def read_item(fp: DicomFileLike) -> Optional[bytes]:
"""Read and return a single Item in the fragmented data stream.
Parameters
----------
fp : filebase.DicomIO
The file-like to read the item from.
Returns
-------
bytes
The Item's raw bytes.
"""
logger = pydicom.config.logger
try:
tag = fp.read_tag()
# already read delimiter before passing data here
# so should just run out
except EOFError:
return None
# No more items, time for sequence to stop reading
if tag == SequenceDelimiterTag:
length = fp.read_UL()
logger.debug(
"%04x: Sequence Delimiter, length 0x%x",
fp.tell() - 8,
length)
if length != 0:
logger.warning(
"Expected 0x00000000 after delimiter, found 0x%x,"
" at data position 0x%x",
length,
fp.tell() - 4)
return None
if tag != ItemTag:
logger.warning(
"Expected Item with tag %s at data position 0x%x",
ItemTag,
fp.tell() - 4)
length = fp.read_UL()
else:
length = fp.read_UL()
logger.debug(
"%04x: Item, length 0x%x",
fp.tell() - 8,
length)
if length == 0xFFFFFFFF:
raise ValueError(
"Encapsulated data fragment had Undefined Length"
" at data position 0x%x" % (fp.tell() - 4, ))
item_data = fp.read(length)
return item_data
def write_dataset_to_bytes(dataset):
# 버퍼 생성
with BytesIO() as buffer:
# DicomFileLike 오브젝트 생성
memory_dataset = DicomFileLike(buffer)
dcmwrite(memory_dataset, dataset)
memory_dataset.seek(0)
return memory_dataset.read()
def get_nr_fragments(fp: DicomFileLike) -> int:
"""Return the number of fragments in `fp`.
.. versionadded:: 1.4
"""
if not fp.is_little_endian:
raise ValueError("'fp.is_little_endian' must be True")
nr_fragments = 0
start = fp.tell()
while True:
try:
tag = Tag(fp.read_tag())
except EOFError:
break
if tag == 0xFFFEE000:
# Item
length = fp.read_UL()
if length == 0xFFFFFFFF:
raise ValueError("Undefined item length at offset {} when "
"parsing the encapsulated pixel data "
"fragments.".format(fp.tell() - 4))
fp.seek(length, 1)
nr_fragments += 1
elif tag == 0xFFFEE0DD:
# Sequence Delimiter
break
else:
raise ValueError("Unexpected tag '{}' at offset {} when parsing "
"the encapsulated pixel data fragment items."
.format(tag, fp.tell() - 4))
fp.seek(start)
return nr_fragments
def write_dataset_to_bytes(dataset):
# create a buffer
with BytesIO() as buffer:
# create a DicomFileLike object that has some properties of DataSet
memory_dataset = DicomFileLike(buffer)
# write the dataset to the DicomFileLike object
dcmwrite(memory_dataset, dataset)
# to read from the object, you have to rewind it
memory_dataset.seek(0)
# read the contents as bytes
return memory_dataset.read()
def write_dataset_to_bytes(dataset):
# 버퍼를 생성한다.
with BytesIO() as buffer:
# Dataset의 속성들을 담을 DicomFileLike 객체를 만든다.
memory_dataset = DicomFileLike(buffer)
# Dataset을 DicomFileLike 객체에 write 한다.
dcmwrite(memory_dataset, dataset)
# 객체에서 읽어오기 위해 rewind 한다.
memory_dataset.seek(0)
# 바이트로 읽어서 리턴한다.
return memory_dataset.read()
def to_bytes(dcm: pydicom.dataset.FileDataset):
"""Converts dicom object to byte sequence,
source https://pydicom.github.io/pydicom/dev/auto_examples/memory_dataset.html"""
with BytesIO() as buffer:
memory_dataset = DicomFileLike(
buffer
) # create a DicomFileLike object that has some properties of DataSet
dcmwrite(memory_dataset,
dcm) # write the dataset to the DicomFileLike object
memory_dataset.seek(
0) # to read from the object, you have to rewind it
return memory_dataset.read() # read the contents as bytes
def test_init_bad_parent(self):
"""Test exceptions raised if parent has no IO methods"""
class IntPlus(int):
def tell(self):
pass
def close(self):
pass
fp = DicomFileLike(IntPlus)
with pytest.raises(IOError,
match=r"This DicomFileLike object has no write\(\) "
r"method"):
fp.write(b'')
with pytest.raises(IOError,
match=r"This DicomFileLike object has no read\(\) "
r"method"):
fp.parent_read(b'')
with pytest.raises(IOError,
match=r"This DicomFileLike object has no seek\(\) "
r"method"):
fp.seek(0, 1)
assert fp.name == '<no filename>'
def test_init_bad_parent(self):
"""Test exceptions raised if parent has no IO methods"""
class IntPlus(int):
def tell(self):
pass
def close(self):
pass
fp = DicomFileLike(IntPlus)
with pytest.raises(IOError,
match="This DicomFileLike object has no write\(\) "
"method"):
fp.write(b'')
with pytest.raises(IOError,
match="This DicomFileLike object has no read\(\) "
"method"):
fp.parent_read(b'')
with pytest.raises(IOError,
match="This DicomFileLike object has no seek\(\) "
"method"):
fp.seek(0, 1)
assert fp.name == '<no filename>'
def write_file(filename, dataset, write_like_original=True):
"""Store a FileDataset to the filename specified.
