def test_invalid_colourspace_warns():
"""Test that using an unknown colourspace gives a warning."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.50')
ds = index['JPEGBaseline_1s_1f_u_08_08.dcm']['ds']
nr_frames = ds.get('NumberOfFrames', 1)
frame = next(generate_pixel_data_frame(ds.PixelData, nr_frames))
msg = r"no colour transformation will be applied"
ds.PhotometricInterpretation = 'ANY'
with pytest.warns(UserWarning, match=msg):
arr = decode_pixel_data(np.frombuffer(frame, 'uint8'), ds)
arr = reshape_pixel_array(ds, arr)
assert arr.flags.writeable
assert 'uint8' == arr.dtype
assert (ds.Rows, ds.Columns) == arr.shape
# Reference values from GDCM handler
assert 76 == arr[5, 50]
assert 167 == arr[15, 50]
assert 149 == arr[25, 50]
assert 203 == arr[35, 50]
assert 29 == arr[45, 50]
assert 142 == arr[55, 50]
assert 1 == arr[65, 50]
assert 64 == arr[75, 50]
assert 192 == arr[85, 50]
assert 255 == arr[95, 50]
def test_multi_frame_varied_ratio(self):
"""Test a multi-frame image where each frames is random fragments"""
# 3 frames, 1st is 1 fragment, 2nd is 3 fragments, 3rd is 2 fragments
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x0C\x00\x00\x00' \
b'\x00\x00\x00\x00' \
b'\x0E\x00\x00\x00' \
b'\x32\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x06\x00\x00\x00\x01\x00\x00\x00\x00\x01' \
b'\xFE\xFF\x00\xE0' \
b'\x02\x00\x00\x00\x02\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00\x02\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x06\x00\x00\x00\x03\x00\x00\x00\x00\x02' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00\x03\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x02\x00\x00\x00\x02\x04'
frames = generate_pixel_data_frame(bytestream)
assert next(frames) == b'\x01\x00\x00\x00\x00\x01'
assert next(frames) == (
b'\x02\x00\x02\x00\x00\x00\x03\x00\x00\x00\x00\x02'
)
assert next(frames) == b'\x03\x00\x00\x00\x02\x04'
pytest.raises(StopIteration, next, frames)
def generate_frames(ds):
"""Yield decompressed pixel data frames as :class:`numpy.ndarray`.
.. deprecated:: 1.2
Use
:func:`~pydicom.pixel_data_handlers.pylibjpeg_handler.generate_frames`
instead
Parameters
----------
ds : pydicom.dataset.Dataset
The dataset containing the pixel data.
Yields
------
numpy.ndarray
A single frame of the decompressed pixel data.
"""
try:
import pydicom
except ImportError:
raise RuntimeError("'generate_frames' requires the pydicom package")
from pydicom.encaps import generate_pixel_data_frame
from pydicom.pixel_data_handlers.util import pixel_dtype
decoders = get_pixel_data_decoders()
decode = decoders[ds.file_meta.TransferSyntaxUID]
p_interp = ds.PhotometricInterpretation
nr_frames = getattr(ds, 'NumberOfFrames', 1)
for frame in generate_pixel_data_frame(ds.PixelData, nr_frames):
arr = decode(frame, ds.group_dataset(0x0028)).view(pixel_dtype(ds))
yield reshape_frame(ds, arr)
def test_multi_frame_three_to_one(self):
"""Test a multi-frame image where each frame is three fragments"""
# 2 frames, each 3 fragments long
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x0C\x00\x00\x00' \
b'\x00\x00\x00\x00' \
b'\x20\x00\x00\x00' \
b'\x40\x00\x00\x00' \
b'\xFE\xFF\x00\xE0\x04\x00\x00\x00\x01\x00\x00\x00' \
b'\xFE\xFF\x00\xE0\x04\x00\x00\x00\x02\x00\x00\x00' \
b'\xFE\xFF\x00\xE0\x04\x00\x00\x00\x03\x00\x00\x00' \
b'\xFE\xFF\x00\xE0\x04\x00\x00\x00\x02\x00\x00\x00' \
b'\xFE\xFF\x00\xE0\x04\x00\x00\x00\x02\x00\x00\x00' \
b'\xFE\xFF\x00\xE0\x04\x00\x00\x00\x03\x00\x00\x00' \
b'\xFE\xFF\x00\xE0\x04\x00\x00\x00\x03\x00\x00\x00' \
b'\xFE\xFF\x00\xE0\x04\x00\x00\x00\x02\x00\x00\x00' \
