matterviz 0.3.1 → 0.3.3

package/dist/trajectory/TrajectoryInfoPane.svelte

@@ -1,175 +1,304 @@
-<script lang="ts">import Icon from '../Icon.svelte';
-import { format_num } from '../labels';
-import DraggablePane from '../overlays/DraggablePane.svelte';
-import { get_electro_neg_formula } from '../composition';
-import { SETTINGS_CONFIG } from '../settings';
-import {} from '../structure';
-import { tooltip as create_tooltip } from 'svelte-multiselect/attachments';
-import { SvelteSet } from 'svelte/reactivity';
-let { trajectory, current_step_idx, current_filename, current_file_path, file_size, file_object, pane_open = $bindable(false), toggle_props, pane_props, ...rest } = $props();
-let copied_items = new SvelteSet();
-async function copy_item(label, value, key) {
+<script lang="ts">
+  import type { InfoItem } from '../layout'
+  import Icon from '../Icon.svelte'
+  import { format_num } from '../labels'
+  import { sanitize_html } from '../sanitize'
+  import DraggablePane from '../overlays/DraggablePane.svelte'
+  import { get_electro_neg_formula } from '../composition'
+  import { SETTINGS_CONFIG } from '../settings'
+  import { type AnyStructure } from '../structure'
+  import type { ComponentProps } from 'svelte'
+  import { tooltip as create_tooltip } from 'svelte-multiselect/attachments'
+  import { SvelteSet } from 'svelte/reactivity'
+  import type { TrajectoryType } from './index'
+
+  let {
+    trajectory,
+    current_step_idx,
+    current_filename,
+    current_file_path,
+    file_size,
+    file_object,
+    pane_open = $bindable(false),
+    toggle_props,
+    pane_props,
+    ...rest
+  }: Omit<ComponentProps<typeof DraggablePane>, `children`> & {
+    trajectory: TrajectoryType
+    current_step_idx: number
+    current_filename?: string | null
+    current_file_path?: string | null
+    file_size?: number | null
+    file_object?: File | null
+    pane_open?: boolean
+    toggle_props?: ComponentProps<typeof DraggablePane>[`toggle_props`]
+    pane_props?: ComponentProps<typeof DraggablePane>[`pane_props`]
+  } = $props()
+
+  let copied_items = new SvelteSet<string>()
+
+  async function copy_item(label: string, value: string | number, key: string) {
     try {
-        await navigator.clipboard.writeText(`${label}: ${value}`);
-        copied_items.add(key);
-        setTimeout(() => {
-            copied_items.delete(key);
-        }, 1000);
+      await navigator.clipboard.writeText(`${label}: ${value}`)
+      copied_items.add(key)
+      setTimeout(() => {
+        copied_items.delete(key)
+      }, 1000)
+    } catch (error) {
+      console.error(`Failed to copy to clipboard:`, error)
     }
-    catch (error) {
-        console.error(`Failed to copy to clipboard:`, error);
-    }
-}
-// Helper functions
-const format_size = (bytes) => bytes > 1024 * 1024
-    ? `${format_num(bytes / (1024 * 1024), `.2~f`)} MB`
-    : `${format_num(bytes / 1024, `.2~f`)} KB`;
-const is_valid_number = (val) => typeof val === `number` && isFinite(val);
-const extract_numeric_array = (frames, prop) => frames.map((frame) => frame.metadata?.[prop]).filter(is_valid_number);
-const format_range = (values, unit = ``, decimals = `.2~f`) => {
-    if (!values.length)
-        return null;
+  }
+
+  // Helper functions
+  const format_size = (bytes: number) =>
+    bytes > 1024 * 1024
+      ? `${format_num(bytes / (1024 * 1024), `.2~f`)} MB`
+      : `${format_num(bytes / 1024, `.2~f`)} KB`
+
+  const is_valid_number = (val: unknown): val is number =>
+    typeof val === `number` && isFinite(val)
+
+  const extract_numeric_array = (frames: typeof trajectory.frames, prop: string) =>
+    frames.map((frame) => frame.metadata?.[prop]).filter(is_valid_number)
+
+  const format_range = (values: number[], unit = ``, decimals = `.2~f`) => {
+    if (!values.length) return null
     if (values.length === 1) {
-        return `${format_num(values[0], decimals)} ${unit}`.trim();
+      return `${format_num(values[0], decimals)} ${unit}`.trim()
     }
-    const [min, max] = [Math.min(...values), Math.max(...values)];
+    const [min, max] = [Math.min(...values), Math.max(...values)]
     return `${format_num(min, decimals)} - ${format_num(max, decimals)} ${unit}`
-        .trim();
-};
-const safe_item = (label, value, key, tooltip) => value ? { label, value, key, tooltip } : null;
-const is_info_item = (item) => Boolean(item);
-const safe_formula = (structure) => {
+      .trim()
+  }
+
+  const safe_item = (
+    label: string,
+    value: string | null,
+    key?: string,
+    tooltip?: string,
+  ): InfoItem | null => value ? { label, value, key, tooltip } : null
+
+  const is_info_item = (item: unknown): item is InfoItem => Boolean(item)
+
+  const safe_formula = (structure: AnyStructure) => {
     try {
-        return get_electro_neg_formula(structure);
-    }
-    catch {
-        return null;
+      return get_electro_neg_formula(structure)
+    } catch {
+      return null
     }
-};
-// Get trajectory info organized by sections
-let info_pane_data = $derived.by(() => {
-    if ((!trajectory?.frames?.length && !trajectory?.total_frames) ||
-        current_step_idx < 0 ||
-        current_step_idx >= (trajectory.total_frames ?? trajectory.frames?.length ?? 0))
-        return [];
+  }
+
+  // Get trajectory info organized by sections
+  let info_pane_data = $derived.by(() => {
+    if (
+      (!trajectory?.frames?.length && !trajectory?.total_frames) ||
+      current_step_idx < 0 ||
+      current_step_idx >= (trajectory.total_frames ?? trajectory.frames?.length ?? 0)
+    ) return []
+
     // For indexed trajectories, we might not have the current frame loaded
-    const current_frame = trajectory.frames?.[current_step_idx];
-    const total_frames = trajectory.total_frames ?? trajectory.frames?.length ?? 0;
-    const sections = [];
+    const current_frame = trajectory.frames?.[current_step_idx]
+    const total_frames = trajectory.total_frames ?? trajectory.frames?.length ?? 0
+
+    const sections: { title: string; items: InfoItem[] }[] = []
+
     // File info section
     const file_items = [
-        current_filename &&
-            safe_item(`Name`, current_filename, `file-name`, current_file_path || undefined),
-        file_size && file_size > 0 &&
-            safe_item(`File Size`, format_size(file_size), `file-size`),
-        file_object?.lastModified &&
-            safe_item(`Modified`, new Date(file_object.lastModified).toLocaleString(), `file-modified`),
-        trajectory.metadata?.source_format &&
-            safe_item(`Format`, String(trajectory.metadata.source_format), `file-format`),
-    ].filter(is_info_item);
+      current_filename &&
+      safe_item(
+        `Name`,
+        current_filename,
+        `file-name`,
+        current_file_path || undefined,
+      ),
+      file_size && file_size > 0 &&
+      safe_item(`File Size`, format_size(file_size), `file-size`),
+      file_object?.lastModified &&
+      safe_item(
+        `Modified`,
+        new Date(file_object.lastModified).toLocaleString(),
+        `file-modified`,
+      ),
+      trajectory.metadata?.source_format &&
+      safe_item(`Format`, String(trajectory.metadata.source_format), `file-format`),
+    ].filter(is_info_item)
+
     if (file_items.length > 0) {
-        sections.push({ title: `File`, items: file_items });
+      sections.push({ title: `File`, items: file_items })
     }
+
     // Trajectory info section (always show this)
     const traj_items = [
-        safe_item(`Total Frames`, `${format_num(total_frames, `.3~s`)} (current: ${format_num(current_step_idx + 1, `.3~s`)})`, `total-frames`),
-        trajectory.is_indexed &&
-            safe_item(`Indexed`, `Yes`, `indexed-mode`, SETTINGS_CONFIG.trajectory.use_indexing.description),
-        trajectory.indexed_frames &&
-            safe_item(`Index Points`, `${trajectory.indexed_frames.length}`, `index-points`, `Number of frames indexed for fast seeking`),
-        trajectory.plot_metadata &&
-            safe_item(`Plot Metadata`, `${trajectory.plot_metadata.length} frames`, `plot-metadata`, `Pre-extracted metadata for plotting`),
-    ].filter(is_info_item);
+      safe_item(
+        `Total Frames`,
+        `${format_num(total_frames, `.3~s`)} (current: ${
+          format_num(current_step_idx + 1, `.3~s`)
+        })`,
+        `total-frames`,
+      ),
+      trajectory.is_indexed &&
+      safe_item(
+        `Indexed`,
+        `Yes`,
+        `indexed-mode`,
+        SETTINGS_CONFIG.trajectory.use_indexing.description,
+      ),
+      trajectory.indexed_frames &&
+      safe_item(
+        `Index Points`,
+        `${trajectory.indexed_frames.length}`,
+        `index-points`,
+        `Number of frames indexed for fast seeking`,
+      ),
+      trajectory.plot_metadata &&
+      safe_item(
+        `Plot Metadata`,
+        `${trajectory.plot_metadata.length} frames`,
+        `plot-metadata`,
+        `Pre-extracted metadata for plotting`,
+      ),
+    ].filter(is_info_item)
+
     if (traj_items.length > 0) {
-        sections.push({ title: `Trajectory`, items: traj_items });
+      sections.push({ title: `Trajectory`, items: traj_items })
     }
+