Parameters
----------
filename : str
Name of file to save new DICOM file to.
dataset : FileDataset
Dataset holding the DICOM information; e.g. an object
read with read_file().
write_like_original : boolean
If True (default), preserves the following information from
the dataset:
-preamble -- if no preamble in read file, than not used here
-hasFileMeta -- if writer did not do file meta information,
then don't write here either
-seq.is_undefined_length -- if original had delimiters, write them now too,
instead of the more sensible length characters
- is_undefined_length_sequence_item -- for datasets that belong to a
sequence, write the undefined length delimiters if that is
what the original had.
If False, produces a "nicer" DICOM file for other readers,
where all lengths are explicit.
See Also
--------
pydicom.dataset.FileDataset
Dataset class with relevant attrs and information.
pydicom.dataset.Dataset.save_as
Write a DICOM file from a dataset that was read in with read_file().
save_as wraps write_file.
Notes
-----
Set dataset.preamble if you want something other than 128 0-bytes.
If the dataset was read from an existing dicom file, then its preamble
was stored at read time. It is up to the user to ensure the preamble is still
correct for its purposes.
If there is no Transfer Syntax tag in the dataset, then set
dataset.is_implicit_VR and dataset.is_little_endian
to determine the transfer syntax used to write the file.
"""
# Decide whether to write DICOM preamble. Should always do so unless trying to mimic the original file read in
preamble = getattr(dataset, "preamble", None)
if not preamble and not write_like_original:
preamble = b"\0" * 128
file_meta = dataset.file_meta
if file_meta is None:
file_meta = Dataset()
if 'TransferSyntaxUID' not in file_meta:
if dataset.is_little_endian and dataset.is_implicit_VR:
file_meta.add_new((2, 0x10), 'UI', ImplicitVRLittleEndian)
elif dataset.is_little_endian and not dataset.is_implicit_VR:
file_meta.add_new((2, 0x10), 'UI', ExplicitVRLittleEndian)
elif not dataset.is_little_endian and not dataset.is_implicit_VR:
file_meta.add_new((2, 0x10), 'UI', ExplicitVRBigEndian)
else:
raise NotImplementedError(
"pydicom has not been verified for Big Endian with Implicit VR"
)
caller_owns_file = True
# Open file if not already a file object
if isinstance(filename, compat.string_types):
fp = DicomFile(filename, 'wb')
# caller provided a file name; we own the file handle
caller_owns_file = False
else:
fp = DicomFileLike(filename)
try:
if preamble:
fp.write(preamble) # blank 128 byte preamble
_write_file_meta_info(fp, file_meta)
# Set file VR, endian. MUST BE AFTER writing META INFO (which changes to Explicit LittleEndian)
fp.is_implicit_VR = dataset.is_implicit_VR
fp.is_little_endian = dataset.is_little_endian
write_dataset(fp, dataset)
finally:
if not caller_owns_file:
fp.close()
def dcmwrite(filename, dataset, write_like_original=True):
"""Write `dataset` to the `filename` specified.
If `write_like_original` is ``True`` then `dataset` will be written as is
(after minimal validation checking) and may or may not contain all or parts
of the File Meta Information (and hence may or may not be conformant with
the DICOM File Format).
If `write_like_original` is ``False``, `dataset` will be stored in the
:dcm:`DICOM File Format <part10/chapter_7.html>`. To do
so requires that the ``Dataset.file_meta`` attribute
exists and contains a :class:`Dataset` with the required (Type 1) *File
Meta Information Group* elements. The byte stream of the `dataset` will be
placed into the file after the DICOM *File Meta Information*.
If `write_like_original` is ``True`` then the :class:`Dataset` will be
written as is (after minimal validation checking) and may or may not
contain all or parts of the *File Meta Information* (and hence may or
may not be conformant with the DICOM File Format).
**File Meta Information**
The *File Meta Information* consists of a 128-byte preamble, followed by
a 4 byte ``b'DICM'`` prefix, followed by the *File Meta Information Group*
elements.
**Preamble and Prefix**
The ``dataset.preamble`` attribute shall be 128-bytes long or ``None`` and
is available for use as defined by the Application Profile or specific
implementations. If the preamble is not used by an Application Profile or
specific implementation then all 128 bytes should be set to ``0x00``. The
actual preamble written depends on `write_like_original` and
``dataset.preamble`` (see the table below).
