fix indices in _read_chunks()

Author: LucaMarconato

src/spatialdata_io/readers/_utils/_image.py

@@ -54,7 +54,6 @@ def _compute_chunks(
 
 
 def _read_chunks(
-    # TODO: expand type hints for ...
     func: Callable[..., NDArray[np.number]],
     slide: Any,
     coords: NDArray[np.int_],
@@ -94,13 +93,23 @@ def _read_chunks(
     Returns
     -------
     list[list[da.array]]
-        List (length: n_row_x) of lists (length: n_row_y) of chunks.
-        Represents all chunks of the full image.
+        (Outer) list (length: n_row_y) of (inner) lists (length: n_row_x) of chunks with axes
+        (c, y, x). Represents all chunks of the full image.
+
+    Notes
+    -------
+    As seen in _compute_chunks(), since coords are in format (x, y, width, height), the
+    inner list there (dim=-1) runs over the y values and the outer list (dim=-2) runs
+    over the x values. In _read_chunks() we have the more common (y, x) format, where
+    the inner list (dim=-1) runs over the x values and the outer list (dim=-2) runs over
+    the y values.
+
+    The above can be confusing, and a way to address this is to define coords to be
+    in format (y, x, height, width) instead of (x, y, width, height).
     """
     func_kwargs = func_kwargs if func_kwargs else {}
 
     # Collect each delayed chunk as item in list of list
-    # TODO: check, wasn't it x, y and not y, x?
     # Inner list becomes dim=-1 (cols/x)
     # Outer list becomes dim=-2 (rows/y)
     # see dask.array.block
@@ -109,21 +118,18 @@ def _read_chunks(
             da.from_delayed(
                 delayed(func)(
                     slide,
-                    x0=coords[y, x, 0],
-                    y0=coords[y, x, 1],
-                    width=coords[y, x, 2],
-                    height=coords[y, x, 3],
+                    x0=coords[x, y, 0],
+                    y0=coords[x, y, 1],
+                    width=coords[x, y, 2],
+                    height=coords[x, y, 3],
                     **func_kwargs,
                 ),
                 dtype=dtype,
-                # TODO: double check the [3, 2] with debugger
                 shape=(n_channel, *coords[y, x, [3, 2]]),
             )
-            # TODO: seems inconsistent with coords docstring
-            for x in range(coords.shape[1])
+            for x in range(coords.shape[0])
         ]
-        # TODO: seems inconsistent with coords docstring
-        for y in range(coords.shape[0])
+        for y in range(coords.shape[1])
     ]
     return chunks
 

src/spatialdata_io/readers/generic.py

@@ -116,7 +116,7 @@ def _tiff_to_chunks(input: Path, axes_dim_mapping: dict[str, int]) -> list[list[
     chunk_coords = _compute_chunks(slide_dimensions, chunk_size=DEFAULT_CHUNKSIZE)
 
     # Define reader func
-    def _reader_func(slide: NDArray[np.number], x0: int, y0: int, width: int, height: int) -> NDArray[np.number]:
+    def _reader_func(slide: np.memmap, x0: int, y0: int, width: int, height: int) -> NDArray[np.number]:
         return np.array(slide[:, y0 : y0 + height, x0 : x0 + width])
 
     return _read_chunks(_reader_func, slide, coords=chunk_coords, n_channel=n_channel, dtype=slide.dtype)
@@ -142,7 +142,6 @@ def image(input: Path, data_axes: Sequence[str], coordinate_system: str) -> Data
 
         # Edge case: Compressed images are not memory-mappable
         except ValueError as e:
-            # TODO: change to logger warning
             logger.warning(
                 f"Exception occurred: {str(e)}\nPossible troubleshooting: image data "
                 "is not memory-mappable, potentially due to compression. Trying to "