def read_dataset(fp, is_implicit_VR, is_little_endian, bytelength=None,
stop_when=None, defer_size=None,
parent_encoding=default_encoding, specific_tags=None):
"""Return a Dataset instance containing the next dataset in the file.
Parameters
----------
fp : an opened file object
is_implicit_VR : boolean
True if file transfer syntax is implicit VR.
is_little_endian : boolean
True if file has little endian transfer syntax.
bytelength : int, None, optional
None to read until end of file or ItemDeliterTag, else
a fixed number of bytes to read
stop_when : None, optional
optional call_back function which can terminate reading.
See help for data_element_generator for details
defer_size : int, None, optional
Size to avoid loading large elements in memory.
See ``dcmread`` for more parameter info.
parent_encoding :
optional encoding to use as a default in case
a Specific Character Set (0008,0005) isn't specified
specific_tags : list or None
See ``dcmread`` for parameter info.
Returns
-------
a Dataset instance
See Also
--------
pydicom.dataset.Dataset
A collection (dictionary) of Dicom `DataElement` instances.
"""
raw_data_elements = dict()
fpStart = fp.tell()
de_gen = data_element_generator(fp, is_implicit_VR, is_little_endian,
stop_when, defer_size, parent_encoding,
specific_tags)
try:
while (bytelength is None) or (fp.tell() - fpStart < bytelength):
raw_data_element = next(de_gen)
# Read data elements. Stop on some errors, but return what was read
tag = raw_data_element.tag
# Check for ItemDelimiterTag --dataset is an item in a sequence
if tag == (0xFFFE, 0xE00D):
break
raw_data_elements[tag] = raw_data_element
except StopIteration:
pass
except EOFError as details:
# XXX is this error visible enough to user code with just logging?
logger.error(str(details) + " in file " +
getattr(fp, "name", "<no filename>"))
except NotImplementedError as details:
logger.error(details)
return Dataset(raw_data_elements)
def read_dataset(fp, is_implicit_VR, is_little_endian, bytelength=None,
stop_when=None, defer_size=None,
parent_encoding=default_encoding, specific_tags=None):
"""Return a Dataset instance containing the next dataset in the file.
Parameters
----------
fp : an opened file object
is_implicit_VR : boolean
True if file transfer syntax is implicit VR.
is_little_endian : boolean
True if file has little endian transfer syntax.
bytelength : int, None, optional
None to read until end of file or ItemDeliterTag, else
a fixed number of bytes to read
stop_when : None, optional
optional call_back function which can terminate reading.
See help for data_element_generator for details
defer_size : int, None, optional
Size to avoid loading large elements in memory.
See ``read_file`` for more parameter info.
parent_encoding :
optional encoding to use as a default in case
a Specific Character Set (0008,0005) isn't specified
specific_tags : list or None
See ``read_file`` for parameter info.
Returns
-------
a Dataset instance
See Also
--------
pydicom.dataset.Dataset
A collection (dictionary) of Dicom `DataElement` instances.
"""
raw_data_elements = dict()
fpStart = fp.tell()
de_gen = data_element_generator(fp, is_implicit_VR, is_little_endian,
stop_when, defer_size, parent_encoding,
specific_tags)
try:
while (bytelength is None) or (fp.tell() - fpStart < bytelength):
raw_data_element = next(de_gen)
# Read data elements. Stop on some errors, but return what was read
tag = raw_data_element.tag
# Check for ItemDelimiterTag --dataset is an item in a sequence
if tag == (0xFFFE, 0xE00D):
break
raw_data_elements[tag] = raw_data_element
except StopIteration:
pass
except EOFError as details:
# XXX is this error visible enough to user code with just logging?
logger.error(str(details) + " in file " +
getattr(fp, "name", "<no filename>"))
except NotImplementedError as details:
logger.error(details)
return Dataset(raw_data_elements)
def read_dataset(fp,
is_implicit_VR,
is_little_endian,
bytelength=None,
stop_when=None,
defer_size=None,
parent_encoding=default_encoding,
specific_tags=None,
at_top_level=True):
"""Return a :class:`~pydicom.dataset.Dataset` instance containing the next
dataset in the file.