+------------------+------------------------------+
| | write_like_original |
+------------------+-------------+----------------+
| dataset.preamble | True | False |
+==================+=============+================+
| None | no preamble | 128 0x00 bytes |
+------------------+-------------+----------------+
| 128 bytes | dataset.preamble |
+------------------+------------------------------+
The prefix shall be the bytestring ``b'DICM'`` and will be written if and
only if the preamble is present.
**File Meta Information Group Elements**
The preamble and prefix are followed by a set of DICOM elements from the
(0002,eeee) group. Some of these elements are required (Type 1) while
others are optional (Type 3/1C). If `write_like_original` is ``True``
then the *File Meta Information Group* elements are all optional. See
:func:`~pydicom.filewriter.write_file_meta_info` for more information on
which elements are required.
The *File Meta Information Group* elements should be included within their
own :class:`~pydicom.dataset.Dataset` in the ``dataset.file_meta``
attribute.
If (0002,0010) *Transfer Syntax UID* is included then the user must ensure
its value is compatible with the values for the
``dataset.is_little_endian`` and ``dataset.is_implicit_VR`` attributes.
For example, if ``is_little_endian`` and ``is_implicit_VR`` are both
``True`` then the Transfer Syntax UID must be 1.2.840.10008.1.2 *Implicit
VR Little Endian*. See the DICOM Standard, Part 5,
:dcm:`Section 10<part05/chapter_10.html>` for more information on Transfer
Syntaxes.
*Encoding*
The preamble and prefix are encoding independent. The File Meta elements
are encoded as *Explicit VR Little Endian* as required by the DICOM
Standard.
**Dataset**
A DICOM Dataset representing a SOP Instance related to a DICOM Information
Object Definition. It is up to the user to ensure the `dataset` conforms
to the DICOM Standard.
*Encoding*
The `dataset` is encoded as specified by the ``dataset.is_little_endian``
and ``dataset.is_implicit_VR`` attributes. It's up to the user to ensure
these attributes are set correctly (as well as setting an appropriate
value for ``dataset.file_meta.TransferSyntaxUID`` if present).
Parameters
----------
filename : str or file-like
Name of file or the file-like to write the new DICOM file to.
dataset : pydicom.dataset.FileDataset
Dataset holding the DICOM information; e.g. an object read with
:func:`~pydicom.filereader.dcmread`.
write_like_original : bool, optional
If ``True`` (default), preserves the following information from
the Dataset (and may result in a non-conformant file):
- preamble -- if the original file has no preamble then none will be
written.
- file_meta -- if the original file was missing any required *File
Meta Information Group* elements then they will not be added or
written.
If (0002,0000) *File Meta Information Group Length* is present then
it may have its value updated.
- seq.is_undefined_length -- if original had delimiters, write them now
too, instead of the more sensible length characters
- is_undefined_length_sequence_item -- for datasets that belong to a
sequence, write the undefined length delimiters if that is
what the original had.
If ``False``, produces a file conformant with the DICOM File Format,
with explicit lengths for all elements.
Raises
------
AttributeError
If either ``dataset.is_implicit_VR`` or ``dataset.is_little_endian``
have not been set.
ValueError
If group 2 elements are in ``dataset`` rather than
``dataset.file_meta``, or if a preamble is given but is not 128 bytes
long, or if Transfer Syntax is a compressed type and pixel data is not
compressed.
See Also
--------
pydicom.dataset.FileDataset
Dataset class with relevant attributes and information.
pydicom.dataset.Dataset.save_as
Write a DICOM file from a dataset that was read in with ``dcmread()``.
``save_as()`` wraps ``dcmwrite()``.
"""
# Ensure is_little_endian and is_implicit_VR are set
if None in (dataset.is_little_endian, dataset.is_implicit_VR):
has_tsyntax = False
try:
tsyntax = dataset.file_meta.TransferSyntaxUID
if not tsyntax.is_private:
dataset.is_little_endian = tsyntax.is_little_endian
dataset.is_implicit_VR = tsyntax.is_implicit_VR
has_tsyntax = True
except AttributeError:
pass
if not has_tsyntax:
raise AttributeError(
"'{0}.is_little_endian' and '{0}.is_implicit_VR' must be "
"set appropriately before saving.".format(
dataset.__class__.__name__))
# Try and ensure that `is_undefined_length` is set correctly
try:
tsyntax = dataset.file_meta.TransferSyntaxUID
if not tsyntax.is_private:
dataset['PixelData'].is_undefined_length = tsyntax.is_compressed
except (AttributeError, KeyError):
pass
# Check that dataset's group 0x0002 elements are only present in the
# `dataset.file_meta` Dataset - user may have added them to the wrong
# place
if dataset.group_dataset(0x0002) != Dataset():
raise ValueError("File Meta Information Group Elements (0002,eeee) "
"should be in their own Dataset object in the "
"'{0}.file_meta' "
"attribute.".format(dataset.__class__.__name__))
# A preamble is required under the DICOM standard, however if
# `write_like_original` is True we treat it as optional
preamble = getattr(dataset, 'preamble', None)
if preamble and len(preamble) != 128:
raise ValueError("'{0}.preamble' must be 128-bytes "
"long.".format(dataset.__class__.__name__))
if not preamble and not write_like_original:
# The default preamble is 128 0x00 bytes.
preamble = b'\x00' * 128
# File Meta Information is required under the DICOM standard, however if
# `write_like_original` is True we treat it as optional
if not write_like_original:
# the checks will be done in write_file_meta_info()
dataset.fix_meta_info(enforce_standard=False)
else:
dataset.ensure_file_meta()
# Check for decompression, give warnings if inconsistencies
# If decompressed, then pixel_array is now used instead of PixelData
if dataset.is_decompressed:
xfer = dataset.file_meta.TransferSyntaxUID
if xfer not in UncompressedPixelTransferSyntaxes:
raise ValueError("file_meta transfer SyntaxUID is compressed type "
"but pixel data has been decompressed")
# Force PixelData to the decompressed version
dataset.PixelData = dataset.pixel_array.tobytes()
caller_owns_file = True
# Open file if not already a file object
if isinstance(filename, compat.string_types):
fp = DicomFile(filename, 'wb')
# caller provided a file name; we own the file handle
caller_owns_file = False
else:
fp = DicomFileLike(filename)
# if we want to write with the same endianess and VR handling as
# the read dataset we want to preserve raw data elements for
# performance reasons (which is done by get_item);
# otherwise we use the default converting item getter
if dataset.is_original_encoding:
get_item = Dataset.get_item
else:
get_item = Dataset.__getitem__
try:
# WRITE FILE META INFORMATION
if preamble:
# Write the 'DICM' prefix if and only if we write the preamble
fp.write(preamble)
fp.write(b'DICM')
if dataset.file_meta: # May be an empty Dataset
# If we want to `write_like_original`, don't enforce_standard
write_file_meta_info(fp,
dataset.file_meta,
enforce_standard=not write_like_original)
# WRITE DATASET
# The transfer syntax used to encode the dataset can't be changed
# within the dataset.
# Write any Command Set elements now as elements must be in tag order
# Mixing Command Set with other elements is non-conformant so we
# require `write_like_original` to be True
command_set = get_item(dataset, slice(0x00000000, 0x00010000))
if command_set and write_like_original:
fp.is_implicit_VR = True
fp.is_little_endian = True
write_dataset(fp, command_set)
# Set file VR and endianness. MUST BE AFTER writing META INFO (which
# requires Explicit VR Little Endian) and COMMAND SET (which requires
# Implicit VR Little Endian)
fp.is_implicit_VR = dataset.is_implicit_VR
fp.is_little_endian = dataset.is_little_endian
# Write non-Command Set elements now
write_dataset(fp, get_item(dataset, slice(0x00010000, None)))
finally:
if not caller_owns_file:
fp.close()
def dcmwrite(filename: Union[PathType, BinaryIO],
dataset: Dataset,
write_like_original: bool = True) -> None:
"""Write `dataset` to the `filename` specified.
If `write_like_original` is ``True`` then the :class:`Dataset` will be
written as is (after minimal validation checking) and may or may not
contain all or parts of the *File Meta Information* (and hence may or
may not be conformant with the DICOM File Format).
If `write_like_original` is ``False``, `dataset` will be stored in the
:dcm:`DICOM File Format <part10/chapter_7.html>`. To do
so requires that the ``Dataset.file_meta`` attribute
exists and contains a :class:`Dataset` with the required (Type 1) *File
Meta Information Group* elements. The byte stream of the `dataset` will be
placed into the file after the DICOM *File Meta Information*.
**File Meta Information**
The *File Meta Information* consists of a 128-byte preamble, followed by
a 4 byte ``b'DICM'`` prefix, followed by the *File Meta Information Group*
elements.
**Preamble and Prefix**
The ``dataset.preamble`` attribute shall be 128-bytes long or ``None`` and
is available for use as defined by the Application Profile or specific
implementations. If the preamble is not used by an Application Profile or
specific implementation then all 128 bytes should be set to ``0x00``. The
actual preamble written depends on `write_like_original` and
``dataset.preamble`` (see the table below).
+------------------+------------------------------+
| | write_like_original |
+------------------+-------------+----------------+
| dataset.preamble | True | False |
+==================+=============+================+
| None | no preamble | 128 0x00 bytes |
+------------------+-------------+----------------+
| 128 bytes | dataset.preamble |
+------------------+------------------------------+
The prefix shall be the bytestring ``b'DICM'`` and will be written if and
only if the preamble is present.
**File Meta Information Group Elements**
The preamble and prefix are followed by a set of DICOM elements from the
(0002,eeee) group. Some of these elements are required (Type 1) while
others are optional (Type 3/1C). If `write_like_original` is ``True``
then the *File Meta Information Group* elements are all optional. See
:func:`~pydicom.filewriter.write_file_meta_info` for more information on
which elements are required.
The *File Meta Information Group* elements should be included within their
own :class:`~pydicom.dataset.Dataset` in the ``dataset.file_meta``
attribute.
