def test_zero_length(self):
"""Test reading BOT with zero length"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x00\x00\x00\x00'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert [0] == get_frame_offsets(fp)
def test_read_be_tag(self):
"""Test DicomIO.read_be_tag indirectly"""
# Tags are 2 + 2 = 4 bytes
bytestream = b'\x01\x02\x03\x04\x05\x06'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = False
assert Tag(fp.read_be_tag()) == 0x01020304
def test_deferred_data_element_deprecated():
"""Test the deprecation warning is working"""
fp = DicomBytesIO()
fp.is_little_endian = True
fp.is_implicit_VR = True
with pytest.deprecated_call():
elem = DeferredDataElement(0x00000000, 'UL', fp, 0, 0, 4)
def test_encapsulate_single_fragment_per_frame_bot(self):
"""Test encapsulating single fragment per frame with BOT values."""
ds = dcmread(JP2K_10FRAME_NOBOT)
frames = decode_data_sequence(ds.PixelData)
assert len(frames) == 10
data = encapsulate(frames, fragments_per_frame=1, has_bot=True)
test_frames = decode_data_sequence(data)
for a, b in zip(test_frames, frames):
assert a == b
fp = DicomBytesIO(data)
fp.is_little_endian = True
offsets = get_frame_offsets(fp)
assert offsets == [
0x0000, # 0
0x0eee, # 3822
0x1df6, # 7670
0x2cf8, # 11512
0x3bfc, # 15356
0x4ade, # 19166
0x59a2, # 22946
0x6834, # 26676
0x76e2, # 30434
0x8594 # 34196
]
def test_charset_patient_names(self, filename, patient_name):
"""Test patient names are correctly decoded and encoded."""
# check that patient names are correctly read
file_path = get_charset_files(filename + '.dcm')[0]
ds = dcmread(file_path)
ds.decode()
assert patient_name == ds.PatientName
# check that patient names are correctly written back
fp = DicomBytesIO()
fp.is_implicit_VR = False
fp.is_little_endian = True
ds.save_as(fp, write_like_original=False)
fp.seek(0)
ds = dcmread(fp)
assert patient_name == ds.PatientName
# check that patient names are correctly written back
# without original byte string (PersonName3 only)
if hasattr(ds.PatientName, 'original_string'):
ds.PatientName.original_string = None
fp = DicomBytesIO()
fp.is_implicit_VR = False
fp.is_little_endian = True
ds.save_as(fp, write_like_original=False)
fp.seek(0)
ds = dcmread(fp)
assert patient_name == ds.PatientName
def test_zero_length(self):
"""Test reading BOT with zero length"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x00\x00\x00\x00'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert [0] == get_frame_offsets(fp)
def test_seq_item_looks_like_explicit_VR(self):
# For issue 999.
# Set up an implicit VR dataset with a "normal" group 8 tag,
# followed by a sequence with an item (dataset) having
# a data element length that looks like a potential valid VR
ds = Dataset()
ds.file_meta = Dataset()
ds.file_meta.MediaStorageSOPClassUID = "1.1.1"
ds.file_meta.MediaStorageSOPInstanceUID = "2.2.2"
ds.is_implicit_VR = True
ds.is_little_endian = True
ds.SOPClassUID = '9.9.9' # First item group 8 in top-level dataset
seq = Sequence()
seq_ds = Dataset()
seq_ds.BadPixelImage = b"\3" * 0x5244 # length looks like "DR"
seq.append(seq_ds)
ds.ReferencedImageSequence = seq
dbio = DicomBytesIO()
ds.save_as(dbio, write_like_original=False)
# Now read the constructed dataset back in
# In original issue, shows warning that has detected what appears
# to be Explicit VR, then throws NotImplemented for the unknown VR
dbio.seek(0)
ds = dcmread(dbio)
ds.remove_private_tags() # forces it to actually parse SQ
def test_encapsulate_single_fragment_per_frame_bot(self):
"""Test encapsulating single fragment per frame with BOT values."""
