Fix reading dicom series error in ITKReader (#6943)

Fixes #6942
fixes #6944.

### Description
When using itk backend reading dicom series and there is only one file
in the folder, return the first name since itk assuming that there must
be more than one file in the tuple.

https://github.com/InsightSoftwareConsortium/ITK/blob/452cb3f9716e95532200de3196d51cd705a0ec5e/Wrapping/Generators/Python/itk/support/extras.py#L1275-L1284

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: KumoLiu <[email protected]>

monai/data/image_reader.py

@@ -244,6 +244,7 @@ def read(self, data: Sequence[PathLike] | PathLike, **kwargs):
                 series_identifier = series_uid[0] if not self.series_name else self.series_name
                 name = names_generator.GetFileNames(series_identifier)
 
+                name = name[0] if len(name) == 1 else name  # type: ignore
                 _obj = itk.imread(name, **kwargs_)
                 if self.series_meta:
                     _reader = itk.ImageSeriesReader.New(FileNames=name)
@@ -631,7 +632,7 @@ def _get_meta_dict(self, img) -> dict:
 
         if self.prune_metadata:
             prune_metadata = {}
-            for key in ["00200037", "00200032", "52009229", "52009230"]:
+            for key in ["00200037", "00200032", "00280030", "52009229", "52009230"]:
                 if key in metadata.keys():
                     prune_metadata[key] = metadata[key]
             return prune_metadata
@@ -661,7 +662,9 @@ def _get_affine(self, metadata: dict, lps_to_ras: bool = True):
         rx, ry, rz, cx, cy, cz = metadata["00200037"]["Value"]
         # "00200032" is the tag of `ImagePositionPatient`
         sx, sy, sz = metadata["00200032"]["Value"]
-        dr, dc = metadata.get("spacing", (1.0, 1.0))[:2]
+        # "00280030" is the tag of `PixelSpacing`
+        spacing = metadata["00280030"]["Value"]
+        dr, dc = metadata.get("spacing", spacing)[:2]
         affine[0, 0] = cx * dr
         affine[0, 1] = rx * dc
         affine[0, 3] = sx
@@ -670,7 +673,7 @@ def _get_affine(self, metadata: dict, lps_to_ras: bool = True):
         affine[1, 3] = sy
         affine[2, 0] = cz * dr
         affine[2, 1] = rz * dc
-        affine[2, 2] = 0
+        affine[2, 2] = 1.0
         affine[2, 3] = sz
 
         # 3d

tests/test_load_image.py

@@ -23,12 +23,13 @@
 from parameterized import parameterized
 from PIL import Image
 
+from monai.apps import download_and_extract
 from monai.data import NibabelReader, PydicomReader
 from monai.data.meta_obj import set_track_meta
 from monai.data.meta_tensor import MetaTensor
 from monai.transforms import LoadImage
 from monai.utils import optional_import
-from tests.utils import assert_allclose
+from tests.utils import assert_allclose, skip_if_downloading_fails, testing_data_config
 
 itk, has_itk = optional_import("itk", allow_namespace_pkg=True)
 ITKReader, _ = optional_import("monai.data", name="ITKReader", as_type="decorator")
@@ -159,6 +160,25 @@ def get_data(self, _obj):
 
 @unittest.skipUnless(has_itk, "itk not installed")
 class TestLoadImage(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        super(__class__, cls).setUpClass()
+        with skip_if_downloading_fails():
+            cls.tmpdir = tempfile.mkdtemp()
+            key = "DICOM_single"
+            url = testing_data_config("images", key, "url")
+            hash_type = testing_data_config("images", key, "hash_type")
+            hash_val = testing_data_config("images", key, "hash_val")
+            download_and_extract(
+                url=url, output_dir=cls.tmpdir, hash_val=hash_val, hash_type=hash_type, file_type="zip"
+            )
+            cls.data_dir = os.path.join(cls.tmpdir, "CT_DICOM_SINGLE")
+
+    @classmethod
+    def tearDownClass(cls):
+        shutil.rmtree(cls.tmpdir)
+        super(__class__, cls).tearDownClass()
+
     @parameterized.expand(
         [TEST_CASE_1, TEST_CASE_2, TEST_CASE_3, TEST_CASE_3_1, TEST_CASE_4, TEST_CASE_4_1, TEST_CASE_5]
     )
@@ -206,6 +226,22 @@ def test_itk_dicom_series_reader(self, input_param, filenames, expected_shape, e
         )
         self.assertTupleEqual(result.shape, expected_np_shape)
 
+    def test_itk_dicom_series_reader_single(self):
+        result = LoadImage(image_only=True, reader="ITKReader")(self.data_dir)
+        self.assertEqual(result.meta["filename_or_obj"], f"{Path(self.data_dir)}")
+        assert_allclose(
+            result.affine,
+            torch.tensor(
+                [
+                    [-0.488281, 0.0, 0.0, 125.0],
+                    [0.0, -0.488281, 0.0, 128.100006],
+                    [0.0, 0.0, 1.0, -99.480003],
+                    [0.0, 0.0, 0.0, 1.0],
+                ]
+            ),
+        )
+        self.assertTupleEqual(result.shape, (16, 16, 1))
+
     def test_itk_reader_multichannel(self):
         test_image = np.random.randint(0, 256, size=(256, 224, 3)).astype("uint8")
         with tempfile.TemporaryDirectory() as tempdir:
@@ -231,6 +267,17 @@ def test_dicom_reader_consistency(self, filenames):
             np.testing.assert_allclose(pydicom_result, itk_result)
             np.testing.assert_allclose(pydicom_result.affine, itk_result.affine)
 
+    def test_dicom_reader_consistency_single(self):
+        itk_param = {"reader": "ITKReader"}
+        pydicom_param = {"reader": "PydicomReader"}
+        for affine_flag in [True, False]:
+            itk_param["affine_lps_to_ras"] = affine_flag
+            pydicom_param["affine_lps_to_ras"] = affine_flag
+            itk_result = LoadImage(image_only=True, **itk_param)(self.data_dir)
+            pydicom_result = LoadImage(image_only=True, **pydicom_param)(self.data_dir)
+            np.testing.assert_allclose(pydicom_result, itk_result.squeeze())
+            np.testing.assert_allclose(pydicom_result.affine, itk_result.affine)
+
     def test_load_nifti_multichannel(self):
         test_image = np.random.randint(0, 256, size=(31, 64, 16, 2)).astype(np.float32)
         with tempfile.TemporaryDirectory() as tempdir:

tests/testing_data/data_config.json

@@ -79,6 +79,11 @@
             "url": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/CT_2D_head_moving.mha",
             "hash_type": "sha256",
             "hash_val": "a37c5fe388c38b3f4ac564f456277d09d3982eda58c4da05ead8ee2332360f47"
+        },
+        "DICOM_single": {
+            "url": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/CT_DICOM_SINGLE.zip",
+            "hash_type": "sha256",
+            "hash_val": "a41f6e93d2e3d68956144f9a847273041d36441da12377d6a1d5ae610e0a7023"
         }
     },
     "videos": {