If (0002,0010) *Transfer Syntax UID* is included then the user must ensure
its value is compatible with the values for the
``dataset.is_little_endian`` and ``dataset.is_implicit_VR`` attributes.
For example, if ``is_little_endian`` and ``is_implicit_VR`` are both
``True`` then the Transfer Syntax UID must be 1.2.840.10008.1.2 *Implicit
VR Little Endian*. See the DICOM Standard, Part 5,
:dcm:`Section 10<part05/chapter_10.html>` for more information on Transfer
Syntaxes.
*Encoding*
The preamble and prefix are encoding independent. The File Meta elements
are encoded as *Explicit VR Little Endian* as required by the DICOM
Standard.
**Dataset**
A DICOM Dataset representing a SOP Instance related to a DICOM Information
Object Definition. It is up to the user to ensure the `dataset` conforms
to the DICOM Standard.
*Encoding*
The `dataset` is encoded as specified by the ``dataset.is_little_endian``
and ``dataset.is_implicit_VR`` attributes. It's up to the user to ensure
these attributes are set correctly (as well as setting an appropriate
value for ``dataset.file_meta.TransferSyntaxUID`` if present).
Parameters
----------
filename : str or PathLike or file-like
Name of file or the file-like to write the new DICOM file to.
dataset : pydicom.dataset.FileDataset
Dataset holding the DICOM information; e.g. an object read with
:func:`~pydicom.filereader.dcmread`.
write_like_original : bool, optional
If ``True`` (default), preserves the following information from
the Dataset (and may result in a non-conformant file):
- preamble -- if the original file has no preamble then none will be
written.
- file_meta -- if the original file was missing any required *File
Meta Information Group* elements then they will not be added or
written.
If (0002,0000) *File Meta Information Group Length* is present then
it may have its value updated.
- seq.is_undefined_length -- if original had delimiters, write them now
too, instead of the more sensible length characters
- is_undefined_length_sequence_item -- for datasets that belong to a
sequence, write the undefined length delimiters if that is
what the original had.
If ``False``, produces a file conformant with the DICOM File Format,
with explicit lengths for all elements.
Raises
------
AttributeError
If either ``dataset.is_implicit_VR`` or ``dataset.is_little_endian``
have not been set.
ValueError
If group 2 elements are in ``dataset`` rather than
``dataset.file_meta``, or if a preamble is given but is not 128 bytes
long, or if Transfer Syntax is a compressed type and pixel data is not
compressed.
See Also
--------
pydicom.dataset.Dataset
Dataset class with relevant attributes and information.
pydicom.dataset.Dataset.save_as
Write a DICOM file from a dataset that was read in with ``dcmread()``.
``save_as()`` wraps ``dcmwrite()``.
"""
# Ensure is_little_endian and is_implicit_VR are set
if None in (dataset.is_little_endian, dataset.is_implicit_VR):
has_tsyntax = False
try:
tsyntax = dataset.file_meta.TransferSyntaxUID
if not tsyntax.is_private:
dataset.is_little_endian = tsyntax.is_little_endian
dataset.is_implicit_VR = tsyntax.is_implicit_VR
has_tsyntax = True
except AttributeError:
pass
if not has_tsyntax:
name = dataset.__class__.__name__
raise AttributeError(
f"'{name}.is_little_endian' and '{name}.is_implicit_VR' must "
f"be set appropriately before saving")
# Try and ensure that `is_undefined_length` is set correctly
try:
tsyntax = dataset.file_meta.TransferSyntaxUID
if not tsyntax.is_private:
dataset['PixelData'].is_undefined_length = tsyntax.is_compressed
except (AttributeError, KeyError):
pass
# Check that dataset's group 0x0002 elements are only present in the
# `dataset.file_meta` Dataset - user may have added them to the wrong
# place
if dataset.group_dataset(0x0002) != Dataset():
raise ValueError(
f"File Meta Information Group Elements (0002,eeee) should be in "
f"their own Dataset object in the "
f"'{dataset.__class__.__name__}.file_meta' attribute.")
# A preamble is required under the DICOM standard, however if
# `write_like_original` is True we treat it as optional
preamble = getattr(dataset, 'preamble', None)
if preamble and len(preamble) != 128:
raise ValueError(
f"'{dataset.__class__.__name__}.preamble' must be 128-bytes long.")
