matterviz 0.3.5 → 0.3.6

package/src/webview/main.ts

@@ -0,0 +1,764 @@
+// Import MatterViz parsing functions and components
+import '$lib/app.css'
+import { COMPRESSION_EXTENSIONS_REGEX } from '$lib/constants'
+import ConvexHull from '$lib/convex-hull/ConvexHull.svelte'
+import type { PhaseData } from '$lib/convex-hull/types'
+import FermiSurface from '$lib/fermi-surface/FermiSurface.svelte'
+import { parse_fermi_file } from '$lib/fermi-surface/parse'
+import { is_fermi_surface_data } from '$lib/fermi-surface/types'
+import { decompress_data, detect_compression_format } from '$lib/io/decompress'
+import { parse_volumetric_file } from '$lib/isosurface/parse'
+import type { VolumetricData } from '$lib/isosurface/types'
+import IsobaricBinaryPhaseDiagram from '$lib/phase-diagram/IsobaricBinaryPhaseDiagram.svelte'
+import type { PhaseDiagramData } from '$lib/phase-diagram/types'
+import { type DefaultSettings, merge } from '$lib/settings'
+import type { AnyStructure } from '$lib/structure'
+import { parse_structure_file } from '$lib/structure/parse'
+import Structure from '$lib/structure/Structure.svelte'
+import { ensure_moyo_wasm_ready } from '$lib/symmetry'
+import { apply_theme_to_dom, is_valid_theme_name, type ThemeName } from '$lib/theme/index'
+import '$lib/theme/themes.mjs'
+import type {
+  FrameIndex,
+  FrameLoader,
+  TrajectoryFrame,
+  TrajectoryMetadata,
+  TrajectoryType,
+} from '$lib/trajectory'
+import { is_trajectory_file, parse_trajectory_data } from '$lib/trajectory/parse'
+import Trajectory from '$lib/trajectory/Trajectory.svelte'
+import { mount, unmount } from 'svelte'
+import type { ViewType } from '../types'
+import { FERMI_FILE_RE, VOLUMETRIC_EXT_RE, VOLUMETRIC_VASP_RE } from '../types'
+import type { RenderableType } from './detect'
+import { detect_view_type } from './detect'
+import JsonBrowser from './JsonBrowser.svelte'
+
+// Maps detect.ts RenderableType to ViewType for direct rendering.
+// Types not listed here fall through to json_browser (which can render all types
+// via its internal mount_into, giving the user a tree view alongside the viz).
+// structure and volumetric have special handling in parse_file_content below.
+const DETECTION_TO_VIEW_TYPE: Partial<Record<RenderableType, ViewType>> = {
+  fermi_surface: `fermi_surface`,
+  band_grid: `fermi_surface`,
+  convex_hull: `convex_hull`,
+  phase_diagram: `phase_diagram`,
+}
+
+export type { ViewType }
+export interface FileData {
+  filename: string
+  content: string
+  is_base64: boolean
+}
+
+export interface MatterVizData {
+  type: ViewType
+  data: FileData
+  theme: ThemeName
+  defaults?: DefaultSettings
+  moyo_wasm_url?: string
+}
+
+export interface ParseResult {
+  type: ViewType
+  data: unknown
+  filename: string
+  // For trajectories that support VS Code streaming
+  streaming_info?: { supports_streaming: boolean; file_path: string }
+}
+
+export interface MatterVizApp {
+  $on?(type: string, callback: (event: Event) => void): () => void
+  $set?(props: Partial<Record<string, unknown>>): void
+}
+
+export interface FileChangeMessage {
+  command: `fileUpdated` | `fileDeleted`
+  file_path?: string
+  data?: FileData
+  type?: ViewType
+  theme?: ThemeName
+}
+
+// VS Code Frame Loader - streams frames via extension communication
+class VSCodeFrameLoader implements FrameLoader {
+  constructor(
+    private readonly file_path: string,
+    private readonly vscode_api: VSCodeAPI,
+  ) {}
+
+  // Only implement the method we actually use
+  async load_frame(
+    _data: string | ArrayBuffer,
+    frame_index: number,
+    timeout: number = 10, // 10 seconds
+  ): Promise<TrajectoryFrame | null> {
+    return new Promise((resolve, reject) => {
+      const request_id = crypto.randomUUID()
+      let timer: ReturnType<typeof setTimeout> | null = null
+      const handler = (event: MessageEvent) => {
+        const { command, request_id: id, error, frame } = event.data
+        if (command === `frame_response` && id === request_id) {