     // Structure info section (only if we have the current frame)
     if (current_frame?.structure?.sites) {
-        const { structure } = current_frame;
-        const lattice = `lattice` in structure ? structure.lattice : null;
-        const { volume, a, b, c, alpha, beta, gamma } = lattice || {};
-        const formula = safe_formula(structure);
-        const structure_items = [
-            safe_item(`Atoms`, `${structure.sites.length}`, `atoms`),
-            formula && safe_item(`Formula`, String(formula), `formula`),
-            is_valid_number(volume) && volume > 0 &&
-                safe_item(`Volume`, `${format_num(volume, `.3~s`)} ų`, `volume`),
-            is_valid_number(volume) && volume > 0 && structure.sites.length > 0 &&
-                safe_item(`Density`, `${format_num(structure.sites.length / volume, `.4~s`)} atoms/ų`, `density`),
-            [a, b, c].every(is_valid_number) &&
-                safe_item(`Cell Lengths`, `${format_num(a, `.3~f`)}, ${format_num(b, `.3~f`)}, ${format_num(c, `.3~f`)} Å`, `cell-lengths`),
-            [alpha, beta, gamma].every(is_valid_number) &&
-                safe_item(`Cell Angles`, `${format_num(alpha, `.2~f`)}°, ${format_num(beta, `.2~f`)}°, ${format_num(gamma, `.2~f`)}°`, `cell-angles`),
-        ].filter(is_info_item);
-        if (structure_items.length > 0) {
-            sections.push({ title: `Structure`, items: structure_items });
-        }
-    }
-    else if (trajectory.is_indexed) {
-        // For indexed trajectories, show a note that frame data is loaded on demand
-        const structure_items = [
-            safe_item(`Frame Loading`, `On-demand`, `frame-loading`, `Structure data loaded when frame is accessed`),
-        ].filter(is_info_item);
-        if (structure_items.length > 0) {
-            sections.push({ title: `Structure`, items: structure_items });
-        }
+      const { structure } = current_frame
+      const lattice = `lattice` in structure ? structure.lattice : null
+      const { volume, a, b, c, alpha, beta, gamma } = lattice || {}
+      const formula = safe_formula(structure)
+
+      const structure_items = [
+        safe_item(`Atoms`, `${structure.sites.length}`, `atoms`),
+        formula && safe_item(`Formula`, String(formula), `formula`),
+        is_valid_number(volume) && volume > 0 &&
+        safe_item(`Volume`, `${format_num(volume, `.3~s`)} ų`, `volume`),
+        is_valid_number(volume) && volume > 0 && structure.sites.length > 0 &&
+        safe_item(
+          `Density`,
+          `${format_num(structure.sites.length / volume, `.4~s`)} atoms/ų`,
+          `density`,
+        ),
+        [a, b, c].every(is_valid_number) &&
+        safe_item(
+          `Cell Lengths`,
+          `${format_num(a as number, `.3~f`)}, ${format_num(b as number, `.3~f`)}, ${
+            format_num(c as number, `.3~f`)
+          } Å`,
+          `cell-lengths`,
+        ),
+        [alpha, beta, gamma].every(is_valid_number) &&
+        safe_item(
+          `Cell Angles`,
+          `${format_num(alpha as number, `.2~f`)}°, ${
+            format_num(beta as number, `.2~f`)
+          }°, ${format_num(gamma as number, `.2~f`)}°`,
+          `cell-angles`,
+        ),
+      ].filter(is_info_item)
+
+      if (structure_items.length > 0) {
+        sections.push({ title: `Structure`, items: structure_items })
+      }
+    } else if (trajectory.is_indexed) {
+      // For indexed trajectories, show a note that frame data is loaded on demand
+      const structure_items = [
+        safe_item(
+          `Frame Loading`,
+          `On-demand`,
+          `frame-loading`,
+          `Structure data loaded when frame is accessed`,
+        ),
+      ].filter(is_info_item)
+
+      if (structure_items.length > 0) {
+        sections.push({ title: `Structure`, items: structure_items })
+      }
     }
+
     // Energy section (only for regular trajectories with multiple frames)
     if (!trajectory.is_indexed && trajectory.frames.length > 1) {
-        const energies = extract_numeric_array(trajectory.frames, `energy`);
-        if (energies.length > 1) {
-            const current_energy = current_frame?.metadata?.energy;
-            const energy_range = format_range(energies, `eV`, `.3~s`);
-            const energy_items = [
-                is_valid_number(current_energy) &&
-                    safe_item(`Current Energy`, `${format_num(current_energy, `.3~s`)} eV`, `energy-current`),
-                energy_range && safe_item(`Energy Range`, energy_range, `energy-range`),
-            ].filter(is_info_item);
