const bytes = new Uint8Array(buffer);
-  const view = new DataView(buffer);
-
-  // ── Parse Header ─────────────────────────────────────────────────
-  const headers = new Map<string, string | number | boolean>();
-  let headerEnd = 0;
-
-  outer: for (let block = 0; block * BLOCK_SIZE < buffer.byteLength; block++) {
-    for (let card = 0; card < CARDS_PER_BLOCK; card++) {
-      const offset = block * BLOCK_SIZE + card * CARD_SIZE;
-      if (offset + CARD_SIZE > buffer.byteLength) break outer;
-
-      const cardStr = decodeASCII(bytes, offset, CARD_SIZE);
-      const keyword = cardStr.substring(0, 8).trim();
-
-      if (keyword === 'END') {
-        headerEnd = (block + 1) * BLOCK_SIZE; // data starts at next block boundary
-        break outer;
-      }
-
-      if (cardStr[8] === '=' && cardStr[9] === ' ') {
-        const valueStr = cardStr.substring(10).split('/')[0].trim();
-        headers.set(keyword, parseCardValue(valueStr));
-      } else if (keyword === 'COMMENT' || keyword === 'HISTORY') {
-        // Skip comment/history cards
-      }
-    }
-  }
-
-  if (headerEnd === 0) {
-    throw new Error('FITS: No END card found in header');
-  }
-
-  // ── Extract Critical Keywords ────────────────────────────────────
-  const bitpix = getNum(headers, 'BITPIX');
-  const naxis = getNum(headers, 'NAXIS');
-
-  const shape: number[] = [];
-  for (let i = 1; i <= naxis; i++) {
-    shape.push(getNum(headers, `NAXIS${i}`));
-  }
-
-  const bscale = getNumOr(headers, 'BSCALE', 1.0);
-  const bzero = getNumOr(headers, 'BZERO', 0.0);
-
-  // ── Parse Data ───────────────────────────────────────────────────
-  const totalPixels = shape.reduce((a, b) => a * b, 1);
-  const bytesPerPixel = Math.abs(bitpix) / 8;
-  const dataOffset = headerEnd;
-
-  if (dataOffset + totalPixels * bytesPerPixel > buffer.byteLength) {
-    throw new Error(
-      `FITS: Data section extends beyond buffer (need ${dataOffset + totalPixels * bytesPerPixel}, have ${buffer.byteLength})`
-    );
-  }
-
-  const data = new Float32Array(totalPixels);
-
-  for (let i = 0; i < totalPixels; i++) {
-    const off = dataOffset + i * bytesPerPixel;
-    let raw: number;
-
-    switch (bitpix) {
-      case 8:
-        raw = bytes[off];
-        break;
-      case 16:
-        raw = view.getInt16(off, false); // big-endian
-        break;
-      case 32:
-        raw = view.getInt32(off, false);
-        break;
-      case -32:
-        raw = view.getFloat32(off, false);
-        break;
-      case -64:
-        raw = view.getFloat64(off, false);
-        break;
-      default:
-        throw new Error(`FITS: Unsupported BITPIX ${bitpix}`);
-    }
-
-    // Apply physical value transformation
-    data[i] = bscale * raw + bzero;
-  }
-
-  // ── Extract WCS ──────────────────────────────────────────────────
-  let wcs: WCSInfo | null = null;
-  if (headers.has('CRVAL1')) {
-    wcs = {
-      crpix: [],
-      crval: [],
-      cdelt: [],
-      ctype: [],
-      cunit: [],
-    };
-    for (let i = 1; i <= naxis; i++) {
-      wcs.crpix.push(getNumOr(headers, `CRPIX${i}`, 1));
-      wcs.crval.push(getNumOr(headers, `CRVAL${i}`, 0));
-      wcs.cdelt.push(getNumOr(headers, `CDELT${i}`, 1));
-      wcs.ctype.push(getStrOr(headers, `CTYPE${i}`, ''));
-      wcs.cunit.push(getStrOr(headers, `CUNIT${i}`, ''));
-    }
-  }
-
-  return {
-    headers,
-    data,
-    shape,
-    wcs,
-    bitpix,
-    object: getStrOr(headers, 'OBJECT', ''),
-    telescope: getStrOr(headers, 'TELESCOP', ''),
-    dateObs: getStrOr(headers, 'DATE-OBS', ''),
-  };
-}
-
-// ── FITS Builder (for tests) ─────────────────────────────────────────────────
-
-/**
- * Build a minimal FITS file as ArrayBuffer (for testing).
- */
-export function buildFITS(opts: {
-  bitpix: number;