+          globalThis.removeEventListener(`message`, handler)
+          if (timer) clearTimeout(timer)
+          if (error) reject(new Error(error))
+          else resolve(frame)
+        }
+      }
+
+      globalThis.addEventListener(`message`, handler)
+      this.vscode_api.postMessage({
+        command: `request_frame`,
+        request_id,
+        file_path: this.file_path,
+        frame_index,
+      })
+
+      timer = setTimeout(() => {
+        globalThis.removeEventListener(`message`, handler)
+        reject(new Error(`Frame ${frame_index} timeout after ${timeout}s`))
+      }, timeout * 1000)
+    })
+  }
+
+  // Unused methods - just throw errors
+  async get_total_frames(): Promise<number> {
+    throw new Error(`Not implemented`)
+  }
+  async build_frame_index(): Promise<FrameIndex[]> {
+    throw new Error(`Not implemented`)
+  }
+  async extract_plot_metadata(): Promise<TrajectoryMetadata[]> {
+    throw new Error(`Not implemented`)
+  }
+}
+
+export interface VSCodeAPI {
+  postMessage(message: unknown): void
+}
+
+// Extend globalThis interface for MatterViz data
+declare global {
+  interface Window {
+    matterviz_data?: MatterVizData
+    initializeMatterViz?: () => Promise<MatterVizApp | null>
+    cleanupMatterViz?: () => Promise<void>
+    download?: (data: string | Blob, filename: string) => void
+  }
+  // Also declare as global var for direct access via globalThis.matterviz_data
+  // Both are needed: Window.matterviz_data is set by extension.ts, accessed via globalThis
+  var matterviz_data: MatterVizData | undefined
+
+  // VSCode webview API
+  function acquireVsCodeApi(): VSCodeAPI
+}
+
+// Store VSCode API instance to avoid multiple acquisitions
+let vscode_api: VSCodeAPI | null = null
+let current_app: MatterVizApp | null = null
+
+// Initialize VSCode API at module level
+try {
+  vscode_api = globalThis.acquireVsCodeApi?.() ?? null
+} catch (error) {
+  console.warn(`VSCode API already acquired or not available:`, error)
+  vscode_api = null
+}
+
+// Set up VSCode-specific download override for file exports
+export const setup_vscode_download = (): void => {
+  if (!vscode_api) return
+  ;(globalThis as unknown as Window).download = (
+    data: string | Blob,
+    filename: string,
+  ): void => {
+    if (!filename?.trim()) {
+      console.error(`Invalid filename provided to download`)
+      return
+    }
+
+    const send_message = (content: string, is_binary: boolean) => {
+      vscode_api?.postMessage({
+        command: `saveAs`,
+        content,
+        filename,
+        is_binary,
+      })
+    }
+
+    try {
+      if (typeof data === `string`) {
+        send_message(data, false)
+      } else {
+        const reader = new FileReader()
+        reader.addEventListener(`load`, () => send_message(reader.result as string, true))
+        reader.addEventListener(`error`, () => {
+          console.error(`Failed to read binary data for download`)
+          vscode_api?.postMessage({
+            command: `error`,
+            text: `Failed to read binary data for download`,
+          })
+        })
+        reader.readAsDataURL(data)
+      }
+    } catch (error) {
+      console.error(`VSCode download failed:`, error)
+      vscode_api?.postMessage({
+        command: `error`,
+        text: `Download failed: ${error}`,
+      })
+    }
+  }
+}
+
+// Handle file change events from extension
+const handle_file_change = async (message: FileChangeMessage): Promise<void> => {
+  if (message.command === `fileDeleted`) {
+    // File was deleted - show error message
+    const container = document.getElementById(`matterviz-app`)
+    if (container) {
+      container.innerHTML = `
+        <div style="padding: 2rem; text-align: center; color: var(--vscode-errorForeground);">
+          <h2>File Deleted</h2>
+          <p>The file "${escape_html(message.file_path ?? ``)}" has been deleted.</p>
+        </div>
+      `
+    }
+    return
+  }
+