b'\xFE\xFF\x00\xE0\x04\x00\x00\x00\x03\x00\x00\x00'
frames = generate_pixel_data_frame(bytestream)
assert next(frames) == (
b'\x01\x00\x00\x00\x02\x00\x00\x00\x03\x00\x00\x00')
assert next(frames) == (
b'\x02\x00\x00\x00\x02\x00\x00\x00\x03\x00\x00\x00')
assert next(frames) == (
b'\x03\x00\x00\x00\x02\x00\x00\x00\x03\x00\x00\x00')
pytest.raises(StopIteration, next, frames)
def test_multi_frame_varied_ratio(self):
"""Test a multi-frame image where each frames is random fragments"""
# 3 frames, 1st is 1 fragment, 2nd is 3 fragments, 3rd is 2 fragments
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x0C\x00\x00\x00' \
b'\x00\x00\x00\x00' \
b'\x0E\x00\x00\x00' \
b'\x32\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x06\x00\x00\x00\x01\x00\x00\x00\x00\x01' \
b'\xFE\xFF\x00\xE0' \
b'\x02\x00\x00\x00\x02\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00\x02\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x06\x00\x00\x00\x03\x00\x00\x00\x00\x02' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00\x03\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x02\x00\x00\x00\x02\x04'
frames = generate_pixel_data_frame(bytestream)
assert next(frames) == b'\x01\x00\x00\x00\x00\x01'
assert next(frames) == (
b'\x02\x00\x02\x00\x00\x00\x03\x00\x00\x00\x00\x02')
assert next(frames) == b'\x03\x00\x00\x00\x02\x04'
pytest.raises(StopIteration, next, frames)
def slice_dicom(self, dcm: U) -> U:
r"""Slices a DICOM object input according to :func:`get_indices`.
.. note:
Unlike :func:`slice_array`, this function can perform slicing on compressed DICOMs
with out needing to decompress all frames. This can provide a substantial performance gain.
"""
# copy dicom and read key tags
dcm = deepcopy(dcm)
num_frames: Optional[SupportsInt] = dcm.get("NumberOfFrames", None)
num_frames = int(num_frames) if num_frames is not None else None
is_compressed: bool = dcm.file_meta.TransferSyntaxUID.is_compressed
start, stop, stride = self.get_indices(num_frames)
# read data
if is_compressed:
frame_iterator: Iterator = generate_pixel_data_frame(
dcm.PixelData, num_frames)
frames = list(islice(frame_iterator, start, stop, stride))
new_pixel_data = encapsulate(frames)
else:
all_frames: np.ndarray = dcm.pixel_array
frames = all_frames[start:stop:stride]
new_pixel_data = frames.tobytes()
out_frames = len(frames)
dcm.NumberOfFrames = out_frames
dcm.PixelData = new_pixel_data
return dcm
def test_multi_frame_three_to_one(self):
"""Test a multi-frame image where each frame is three fragments"""
# 2 frames, each 3 fragments long
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x0C\x00\x00\x00' \
b'\x00\x00\x00\x00' \
b'\x20\x00\x00\x00' \
b'\x40\x00\x00\x00' \
b'\xFE\xFF\x00\xE0\x04\x00\x00\x00\x01\x00\x00\x00' \
b'\xFE\xFF\x00\xE0\x04\x00\x00\x00\x02\x00\x00\x00' \
b'\xFE\xFF\x00\xE0\x04\x00\x00\x00\x03\x00\x00\x00' \
b'\xFE\xFF\x00\xE0\x04\x00\x00\x00\x02\x00\x00\x00' \
b'\xFE\xFF\x00\xE0\x04\x00\x00\x00\x02\x00\x00\x00' \
b'\xFE\xFF\x00\xE0\x04\x00\x00\x00\x03\x00\x00\x00' \
b'\xFE\xFF\x00\xE0\x04\x00\x00\x00\x03\x00\x00\x00' \
b'\xFE\xFF\x00\xE0\x04\x00\x00\x00\x02\x00\x00\x00' \
b'\xFE\xFF\x00\xE0\x04\x00\x00\x00\x03\x00\x00\x00'
frames = generate_pixel_data_frame(bytestream)
assert next(frames) == (
b'\x01\x00\x00\x00\x02\x00\x00\x00\x03\x00\x00\x00'
)
assert next(frames) == (
b'\x02\x00\x00\x00\x02\x00\x00\x00\x03\x00\x00\x00'
)
assert next(frames) == (
b'\x03\x00\x00\x00\x02\x00\x00\x00\x03\x00\x00\x00'
)
pytest.raises(StopIteration, next, frames)
def test_empty_bot_too_few_fragments(self):
"""Test parsing with too few fragments."""
