matterviz 0.3.5 → 0.3.6

package/dist/xrd/XrdPlot.svelte

@@ -1,615 +0,0 @@
-<script lang="ts">
-  import { add_alpha, PLOT_COLORS } from '../colors'
-  import EmptyState from '../EmptyState.svelte'
-  import StatusMessage from '../feedback/StatusMessage.svelte'
-  import {
-    decompress_data_binary,
-    decompress_file,
-    detect_compression_format,
-    handle_url_drop,
-  } from '../io'
-  import { format_value } from '../labels'
-  import { sanitize_html } from '../sanitize'
-  import SettingsSection from '../layout/SettingsSection.svelte'
-  import type { Vec2 } from '../math'
-  import type {
-    AxisConfig,
-    BarHandlerProps,
-    BarSeries,
-    ControlsConfig,
-    DataSeries,
-    ScatterHandlerProps,
-  } from '../plot'
-  import { BarPlot, ScatterPlot } from '../plot'
-  import { add_xrd_pattern } from './calc-xrd'
-  import type { ComponentProps } from 'svelte'
-  import type { BroadeningParams } from './broadening'
-  import { compute_broadened_pattern, DEFAULT_BROADENING } from './broadening'
-  import type { Hkl, HklFormat, PatternEntry, XrdPattern } from './index'
-
-  function is_xrd_pattern(obj: unknown): obj is XrdPattern {
-    if (!obj || typeof obj !== `object`) return false
-    const pattern_obj = obj as { x?: unknown; y?: unknown }
-    const x = pattern_obj.x
-    const y = pattern_obj.y
-    return (
-      Array.isArray(x) &&
-      Array.isArray(y) &&
-      x.length === y.length
-    )
-  }
-
-  function format_hkl(hkl: Hkl, format: HklFormat): string {
-    if (format === `compact`) {
-      // Use crystallographic overbar notation for negative indices (e.g. 1̄ instead of -1)
-      // Note: Requires font support for Unicode combining characters (U+0305)
-      return hkl
-        .map((val) => {
-          // Use combining overline character (U+0305) for negative values
-          // Apply overbar to each digit for multi-digit numbers
-          if (val < 0) {
-            const digits = String(Math.abs(val))
-            return digits
-              .split(``)
-              .map((digit) => `${digit}\u0305`)
-              .join(``)
-          }
-          return `${val}`
-        })
-        .join(``)
-    }
-    if (format === `full`) return `(${hkl.join(`, `)})`
-    return ``
-  }
-
-  let {
-    patterns,
-    peak_width = 0.5,
-    annotate_peaks = 5,
-    hkl_format = `compact`,
-    show_angles = null,
-    orientation = `vertical`,
-    wavelength = null,
-    x_axis = {},
-    y_axis = {},
-    allow_file_drop = true,
-    on_file_drop,
-    loading = $bindable(false),
-    error_msg = $bindable(),
-    broadening_enabled = $bindable(false),
-    broadening_params = $bindable({ ...DEFAULT_BROADENING }),
-    controls = {},
-    ...rest
-  }:
-    & ComponentProps<typeof BarPlot>
-    & ComponentProps<typeof ScatterPlot>
-    & {
-      patterns:
-        | XrdPattern
-        | Record<string, XrdPattern | { pattern: XrdPattern; color?: string }>
-        | PatternEntry[]
-      peak_width?: number
-      annotate_peaks?: number // int => top-k, float in (0,1) => threshold of max
-      hkl_format?: HklFormat
-      show_angles?: boolean | null
-      wavelength?: number | null
-      x_axis?: AxisConfig
-      y_axis?: AxisConfig
-      allow_file_drop?: boolean
-      on_file_drop?: (content: string | ArrayBuffer, filename: string) => void
-      loading?: boolean
-      error_msg?: string
-      broadening_enabled?: boolean
-      broadening_params?: BroadeningParams
-      controls?: ControlsConfig
-    } = $props()
-
-  let dragover = $state(false)
-  let dropped_entries = $state<PatternEntry[]>([])
-
-  // Normalize various input shapes to a consistent array of { label, pattern, color }
-  const pattern_entries = $derived.by<PatternEntry[]>(() => {
-    if (!patterns) return []
-    const base_entries = Array.isArray(patterns)
-      ? (patterns as PatternEntry[])
-      : is_xrd_pattern(patterns)