+  if (message.command === `fileUpdated` && message.data) {
+    try {
+      if (message.theme && is_valid_theme_name(message.theme)) {
+        apply_theme_to_dom(message.theme)
+      }
+
+      const { content, filename, is_base64 } = message.data
+      const result = await parse_file_content(content, filename, is_base64)
+
+      // Update the display
+      const container = document.getElementById(`matterviz-app`)
+      if (container && current_app) {
+        await unmount(current_app) // unmount the existing component to prevent memory leaks
+        current_app = create_display(container, result, result.filename)
+      }
+
+      vscode_api?.postMessage({ command: `info`, text: `File reloaded successfully` })
+    } catch (error) {
+      console.error(`Failed to reload file:`, error)
+      vscode_api?.postMessage({
+        command: `error`,
+        text: `Failed to reload file: ${error}`,
+      })
+    }
+  }
+}
+
+// Convert base64 to ArrayBuffer for binary files
+export function base64_to_array_buffer(base64: string): ArrayBuffer {
+  const binary = atob(base64)
+  const bytes = new Uint8Array(binary.length)
+  for (let idx = 0; idx < binary.length; idx++) {
+    bytes[idx] = binary.charCodeAt(idx)
+  }
+  return bytes.buffer
+}
+
+// Type for parsed trajectory response from large file requests
+type ParsedTrajectoryResponse = {
+  trajectory: TrajectoryType
+  supports_streaming: boolean
+  file_path: string
+}
+
+// Request large file content from the extension using chunked streaming
+function request_large_file_content(
+  file_path: string,
+  filename: string,
+  is_compressed: boolean,
+  timeout: number = 30_000, // 30 seconds
+): Promise<string | ParsedTrajectoryResponse> {
+  if (!vscode_api) throw new Error(`VS Code API not available`)
+
+  return new Promise((resolve, reject) => {
+    const request_id = crypto.randomUUID()
+
+    let timer: ReturnType<typeof setTimeout> | null = null
+    const handler = (event: MessageEvent) => {
+      const { command, request_id: id, error, parsed_trajectory } = event.data
+      const { is_parsed, stage, progress } = event.data
+      if (command === `large_file_progress` && id === request_id) {
+        // TODO maybe forward file load progress to UI
+        console.info(`Progress: ${stage} - ${progress}%`)
+        return
+      }
+      if (command === `large_file_response` && id === request_id) {
+        globalThis.removeEventListener(`message`, handler)
+        if (timer) clearTimeout(timer)
+        if (error) return reject(new Error(error))
+        if (is_parsed && parsed_trajectory) {
+          return resolve({
+            trajectory: parsed_trajectory,
+            supports_streaming: true,
+            file_path,
+          })
+        }
+        resolve(event.data.content)
+      }
+    }
+
+    globalThis.addEventListener(`message`, handler)
+    const command = `request_large_file`
+    vscode_api.postMessage({ command, request_id, file_path, filename, is_compressed })
+
+    timer = setTimeout(() => {
+      globalThis.removeEventListener(`message`, handler)
+      reject(new Error(`Large file timeout`))
+    }, timeout)
+  })
+}
+
+// Parse file content and determine if it's a structure or trajectory
+const parse_file_content = async (
+  content: string,
+  filename: string,
+  is_compressed: boolean = false,
+  recursion_depth: number = 0,
+): Promise<ParseResult> => {
+  if (recursion_depth > 2) {
+    throw new Error(
+      `parse_file_content exceeded max recursion depth=2 while parsing file ${filename}`,
+    )
+  }
+
+  // Check if this is a large file marker from the extension
+  if (content.startsWith(`LARGE_FILE:`)) {
+    const [, file_path, file_size_str] = content.split(`:`)
+    const file_size = parseInt(file_size_str, 10)
+
+    console.info(`Handling large file: ${filename} (${Math.round(file_size / 1024 / 1024)}MB)`)
+
+    const parsed_trajectory = await request_large_file_content(
+      file_path,
+      filename,
+      is_compressed,
