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_valid_no_warning(self, recwarn):
"""Test no warning issued when dataset matches JPEG data."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.90')
ds = index['966_fixed.dcm']['ds']
ds.pixel_array
assert len(recwarn) == 0
def test_bad_decode():
"""Test trying to decode bad data."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.90')
ds = index['966.dcm']['ds']
frame = next(generate_frames(ds))
msg = r"Error decoding the J2K data: failed to decode image"
with pytest.raises(RuntimeError, match=msg):
decode(frame)
def test_decode_format_raises(self):
"""Test decoding using invalid format raises."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.90')
ds = index['693_J2KR.dcm']['ds']
frame = next(generate_frames(ds))
msg = r"Unsupported 'j2k_format' value: 3"
with pytest.raises(ValueError, match=msg):
get_parameters(frame, j2k_format=3)
def test_non_conformant_raises(self):
"""Test that a non-conformant JPEG image raises an exception."""
ds_list = get_indexed_datasets('1.2.840.10008.1.2.4.90')
# Image has invalid Se value in the SOS marker segment
item = ds_list['966.dcm']
assert 0xC000 == item['Status'][1]
msg = r"Error decoding the J2K data: failed to decode image"
with pytest.raises(RuntimeError, match=msg):
item['ds'].pixel_array
def test_decode_reshape_false(self):
"""Test decoding using invalid jpeg format raises."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.90')
ds = index['US1_J2KR.dcm']['ds']
frame = next(generate_frames(ds))
arr = decode(frame, reshape=False)
assert arr.flags.writeable
assert (ds.Rows * ds.Columns * ds.SamplesPerPixel, ) == arr.shape
def test_unsupported_syntax_raises(self):
"""Test exception gets raised if unsupported transfer syntax."""
index = get_indexed_datasets('1.2.840.10008.1.2.1')
ds = index['CT_small.dcm']['ds']
assert '1.2.840.10008.1.2.1' == ds.file_meta.TransferSyntaxUID
msg = (r"Unable to convert the pixel data as the transfer syntax "
r"is not supported by the openjpeg pixel data handler.")
with pytest.raises(NotImplementedError, match=msg):
handler.get_pixeldata(ds)
def test_decode_bad_format_raises(self):
"""Test decoding using invalid jpeg format raises."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.90')
ds = index['MR_small_jp2klossless.dcm']['ds']
frame = next(generate_frames(ds))
msg = r"Unsupported 'j2k_format' value: 3"
with pytest.raises(ValueError, match=msg):
decode(frame, j2k_format=3)
def test_no_dataset(self):
index = get_indexed_datasets('1.2.840.10008.1.2.4.90')
ds = index['MR_small_jp2klossless.dcm']['ds']
frame = next(generate_frames(ds))
arr = decode_pixel_data(frame)
assert arr.flags.writeable
assert 'uint8' == arr.dtype
length = ds.Rows * ds.Columns * ds.SamplesPerPixel * ds.BitsAllocated / 8
assert (length, ) == arr.shape
def setup(self):
add_handler()
self.ds = get_indexed_datasets(self.uid)
# Check if is already supported, and if not add it
self.has_tsyntax = True
if self.uid not in handler.SUPPORTED_TRANSFER_SYNTAXES:
self.has_tsyntax = False
handler.SUPPORTED_TRANSFER_SYNTAXES.append(self.uid)
def test_invalid_pixel_data(self):
"""Test that warning issued if Pixel Data is not a J2K codestream."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.90')
ds = index['GDCMJ2K_TextGBR.dcm']['ds']
msg = (r"The \(7FE0,0010\) Pixel Data contains a JPEG 2000 codestream "
r"with the optional JP2 file format header, which is "
r"non-conformant to the DICOM Standard \(Part 5, Annex A.4.4\)")
with pytest.warns(UserWarning, match=msg):
ds.pixel_array
def test_missing_element_raises(self):
"""Test exception gets raised if required element missing."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.90')
ds = index['US1_J2KR.dcm']['ds']
del ds.BitsAllocated
assert 'BitsAllocated' not in ds
msg = (r"Unable to convert the pixel data as the following required "
r"elements are missing from the dataset: BitsAllocated")
with pytest.raises(AttributeError, match=msg):