-      ? [{ label: `XRD Pattern`, pattern: patterns as XrdPattern }]
-      : Object.entries(
-        patterns as Record<
-          string,
-          XrdPattern | { pattern: XrdPattern; color?: string }
-        >,
-      ).map(([label, value]) =>
-        `pattern` in value
-          ? { label, ...value }
-          : { label, pattern: value as XrdPattern }
-      )
-    // Merge user-provided patterns with any dropped-on-the-fly entries
-    return [...base_entries, ...dropped_entries]
-  })
-
-  // Decide default show_angles
-  const actual_show_angles = $derived(
-    show_angles ?? pattern_entries.length <= 2,
-  )
-
-  // Compute global max intensity for normalization (as in pymatviz xrd_pattern)
-  const global_max_intensity = $derived.by(() => {
-    let max_val = 0
-    for (const entry of pattern_entries) {
-      for (const y of entry.pattern.y) if (y > max_val) max_val = y
-    }
-    return max_val || 1
-  })
-
-  // Compute overall 2θ domain (degrees)
-  const angle_range = $derived.by((): Vec2 => {
-    const valid = pattern_entries.filter((entry) => entry.pattern.x.length > 0)
-    if (valid.length === 0) return [0, 90]
-    let [min_x, max_x] = [Infinity, 0]
-    for (const entry of valid) {
-      const entry_min = Math.min(...entry.pattern.x)
-      const entry_max = Math.max(...entry.pattern.x)
-      if (entry_min < min_x) min_x = entry_min
-      if (entry_max > max_x) max_x = entry_max
-    }
-    const x_min = min_x > 10 ? Math.floor(min_x) : 0
-    return [x_min, Math.ceil(max_x)]
-  })
-
-  // Scaled intensities are normalized to 0..100, add 10% top padding for peak labels
-  const intensity_range: [number, number] = [0, 110]
-
-  // Build BarPlot series from entries (for Discrete/Stick view)
-  const bar_series = $derived.by<BarSeries[]>(() => {
-    if (broadening_enabled) return [] // Optimization: skip if not used
-
-    const include_name = pattern_entries.length > 1
-    // Add transparency when multiple series overlap
-    const alpha = pattern_entries.length > 1 ? 0.6 : 1
-    const scale = (y: number) => (y / global_max_intensity) * 100
-    return pattern_entries.map((entry, entry_idx) => {
-      const xs = entry.pattern.x
-      const ys = entry.pattern.y.map((val) => scale(val || 0))
-      const metadata: Record<string, unknown>[] = []
-      const labels: (string | null)[] = []
-
-      // Determine which peaks to annotate
-      const intens = ys
-      let selected_indices: number[] = []
-      if (annotate_peaks && annotate_peaks > 0) {
-        let candidates: { idx: number; y_val: number }[] = []
-        if (annotate_peaks > 0 && annotate_peaks < 1) {
-          const thresh = annotate_peaks * 100
-          candidates = intens
-            .map((y_val, idx) => ({ y_val, idx }))
-            .filter(({ y_val }) => y_val > thresh)
-        } else {
-          const max_peaks = Math.min(intens.length, Math.floor(annotate_peaks))
-          candidates = intens
-            .map((y_val, idx) => ({ y_val, idx }))
-            .sort((a, b) => b.y_val - a.y_val)
-            .slice(0, max_peaks)
-        }
-
-        // Filter out overlapping labels: keep higher intensity peaks when x values are close
-        // Min spacing as fraction of x-range to avoid overlaps (roughly 3% of range)
-        const x_range = Math.max(...xs) - Math.min(...xs)
-        const min_spacing = x_range * 0.03
-        // Sort by intensity descending so we keep highest peaks first
-        candidates.sort((a, b) => b.y_val - a.y_val)
-        const kept: { idx: number; y_val: number }[] = []
-        for (const cand of candidates) {
-          const cand_x = xs[cand.idx]
-          // Check if any already-kept peak is too close
-          const too_close = kept.some(
-            (kept_peak) => Math.abs(xs[kept_peak.idx] - cand_x) < min_spacing,
-          )
-          if (!too_close) kept.push(cand)
-        }
-        selected_indices = kept.map((kept_peak) => kept_peak.idx)