+    )
+
+    // Check if we received a pre-parsed trajectory with VS Code streaming support
+    if (
+      parsed_trajectory &&
+      typeof parsed_trajectory === `object` &&
+      `trajectory` in parsed_trajectory &&
+      `supports_streaming` in parsed_trajectory
+    ) {
+      const { trajectory, supports_streaming, file_path } = parsed_trajectory
+      const streaming_info = { supports_streaming, file_path }
+      return { type: `trajectory`, data: trajectory, filename, streaming_info }
+    }
+
+    // Fallback: if not pre-parsed, treat as raw content
+    return parse_file_content(
+      parsed_trajectory as string,
+      filename,
+      is_compressed,
+      recursion_depth + 1,
+    )
+  }
+
+  // Handle compressed/binary files by converting from base64 first
+  if (is_compressed) {
+    const buffer = base64_to_array_buffer(content)
+
+    // Binary trajectory formats: pass buffer directly to trajectory parser
+    if (/\.(h5|hdf5|traj)$/i.test(filename)) {
+      const data = await parse_trajectory_data(buffer, filename)
+      return { type: `trajectory`, filename, data }
+    }
+
+    // Unified handling for all supported compression formats
+    const format = detect_compression_format(filename)
+    if (format && format !== `zip`) {
+      // Skip ZIP as it's not supported in browser
+      content = await decompress_data(buffer, format)
+      filename = filename.replace(COMPRESSION_EXTENSIONS_REGEX, ``)
+    }
+  }
+
+  // Try trajectory parsing first if it looks like a trajectory
+  if (is_trajectory_file(filename, content)) {
+    const data = await parse_trajectory_data(content, filename)
+    return { type: `trajectory`, data, filename }
+  }
+
+  // Fermi surface files (.bxsf, .frmsf)
+  // Use basename for regex matching in case filename retains a directory prefix
+  const basename = filename.split(`/`).pop() ?? filename
+  if (FERMI_FILE_RE.test(basename)) {
+    const data = parse_fermi_file(content, filename)
+    if (data) return { type: `fermi_surface`, data, filename }
+    throw new Error(`Failed to parse Fermi surface file: ${filename}`)
+  }
+
+  // Volumetric data files (.cube, CHGCAR, AECCAR*, ELFCAR, LOCPOT, PARCHG)
+  if (VOLUMETRIC_EXT_RE.test(basename) || VOLUMETRIC_VASP_RE.test(basename)) {
+    const data = parse_volumetric_file(content, filename)
+    if (data) return { type: `isosurface`, data, filename }
+    throw new Error(`Failed to parse volumetric file: ${filename}`)
+  }
+
+  // JSON files: use smart detection + JSON browser
+  if (/\.json$/i.test(filename)) {
+    try {
+      const parsed = JSON.parse(content)
+      // Check if the top-level value matches a known visualization type
+      const detected = detect_view_type(parsed)
+      if (detected) {
+        // Structure JSON needs normalization (OPTIMADE, fractional coords, etc.)
+        if (detected === `structure`) {
+          const structure = parse_structure_file(content, filename)
+          if (structure?.sites) {
+            return {
+              type: `structure`,
+              data: { ...structure, id: filename.replace(/\.[^/.]+$/, ``) },
+              filename,
+            }
+          }
+        }
+        // Volumetric JSON needs wrapping in { structure, volumes } for the isosurface renderer
+        if (detected === `volumetric`) {
+          const vol = parsed as { lattice?: unknown }
+          return {
+            type: `isosurface`,
+            data: { structure: { sites: [], lattice: vol.lattice }, volumes: [parsed] },
+            filename,
+          }
+        }
+        return {
+          type: DETECTION_TO_VIEW_TYPE[detected] ?? `json_browser`,
+          data: parsed,
+          filename,
+        }
+      }
+      // No top-level match -- show JSON browser for navigation
+      return { type: `json_browser`, data: parsed, filename }
+    } catch {
+      // JSON parse failed, fall through to structure parser
+    }
+  }
+
+  // Parse as structure (CIF, POSCAR, XYZ, etc.)
