def test_pixel_array(self):
index = get_indexed_datasets(self.uid)
ds = index['US1_J2KR.dcm']['ds']
arr = ds.pixel_array
assert arr.flags.writeable
assert 'uint8' == arr.dtype
assert (ds.Rows, ds.Columns, ds.SamplesPerPixel) == arr.shape
# Values checked against GDCM
assert [
[180, 26, 0],
[172, 15, 0],
[162, 9, 0],
[152, 4, 0],
[145, 0, 0],
[132, 0, 0],
[119, 0, 0],
[106, 0, 0],
[ 87, 0, 0],
[ 37, 0, 0],
[ 0, 0, 0],
[ 50, 0, 0],
[100, 0, 0],
[109, 0, 0],
[122, 0, 0],
[135, 0, 0],
[145, 0, 0],
[155, 5, 0],
[165, 11, 0],
[175, 17, 0]] == arr[175:195, 28, :].tolist()
def test_get_pixeldata_no_lj_syntax(self):
"""Test exception raised if syntax not supported."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.50')
ds = index['JPEGBaseline_1s_1f_u_08_08.dcm']['ds']
msg = (r"Unable to convert the pixel data as there are no pylibjpeg "
r"plugins available to decode pixel data encoded using 'JPEG")
with pytest.raises(NotImplementedError, match=msg):
handler.get_pixeldata(ds)
def test_missing_required(self):
"""Test missing required element raises."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.50')
ds = index['JPEGBaseline_1s_1f_u_08_08.dcm']['ds']
del ds.SamplesPerPixel
msg = r"'FileDataset' object has no attribute 'SamplesPerPixel'"
with pytest.raises(AttributeError, match=msg):
ds.pixel_array
def test_missing_required(self):
"""Test missing required element raises."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.50')
ds = index['JPEGBaseline_1s_1f_u_08_08.dcm']['ds']
del ds.SamplesPerPixel
msg = (r"Unable to convert the pixel data as the following required "
r"elements are missing from the dataset: SamplesPerPixel")
with pytest.raises(AttributeError, match=msg):
ds.pixel_array
def test_pixel_array(self):
# Should basically just not mess up the usual pydicom behaviour
index = get_indexed_datasets('1.2.840.10008.1.2.4.50')
ds = index['JPEGBaseline_1s_1f_u_08_08.dcm']['ds']
msg = (
r"Unable to convert the Pixel Data as the 'pylibjpeg-libjpeg' "
r"plugin is not installed"
)
with pytest.raises(RuntimeError, match=msg):
ds.pixel_array
def test_get_pixeldata_no_syntax(self):
"""Test exception raised if syntax not supported."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.50')
ds = index['JPEGBaseline_1s_1f_u_08_08.dcm']['ds']
ds.file_meta.TransferSyntaxUID = '1.2.3.4'
msg = (
r"Unable to convert the pixel data as there are no pylibjpeg "
r"plugins available to decode pixel data encoded using '1.2.3.4'")
with pytest.raises(RuntimeError, match=msg):
handler.get_pixeldata(ds)
def test_pixel_array(self):
# Should basically just not mess up the usual pydicom behaviour
index = get_indexed_datasets('1.2.840.10008.1.2.4.50')
ds = index['JPEGBaseline_1s_1f_u_08_08.dcm']['ds']
msg = (
r"The following handlers are available to decode the pixel data "
r"however they are missing required dependencies: GDCM \(req. "
r"GDCM\), Pillow \(req. Pillow\)")
with pytest.raises(RuntimeError, match=msg):
ds.pixel_array
def test_generate_frames_1s(self):
"""Test with multiple frames, 1 sample/px."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.90')
ds = index['emri_small_jpeg_2k_lossless.dcm']['ds']
assert ds.NumberOfFrames > 1
assert 1 == ds.SamplesPerPixel
frames = generate_frames(ds)
arr = next(frames)
assert arr.flags.writeable
assert 'uint16' == arr.dtype
assert (ds.Rows, ds.Columns) == arr.shape
assert 163 == arr[12, 23]
def test_pixel_array(self):
index = get_indexed_datasets(self.uid)
ds = index['MR_small_jpeg_ls_lossless.dcm']['ds']
assert self.uid == ds.file_meta.TransferSyntaxUID
arr = ds.pixel_array
assert arr.flags.writeable
assert 'int16' == arr.dtype
assert (ds.Rows, ds.Columns) == arr.shape
# Reference values from GDCM handler
assert [1194, 879, 127, 661, 1943, 1885, 1857, 1746,
1699] == (arr[55:65, 38].tolist())
def test_generate_frames_3s_0p(self):
"""Test with multiple frames, 3 sample/px, 0 planar conf."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.50')
ds = index['color3d_jpeg_baseline.dcm']['ds']
assert ds.NumberOfFrames > 1
assert 3 == ds.SamplesPerPixel
assert 0 == ds.PlanarConfiguration
frames = generate_frames(ds)
arr = next(frames)
assert arr.flags.writeable
assert 'uint8' == arr.dtype
assert (ds.Rows, ds.Columns, 3) == arr.shape
assert [48, 128, 128] == arr[159, 290, :].tolist()
def test_pixel_representation_mismatch(self):
"""Test mismatch between Pixel Representation and the J2K data."""