Parameters
----------
fp : file-like
An opened file-like object.
is_implicit_VR : bool
``True`` if file transfer syntax is implicit VR.
is_little_endian : bool
``True`` if file has little endian transfer syntax.
bytelength : int, None, optional
``None`` to read until end of file or ItemDeliterTag, else a fixed
number of bytes to read
stop_when : None, optional
Optional call_back function which can terminate reading. See help for
:func:`data_element_generator` for details
defer_size : int, None, optional
Size to avoid loading large elements in memory. See :func:`dcmread` for
more parameter info.
parent_encoding :
Optional encoding to use as a default in case (0008,0005) *Specific
Character Set* isn't specified.
specific_tags : list or None
See :func:`dcmread` for parameter info.
at_top_level: bool
If dataset is top level (not within a sequence).
Used to turn off explicit VR heuristic within sequences
Returns
-------
dataset.Dataset
A Dataset instance.
See Also
--------
:class:`~pydicom.dataset.Dataset`
A collection (dictionary) of DICOM
:class:`~pydicom.dataelem.DataElement` instances.
"""
raw_data_elements = dict()
fp_start = fp.tell()
if at_top_level:
is_implicit_VR = _is_implicit_vr(fp, is_implicit_VR, is_little_endian,
stop_when)
fp.seek(fp_start)
de_gen = data_element_generator(fp, is_implicit_VR, is_little_endian,
stop_when, defer_size, parent_encoding,
specific_tags)
try:
while (bytelength is None) or (fp.tell() - fp_start < bytelength):
raw_data_element = next(de_gen)
# Read data elements. Stop on some errors, but return what was read
tag = raw_data_element.tag
# Check for ItemDelimiterTag --dataset is an item in a sequence
if tag == BaseTag(0xFFFEE00D):
break
raw_data_elements[tag] = raw_data_element
except StopIteration:
pass
except EOFError as details:
if config.enforce_valid_values:
raise
msg = str(details) + " in file " + getattr(fp, "name", "<no filename>")
warnings.warn(msg, UserWarning)
except NotImplementedError as details:
logger.error(details)
ds = Dataset(raw_data_elements)
if 0x00080005 in raw_data_elements:
char_set = DataElement_from_raw(raw_data_elements[0x00080005])
encoding = convert_encodings(char_set)
else:
encoding = parent_encoding
ds.set_original_encoding(is_implicit_VR, is_little_endian, encoding)
return ds
def read_undefined_length_value(fp,
is_little_endian,
delimiter_tag,
defer_size=None,
read_size=1024 * 8):
"""Read until the delimiter tag found and return the value;
ignore the delimiter.
On completion, the file will be set to the first byte after the delimiter
and its following four zero bytes.
Parameters
----------
fp : a file-like object
is_little_endian : boolean
True if file transfer syntax is little endian, else False.
delimiter_tag : BaseTag
tag used as and marker for reading
defer_size : int, None, optional
Size to avoid loading large elements in memory.
See ``filereader.dcmread`` for more parameter info.
read_size : int
Number of bytes to read at one time.
Returns
-------
delimiter : str, None
The file delimiter
Raises
------
EOFError
If EOF is reached before delimiter found.
"""
data_start = fp.tell()
search_rewind = 3
if is_little_endian:
bytes_format = b"<HH"
else:
bytes_format = b">HH"
bytes_to_find = pack(bytes_format, delimiter_tag.group, delimiter_tag.elem)
found = False
eof = False
value_chunks = []
defer_size = size_in_bytes(defer_size)
byte_count = 0 # for defer_size checks
while not found:
chunk_start = fp.tell()
bytes_read = fp.read(read_size)
if len(bytes_read) < read_size:
# try again - if still don't get required amount,
# this is the last block
new_bytes = fp.read(read_size - len(bytes_read))
bytes_read += new_bytes
if len(bytes_read) < read_size:
eof = True # but will still check whatever we did get
index = bytes_read.find(bytes_to_find)
if index != -1:
found = True
new_bytes = bytes_read[:index]
byte_count += len(new_bytes)
if defer_size is None or byte_count < defer_size:
value_chunks.append(bytes_read[:index])
fp.seek(chunk_start + index + 4) # rewind to end of delimiter
length = fp.read(4)
if length != b"\0\0\0\0":
msg = ("Expected 4 zero bytes after undefined length delimiter"
" at pos {0:04x}")
logger.error(msg.format(fp.tell() - 4))
elif eof:
fp.seek(data_start)
raise EOFError(
"End of file reached before delimiter {0!r} found".format(
delimiter_tag))
else:
# rewind a bit in case delimiter crossed read_size boundary
fp.seek(fp.tell() - search_rewind)
# accumulate the bytes read (not including the rewind)
new_bytes = bytes_read[:-search_rewind]
byte_count += len(new_bytes)
if defer_size is None or byte_count < defer_size:
value_chunks.append(new_bytes)
# if get here then have found the byte string
if defer_size is not None and byte_count >= defer_size:
return None
else:
return b"".join(value_chunks)
def from_json(cls,
dataset_class,
tag,
vr,
value,
value_key,
bulk_data_uri_handler=None,
encodings=None):
"""Creates a DataElement from JSON.