+  const structure = parse_structure_file(content, filename)
+  if (!structure?.sites) {
+    throw new Error(`Failed to parse file or no atoms found`)
+  }
+
+  const data = { ...structure, id: filename.replace(/\.[^/.]+$/, ``) }
+  return { type: `structure`, data, filename }
+}
+
+// Escape HTML special chars to prevent XSS when inserting into innerHTML
+const escape_html = (text: string): string =>
+  text
+    .replace(/&/g, `&amp;`)
+    .replace(/</g, `&lt;`)
+    .replace(/>/g, `&gt;`)
+    .replace(/"/g, `&quot;`)
+    .replace(/'/g, `&#39;`)
+
+// Create error display in container
+const create_error_display = (
+  container: HTMLElement,
+  error: Error,
+  filename: string,
+): void => {
+  container.innerHTML = `
+    <div style="padding: 20px; text-align: center; color: var(--vscode-errorForeground, #f85149);
+                background: var(--vscode-editor-background, #1e1e1e); height: 100%;
+                display: flex; flex-direction: column; justify-content: center; align-items: center;">
+      <div style="font-size: 48px; margin-bottom: 20px;">❌</div>
+      <h2 style="margin: 0 0 15px 0;">Failed to Parse File</h2>
+      <div style="background: rgba(255,255,255,0.1); padding: 20px; border-radius: 8px; max-width: 600px;">
+        <p style="margin: 0 0 10px 0;"><strong>File:</strong> ${escape_html(filename)}</p>
+        <p style="margin: 0 0 10px 0;"><strong>Error:</strong> ${escape_html(error.message)}</p>
+        <p style="margin: 0; font-size: 14px; opacity: 0.8;">
+          Supported formats: XYZ, CIF, JSON, POSCAR, trajectory files (.traj, .h5, .extxyz), etc.
+        </p>
+      </div>
+    </div>`
+}
+
+// Mount Svelte component and create display
+const create_display = (
+  container: HTMLElement,
+  result: ParseResult,
+  filename: string,
+): MatterVizApp => {
+  Object.assign(container.style, {
+    width: `100%`,
+    height: `100%`,
+    position: `absolute`,
+    top: `0`,
+    left: `0`,
+    right: `0`,
+    bottom: `0`,
+    background: `var(--vscode-editor-background, #1e1e1e)`,
+    color: `var(--vscode-editor-foreground, #d4d4d4)`,
+    overflow: `hidden`,
+  })
+  container.innerHTML = ``
+
+  // Get defaults and create props
+  const defaults = merge(globalThis.matterviz_data?.defaults)
+  const common_props = {
+    allow_file_drop: false,
+    style: `height: 100%; border-radius: 0`,
+    enable_tips: false,
+    fullscreen_toggle: false,
+  }
+
+  let app: MatterVizApp
+  let log_message: string
+
+  if (result.type === `trajectory`) {
+    // Type for trajectory with optional frame loader for streaming
+    type StreamingTrajectory = TrajectoryType & { frame_loader?: FrameLoader }
+
+    // Prepare trajectory data for VS Code streaming if supported
+    let final_trajectory: TrajectoryType | StreamingTrajectory = result.data as TrajectoryType
+
+    if (result.streaming_info?.supports_streaming) {
+      const trajectory = result.data as TrajectoryType
+      if (vscode_api && result.streaming_info.file_path) {
+        final_trajectory = {
+          ...trajectory,
+          is_indexed: true,
+          frames: trajectory.frames || [],
+          frame_loader: new VSCodeFrameLoader(result.streaming_info.file_path, vscode_api),
+        }
+      }
+    }
+
+    app = mount(Trajectory, {
+      target: container,
+      props: {
+        trajectory: final_trajectory,
+        ...trajectory_props(defaults),
+        ...common_props,
+      },
+    })
+    log_message = `Trajectory rendered: ${filename} (${
+      final_trajectory.frames?.length ?? 0
+    } initial frames, ${final_trajectory.total_frames ?? `unknown`} total)`
+  } else if (result.type === `fermi_surface`) {
+    const fermi_props: Record<string, unknown> = { ...common_props }
