def write_sequence_item(fp: DicomIO, dataset: Dataset,
encodings: List[str]) -> None:
"""Write a `dataset` in a sequence to the file-like `fp`.
This is similar to writing a data_element, but with a specific tag for
Sequence Item.
See DICOM Standard, Part 5, :dcm:`Section 7.5<sect_7.5.html>`.
Parameters
----------
fp : file-like
The file-like to write the encoded data to.
dataset : Dataset
The :class:`Dataset<pydicom.dataset.Dataset>` to write to `fp`.
encodings : list of str
The character encodings to use on text values.
"""
fp.write_tag(ItemTag) # marker for start of Sequence Item
length_location = fp.tell() # save location for later.
# will fill in real value later if not undefined length
fp.write_UL(0xffffffff)
write_dataset(fp, dataset, parent_encoding=encodings)
if getattr(dataset, "is_undefined_length_sequence_item", False):
fp.write_tag(ItemDelimiterTag)
fp.write_UL(0) # 4-bytes 'length' field for delimiter item
else: # we will be nice and set the lengths for the reader of this file
location = fp.tell()
fp.seek(length_location)
fp.write_UL(location - length_location - 4) # 4 is length of UL
fp.seek(location) # ready for next data_element
def write_ATvalue(fp: DicomIO, elem: DataElement) -> None:
"""Write a data_element tag to a file."""
try:
iter(cast(Sequence[Any], elem.value)) # see if is multi-valued AT;
# Note will fail if Tag ever derived from true tuple rather than being
# a long
except TypeError:
# make sure is expressed as a Tag instance
tag = Tag(cast(int, elem.value))
fp.write_tag(tag)
else:
tags = [Tag(tag) for tag in cast(Sequence[int], elem.value)]
for tag in tags:
fp.write_tag(tag)
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
