fix: stringify HDF5 reference attributes in the h5 browser

Fixes #9

Author: PierreRaybaut

CHANGELOG.md

@@ -15,6 +15,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/)
 
 - **Saving and opening TIFF images**: saving (or opening) an image in TIFF format no longer fails with an internal `No module named 'tifffile'` error. The library required for TIFF support is now installed alongside the rest of the scientific stack at startup, so `.tif`/`.tiff` files can be written and read like any other image format.
 - **Command palette search**: short queries no longer flood the results with unrelated commands. Typing `rota` (looking for _Rotation_) used to also match entries like _Import annotations_, _Polynomial calibration_ or _Horizontal projection_, because the search accepted any command whose letters appeared in order, however scattered. The search now keeps only commands that either contain the query as-is or match it word-by-word (initials), so results stay relevant while still finding commands like `fft` or `fan` → _Fourier analysis_.
+- **HDF5 files converted from HDF4**: opening an HDF5 file produced by `h4toh5convert` no longer breaks the Properties panel (with a `could not be cloned` error) nor the display of imported signals and images. Such files carry HDF5 object-reference attributes (e.g. `DIMENSION_LIST`) that could not be transferred out of the computation worker; these attributes are now shown as plain text instead, so the data imports and displays normally.
 
 ## [0.6.2] - 2026-06-26
 

src/runtime/dlw_h5browser.py

@@ -431,9 +431,19 @@ def _collect_attrs(dset: Any) -> dict[str, Any]:
         if isinstance(value, bytes):
             value = _safe_decode_bytes(value)
         if isinstance(value, np.ndarray):
-            try:
-                value = value.tolist()
-            except Exception:  # noqa: BLE001
+            # Numeric, boolean and string arrays convert cleanly to
+            # JSON-friendly lists. ``object``/``void`` dtypes are how h5py
+            # exposes HDF5 object/region *reference* attributes (e.g.
+            # ``DIMENSION_LIST`` / ``REFERENCE_LIST`` produced by
+            # ``h4toh5convert``): ``tolist()`` would yield ``h5py.h5r.Reference``
+            # elements that cannot cross the worker→main-thread ``postMessage``
+            # boundary ("could not be cloned"), so stringify them instead.
+            if value.dtype.kind in "biufcSU":
+                try:
+                    value = value.tolist()
+                except Exception:  # noqa: BLE001
+                    value = repr(value)
+            else:
                 value = repr(value)
         elif isinstance(value, (np.integer,)):
             value = int(value)

tests/python/test_h5browser.py

@@ -91,6 +91,47 @@ def test_node_attrs_exposes_attributes(opened):
     assert attrs["attributes"].get("units") == "V"
 
 
+def _assert_no_h5_references(value):
+    """Recursively assert *value* holds no ``h5py.h5r.Reference`` object."""
+    assert not isinstance(value, h5py.h5r.Reference)
+    if isinstance(value, dict):
+        for item in value.values():
+            _assert_no_h5_references(item)
+    elif isinstance(value, (list, tuple)):
+        for item in value:
+            _assert_no_h5_references(item)
+
+
+def test_node_attrs_stringifies_reference_attributes(tmp_path):
+    """HDF5 reference attributes must not leak non-cloneable objects.
+
+    Files converted with ``h4toh5convert`` carry object-reference attributes
+    (e.g. ``DIMENSION_LIST``) that h5py exposes as ``object``-dtype arrays of
+    :class:`h5py.h5r.Reference`. Such objects cannot cross the worker→main
+    thread ``postMessage`` boundary ("could not be cloned"), so
+    ``_collect_attrs`` must stringify them rather than ``tolist()`` them.
+    """
+    path = tmp_path / "ref.h5"
+    ref_dtype = h5py.special_dtype(ref=h5py.Reference)
+    with h5py.File(path, "w") as f:
+        img = f.create_dataset("img", data=np.arange(64, dtype=float).reshape(8, 8))
+        s0 = f.create_dataset("scale0", data=np.arange(8))
+        s1 = f.create_dataset("scale1", data=np.arange(8))
+        img.attrs.create("DIMENSION_LIST", np.array([s0.ref, s1.ref], dtype=ref_dtype))
+        img.attrs["REFERENCE"] = s0.ref
+        img.attrs["units"] = "px"
+    result = h5b.open_file("ref.h5", path.read_bytes())
+    try:
+        attrs = h5b.node_attrs(result["file_id"], "/img")["attributes"]
+        assert attrs["units"] == "px"
+        # Reference attributes survive only as harmless strings.
+        assert isinstance(attrs["DIMENSION_LIST"], str)
+        assert isinstance(attrs["REFERENCE"], str)
+        _assert_no_h5_references(attrs)
+    finally:
+        h5b.close_all()
+
+
 def test_preview_signal(opened):
     file_id = opened["file_id"]
     prev = h5b.preview(file_id, "/sig")