Parameters
----------
dataset_class: Dataset derived class
class used to create sequence items
tag: pydicom.tag.Tag
data element tag
vr: str
data element value representation
value: list
data element value(s)
value_key: Union[str, None]
key of the data element that contains the value
(options: ``{"Value", "InlineBinary", "BulkDataURI"}``)
bulk_data_uri_handler: Union[Callable, None]
callable that accepts the "BulkDataURI" of the JSON representation
of a data element and returns the actual value of that data element
(retrieved via DICOMweb WADO-RS)
Returns
-------
pydicom.dataelem.DataElement
"""
# TODO: test wado-rs retrieve wrapper
try:
vm = dictionary_VM(tag)
except KeyError:
# Private tag
vm = str(len(value))
if value_key == 'Value':
if not (isinstance(value, list)):
fmt = '"{}" of data element "{}" must be a list.'
raise TypeError(fmt.format(value_key, tag))
elif value_key in {'InlineBinary', 'BulkDataURI'}:
if isinstance(value, list):
fmt = '"{}" of data element "{}" must be a {}.'
expected_type = ('string' if value_key == 'BulkDataURI' else
'bytes-like object')
raise TypeError(fmt.format(value_key, tag, expected_type))
if vr == 'SQ':
elem_value = []
for value_item in value:
ds = dataset_class()
if value_item:
for key, val in value_item.items():
if 'vr' not in val:
fmt = 'Data element "{}" must have key "vr".'
raise KeyError(fmt.format(tag))
unique_value_keys = tuple(
set(val.keys()) & set(jsonrep.JSON_VALUE_KEYS))
if len(unique_value_keys) == 0:
logger.debug(
'data element has neither key "{}".'.format(
'" nor "'.join(jsonrep.JSON_VALUE_KEYS)))
elem = DataElement(tag=tag, value='', VR=vr)
else:
value_key = unique_value_keys[0]
elem = cls.from_json(dataset_class, key, val['vr'],
val[value_key], value_key)
ds.add(elem)
elem_value.append(ds)
elif vr == 'PN':
# Special case, see DICOM Part 18 Annex F2.2
elem_value = []
for v in value:
if not isinstance(v, dict):
# Some DICOMweb services get this wrong, so we
# workaround the issue and warn the user
# rather than raising an error.
logger.error(
'value of data element "{}" with VR Person Name (PN) '
'is not formatted correctly'.format(tag))
elem_value.append(v)
else:
elem_value.extend(list(v.values()))
if vm == '1':
try:
elem_value = elem_value[0]
except IndexError:
elem_value = ''
else:
if vm == '1':
if value_key == 'InlineBinary':
elem_value = base64.b64decode(value)
elif value_key == 'BulkDataURI':
if bulk_data_uri_handler is None:
logger.warning(
'no bulk data URI handler provided for retrieval '
'of value of data element "{}"'.format(tag))
elem_value = b''
else:
elem_value = bulk_data_uri_handler(value)
else:
if value:
elem_value = value[0]
else:
elem_value = value
else:
elem_value = value
if elem_value is None:
logger.warning('missing value for data element "{}"'.format(tag))
elem_value = ''
elem_value = jsonrep.convert_to_python_number(elem_value, vr)
try:
if compat.in_py2 and vr == "PN":
elem_value = PersonNameUnicode(elem_value, 'UTF8')
return DataElement(tag=tag, value=elem_value, VR=vr)
except Exception:
raise ValueError(
'Data element "{}" could not be loaded from JSON: {}'.format(
tag, elem_value))
def read_undefined_length_value(fp,
is_little_endian,
delimiter_tag,
defer_size=None,
read_size=1024*8):
"""Read until the delimiter tag found and return the value;
ignore the delimiter.
On completion, the file will be set to the first byte after the delimiter
and its following four zero bytes.
Parameters
----------
fp : a file-like object
is_little_endian : boolean
True if file transfer syntax is little endian, else False.
delimiter_tag : BaseTag
tag used as and marker for reading
defer_size : int, None, optional
Size to avoid loading large elements in memory.