ds = dcmread(JP2K_10FRAME_NOBOT)
frames = decode_data_sequence(ds.PixelData)
assert len(frames) == 10
data = encapsulate(frames, fragments_per_frame=1, has_bot=True)
test_frames = decode_data_sequence(data)
for a, b in zip(test_frames, frames):
assert a == b
fp = DicomBytesIO(data)
fp.is_little_endian = True
length, offsets = get_frame_offsets(fp)
assert offsets == [
0x0000, # 0
0x0eee, # 3822
0x1df6, # 7670
0x2cf8, # 11512
0x3bfc, # 15356
0x4ade, # 19166
0x59a2, # 22946
0x6834, # 26676
0x76e2, # 30434
0x8594 # 34196
]
def test_read_be_tag(self):
"""Test DicomIO.read_be_tag indirectly"""
# Tags are 2 + 2 = 4 bytes
bytestream = b'\x01\x02\x03\x04\x05\x06'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = False
assert Tag(fp.read_be_tag()) == 0x01020304
def test_not_little_endian(self):
"""Test reading big endian raises exception"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x00\x00\x00\x00'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = False
assert_raises_regex(ValueError, "'fp.is_little_endian' must be True",
get_frame_offsets, fp)
def test_single_fragment_no_delimiter(self):
"""Test single fragment is returned OK"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert read_item(fp) == b'\x01\x00\x00\x00'
def test_read_exact_length_raises(self):
"""Test DicomIO.read exact length raises if short"""
fp = DicomBytesIO(b'\x00\x01\x03')
fp.is_little_endian = True
with pytest.raises(EOFError,
match="Unexpected end of file. Read 3 bytes of 4 "
"expected starting at position 0x0"):
fp.read(length=4, need_exact_length=True)
def test_single_frame(self):
"""Test reading single-frame BOT item"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x00\x00\x00\x00'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert [0] == get_frame_offsets(fp)
def test_single_fragment_no_delimiter(self):
"""Test single fragment is returned OK"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert read_item(fp) == b'\x01\x00\x00\x00'
def encode(ds, is_implicit_VR, is_little_endian):
f = DicomBytesIO()
f.is_implicit_VR = is_implicit_VR
f.is_little_endian = is_little_endian
write_dataset(f, ds)
rawstr = f.parent.getvalue()
f.close()
return rawstr
def encode_element(el, is_implicit_VR, is_little_endian):
f = DicomBytesIO()
f.is_implicit_VR = is_implicit_VR
f.is_little_endian = is_little_endian
write_data_element(f, el)
rawstr = f.parent.getvalue()
f.close()
return rawstr
def test_single_frame(self):
"""Test reading single-frame BOT item"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x00\x00\x00\x00'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert [0] == get_frame_offsets(fp)
def test_read_exact_length_raises(self):
"""Test DicomIO.read exact length raises if short"""
fp = DicomBytesIO(b'\x00\x01\x03')
fp.is_little_endian = True
with pytest.raises(EOFError,
match="Unexpected end of file. Read 3 bytes of 4 "
"expected starting at position 0x0"):
fp.read(length=4, need_exact_length=True)
def test_lut_descriptor_empty(self):
"""Regression test for #1049: LUT empty raises."""
bs = DicomBytesIO(b'\x28\x00\x01\x11\x53\x53\x00\x00')
bs.is_little_endian = True
bs.is_implicit_VR = False
ds = dcmread(bs, force=True)
elem = ds[0x00281101]
assert elem.value is None
assert elem.VR == 'SS'
def test_read_le_ul(self):
"""Test DicomIO.read_leUL indirectly"""
# UL are 4 bytes fixed
bytestream = b'\x00\x00\x00\x00\xFF\xFF\x00\x00\xFE\xFF\xFF\xFF'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert fp.read_leUL() == 0
assert fp.read_leUL() == 0xFFFF
assert fp.read_leUL() == 0xFFFFFFFE
def test_item_undefined_length(self):
"""Test exception raised if item length undefined."""