+    if (is_fermi_surface_data(result.data as Parameters<typeof is_fermi_surface_data>[0])) {
+      fermi_props.fermi_data = result.data
+    } else {
+      fermi_props.band_data = result.data
+    }
+    app = mount(FermiSurface, { target: container, props: fermi_props })
+    log_message = `Fermi surface rendered: ${filename}`
+  } else if (result.type === `isosurface`) {
+    // VolumetricFileData has structure + volumes; render via Structure with volumetric_data
+    const vol_file = result.data as { structure: AnyStructure; volumes: VolumetricData[] }
+    app = mount(Structure, {
+      target: container,
+      props: {
+        structure: vol_file.structure,
+        volumetric_data: vol_file.volumes,
+        ...structure_props(defaults),
+        ...common_props,
+      },
+    })
+    log_message = `Volumetric data rendered: ${filename}`
+  } else if (result.type === `convex_hull`) {
+    const entries = result.data as PhaseData[]
+    app = mount(ConvexHull, {
+      target: container,
+      props: { entries, ...common_props },
+    })
+    log_message = `Convex hull rendered: ${filename} (${entries.length} entries)`
+  } else if (result.type === `phase_diagram`) {
+    app = mount(IsobaricBinaryPhaseDiagram, {
+      target: container,
+      props: { data: result.data as PhaseDiagramData, ...common_props },
+    })
+    log_message = `Phase diagram rendered: ${filename}`
+  } else if (result.type === `json_browser`) {
+    app = mount(JsonBrowser, {
+      target: container,
+      props: { value: result.data, defaults, filename },
+    })
+    log_message = `JSON browser opened: ${filename}`
+  } else {
+    // Default: structure
+    const structure = result.data as AnyStructure
+    app = mount(Structure, {
+      target: container,
+      props: {
+        structure,
+        ...structure_props(defaults),
+        ...common_props,
+      },
+    })
+    log_message = `Structure rendered: ${filename} (${structure.sites?.length ?? 0} sites)`
+  }
+
+  vscode_api?.postMessage({ command: `info`, text: log_message })
+  return app
+}
+
+// Map defaults in settings.ts to structure component props
+// TIGHT COUPLING WARNING: settings-to-props mapping functions create a direct dependency between the centralized settings schema
+// (src/lib/settings.ts) and component prop interfaces. Changes to either side
+// require manual updates here.
+const structure_props = (defaults: DefaultSettings) => {
+  const { structure } = defaults
+  return {
+    scene_props: { ...structure, gizmo: structure.show_gizmo },
+    lattice_props: {
+      show_cell_vectors: structure.show_cell_vectors,
+      cell_edge_opacity: structure.cell_edge_opacity,
+      cell_surface_opacity: structure.cell_surface_opacity,
+      cell_edge_color: structure.cell_edge_color,
+      cell_surface_color: structure.cell_surface_color,
+    },
+    color_scheme: defaults.color_scheme,
+    background_color: defaults.background_color,
+    background_opacity: defaults.background_opacity,
+    show_image_atoms: structure.show_image_atoms,
+  }
+}
+
+// Map defaults to trajectory component props
+const trajectory_props = (defaults: DefaultSettings) => {
+  const { trajectory, plot, scatter, histogram } = defaults
+  return {
+    ...trajectory,
+    structure_props: structure_props(defaults),
+    loading_options: {
+      bin_file_threshold: trajectory.bin_file_threshold,
+      text_file_threshold: trajectory.text_file_threshold,
+      use_indexing: trajectory.use_indexing,
+      chunk_size: trajectory.chunk_size,
+      max_frames_in_memory: trajectory.max_frames_in_memory,
+      enable_performance_monitoring: trajectory.enable_performance_monitoring,
+      prefetch_frames: trajectory.prefetch_frames,
+      cache_parsed_data: trajectory.cache_parsed_data,