See ``filereader.read_file`` for more parameter info.
read_size : int
Number of bytes to read at one time.
Returns
-------
delimiter : str, None
The file delimiter
Raises
------
EOFError
If EOF is reached before delimiter found.
"""
data_start = fp.tell()
search_rewind = 3
if is_little_endian:
bytes_format = b"<HH"
else:
bytes_format = b">HH"
bytes_to_find = pack(bytes_format, delimiter_tag.group, delimiter_tag.elem)
found = False
eof = False
value_chunks = []
defer_size = size_in_bytes(defer_size)
byte_count = 0 # for defer_size checks
while not found:
chunk_start = fp.tell()
bytes_read = fp.read(read_size)
if len(bytes_read) < read_size:
# try again - if still don't get required amount,
# this is the last block
new_bytes = fp.read(read_size - len(bytes_read))
bytes_read += new_bytes
if len(bytes_read) < read_size:
eof = True # but will still check whatever we did get
index = bytes_read.find(bytes_to_find)
if index != -1:
found = True
new_bytes = bytes_read[:index]
byte_count += len(new_bytes)
if defer_size is None or byte_count < defer_size:
value_chunks.append(bytes_read[:index])
fp.seek(chunk_start + index + 4) # rewind to end of delimiter
length = fp.read(4)
if length != b"\0\0\0\0":
msg = ("Expected 4 zero bytes after undefined length delimiter"
" at pos {0:04x}")
logger.error(msg.format(fp.tell() - 4))
elif eof:
fp.seek(data_start)
raise EOFError("End of file reached before delimiter {0!r} found".
format(delimiter_tag))
else:
# rewind a bit in case delimiter crossed read_size boundary
fp.seek(fp.tell() - search_rewind)
# accumulate the bytes read (not including the rewind)
new_bytes = bytes_read[:-search_rewind]
byte_count += len(new_bytes)
if defer_size is None or byte_count < defer_size:
value_chunks.append(new_bytes)
# if get here then have found the byte string
if defer_size is not None and byte_count >= defer_size:
return None
else:
return b"".join(value_chunks)
def read_dataset(fp: BinaryIO,
is_implicit_VR: bool,
is_little_endian: bool,
bytelength: Optional[int] = None,
stop_when: Optional[Callable[[BaseTag, Optional[str], int],
bool]] = None,
defer_size: Optional[Union[str, int, float]] = None,
parent_encoding: Union[
str, MutableSequence[str]] = default_encoding,
specific_tags: Optional[List[BaseTag]] = None,
at_top_level: bool = True) -> Dataset:
"""Return a :class:`~pydicom.dataset.Dataset` instance containing the next
dataset in the file.
Parameters
----------
fp : file-like
An opened file-like object.
is_implicit_VR : bool
``True`` if file transfer syntax is implicit VR.
is_little_endian : bool
``True`` if file has little endian transfer syntax.
bytelength : int, None, optional
``None`` to read until end of file or ItemDeliterTag, else a fixed
number of bytes to read
stop_when : None, optional
Optional call_back function which can terminate reading. See help for
:func:`data_element_generator` for details
defer_size : int, str or float, optional
Size to avoid loading large elements in memory. See :func:`dcmread` for
more parameter info.
parent_encoding : str or List[str]
Optional encoding to use as a default in case (0008,0005) *Specific
Character Set* isn't specified.
specific_tags : list of BaseTag, optional
See :func:`dcmread` for parameter info.
at_top_level: bool
If dataset is top level (not within a sequence).
Used to turn off explicit VR heuristic within sequences
Returns
-------
dataset.Dataset
A Dataset instance.
See Also
--------
:class:`~pydicom.dataset.Dataset`
A collection (dictionary) of DICOM
:class:`~pydicom.dataelem.DataElement` instances.