bytestream = (b'\xFE\xFF\x00\xE0'
b'\xFF\xFF\xFF\xFF'
b'\x00\x00\x00\x01')
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
with pytest.raises(ValueError):
get_nr_fragments(fp)
def test_not_little_endian(self):
"""Test reading big endian raises exception"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x00\x00\x00\x00'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = False
with pytest.raises(ValueError,
match="'fp.is_little_endian' must be True"):
get_frame_offsets(fp)
def test_read_be_us(self):
"""Test DicomIO.read_beUS indirectly"""
# US are 2 bytes fixed
bytestream = b'\x00\x00\x00\xFF\xFF\xFE'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert fp.read_beUS() == 0
assert fp.read_beUS() == 255
assert fp.read_beUS() == 0xFFFE
def test_not_little_endian(self):
"""Test reading big endian raises exception"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x00\x00\x00\x00'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = False
with pytest.raises(ValueError,
match="'fp.is_little_endian' must be True"):
get_frame_offsets(fp)
def test_read_le_ul(self):
"""Test DicomIO.read_leUL indirectly"""
# UL are 4 bytes fixed
bytestream = b'\x00\x00\x00\x00\xFF\xFF\x00\x00\xFE\xFF\xFF\xFF'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert fp.read_leUL() == 0
assert fp.read_leUL() == 0xFFFF
assert fp.read_leUL() == 0xFFFFFFFE
def test_read_be_us(self):
"""Test DicomIO.read_beUS indirectly"""
# US are 2 bytes fixed
bytestream = b'\x00\x00\x00\xFF\xFF\xFE'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert fp.read_beUS() == 0
assert fp.read_beUS() == 255
assert fp.read_beUS() == 0xFFFE
def test_single_fragment_delimiter(self):
"""Test single fragment is returned OK with sequence delimiter item"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00' \
b'\xFE\xFF\xDD\xE0'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert 1 == get_nr_fragments(fp)
def test_item_undefined_length(self):
"""Test exception raised if item length undefined."""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\xFF\xFF\xFF\xFF' \
b'\x00\x00\x00\x01'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert_raises_regex(
ValueError, "Encapsulated data fragment had Undefined Length"
" at data position 0x4", read_item, fp)
def test_single_fragment_no_delimiter(self):
"""Test single fragment is returned OK"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
fragments = generate_pixel_data_fragment(fp)
assert next(fragments) == b'\x01\x00\x00\x00'
pytest.raises(StopIteration, next, fragments)
def test_lut_descriptor_singleton(self):
"""Test LUT Descriptor with VM = 1"""
bs = DicomBytesIO(b'\x28\x00\x01\x11\x53\x53\x02\x00\x00\xf5')
bs.is_little_endian = True
bs.is_implicit_VR = False
ds = dcmread(bs, force=True)
elem = ds[0x00281101]
# No conversion to US if not a triplet
assert elem.value == -2816
assert elem.VR == 'SS'
def test_single_fragment_no_delimiter(self):
"""Test single fragment is returned OK"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
fragments = generate_pixel_data_fragment(fp)
assert next(fragments) == b'\x01\x00\x00\x00'
pytest.raises(StopIteration, next, fragments)
def test_item_undefined_length(self):
"""Test exception raised if item length undefined."""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\xFF\xFF\xFF\xFF' \
b'\x00\x00\x00\x01'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
with pytest.raises(ValueError,
match="Encapsulated data fragment had Undefined "
"Length at data position 0x4"):
read_item(fp)
def test_multi_frame(self):
"""Test reading multi-frame BOT item"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x10\x00\x00\x00' \
b'\x00\x00\x00\x00' \
b'\x66\x13\x00\x00' \
b'\xF4\x25\x00\x00' \
b'\xFE\x37\x00\x00'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert [0, 4966, 9716, 14334] == get_frame_offsets(fp)
def test_bad_length_multiple(self):
"""Test raises exception if the item length is not a multiple of 4."""
