fix #382: handle 'layers' as h5py.Dataset in read_stereo_h5ad

stereo/io/reader.py

@@ -315,11 +315,14 @@ def _read_stereo_h5ad_from_group(f: Union[h5py.File, h5py.Group], data: StereoEx
                     batch, sn = row[0], row[1]
                     data.sn[str(batch)] = str(sn)
         elif k == 'layers':
-            for layer_key in f[k].keys():
-                if isinstance(f[k][layer_key], h5py.Group):
-                    data.layers[layer_key] = h5ad.read_group(f[k][layer_key])
-                else:
-                    data.layers[layer_key] = h5ad.read_dataset(f[k][layer_key])
+            if isinstance(f[k], h5py.Group):
+                for layer_key in f[k].keys():
+                    if isinstance(f[k][layer_key], h5py.Group):
+                        data.layers[layer_key] = h5ad.read_group(f[k][layer_key])
+                    else:
+                        data.layers[layer_key] = h5ad.read_dataset(f[k][layer_key])
+            else:
+                data.layers[k] = h5ad.read_dataset(f[k])
 
     # read raw
     if use_raw is True and 'exp_matrix@raw' in f.keys():

tests/test_read_h5ad_layers.py

@@ -0,0 +1,89 @@
+"""Tests for reading 'layers' key from Stereopy-format H5AD files.
+
+Verifies that both h5py.Group and h5py.Dataset formats for the 'layers'
+key are handled correctly in _read_stereo_h5ad_from_group (issue #382).
+"""
+
+import os
+import tempfile
+
+import h5py
+import numpy as np
+import pytest
+
+from stereo.io.reader import _read_stereo_h5ad_from_group
+from stereo.core.stereo_exp_data import StereoExpData
+
+
+def _make_minimal_h5(path, layers_as_dataset=False):
+    """Create a minimal Stereopy-format H5AD file with a 'layers' key.
+
+    Parameters
+    ----------
+    path
+        Path to write the HDF5 file.
+    layers_as_dataset
+        If True, store 'layers' as an h5py.Dataset (flat array).
+        If False, store 'layers' as an h5py.Group with a sub-dataset.
+    """
+    n_cells, n_genes = 5, 10
+    with h5py.File(path, 'w') as f:
+        f.create_dataset('exp_matrix', data=np.ones((n_cells, n_genes), dtype=np.float32))
+        cells_grp = f.create_group('cells')
+        cells_grp.create_dataset('cell_name', data=np.array([b'c0', b'c1', b'c2', b'c3', b'c4']))
+        genes_grp = f.create_group('genes')
+        genes_grp.create_dataset('gene_name', data=np.array([
+            b'g0', b'g1', b'g2', b'g3', b'g4', b'g5', b'g6', b'g7', b'g8', b'g9'
+        ]))
+        if layers_as_dataset:
+            f.create_dataset('layers', data=np.zeros((n_cells, n_genes), dtype=np.float32))
+        else:
+            layers_grp = f.create_group('layers')
+            layers_grp.create_dataset('raw_counts', data=np.full((n_cells, n_genes), 2.0, dtype=np.float32))
+
+
+@pytest.fixture
+def h5_with_layers_group(tmp_path):
+    path = str(tmp_path / "layers_group.h5ad")
+    _make_minimal_h5(path, layers_as_dataset=False)
+    return path
+
+
+@pytest.fixture
+def h5_with_layers_dataset(tmp_path):
+    path = str(tmp_path / "layers_dataset.h5ad")
+    _make_minimal_h5(path, layers_as_dataset=True)
+    return path
+
+
+class TestReadH5adLayers:
+    """Test that _read_stereo_h5ad_from_group handles layers as Group or Dataset."""
+
+    def test_layers_as_group(self, h5_with_layers_group):
+        """When 'layers' is an h5py.Group, each sub-key should be read into data.layers."""
+        data = StereoExpData(file_path=h5_with_layers_group)
+        with h5py.File(h5_with_layers_group, 'r') as f:
+            _read_stereo_h5ad_from_group(f, data, use_raw=False, use_result=False)
+        assert 'raw_counts' in data.layers
+        assert data.layers['raw_counts'].shape == (5, 10)
+        np.testing.assert_array_equal(data.layers['raw_counts'], np.full((5, 10), 2.0))
+
+    def test_layers_as_dataset(self, h5_with_layers_dataset):
+        """When 'layers' is an h5py.Dataset, it should be read directly without error."""
+        data = StereoExpData(file_path=h5_with_layers_dataset)
+        with h5py.File(h5_with_layers_dataset, 'r') as f:
+            _read_stereo_h5ad_from_group(f, data, use_raw=False, use_result=False)
+        assert 'layers' in data.layers
+        assert data.layers['layers'].shape == (5, 10)
+        np.testing.assert_array_equal(data.layers['layers'], np.zeros((5, 10)))
+
+    def test_layers_as_dataset_no_attribute_error(self, h5_with_layers_dataset):
+        """Regression test: reading a Dataset-type 'layers' must not raise AttributeError."""
+        data = StereoExpData(file_path=h5_with_layers_dataset)
+        with h5py.File(h5_with_layers_dataset, 'r') as f:
+            try:
+                _read_stereo_h5ad_from_group(f, data, use_raw=False, use_result=False)
+            except AttributeError as e:
+                pytest.fail(
+                    "AttributeError raised when reading layers as Dataset: {}".format(e)
+                )