if not preamble and not write_like_original:
# The default preamble is 128 0x00 bytes.
preamble = b'\x00' * 128
# File Meta Information is required under the DICOM standard, however if
# `write_like_original` is True we treat it as optional
if not write_like_original:
# the checks will be done in write_file_meta_info()
dataset.fix_meta_info(enforce_standard=False)
else:
dataset.ensure_file_meta()
# Check for decompression, give warnings if inconsistencies
# If decompressed, then pixel_array is now used instead of PixelData
if dataset.is_decompressed:
if dataset.file_meta.TransferSyntaxUID.is_compressed:
raise ValueError(
f"The Transfer Syntax UID element in "
f"'{dataset.__class__.__name__}.file_meta' is compressed "
f"but the pixel data has been decompressed")
# Force PixelData to the decompressed version
dataset.PixelData = dataset.pixel_array.tobytes()
caller_owns_file = True
# Open file if not already a file object
filename = path_from_pathlike(filename)
if isinstance(filename, str):
fp = DicomFile(filename, 'wb')
# caller provided a file name; we own the file handle
caller_owns_file = False
else:
try:
fp = DicomFileLike(filename)
except AttributeError:
raise TypeError("dcmwrite: Expected a file path or a file-like, "
"but got " + type(filename).__name__)
try:
# WRITE FILE META INFORMATION
if preamble:
# Write the 'DICM' prefix if and only if we write the preamble
fp.write(preamble)
fp.write(b'DICM')
tsyntax: Optional[UID] = None # type: ignore[no-redef]
if dataset.file_meta: # May be an empty Dataset
# If we want to `write_like_original`, don't enforce_standard
write_file_meta_info(fp,
dataset.file_meta,
enforce_standard=not write_like_original)
tsyntax = getattr(dataset.file_meta, "TransferSyntaxUID", None)
if (tsyntax == DeflatedExplicitVRLittleEndian):
# See PS3.5 section A.5
# when writing, the entire dataset following
# the file metadata is prepared the normal way,
# then "deflate" compression applied.
buffer = DicomBytesIO()
_write_dataset(buffer, dataset, write_like_original)
# Compress the encoded data and write to file
compressor = zlib.compressobj(wbits=-zlib.MAX_WBITS)
deflated = compressor.compress(
buffer.parent.getvalue() # type: ignore[union-attr]
)
deflated += compressor.flush()
if len(deflated) % 2:
deflated += b'\x00'
fp.write(deflated)
else:
_write_dataset(fp, dataset, write_like_original)
finally:
if not caller_owns_file:
fp.close()
def dcmwrite(filename, dataset, write_like_original=True):
"""Write `dataset` to the `filename` specified.
If `write_like_original` is True then `dataset` will be written as is
(after minimal validation checking) and may or may not contain all or parts
of the File Meta Information (and hence may or may not be conformant with
the DICOM File Format).
If `write_like_original` is False, `dataset` will be stored in the DICOM
File Format in accordance with DICOM Standard Part 10 Section 7. The byte
stream of the `dataset` will be placed into the file after the DICOM File
Meta Information.
File Meta Information
---------------------
The File Meta Information consists of a 128-byte preamble, followed by a 4
byte DICOM prefix, followed by the File Meta Information Group elements.
Preamble and Prefix
~~~~~~~~~~~~~~~~~~~
The `dataset.preamble` attribute shall be 128-bytes long or None and is
available for use as defined by the Application Profile or specific
implementations. If the preamble is not used by an Application Profile or
specific implementation then all 128 bytes should be set to 0x00. The
actual preamble written depends on `write_like_original` and
`dataset.preamble` (see the table below).
+------------------+------------------------------+
| | write_like_original |
+------------------+-------------+----------------+
| dataset.preamble | True | False |
+==================+=============+================+
| None | no preamble | 128 0x00 bytes |
+------------------+------------------------------+
| 128 bytes | dataset.preamble |
+------------------+------------------------------+
The prefix shall be the string 'DICM' and will be written if and only if
the preamble is present.
File Meta Information Group Elements
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The preamble and prefix are followed by a set of DICOM Elements from the
(0002,eeee) group. Some of these elements are required (Type 1) while
others are optional (Type 3/1C). If `write_like_original` is True then the
File Meta Information Group elements are all optional. See
pydicom.filewriter.write_file_meta_info for more information on which
elements are required.
The File Meta Information Group elements should be included within their
own Dataset in the `dataset.file_meta` attribute.
If (0002,0010) 'Transfer Syntax UID' is included then the user must ensure
it's value is compatible with the values for the `dataset.is_little_endian`
and `dataset.is_implicit_VR` attributes. For example, if is_little_endian
and is_implicit_VR are both True then the Transfer Syntax UID must be
1.2.840.10008.1.2 'Implicit VR Little Endian'. See the DICOM standard
Part 5 Section 10 for more information on Transfer Syntaxes.
Encoding
~~~~~~~~
The preamble and prefix are encoding independent. The File Meta Elements
are encoded as Explicit VR Little Endian as required by the DICOM standard.
Dataset
-------
A DICOM Dataset representing a SOP Instance related to a DICOM Information
Object Definition. It is up to the user to ensure the `dataset` conforms
to the DICOM standard.
Encoding
~~~~~~~~
The `dataset` is encoded as specified by the `dataset.is_little_endian`
and `dataset.is_implicit_VR` attributes. It's up to the user to ensure
these attributes are set correctly (as well as setting an appropriate value
for `dataset.file_meta.TransferSyntaxUID` if present).
