def time_decode_16bit_1sample_10frame(self):
"""Time decoding the pixel data from 10 RLE frames."""
for ii in range(self.no_runs):
for frame in self.frames:
_rle_decode_frame(frame, self.ds.Rows, self.ds.Columns,
self.ds.SamplesPerPixel,
self.ds.BitsAllocated)
def time_decode_16bit_1sample_1frame(self):
"""Time decoding the pixel data from a single RLE frame."""
for ii in range(self.no_runs):
_rle_decode_frame(self.frames[0],
self.ds.Rows,
self.ds.Columns,
self.ds.SamplesPerPixel,
self.ds.BitsAllocated)
def test_unsupported_bits_allocated_raises(self):
"""Test exception raised for BitsAllocated not a multiple of 8."""
msg = (
r"Unable to decode RLE encoded pixel data with a \(0028,0100\) "
r"'Bits Allocated' value of 12"
)
with pytest.raises(NotImplementedError, match=msg):
_rle_decode_frame(b'\x00\x00\x00\x00', 1, 1, 1, 12)
def time_decode_16bit_1sample_10frame(self):
"""Time decoding the pixel data from 10 RLE frames."""
for ii in range(self.no_runs):
for frame in self.frames:
_rle_decode_frame(frame,
self.ds.Rows,
self.ds.Columns,
self.ds.SamplesPerPixel,
self.ds.BitsAllocated)
def test_invalid_nr_segments_raises(self, header, samples, bits):
"""Test having too many segments in the data raises exception."""
# This should probably be ValueError
with pytest.raises(AttributeError,
match='Unexpected number of planes'):
_rle_decode_frame(header,
rows=1,
columns=1,
samples_per_pixel=samples,
bits_allocated=bits)
def test_invalid_segment_data_raises(self):
"""Test invalid segment data raises exception"""
ds = dcmread(RLE_16_1_1F)
pixel_data = defragment_data(ds.PixelData)
msg = r"amount \(4095 vs. 4096 bytes\)"
with pytest.raises(ValueError, match=msg):
_rle_decode_frame(
pixel_data[:-1],
ds.Rows,
ds.Columns,
ds.SamplesPerPixel,
ds.BitsAllocated
)
def test_invalid_nr_segments_raises(self, header, samples, bits):
"""Test having too many segments in the data raises exception."""
# This should probably be ValueError
expected = samples * bits // 8
actual = unpack('<L', header)[0]
header += b'\x00' * (64 - len(header))
msg = (
r"expected amount \({} vs. {} segments\)".format(actual, expected)
)
with pytest.raises(ValueError, match=msg):
_rle_decode_frame(
header, rows=1, columns=1, nr_samples=samples, nr_bits=bits
)
def test_invalid_frame_data_raises(self):
"""Test that invalid segment data raises exception."""
ds = dcmread(MR_RLE_1F)
pixel_data = defragment_data(ds.PixelData)
# Missing byte
with pytest.raises(ValueError,
match=r'amount \(4095 vs. 4096 bytes\)'):
_rle_decode_frame(pixel_data[:-1], ds.Rows, ds.Columns,
ds.SamplesPerPixel, ds.BitsAllocated)
# Extra byte
with pytest.raises(ValueError,
match=r'amount \(4097 vs. 4096 bytes\)'):
_rle_decode_frame(pixel_data + b'\x00\x01', ds.Rows, ds.Columns,
ds.SamplesPerPixel, ds.BitsAllocated)
def test_16bit_3sample(self):
"""Test decoding 16-bit, 3 sample/pixel."""