# Length 10
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x0A\x00\x00\x00' \
b'\x01\x02\x03\x04\x05\x06\x07\x08\x09\x0A'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert_raises_regex(
ValueError, "The length of the Basic Offset Table item is not "
"a multiple of 4.", get_frame_offsets, fp)
def test_multi_frame(self):
"""Test reading multi-frame BOT item"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x10\x00\x00\x00' \
b'\x00\x00\x00\x00' \
b'\x66\x13\x00\x00' \
b'\xF4\x25\x00\x00' \
b'\xFE\x37\x00\x00'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert [0, 4966, 9716, 14334] == get_frame_offsets(fp)
def test_not_little_endian(self):
"""Test reading big endian raises exception"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = False
fragments = generate_pixel_data_fragment(fp)
assert_raises_regex(ValueError, "'fp.is_little_endian' must be True",
next, fragments)
pytest.raises(StopIteration, next, fragments)
def test_item_undefined_length(self):
"""Test exception raised if item length undefined."""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\xFF\xFF\xFF\xFF' \
b'\x00\x00\x00\x01'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
with pytest.raises(ValueError,
match="Encapsulated data fragment had Undefined "
"Length at data position 0x4"):
read_item(fp)
def test_multi_fragments_no_delimiter(self):
"""Test multi fragments are returned OK"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x06\x00\x00\x00' \
b'\x01\x02\x03\x04\x05\x06'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert 2 == get_nr_fragments(fp)
def test_bad_tag(self):
"""Test raises exception if no item tag."""
# (fffe,e100)
bytestream = b'\xFE\xFF\x00\xE1' \
b'\x08\x00\x00\x00' \
b'\x01\x02\x03\x04\x05\x06\x07\x08'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert_raises_regex(
ValueError, "Unexpected tag '\(fffe, e100\)' when "
"parsing the Basic Table Offset item.", get_frame_offsets, fp)
def test_changed_character_set(self):
# Regression test for #629
multiPN_name = get_charset_files("chrFrenMulti.dcm")[0]
ds = dcmread(multiPN_name) # is Latin-1
ds.SpecificCharacterSet = 'ISO_IR 192'
from pydicom.filebase import DicomBytesIO
fp = DicomBytesIO()
ds.save_as(fp, write_like_original=False)
fp.seek(0)
ds_out = dcmread(fp)
# we expect UTF-8 encoding here
assert b'Buc^J\xc3\xa9r\xc3\xb4me' == ds_out.get_item(0x00100010).value
def test_not_little_endian(self):
"""Test reading big endian raises exception"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = False
fragments = generate_pixel_data_fragment(fp)
with pytest.raises(ValueError,
match="'fp.is_little_endian' must be True"):
next(fragments)
pytest.raises(StopIteration, next, fragments)
def test_multi_fragments_no_delimiter(self):
"""Test multi fragments are returned OK"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x06\x00\x00\x00' \
b'\x01\x02\x03\x04\x05\x06'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert read_item(fp) == b'\x01\x00\x00\x00'
assert read_item(fp) == b'\x01\x02\x03\x04\x05\x06'
def test_changed_character_set(self):
# Regression test for #629
multiPN_name = get_charset_files("chrFrenMulti.dcm")[0]
ds = dcmread(multiPN_name) # is Latin-1
ds.SpecificCharacterSet = 'ISO_IR 192'
from pydicom.filebase import DicomBytesIO
fp = DicomBytesIO()
ds.save_as(fp, write_like_original=False)
fp.seek(0)
ds_out = dcmread(fp)
# we expect UTF-8 encoding here
assert b'Buc^J\xc3\xa9r\xc3\xb4me' == ds_out.get_item(0x00100010).value
def test_bad_length_multiple(self):
"""Test raises exception if the item length is not a multiple of 4."""
# Length 10
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x0A\x00\x00\x00' \
b'\x01\x02\x03\x04\x05\x06\x07\x08\x09\x0A'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
with pytest.raises(ValueError,
match="The length of the Basic Offset Table item"
" is not a multiple of 4."):
get_frame_offsets(fp)
def test_bad_tag(self):
"""Test raises exception if no item tag."""
# (fffe,e100)
bytestream = b'\xFE\xFF\x00\xE1' \
b'\x08\x00\x00\x00' \
b'\x01\x02\x03\x04\x05\x06\x07\x08'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
with pytest.raises(ValueError,
match="Unexpected tag '\(fffe, e100\)' when "
"parsing the Basic Table Offset item."):
get_frame_offsets(fp)
def test_bad_length_multiple(self):
"""Test raises exception if the item length is not a multiple of 4."""
