def test_kwargs_from_ds(self):
"""Test Encoder.kwargs_from_ds()"""
# Note no NumberOfFrames element
ds = Dataset()
ds.Rows = 10
ds.Columns = 12
ds.SamplesPerPixel = 1
ds.BitsAllocated = 8
ds.BitsStored = 8
ds.PixelRepresentation = 0
ds.PhotometricInterpretation = 'RGB'
enc = Encoder(RLELossless)
kwargs = enc.kwargs_from_ds(ds)
assert 1 == kwargs['number_of_frames']
assert enc._check_kwargs(kwargs) is None
# Test conversion of empty *Number of Frames*
ds.NumberOfFrames = None
kwargs = enc.kwargs_from_ds(ds)
assert 1 == kwargs['number_of_frames']
# Test already present *Number of Frames* is unaffected
ds.NumberOfFrames = 10
kwargs = enc.kwargs_from_ds(ds)
assert 10 == kwargs['number_of_frames']
# Test missing elements
del ds.Columns
del ds.BitsAllocated
msg = (
r"The following required elements are missing from the dataset: "
r"'Columns', 'BitsAllocated'")
with pytest.raises(AttributeError, match=msg):
enc.kwargs_from_ds(ds)
# Test VM 0
ds.Columns = None
ds.BitsAllocated = None
msg = (r"The following required dataset elements have a VM of 0: "
r"'Columns', 'BitsAllocated'")
with pytest.raises(AttributeError, match=msg):
enc.kwargs_from_ds(ds)
class TestEncoder_Preprocess:
"""Tests for Encoder._preprocess()."""
def setup(self):
self.e = Encoder(JPEG2000Lossless)
self.ds = ds = Dataset()
ds.Rows = 1
ds.Columns = 3
ds.SamplesPerPixel = 1
ds.PixelRepresentation = 0
ds.BitsAllocated = 8
ds.BitsStored = 8
ds.NumberOfFrames = 1
ds.PhotometricInterpretation = 'RGB'
self.arr_3s = np.asarray([
[[1, 2, 3], [4, 5, 6]],
[[7, 8, 9], [10, 11, 12]],
[[13, 14, 15], [16, 17, 18]],
[[19, 20, 21], [22, 23, 24]],
], '|u1')
assert self.arr_3s.shape == (4, 2, 3)
def test_invalid_arr_shape_raises(self):
"""Test that an array size and dataset mismatch raise exceptions"""
# 1D arrays
arr = np.asarray((1, 2, 3, 4))
msg = (r"Unable to encode as the shape of the ndarray \(4,\) "
r"doesn't match the values for the rows, columns and samples "
r"per pixel")
kwargs = self.e.kwargs_from_ds(self.ds)
assert arr.shape == (4, )
with pytest.raises(ValueError, match=msg):
self.e._preprocess(arr, **kwargs)
# 2D arrays
arr = np.asarray([[1, 2, 3, 4]])
assert arr.shape == (1, 4)
msg = r"Unable to encode as the shape of the ndarray \(1, 4\) "
with pytest.raises(ValueError, match=msg):
self.e._preprocess(arr, **kwargs)
self.ds.Rows = 2
self.ds.Columns = 2
self.ds.SamplesPerPixel = 3
arr = np.asarray([[1, 2], [3, 4]])
assert arr.shape == (2, 2)
msg = r"Unable to encode as the shape of the ndarray \(2, 2\) "
with pytest.raises(ValueError, match=msg):
self.e._preprocess(arr, **kwargs)
# 3D arrays
self.ds.Rows = 3
arr = np.asarray([[[1, 2, 1], [3, 4, 1]]])
assert arr.shape == (1, 2, 3)
msg = r"Unable to encode as the shape of the ndarray \(1, 2, 3\) "
with pytest.raises(ValueError, match=msg):
self.e._preprocess(arr, **kwargs)
def test_invalid_arr_dtype_raises(self):
"""Test an invalid arr dtype raises exception."""
arr = np.asarray(('a', 'b', 'c'))
msg = (
r"Unable to encode as the ndarray's dtype '<U1' is not supported")
kwargs = self.e.kwargs_from_ds(self.ds)
with pytest.raises(ValueError, match=msg):
self.e._preprocess(arr, **kwargs)
def test_invalid_pixel_representation_raises(self):
"""Test exception raised if pixel representation/dtype mismatch"""
self.ds.BitsAllocated = 8
self.ds.BitsStored = 8
self.ds.SamplesPerPixel = 1
self.ds.PixelRepresentation = 0
self.ds.Rows = 1
self.ds.Columns = 3
kwargs = self.e.kwargs_from_ds(self.ds)
arr = np.asarray([1, 2, 3], dtype='|i1')
msg = (r"Unable to encode as the ndarray's dtype 'int8' is not "
r"consistent with pixel representation '0' \(unsigned int\)")
with pytest.raises(ValueError, match=msg):
self.e._preprocess(arr, **kwargs)
arr = np.asarray([1, 2, 3], dtype='|u1')
kwargs['pixel_representation'] = 1
msg = (r"Unable to encode as the ndarray's dtype 'uint8' is not "
r"consistent with pixel representation '1' \(signed int\)")
with pytest.raises(ValueError, match=msg):
self.e._preprocess(arr, **kwargs)
def test_invalid_bits_allocated_raises(self):
"""Test exception raised for invalid Bits Allocated"""
self.ds.BitsAllocated = 8
self.ds.BitsStored = 8
self.ds.SamplesPerPixel = 1
self.ds.PixelRepresentation = 0
self.ds.Rows = 1
self.ds.Columns = 3
kwargs = self.e.kwargs_from_ds(self.ds)
arr = np.asarray([1, 2, 3], dtype='|u1')
kwargs['bits_stored'] = 9
msg = (
r"Unable to encode as the bits stored value is greater than the "
r"bits allocated value")
with pytest.raises(ValueError, match=msg):
self.e._preprocess(arr, **kwargs)
kwargs['bits_stored'] = 8
kwargs['bits_allocated'] = 9
msg = (r"Unable to encode as a bits allocated value of 9 is not "
r"supported \(must be a multiple of 8\)")
with pytest.raises(ValueError, match=msg):
self.e._preprocess(arr, **kwargs)
kwargs['bits_allocated'] = 16
msg = (r"Unable to encode as the ndarray's dtype 'uint8' is not "
r"consistent with a bits allocated value of 16")
with pytest.raises(ValueError, match=msg):
self.e._preprocess(arr, **kwargs)
def test_invalid_samples_per_pixel_raises(self):
"""Test exception raised spp is invalid"""
self.ds.BitsAllocated = 8
self.ds.BitsStored = 8
self.ds.SamplesPerPixel = 2
self.ds.PixelRepresentation = 0
self.ds.Rows = 2
self.ds.Columns = 2
kwargs = self.e.kwargs_from_ds(self.ds)
arr = np.asarray([1, 2, 3], dtype='|i1')
msg = (r"Unable to encode as a samples per pixel value of 2 is not "
r"supported \(must be 1 or 3\)")
with pytest.raises(ValueError, match=msg):
self.e._preprocess(arr, **kwargs)
arr = np.asarray([[1, 2], [1, 3]], dtype='|i1')
kwargs['samples_per_pixel'] = 3
msg = (r"Unable to encode as the shape of the ndarray \(2, 2\) is not "
r"consistent with a samples per pixel value of 3")
with pytest.raises(ValueError, match=msg):
self.e._preprocess(arr, **kwargs)
def test_u08_1s(self):
"""Test processing u8/1s"""
self.ds.BitsAllocated = 8
self.ds.BitsStored = 8
self.ds.SamplesPerPixel = 1
self.ds.PixelRepresentation = 0
self.ds.Rows = 1