ds = dcmread(JP2K_10FRAME_NOBOT)
assert 10 == ds.NumberOfFrames
msg = (r"Unable to parse encapsulated pixel data as the Basic "
r"Offset Table is empty and there are fewer fragments then "
r"frames; the dataset may be corrupt")
with pytest.raises(ValueError, match=msg):
next(generate_pixel_data_frame(ds.PixelData, 20))
def test_empty_bot_single_fragment(self):
"""Test a single-frame image where the frame is one fragments"""
# 1 frame, 1 fragment long
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x00\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00'
frames = generate_pixel_data_frame(bytestream)
assert next(frames) == b'\x01\x00\x00\x00'
pytest.raises(StopIteration, next, frames)
def test_empty_bot_multi_fragments_per_frame(self):
"""Test multi-frame where multiple frags per frame and no BOT."""
# Regression test for #685
ds = dcmread(JP2K_10FRAME_NOBOT)
assert 10 == ds.NumberOfFrames
frame_gen = generate_pixel_data_frame(ds.PixelData, ds.NumberOfFrames)
for ii in range(10):
next(frame_gen)
with pytest.raises(StopIteration):
next(frame_gen)
def test_empty_bot_single_fragment(self):
"""Test a single-frame image where the frame is one fragments"""
# 1 frame, 1 fragment long
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x00\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00'
frames = generate_pixel_data_frame(bytestream)
assert next(frames) == b'\x01\x00\x00\x00'
pytest.raises(StopIteration, next, frames)
def test_non_conformant_raises():
"""Test that a non-conformant JPEG image raises an exception."""
ds_list = get_indexed_datasets('1.2.840.10008.1.2.4.51')
# Image has invalid Se value in the SOS marker segment
item = ds_list['JPEG-lossy.dcm']
assert 0xC000 == item['Status'][1]
ds = item['ds']
nr_frames = ds.get('NumberOfFrames', 1)
frame = next(generate_pixel_data_frame(ds.PixelData, nr_frames))
msg = (
r"libjpeg error code '-1038' returned from GetJPEGParameters\(\): A "
r"misplaced marker segment was found - scan start must be zero "
r"and scan stop must be 63 for the sequential operating modes")
with pytest.raises(RuntimeError, match=msg):
get_parameters(frame)
def test_empty_bot_triple_fragment_single_frame(self):
"""Test a single-frame image where the frame is three fragments"""
# 1 frame, 3 fragments long
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x00\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x02\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x03\x00\x00\x00'
frames = generate_pixel_data_frame(bytestream, 1)
assert next(frames) == (
b'\x01\x00\x00\x00\x02\x00\x00\x00\x03\x00\x00\x00')
pytest.raises(StopIteration, next, frames)
def test_bot_triple_fragment_single_frame(self):
"""Test a single-frame image where the frame is three fragments"""
# 1 frame, 3 fragments long
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x00\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x02\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x03\x00\x00\x00'
frames = generate_pixel_data_frame(bytestream)
assert next(frames) == (
b'\x01\x00\x00\x00\x02\x00\x00\x00\x03\x00\x00\x00'
)
pytest.raises(StopIteration, next, frames)
def test_decode_bytes():
"""Test decode using bytes."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.50')