-      }
-
-      for (let idx = 0; idx < xs.length; idx++) {
-        const hkls_objs = entry.pattern.hkls?.[idx] ?? []
-        const hkls: Hkl[] = hkls_objs
-          .map((hkl_obj) => (Array.isArray(hkl_obj?.hkl) ? hkl_obj.hkl : null))
-          .filter((hkl_val): hkl_val is Hkl => Array.isArray(hkl_val) && hkl_val.length === 3)
-        const d_hkl = entry.pattern.d_hkls?.[idx]
-        metadata.push({ hkls, d: d_hkl, label: entry.label })
-
-        if (selected_indices.includes(idx)) {
-          const angle_text = actual_show_angles
-            ? `${format_value(xs[idx], `.2f`)}°`
-            : ``
-          const hkl_text = hkls && hkl_format
-            ? hkls.map((hkl_val) => format_hkl(hkl_val, hkl_format)).join(`, `)
-            : ``
-          // Use @ separator between hkl and angle for better clarity
-          const separator = hkl_text && angle_text ? ` @ ` : ``
-          const text = [hkl_text, angle_text].filter(Boolean).join(separator)
-          labels.push(text)
-        } else labels.push(null)
-      }
-
-      const base_color = entry.color ?? PLOT_COLORS[entry_idx % PLOT_COLORS.length]
-      return {
-        x: xs,
-        y: ys,
-        label: include_name ? entry.label : ``,
-        color: add_alpha(base_color, alpha),
-        bar_width: Math.max(peak_width, 0.8),
-        visible: true,
-        metadata,
-        labels,
-      }
-    })
-  })
-
-  // Build ScatterPlot series (for Broadened Profile view)
-  const scatter_series = $derived.by<DataSeries[]>(() => {
-    if (!broadening_enabled) return []
-
-    const include_name = pattern_entries.length > 1
-    // We rescale after broadening so that max peak is 100, matching stick view scale
-    return pattern_entries
-      .map((entry, entry_idx) => {
-        const broadened = compute_broadened_pattern(
-          entry.pattern,
-          broadening_params,
-          angle_range,
-        )
-
-        // Normalize broadened profile relative to GLOBAL max intensity of stick patterns?
-        // Or normalize to 100 for *this* profile?
-        // Usually we want relative intensities between patterns to be preserved if possible.
-        // But broadening spreads intensity, so peak heights drop.
-        // If we normalize each profile to 100 independently, we lose relative scaling between patterns.
-        // If we normalize by global_max_intensity (from sticks), broadened peaks will be tiny.
-        // Let's normalize such that the highest peak across ALL broadened patterns is 100.
-
-        return {
-          broadened,
-          entry,
-          entry_idx,
-        }
-      })
-      .map(({ broadened, entry, entry_idx }, _, all_processed) => {
-        // Find global max of all broadened patterns to normalize
-        const all_ys = all_processed.flatMap((processed) => processed.broadened.y)
-        const max_y = Math.max(...all_ys, 1) // Avoid div by zero
-
-        const scale = (y: number) => (y / max_y) * 100
-        const base_color = entry.color ?? PLOT_COLORS[entry_idx % PLOT_COLORS.length]
-        // Add transparency when multiple series overlap
-        const alpha = all_processed.length > 1 ? 0.6 : 1
-
-        return {
-          x: broadened.x,
-          y: broadened.y.map(scale),
-          label: include_name ? entry.label : ``,
-          color: add_alpha(base_color, alpha),
-          markers: `line`, // Only line for profile
-          line_style: { stroke_width: 2 },
-          visible: true,
-        } as DataSeries
-      })
-  })
-
-  async function handle_file_drop(event: DragEvent) {
-    event.preventDefault()
-    dragover = false
-    if (!allow_file_drop) return
-    loading = true
-    error_msg = undefined
-
-    const compute_and_add = async (
-      content: string | ArrayBuffer,
-      filename: string,
-    ) => {
-      const result = await add_xrd_pattern(content, filename, wavelength)
-      if (result.error) {
-        error_msg = result.error
