Merge pull request #148 from sbesson/hcs_axes_fix

Fix remaining assumptions on 5D dimensions

Author: sbesson

ome_zarr/reader.py

@@ -57,7 +57,7 @@ def __init__(
             self.specs.append(PlateLabels(self))
         elif Plate.matches(zarr):
             self.specs.append(Plate(self))
-            self.add(zarr, plate_labels=True)
+            # self.add(zarr, plate_labels=True)
         if Well.matches(zarr):
             self.specs.append(Well(self))
 
@@ -412,6 +412,8 @@ def __init__(self, node: Node) -> None:
         # Use first Field for rendering settings, shape etc.
         image_zarr = self.zarr.create(image_paths[0])
         image_node = Node(image_zarr, node)
+        x_index = len(image_node.metadata["axes"]) - 1
+        y_index = len(image_node.metadata["axes"]) - 2
         level = 0  # load full resolution image
         self.numpy_type = image_node.data[level].dtype
         self.img_metadata = image_node.metadata
@@ -448,8 +450,8 @@ def get_lazy_well() -> da.Array:
                         dtype=self.numpy_type,
                     )
                     lazy_row.append(lazy_tile)
-                lazy_rows.append(da.concatenate(lazy_row, axis=4))
-            return da.concatenate(lazy_rows, axis=3)
+                lazy_rows.append(da.concatenate(lazy_row, axis=x_index))
+            return da.concatenate(lazy_rows, axis=y_index)
 
         node.data = [get_lazy_well()]
         node.metadata = image_node.metadata
@@ -470,7 +472,7 @@ def get_pyramid_lazy(self, node: Node) -> None:
         stitched full-resolution images.
         """
         self.plate_data = self.lookup("plate", {})
-        LOGGER.info("plate_data", self.plate_data)
+        LOGGER.info("plate_data: %s", self.plate_data)
         self.rows = self.plate_data.get("rows")
         self.columns = self.plate_data.get("columns")
         self.first_field = "0"
@@ -491,10 +493,11 @@ def get_pyramid_lazy(self, node: Node) -> None:
             raise Exception("could not find first well")
         self.numpy_type = well_spec.numpy_type
 
-        LOGGER.debug("img_pyramid_shapes", well_spec.img_pyramid_shapes)
+        LOGGER.debug(f"img_pyramid_shapes: {well_spec.img_pyramid_shapes}")
 
-        size_y = well_spec.img_shape[3]
-        size_x = well_spec.img_shape[4]
+        self.axes = well_spec.img_metadata["axes"]
+        size_y = well_spec.img_shape[len(self.axes) - 2]
+        size_x = well_spec.img_shape[len(self.axes) - 1]
 
         # FIXME - if only returning a single stiched plate (not a pyramid)
         # need to decide optimal size. E.g. longest side < 1500
@@ -511,7 +514,7 @@ def get_pyramid_lazy(self, node: Node) -> None:
             if longest_side <= TARGET_SIZE:
                 break
 
-        LOGGER.debug("target_level", target_level)
+        LOGGER.debug(f"target_level: {target_level}")
 
         pyramid = []
 
@@ -541,16 +544,19 @@ def get_tile_path(self, level: int, row: int, col: int) -> str:
         )
 
     def get_stitched_grid(self, level: int, tile_shape: tuple) -> da.core.Array:
+        LOGGER.debug(f"get_stitched_grid() level: {level}, tile_shape: {tile_shape}")
+
         def get_tile(tile_name: str) -> np.ndarray:
             """tile_name is 'level,z,c,t,row,col'"""
             row, col = (int(n) for n in tile_name.split(","))
             path = self.get_tile_path(level, row, col)
-            LOGGER.debug(f"LOADING tile... {path}")
+            LOGGER.debug(f"LOADING tile... {path} with shape: {tile_shape}")
 
             try:
                 data = self.zarr.load(path)
-            except ValueError:
+            except ValueError as e:
                 LOGGER.error(f"Failed to load {path}")
+                LOGGER.debug(f"{e}")
                 data = np.zeros(tile_shape, dtype=self.numpy_type)
             return data
 
