matterviz 0.4.1 → 0.4.3

package/dist/xrd/XrdPlot.svelte

@@ -2,13 +2,7 @@
   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,
-    drag_over_handlers,
-    handle_url_drop,
-  } from '../io'
+  import * as io from '../io'
   import { format_value } from '../labels'
   import { sanitize_html } from '../sanitize'
   import SettingsSection from '../layout/SettingsSection.svelte'
@@ -34,11 +28,7 @@
     const pattern_obj = obj as { x?: unknown; y?: unknown }
     const x_vals = pattern_obj.x
     const y_vals = pattern_obj.y
-    return (
-      Array.isArray(x_vals) &&
-      Array.isArray(y_vals) &&
-      x_vals.length === y_vals.length
-    )
+    return Array.isArray(x_vals) && Array.isArray(y_vals) && x_vals.length === y_vals.length
   }
 
   function format_hkl(hkl: Hkl, format: HklFormat): string {
@@ -82,10 +72,8 @@
     broadening_params = $bindable({ ...DEFAULT_BROADENING }),
     controls = {},
     ...rest
-  }:
-    & ComponentProps<typeof BarPlot>
-    & ComponentProps<typeof ScatterPlot>
-    & {
+  }: ComponentProps<typeof BarPlot> &
+    ComponentProps<typeof ScatterPlot> & {
       patterns:
         | XrdPattern
         | Record<string, XrdPattern | { pattern: XrdPattern; color?: string }>
@@ -115,25 +103,18 @@
     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 }
-      )
+        ? [{ 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,
-  )
+  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(() => {
@@ -177,18 +158,17 @@
       const labels: (string | null)[] = []
 
       // Determine which peaks to annotate
-      const intens = ys
       let selected_indices: number[] = []
-      if (annotate_peaks && annotate_peaks > 0) {
+      if (annotate_peaks > 0) {
         let candidates: { idx: number; y_val: number }[] = []
-        if (annotate_peaks > 0 && annotate_peaks < 1) {
+        if (annotate_peaks < 1) {
           const thresh = annotate_peaks * 100
-          candidates = intens
+          candidates = ys
             .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
+          const max_peaks = Math.min(ys.length, Math.floor(annotate_peaks))
+          candidates = ys
             .map((y_val, idx) => ({ y_val, idx }))
             .sort((a, b) => b.y_val - a.y_val)
             .slice(0, max_peaks)
@@ -221,10 +201,8 @@
         metadata.push({ hkls, d: d_hkl, label: entry.label })
 
         if (selected_indices.includes(idx)) {
-          const angle_text = actual_show_angles
-            ? `${format_value(xs[idx], `.2f`)}°`
-            : ``
-          const hkl_text = hkls && hkl_format
+          const angle_text = actual_show_angles ? `${format_value(xs[idx], `.2f`)}°` : ``
+          const hkl_text = hkl_format
             ? hkls.map((hkl_val) => format_hkl(hkl_val, hkl_format)).join(`, `)
             : ``
           // Use @ separator between hkl and angle for better clarity
@@ -253,49 +231,32 @@
     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_val: number) => (y_val / 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
-      })
+    // Normalize so the highest peak across ALL broadened profiles is 100: per-profile
+    // normalization would lose relative scaling between patterns, while the stick-view
+    // global max would make broadened peaks tiny (broadening spreads intensity)
+    const broadened = pattern_entries.map((entry) =>
+      compute_broadened_pattern(entry.pattern, broadening_params, angle_range),
+    )
+    let max_y = 1 // avoid div by zero
+    for (const profile of broadened) {
+      for (const y_val of profile.y) max_y = Math.max(max_y, y_val)
+    }
+    // Add transparency when multiple series overlap
+    const alpha = pattern_entries.length > 1 ? 0.6 : 1
+
+    return broadened.map((profile, entry_idx) => {
+      const entry = pattern_entries[entry_idx]
+      const base_color = entry.color ?? PLOT_COLORS[entry_idx % PLOT_COLORS.length]
+      return {
+        x: profile.x,
+        y: profile.y.map((y_val) => (y_val / max_y) * 100),
+        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) {
@@ -305,10 +266,7 @@
     loading = true
     error_msg = undefined
 
-    const compute_and_add = async (
-      content: string | ArrayBuffer,
-      filename: string,
-    ) => {
+    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
@@ -319,20 +277,19 @@
 
     try {
       // Handle URL-based drops
-      const handled = await handle_url_drop(
-        event,
-        on_file_drop || compute_and_add,
-      ).catch(() => false)
+      const handled = await io
+        .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)
+          const compression_format = io.detect_compression_format(lower_name)
           // Get base filename without compression extension
           const base_name = compression_format
-            ? lower_name.replace(/\.(gz|gzip)$/i, ``)
+            ? lower_name.replace(/\.(?:gz|gzip)$/i, ``)
             : lower_name
           const base_ext = base_name.split(`.`).pop()
 