Parameters
----------
filename : str or file-like
Name of file or the file-like to write the new DICOM file to.
dataset : pydicom.dataset.FileDataset
Dataset holding the DICOM information; e.g. an object read with
pydicom.dcmread().
write_like_original : bool
If True (default), preserves the following information from
the Dataset (and may result in a non-conformant file):
- preamble -- if the original file has no preamble then none will be
written.
- file_meta -- if the original file was missing any required File Meta
Information Group elements then they will not be added or written.
If (0002,0000) 'File Meta Information Group Length' is present then
it may have its value updated.
- seq.is_undefined_length -- if original had delimiters, write them now
too, instead of the more sensible length characters
- is_undefined_length_sequence_item -- for datasets that belong to a
sequence, write the undefined length delimiters if that is
what the original had.
If False, produces a file conformant with the DICOM File Format, with
explicit lengths for all elements.
See Also
--------
pydicom.dataset.FileDataset
Dataset class with relevant attributes and information.
pydicom.dataset.Dataset.save_as
Write a DICOM file from a dataset that was read in with dcmread().
save_as wraps dcmwrite.
"""
# Check that dataset's group 0x0002 elements are only present in the
# `dataset.file_meta` Dataset - user may have added them to the wrong
# place
if dataset.group_dataset(0x0002) != Dataset():
raise ValueError("File Meta Information Group Elements (0002,eeee) "
"should be in their own Dataset object in the "
"'{0}.file_meta' "
"attribute.".format(dataset.__class__.__name__))
# A preamble is required under the DICOM standard, however if
# `write_like_original` is True we treat it as optional
preamble = getattr(dataset, 'preamble', None)
if preamble and len(preamble) != 128:
raise ValueError("'{0}.preamble' must be 128-bytes "
"long.".format(dataset.__class__.__name__))
if not preamble and not write_like_original:
# The default preamble is 128 0x00 bytes.
preamble = b'\x00' * 128
# File Meta Information is required under the DICOM standard, however if
# `write_like_original` is True we treat it as optional
file_meta = getattr(dataset, 'file_meta', None)
if not file_meta and not write_like_original:
dataset.file_meta = Dataset()
file_meta = dataset.file_meta
# If enforcing the standard, correct the TransferSyntaxUID where possible,
# noting that the transfer syntax for is_implicit_VR = False and
# is_little_endian = True is ambiguous as it may be an encapsulated
# transfer syntax
if not write_like_original:
if dataset.is_little_endian and dataset.is_implicit_VR:
file_meta.TransferSyntaxUID = ImplicitVRLittleEndian
elif not dataset.is_little_endian and not dataset.is_implicit_VR:
file_meta.TransferSyntaxUID = ExplicitVRBigEndian
elif not dataset.is_little_endian and dataset.is_implicit_VR:
raise NotImplementedError("Implicit VR Big Endian is not a"
"supported Transfer Syntax.")
if 'SOPClassUID' in dataset:
file_meta.MediaStorageSOPClassUID = dataset.SOPClassUID
if 'SOPInstanceUID' in dataset:
file_meta.MediaStorageSOPInstanceUID = dataset.SOPInstanceUID
caller_owns_file = True
# Open file if not already a file object
if isinstance(filename, compat.string_types):
fp = DicomFile(filename, 'wb')
# caller provided a file name; we own the file handle
caller_owns_file = False
else:
fp = DicomFileLike(filename)
try:
# WRITE FILE META INFORMATION
if preamble:
# Write the 'DICM' prefix if and only if we write the preamble
fp.write(preamble)
fp.write(b'DICM')
if file_meta is not None: # May be an empty Dataset
# If we want to `write_like_original`, don't enforce_standard
write_file_meta_info(fp,
file_meta,
enforce_standard=not write_like_original)
# WRITE DATASET
# The transfer syntax used to encode the dataset can't be changed
# within the dataset.
# Write any Command Set elements now as elements must be in tag order
# Mixing Command Set with other elements is non-conformant so we
# require `write_like_original` to be True
command_set = dataset[0x00000000:0x00010000]
if command_set and write_like_original:
fp.is_implicit_VR = True
fp.is_little_endian = True
write_dataset(fp, command_set)
# Set file VR and endianness. MUST BE AFTER writing META INFO (which
# requires Explicit VR Little Endian) and COMMAND SET (which requires
# Implicit VR Little Endian)
fp.is_implicit_VR = dataset.is_implicit_VR
fp.is_little_endian = dataset.is_little_endian
# Write non-Command Set elements now
write_dataset(fp, dataset[0x00010000:])
finally:
if not caller_owns_file:
fp.close()
def test_context(self):
"""Test using DicomFileLike as a context"""
with DicomFileLike(BytesIO(b'\x00\x01')) as fp:
assert fp.parent_read(2) == b'\x00\x01'
def test_init_good_parent(self):
"""Test methods are set OK if parent is good"""
fp = DicomFileLike(BytesIO())
assert fp.parent_read == fp.parent.read
assert fp.write == fp.parent.write
assert fp.seek == fp.parent.seek
def generate_pixel_data_fragment(
fp: DicomFileLike) -> Generator[bytes, None, None]:
"""Yield the encapsulated pixel data fragments.
