swap axes instead of transposing

angelolab · Sep 5, 2023 · e1292c6 · e1292c6
1 parent 76f83d5
commit e1292c6
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Showing 2 changed files with 25 additions and 5 deletions.
diff --git a/src/alpineer/load_utils.py b/src/alpineer/load_utils.py
@@ -532,11 +532,22 @@ def fov_to_ome(
     # Reorder the DataArray as OME-TIFFs require [Channel, Y, X]
     fov_xr: xr.DataArray = load_imgs_from_tree(
         data_dir=data_dir, img_sub_folder=img_sub_folder, fovs=fovs, channels=channels
-    ).transpose("fovs", "channels", "cols", "rows")
+    )
+
+    # convert to numpy for axes swapping without image rotation
+    fov_np = fov_xr.as_numpy()
+    fov_np = np.swapaxes(fov_np, 2, 3)
+    fov_np = np.swapaxes(fov_np, 1, 2)
+
+    fov_xr_reordered = xr.DataArray(
+        fov_np,
+        coords=[fov_xr.fovs, fov_xr.channels, fov_xr.rows, fov_xr.cols],
+        dims=["fovs", "channels", "rows", "cols"],
+    )
 
     _compression: dict = {"algorithm": "zlib", "args": {"level": 6}}
 
-    for fov in fov_xr:
+    for fov in fov_xr_reordered:
         fov_name: str = fov.fovs.values
         ome_file_path: pathlib.Path = pathlib.Path(ome_save_dir) / f"{fov_name}.ome.tiff"
 
@@ -613,6 +624,6 @@ def ome_to_fov(ome: Union[str, pathlib.Path], data_dir: Union[str, pathlib.Path]
 
             image_utils.save_image(
                 fname=save_dir / f"{channel}.tiff",
-                data=ome_tiff_page.asarray().transpose(),
+                data=ome_tiff_page.asarray(),
                 compression_level=6,
             )
diff --git a/tests/load_utils_test.py b/tests/load_utils_test.py
@@ -665,7 +665,16 @@ def create_img_data(tmp_path_factory) -> Iterator[Tuple[pathlib.Path, xr.DataArr
 
     # Create OME-TIFFs
     _compression: dict = {"algorithm": "zlib", "args": {"level": 6}}
-    data_xr_transposed = data_xr.transpose("fovs", "channels", "cols", "rows")
+    data_np = data_xr.as_numpy()
+    data_np = np.swapaxes(data_np, 2, 3)
+    data_np = np.swapaxes(data_np, 1, 2)
+
+    data_xr_transposed = xr.DataArray(
+        data_np,
+        coords=[data_xr.fovs, data_xr.channels, data_xr.rows, data_xr.cols],
+        dims=["fovs", "channels", "rows", "cols"],
+    )
+
     for fov in data_xr_transposed:
         fov_name: str = fov.fovs.values
         ome_file_path: pathlib.Path = pathlib.Path(test_dir) / f"{fov_name}.ome.tiff"
@@ -726,7 +735,7 @@ def test_fov_to_ome(self, fovs, channels) -> None:
 
                 # Assert that the channel values in the OME-TIFF are correct.
                 for page, chan in zip(ome_tiff.pages, channels):
-                    actual_data = page.asarray().transpose()
+                    actual_data = page.asarray()
                     desired_data = self.data_xr.sel(fovs=fov_name, channels=chan).values
                     np.testing.assert_equal(actual_data, desired_data)