@@ -341,7 +298,7 @@
             let buffer = await file.arrayBuffer()
             // Decompress if gzipped
             if (compression_format === `gzip`) {
-              buffer = await decompress_data_binary(buffer, `gzip`)
+              buffer = await io.decompress_data_binary(buffer, `gzip`)
             }
             const output_name = base_name.endsWith(`.brml`)
               ? base_name
@@ -349,13 +306,11 @@
             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)
+            const { content, filename } = await io.decompress_file(file)
             if (content) await (on_file_drop || compute_and_add)(content, filename)
           }
         } catch (exc) {
-          error_msg = `Failed to load file ${file.name}: ${
-            to_error(exc).message
-          }`
+          error_msg = `Failed to load file ${file.name}: ${to_error(exc).message}`
         }
       }
     } finally {
@@ -381,11 +336,9 @@
     </label>
 
     {#if broadening_enabled}
-      <div
-        class="pane-grid"
-        style="display: grid; grid-template-columns: 1fr 1fr; gap: 1ex"
-      >
-        <label title="Caglioti U parameter">U:
+      <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"
@@ -393,7 +346,8 @@
             class="param-input"
           />
         </label>
-        <label title="Caglioti V parameter">V:
+        <label title="Caglioti V parameter"
+          >V:
           <input
             type="number"
             step="0.001"
@@ -401,7 +355,8 @@
             class="param-input"
           />
         </label>
-        <label title="Caglioti W parameter">W:
+        <label title="Caglioti W parameter"
+          >W:
           <input
             type="number"
             step="0.001"
@@ -409,7 +364,8 @@
             class="param-input"
           />
         </label>
-        <label title="Pseudo-Voigt shape factor (0=Gaussian, 1=Lorentzian)">η:
+        <label title="Pseudo-Voigt shape factor (0=Gaussian, 1=Lorentzian)"
+          >η:
           <input
             type="number"
             min="0"
@@ -438,8 +394,8 @@
     {: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`}
+          ? `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>
@@ -475,24 +431,26 @@
         }}
         {tooltip}
         ondrop={handle_file_drop}
-        {...drag_over_handlers({ allow: () => allow_file_drop, set_dragover: (over) => dragover = over })}
-        class={(rest.class ?? ``) + (dragover ? ` dragover` : ``)}
+        {...io.drag_over_handlers({
+          allow: () => allow_file_drop,
+          set_dragover: (over) => (dragover = over),
+        })}
+        class={[rest.class, dragover && `dragover`]}
         style={`overflow: visible; ${rest.style ?? ``}`}
         {controls}
         controls_extra={broadening_controls_snippet}
       />
     {:else}
       <!-- Discrete Stick View -->
-      {#snippet tooltip(
-    info: BarHandlerProps<{ label?: string; hkls?: Hkl[]; d?: number }>,
-  )}
+      {#snippet tooltip(info: BarHandlerProps<{ label?: string; hkls?: Hkl[]; d?: number }>)}
         {@const angle_text = `${format_value(info.x, `.2f`)}°`}
         {@const intensity_text = `${format_value(info.y, `.1f`)}`}
         {@const hkls = info.metadata?.hkls}
         {@const d_spacing = info.metadata?.d}
-        {@const hkl_text = hkls && hkl_format
-      ? hkls.map((hkl: Hkl) => format_hkl(hkl, hkl_format)).join(`, `)
-      : ``}
+        {@const hkl_text =
+          hkls && hkl_format
+            ? hkls.map((hkl: Hkl) => format_hkl(hkl, hkl_format)).join(`, `)
+            : ``}
         {@const d_text = d_spacing != null ? `${format_value(d_spacing, `.3f`)} Å` : ``}
         {@html sanitize_html(info.metadata?.label ?? ``)}<br />
         2θ: {angle_text}<br />
@@ -526,8 +484,11 @@
         }}
         {tooltip}
         ondrop={handle_file_drop}
-        {...drag_over_handlers({ allow: () => allow_file_drop, set_dragover: (over) => dragover = over })}
-        class={(rest.class ?? ``) + (dragover ? ` dragover` : ``)}
+        {...io.drag_over_handlers({
+          allow: () => allow_file_drop,
+          set_dragover: (over) => (dragover = over),
+        })}
+        class={[rest.class, dragover && `dragover`]}
         style={`overflow: visible; ${rest.style ?? ``}`}
         show_controls={controls.show}
         controls_open={controls.open}

package/dist/xrd/broadening.js

@@ -1,3 +1,4 @@
+import { clamp01 } from '../utils';
 const LOG_2 = Math.log(2);
 export const DEFAULT_BROADENING = {
     U: 0.04,
@@ -43,7 +44,7 @@ fwhm, // Full Width at Half Maximum
 eta) {
     // Intensity at x
     // Clamp eta to [0, 1]
-    const safe_eta = Math.max(0, Math.min(1, eta));
+    const safe_eta = clamp01(eta);
     return safe_eta * lorentzian(x, x0, fwhm) + (1 - safe_eta) * gaussian(x, x0, fwhm);
 }
 // Computes a broadened XRD pattern from discrete peaks.

