def test_little_endian_segment_order(self):
"""Test interpreting segment order as little endian."""
ds = dcmread(MR_RLE_1F)
assert ds.file_meta.TransferSyntaxUID == RLELossless
assert ds.BitsAllocated == 16
assert ds.SamplesPerPixel == 1
assert 'NumberOfFrames' not in ds
assert ds.PixelRepresentation == 1 # signed
# Big endian
arr = get_pixeldata(ds, rle_segment_order='>')
arr = reshape_pixel_array(ds, arr)
assert (64, 64) == arr.shape
assert (422, 319, 361) == tuple(arr[0, 31:34])
assert (366, 363, 322) == tuple(arr[31, :3])
assert (1369, 1129, 862) == tuple(arr[-1, -3:])
# Little endian
arr = get_pixeldata(ds, rle_segment_order='<')
arr = reshape_pixel_array(ds, arr)
assert (64, 64) == arr.shape
assert (-23039, 16129, 26881) == tuple(arr[0, 31:34])
assert (28161, 27393, 16897) == tuple(arr[31, :3])
assert (22789, 26884, 24067) == tuple(arr[-1, -3:])
def test_invalid_nr_frames_raises(self):
"""Test an invalid Number of Frames value raises exception."""
self.ds.SamplesPerPixel = 1
self.ds.NumberOfFrames = 0
# Need to escape brackets
with pytest.raises(ValueError, match=r"value of 0 for \(0028,0008\)"):
reshape_pixel_array(self.ds, RESHAPE_ARRAYS['1frame_1sample'])
def test_invalid_planar_conf_raises(self):
self.ds.SamplesPerPixel = 3
self.ds.PlanarConfiguration = 2
# Need to escape brackets
with pytest.raises(ValueError, match=r"value of 2 for \(0028,0006\)"):
reshape_pixel_array(self.ds,
RESHAPE_ARRAYS['1frame_3sample_0config'])
def test_invalid_samples_raises(self):
"""Test an invalid Samples per Pixel value raises exception."""
self.ds.SamplesPerPixel = 0
# Need to escape brackets
with pytest.raises(ValueError,
match=r"value of 0 for \(0028,0002\)"):
reshape_pixel_array(self.ds, RESHAPE_ARRAYS['1frame_1sample'])
def test_invalid_planar_conf_raises(self):
self.ds.SamplesPerPixel = 3
self.ds.PlanarConfiguration = 2
# Need to escape brackets
with pytest.raises(ValueError,
match=r"value of 2 for \(0028,0006\)"):
reshape_pixel_array(self.ds,
RESHAPE_ARRAYS['1frame_3sample_0config'])
def test_2frame_1sample(self):
"""Test reshaping 2 frame, 1 sample/pixel."""
self.ds.NumberOfFrames = 2
self.ds.SamplesPerPixel = 1
arr = reshape_pixel_array(self.ds, RESHAPE_ARRAYS['2frame_1sample'])
assert (2, 4, 5) == arr.shape
assert np.array_equal(arr, self.ref_2_1)
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_2frame_1sample(self):
"""Test reshaping 2 frame, 1 sample/pixel."""
self.ds.NumberOfFrames = 2
self.ds.SamplesPerPixel = 1
arr = reshape_pixel_array(self.ds, RESHAPE_ARRAYS['2frame_1sample'])
assert (2, 4, 5) == arr.shape
assert np.array_equal(arr, self.ref_2_1)
def test_jpeg2000i(self, fname, info):
"""Test get_parameters() for the j2k datasets."""