header = (
b'\x06\x00\x00\x00' # 6 segments
b'\x40\x00\x00\x00' # 64
b'\x47\x00\x00\x00' # 71
b'\x4E\x00\x00\x00' # 78
b'\x55\x00\x00\x00' # 85
b'\x5C\x00\x00\x00' # 92
b'\x63\x00\x00\x00' # 99
)
header += (64 - len(header)) * b'\x00'
# 2 x 3 data
data = (
# 0, 1, 256, 255, 65280, 65535
b'\x05\x00\x00\x01\x00\xFF\xFF' # MSB
b'\x05\x00\x01\x00\xFF\x00\xFF' # LSB
b'\x05\xFF\x00\x01\x00\xFF\x00' # MSB
b'\x05\xFF\x01\x00\xFF\x00\x00' # LSB
b'\x05\x00\x00\x01\x00\xFF\xFF' # MSB
b'\x05\x01\x01\x00\xFF\x00\xFE' # LSB
)
decoded = _rle_decode_frame(header + data, 2, 3, 3, 16)
arr = np.frombuffer(decoded, np.dtype('>u2'))
assert [0, 1, 256, 255, 65280, 65535] == arr[:6].tolist()
assert [65535, 1, 256, 255, 65280, 0] == arr[6:12].tolist()
assert [1, 1, 256, 255, 65280, 65534] == arr[12:].tolist()
def test_8bit_1sample(self):
"""Test decoding 8-bit, 1 sample/pixel."""
header = (b'\x01\x00\x00\x00' b'\x40\x00\x00\x00')
header += (64 - len(header)) * b'\x00'
# 2 x 3 data
# 0, 64, 128, 160, 192, 255
data = b'\x05\x00\x40\x80\xA0\xC0\xFF'
decoded = _rle_decode_frame(header + data, 2, 3, 1, 8)
arr = np.frombuffer(decoded, np.dtype('>u1'))
assert [0, 64, 128, 160, 192, 255] == arr.tolist()
def test_invalid_frame_data_raises(self):
"""Test that invalid segment data raises exception."""
ds = dcmread(MR_RLE_1F)
pixel_data = defragment_data(ds.PixelData)
# Missing byte
# This should probably be ValueError
with pytest.raises(AttributeError, match='Different number of bytes'):
_rle_decode_frame(pixel_data[:-1],
ds.Rows,
ds.Columns,
ds.SamplesPerPixel,
ds.BitsAllocated)
# Extra byte
with pytest.raises(AttributeError, match='Different number of bytes'):
_rle_decode_frame(pixel_data + b'\x00\x01',
ds.Rows,
ds.Columns,
ds.SamplesPerPixel,
ds.BitsAllocated)
def test_16bit_1sample(self):
"""Test decoding 16-bit, 1 sample/pixel."""
header = (b'\x02\x00\x00\x00' b'\x40\x00\x00\x00' b'\x47\x00\x00\x00')
header += (64 - len(header)) * b'\x00'
# 2 x 3 data
data = (
# 0, 1, 256, 255, 65280, 65535
b'\x05\x00\x00\x01\x00\xFF\xFF' # MSB
b'\x05\x00\x01\x00\xFF\x00\xFF' # LSB
)
decoded = _rle_decode_frame(header + data, 2, 3, 1, 16)
arr = np.frombuffer(decoded, np.dtype('>u2'))
assert [0, 1, 256, 255, 65280, 65535] == arr.tolist()
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_cycle_u8_1s_1f(self):
"""Test an encode/decode cycle for 8-bit 1 sample/pixel."""
ds = dcmread(EXPL_8_1_1F)
ref = ds.pixel_array
assert ds.BitsAllocated == 8
assert ds.SamplesPerPixel == 1
assert ds.PixelRepresentation == 0
assert ds.PhotometricInterpretation == 'PALETTE COLOR'
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, '|u1')
assert np.array_equal(ref.ravel(), arr)
def test_nonconf_segment_padding_warns(self):
"""Test non-conformant segment padding warns"""
ds = dcmread(RLE_16_1_1F)
pixel_data = defragment_data(ds.PixelData)
msg = (
r"The decoded RLE segment contains non-conformant padding - 4097 "
r"vs. 4096 bytes expected"
)
with pytest.warns(UserWarning, match=msg):
frame = _rle_decode_frame(
pixel_data + b'\x00\x01',
4096,
1,
ds.SamplesPerPixel,
ds.BitsAllocated
)
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_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_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 test_32bit_1sample(self):
"""Test decoding 32-bit, 1 sample/pixel."""
