Merge pull request #314 from ImagingDataCommons/bug/get_bot_pydicom3

Fix for BOT construction, add test

Author: CPBridge

data/test_files/sm_image_jpegls.dcm

@@ -185,7 +185,7 @@ def _build_bot(fp: DicomFileLike, number_of_frames: int) -> List[int]:
                 f'Length of Frame item #{i} is zero.'
             )
 
-        first_two_bytes = fp.read(2, True)
+        first_two_bytes = fp.read(2)
         if not fp.is_little_endian:
             first_two_bytes = first_two_bytes[::-1]
         # In case of fragmentation, we only want to get the offsets to the

data/test_files/sm_image_jpegls_nobot.dcm

@@ -73,6 +73,26 @@ def test_read_multi_frame_sm_image_native(self):
                 )
                 np.testing.assert_array_equal(frame, pixel_array[i, ...])
 
+    def test_read_multi_frame_sm_image_jpegls(self):
+        filename = str(self._test_dir.joinpath('sm_image_jpegls.dcm'))
+        dataset = dcmread(filename)
+        pixel_array = dataset.pixel_array
+        with ImageFileReader(filename) as reader:
+            assert reader.number_of_frames == 25
+            indices = list(range(reader.number_of_frames))
+            shuffle(indices)
+            for i in indices:
+                frame = reader.read_frame(i, correct_color=False)
+                assert isinstance(frame, np.ndarray)
+                assert frame.ndim == 3
+                assert frame.dtype == np.uint8
+                assert frame.shape == (
+                    reader.metadata.Rows,
+                    reader.metadata.Columns,
+                    reader.metadata.SamplesPerPixel,
+                )
+                np.testing.assert_array_equal(frame, pixel_array[i, ...])
+
     def test_read_multi_frame_sm_image_numbers_native(self):
         filename = str(self._test_dir.joinpath('sm_image_numbers.dcm'))
         dataset = dcmread(filename)
@@ -212,3 +232,87 @@ def test_read_single_frame_ct_image_dicom_file_like_opened(self):
                 reader.metadata.Columns,
             )
             np.testing.assert_array_equal(frame, pixel_array)
+
+    def test_read_single_frame_sm_image_jpegls_dicom_bytes_io(self):
+        filename = str(self._test_dir.joinpath("sm_image_jpegls.dcm"))
+        dcm = DicomBytesIO(open(filename, "rb").read())
+
+        dataset = dcmread(filename)
+        pixel_array = dataset.pixel_array
+        with ImageFileReader(dcm) as reader:
+            assert reader.number_of_frames == 25
+            for fno in range(reader.number_of_frames):
+                frame = reader.read_frame(fno)
+                assert isinstance(frame, np.ndarray)
+                assert frame.ndim == 3
+                assert frame.dtype == np.uint8
+                assert frame.shape == (
+                    reader.metadata.Rows,
+                    reader.metadata.Columns,
+                    3,
+                )
+                np.testing.assert_array_equal(frame, pixel_array[fno])
+
+    def test_read_single_frame_sm_image_jpegls_nobot_dicom_bytes_io(self):
+        filename = str(self._test_dir.joinpath("sm_image_jpegls_nobot.dcm"))
+        dcm = DicomBytesIO(open(filename, "rb").read())
+
+        dataset = dcmread(filename)
+        pixel_array = dataset.pixel_array
+        with ImageFileReader(dcm) as reader:
+            assert reader.number_of_frames == 25
+            for fno in range(reader.number_of_frames):
+                frame = reader.read_frame(fno)
+                assert isinstance(frame, np.ndarray)
+                assert frame.ndim == 3
+                assert frame.dtype == np.uint8
+                assert frame.shape == (
+                    reader.metadata.Rows,
+                    reader.metadata.Columns,
+                    3,
+                )
+                np.testing.assert_array_equal(frame, pixel_array[fno])
+
+    def test_read_single_frame_sm_image_jpegls_dicom_file_like_opened(self):
+        # Test reading frames from an opened DicomFileLike file
+        filename = self._test_dir.joinpath("sm_image_jpegls.dcm")
+        dcm = DicomFileLike(filename.open("rb"))
+
+        dataset = dcmread(filename)
+        pixel_array = dataset.pixel_array
+        with ImageFileReader(dcm) as reader:
+            assert reader.number_of_frames == 25
+            for fno in range(reader.number_of_frames):
+                frame = reader.read_frame(fno)
+                assert isinstance(frame, np.ndarray)
+                assert frame.ndim == 3
+                assert frame.dtype == np.uint8
+                assert frame.shape == (
+                    reader.metadata.Rows,
+                    reader.metadata.Columns,
+                    3,
+                )
+                np.testing.assert_array_equal(frame, pixel_array[fno])
+
+    def test_read_single_frame_sm_image_jpegls_nobot_dicom_file_like_opened(
+        self
+    ):
+        # Test reading frames from an opened DicomFileLike file
+        filename = self._test_dir.joinpath("sm_image_jpegls_nobot.dcm")
+        dcm = DicomFileLike(filename.open("rb"))
+
+        dataset = dcmread(filename)
+        pixel_array = dataset.pixel_array
+        with ImageFileReader(dcm) as reader:
+            assert reader.number_of_frames == 25
+            for fno in range(reader.number_of_frames):
+                frame = reader.read_frame(fno)
+                assert isinstance(frame, np.ndarray)
+                assert frame.ndim == 3
+                assert frame.dtype == np.uint8
+                assert frame.shape == (
+                    reader.metadata.Rows,
+                    reader.metadata.Columns,
+                    3,
+                )
+                np.testing.assert_array_equal(frame, pixel_array[fno])