#info: (rows, columns, spp, bps)
index = get_indexed_datasets('1.2.840.10008.1.2.4.91')
ds = index[fname]['ds']
frame = next(generate_frames(ds))
arr = decode(BytesIO(frame), reshape=False)
assert arr.flags.writeable
ds.NumberOfFrames = 1
arr = arr.view(pixel_dtype(ds))
arr = reshape_pixel_array(ds, arr)
#plt.imshow(arr)
#plt.show()
if info[2] == 1:
assert (info[0], info[1]) == arr.shape
else:
assert (info[0], info[1], info[2]) == arr.shape
if 1 <= info[3] <= 8:
if info[4] == 1:
assert arr.dtype == 'int8'
else:
assert arr.dtype == 'uint8'
if 9 <= info[3] <= 16:
if info[4] == 1:
assert arr.dtype == 'int16'
else:
assert arr.dtype == 'uint16'
def test_uncompressed_syntaxes(self):
"""Test that uncompressed syntaxes use the dataset planar conf."""
for uid in UncompressedPixelTransferSyntaxes:
self.ds.file_meta.TransferSyntaxUID = uid
self.ds.PlanarConfiguration = 0
self.ds.NumberOfFrames = 1
self.ds.SamplesPerPixel = 3
arr = reshape_pixel_array(self.ds,
RESHAPE_ARRAYS['1frame_3sample_0config'])
assert (4, 5, 3) == arr.shape
assert np.array_equal(arr, self.ref_1_3)
self.ds.PlanarConfiguration = 1
arr = reshape_pixel_array(self.ds,
RESHAPE_ARRAYS['1frame_3sample_1config'])
assert (4, 5, 3) == arr.shape
assert np.array_equal(arr, self.ref_1_3)
def test_2frame_3sample_1conf(self):
"""Test reshaping 2 frame, 3 sample/pixel for 1 planar config."""
self.ds.NumberOfFrames = 2
self.ds.SamplesPerPixel = 3
self.ds.PlanarConfiguration = 1
arr = reshape_pixel_array(self.ds,
RESHAPE_ARRAYS['2frame_3sample_1config'])
assert (2, 4, 5, 3) == arr.shape
assert np.array_equal(arr, self.ref_2_3)
def test_1frame_3sample_0conf(self):
"""Test reshaping 1 frame, 3 sample/pixel for 0 planar config."""
self.ds.NumberOfFrames = 1
self.ds.SamplesPerPixel = 3
self.ds.PlanarConfiguration = 0
arr = reshape_pixel_array(self.ds,
RESHAPE_ARRAYS['1frame_3sample_0config'])
assert (4, 5, 3) == arr.shape
assert np.array_equal(arr, self.ref_1_3)
def test_1frame_3sample_0conf(self):
"""Test reshaping 1 frame, 3 sample/pixel for 0 planar config."""
self.ds.NumberOfFrames = 1
self.ds.SamplesPerPixel = 3
self.ds.PlanarConfiguration = 0
arr = reshape_pixel_array(self.ds,
RESHAPE_ARRAYS['1frame_3sample_0config'])
assert (4, 5, 3) == arr.shape
assert np.array_equal(arr, self.ref_1_3)
def test_2frame_3sample_1conf(self):
"""Test reshaping 2 frame, 3 sample/pixel for 1 planar config."""
self.ds.NumberOfFrames = 2
self.ds.SamplesPerPixel = 3
self.ds.PlanarConfiguration = 1
arr = reshape_pixel_array(self.ds,
RESHAPE_ARRAYS['2frame_3sample_1config'])
assert (2, 4, 5, 3) == arr.shape
assert np.array_equal(arr, self.ref_2_3)
def test_uncompressed_syntaxes(self):
"""Test that uncompressed syntaxes use the dataset planar conf."""
for uid in UncompressedPixelTransferSyntaxes:
self.ds.file_meta.TransferSyntaxUID = uid
self.ds.PlanarConfiguration = 0
self.ds.NumberOfFrames = 1
self.ds.SamplesPerPixel = 3
arr = reshape_pixel_array(self.ds,
RESHAPE_ARRAYS['1frame_3sample_0config'])
assert (4, 5, 3) == arr.shape
assert np.array_equal(arr, self.ref_1_3)
self.ds.PlanarConfiguration = 1
arr = reshape_pixel_array(self.ds,
RESHAPE_ARRAYS['1frame_3sample_1config'])
assert (4, 5, 3) == arr.shape
assert np.array_equal(arr, self.ref_1_3)
def test_compressed_syntaxes_1conf(self):
"""Test the compressed syntaxes that are always 1 planar conf."""