ds = index['JPEGBaseline_1s_1f_u_08_08.dcm']['ds']
nr_frames = ds.get('NumberOfFrames', 1)
frame = next(generate_pixel_data_frame(ds.PixelData, nr_frames))
arr = decode(frame)
assert arr.flags.writeable
assert 'uint8' == arr.dtype
assert (ds.Rows, ds.Columns) == arr.shape
# Reference values from GDCM handler
assert 76 == arr[5, 50]
assert 167 == arr[15, 50]
assert 149 == arr[25, 50]
assert 203 == arr[35, 50]
assert 29 == arr[45, 50]
assert 142 == arr[55, 50]
assert 1 == arr[65, 50]
assert 64 == arr[75, 50]
assert 192 == arr[85, 50]
assert 255 == arr[95, 50]
def test_multi_frame_one_to_one(self):
"""Test a multi-frame image where each frame is one fragment"""
# 3 frames, each 1 fragment long
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x0C\x00\x00\x00' \
b'\x00\x00\x00\x00' \
b'\x0C\x00\x00\x00' \
b'\x18\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x02\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x03\x00\x00\x00'
frames = generate_pixel_data_frame(bytestream)
assert next(frames) == b'\x01\x00\x00\x00'
assert next(frames) == b'\x02\x00\x00\x00'
assert next(frames) == b'\x03\x00\x00\x00'
pytest.raises(StopIteration, next, frames)
def test_multi_frame_one_to_one(self):
"""Test a multi-frame image where each frame is one fragment"""
# 3 frames, each 1 fragment long
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x0C\x00\x00\x00' \
b'\x00\x00\x00\x00' \
b'\x0C\x00\x00\x00' \
b'\x18\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x02\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x03\x00\x00\x00'
frames = generate_pixel_data_frame(bytestream)
assert next(frames) == b'\x01\x00\x00\x00'
assert next(frames) == b'\x02\x00\x00\x00'
assert next(frames) == b'\x03\x00\x00\x00'
pytest.raises(StopIteration, next, frames)
def generate_frames(ds):
"""Yield decompressed pixel data frames as :class:`numpy.ndarray`.
Parameters
----------
ds : pydicom.dataset.Dataset
The dataset containing the pixel data.
Yields
------
numpy.ndarray
A single frame of the decompressed pixel data.
"""
from pydicom.encaps import generate_pixel_data_frame
from pydicom.pixel_data_handlers.util import pixel_dtype
decoders = get_pixel_data_decoders()
decode = decoders[ds.file_meta.TransferSyntaxUID]
p_interp = ds.PhotometricInterpretation
nr_frames = getattr(ds, 'NumberOfFrames', 1)
for frame in generate_pixel_data_frame(ds.PixelData, nr_frames):
arr = decode(frame, ds.group_dataset(0x0028)).view(pixel_dtype(ds))
yield reshape_frame(ds, arr)
def generate_frames(ds: "Dataset", reshape: bool = True) -> "np.ndarray":
"""Yield a *Pixel Data* frame from `ds` as an :class:`~numpy.ndarray`.
.. versionadded:: 2.1
Parameters
----------
ds : pydicom.dataset.Dataset
The :class:`Dataset` containing an :dcm:`Image Pixel
<part03/sect_C.7.6.3.html>` module and the *Pixel Data* to be
converted.
reshape : bool, optional
If ``True`` (default), then the returned :class:`~numpy.ndarray` will
be reshaped to the correct dimensions. If ``False`` then no reshaping
will be performed.
Yields
-------
numpy.ndarray
A single frame of (7FE0,0010) *Pixel Data* as an
:class:`~numpy.ndarray` with an appropriate dtype for the data.
Raises
------
AttributeError
If `ds` is missing a required element.