-            if (energy_items.length > 0) {
-                sections.push({ title: `Energy`, items: energy_items });
-            }
+      const energies = extract_numeric_array(trajectory.frames, `energy`)
+      if (energies.length > 1) {
+        const current_energy = current_frame?.metadata?.energy
+        const energy_range = format_range(energies, `eV`, `.3~s`)
+
+        const energy_items = [
+          is_valid_number(current_energy) &&
+          safe_item(
+            `Current Energy`,
+            `${format_num(current_energy, `.3~s`)} eV`,
+            `energy-current`,
+          ),
+          energy_range && safe_item(`Energy Range`, energy_range, `energy-range`),
+        ].filter(is_info_item)
+
+        if (energy_items.length > 0) {
+          sections.push({ title: `Energy`, items: energy_items })
         }
+      }
     }
+
     // Forces section (only for regular trajectories with multiple frames)
     if (!trajectory.is_indexed && trajectory.frames.length > 1) {
-        const forces = extract_numeric_array(trajectory.frames, `force_max`);
-        if (forces.length > 1) {
-            const current_force = current_frame?.metadata?.force_max;
-            const force_range = format_range(forces, `eV/Å`, `.3~s`);
-            const force_items = [
-                is_valid_number(current_force) &&
-                    safe_item(`Max Force`, `${format_num(current_force, `.3~s`)} eV/Å`, `force-current`),
-                force_range && safe_item(`Force Range`, force_range, `force-range`),
-            ].filter(is_info_item);
-            if (force_items.length > 0) {
-                sections.push({ title: `Forces`, items: force_items });
-            }
+      const forces = extract_numeric_array(trajectory.frames, `force_max`)
+      if (forces.length > 1) {
+        const current_force = current_frame?.metadata?.force_max
+        const force_range = format_range(forces, `eV/Å`, `.3~s`)
+
+        const force_items = [
+          is_valid_number(current_force) &&
+          safe_item(
+            `Max Force`,
+            `${format_num(current_force, `.3~s`)} eV/Å`,
+            `force-current`,
+          ),
+          force_range && safe_item(`Force Range`, force_range, `force-range`),
+        ].filter(is_info_item)
+
+        if (force_items.length > 0) {
+          sections.push({ title: `Forces`, items: force_items })
         }
+      }
     }
+
     // Volume change section (only for regular trajectories)
-    if (!trajectory.is_indexed && current_frame?.structure &&
-        trajectory.frames.length > 1) {
-        const lattice = `lattice` in current_frame.structure
-            ? current_frame.structure.lattice
-            : null;
-        if (lattice) {
-            const volumes = trajectory.frames.map(({ structure }) => (`lattice` in structure && structure.lattice?.volume))
-                .filter(is_valid_number)
-                .filter((v) => v > 0);
-            if (volumes.length > 1) {
-                const vol_change = (Math.max(...volumes) - Math.min(...volumes)) /
-                    Math.min(...volumes);
-                if (Math.abs(vol_change) > 0.1 && is_valid_number(vol_change)) {
-                    const vol_items = [safe_item(`Volume Change`, `${format_num(vol_change, `.2~%`)}`, `vol-change`)].filter(is_info_item);
-                    if (vol_items.length > 0) {
-                        sections.push({ title: `Volume`, items: vol_items });
-                    }
-                }
+    if (
+      !trajectory.is_indexed && current_frame?.structure &&
+      trajectory.frames.length > 1
+    ) {
+      const lattice = `lattice` in current_frame.structure
+        ? current_frame.structure.lattice
+        : null
+      if (lattice) {
+        const volumes = trajectory.frames.map((
+          { structure },
+        ) => (`lattice` in structure && structure.lattice?.volume))
+          .filter(is_valid_number)
+          .filter((v) => v > 0)
+
+        if (volumes.length > 1) {
+          const vol_change = (Math.max(...volumes) - Math.min(...volumes)) /
+            Math.min(...volumes)
+          if (Math.abs(vol_change) > 0.1 && is_valid_number(vol_change)) {
+            const vol_items = [safe_item(
+              `Volume Change`,
+              `${format_num(vol_change, `.2~%`)}`,
+              `vol-change`,
+            )].filter(is_info_item)
+
+            if (vol_items.length > 0) {
+              sections.push({ title: `Volume`, items: vol_items })
             }
+          }
         }
+      }
     }
-    return sections;
-});
+
+    return sections
+  })
 </script>
 