package/dist/xrd/calc-xrd.js

@@ -121,20 +121,14 @@ export function compute_xrd_pattern(structure, options = {}) {
         }
         wavelength = WAVELENGTHS[wl_input];
     }
-    // Symmetry refinement (symprec > 0) is not implemented in TS version.
-    // Option retained for API parity.
-    // const symprec = options.symprec ?? 0
+    // Symmetry refinement (symprec > 0) is not implemented in TS version. Option retained for API parity.
     // For row-wise lattice matrix A (rows are a, b, c), reciprocal rows are inv(A)^T
     const recip_rows = math.transpose_3x3_matrix(math.matrix_inverse_3x3(structure.lattice.matrix));
     // Bragg condition bounds: reciprocal vector length r = 2 sin(theta) / lambda
     const two_theta_range = options.two_theta_range === null ? null : (options.two_theta_range ?? [0, 180]);
     const [min_radius, max_radius] = two_theta_range === null
         ? [0, 2 / wavelength]
-        : (([t_min, t_max]) => {
-            const r_min = (2 * Math.sin((t_min / 2) * (Math.PI / 180))) / wavelength;
-            const r_max = (2 * Math.sin((t_max / 2) * (Math.PI / 180))) / wavelength;
-            return [r_min, r_max];
-        })(two_theta_range);
+        : two_theta_range.map((angle) => (2 * Math.sin((angle / 2) * (Math.PI / 180))) / wavelength);
     const recip_points = enumerate_reciprocal_points(recip_rows, structure.lattice.matrix, max_radius, min_radius);
     const coeffs = [];
     const frac_coords = [];
@@ -151,16 +145,11 @@ export function compute_xrd_pattern(structure, options = {}) {
             if (!raw_coeff) {
                 throw new Error(`No atomic scattering coefficients for ${element_symbol}. Extend ATOMIC_SCATTERING_PARAMS.`);
             }
-            let coeff_entry;
-            if (Array.isArray(raw_coeff)) {
-                const a_arr = raw_coeff.map(([a]) => a);
-                const b_arr = raw_coeff.map(([_, b]) => b);
-                coeff_entry = { a: a_arr, b: b_arr, z: ELEMENT_Z[element_symbol] };
-            }
-            else {
-                coeff_entry = { a: raw_coeff.a.slice(), b: raw_coeff.b.slice(), c: raw_coeff.c };
-            }
-            coeffs.push(coeff_entry);
+            coeffs.push({
+                a: raw_coeff.map((row) => row[0]),
+                b: raw_coeff.map((row) => row[1]),
+                z: ELEMENT_Z[element_symbol],
+            });
             frac_coords.push(site.abc);
             occus.push(species.occu);
             dw_factors.push(debye_waller_factors[element_symbol] ?? 0);
@@ -171,9 +160,7 @@ export function compute_xrd_pattern(structure, options = {}) {
     const two_thetas = [];
     const merge_tol = options.peak_merge_tol ?? TWO_THETA_TOL;
     const scaled_tol = options.scaled_intensity_tol ?? SCALED_INTENSITY_TOL;
-    for (const entry of recip_points) {
-        const hkl = entry.hkl;
-        const g_norm = entry.g_norm;
+    for (const { hkl, g_norm } of recip_points) {
         if (g_norm === 0)
             continue;
         const asin_arg = (wavelength * g_norm) / 2;
@@ -184,18 +171,10 @@ export function compute_xrd_pattern(structure, options = {}) {
         const sin_theta_over_lambda_sq = sin_theta_over_lambda * sin_theta_over_lambda;
         // g.r for all fractional coords
         const g_dot_r_all = frac_coords.map((frac_coord) => math.dot(frac_coord, hkl));
-        // Atomic scattering factors (vectorized style)
-        const f_scattering = coeffs.map((coeff_entry) => {
-            const { a: a_arr, b: b_arr, z: atomic_number } = coeff_entry;
-            const num_terms = Math.min(a_arr.length, b_arr.length);
-            const sum_terms = a_arr
-                .slice(0, num_terms)
-                .reduce((sum, a_i, term_idx) => sum + a_i * Math.exp(-b_arr[term_idx] * sin_theta_over_lambda_sq), 0);
-            // pymatgen-style fitted params: f = Z − 41.78214·s²·Σ aᵢ·exp(−bᵢ·s²)
-            if (atomic_number !== undefined) {
-                return atomic_number - 41.78214 * sin_theta_over_lambda_sq * sum_terms;
-            }
-            return sum_terms + (coeff_entry.c ?? 0);
+        // Atomic scattering factors: f = Z − 41.78214·s²·Σ aᵢ·exp(−bᵢ·s²) (pymatgen fitted params)
+        const f_scattering = coeffs.map(({ a: a_arr, b: b_arr, z: atomic_number }) => {