-      } else if (result.pattern) {
-        dropped_entries = [result.pattern, ...dropped_entries]
-      }
-    }
-
-    try {
-      // Handle URL-based drops
-      const handled = await handle_url_drop(
-        event,
-        on_file_drop || compute_and_add,
-      ).catch(() => false)
-      if (handled) return
-
-      const file = event.dataTransfer?.files?.[0]
-      if (file) {
-        try {
-          const lower_name = file.name.toLowerCase()
-          const compression_format = detect_compression_format(lower_name)
-          // Get base filename without compression extension
-          const base_name = compression_format
-            ? lower_name.replace(/\.(gz|gzip)$/i, ``)
-            : lower_name
-          const base_ext = base_name.split(`.`).pop()
-
-          // Handle .brml files (ZIP archives) - both plain and gzipped
-          if (base_ext === `brml`) {
-            let buffer = await file.arrayBuffer()
-            // Decompress if gzipped
-            if (compression_format === `gzip`) {
-              buffer = await decompress_data_binary(buffer, `gzip`)
-            }
-            const output_name = base_name.endsWith(`.brml`)
-              ? base_name
-              : file.name.replace(/\.gz$/i, ``)
-            await (on_file_drop || compute_and_add)(buffer, output_name)
-          } else {
-            // Text-based formats (.xy, .xye, .xrdml) - decompress_file handles .gz
-            const { content, filename } = await decompress_file(file)
-            if (content) await (on_file_drop || compute_and_add)(content, filename)
-          }
-        } catch (exc) {
-          error_msg = `Failed to load file ${file.name}: ${
-            exc instanceof Error ? exc.message : String(exc)
-          }`
-        }
-      }
-    } finally {
-      loading = false
-    }
-  }
-
-  const [angle_label, intensity_label] = [`2θ (degrees)`, `Intensity (a.u.)`]
-</script>
-
-{#snippet broadening_controls_snippet()}
-  <SettingsSection
-    title="Broadening"
-    current_values={broadening_params}
-    on_reset={() => {
-      broadening_params = { ...DEFAULT_BROADENING }
-      broadening_enabled = false
-    }}
-  >
-    <label class="toggle">
-      <input type="checkbox" bind:checked={broadening_enabled} />
-      Simulate Broadening
-    </label>
-
-    {#if broadening_enabled}
-      <div
-        class="pane-grid"
-        style="display: grid; grid-template-columns: 1fr 1fr; gap: 1ex"
-      >
-        <label title="Caglioti U parameter">U:
-          <input
-            type="number"
-            step="0.001"
-            bind:value={broadening_params.U}
-            class="param-input"
-          />
-        </label>
-        <label title="Caglioti V parameter">V:
-          <input
-            type="number"
-            step="0.001"
-            bind:value={broadening_params.V}
-            class="param-input"
-          />
-        </label>
-        <label title="Caglioti W parameter">W:
-          <input
-            type="number"
-            step="0.001"
-            bind:value={broadening_params.W}
-            class="param-input"
-          />
-        </label>
-        <label title="Pseudo-Voigt shape factor (0=Gaussian, 1=Lorentzian)">η:
-          <input
-            type="number"
-            min="0"
-            max="1"
-            step="0.05"
-            bind:value={broadening_params.shape_factor}
-            class="param-input"
-          />
-        </label>
-      </div>
-    {/if}
-  </SettingsSection>
-{/snippet}
-
-{#if pattern_entries.length === 0}
-  <EmptyState
-    class="xrd-empty-state"
-    style={rest.style}
-    ondrop={allow_file_drop ? handle_file_drop : undefined}
-    ondragover={allow_file_drop ? (evt) => evt.preventDefault() : undefined}
-    role="region"
-    aria-label="XRD drop zone"
-  >
-    {#if error_msg}
-      <StatusMessage bind:message={error_msg} type="error" dismissible />