 <DraggablePane
@@ -207,8 +336,8 @@ let info_pane_data = $derived.by(() => {
             }
           }}
         >
-          <span>{@html label}</span>
-          <span title={tooltip} {@attach create_tooltip()}>{@html value}</span>
+          <span>{@html sanitize_html(label)}</span>
+          <span title={tooltip} {@attach create_tooltip()}>{@html sanitize_html(value)}</span>
           {#if copied_items.has(key ?? label)}
             <Icon
               icon="Check"

package/dist/trajectory/constants.d.ts

@@ -0,0 +1,6 @@
+export declare const MAX_SAFE_STRING_LENGTH: number;
+export declare const MAX_METADATA_SIZE: number;
+export declare const LARGE_FILE_THRESHOLD: number;
+export declare const INDEX_SAMPLE_RATE = 100;
+export declare const MAX_BIN_FILE_SIZE: number;
+export declare const MAX_TEXT_FILE_SIZE: number;

package/dist/trajectory/constants.js

@@ -0,0 +1,7 @@
+// Constants for trajectory parsing and large file handling
+export const MAX_SAFE_STRING_LENGTH = 0x1fffffe8 * 0.5; // 50% of JS max string length as safety
+export const MAX_METADATA_SIZE = 50 * 1024 * 1024; // 50MB limit for metadata
+export const LARGE_FILE_THRESHOLD = 400 * 1024 * 1024; // 400MB
+export const INDEX_SAMPLE_RATE = 100; // Default sample rate for frame indexing
+export const MAX_BIN_FILE_SIZE = 100 * 1024 * 1024; // 100MB default for ArrayBuffer files
+export const MAX_TEXT_FILE_SIZE = 50 * 1024 * 1024; // 50MB default for string files

