fixes #6007

Signed-off-by: Wenqi Li <[email protected]>

monai/data/image_reader.py

@@ -1141,13 +1141,17 @@ class PILReader(ImageReader):
     Args:
         converter: additional function to convert the image data after `read()`.
             for example, use `converter=lambda image: image.convert("LA")` to convert image format.
+        reverse_indexing: whether to swap axis 0 and 1 after loading the array, this is enabled by default,
+            so that output of the reader is consistent with the other readers. Set this option to ``False`` to use
+            the PIL backend's original spatial axes convention.
         kwargs: additional args for `Image.open` API in `read()`, mode details about available args:
             https://pillow.readthedocs.io/en/stable/reference/Image.html#PIL.Image.open
     """
 
-    def __init__(self, converter: Callable | None = None, **kwargs):
+    def __init__(self, converter: Callable | None = None, reverse_indexing: bool = True, **kwargs):
         super().__init__()
         self.converter = converter
+        self.reverse_indexing = reverse_indexing
         self.kwargs = kwargs
 
     def verify_suffix(self, filename: Sequence[PathLike] | PathLike) -> bool:
@@ -1207,7 +1211,7 @@ def get_data(self, img) -> tuple[np.ndarray, dict]:
         for i in ensure_tuple(img):
             header = self._get_meta_dict(i)
             header[MetaKeys.SPATIAL_SHAPE] = self._get_spatial_shape(i)
-            data = np.moveaxis(np.asarray(i), 0, 1)
+            data = np.moveaxis(np.asarray(i), 0, 1) if self.reverse_indexing else np.asarray(i)
             img_array.append(data)
             header[MetaKeys.ORIGINAL_CHANNEL_DIM] = (
                 "no_channel" if len(data.shape) == len(header[MetaKeys.SPATIAL_SHAPE]) else -1

tests/test_pil_reader.py

@@ -25,7 +25,7 @@
 
 TEST_CASE_2 = [(128, 128, 3), ["test_image.png"], (128, 128, 3), (128, 128)]
 
-TEST_CASE_3 = [(128, 128, 4), ["test_image.png"], (128, 128, 4), (128, 128)]
+TEST_CASE_3 = [(128, 128, 4), ["test_image.png"], (128, 128, 4), (128, 128), False]
 
 TEST_CASE_4 = [(128, 128), ["test_image1.png", "test_image2.png", "test_image3.png"], (3, 128, 128), (128, 128)]
 
@@ -38,20 +38,21 @@
 
 class TestPNGReader(unittest.TestCase):
     @parameterized.expand([TEST_CASE_1, TEST_CASE_2, TEST_CASE_3, TEST_CASE_4, TEST_CASE_5, TEST_CASE_6])
-    def test_shape_value(self, data_shape, filenames, expected_shape, meta_shape):
+    def test_shape_value(self, data_shape, filenames, expected_shape, meta_shape, reverse=True):
         test_image = np.random.randint(0, 256, size=data_shape)
         with tempfile.TemporaryDirectory() as tempdir:
             for i, name in enumerate(filenames):
                 filenames[i] = os.path.join(tempdir, name)
                 Image.fromarray(test_image.astype("uint8")).save(filenames[i])
-            reader = PILReader(mode="r")
+            reader = PILReader(mode="r", reverse_indexing=reverse)
             result = reader.get_data(reader.read(filenames))
             # load image by PIL and compare the result
             test_image = np.asarray(Image.open(filenames[0]))
 
         self.assertTupleEqual(tuple(result[1]["spatial_shape"]), meta_shape)
         self.assertTupleEqual(result[0].shape, expected_shape)
-        test_image = np.moveaxis(test_image, 0, 1)
+        if reverse:
+            test_image = np.moveaxis(test_image, 0, 1)
         if result[0].shape == test_image.shape:
             np.testing.assert_allclose(result[0], test_image)
         else: