def test_jpeg_rgb_wrong_photometric_interpretation(self):
with pytest.raises(ValueError):
decode_frame(value=b'',
transfer_syntax_uid=JPEGBaseline,
rows=16,
columns=32,
samples_per_pixel=3,
bits_allocated=8,
bits_stored=8,
photometric_interpretation='MONOCHROME',
pixel_representation=0,
planar_configuration=0)
def read_frame(self, index: int, correct_color: bool = True) -> np.ndarray:
"""Reads and decodes the pixel data of an individual frame item.
Parameters
----------
index: int
Zero-based frame index
correct_color: bool, optional
Whether colors should be corrected by applying an ICC
transformation. Will only be performed if metadata contain an
ICC Profile.
Returns
-------
numpy.ndarray
Array of decoded pixels of the frame with shape (Rows x Columns)
in case of a monochrome image or (Rows x Columns x SamplesPerPixel)
in case of a color image.
Raises
------
IOError
When frame could not be read
"""
frame_data = self.read_frame_raw(index)
logger.debug(f'decode frame #{index}')
if self.metadata.BitsAllocated == 1:
unpacked_frame = unpack_bits(frame_data)
rows, columns = self.metadata.Rows, self.metadata.Columns
n_pixels = self._pixels_per_frame
pixel_offset = int(((index * n_pixels / 8) % 1) * 8)
pixel_array = unpacked_frame[pixel_offset:pixel_offset + n_pixels]
return pixel_array.reshape(rows, columns)
frame_array = decode_frame(
frame_data,
rows=self.metadata.Rows,
columns=self.metadata.Columns,
samples_per_pixel=self.metadata.SamplesPerPixel,
transfer_syntax_uid=self.metadata.file_meta.TransferSyntaxUID,
bits_allocated=self.metadata.BitsAllocated,
bits_stored=self.metadata.BitsStored,
photometric_interpretation=self.metadata.PhotometricInterpretation,
pixel_representation=self.metadata.PixelRepresentation,
planar_configuration=getattr(self.metadata, 'PlanarConfiguration',
None))
# We don't use the color_correct_frame() function here, since we cache
# the ICC transform on the reader instance for improved performance.
if correct_color and self._color_manager is not None:
logger.debug(f'correct color of frame #{index}')
return self._color_manager.transform_frame(frame_array)
return frame_array
def test_jpeg_rgb(self):
filepath = str(self._test_files_dir.joinpath('frame_rgb_empty.jpeg'))
with open(filepath, 'br') as fp:
compressed_frame = fp.read()
rows = 16
columns = 32
samples_per_pixel = 3
bits_allocated = 8
frame = decode_frame(value=compressed_frame,
transfer_syntax_uid=JPEGBaseline,
rows=rows,
columns=columns,
samples_per_pixel=samples_per_pixel,
bits_allocated=bits_allocated,
bits_stored=bits_allocated,
photometric_interpretation='YBR_FULL',
pixel_representation=0,
planar_configuration=0)
assert frame.shape[0] == rows
assert frame.shape[1] == columns
assert frame.shape[2] == samples_per_pixel
assert str(frame.dtype) == f'uint{bits_allocated}'
def test_jpeg2000_monochrome(self):
bits_allocated = 16
frame = np.zeros((16, 32), dtype=np.dtype(f'uint{bits_allocated}'))
compressed_frame = encode_frame(
frame,
transfer_syntax_uid=JPEG2000Lossless,
bits_allocated=bits_allocated,
bits_stored=bits_allocated,
photometric_interpretation='MONOCHROME1',
pixel_representation=0,
)
assert compressed_frame.startswith(b'\x00\x00\x00\x0C\x6A\x50\x20')
assert compressed_frame.endswith(b'\xFF\xD9')
decoded_frame = decode_frame(value=compressed_frame,
transfer_syntax_uid=JPEG2000Lossless,
rows=frame.shape[0],
columns=frame.shape[1],
samples_per_pixel=1,
bits_allocated=bits_allocated,
bits_stored=bits_allocated,
photometric_interpretation='MONOCHROME1',
pixel_representation=0,
planar_configuration=0)
np.testing.assert_array_equal(frame, decoded_frame)
def test_jpeg2000_rgb(self):
bits_allocated = 8
frame = np.ones((16, 32, 3), dtype=np.dtype(f'uint{bits_allocated}'))
frame *= 255
compressed_frame = encode_frame(frame,
transfer_syntax_uid=JPEG2000Lossless,
bits_allocated=bits_allocated,
bits_stored=bits_allocated,
photometric_interpretation='YBR_FULL',
pixel_representation=0,
planar_configuration=0)
assert compressed_frame.startswith(b'\x00\x00\x00\x0C\x6A\x50\x20')
assert compressed_frame.endswith(b'\xFF\xD9')
decoded_frame = decode_frame(value=compressed_frame,
transfer_syntax_uid=JPEG2000Lossless,
rows=frame.shape[0],
columns=frame.shape[1],
samples_per_pixel=frame.shape[2],
bits_allocated=bits_allocated,
bits_stored=bits_allocated,
photometric_interpretation='YBR_FULL',
pixel_representation=0,
planar_configuration=0)
np.testing.assert_array_equal(frame, decoded_frame)