Fix native floating-point frame decoding

src/highdicom/io.py

@@ -31,6 +31,7 @@
 )
 from pydicom.uid import UID, DeflatedExplicitVRLittleEndian
 
+from highdicom.enum import PixelDataKeywords
 from highdicom.frame import decode_frame
 from highdicom.color import ColorManager
 from highdicom.uid import UID as hd_UID
@@ -41,6 +42,11 @@
 _FLOAT_PIXEL_DATA_TAGS = {0x7FE00008, 0x7FE00009, }
 _UINT_PIXEL_DATA_TAGS = {0x7FE00010, }
 _PIXEL_DATA_TAGS = _FLOAT_PIXEL_DATA_TAGS.union(_UINT_PIXEL_DATA_TAGS)
+_PIXEL_DATA_KEYWORDS = {
+    0x7FE00008: PixelDataKeywords.FLOAT_PIXEL_DATA,
+    0x7FE00009: PixelDataKeywords.DOUBLE_FLOAT_PIXEL_DATA,
+    0x7FE00010: PixelDataKeywords.PIXEL_DATA,
+}
 
 _JPEG_SOI_MARKER = b'\xFF\xD8'  # also JPEG-LS
 _JPEG_EOI_MARKER = b'\xFF\xD9'  # also JPEG-LS
@@ -545,9 +551,7 @@ def _read_metadata(self) -> None:
             raise ValueError(
                 'Dataset does not represent an image information entity.'
             )
-        self._as_float = False
-        if int(tag) in _FLOAT_PIXEL_DATA_TAGS:
-            self._as_float = True
+        self._pixel_keyword = _PIXEL_DATA_KEYWORDS[int(tag)]
 
         # Reset the file pointer to the beginning of the Pixel Data element
         self._fp.seek(self._pixel_data_offset, 0)
@@ -759,20 +763,28 @@ def read_frame(self, index: int, correct_color: bool = True) -> np.ndarray:
 
         logger.debug(f'decode frame #{index}')
 
+        if self._pixel_keyword == PixelDataKeywords.PIXEL_DATA:
+            bits_stored = self.metadata.BitsStored
+            pixel_representation = self.metadata.PixelRepresentation
+        else:
+            bits_stored = self.metadata.BitsAllocated
+            pixel_representation = None
+
         frame_array = decode_frame(
             frame_data,
             rows=self.metadata.Rows,
             columns=self.metadata.Columns,
             samples_per_pixel=self.metadata.SamplesPerPixel,
             transfer_syntax_uid=self.transfer_syntax_uid,
             bits_allocated=self.metadata.BitsAllocated,
-            bits_stored=self.metadata.BitsStored,
+            bits_stored=bits_stored,
             photometric_interpretation=self.metadata.PhotometricInterpretation,
-            pixel_representation=self.metadata.PixelRepresentation,
+            pixel_representation=pixel_representation,
             planar_configuration=getattr(
                 self.metadata, 'PlanarConfiguration', None
             ),
             index=index,
+            pixel_keyword=self._pixel_keyword,
         )
 
         # We don't use the color_correct_frame() function here, since we cache

tests/test_io.py

@@ -6,7 +6,13 @@
 import numpy as np
 from pydicom import dcmread
 from pydicom.data import get_testdata_file
+from pydicom.dataset import FileDataset, FileMetaDataset
 from pydicom.filebase import DicomBytesIO, DicomFileLike, DicomFile
+from pydicom.uid import (
+    ExplicitVRLittleEndian,
+    ParametricMapStorage,
+    generate_uid,
+)
 import pytest
 
 from highdicom.io import ImageFileReader
@@ -39,6 +45,55 @@ def test_read_single_frame_ct_image_native(self):
             )
             np.testing.assert_array_equal(frame, pixel_array)
 
+    def test_read_float_pixel_data(self):
+        cases = [
+            (np.float32, 'FloatPixelData', 32),
+            (np.float64, 'DoubleFloatPixelData', 64),
+        ]
+        with TemporaryDirectory() as temp_dir:
+            for dtype, pixel_keyword, bits_allocated in cases:
+                filename = Path(temp_dir) / f"{pixel_keyword}.dcm"
+                file_meta = FileMetaDataset()
+                file_meta.TransferSyntaxUID = ExplicitVRLittleEndian
+                file_meta.MediaStorageSOPClassUID = ParametricMapStorage
+                file_meta.MediaStorageSOPInstanceUID = generate_uid()
+                file_meta.ImplementationClassUID = generate_uid()
+                dataset = FileDataset(
+                    filename,
+                    {},
+                    file_meta=file_meta,
+                    preamble=b"\0" * 128,
+                )
+                dataset.SOPClassUID = file_meta.MediaStorageSOPClassUID
+                dataset.SOPInstanceUID = file_meta.MediaStorageSOPInstanceUID
+                dataset.Rows = 3
+                dataset.Columns = 4
+                dataset.SamplesPerPixel = 1
+                dataset.PhotometricInterpretation = 'MONOCHROME2'
+                dataset.NumberOfFrames = 2
+                dataset.BitsAllocated = bits_allocated
+                pixel_array = np.linspace(
+                    -3.5,
+                    2.25,
+                    num=24,
+                    dtype=dtype,
+                ).reshape(2, 3, 4)
+                setattr(dataset, pixel_keyword, pixel_array.tobytes())
+                dataset.save_as(
+                    filename,
+                    implicit_vr=False,
+                    little_endian=True,
+                )
+
+                with ImageFileReader(filename) as reader:
+                    for frame_index in range(2):
+                        frame = reader.read_frame(frame_index)
+                        assert frame.dtype == dtype
+                        np.testing.assert_array_equal(
+                            frame,
+                            pixel_array[frame_index],
+                        )
+
     def test_read_multi_frame_ct_image_native(self):
         filename = str(get_testdata_file('eCT_Supplemental.dcm'))
         dataset = dcmread(filename)