Merge pull request #300 from aeisenbarth/field-of-view-paths

Avoid hard-coded field-of-view path "0"

ome_zarr/reader.py

@@ -424,7 +424,8 @@ def get_field(tile_name: str, level: int) -> np.ndarray:
             """tile_name is 'row,col'"""
             row, col = (int(n) for n in tile_name.split(","))
             field_index = (column_count * row) + col
-            path = f"{field_index}/{level}"
+            image_path = image_paths[field_index]
+            path = f"{image_path}/{level}"
             LOGGER.debug("LOADING tile... %s", path)
             try:
                 data = self.zarr.load(path)
@@ -486,7 +487,6 @@ def get_pyramid_lazy(self, node: Node) -> None:
         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"
         self.row_names = [row["name"] for row in self.rows]
         self.col_names = [col["name"] for col in self.columns]
 
@@ -502,6 +502,7 @@ def get_pyramid_lazy(self, node: Node) -> None:
         well_spec: Optional[Well] = well_node.first(Well)
         if well_spec is None:
             raise Exception("Could not find first well")
+        self.first_field_path = well_spec.well_data["images"][0]["path"]
         self.numpy_type = well_spec.numpy_type
 
         LOGGER.debug("img_pyramid_shapes: %s", well_spec.img_pyramid_shapes)
@@ -528,7 +529,7 @@ def get_numpy_type(self, image_node: Node) -> np.dtype:
     def get_tile_path(self, level: int, row: int, col: int) -> str:
         return (
             f"{self.row_names[row]}/"
-            f"{self.col_names[col]}/{self.first_field}/{level}"
+            f"{self.col_names[col]}/{self.first_field_path}/{level}"
         )
 
     def get_stitched_grid(self, level: int, tile_shape: tuple) -> da.core.Array:
@@ -568,7 +569,7 @@ def get_tile_path(self, level: int, row: int, col: int) -> str:  # pragma: no co
         """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}"
+            f"{self.first_field_path}/labels/0/{level}"
         )
         return path
 
@@ -590,7 +591,7 @@ def get_pyramid_lazy(self, node: Node) -> None:  # pragma: no cover
         properties: Dict[int, Dict[str, Any]] = {}
         for row in self.row_names:
             for col in self.col_names:
-                path = f"{row}/{col}/{self.first_field}/labels/0/.zattrs"
+                path = f"{row}/{col}/{self.first_field_path}/labels/0/.zattrs"
                 labels_json = self.zarr.get_json(path).get("image-label", {})
                 # NB: assume that 'label_val' is unique across all images
                 props_list = labels_json.get("properties", [])

tests/test_reader.py

@@ -1,6 +1,7 @@
+import numpy as np
 import pytest
 import zarr
-from numpy import zeros
+from numpy import ones, zeros
 
 from ome_zarr.data import create_zarr
 from ome_zarr.io import parse_url
@@ -75,7 +76,8 @@ def test_minimal_plate(self):
         # assert len(nodes[1].specs) == 1
         # assert isinstance(nodes[1].specs[0], PlateLabels)
 
-    def test_multiwells_plate(self):
+    @pytest.mark.parametrize("field_paths", [["0", "1", "2"], ["img1", "img2", "img3"]])
+    def test_multiwells_plate(self, field_paths):
         row_names = ["A", "B", "C"]
         col_names = ["1", "2", "3", "4"]
         well_paths = ["A/1", "A/2", "A/4", "B/2", "B/3", "C/1", "C/3", "C/4"]
@@ -84,16 +86,25 @@ def test_multiwells_plate(self):
             row, col = wp.split("/")
             row_group = self.root.require_group(row)
             well = row_group.require_group(col)
-            write_well_metadata(well, ["0", "1", "2"])
-            for field in range(3):
+            write_well_metadata(well, field_paths)
+            for field in field_paths:
                 image = well.require_group(str(field))
-                write_image(zeros((1, 1, 1, 256, 256)), image)
+                write_image(ones((1, 1, 1, 256, 256)), image)
 
         reader = Reader(parse_url(str(self.path)))
         nodes = list(reader())
         # 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)
+        plate_node = nodes[0]
+        assert len(plate_node.specs) == 1
+        assert isinstance(plate_node.specs[0], Plate)
+        # Get the plate node's array. It should be fused from the first field of all
+        # well arrays (which in this test are non-zero), with zero values for wells
+        # that failed to load (not expected) or the surplus area not filled by a well.
+        expected_num_pixels = (
+            len(well_paths) * len(field_paths[:1]) * np.prod((1, 1, 1, 256, 256))
+        )
+        pyramid_0 = plate_node.data[0]
+        assert np.asarray(pyramid_0).sum() == expected_num_pixels
         # assert len(nodes[1].specs) == 1
         # assert isinstance(nodes[1].specs[0], PlateLabels)