-    {:else}
-      <StatusMessage
-        message={allow_file_drop
-        ? `Drag and drop structure files (.cif, .json, etc.) or XRD data files (.xy, .csv, .ras, .uxd, .gsas, .xrdml, .brml, .raw, + .gz) here`
-        : `No XRD data to display`}
-      />
-    {/if}
-  </EmptyState>
-{:else}
-  <div class="xrd-plot-container" style={`position: relative; ${rest.style ?? ``}`}>
-    {#if error_msg}
-      <div class="error-overlay">
-        <StatusMessage bind:message={error_msg} type="error" dismissible />
-      </div>
-    {/if}
-    {#if broadening_enabled}
-      <!-- Broadened Profile View -->
-      {#snippet tooltip(info: ScatterHandlerProps)}
-        {@const angle_text = `${format_value(info.x, `.2f`)}°`}
-        {@const intensity_text = `${format_value(info.y, `.1f`)}`}
-        {@html sanitize_html(info.label ?? ``)}<br />
-        2θ: {angle_text}<br />
-        Intensity: {intensity_text}
-      {/snippet}
-
-      <ScatterPlot
-        {...rest}
-        series={scatter_series}
-        x_axis={{
-          label: angle_label,
-          ...x_axis,
-          range: angle_range,
-        }}
-        y_axis={{
-          label: intensity_label,
-          ...y_axis,
-          range: intensity_range,
-        }}
-        {tooltip}
-        ondrop={handle_file_drop}
-        ondragover={(event) => {
-          event.preventDefault()
-          if (!allow_file_drop) return
-          dragover = true
-        }}
-        ondragleave={(event) => {
-          event.preventDefault()
-          dragover = false
-        }}
-        class={(rest.class ?? ``) + (dragover ? ` dragover` : ``)}
-        style={`overflow: visible; ${rest.style ?? ``}`}
-        {controls}
-        controls_extra={broadening_controls_snippet}
-      />
-    {:else}
-      <!-- Discrete Stick View -->
-      {#snippet tooltip(
-    info: BarHandlerProps<{ label?: string; hkls?: Hkl[]; d?: number }>,
-  )}
-        {@const angle_text = `${format_value(info.x, `.2f`)}°`}
-        {@const intensity_text = `${format_value(info.y, `.1f`)}`}
-        {@const hkls = info.metadata?.hkls}
-        {@const d = info.metadata?.d}
-        {@const hkl_text = hkls && hkl_format
-      ? hkls.map((hkl: Hkl) => format_hkl(hkl, hkl_format)).join(`, `)
-      : ``}
-        {@const d_text = d != null ? `${format_value(d, `.3f`)} Å` : ``}
-        {@html sanitize_html(info.metadata?.label ?? ``)}<br />
-        2θ: {angle_text}<br />
-        Intensity: {intensity_text}
-        {#if hkl_text}<br />hkl: {hkl_text}{/if}
-        {#if d_text}<br />d: {d_text}{/if}
-      {/snippet}
-
-      <BarPlot
-        {...rest}
-        series={bar_series}
-        bind:orientation
-        x_axis={{
-          label: orientation === `horizontal` ? intensity_label : angle_label,
-
-          ...(orientation === `horizontal` ? y_axis : x_axis),
-          label_shift: {
-            y: 20,
-            ...(orientation === `horizontal` ? y_axis : x_axis).label_shift,
-          },
-          range: orientation === `horizontal` ? intensity_range : angle_range,
-        }}
-        y_axis={{
-          label: orientation === `horizontal` ? angle_label : intensity_label,
-          ...(orientation === `horizontal` ? x_axis : y_axis),
-          label_shift: {
-            x: 2,
-            ...(orientation === `horizontal` ? x_axis : y_axis).label_shift,
-          },
-          range: orientation === `horizontal` ? angle_range : intensity_range,
-        }}
-        {tooltip}
-        ondrop={handle_file_drop}
-        ondragover={(event) => {
-          event.preventDefault()
-          if (!allow_file_drop) return
-          dragover = true
-        }}
-        ondragleave={(event) => {
-          event.preventDefault()
-          dragover = false
-        }}
-        class={(rest.class ?? ``) + (dragover ? ` dragover` : ``)}
-        style={`overflow: visible; ${rest.style ?? ``}`}
-        show_controls={controls.show}
