def write_data_element(fp, data_element, encodings=None):
"""Write the data_element to file fp according to
dicom media storage rules.
"""
# Write element's tag
fp.write_tag(data_element.tag)
# write into a buffer to avoid seeking back which can be expansive
buffer = DicomBytesIO()
buffer.is_little_endian = fp.is_little_endian
buffer.is_implicit_VR = fp.is_implicit_VR
VR = data_element.VR
if not fp.is_implicit_VR and len(VR) != 2:
msg = ("Cannot write ambiguous VR of '{}' for data element with "
"tag {}.\nSet the correct VR before writing, or use an "
"implicit VR transfer syntax".format(VR,
repr(data_element.tag)))
raise ValueError(msg)
if data_element.is_raw:
# raw data element values can be written as they are
buffer.write(data_element.value)
is_undefined_length = data_element.length == 0xFFFFFFFF
else:
if VR not in writers:
raise NotImplementedError(
"write_data_element: unknown Value Representation "
"'{0}'".format(VR))
encodings = encodings or [default_encoding]
encodings = convert_encodings(encodings)
writer_function, writer_param = writers[VR]
is_undefined_length = data_element.is_undefined_length
if not data_element.is_empty:
if VR in text_VRs or VR in ('PN', 'SQ'):
writer_function(buffer, data_element, encodings=encodings)
else:
# Many numeric types use the same writer but with
# numeric format parameter
if writer_param is not None:
writer_function(buffer, data_element, writer_param)
else:
writer_function(buffer, data_element)
# valid pixel data with undefined length shall contain encapsulated
# data, e.g. sequence items - raise ValueError otherwise (see #238)
if is_undefined_length and data_element.tag == 0x7fe00010:
encap_item = b'\xfe\xff\x00\xe0'
if not fp.is_little_endian:
# Non-conformant endianness
encap_item = b'\xff\xfe\xe0\x00'
if not data_element.value.startswith(encap_item):
raise ValueError(
"(7FE0,0010) Pixel Data has an undefined length indicating "
"that it's compressed, but the data isn't encapsulated as "
"required. See pydicom.encaps.encapsulate() for more "
"information")
value_length = buffer.tell()
if (not fp.is_implicit_VR and VR not in extra_length_VRs
and not is_undefined_length and value_length > 0xffff):
# see PS 3.5, section 6.2.2 for handling of this case
msg = ('The value for the data element {} exceeds the size '
'of 64 kByte and cannot be written in an explicit transfer '
'syntax. The data element VR is changed from "{}" to "UN" '
'to allow saving the data.'.format(data_element.tag, VR))
warnings.warn(msg)
VR = 'UN'
# write the VR for explicit transfer syntax
if not fp.is_implicit_VR:
if not in_py2:
fp.write(bytes(VR, default_encoding))
else:
fp.write(VR)
if VR in extra_length_VRs:
fp.write_US(0) # reserved 2 bytes
if (not fp.is_implicit_VR and VR not in extra_length_VRs
and not is_undefined_length):
fp.write_US(value_length) # Explicit VR length field is 2 bytes
else:
# write the proper length of the data_element in the length slot,
# unless is SQ with undefined length.
fp.write_UL(0xFFFFFFFF if is_undefined_length else value_length)
fp.write(buffer.getvalue())
if is_undefined_length:
fp.write_tag(SequenceDelimiterTag)
fp.write_UL(0) # 4-byte 'length' of delimiter data item
def write_data_element(
fp: DicomIO,
elem: Union[DataElement, RawDataElement],
encodings: Optional[Union[str, List[str]]] = None) -> None:
"""Write the data_element to file fp according to
dicom media storage rules.
