matterviz 0.4.0 → 0.4.2

package/dist/xrd/XrdPlot.svelte

@@ -6,6 +6,7 @@
     decompress_data_binary,
     decompress_file,
     detect_compression_format,
+    drag_over_handlers,
     handle_url_drop,
   } from '../io'
   import { format_value } from '../labels'
@@ -31,13 +32,9 @@
   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
-    )
+    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
   }
 
   function format_hkl(hkl: Hkl, format: HklFormat): string {
@@ -81,10 +78,8 @@
     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 }>
@@ -114,31 +109,24 @@
     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(() => {
     let max_val = 0
     for (const entry of pattern_entries) {
-      for (const y of entry.pattern.y) if (y > max_val) max_val = y
+      for (const intensity of entry.pattern.y) if (intensity > max_val) max_val = intensity
     }
     return max_val || 1
   })
@@ -159,7 +147,7 @@
   })
 
   // Scaled intensities are normalized to 0..100, add 10% top padding for peak labels
-  const intensity_range: [number, number] = [0, 110]
+  const intensity_range: Vec2 = [0, 110]
 
   // Build BarPlot series from entries (for Discrete/Stick view)
   const bar_series = $derived.by<BarSeries[]>(() => {
@@ -168,7 +156,7 @@
     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
+    const scale = (y_val: number) => (y_val / 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))
@@ -220,12 +208,11 @@
         metadata.push({ hkls, d: d_hkl, label: entry.label })
 
         if (selected_indices.includes(idx)) {
-          const angle_text = actual_show_angles
-            ? `${format_value(xs[idx], `.2f`)}°`
-            : ``
-          const hkl_text = hkls && hkl_format
-            ? hkls.map((hkl_val) => format_hkl(hkl_val, hkl_format)).join(`, `)
-            : ``
+          const angle_text = actual_show_angles ? `${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)
@@ -280,7 +267,7 @@
         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 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
@@ -304,10 +291,7 @@
     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
@@ -318,10 +302,9 @@
 
     try {
       // Handle URL-based drops
-      const handled = await handle_url_drop(
-        event,
-        on_file_drop || compute_and_add,
-      ).catch(() => false)
+      const handled = await handle_url_drop(event, on_file_drop || compute_and_add).catch(
+        () => false,
+      )
       if (handled) return
 
       const file = event.dataTransfer?.files?.[0]
@@ -331,7 +314,7 @@
           const compression_format = detect_compression_format(lower_name)
           // Get base filename without compression extension
           const base_name = compression_format
-            ? lower_name.replace(/\.(gz|gzip)$/i, ``)
+            ? lower_name.replace(/\.(?:gz|gzip)$/i, ``)
             : lower_name
           const base_ext = base_name.split(`.`).pop()
 
@@ -352,9 +335,7 @@
             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 {
@@ -380,11 +361,9 @@
     </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"
@@ -392,7 +371,8 @@
             class="param-input"
           />
         </label>
-        <label title="Caglioti V parameter">V:
+        <label title="Caglioti V parameter"
+          >V:
           <input
             type="number"
             step="0.001"
@@ -400,7 +380,8 @@
             class="param-input"
           />
         </label>
-        <label title="Caglioti W parameter">W:
+        <label title="Caglioti W parameter"
+          >W:
           <input
             type="number"
             step="0.001"
@@ -408,7 +389,8 @@
             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"
@@ -437,8 +419,8 @@
     {: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>
@@ -474,33 +456,27 @@
         }}
         {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` : ``)}
+        {...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 = `${format_value(info.y, `.1f`)}`}
         {@const hkls = info.metadata?.hkls}
-        {@const d = info.metadata?.d}
-        {@const hkl_text = hkls && hkl_format
-      ? hkls.map((hkl: Hkl) => format_hkl(hkl, hkl_format)).join(`, `)
-      : ``}
-        {@const d_text = d != null ? `${format_value(d, `.3f`)} Å` : ``}
+        {@const d_spacing = info.metadata?.d}
+        {@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 />
         Intensity: {intensity_text}
@@ -533,16 +509,11 @@
         }}
         {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` : ``)}
+        {...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.d.ts

@@ -1,3 +1,4 @@
+import type { Vec2 } from '../math';
 import type { XrdPattern } from './index';
 export type BroadeningParams = {
     U: number;
@@ -16,5 +17,5 @@ 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
+range: Vec2, // Angular range [min, max] in degrees
 step_size?: number): XrdPattern;

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

@@ -67,13 +67,6 @@ function get_unique_families(hkls) {
     }
     return family_map;
 }
-function compute_reciprocal_lattice_rows(structure) {
-    // For row-wise lattice matrix A (rows are a, b, c), reciprocal rows are inv(A)^T
-    const direct = structure.lattice.matrix;
-    const inv = math.matrix_inverse_3x3(direct);
-    const recip = math.transpose_3x3_matrix(inv);
-    return recip;
-}
 function enumerate_reciprocal_points(recip_rows, direct_rows, max_radius, min_radius) {
     const recip_b1 = recip_rows[0];
     const recip_b2 = recip_rows[1];
@@ -128,10 +121,9 @@ 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
-    const recip_rows = compute_reciprocal_lattice_rows(structure);
+    // 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
@@ -192,14 +184,15 @@ export function compute_xrd_pattern(structure, options = {}) {
         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 } = 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 (z !== undefined)
-                return z - 41.78214 * sin_theta_over_lambda_sq * sum_terms;
+            if (atomic_number !== undefined) {
+                return atomic_number - 41.78214 * sin_theta_over_lambda_sq * sum_terms;
+            }
             return sum_terms + (coeff_entry.c ?? 0);
         });
         const dw_corr = dw_factors.map((dw_b) => Math.exp(-dw_b * sin_theta_over_lambda_sq));
@@ -264,7 +257,7 @@ 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);

package/dist/xrd/index.d.ts

@@ -1,5 +1,5 @@
 import type { CompositionType } from '../composition';
-import type { Vec3 } from '../math';
+import type { Vec2, Vec3 } from '../math';
 import type { RadiationKey } from './calc-xrd';
 export * from './broadening';
 export * from './calc-xrd';
@@ -26,7 +26,7 @@ export type XrdOptions = {
     symprec?: number;
     debye_waller_factors?: CompositionType;
     scaled?: boolean;
-    two_theta_range?: [number, number] | null;
+    two_theta_range?: Vec2 | null;
     peak_merge_tol?: number;
     scaled_intensity_tol?: number;
 };

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;