# Length 10
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x0A\x00\x00\x00' \
b'\x01\x02\x03\x04\x05\x06\x07\x08\x09\x0A'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
with pytest.raises(ValueError,
match="The length of the Basic Offset Table item"
" is not a multiple of 4."):
get_frame_offsets(fp)
def test_multi_fragments_delimiter(self):
"""Test multi fragments are returned OK with sequence delimiter item"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x06\x00\x00\x00' \
b'\x01\x02\x03\x04\x05\x06' \
b'\xFE\xFF\xDD\xE0'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert read_item(fp) == b'\x01\x00\x00\x00'
assert read_item(fp) == b'\x01\x02\x03\x04\x05\x06'
def test_item_sequence_delimiter(self):
"""Test that the fragments are returned if seq delimiter hit."""
bytestream = (b'\xFE\xFF\x00\xE0'
b'\x04\x00\x00\x00'
b'\x01\x00\x00\x00'
b'\xFE\xFF\xDD\xE0'
b'\x00\x00\x00\x00'
b'\xFE\xFF\x00\xE0'
b'\x04\x00\x00\x00'
b'\x02\x00\x00\x00')
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert 1 == get_nr_fragments(fp)
def test_item_undefined_length(self):
"""Test exception raised if item length undefined."""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\xFF\xFF\xFF\xFF' \
b'\x00\x00\x00\x01'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
fragments = generate_pixel_data_fragment(fp)
assert_raises_regex(
ValueError, "Undefined item length at offset 4 when "
"parsing the encapsulated pixel data "
"fragments.", next, fragments)
pytest.raises(StopIteration, next, fragments)
def decode(bytestring, is_implicit_vr, is_little_endian, deflated=False):
"""Decode `bytestring` to a *pydicom* :class:`~pydicom.dataset.Dataset`.
.. versionchanged:: 1.5
Added `deflated` keyword parameter
Parameters
----------
byestring : io.BytesIO
The encoded dataset in the DIMSE Message sent from the peer AE.
is_implicit_vr : bool
The dataset is encoded as implicit (``True``) or explicit VR
(``False``).
is_little_endian : bool
The byte ordering of the encoded dataset, ``True`` for little endian,
``False`` for big endian.
deflated : bool, optional
``True`` if the dataset has been encoded using *Deflated Explicit VR
Little Endian* transfer syntax (default ``False``).
Returns
-------
pydicom.dataset.Dataset
The decoded dataset.
"""
## Logging
transfer_syntax = ''
if deflated:
transfer_syntax = "Deflated "
transfer_syntax += "Little Endian" if is_little_endian else "Big Endian"
if is_implicit_vr:
transfer_syntax += " Implicit"
else:
transfer_syntax += " Explicit"
LOGGER.debug('pydicom.read_dataset() TransferSyntax="%s"', transfer_syntax)
# Rewind to the start of the stream
bytestring.seek(0)
if deflated:
# Decompress the dataset
bytestring = DicomBytesIO(
zlib.decompress(bytestring.getvalue(), -zlib.MAX_WBITS))
bytestring.is_implicit_VR = is_implicit_vr
bytestring.is_little_endian = is_little_endian
# Decode the dataset
return read_dataset(bytestring, is_implicit_vr, is_little_endian)
def test_multi_fragments_no_delimiter(self):
"""Test multi fragments are returned OK"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x06\x00\x00\x00' \
b'\x01\x02\x03\x04\x05\x06'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
fragments = generate_pixel_data_fragment(fp)
assert next(fragments) == b'\x01\x00\x00\x00'
assert next(fragments) == b'\x01\x02\x03\x04\x05\x06'
pytest.raises(StopIteration, next, fragments)
def test_multi_fragments_no_delimiter(self):
"""Test multi fragments are returned OK"""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x06\x00\x00\x00' \
b'\x01\x02\x03\x04\x05\x06'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
fragments = generate_pixel_data_fragment(fp)
assert next(fragments) == b'\x01\x00\x00\x00'
assert next(fragments) == b'\x01\x02\x03\x04\x05\x06'