package/dist/trajectory/extract.js

@@ -15,8 +15,7 @@ export const energy_data_extractor = (frame, _trajectory) => {
             `total_energy`,
         ];
         for (const field of energy_fields) {
-            if (field in frame.metadata &&
-                typeof frame.metadata[field] === `number`) {
+            if (field in frame.metadata && typeof frame.metadata[field] === `number`) {
                 data[field] = frame.metadata[field];
             }
         }
@@ -36,36 +35,26 @@ export const force_stress_data_extractor = (frame, _trajectory) => {
                 const force_magnitudes = forces.map((force) => Math.hypot(...force));
                 data.force_max = Math.max(...force_magnitudes);
                 // Calculate RMS (root mean square) of force magnitudes
-                data.force_norm = Math.sqrt(force_magnitudes.reduce((sum, f) => sum + f ** 2, 0) /
-                    force_magnitudes.length);
+                data.force_norm = Math.sqrt(force_magnitudes.reduce((sum, f) => sum + f ** 2, 0) / force_magnitudes.length);
             }
         }
         else {
             // Fallback to metadata values if forces array not available
-            if (frame.metadata.force_max &&
-                typeof frame.metadata.force_max === `number`) {
+            if (frame.metadata.force_max && typeof frame.metadata.force_max === `number`) {
                 data.force_max = frame.metadata.force_max;
             }
             // Prefer force_norm if available, fall back to force_rms
-            if (frame.metadata.force_norm &&
-                typeof frame.metadata.force_norm === `number`) {
+            if (frame.metadata.force_norm && typeof frame.metadata.force_norm === `number`) {
                 data.force_norm = frame.metadata.force_norm;
             }
-            else if (frame.metadata.force_rms &&
-                typeof frame.metadata.force_rms === `number`) {
+            else if (frame.metadata.force_rms && typeof frame.metadata.force_rms === `number`) {
                 data.force_norm = frame.metadata.force_rms; // Use force_rms as fallback
             }
         }
         // Extract other stress and pressure properties (no duplicates expected)
-        const other_stress_fields = [
-            `stress_max`,
-            `stress_frobenius`,
-            `stress_trace`,
-            `pressure`,
-        ];
+        const other_stress_fields = [`stress_max`, `stress_frobenius`, `stress_trace`, `pressure`];
         for (const field of other_stress_fields) {
-            if (field in frame.metadata &&
-                typeof frame.metadata[field] === `number`) {
+            if (field in frame.metadata && typeof frame.metadata[field] === `number`) {
                 data[field] = frame.metadata[field];
             }
         }
@@ -92,8 +81,7 @@ export const structural_data_extractor = (frame, _trajectory) => {
         // Extract other structural properties, avoiding volume duplicate
         const structural_fields = [`temperature`];
         for (const field of structural_fields) {
-            if (field in frame.metadata &&
-                typeof frame.metadata[field] === `number`)
+            if (field in frame.metadata && typeof frame.metadata[field] === `number`)
                 data[field] = frame.metadata[field];
         }
         // Handle density separately - prefer metadata, but calculate if not available
@@ -109,9 +97,7 @@ export const structural_data_extractor = (frame, _trajectory) => {
             }
         }
         // Only use metadata volume if lattice volume is not available
-        if (!data.volume &&
-            frame.metadata.volume &&
-            typeof frame.metadata.volume === `number`) {
+        if (!data.volume && frame.metadata.volume && typeof frame.metadata.volume === `number`) {
             data.volume = frame.metadata.volume;
         }
         // Note: pressure is handled by force_stress_data_extractor to avoid duplication
@@ -136,15 +122,11 @@ function property_varies(trajectory, property_key, tolerance = 1e-10) {
         // Check both direct structure properties and metadata
         let value;
         if (`lattice` in frame.structure) {
-            const lattice = frame.structure.lattice;
-            if (property_key in lattice &&
-                typeof lattice[property_key] === `number`) {
-                value = lattice[property_key];
-            }
+            const lattice_value = frame.structure.lattice[property_key];
+            if (typeof lattice_value === `number`)
+                value = lattice_value;
         }
-        if (value === undefined &&
-            frame.metadata &&
-            property_key in frame.metadata) {
+        if (value === undefined && frame.metadata && property_key in frame.metadata) {
             const metadata_value = frame.metadata[property_key];
             if (typeof metadata_value === `number`) {
                 value = metadata_value;

package/dist/trajectory/format-detect.d.ts

@@ -0,0 +1,9 @@
+export declare function strip_compression_extensions(filename: string): string;
+export declare const FORMAT_PATTERNS: {
+    readonly ase: (data: unknown, filename?: string) => boolean;
+    readonly hdf5: (data: unknown, filename?: string) => boolean;
+    readonly vasp: (data: string, filename?: string) => boolean;
+    readonly xyz_multi: (data: string, filename?: string) => boolean;
+    readonly lammpstrj: (data: string, filename?: string) => boolean;
+};
+export declare function is_trajectory_file(filename: string, content?: string): boolean;