-  shape: number[];
-  data: number[];
-  bscale?: number;
-  bzero?: number;
-  headers?: Record<string, string | number>;
-}): ArrayBuffer {
-  const cards: string[] = [];
-
-  cards.push(fmtCard('SIMPLE', true));
-  cards.push(fmtCard('BITPIX', opts.bitpix));
-  cards.push(fmtCard('NAXIS', opts.shape.length));
-  for (let i = 0; i < opts.shape.length; i++) {
-    cards.push(fmtCard(`NAXIS${i + 1}`, opts.shape[i]));
-  }
-  if (opts.bscale !== undefined) cards.push(fmtCard('BSCALE', opts.bscale));
-  if (opts.bzero !== undefined) cards.push(fmtCard('BZERO', opts.bzero));
-
-  if (opts.headers) {
-    for (const [key, val] of Object.entries(opts.headers)) {
-      cards.push(fmtCard(key, val));
-    }
-  }
-
-  cards.push('END'.padEnd(CARD_SIZE));
-
-  // Pad header to block boundary
-  while (cards.length % CARDS_PER_BLOCK !== 0) {
-    cards.push(' '.repeat(CARD_SIZE));
-  }
-
-  const headerBytes = new Uint8Array(cards.length * CARD_SIZE);
-  for (let i = 0; i < cards.length; i++) {
-    for (let j = 0; j < CARD_SIZE; j++) {
-      headerBytes[i * CARD_SIZE + j] = cards[i].charCodeAt(j);
-    }
-  }
-
-  // Write data
-  const bytesPerPixel = Math.abs(opts.bitpix) / 8;
-  const dataSize = opts.data.length * bytesPerPixel;
-  const paddedDataSize = Math.ceil(dataSize / BLOCK_SIZE) * BLOCK_SIZE;
-  const dataBytes = new ArrayBuffer(paddedDataSize);
-  const dataView = new DataView(dataBytes);
-
-  for (let i = 0; i < opts.data.length; i++) {
-    const off = i * bytesPerPixel;
-    switch (opts.bitpix) {
-      case 8:
-        new Uint8Array(dataBytes)[off] = opts.data[i];
-        break;
-      case 16:
-        dataView.setInt16(off, opts.data[i], false);
-        break;
-      case 32:
-        dataView.setInt32(off, opts.data[i], false);
-        break;
-      case -32:
-        dataView.setFloat32(off, opts.data[i], false);
-        break;
-      case -64:
-        dataView.setFloat64(off, opts.data[i], false);
-        break;
-    }
-  }
-
-  // Combine
-  const result = new Uint8Array(headerBytes.length + paddedDataSize);
-  result.set(headerBytes);
-  result.set(new Uint8Array(dataBytes), headerBytes.length);
-  return result.buffer;
-}
-
-// ── Helpers ──────────────────────────────────────────────────────────────────
-
-function decodeASCII(bytes: Uint8Array, offset: number, length: number): string {
-  let s = '';
-  for (let i = 0; i < length; i++) {
-    s += String.fromCharCode(bytes[offset + i]);
-  }
-  return s;
-}
-
-function parseCardValue(s: string): string | number | boolean {
-  if (s === 'T') return true;
-  if (s === 'F') return false;
-  if (s.startsWith("'")) return s.replace(/^'|'$/g, '').trim();
-  const n = Number(s);
-  return Number.isNaN(n) ? s : n;
-}
-
-function getNum(headers: Map<string, string | number | boolean>, key: string): number {
-  const v = headers.get(key);
-  if (typeof v !== 'number') throw new Error(`FITS: Missing or non-numeric header ${key}`);
-  return v;
-}
-
-function getNumOr(
-  headers: Map<string, string | number | boolean>,
-  key: string,
-  def: number
-): number {
-  const v = headers.get(key);
-  return typeof v === 'number' ? v : def;
-}
-
-function getStrOr(
-  headers: Map<string, string | number | boolean>,
-  key: string,
-  def: string
-): string {
-  const v = headers.get(key);
-  return typeof v === 'string' ? v : def;
-}
-
-function fmtCard(keyword: string, value: string | number | boolean): string {
-  const kw = keyword.padEnd(8);
-  let valStr: string;
-  if (typeof value === 'boolean') {
-    valStr = value ? 'T' : 'F';
-    valStr = valStr.padStart(20);
-  } else if (typeof value === 'number') {
-    valStr = String(value).padStart(20);
-  } else {
-    valStr = `'${value}'`.padEnd(20);
-  }
-  return `${kw}= ${valStr}`.padEnd(CARD_SIZE);
-}