handler.get_pixeldata(ds)
def test_invalid_pixel_representation(self):
"""Test that warning issued when Pixel Representation doesn't match."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.90')
ds = index['TOSHIBA_J2K_SIZ0_PixRep1.dcm']['ds']
msg = (
r"The \(0028,0103\) Pixel Representation value '1' \(signed\) in "
r"the dataset does not match the format of the values found in "
r"the JPEG 2000 data 'unsigned'")
with pytest.warns(UserWarning, match=msg):
ds.pixel_array
def test_invalid_bits_stored(self):
"""Test that warning issued when Bits Stored doesn't match."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.91')
ds = index['OsirixFake16BitsStoredFakeSpacing.dcm']['ds']
msg = (
r"The \(0028,0101\) Bits Stored value '16' in the dataset does "
r"not match the component precision value '11' found in the JPEG "
r"2000 data. It's recommended that you change the Bits Stored "
r"value to produce the correct output")
with pytest.warns(UserWarning, match=msg):
ds.pixel_array
def test_jpeg2000i(self, fname, info):
"""Test get_parameters() for the baseline datasets."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.91')
ds = index[fname]['ds']
frame = next(generate_frames(ds))
params = get_parameters(frame)
assert (info[0], info[1]) == (params['rows'], params['columns'])
assert info[2] == params['nr_components']
assert info[3] == params['precision']
assert info[4] == params['is_signed']
def test_signed_error(self):
"""Regression test for #30."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.90')
ds = index['693_J2KR.dcm']['ds']
frame = next(generate_frames(ds))
arr = decode(frame)
#print(arr)
#import matplotlib.pyplot as plt
#plt.imshow(arr)
#plt.show()
assert -2000 == arr[0, 0]
def test_decode_bad_type_raises(self):
"""Test decoding using invalid type raises."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.90')
ds = index['MR_small_jp2klossless.dcm']['ds']
frame = tuple(next(generate_frames(ds)))
assert not hasattr(frame, 'tell') and not isinstance(frame, bytes)
msg = (
r"The Python object containing the encoded JPEG 2000 data must "
r"either be bytes or have read\(\), tell\(\) and seek\(\) methods."
)
with pytest.raises(TypeError, match=msg):
decode(frame)
def test_invalid_samples_per_pixel(self):
"""Test that warning issued when Samples Per Pixel doesn't match."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.90')
ds = index['693_J2KR.dcm']['ds']
ds.SamplesPerPixel = 3
msg = (
r"The \(0028,0002\) Samples per Pixel value '3' in the dataset "
r"does not match the number of components '1' found in the JPEG "
r"2000 data. It's recommended that you change the Samples per "
r"Pixel value to produce the correct output")
with pytest.warns(UserWarning, match=msg):
with pytest.raises(ValueError):
ds.pixel_array
def test_decode_reshape_true(self):
"""Test decoding using invalid jpeg format raises."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.90')
ds = index['US1_J2KR.dcm']['ds']
frame = next(generate_frames(ds))
arr = decode(frame)
assert arr.flags.writeable
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_decode_bytes(self):
"""Test decoding using bytes."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.90')
ds = index['MR_small_jp2klossless.dcm']['ds']
frame = next(generate_frames(ds))
assert isinstance(frame, bytes)
arr = decode(frame)
assert arr.flags.writeable
assert 'int16' == arr.dtype
assert (ds.Rows, ds.Columns) == arr.shape
# It'd be nice to standardise the pixel value testing...
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:])
assert 862 == arr[-1, -1]
def setup(self):
add_handler()
self.ds = get_indexed_datasets(self.uid)
def setup(self):
self.ds = get_indexed_datasets(self.uid)
def test_should_change_pi(self):
"""Test the pointless function."""
index = get_indexed_datasets('1.2.840.10008.1.2.4.90')
ds = index['US1_J2KR.dcm']['ds']
func = (handler.should_change_PhotometricInterpretation_to_RGB)
assert not func(ds)