self.ds.Columns = 3
# Override the encoding profile validation
self.e._uid = None
arr = np.asarray([1, 2, 3], dtype='|u1')
assert arr.dtype.itemsize == 1
kwargs = self.e.kwargs_from_ds(self.ds)
out = self.e._preprocess(arr, **kwargs)
assert len(out) == 3
assert b"\x01\x02\x03" == out
def test_u08_3s(self):
"""Test processing u8/3s"""
self.ds.BitsAllocated = 8
self.ds.BitsStored = 8
self.ds.PixelRepresentation = 0
self.ds.Rows = 4
self.ds.Columns = 2
self.ds.SamplesPerPixel = 3
# Override the encoding profile validation
self.e._uid = None
arr = self.arr_3s.astype('|u1')
assert arr.dtype.itemsize == 1
kwargs = self.e.kwargs_from_ds(self.ds)
out = self.e._preprocess(arr, **kwargs)
assert len(out) == 24
assert out == bytes(range(1, 25))
def test_i08_1s(self):
"""Test processing i8/1s"""
self.ds.BitsAllocated = 8
self.ds.BitsStored = 8
self.ds.SamplesPerPixel = 1
self.ds.PixelRepresentation = 1
self.ds.Rows = 1
self.ds.Columns = 3
# Override the encoding profile validation
self.e._uid = None
arr = np.asarray([-128, 0, 127], dtype='|i1')
assert arr.dtype.itemsize == 1
kwargs = self.e.kwargs_from_ds(self.ds)
out = self.e._preprocess(arr, **kwargs)
assert len(out) == 3
assert out == b"\x80\x00\x7f"
def test_i08_3s(self):
"""Test processing i8/3s"""
self.ds.BitsAllocated = 8
self.ds.BitsStored = 8
self.ds.PixelRepresentation = 1
self.ds.Rows = 4
self.ds.Columns = 2
self.ds.SamplesPerPixel = 3
# Override the encoding profile validation
self.e._uid = None
arr = self.arr_3s.astype('|i1')
assert arr.dtype.itemsize == 1
kwargs = self.e.kwargs_from_ds(self.ds)
out = self.e._preprocess(arr, **kwargs)
assert len(out) == 24
assert out == bytes(range(1, 25))
def test_u16_1s(self):
"""Test processing u16/1s"""
self.ds.BitsAllocated = 16
self.ds.BitsStored = 16
self.ds.PixelRepresentation = 0
self.ds.Rows = 1
self.ds.Columns = 3
self.ds.SamplesPerPixel = 1
# Override the encoding profile validation
self.e._uid = None
for dtype in ('>u2', '<u2', '=u2'):
arr = np.asarray([1, 2, 3], dtype=dtype)
assert arr.dtype.itemsize == 2
kwargs = self.e.kwargs_from_ds(self.ds)
out = self.e._preprocess(arr, **kwargs)
assert len(out) == 6
assert out == b"\x01\x00\x02\x00\x03\x00"
def test_u16_3s(self):
"""Test processing u16/3s"""
self.ds.BitsAllocated = 16
self.ds.BitsStored = 16
self.ds.SamplesPerPixel = 3
self.ds.PixelRepresentation = 0
self.ds.Rows = 4
self.ds.Columns = 2
ref = b''.join([bytes([b]) + b'\x00' for b in bytes(range(1, 25))])
# Override the encoding profile validation
self.e._uid = None
for dtype in ('>u2', '<u2', '=u2'):
arr = self.arr_3s.astype(dtype)
assert arr.dtype.itemsize == 2
kwargs = self.e.kwargs_from_ds(self.ds)
out = self.e._preprocess(arr, **kwargs)
assert len(out) == 48
assert out == ref
def test_i16_1s(self):
"""Test processing i16/1s"""
self.ds.BitsAllocated = 16
self.ds.BitsStored = 16
self.ds.PixelRepresentation = 1
self.ds.Rows = 1
self.ds.Columns = 3
self.ds.SamplesPerPixel = 1
# Override the encoding profile validation
self.e._uid = None