package/src/fits/FITSToGrid.ts

@@ -1,96 +0,0 @@
-/**
- * FITSToGrid — Convert parsed FITS data to HoloScript grid structures.
- *
- * Maps FITS spectral cubes (RA × Dec × Freq) and 2D images to
- * RegularGrid3D for visualization via ScalarFieldOverlay or SimResultsMesh.
- */
-
-import { RegularGrid3D } from '@holoscript/engine/simulation';
-import type { FITSFile } from './FITSParser';
-
-/**
- * Convert a parsed FITS file to a RegularGrid3D.
- *
- * - 3D cubes (NAXIS=3): maps directly to grid
- * - 2D images (NAXIS=2): creates a 1-deep grid (nx × ny × 1)
- * - 1D spectra (NAXIS=1): creates a 1×1×n grid
- */
-export function fitsToGrid3D(fits: FITSFile): RegularGrid3D {
-  const shape = fits.shape;
-
-  let nx: number, ny: number, nz: number;
-
-  if (shape.length >= 3) {
-    nx = shape[0];
-    ny = shape[1];
-    nz = shape[2];
-  } else if (shape.length === 2) {
-    nx = shape[0];
-    ny = shape[1];
-    nz = 1;
-  } else if (shape.length === 1) {
-    nx = shape[0];
-    ny = 1;
-    nz = 1;
-  } else {
-    throw new Error(`FITS: Cannot convert ${shape.length}D data to grid`);
-  }
-
-  const grid = new RegularGrid3D([nx, ny, nz], [nx, ny, nz]);
-
-  // FITS stores data in FORTRAN order (column-major: NAXIS1 varies fastest)
-  // RegularGrid3D uses row-major (x varies fastest in our convention)
-  // Since NAXIS1 = x and it varies fastest in both, direct copy works
-  const data = fits.data;
-  const gridData = grid.data;
-  const len = Math.min(data.length, gridData.length);
-
-  for (let i = 0; i < len; i++) {
-    gridData[i] = data[i];
-  }
-
-  return grid;
-}
-
-/**
- * Extract a single frequency channel (z-slice) from a 3D FITS cube.
- * Returns a 2D Float32Array (nx × ny) for use as a ScalarFieldOverlay.
- */
-export function extractChannel(fits: FITSFile, channel: number): Float32Array {
-  if (fits.shape.length < 3) {
-    // 2D image — return the whole thing
-    return new Float32Array(fits.data);
-  }
-
-  const nx = fits.shape[0];
-  const ny = fits.shape[1];
-  const nz = fits.shape[2];
-
-  if (channel < 0 || channel >= nz) {
-    throw new Error(`Channel ${channel} out of range [0, ${nz - 1}]`);
-  }
-
-  const slice = new Float32Array(nx * ny);
-  const offset = channel * nx * ny;
-
-  for (let i = 0; i < nx * ny; i++) {
-    slice[i] = fits.data[offset + i];
-  }
-
-  return slice;
-}
-
-/**
- * Get data range (min/max) for the FITS data.
- * Useful for colormap normalization.
- */
-export function fitsDataRange(fits: FITSFile): [number, number] {
-  let min = Infinity,
-    max = -Infinity;
-  for (let i = 0; i < fits.data.length; i++) {
-    const v = fits.data[i];
-    if (v < min) min = v;
-    if (v > max) max = v;
-  }
-  return [min, max];
-}