pytest.raises(StopIteration, next, fragments)
def test_item_undefined_length(self):
"""Test exception raised if item length undefined."""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\xFF\xFF\xFF\xFF' \
b'\x00\x00\x00\x01'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
fragments = generate_pixel_data_fragment(fp)
with pytest.raises(ValueError,
match="Undefined item length at offset 4 when "
"parsing the encapsulated pixel data "
"fragments."):
next(fragments)
pytest.raises(StopIteration, next, fragments)
def test_write_tag(self):
"""Test DicomIO.write_tag indirectly"""
tag = Tag(0x01020304)
# Little endian
fp = DicomBytesIO()
fp.is_little_endian = True
fp.write_tag(tag)
assert fp.getvalue() == b'\x02\x01\x04\x03'
# Big endian
fp = DicomBytesIO()
fp.is_little_endian = False
fp.write_tag(tag)
assert fp.getvalue() == b'\x01\x02\x03\x04'
def test_item_sequence_delimiter_zero_length(self):
"""Test that the fragments are returned if seq delimiter hit."""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00' \
b'\xFE\xFF\xDD\xE0' \
b'\x00\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x02\x00\x00\x00'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert read_item(fp) == b'\x01\x00\x00\x00'
assert read_item(fp) is None
assert read_item(fp) == b'\x02\x00\x00\x00'
def test_item_sequence_delimiter(self):
"""Test non-zero length seq delimiter reads correctly."""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00' \
b'\xFE\xFF\xDD\xE0' \
b'\x04\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x02\x00\x00\x00'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert read_item(fp) == b'\x01\x00\x00\x00'
assert read_item(fp) is None
assert read_item(fp) == b'\x02\x00\x00\x00'
def test_item_sequence_delimiter(self):
"""Test that the fragments are returned if seq delimiter hit."""
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00' \
b'\xFE\xFF\xDD\xE0' \
b'\x00\x00\x00\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x02\x00\x00\x00'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
fragments = generate_pixel_data_fragment(fp)
assert next(fragments) == b'\x01\x00\x00\x00'
pytest.raises(StopIteration, next, fragments)
def test_dcmread_does_not_raise(self):
"""Test that reading from DicomBytesIO does not raise on EOF.
Regression test for #358."""
ds = dcmread(mr_name)
fp = DicomBytesIO()
ds.save_as(fp, write_like_original=True)
fp.seek(0)
de_gen = data_element_generator(fp, False, True)
try:
while True:
next(de_gen)
except StopIteration:
pass
except EOFError:
self.fail('Unexpected EOFError raised')
def test_item_bad_tag(self):
"""Test item is read if it has an unexpected tag"""
# This should raise an exception instead
bytestream = b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x01\x00\x00\x00' \
b'\x10\x00\x10\x00' \
b'\x04\x00\x00\x00' \
b'\xFF\x00\xFF\x00' \
b'\xFE\xFF\x00\xE0' \
b'\x04\x00\x00\x00' \
b'\x02\x00\x00\x00'
fp = DicomBytesIO(bytestream)
fp.is_little_endian = True
assert read_item(fp) == b'\x01\x00\x00\x00'
assert read_item(fp) == b'\xFF\x00\xFF\x00'
assert read_item(fp) == b'\x02\x00\x00\x00'
def encode(ds, is_implicit_VR, is_little_endian):
"""
Given a pydicom Dataset, encode it to a byte stream
Parameters
----------
ds - pydicom.dataset.Dataset
The dataset to encode
is_implicit_VR - bool
Transfer syntax implicit/explicit VR
is_little_endian - bool
Transfer syntax byte ordering
Returns
-------
bytes or None
The encoded dataset (if successful), None if encoding failed.
"""
f = DicomBytesIO()
f.is_implicit_VR = is_implicit_VR
f.is_little_endian = is_little_endian
try:
write_dataset(f, ds)
except Exception as e:
logger.error("pydicom.write_dataset() failed:")
logger.error(e)
f.close()
return None
rawstr = f.parent.getvalue()
f.close()
return rawstr