-        controls_open={controls.open}
-        controls_toggle_props={controls.toggle_props}
-        controls_pane_props={controls.pane_props}
-        controls_extra={broadening_controls_snippet}
-      />
-    {/if}
-  </div>
-{/if}
-
-<style>
-  .xrd-plot-container {
-    display: flex;
-    flex-direction: column;
-    gap: 1rem;
-    width: 100%;
-    height: 100%;
-  }
-  /* Hide controls toggle by default, show on hover */
-  .xrd-plot-container :global(.pane-toggle) {
-    opacity: 0;
-    transition: opacity 0.2s;
-  }
-  .xrd-plot-container:hover :global(.pane-toggle),
-  .xrd-plot-container :global(.pane-toggle:focus-visible),
-  .xrd-plot-container :global(.pane-toggle[aria-expanded='true']) {
-    opacity: 1;
-  }
-  .toggle {
-    display: flex;
-    align-items: center;
-    gap: 0.5rem;
-    cursor: pointer;
-    font-weight: 500;
-  }
-  .param-input {
-    width: 4.5em;
-    padding: 2px 4px;
-    border: 1px solid var(--border-color, #ccc);
-    box-sizing: border-box;
-    border-radius: 3px;
-    background: transparent;
-    color: inherit;
-  }
-  :global(.xrd-plot-container .dragover) {
-    outline: 2px dashed var(--primary-color, cornflowerblue);
-    outline-offset: -2px;
-    background: rgba(100, 149, 237, 0.1);
-  }
-  :global(.xrd-empty-state) {
-    min-height: 200px;
-    border: 2px dashed var(--border-color, #ccc);
-    border-radius: 8px;
-    background: light-dark(rgba(0, 0, 0, 0.02), rgba(255, 255, 255, 0.02));
-  }
-  :global(.xrd-empty-state .message) {
-    max-width: 80%;
-  }
-  .error-overlay {
-    position: absolute;
-    top: 50%;
-    left: 50%;
-    transform: translate(-50%, -50%);
-    z-index: 10;
-    max-width: 80%;
-  }
-  .error-overlay :global(.message) {
-    box-shadow: 0 4px 12px rgba(0, 0, 0, 0.15);
-  }
-</style>

package/dist/xrd/XrdPlot.svelte.d.ts

@@ -1,28 +0,0 @@
-import type { AxisConfig, ControlsConfig } from '../plot';
-import { BarPlot, ScatterPlot } from '../plot';
-import type { ComponentProps } from 'svelte';
-import type { BroadeningParams } from './broadening';
-import type { HklFormat, PatternEntry, XrdPattern } from './index';
-type $$ComponentProps = ComponentProps<typeof BarPlot> & ComponentProps<typeof ScatterPlot> & {
-    patterns: XrdPattern | Record<string, XrdPattern | {
-        pattern: XrdPattern;
-        color?: string;
-    }> | PatternEntry[];
-    peak_width?: number;
-    annotate_peaks?: number;
-    hkl_format?: HklFormat;
-    show_angles?: boolean | null;
-    wavelength?: number | null;
-    x_axis?: AxisConfig;
-    y_axis?: AxisConfig;
-    allow_file_drop?: boolean;
-    on_file_drop?: (content: string | ArrayBuffer, filename: string) => void;
-    loading?: boolean;
-    error_msg?: string;
-    broadening_enabled?: boolean;
-    broadening_params?: BroadeningParams;
-    controls?: ControlsConfig;
-};
-declare const XrdPlot: import("svelte").Component<$$ComponentProps, {}, "loading" | "error_msg" | "broadening_enabled" | "broadening_params">;
-type XrdPlot = ReturnType<typeof XrdPlot>;
-export default XrdPlot;

package/dist/xrd/broadening.d.ts

@@ -1,20 +0,0 @@
-import type { XrdPattern } from './index';
-export type BroadeningParams = {
-    U: number;
-    V: number;
-    W: number;
-    shape_factor: number;
-};
-export declare const DEFAULT_BROADENING: BroadeningParams;
-export declare function caglioti_fwhm(two_theta: number, // Angle in degrees (2θ)
-U: number, // Caglioti parameter U
-V: number, // Caglioti parameter V
-W: number): number;
-export declare function pseudo_voigt(x: number, // Position
-x0: number, // Peak center
-fwhm: number, // Full Width at Half Maximum
-eta: number): number;
-export declare function compute_broadened_pattern(pattern: XrdPattern, // Discrete XRD pattern (peaks)
-params: BroadeningParams, // Broadening parameters (U, V, W, shape_factor)
-range: [number, number], // Angular range [min, max] in degrees
-step_size?: number): XrdPattern;