fix: Fix images where widthPx x Bytes is not the same as expected width Bytes

src/nd2/_sdk/latest.pyx

@@ -113,6 +113,17 @@ cdef class ND2Reader:
             cont = self._metadata().get('contents')
             attrs = self._attributes()
             nC = cont.get('channelCount') if cont else attrs.get("componentCount", 1)
+            # widthPx doesn't always equal widthBytes / bytesPerPixel ... but when it doesn't
+            # the image is slanted anyway. For now, we just force it here.
+            w = attrs.get('widthBytes') // (attrs.get("componentCount", 1) * attrs.get('bitsPerComponentInMemory') // 8)
+            if w != attrs['widthPx']:
+                wb = attrs.get('widthBytes')
+                bpp = (attrs.get('bitsPerComponentInMemory') // 8)
+                warnings.warn(
+                    f"widthPx ({attrs['widthPx']}) != widthBytes ({wb}) / bytesPerPixel ({bpp}). "
+                    f"Forcing widthPx to {w} (widthBytes / bytesPerPixel)."
+                )
+                attrs['widthPx'] = w
             self.__attributes = structures.Attributes(**attrs, channelCount=nC)
         return self.__attributes
 

src/nd2/nd2file.py

@@ -399,7 +399,7 @@ def _dask_block(self, copy: bool, block_id: Tuple[int]) -> np.ndarray:
                             f"Cannot get chunk {block_id} for single frame image."
                         )
                     idx = 0
-                data = self._get_frame(cast(int, idx))
+                data = self._get_frame(int(idx))  # type: ignore
                 data = data.copy() if copy else data
                 return data[(np.newaxis,) * ncoords]
             finally:
@@ -498,8 +498,8 @@ def _coord_shape(self) -> Tuple[int, ...]:
     def _frame_count(self) -> int:
         return int(np.prod(self._coord_shape))
 
-    def _get_frame(self, index: int) -> np.ndarray:
-        frame = self._rdr._read_image(index)
+    def _get_frame(self, index: SupportsInt) -> np.ndarray:
+        frame = self._rdr._read_image(int(index))
         frame.shape = self._raw_frame_shape
         return frame.transpose((2, 0, 1, 3)).squeeze()
 

tests/test_reader.py

@@ -2,6 +2,7 @@
 import os
 import pickle
 import sys
+from contextlib import nullcontext
 from pathlib import Path
 
 import dask.array as da
@@ -16,15 +17,31 @@
 DATA = Path(__file__).parent / "data"
 
 
-def test_metadata_extraction(new_nd2):
+def _warning_ctx(fname: Path):
+    if fname.name in {
+        "jonas_control002.nd2",
+        "jonas_JJ1473_control_24h_JJ1473_control_24h_03.nd2",
+    }:
+        return pytest.warns(UserWarning, match="widthPx")
+    return nullcontext()
+
+
+def test_metadata_extraction(new_nd2: Path):
     assert ND2File.is_supported_file(new_nd2)
-    with ND2File(new_nd2) as nd:
+    with _warning_ctx(new_nd2), ND2File(new_nd2) as nd:
         assert nd.path == str(new_nd2)
         assert not nd.closed
 
         # assert isinstance(nd._rdr._seq_count(), int)
         assert isinstance(nd.attributes, structures.Attributes)
 
+        # this is one of the "skewed" files where widthPx seems
+        # to be set incorrectly in the actual metadata
+        if new_nd2.name == "jonas_control002.nd2":
+            assert nd.attributes.widthPx == 248
+            assert nd.shape == (65, 9, 152, 248)
+            assert nd.sizes["X"] == 248
+
         # TODO: deal with typing when metadata is completely missing
         assert isinstance(nd.metadata, structures.Metadata)
         assert isinstance(nd.frame_metadata(0), structures.FrameMetadata)
@@ -41,7 +58,7 @@ def test_metadata_extraction(new_nd2):
 
 
 def test_read_safety(new_nd2: Path):
-    with ND2File(new_nd2) as nd:
+    with _warning_ctx(new_nd2), ND2File(new_nd2) as nd:
         for i in range(nd._frame_count):
             nd._rdr._read_image(i)
 
@@ -50,7 +67,7 @@ def test_position(new_nd2):
     """use position to extract a single stage position with asarray."""
     if new_nd2.stat().st_size > 250_000_000:
         pytest.skip("skipping read on big files")
-    with ND2File(new_nd2) as nd:
+    with _warning_ctx(new_nd2), ND2File(new_nd2) as nd:
         dx = nd.to_xarray(delayed=True, position=0, squeeze=False)
         nx = nd.to_xarray(delayed=False, position=0, squeeze=False)
         assert dx.sizes[AXIS.POSITION] == 1
@@ -62,7 +79,7 @@ def test_position(new_nd2):
 
 
 def test_dask(new_nd2):
-    with ND2File(new_nd2) as nd:
+    with _warning_ctx(new_nd2), ND2File(new_nd2) as nd:
         dsk = nd.to_dask()
         assert isinstance(dsk, da.Array)
         assert dsk.shape == nd.shape
@@ -79,7 +96,7 @@ def test_dask_closed(single_nd2):
 
 @pytest.mark.skipif(bool(os.getenv("CIBUILDWHEEL")), reason="slow")
 def test_full_read(new_nd2):
-    with ND2File(new_nd2) as nd:
+    with _warning_ctx(new_nd2), ND2File(new_nd2) as nd:
         if new_nd2.stat().st_size > 500_000_000:
             pytest.skip("skipping full read on big files")
         delayed_xarray: np.ndarray = np.asarray(nd.to_xarray(delayed=True))
@@ -109,7 +126,7 @@ def test_full_read_legacy(old_nd2):
 
 
 def test_xarray(new_nd2):
-    with ND2File(new_nd2) as nd:
+    with _warning_ctx(new_nd2), ND2File(new_nd2) as nd:
         xarr = nd.to_xarray()
         assert isinstance(xarr, xr.DataArray)
         assert isinstance(xarr.data, da.Array)
@@ -176,7 +193,7 @@ def test_bioformats_parity(new_nd2: Path, bfshapes: dict):
         bf_info = {k: v for k, v in bfshapes[new_nd2.name]["shape"].items() if v > 1}
     except KeyError:
         pytest.skip(f"{new_nd2.name} not in stats")
-    with ND2File(new_nd2) as nd:
+    with _warning_ctx(new_nd2), ND2File(new_nd2) as nd:
         # doing these weird checks/asserts for better error messages
         if len(bf_info) != len(nd.sizes):
             assert bf_info == nd.sizes

tests/test_sdk.py

@@ -1,3 +1,4 @@
+from contextlib import nullcontext
 from pathlib import Path
 
 import numpy as np
@@ -6,8 +7,18 @@
 from nd2._sdk import latest
 
 
+# duplicated in test_reader
+def _warning_ctx(fname: Path):
+    if fname.name in {
+        "jonas_control002.nd2",
+        "jonas_JJ1473_control_24h_JJ1473_control_24h_03.nd2",
+    }:
+        return pytest.warns(UserWarning, match="widthPx")
+    return nullcontext()
+
+
 def test_new_sdk(new_nd2: Path):
-    with latest.ND2Reader(new_nd2, read_using_sdk=True) as nd:
+    with _warning_ctx(new_nd2), latest.ND2Reader(new_nd2, read_using_sdk=True) as nd:
         a = nd._attributes()
         assert isinstance(a, dict)
         assert isinstance(nd._metadata(), dict)