merge dev into main

Author: lguerard

src/patchworks/plugins/ome_zarr.py

@@ -725,7 +725,21 @@ def _open_tiff_sequence(
         ) from exc
 
     ts = tifffile.TiffSequence(pattern, pattern=sequence_pattern)
+
+    # Each file should be a single 2D (y, x) plane, but tifffile.imread can
+    # report extra leading singleton dims (e.g. a page/sample axis) even for
+    # a plain single-page TIFF — drop those so one file maps to exactly (y, x).
+    chunkshape = tifffile.imread(ts[0]).shape
+    lead = len(chunkshape) - 2
+    if lead < 0 or any(s != 1 for s in chunkshape[:lead]):
+        raise ValueError(
+            f"expected single 2D (y, x) planes per file, got shape "
+            f"{chunkshape} for {ts[0]!r}"
+        )
+
     arr = da.from_zarr(zarr.open(store=ts.aszarr()))
+    if lead:
+        arr = arr[(slice(None),) * len(ts.axes) + (0,) * lead]
     full_axes = ts.axes.lower() + "yx"
 
     # Canonicalise to patchworks' tczyx axis order regardless of the order

tests/test_ome_zarr.py

@@ -122,12 +122,18 @@ def test_tiff_sequence_conversion(tmp_path):
 
 
 def test_tiff_sequence_drops_singleton_time_axis(tmp_path):
-    """A constant T in the pattern is dropped, keeping channel at axis 0."""
+    """A constant T in the pattern is dropped, keeping channel at axis 0.
+
+    Each file's own array has leading singleton dims (1, 1, y, x) — what
+    tifffile.imread reports even for a plain single-page TIFF in practice —
+    to make sure those get stripped instead of being mistaken for real
+    sequence axes.
+    """
     tifffile = pytest.importorskip("tifffile")
     n_z, n_c, size = 2, 3, 8
     for z in range(n_z):
         for c in range(n_c):
-            img = np.full((size, size), z * 10 + c, dtype="uint16")
+            img = np.full((1, 1, size, size), z * 10 + c, dtype="uint16")
             tifffile.imwrite(tmp_path / f"sample_T0_Z{z:03d}_C{c}_V0.tif", img)
 
     out = tmp_path / "out.zarr"