"""
raw_data_elements: Dict[BaseTag, Union[RawDataElement, DataElement]] = {}
fp_start = fp.tell()
is_implicit_VR = _is_implicit_vr(fp,
is_implicit_VR,
is_little_endian,
stop_when,
is_sequence=not at_top_level)
fp.seek(fp_start)
de_gen = data_element_generator(
fp,
is_implicit_VR,
is_little_endian,
stop_when,
defer_size,
parent_encoding,
specific_tags,
)
try:
while (bytelength is None) or (fp.tell() - fp_start < bytelength):
raw_data_element = next(de_gen)
# Read data elements. Stop on some errors, but return what was read
tag = raw_data_element.tag
# Check for ItemDelimiterTag --dataset is an item in a sequence
if tag == BaseTag(0xFFFEE00D):
break
raw_data_elements[tag] = raw_data_element
except StopIteration:
pass
except EOFError as details:
if config.settings.reading_validation_mode == config.RAISE:
raise
msg = str(details) + " in file " + getattr(fp, "name", "<no filename>")
warnings.warn(msg, UserWarning)
except NotImplementedError as details:
logger.error(details)
ds = Dataset(raw_data_elements)
encoding: Union[str, MutableSequence[str]]
if 0x00080005 in raw_data_elements:
elem = cast(RawDataElement, raw_data_elements[BaseTag(0x00080005)])
char_set = cast(Optional[Union[str, MutableSequence[str]]],
DataElement_from_raw(elem).value)
encoding = convert_encodings(char_set) # -> List[str]
else:
encoding = parent_encoding # -> Union[str, MutableSequence[str]]
ds.set_original_encoding(is_implicit_VR, is_little_endian, encoding)
return ds
def read_undefined_length_value(fp: BinaryIO,
is_little_endian: bool,
delimiter_tag: BaseTag,
defer_size: Optional[Union[int, float]] = None,
read_size: int = 1024 * 8) -> Optional[bytes]:
"""Read until `delimiter_tag` and return the value up to that point.
On completion, the file will be set to the first byte after the delimiter
and its following four zero bytes.
Parameters
----------
fp : file-like
The file-like to read.
is_little_endian : bool
``True`` if file transfer syntax is little endian, else ``False``.
delimiter_tag : BaseTag
Tag used as end marker for reading
defer_size : int or None, optional
Size to avoid loading large elements in memory. See
:func:`~pydicom.filereader.dcmread` for more parameter info.
read_size : int, optional
Number of bytes to read at one time.
Returns
-------
delimiter : bytes or None
The file delimiter.
Raises
------
EOFError
If EOF is reached before delimiter found.
"""
data_start = fp.tell()
defer_size = size_in_bytes(defer_size)
# It's common for an undefined length value item to be an
# encapsulated pixel data as defined in PS3.5 section A.4.
# Attempt to parse the data under that assumption, since the method
# 1. is proof against coincidental embedded sequence delimiter tags
# 2. avoids accumulating any data in memory if the element is large
# enough to be deferred
# 3. does not double-accumulate data (in chunks and then joined)
#
# Unfortunately, some implementations deviate from the standard and the
# encapsulated pixel data-parsing algorithm fails. In that case, we fall
# back to a method of scanning the entire element value for the
# sequence delimiter, as was done historically.
if delimiter_tag == SequenceDelimiterTag:
was_value_found, value = _try_read_encapsulated_pixel_data(
fp, is_little_endian, defer_size)
if was_value_found:
return value
search_rewind = 3
if is_little_endian:
bytes_format = b"<HH"
else:
bytes_format = b">HH"
bytes_to_find = pack(bytes_format, delimiter_tag.group, delimiter_tag.elem)
found = False
eof = False
value_chunks = []
byte_count = 0 # for defer_size checks
while not found:
chunk_start = fp.tell()
bytes_read = fp.read(read_size)
if len(bytes_read) < read_size:
# try again - if still don't get required amount,
# this is the last block
new_bytes = fp.read(read_size - len(bytes_read))
bytes_read += new_bytes
if len(bytes_read) < read_size:
eof = True # but will still check whatever we did get
index = bytes_read.find(bytes_to_find)
if index != -1:
found = True
new_bytes = bytes_read[:index]
byte_count += len(new_bytes)
if defer_size is None or byte_count < defer_size:
value_chunks.append(new_bytes)
fp.seek(chunk_start + index + 4) # rewind to end of delimiter
length = fp.read(4)
if length != b"\0\0\0\0":
msg = ("Expected 4 zero bytes after undefined length delimiter"
" at pos {0:04x}")
logger.error(msg.format(fp.tell() - 4))
elif eof:
fp.seek(data_start)
raise EOFError(
"End of file reached before delimiter {0!r} found".format(
delimiter_tag))
else:
# rewind a bit in case delimiter crossed read_size boundary
fp.seek(fp.tell() - search_rewind)
# accumulate the bytes read (not including the rewind)
new_bytes = bytes_read[:-search_rewind]
byte_count += len(new_bytes)
if defer_size is None or byte_count < defer_size:
value_chunks.append(new_bytes)
# if get here then have found the byte string
if defer_size is not None and byte_count >= defer_size:
return None
else:
return b"".join(value_chunks)