RuntimeError
If the plugin required to decode the pixel data is not installed.
"""
tsyntax = ds.file_meta.TransferSyntaxUID
# The check of transfer syntax must be first
if tsyntax not in _DECODERS:
if tsyntax in _OPENJPEG_SYNTAXES:
plugin = "pylibjpeg-openjpeg"
else:
plugin = "pylibjpeg-libjpeg"
raise RuntimeError(
f"Unable to convert the Pixel Data as the '{plugin}' plugin is "
f"not installed")
# Check required elements
required_elements = [
"BitsAllocated",
"Rows",
"Columns",
"PixelRepresentation",
"SamplesPerPixel",
"PhotometricInterpretation",
"PixelData",
]
missing = [elem for elem in required_elements if elem not in ds]
if missing:
raise AttributeError(
"Unable to convert the pixel data as the following required "
"elements are missing from the dataset: " + ", ".join(missing))
decoder = _DECODERS[tsyntax]
LOGGER.debug(f"Decoding {tsyntax.name} encoded Pixel Data using {decoder}")
nr_frames = getattr(ds, "NumberOfFrames", 1)
image_px_module = ds.group_dataset(0x0028)
dtype = pixel_dtype(ds)
for frame in generate_pixel_data_frame(ds.PixelData, nr_frames):
arr = decoder(frame, image_px_module)
# Re-view as pylibjpeg returns a 1D uint8 ndarray
arr = arr.view(dtype)
if not reshape:
yield arr
continue
if ds.SamplesPerPixel == 1:
yield arr.reshape(ds.Rows, ds.Columns)
else:
# JPEG, JPEG-LS and JPEG 2000 are all Planar Configuration 0
yield arr.reshape(ds.Rows, ds.Columns, ds.SamplesPerPixel)
def generate_frames(ds):
"""Return a frame generator for DICOM datasets."""
nr_frames = ds.get('NumberOfFrames', 1)
return generate_pixel_data_frame(ds.PixelData, nr_frames)
def generate_frames(self, ds):
"""Return a generator object with the dataset's pixel data frames."""
nr_frames = ds.get('NumberOfFrames', 1)
return generate_pixel_data_frame(ds.PixelData, nr_frames)
def get_pixeldata(ds):
"""Return a :class:`numpy.ndarray` of the pixel data.
Parameters
----------
ds : Dataset
The :class:`Dataset` containing an Image Pixel, Floating Point Image
Pixel or Double Floating Point Image Pixel module and the
*Pixel Data*, *Float Pixel Data* or *Double Float Pixel Data* to be
converted. If (0028,0004) *Photometric Interpretation* is
`'YBR_FULL_422'` then the pixel data will be
resampled to 3 channel data as per Part 3, :dcm:`Annex C.7.6.3.1.2
<part03/sect_C.7.6.3.html#sect_C.7.6.3.1.2>` of the DICOM Standard.
Returns
-------
np.ndarray
The contents of (7FE0,0010) *Pixel Data* as a 1D array.
"""
tsyntax = ds.file_meta.TransferSyntaxUID
# The check of transfer syntax must be first
if tsyntax not in SUPPORTED_TRANSFER_SYNTAXES:
raise NotImplementedError(
"Unable to convert the pixel data as the transfer syntax "
"is not supported by the pylibjpeg pixel data handler."