@@ -566,23 +572,29 @@ def get_tile(tile_name: str) -> np.ndarray:
                     lazy_reader(tile_name), shape=tile_shape, dtype=self.numpy_type
                 )
                 lazy_row.append(lazy_tile)
-            lazy_rows.append(da.concatenate(lazy_row, axis=4))
-        return da.concatenate(lazy_rows, axis=3)
+            lazy_rows.append(da.concatenate(lazy_row, axis=len(self.axes) - 1))
+        return da.concatenate(lazy_rows, axis=len(self.axes) - 2)
 
 
 class PlateLabels(Plate):
-    def get_tile_path(self, level: int, row: int, col: int) -> str:
+    def get_tile_path(self, level: int, row: int, col: int) -> str:  # pragma: no cover
         """251.zarr/A/1/0/labels/0/3/"""
         path = (
             f"{self.row_names[row]}/{self.col_names[col]}/"
             f"{self.first_field}/labels/0/{level}"
         )
         return path
 
-    def get_pyramid_lazy(self, node: Node) -> None:
+    def get_pyramid_lazy(self, node: Node) -> None:  # pragma: no cover
         super().get_pyramid_lazy(node)
         # pyramid data may be multi-channel, but we only have 1 labels channel
-        node.data[0] = node.data[0][:, 0:1, :, :, :]
+        # TODO: when PlateLabels are re-enabled, update the logic to handle
+        # 0.4 axes (list of dictionaries)
+        if "c" in self.axes:
+            c_index = self.axes.index("c")
+            idx = [slice(None)] * len(self.axes)
+            idx[c_index] = slice(0, 1)
+            node.data[0] = node.data[0][tuple(idx)]
         # remove image metadata
         node.metadata = {}
 
@@ -602,7 +614,7 @@ def get_pyramid_lazy(self, node: Node) -> None:
                         del properties[label_val]["label-value"]
         node.metadata["properties"] = properties
 
-    def get_numpy_type(self, image_node: Node) -> np.dtype:
+    def get_numpy_type(self, image_node: Node) -> np.dtype:  # pragma: no cover
         # FIXME - don't assume Well A1 is valid
         path = self.get_tile_path(0, 0, 0)
         label_zarr = self.zarr.load(path)

tests/test_node.py

@@ -109,7 +109,6 @@ def test_multiwells_plate(self, fmt):
         for wp in empty_wells:
             assert parse_url(str(self.path / wp)) is None
 
-    @pytest.mark.xfail(reason="https://github.com/ome/ome-zarr-py/issues/145")
     @pytest.mark.parametrize(
         "axes, dims",
         (

tests/test_reader.py

@@ -4,7 +4,7 @@
 
 from ome_zarr.data import create_zarr
 from ome_zarr.io import parse_url
-from ome_zarr.reader import Node, Plate, PlateLabels, Reader
+from ome_zarr.reader import Node, Plate, Reader
 from ome_zarr.writer import write_image, write_plate_metadata, write_well_metadata
 
 
@@ -50,11 +50,12 @@ def test_minimal_plate(self):
 
         reader = Reader(parse_url(str(self.path)))
         nodes = list(reader())
-        assert len(nodes) == 2
+        # currently reading plate labels disabled. Only 1 node
+        assert len(nodes) == 1
         assert len(nodes[0].specs) == 1
         assert isinstance(nodes[0].specs[0], Plate)
-        assert len(nodes[1].specs) == 1
-        assert isinstance(nodes[1].specs[0], PlateLabels)
+        # assert len(nodes[1].specs) == 1
+        # assert isinstance(nodes[1].specs[0], PlateLabels)
 
     def test_multiwells_plate(self):
         row_names = ["A", "B", "C"]
@@ -72,8 +73,9 @@ def test_multiwells_plate(self):
 
         reader = Reader(parse_url(str(self.path)))
         nodes = list(reader())
-        assert len(nodes) == 2
+        # currently reading plate labels disabled. Only 1 node
+        assert len(nodes) == 1
         assert len(nodes[0].specs) == 1
         assert isinstance(nodes[0].specs[0], Plate)
-        assert len(nodes[1].specs) == 1
-        assert isinstance(nodes[1].specs[0], PlateLabels)
+        # assert len(nodes[1].specs) == 1
+        # assert isinstance(nodes[1].specs[0], PlateLabels)