for uid in ['1.2.840.10008.1.2.4.80',
'1.2.840.10008.1.2.4.81',
'1.2.840.10008.1.2.5']:
self.ds.file_meta.TransferSyntaxUID = uid
self.ds.PlanarConfiguration = 0
self.ds.NumberOfFrames = 1
self.ds.SamplesPerPixel = 3
arr = reshape_pixel_array(self.ds,
RESHAPE_ARRAYS['1frame_3sample_1config'])
assert (4, 5, 3) == arr.shape
assert np.array_equal(arr, self.ref_1_3)
def test_compressed_syntaxes_1conf(self):
"""Test the compressed syntaxes that are always 1 planar conf."""
for uid in [
'1.2.840.10008.1.2.4.80', '1.2.840.10008.1.2.4.81',
'1.2.840.10008.1.2.5'
]:
self.ds.file_meta.TransferSyntaxUID = uid
self.ds.PlanarConfiguration = 0
self.ds.NumberOfFrames = 1
self.ds.SamplesPerPixel = 3
arr = reshape_pixel_array(self.ds,
RESHAPE_ARRAYS['1frame_3sample_1config'])
assert (4, 5, 3) == arr.shape
assert np.array_equal(arr, self.ref_1_3)
def test_cycle_32bit_1sample(self):
"""Test an encode/decode cycle for 32-bit 1 sample/pixel."""
ds = dcmread(EXPL_32_1_1F)
ref = ds.pixel_array
assert 32 == ds.BitsAllocated
assert 1 == ds.SamplesPerPixel
kwargs = RLELosslessEncoder.kwargs_from_ds(ds)
encoded = _encode_frame(ds.PixelData, **kwargs)
decoded = _rle_decode_frame(
encoded, ds.Rows, ds.Columns, ds.SamplesPerPixel, ds.BitsAllocated
)
arr = np.frombuffer(decoded, '<u4')
arr = reshape_pixel_array(ds, arr)
assert np.array_equal(ref, arr)
def test_functional(self):
"""Test function works OK."""
ds = dcmread(EXPL_16_3_1F)
ref = ds.pixel_array
assert ds.BitsAllocated == 16
assert ds.SamplesPerPixel == 3
assert ds.PixelRepresentation == 0
encoded = rle_encode_frame(ref)
decoded = _rle_decode_frame(
encoded, ds.Rows, ds.Columns, ds.SamplesPerPixel, ds.BitsAllocated
)
ds.PlanarConfiguration = 1
arr = np.frombuffer(decoded, '<u2')
arr = reshape_pixel_array(ds, arr)
assert np.array_equal(ref, arr)
def test_cycle_u32_1s_1f(self):
"""Test an encode/decode cycle for 32-bit 1 sample/pixel."""
ds = dcmread(EXPL_32_1_1F)
ref = ds.pixel_array
assert ds.BitsAllocated == 32
assert ds.SamplesPerPixel == 1
assert ds.PixelRepresentation == 0
assert ds.PhotometricInterpretation == 'MONOCHROME2'
enc = RLELosslessEncoder
encoded = enc.encode(ds, idx=0, encoding_plugin='gdcm')
decoded = _rle_decode_frame(encoded, ds.Rows, ds.Columns,
ds.SamplesPerPixel, ds.BitsAllocated)
arr = np.frombuffer(decoded, '>u4')
arr = reshape_pixel_array(ds, arr)
assert np.array_equal(ref, arr)
def test_cycle_32bit_3sample(self):
"""Test an encode/decode cycle for 32-bit 3 sample/pixel."""