)
# Check required elements
required_elements = [
'BitsAllocated', 'Rows', 'Columns', 'PixelRepresentation',
'SamplesPerPixel', 'PhotometricInterpretation', 'PixelData',
]
missing = [elem for elem in required_elements if elem not in ds]
if missing:
raise AttributeError(
"Unable to convert the pixel data as the following required "
"elements are missing from the dataset: " + ", ".join(missing)
)
# Calculate the expected length of the pixel data (in bytes)
# Note: this does NOT include the trailing null byte for odd length data
expected_len = get_expected_length(ds)
if ds.PhotometricInterpretation == 'YBR_FULL_422':
# libjpeg has already resampled the pixel data, see PS3.3 C.7.6.3.1.2
expected_len = expected_len // 2 * 3
p_interp = ds.PhotometricInterpretation
# How long each frame is in bytes
nr_frames = getattr(ds, 'NumberOfFrames', 1)
frame_len = expected_len // nr_frames
# The decoded data will be placed here
arr = np.empty(expected_len, np.uint8)
# Generators for the encoded JPG image frame(s) and insertion offsets
generate_frames = generate_pixel_data_frame(ds.PixelData, nr_frames)
generate_offsets = range(0, expected_len, frame_len)
for frame, offset in zip(generate_frames, generate_offsets):
# Encoded JPG data to be sent to the decoder
frame = np.frombuffer(frame, np.uint8)
arr[offset:offset + frame_len] = decode_pixel_data(
frame, ds.group_dataset(0x0028)
)
return arr.view(pixel_dtype(ds))
def get_pixeldata(ds):
"""Return a :class:`numpy.ndarray` of the pixel data.
Parameters
----------
ds : pydicom.dataset.Dataset
The :class:`Dataset` containing an Image Pixel module and the
*Pixel Data* to be converted.
Returns
-------
numpy.ndarray
The contents of (7FE0,0010) *Pixel Data* as a 1D array.
Raises
------
AttributeError
If `ds` is missing a required element.
NotImplementedError
If `ds` contains pixel data in an unsupported format.
ValueError
If the actual length of the pixel data doesn't match the expected
length.
"""
tsyntax = ds.file_meta.TransferSyntaxUID
# The check of transfer syntax must be first
if tsyntax not in SUPPORTED_TRANSFER_SYNTAXES:
raise NotImplementedError(
"Unable to convert the pixel data as there are no pylibjpeg "
"plugins available to decode pixel data encoded using '{}'".format(
tsyntax.name))
# Check required elements
required_elements = [
'BitsAllocated',
'Rows',
'Columns',
'PixelRepresentation',
'SamplesPerPixel',
'PhotometricInterpretation',
'PixelData',
]
missing = [elem for elem in required_elements if elem not in ds]
if missing:
raise AttributeError(
"Unable to convert the pixel data as the following required "
"elements are missing from the dataset: " + ", ".join(missing))
# Calculate the expected length of the pixel data (in bytes)
# Note: this does NOT include the trailing null byte for odd length data
expected_len = get_expected_length(ds)
if ds.PhotometricInterpretation == 'YBR_FULL_422':
# JPEG Transfer Syntaxes
# Plugin should have already resampled the pixel data
# see PS3.3 C.7.6.3.1.2
expected_len = expected_len // 2 * 3
p_interp = ds.PhotometricInterpretation
# How long each frame is in bytes
nr_frames = getattr(ds, 'NumberOfFrames', 1)
frame_len = expected_len // nr_frames
# The decoded data will be placed here
arr = np.empty(expected_len, np.uint8)
decoder = _DECODERS[tsyntax]
LOGGER.debug("Decoding {} Pixel Data using {}".format(tsyntax, decoder))
# Generators for the encoded JPEG image frame(s) and insertion offsets
generate_frames = generate_pixel_data_frame(ds.PixelData, nr_frames)
generate_offsets = range(0, expected_len, frame_len)
pixel_module = ds.group_dataset(0x0028)
for frame, offset in zip(generate_frames, generate_offsets):
# Encoded JPEG data to be sent to the decoder
arr[offset:offset + frame_len] = decoder(frame, pixel_module)
if tsyntax in [JPEG2000, JPEG2000Lossless] and APPLY_J2K_CORRECTIONS:
j2k_parameters = get_j2k_parameters(frame)
if j2k_parameters:
shift = ds.BitsAllocated - j2k_parameters['precision']
if (shift and not j2k_parameters['is_signed']
and bool(ds.PixelRepresentation)):
# Correct for a mismatch between J2K and Pixel Representation
# by converting unsigned data to signed (2's complement)
pixel_module.PixelRepresentation = 0
# This probably isn't very efficient
arr = arr.view(pixel_dtype(pixel_module))
np.left_shift(arr, shift, out=arr)
arr = arr.astype(pixel_dtype(ds))
return np.right_shift(arr, shift)
return arr.view(pixel_dtype(ds))
def generate_frames(ds: "Dataset",
reshape: bool = True) -> Iterable["np.ndarray"]:
"""Yield a *Pixel Data* frame from `ds` as an :class:`~numpy.ndarray`.