index = get_indexed_datasets(self.uid)
ds = index['J2K_pixelrep_mismatch.dcm']['ds']
arr = ds.pixel_array
assert arr.flags.writeable
assert 'int16' == arr.dtype
assert (512, 512) == arr.shape
assert -2000 == arr[0, 0]
assert [621, 412, 138, -193, -520, -767, -907, -966, -988,
-995] == (arr[47:57, 279].tolist())
assert [-377, -121, 141, 383, 633, 910, 1198, 1455, 1638,
1732] == (arr[328:338, 106].tolist())
def test_generate_frames_single_1s(self):
"""Test with single frame, 1 sample/px."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.90')
ds = index['693_J2KR.dcm']['ds']
assert 1 == getattr(ds, 'NumberOfFrames', 1)
assert 1 == ds.SamplesPerPixel
frame_gen = generate_frames(ds)
arr = next(frame_gen)
with pytest.raises(StopIteration):
next(frame_gen)
assert arr.flags.writeable
assert 'int16' == arr.dtype
assert (ds.Rows, ds.Columns) == arr.shape
assert ([1022, 1051, 1165, 1442, 1835, 2096, 2074, 1868, 1685,
1603] == arr[290, 135:145].tolist())
def test_pixel_array(self):
index = get_indexed_datasets(self.uid)
ds = index['JPEGBaseline_1s_1f_u_08_08.dcm']['ds']
assert self.uid == ds.file_meta.TransferSyntaxUID
arr = ds.pixel_array
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_pixel_array(self):
# Should basically just not mess up the usual pydicom behaviour
index = get_indexed_datasets('1.2.840.10008.1.2.4.50')
ds = index['JPEGBaseline_1s_1f_u_08_08.dcm']['ds']
arr = ds.pixel_array
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_pixel_representation_mismatch(self):
"""Test mismatch between Pixel Representation and the J2K data."""
index = get_indexed_datasets(self.uid)
ds = index['J2K_pixelrep_mismatch.dcm']['ds']
msg = (
r"value '1' \(signed\) in the dataset does not match the format "
r"of the values found in the JPEG 2000 data 'unsigned'"
)
with pytest.warns(UserWarning, match=msg):
arr = ds.pixel_array
assert arr.flags.writeable
assert 'int16' == arr.dtype
assert (512, 512) == arr.shape
assert -2000 == arr[0, 0]
assert [621, 412, 138, -193, -520, -767, -907, -966, -988, -995] == (
arr[47:57, 279].tolist()
)
assert [-377, -121, 141, 383, 633, 910, 1198, 1455, 1638, 1732] == (
arr[328:338, 106].tolist()
)
def test_ybr_full_422(self):
"""Test YBR_FULL_422 data decoded."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.50')
ds = index['SC_rgb_dcmtk_+eb+cy+np.dcm']['ds']
assert 'YBR_FULL_422' == ds.PhotometricInterpretation
arr = ds.pixel_array