"""
# Write element's tag
fp.write_tag(elem.tag)
# write into a buffer to avoid seeking back which can be expansive
buffer = DicomBytesIO()
buffer.is_little_endian = fp.is_little_endian
buffer.is_implicit_VR = fp.is_implicit_VR
VR: Optional[str] = elem.VR
if not fp.is_implicit_VR and VR and len(VR) != 2:
msg = (f"Cannot write ambiguous VR of '{VR}' for data element with "
f"tag {repr(elem.tag)}.\nSet the correct VR before "
f"writing, or use an implicit VR transfer syntax")
raise ValueError(msg)
if elem.is_raw:
elem = cast(RawDataElement, elem)
# raw data element values can be written as they are
buffer.write(cast(bytes, elem.value))
is_undefined_length = elem.length == 0xFFFFFFFF
else:
elem = cast(DataElement, elem)
if VR not in writers:
raise NotImplementedError(
f"write_data_element: unknown Value Representation '{VR}'")
encodings = encodings or [default_encoding]
encodings = convert_encodings(encodings)
fn, param = writers[VR]
is_undefined_length = elem.is_undefined_length
if not elem.is_empty:
if VR in text_VRs or VR in ('PN', 'SQ'):
fn(buffer, elem, encodings=encodings) # type: ignore[operator]
else:
# Many numeric types use the same writer but with
# numeric format parameter
if param is not None:
fn(buffer, elem, param) # type: ignore[operator]
else:
fn(buffer, elem) # type: ignore[operator]
# valid pixel data with undefined length shall contain encapsulated
# data, e.g. sequence items - raise ValueError otherwise (see #238)
if is_undefined_length and elem.tag == 0x7fe00010:
encap_item = b'\xfe\xff\x00\xe0'
if not fp.is_little_endian:
# Non-conformant endianness
encap_item = b'\xff\xfe\xe0\x00'
if not cast(bytes, elem.value).startswith(encap_item):
raise ValueError(
"(7FE0,0010) Pixel Data has an undefined length indicating "
"that it's compressed, but the data isn't encapsulated as "
"required. See pydicom.encaps.encapsulate() for more "
"information")
value_length = buffer.tell()
if (not fp.is_implicit_VR and VR not in extra_length_VRs
and not is_undefined_length and value_length > 0xffff):
# see PS 3.5, section 6.2.2 for handling of this case
msg = (
f"The value for the data element {elem.tag} exceeds the "
f"size of 64 kByte and cannot be written in an explicit transfer "
f"syntax. The data element VR is changed from '{VR}' to 'UN' "
f"to allow saving the data.")
warnings.warn(msg)
VR = 'UN'
# write the VR for explicit transfer syntax
if not fp.is_implicit_VR:
VR = cast(str, VR)
fp.write(bytes(VR, default_encoding))
if VR in extra_length_VRs:
fp.write_US(0) # reserved 2 bytes
if (not fp.is_implicit_VR and VR not in extra_length_VRs
and not is_undefined_length):
fp.write_US(value_length) # Explicit VR length field is 2 bytes
else:
# write the proper length of the data_element in the length slot,
# unless is SQ with undefined length.
fp.write_UL(0xFFFFFFFF if is_undefined_length else value_length)
fp.write(buffer.getvalue())
if is_undefined_length:
fp.write_tag(SequenceDelimiterTag)
fp.write_UL(0) # 4-byte 'length' of delimiter data item
def write_data_element(fp, data_element, encodings=None):
"""Write the data_element to file fp according to
dicom media storage rules.
"""
# Write element's tag
fp.write_tag(data_element.tag)
# If explicit VR, write the VR
VR = data_element.VR
if not fp.is_implicit_VR:
if len(VR) != 2:
msg = ("Cannot write ambiguous VR of '{}' for data element with "
"tag {}.\nSet the correct VR before writing, or use an "
"implicit VR transfer syntax".format(
VR, repr(data_element.tag)))
raise ValueError(msg)
if not in_py2:
fp.write(bytes(VR, default_encoding))
else:
fp.write(VR)
if VR in extra_length_VRs:
fp.write_US(0) # reserved 2 bytes
# write into a buffer to avoid seeking back which can be expansive
buffer = DicomBytesIO()
buffer.is_little_endian = fp.is_little_endian
buffer.is_implicit_VR = fp.is_implicit_VR
if data_element.is_raw:
# raw data element values can be written as they are
buffer.write(data_element.value)
is_undefined_length = data_element.length == 0xFFFFFFFF
else:
if VR not in writers:
raise NotImplementedError(
"write_data_element: unknown Value Representation "
"'{0}'".format(VR))
encodings = encodings or [default_encoding]
encodings = convert_encodings(encodings)
writer_function, writer_param = writers[VR]
is_undefined_length = data_element.is_undefined_length
if VR in text_VRs or VR in ('PN', 'SQ'):
writer_function(buffer, data_element, encodings=encodings)
else:
# Many numeric types use the same writer but with numeric format
# parameter
if writer_param is not None:
writer_function(buffer, data_element, writer_param)
else:
writer_function(buffer, data_element)
# valid pixel data with undefined length shall contain encapsulated
# data, e.g. sequence items - raise ValueError otherwise (see #238)
if is_undefined_length and data_element.tag == 0x7fe00010:
val = data_element.value
if (fp.is_little_endian and not val.startswith(b'\xfe\xff\x00\xe0')
or not fp.is_little_endian
and not val.startswith(b'\xff\xfe\xe0\x00')):
raise ValueError('Pixel Data with undefined length must '
'start with an item tag')
value_length = buffer.tell()
if (not fp.is_implicit_VR and VR not in extra_length_VRs
and not is_undefined_length):
fp.write_US(value_length) # Explicit VR length field is only 2 bytes
else:
# write the proper length of the data_element in the length slot,
# unless is SQ with undefined length.
fp.write_UL(0xFFFFFFFF if is_undefined_length else value_length)
fp.write(buffer.getvalue())
if is_undefined_length:
fp.write_tag(SequenceDelimiterTag)
fp.write_UL(0) # 4-byte 'length' of delimiter data item
def write_data_element(fp, data_element, encodings=None):
"""Write the data_element to file fp according to
dicom media storage rules.
"""
# Write element's tag
fp.write_tag(data_element.tag)
# If explicit VR, write the VR
VR = data_element.VR
if not fp.is_implicit_VR:
if len(VR) != 2:
msg = ("Cannot write ambiguous VR of '{}' for data element with "
"tag {}.\nSet the correct VR before writing, or use an "
"implicit VR transfer syntax".format(
VR, repr(data_element.tag)))
raise ValueError(msg)
if not in_py2:
fp.write(bytes(VR, default_encoding))
else:
fp.write(VR)
if VR in extra_length_VRs:
fp.write_US(0) # reserved 2 bytes
# write into a buffer to avoid seeking back which can be expansive
buffer = DicomBytesIO()
buffer.is_little_endian = fp.is_little_endian
buffer.is_implicit_VR = fp.is_implicit_VR
if data_element.is_raw:
# raw data element values can be written as they are
buffer.write(data_element.value)
is_undefined_length = data_element.length == 0xFFFFFFFF
else:
if VR not in writers:
raise NotImplementedError(
"write_data_element: unknown Value Representation "
"'{0}'".format(VR))
encodings = encodings or [default_encoding]
encodings = convert_encodings(encodings)
writer_function, writer_param = writers[VR]
is_undefined_length = data_element.is_undefined_length
if VR in text_VRs or VR in ('PN', 'SQ'):
writer_function(buffer, data_element, encodings=encodings)
else:
# Many numeric types use the same writer but with numeric format
# parameter
if writer_param is not None:
writer_function(buffer, data_element, writer_param)
else:
writer_function(buffer, data_element)
# valid pixel data with undefined length shall contain encapsulated
# data, e.g. sequence items - raise ValueError otherwise (see #238)
if is_undefined_length and data_element.tag == 0x7fe00010:
val = data_element.value
if (fp.is_little_endian and not
val.startswith(b'\xfe\xff\x00\xe0') or
not fp.is_little_endian and
not val.startswith(b'\xff\xfe\xe0\x00')):
raise ValueError('Pixel Data with undefined length must '
'start with an item tag')
value_length = buffer.tell()
if (not fp.is_implicit_VR and VR not in extra_length_VRs and
not is_undefined_length):
try:
fp.write_US(value_length) # Explicit VR length field is 2 bytes
except struct.error:
msg = ('The value for the data element {} exceeds the size '
'of 64 kByte and cannot be written in an explicit transfer '
'syntax. You can save it using Implicit Little Endian '
'transfer syntax, or you have to truncate the value to not '
'exceed the maximum size of 64 kByte.'
.format(data_element.tag))
raise ValueError(msg)
else:
# write the proper length of the data_element in the length slot,
# unless is SQ with undefined length.
fp.write_UL(0xFFFFFFFF if is_undefined_length else value_length)
fp.write(buffer.getvalue())
if is_undefined_length:
fp.write_tag(SequenceDelimiterTag)
fp.write_UL(0) # 4-byte 'length' of delimiter data item