header = (
b'\x04\x00\x00\x00' # 4 segments
b'\x40\x00\x00\x00' # 64 offset
b'\x47\x00\x00\x00' # 71 offset
b'\x4E\x00\x00\x00' # 78 offset
b'\x55\x00\x00\x00' # 85 offset
)
header += (64 - len(header)) * b'\x00'
# 2 x 3 data
data = (
# 0, 16777216, 65536, 256, 4294967295
b'\x05\x00\x01\x00\x00\x00\xFF' # MSB
b'\x05\x00\x00\x01\x00\x00\xFF'
b'\x05\x00\x00\x00\x01\x00\xFF'
b'\x05\x00\x00\x00\x00\x01\xFF' # LSB
)
decoded = _rle_decode_frame(header + data, 2, 3, 1, 32)
arr = np.frombuffer(decoded, np.dtype('>u4'))
assert [0, 16777216, 65536, 256, 1, 4294967295] == arr.tolist()
def test_8bit_3sample(self):
"""Test decoding 8-bit, 3 sample/pixel."""
header = (
b'\x03\x00\x00\x00' # 3 segments
b'\x40\x00\x00\x00' # 64
b'\x47\x00\x00\x00' # 71
b'\x4E\x00\x00\x00' # 78
)
header += (64 - len(header)) * b'\x00'
# 2 x 3 data
# 0, 64, 128, 160, 192, 255
data = (
b'\x05\x00\x40\x80\xA0\xC0\xFF' # R
b'\x05\xFF\xC0\x80\x40\x00\xFF' # B
b'\x05\x01\x40\x80\xA0\xC0\xFE' # G
)
decoded = _rle_decode_frame(header + data, 2, 3, 3, 8)
arr = np.frombuffer(decoded, np.dtype('>u1'))
# Ordered all R, all G, all B
assert [0, 64, 128, 160, 192, 255] == arr[:6].tolist()
assert [255, 192, 128, 64, 0, 255] == arr[6:12].tolist()
assert [1, 64, 128, 160, 192, 254] == arr[12:].tolist()
def test_32bit_3sample(self):
"""Test decoding 32-bit, 3 sample/pixel."""
header = (
b'\x0C\x00\x00\x00' # 12 segments
b'\x40\x00\x00\x00' # 64
b'\x47\x00\x00\x00' # 71
b'\x4E\x00\x00\x00' # 78
b'\x55\x00\x00\x00' # 85
b'\x5C\x00\x00\x00' # 92
b'\x63\x00\x00\x00' # 99
b'\x6A\x00\x00\x00' # 106
b'\x71\x00\x00\x00' # 113
b'\x78\x00\x00\x00' # 120
b'\x7F\x00\x00\x00' # 127
b'\x86\x00\x00\x00' # 134
b'\x8D\x00\x00\x00' # 141
)
header += (64 - len(header)) * b'\x00'
# 2 x 3 data
data = (
# 0, 16777216, 65536, 256, 4294967295
b'\x05\x00\x01\x00\x00\x00\xFF' # MSB
b'\x05\x00\x00\x01\x00\x00\xFF'
b'\x05\x00\x00\x00\x01\x00\xFF'
b'\x05\x00\x00\x00\x00\x01\xFF' # LSB
b'\x05\xFF\x01\x00\x00\x00\x00' # MSB
b'\x05\xFF\x00\x01\x00\x00\x00'
b'\x05\xFF\x00\x00\x01\x00\x00'
b'\x05\xFF\x00\x00\x00\x01\x00' # LSB
b'\x05\x00\x01\x00\x00\x00\xFF' # MSB
b'\x05\x00\x00\x01\x00\x00\xFF'
b'\x05\x00\x00\x00\x01\x00\xFF'
b'\x05\x01\x00\x00\x00\x01\xFE' # LSB
)
decoded = _rle_decode_frame(header + data, 2, 3, 3, 32)
arr = np.frombuffer(decoded, np.dtype('>u4'))
assert [0, 16777216, 65536, 256, 1, 4294967295] == arr[:6].tolist()
assert [4294967295, 16777216, 65536, 256, 1, 0] == arr[6:12].tolist()
assert [1, 16777216, 65536, 256, 1, 4294967294] == arr[12:].tolist()
def test_unsupported_bits_allocated_raises(self):
"""Test exception raised for BitsAllocated not a multiple of 8."""
with pytest.raises(NotImplementedError, match='multiple of bytes'):
_rle_decode_frame(b'\x00\x00\x00\x00', 1, 1, 1, 12)