package/src/index.ts

@@ -1,37 +0,0 @@
-import { RADIO_ASTRONOMY_TRAITS, RadioAstronomyTraitName } from './constants/astronomy-traits';
-import { PythonAstropyBridge, AstropyResult } from './bridge/python-runner';
-
-/**
- * @holoscript/radio-astronomy-plugin
- *
- * Domain plugin bridging Radio Astrophysics simulation concepts into the HoloScript Universal pipeline.
- * Extends standard traits without bloating core. Provides an astropy python bridge for logic evaluation.
- */
-
-// Export vocabulary
-export { RADIO_ASTRONOMY_TRAITS, type RadioAstronomyTraitName };
-
-// Export Bridges
-export { PythonAstropyBridge, type AstropyResult };
-
-// Export FITS parsing and visualization
-export { parseFITS, buildFITS, type FITSFile, type WCSInfo } from './fits/FITSParser';
-export { fitsToGrid3D, extractChannel, fitsDataRange } from './fits/FITSToGrid';
-export {
-  SpectralCubeViewer,
-  FITSViewerPanel,
-  type SpectralCubeViewerProps,
-  type FITSViewerPanelProps,
-} from './components/SpectralCubeViewer';
-
-/**
- * Metadata exposing domain capabilities to the Studio / Schema Mapper.
- */
-export const DOMAIN_MANIFEST = {
-  id: 'domain.science.astronomy.radio',
-  name: 'Radio Astronomy Plugin',
-  version: '1.0.0',
-  description: 'Extends HoloScript spatial environments with radio astrophysics primitives.',
-  keywords: ['interferometer', 'radio emitting', 'synchrotron radiation', 'pulsar'],
-  traits: RADIO_ASTRONOMY_TRAITS,
-};

package/tsconfig.json

@@ -1,26 +0,0 @@
-{
-  "compilerOptions": {
-    "target": "ES2020",
-    "module": "ESNext",
-    "moduleResolution": "bundler",
-    "lib": ["ES2020", "DOM"],
-    "declaration": true,
-    "declarationMap": true,
-    "sourceMap": true,
-    "strict": true,
-    "noImplicitAny": true,
-    "strictNullChecks": true,
-    "noUnusedLocals": false,
-    "noUnusedParameters": false,
-    "resolveJsonModule": true,
-    "esModuleInterop": true,
-    "skipLibCheck": true,
-    "forceConsistentCasingInFileNames": true,
-    "outDir": "./dist",
-    "rootDir": "./src",
-    "experimentalDecorators": true,
-    "jsx": "react-jsx"
-  },
-  "include": ["src/**/*"],
-  "exclude": ["node_modules", "dist", "src/**/*.test.ts", "src/**/*.bench.ts", "src/__tests__/**/*"]
-}

package/vitest.config.ts

@@ -1,10 +0,0 @@
-import { defineConfig } from 'vitest/config';
-
-export default defineConfig({
-  test: {
-    globals: true,
-    environment: 'node',
-    include: ['src/**/*.test.ts'],
-    passWithNoTests: true,
-  },
-});