ds = dcmread(EXPL_32_3_1F)
ref = ds.pixel_array
assert ds.BitsAllocated == 32
assert ds.SamplesPerPixel == 3
assert ds.PixelRepresentation == 0
kwargs = RLELosslessEncoder.kwargs_from_ds(ds)
encoded = _encode_frame(ds.PixelData, **kwargs)
decoded = _rle_decode_frame(
encoded, ds.Rows, ds.Columns, ds.SamplesPerPixel, ds.BitsAllocated
)
# The decoded data is planar configuration 1
ds.PlanarConfiguration = 1
arr = np.frombuffer(decoded, '<u4')
arr = reshape_pixel_array(ds, arr)
assert np.array_equal(ref, arr)
def test_cycle_u16_3s_1f(self):
"""Test an encode/decode cycle for 16-bit 3 sample/pixel."""
ds = dcmread(EXPL_16_3_1F)
ref = ds.pixel_array
assert ds.BitsAllocated == 16
assert ds.SamplesPerPixel == 3
assert ds.PixelRepresentation == 0
assert ds.PhotometricInterpretation == 'RGB'
assert ds.PlanarConfiguration == 0
enc = RLELosslessEncoder
encoded = enc.encode(ds, idx=0, encoding_plugin='gdcm')
decoded = _rle_decode_frame(encoded, ds.Rows, ds.Columns,
ds.SamplesPerPixel, ds.BitsAllocated)
arr = np.frombuffer(decoded, '<u2')
# The decoded data is planar configuration 1
ds.PlanarConfiguration = 1
arr = reshape_pixel_array(ds, arr)
assert np.array_equal(ref, arr)
def test_big_endian_arr(self):
"""Test using a big endian array works."""
ds = dcmread(EXPL_16_3_1F)
ref = ds.pixel_array
assert ds.BitsAllocated == 16
assert ds.SamplesPerPixel == 3
assert ds.PixelRepresentation == 0
arr = ref.newbyteorder('>')
assert id(arr) != id(ref)
assert arr.dtype == '>u2'
encoded = rle_encode_frame(arr)
decoded = _rle_decode_frame(
encoded, ds.Rows, ds.Columns, ds.SamplesPerPixel, ds.BitsAllocated
)
ds.PlanarConfiguration = 1
arr = np.frombuffer(decoded, '<u2')
arr = reshape_pixel_array(ds, arr)
assert np.array_equal(ref, arr)
def as_array(ds: "Dataset") -> "np.ndarray":
"""Return the entire *Pixel Data* 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.
Returns
-------
numpy.ndarray
The contents of (7FE0,0010) *Pixel Data* as an :class:`~numpy.ndarray`
with shape (rows, columns), (rows, columns, components), (frames,
rows, columns), or (frames, rows, columns, components) depending on
the dataset.
"""
return reshape_pixel_array(ds, get_pixeldata(ds))
def test_1frame_1sample(self):
"""Test reshaping 1 frame, 1 sample/pixel."""
self.ds.SamplesPerPixel = 1
arr = reshape_pixel_array(self.ds, RESHAPE_ARRAYS['1frame_1sample'])
assert (4, 5) == arr.shape
assert np.array_equal(arr, self.ref_1_1)
def test_reshape_pixel_array_raises(self):
"""Test that reshape_pixel_array raises exception without numpy."""
with pytest.raises(ImportError,
match="Numpy is required to reshape"):
reshape_pixel_array(None, None)
def test_reshape_pixel_array_raises(self):
"""Test that reshape_pixel_array raises exception without numpy."""
with pytest.raises(ImportError, match="Numpy is required to reshape"):
reshape_pixel_array(None, None)
def test_1frame_1sample(self):
"""Test reshaping 1 frame, 1 sample/pixel."""
self.ds.SamplesPerPixel = 1
arr = reshape_pixel_array(self.ds, RESHAPE_ARRAYS['1frame_1sample'])
assert (4, 5) == arr.shape
assert np.array_equal(arr, self.ref_1_1)