for dtype in ('>i2', '<i2', '=i2'):
arr = np.asarray([-128, 0, 127], dtype=dtype)
assert arr.dtype.itemsize == 2
kwargs = self.e.kwargs_from_ds(self.ds)
out = self.e._preprocess(arr, **kwargs)
assert len(out) == 6
assert out == b"\x80\xff\x00\x00\x7f\x00"
def test_i16_3s(self):
"""Test processing i16/3s"""
self.ds.BitsAllocated = 16
self.ds.BitsStored = 16
self.ds.SamplesPerPixel = 3
self.ds.PixelRepresentation = 1
self.ds.Rows = 4
self.ds.Columns = 2
ref = b''.join([bytes([b]) + b'\x00' for b in bytes(range(1, 25))])
# Override the encoding profile validation
self.e._uid = None
for dtype in ('>i2', '<i2', '=i2'):
arr = self.arr_3s.astype(dtype)
assert arr.dtype.itemsize == 2
kwargs = self.e.kwargs_from_ds(self.ds)
out = self.e._preprocess(arr, **kwargs)
assert len(out) == 48
assert out == ref
def test_u32_1s(self):
"""Test processing u32/1s"""
self.ds.BitsAllocated = 32
self.ds.BitsStored = 32
self.ds.SamplesPerPixel = 1
self.ds.PixelRepresentation = 0
self.ds.Rows = 1
self.ds.Columns = 3
ref = b"\x01\x00\x00\x00\x02\x00\x00\x00\x03\x00\x00\x00"
# Override the encoding profile validation
self.e._uid = None
for dtype in ('>u4', '<u4', '=u4'):
arr = np.asarray([1, 2, 3], dtype=dtype)
assert arr.dtype.itemsize == 4
kwargs = self.e.kwargs_from_ds(self.ds)
out = self.e._preprocess(arr, **kwargs)
assert len(out) == 12
assert out == ref
def test_u32_3s(self):
"""Test processing u32/3s"""
self.ds.BitsAllocated = 32
self.ds.BitsStored = 32
self.ds.SamplesPerPixel = 3
self.ds.PixelRepresentation = 0
self.ds.Rows = 4
self.ds.Columns = 2
ref = b''.join([bytes([b]) + b'\x00' * 3 for b in bytes(range(1, 25))])
# Override the encoding profile validation
self.e._uid = None
for dtype in ('>u4', '<u4', '=u4'):
arr = self.arr_3s.astype(dtype)
assert arr.dtype.itemsize == 4
kwargs = self.e.kwargs_from_ds(self.ds)
out = self.e._preprocess(arr, **kwargs)
assert len(out) == 96
assert out == ref
def test_i32_1s(self):
"""Test processing i32/1s"""
self.ds.BitsAllocated = 32
self.ds.BitsStored = 32
self.ds.SamplesPerPixel = 1
self.ds.PixelRepresentation = 1
self.ds.Rows = 1
self.ds.Columns = 3
ref = b"\x80\xff\xff\xff\x00\x00\x00\x00\x7f\x00\x00\x00"
# Override the encoding profile validation
self.e._uid = None
for dtype in ('>i4', '<i4', '=i4'):
arr = np.asarray([-128, 0, 127], dtype=dtype)
assert arr.dtype.itemsize == 4
kwargs = self.e.kwargs_from_ds(self.ds)
out = self.e._preprocess(arr, **kwargs)
assert len(out) == 12
assert out == ref
def test_i32_3s(self):
"""Test processing i32/3s"""
self.ds.BitsAllocated = 32
self.ds.BitsStored = 32
self.ds.SamplesPerPixel = 3
self.ds.PixelRepresentation = 1
self.ds.Rows = 4
self.ds.Columns = 2
ref = b''.join([bytes([b]) + b'\x00' * 3 for b in bytes(range(1, 25))])
# Override the encoding profile validation
self.e._uid = None
for dtype in ('>i4', '<i4', '=i4'):
arr = self.arr_3s.astype(dtype)
assert arr.dtype.itemsize == 4
kwargs = self.e.kwargs_from_ds(self.ds)
out = self.e._preprocess(arr, **kwargs)
assert len(out) == 96
assert out == ref