.. versionadded:: 2.1
Parameters
----------
ds : pydicom.dataset.Dataset
The :class:`Dataset` containing an :dcm:`Image Pixel
<part03/sect_C.7.6.3.html>` module and the *Pixel Data* to be
converted.
reshape : bool, optional
If ``True`` (default), then the returned :class:`~numpy.ndarray` will
be reshaped to the correct dimensions. If ``False`` then no reshaping
will be performed.
Yields
-------
numpy.ndarray
A single frame of (7FE0,0010) *Pixel Data* as an
:class:`~numpy.ndarray` with an appropriate dtype for the data.
Raises
------
AttributeError
If `ds` is missing a required element.
RuntimeError
If the plugin required to decode the pixel data is not installed.
"""
tsyntax = ds.file_meta.TransferSyntaxUID
# The check of transfer syntax must be first
if tsyntax not in _DECODERS:
if tsyntax in _OPENJPEG_SYNTAXES:
plugin = "pylibjpeg-openjpeg"
elif tsyntax in _LIBJPEG_SYNTAXES:
plugin = "pylibjpeg-libjpeg"
else:
plugin = "pylibjpeg-rle"
raise RuntimeError(
f"Unable to convert the Pixel Data as the '{plugin}' plugin is "
f"not installed")
# Check required elements
required_elements = [
"BitsAllocated",
"Rows",
"Columns",
"PixelRepresentation",
"SamplesPerPixel",
"PhotometricInterpretation",
"PixelData",
]
missing = [elem for elem in required_elements if elem not in ds]
if missing:
raise AttributeError(
"Unable to convert the pixel data as the following required "
"elements are missing from the dataset: " + ", ".join(missing))
decoder = _DECODERS[tsyntax]
LOGGER.debug(f"Decoding {tsyntax.name} encoded Pixel Data using {decoder}")
nr_frames = getattr(ds, "NumberOfFrames", 1)
pixel_module = ds.group_dataset(0x0028)
dtype = pixel_dtype(ds)
bits_stored = cast(int, ds.BitsStored)
bits_allocated = cast(int, ds.BitsAllocated)
for frame in generate_pixel_data_frame(ds.PixelData, nr_frames):
arr = decoder(frame, pixel_module)
if (tsyntax in [JPEG2000, JPEG2000Lossless]
and config.APPLY_J2K_CORRECTIONS):
param = get_j2k_parameters(frame)
j2k_sign = param.setdefault('is_signed', True)
j2k_precision = cast(int, param.setdefault('precision',
bits_stored))
shift = bits_allocated - j2k_precision
if shift and not j2k_sign and j2k_sign != ds.PixelRepresentation:
# Convert unsigned J2K data to 2s complement
# Can only get here if parsed J2K codestream OK
pixel_module.PixelRepresentation = 0
arr = arr.view(pixel_dtype(pixel_module))
arr = np.left_shift(arr, shift)
arr = arr.astype(dtype)
arr = np.right_shift(arr, shift)
if arr.dtype != dtype:
# Re-view as pylibjpeg returns a 1D uint8 ndarray
arr = arr.view(dtype)
if not reshape:
yield arr
continue
if ds.SamplesPerPixel == 1:
yield arr.reshape(ds.Rows, ds.Columns)
else:
if tsyntax == RLELossless:
# RLE Lossless is Planar Configuration 1
arr = arr.reshape(ds.SamplesPerPixel, ds.Rows, ds.Columns)
yield arr.transpose(1, 2, 0)
else:
# JPEG, JPEG-LS and JPEG 2000 are all Planar Configuration 0
yield arr.reshape(ds.Rows, ds.Columns, ds.SamplesPerPixel)