For compressed (encapsulated) Transfer Syntaxes, the (7FE0,0010) *Pixel
Data* element is encoded in an encapsulated format.
**Encapsulation**
The encoded pixel data stream is fragmented into one or more Items. The
stream may represent a single or multi-frame image.
Each *Data Stream Fragment* shall have tag of (FFFE,E000), followed by a 4
byte *Item Length* field encoding the explicit number of bytes in the Item.
All Items containing an encoded fragment shall have an even number of bytes
greater than or equal to 2, with the last fragment being padded if
necessary.
The first Item in the Sequence of Items shall be a 'Basic Offset Table',
however the Basic Offset Table item value is not required to be present.
It is assumed that the Basic Offset Table item has already been read prior
to calling this function (and that `fp` is positioned past this item).
The remaining items in the Sequence of Items are the pixel data fragments
and it is these items that will be read and returned by this function.
The Sequence of Items is terminated by a (FFFE,E0DD) *Sequence Delimiter
Item* with an Item Length field of value ``0x00000000``. The presence
or absence of the *Sequence Delimiter Item* in `fp` has no effect on the
returned fragments.
*Encoding*
The encoding of the data shall be little endian.
Parameters
----------
fp : filebase.DicomFileLike
The encoded (7FE0,0010) *Pixel Data* element value, positioned at the
start of the item tag for the first item after the Basic Offset Table
item. ``fp.is_little_endian`` should be set to ``True``.
Yields
------
bytes
A pixel data fragment.
Raises
------
ValueError
If the data contains an item with an undefined length or an unknown
tag.
References
----------
DICOM Standard Part 5, :dcm:`Annex A.4 <part05/sect_A.4.html>`
"""
if not fp.is_little_endian:
raise ValueError("'fp.is_little_endian' must be True")
# We should be positioned at the start of the Item Tag for the first
# fragment after the Basic Offset Table
while True:
try:
tag = Tag(fp.read_tag())
except EOFError:
break
if tag == 0xFFFEE000:
# Item
length = fp.read_UL()
if length == 0xFFFFFFFF:
raise ValueError(
f"Undefined item length at offset {fp.tell() - 4} when "
"parsing the encapsulated pixel data fragments")
yield fp.read(length)
elif tag == 0xFFFEE0DD:
# Sequence Delimiter
# Behave nicely and rewind back to the end of the items
fp.seek(-4, 1)
break
else:
raise ValueError(
f"Unexpected tag '{tag}' at offset {fp.tell() - 4} when "
"parsing the encapsulated pixel data fragment items")
def get_frame_offsets(fp: DicomFileLike) -> Tuple[bool, List[int]]:
"""Return a list of the fragment offsets from the Basic Offset Table.
**Basic Offset Table**
The Basic Offset Table Item must be present and have a tag (FFFE,E000) and
a length, however it may or may not have a value.
Basic Offset Table with no value
::
Item Tag | Length |
FE FF 00 E0 00 00 00 00
Basic Offset Table with value (2 frames)
::
Item Tag | Length | Offset 1 | Offset 2 |
FE FF 00 E0 08 00 00 00 00 00 00 00 10 00 00 00
For single or multi-frame images with only one frame, the Basic Offset
Table may or may not have a value. When it has no value then its length
shall be ``0x00000000``.
For multi-frame images with more than one frame, the Basic Offset Table
should have a value containing concatenated 32-bit unsigned integer values
that are the byte offsets to the first byte of the Item tag of the first
fragment of each frame as measured from the first byte of the first item
tag following the Basic Offset Table Item.
All decoders, both for single and multi-frame images should accept both
an empty Basic Offset Table and one containing offset values.
.. versionchanged:: 1.4
Changed to return (is BOT empty, list of offsets).
Parameters
----------
fp : filebase.DicomFileLike
The encapsulated pixel data positioned at the start of the Basic Offset
Table. ``fp.is_little_endian`` should be set to ``True``.
Returns
-------
bool, list of int
Whether or not the BOT is empty, and a list of the byte offsets
to the first fragment of each frame, as measured from the start of the
first item following the Basic Offset Table item.
Raises
------
ValueError
If the Basic Offset Table item's tag is not (FFEE,E000) or if the
length in bytes of the item's value is not a multiple of 4.
References
----------
DICOM Standard, Part 5, :dcm:`Annex A.4 <part05/sect_A.4.html>`
"""
if not fp.is_little_endian:
raise ValueError("'fp.is_little_endian' must be True")
tag = Tag(fp.read_tag())
if tag != 0xfffee000:
raise ValueError(
f"Unexpected tag '{tag}' when parsing the Basic Table Offset item")
length = fp.read_UL()
if length % 4:
raise ValueError(
"The length of the Basic Offset Table item is not a multiple of 4")
offsets = []
# Always return at least a 0 offset
if length == 0:
offsets.append(0)
for ii in range(length // 4):
offsets.append(fp.read_UL())
return bool(length), offsets