+    },
+    scatter_props: {
+      markers: scatter.symbol_type,
+      line_width: scatter.line.width,
+      point_size: scatter.point.size,
+      show_legend: scatter.show_legend,
+      enable_zoom: plot.enable_zoom,
+      zoom_factor: plot.zoom_factor,
+      auto_fit_range: plot.auto_fit_range,
+      show_grid: plot.grid_lines,
+      show_axis_labels: plot.axis_labels,
+      animation_duration: plot.animation_duration,
+      legend: { show: scatter.show_legend },
+    },
+    histogram_props: {
+      mode: histogram.mode,
+      show_legend: histogram.show_legend,
+      bin_count: histogram.bin_count,
+      enable_zoom: plot.enable_zoom,
+      zoom_factor: plot.zoom_factor,
+      auto_fit_range: plot.auto_fit_range,
+      show_grid: plot.grid_lines,
+      show_axis_labels: plot.axis_labels,
+      animation_duration: plot.animation_duration,
+      legend: { show: histogram.show_legend },
+    },
+    spinner_props: { show_progress: trajectory.show_parsing_progress },
+    ELEM_PROPERTY_LABELS: {},
+  }
+}
+
+// Initialize the MatterViz application
+async function initialize() {
+  // Get MatterViz data passed from extension
+  const { content, filename, is_base64 } = globalThis.matterviz_data?.data || {}
+  const theme = globalThis.matterviz_data?.theme
+  const moyo_wasm_url = globalThis.matterviz_data?.moyo_wasm_url
+  if (!content || !filename) {
+    throw new Error(`No data provided to MatterViz app`)
+  }
+
+  // Initialize WASM early with URL from extension (for symmetry analysis)
+  if (moyo_wasm_url) await ensure_moyo_wasm_ready(moyo_wasm_url)
+
+  // Set up VSCode-specific download override
+  setup_vscode_download()
+
+  // Apply theme early
+  if (theme) apply_theme_to_dom(theme)
+
+  const container = document.getElementById(`matterviz-app`)
+  if (!container) throw new Error(`Target container not found in DOM`)
+
+  const result = await parse_file_content(content, filename, is_base64)
+  const app = create_display(container, result, result.filename)
+
+  // Store the app instance for file watching
+  current_app = app
+
+  // Set up file change monitoring
+  if (vscode_api) {
+    // Listen for file change messages from extension
+    globalThis.addEventListener(`message`, (event) => {
+      if ([`fileUpdated`, `fileDeleted`].includes(event.data.command)) {
+        handle_file_change(event.data)
+      }
+    })
+  }
+
+  return app
+}
+
+// Cleanup function to properly dispose of components
+async function cleanup_matterviz(): Promise<void> {
+  if (current_app) {
+    await unmount(current_app)
+    current_app = null
+  }
+} // Export initialization and cleanup functions to global scope
+
+;(
+  globalThis as unknown as {
+    initializeMatterViz?: () => Promise<MatterVizApp | null>
+    cleanupMatterViz?: () => Promise<void>
+  }
+).initializeMatterViz = async (): Promise<MatterVizApp | null> => {
+  if (!globalThis.matterviz_data) {
+    console.warn(`No matterviz_data found on window`)
+    return null
+  }
+
+  try {
+    const app = await initialize()
+    current_app = app
+    return app
+  } catch (error) {
+    const err = error instanceof Error ? error : new Error(String(error))
+    const container = document.getElementById(`matterviz-app`)
+    if (container) {
+      create_error_display(
+        container,
+        err,
+        globalThis.matterviz_data?.data?.filename || `Unknown file`,
+      )
+    }
+    vscode_api?.postMessage({
+      command: `error`,
+      text: `Error rendering ${
+        globalThis.matterviz_data?.data?.filename || `Unknown file`
+      }: ${err.message}`,
+    })
+    return null
+  }
+}
+;(globalThis as unknown as { cleanupMatterViz?: () => Promise<void> }).cleanupMatterViz =
+  cleanup_matterviz