fix(lif): drop stale tile Y/X coords in grid- and stage-stitch reassemblers (cut v0.6.0)

CHANGELOG.md

@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.6.0] - 2026-07-02
+
 ### Added
 
 - Fourth value on `lif_mosaic`: `"stage-stitch"` reassembles a single canvas
@@ -28,6 +30,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   `zarrmony.metadata.lif_tiles.compute_stage_placements`,
   `reassemble_stage`, and `stage_overlap_discrepancy`. (#40)
 
+### Fixed
+
+- `lif_mosaic="grid-stitch"` and `"stage-stitch"` no longer crash with
+  `CoordinateValidationError: conflicting sizes for dimension 'Y'` when the
+  reader attaches per-tile Y/X pixel-space coords. Both reassemblers now
+  drop stale Y/X coords along with the M-indexed coords, so a canvas whose
+  Y/X size no longer matches a single tile stays consistent. Surfaced on a
+  real Leica LIF (3×3 mosaic, 2048×2048 tiles → 6144×6144 canvas); the
+  synthetic fixtures happened not to carry Y/X coords so the fault didn't
+  show up in CI. (#41)
+
 ## [0.5.0] - 2026-07-01
 
 ### Added

src/zarrmony/metadata/lif_tiles.py

@@ -317,10 +317,14 @@ def reassemble_grid(tiles_xarr: xr.DataArray, tile_layout: dict | None) -> xr.Da
         row_arrays.append(da.concatenate(row_tiles, axis=x_axis))
     canvas_data = da.concatenate(row_arrays, axis=y_axis)
 
+    # Y/X coords carry per-tile pixel positions — they no longer size-match
+    # the enlarged canvas, so drop them along with any other spatial coord
+    # whose dims touch Y or X. Non-spatial coords (T/C/Z, channel names, etc.)
+    # survive untouched.
     preserved_coords = {
         name: coord
         for name, coord in tiles_xarr.coords.items()
-        if "M" not in coord.dims
+        if "M" not in coord.dims and "Y" not in coord.dims and "X" not in coord.dims
     }
     return xr.DataArray(canvas_data, dims=non_m_dims, coords=preserved_coords)
 
@@ -552,10 +556,12 @@ def reassemble_stage(
     )
     canvas_data = da.from_delayed(delayed_canvas, shape=canvas_shape_t, dtype=dtype)
 
+    # See reassemble_grid: Y/X coords carry per-tile positions and can't
+    # be reused on a canvas of a different size.
     preserved_coords = {
         name: coord
         for name, coord in tiles_xarr.coords.items()
-        if "M" not in coord.dims
+        if "M" not in coord.dims and "Y" not in coord.dims and "X" not in coord.dims
     }
     return xr.DataArray(canvas_data, dims=non_m_dims, coords=preserved_coords)
 

tests/test_lif_tiles.py

@@ -367,6 +367,32 @@ def test_reassemble_grid_preserves_non_m_coords() -> None:
     assert list(canvas.coords["C"].values) == ["DAPI"]
 
 
+def test_reassemble_grid_drops_stale_tile_yx_coords() -> None:
+    # Real bioio-lif readers attach Y/X pixel-space coords sized for a single
+    # tile. The reassembled canvas is N× wider, so those coords no longer
+    # size-match — reassemble_grid must drop them (regression from a real
+    # Leica LIF where the 2048-long Y coord clashed with a 6144-tall canvas).
+    m_order = [(0, 0), (1, 0), (0, 1), (1, 1)]
+    tile_h, tile_w = 4, 4
+    tiles_xarr = _tiles_xarr(m_order, tile_h=tile_h, tile_w=tile_w)
+    tiles_xarr = tiles_xarr.assign_coords(
+        Y=np.arange(tile_h, dtype=np.float64),
+        X=np.arange(tile_w, dtype=np.float64),
+    )
+    tile_layout = {
+        "tiles": _tiles_from_grid(m_order),
+        "intended_overlap_x_pct": None,
+        "intended_overlap_y_pct": None,
+    }
+
+    canvas = reassemble_grid(tiles_xarr, tile_layout)
+
+    assert canvas.sizes["Y"] == 2 * tile_h
+    assert canvas.sizes["X"] == 2 * tile_w
+    assert "Y" not in canvas.coords
+    assert "X" not in canvas.coords
+
+
 # --- compute_stage_placements ---------------------------------------------
 
 
@@ -537,3 +563,22 @@ def test_reassemble_stage_raises_on_offsets_m_count_mismatch() -> None:
     tiles_xarr = xr.DataArray(da.from_array(arr), dims=["M", "T", "C", "Y", "X"])
     with pytest.raises(ValueError, match=r"offsets count \(1\).*M dim \(2\)"):
         reassemble_stage(tiles_xarr, [(0, 0)], canvas_shape_yx=(4, 8))
+
+
+def test_reassemble_stage_drops_stale_tile_yx_coords() -> None:
+    # Same shape-mismatch as reassemble_grid: the reader's tile-sized Y/X
+    # coords can't be reused on a canvas of a different size.
+    tile_h, tile_w = 4, 4
+    arr = np.zeros((2, 1, 1, tile_h, tile_w), dtype=np.uint16)
+    tiles_xarr = xr.DataArray(da.from_array(arr), dims=["M", "T", "C", "Y", "X"])
+    tiles_xarr = tiles_xarr.assign_coords(
+        Y=np.arange(tile_h, dtype=np.float64),
+        X=np.arange(tile_w, dtype=np.float64),
+    )
+
+    canvas = reassemble_stage(tiles_xarr, [(0, 0), (0, 2)], canvas_shape_yx=(4, 6))
+
+    assert canvas.sizes["Y"] == 4
+    assert canvas.sizes["X"] == 6
+    assert "Y" not in canvas.coords
+    assert "X" not in canvas.coords