MATLAB .mat file reader addition

apps/cadecon/src/components/import/FileDropZone.tsx

@@ -1,5 +1,6 @@
 import { createSignal, Show, type JSX } from 'solid-js';
-import { parseNpy, parseNpz, processNpyResult } from '@calab/io';
+import { parseNpy, parseNpz, parseMat, processNpyResult } from '@calab/io';
+import type { NpzResult } from '@calab/core';
 import {
   rawFile,
   setRawFile,
@@ -19,12 +20,36 @@ export function FileDropZone(): JSX.Element {
     return mb >= 1 ? `${mb.toFixed(1)} MB` : `${(bytes / 1024).toFixed(1)} KB`;
   };
 
+  // Shared handling for multi-array containers (.npz and .mat): pick the single
+  // 2D array automatically, or hand off to the array selector when ambiguous.
+  const handleMultiArrayResult = (result: NpzResult, ext: string) => {
+    const twoDArrayNames = result.arrayNames.filter(
+      (name) => result.arrays[name].shape.length === 2,
+    );
+
+    if (twoDArrayNames.length === 0) {
+      setImportError(
+        `No 2D arrays found in .${ext} file. CaDecon requires a 2D array (cells x timepoints).`,
+      );
+      return;
+    }
+
+    if (twoDArrayNames.length === 1) {
+      // Auto-select the only 2D array
+      const processed = processNpyResult(result.arrays[twoDArrayNames[0]]);
+      setParsedData(processed);
+    } else {
+      // Multiple 2D arrays: let user select
+      setNpzArrays(result);
+    }
+  };
+
   const handleFile = async (file: File) => {
     const ext = file.name.split('.').pop()?.toLowerCase();
 
-    if (ext !== 'npy' && ext !== 'npz') {
+    if (ext !== 'npy' && ext !== 'npz' && ext !== 'mat') {
       setImportError(
-        `Unsupported file format: .${ext ?? 'unknown'}. Please use .npy or .npz files.`,
+        `Unsupported file format: .${ext ?? 'unknown'}. Please use .npy, .npz, or .mat files.`,
       );
       return;
     }
@@ -37,28 +62,9 @@ export function FileDropZone(): JSX.Element {
       const buffer = await file.arrayBuffer();
 
       if (ext === 'npz') {
-        const npzResult = parseNpz(buffer);
-        // Filter to only 2D numeric arrays
-        const twoDArrayNames = npzResult.arrayNames.filter((name) => {
-          const arr = npzResult.arrays[name];
-          return arr.shape.length === 2;
-        });
-
-        if (twoDArrayNames.length === 0) {
-          setImportError(
-            'No 2D arrays found in .npz file. CaDecon requires a 2D array (cells x timepoints).',
-          );
-          return;
-        }
-
-        if (twoDArrayNames.length === 1) {
-          // Auto-select the only 2D array
-          const processed = processNpyResult(npzResult.arrays[twoDArrayNames[0]]);
-          setParsedData(processed);
-        } else {
-          // Multiple 2D arrays: let user select
-          setNpzArrays(npzResult);
-        }
+        handleMultiArrayResult(parseNpz(buffer), 'npz');
+      } else if (ext === 'mat') {
+        handleMultiArrayResult(parseMat(buffer), 'mat');
       } else {
         // .npy file
         const result = parseNpy(buffer);
@@ -121,13 +127,13 @@ export function FileDropZone(): JSX.Element {
           </svg>
         </div>
         <p class="drop-zone__text">
-          Drop a <strong>.npy</strong> or <strong>.npz</strong> file here
+          Drop a <strong>.npy</strong>, <strong>.npz</strong>, or <strong>.mat</strong> file here
         </p>
         <p class="drop-zone__subtext">or click to browse</p>
         <input
           ref={inputRef}
           type="file"
-          accept=".npy,.npz"
+          accept=".npy,.npz,.mat"
           style="display:none"
           onChange={handleInputChange}
         />

apps/cadecon/src/components/import/NpzArraySelector.tsx

@@ -37,8 +37,8 @@ export function NpzArraySelector(): JSX.Element {
       <div class="card">
         <h3 class="card__title">Select Array</h3>
         <p class="text-secondary">
-          This .npz file contains {twoDArrays().length} arrays with 2D data. Select the one
-          containing your calcium traces:
+          This file contains {twoDArrays().length} arrays with 2D data. Select the one containing
+          your calcium traces:
         </p>
         <div class="npz-array-list">
           <For each={twoDArrays()}>

packages/io/src/__fixtures__/gen-mat-fixtures.py

@@ -0,0 +1,47 @@
+#!/usr/bin/env python3
+"""Regenerate the real MATLAB .mat fixtures used by mat-parser.test.ts.
+
+These fixtures are written by scipy (a genuine MATLAB Level-5 writer), which is
+the whole point: hand-built .mat bytes can only encode our *assumptions* about
+the format, including wrong ones. A real writer catches format-reality bugs --
+e.g. that compressed data elements are NOT padded to an 8-byte boundary, which
+a synthetic builder happily got wrong.
+
+Keep the arrays tiny (fixtures are committed to the repo) and use integer values
+so the TypeScript test can assert exact round-trip values.
+
+Usage:
+    python gen-mat-fixtures.py          # requires numpy + scipy
+
+Produces, next to this script:
+    traces_v6.mat     uncompressed (savemat do_compression=False, ~= MATLAB -v6)
+    traces_v7.mat     zlib-compressed (do_compression=True,        ~= MATLAB -v7)
+    traces_multi.mat  compressed, multiple variables (traces + fps + tvec)
+"""
+
+import os
+
+import numpy as np
+import scipy.io as sio
+
+HERE = os.path.dirname(os.path.abspath(__file__))
+
+# 3 cells x 5 timepoints, row-major logical layout [[1..5],[6..10],[11..15]].
+TRACES = np.arange(1, 16, dtype=np.float64).reshape(3, 5)
+
+
+def main() -> None:
+    sio.savemat(os.path.join(HERE, "traces_v6.mat"), {"traces": TRACES}, do_compression=False)
+    sio.savemat(os.path.join(HERE, "traces_v7.mat"), {"traces": TRACES}, do_compression=True)
+    sio.savemat(
+        os.path.join(HERE, "traces_multi.mat"),
+        {"traces": TRACES, "fps": 30.0, "tvec": np.arange(5.0)},
+        do_compression=True,
+    )
+    for name in ("traces_v6.mat", "traces_v7.mat", "traces_multi.mat"):
+        path = os.path.join(HERE, name)
+        print(f"wrote {name}: {os.path.getsize(path)} bytes")
+
+
+if __name__ == "__main__":
+    main()