+            const sum_terms = a_arr.reduce((sum, a_i, term_idx) => sum + a_i * Math.exp(-b_arr[term_idx] * sin_theta_over_lambda_sq), 0);
+            return atomic_number - 41.78214 * sin_theta_over_lambda_sq * sum_terms;
         });
         const dw_corr = dw_factors.map((dw_b) => Math.exp(-dw_b * sin_theta_over_lambda_sq));
         // Structure factor sum: sum(fs * occu * exp(2πi g·r) * DW)
@@ -214,28 +193,16 @@ export function compute_xrd_pattern(structure, options = {}) {
         const lorentz = (1 + Math.cos(2 * theta) ** 2) / denom;
         const intensity_hkl = (f_real * f_real + f_imag * f_imag) * lorentz;
         const two_theta = math.to_degrees(2 * theta);
-        // Use (h, k, l) always. For hexagonal systems, pymatgen presents Miller–Bravais (h, k, i, l),
-        // but downstream components expect 3-index HKL. Keep 3-index form to match types/consumers.
-        const hkl_to_store = [hkl[0], hkl[1], hkl[2]];
-        // Merge peaks within tolerance
-        let found_index = null;
-        for (let idx = 0; idx < two_thetas.length; idx++) {
-            if (Math.abs(two_thetas[idx] - two_theta) < merge_tol) {
-                found_index = idx;
-                break;
-            }
-        }
-        if (found_index !== null) {
-            const key = two_thetas[found_index];
-            const item = peaks.get(key);
-            if (item) {
-                item.intensity += intensity_hkl;
-                item.hkls.push(hkl_to_store);
-            }
+        // Merge peaks within tolerance. hkls stay 3-index (h, k, l) even for hexagonal
+        // systems where pymatgen presents Miller–Bravais (h, k, i, l), matching consumers.
+        const merge_key = two_thetas.find((angle) => Math.abs(angle - two_theta) < merge_tol);
+        const existing = merge_key === undefined ? undefined : peaks.get(merge_key);
+        if (existing) {
+            existing.intensity += intensity_hkl;
+            existing.hkls.push(hkl);
         }
         else {
-            const d_hkl = 1 / g_norm;
-            peaks.set(two_theta, { intensity: intensity_hkl, hkls: [hkl_to_store], d_hkl });
+            peaks.set(two_theta, { intensity: intensity_hkl, hkls: [hkl], d_hkl: 1 / g_norm });
             two_thetas.push(two_theta);
         }
     }
@@ -259,7 +226,7 @@ export function compute_xrd_pattern(structure, options = {}) {
             const fam = get_unique_families(item.hkls);
             const fam_array = [];
             for (const [repr_key, multiplicity] of fam.entries()) {
-                const repr = repr_key.split(`,`).map((num_str) => parseInt(num_str, 10));
+                const repr = repr_key.split(`,`).map(Number);
                 fam_array.push({ hkl: repr, multiplicity });
             }
             hkls_out.push(fam_array);
@@ -285,14 +252,9 @@ wavelength) {
         // Check if file is a direct XRD data file (.xy, .brml)
         if (is_xrd_data_file(filename)) {
             // Convert ArrayBufferLike to ArrayBuffer if needed (handles SharedArrayBuffer)
-            let buffer_content;
-            if (typeof content === `string`) {
-                buffer_content = content;
-            }
-            else {
-                buffer_content =
-                    content instanceof ArrayBuffer ? content : new Uint8Array(content).slice().buffer;
-            }
+            const buffer_content = typeof content === `string` || content instanceof ArrayBuffer
+                ? content
+                : new Uint8Array(content).slice().buffer;
             const pattern = await parse_xrd_file(buffer_content, filename);
             if (pattern && pattern.x.length > 0) {
                 return { pattern: { label: filename || `XRD data`, pattern } };

package/dist/xrd/parse.d.ts

@@ -1,6 +1,5 @@
 import type { XrdPattern } from './index';
 export declare function parse_xy_file(content: string): XrdPattern | null;
-export declare function parse_xye_file(content: string): XrdPattern | null;
 export declare function parse_ras_file(content: string): XrdPattern | null;
 export declare function parse_uxd_file(content: string): XrdPattern | null;
 export declare function parse_gsas_file(content: string): XrdPattern | null;