def write_data_element(fp, data_element, encoding=default_encoding):
"""Write the data_element to file fp according to dicom media storage rules.
"""
fp.write_tag(data_element.tag)
VR = data_element.VR
if not fp.is_implicit_VR:
if len(VR) != 2:
msg = "Cannot write ambiguous VR of '%s' for data element with tag %r." % (VR, data_element.tag)
msg += "\nSet the correct VR before writing, or use an implicit VR transfer syntax"
raise ValueError(msg)
if in_py3:
fp.write(bytes(VR, default_encoding))
else:
fp.write(VR)
if VR in extra_length_VRs:
fp.write_US(0) # reserved 2 bytes
if VR not in writers:
raise NotImplementedError("write_data_element: unknown Value Representation '{0}'".format(VR))
length_location = fp.tell() # save location for later.
if not fp.is_implicit_VR and VR not in ['OB', 'OW', 'OF', 'SQ', 'UT', 'UN']:
fp.write_US(0) # Explicit VR length field is only 2 bytes
else:
fp.write_UL(0xFFFFFFFFL) # will fill in real length value later if not undefined length item
encoding = convert_encodings(encoding)
writer_function, writer_param = writers[VR]
if VR in text_VRs:
writer_function(fp, data_element, encoding=encoding[1])
elif VR in ('PN', 'SQ'):
writer_function(fp, data_element, encoding=encoding)
else:
# Many numeric types use the same writer but with numeric format parameter
if writer_param is not None:
writer_function(fp, data_element, writer_param)
else:
writer_function(fp, data_element)
# print DataElement(tag, VR, value)
is_undefined_length = False
if hasattr(data_element, "is_undefined_length") and data_element.is_undefined_length:
is_undefined_length = True
location = fp.tell()
fp.seek(length_location)
if not fp.is_implicit_VR and VR not in ['OB', 'OW', 'OF', 'SQ', 'UT', 'UN']:
fp.write_US(location - length_location - 2) # 2 is length of US
else:
# write the proper length of the data_element back in the length slot, unless is SQ with undefined length.
if not is_undefined_length:
fp.write_UL(location - length_location - 4) # 4 is length of UL
fp.seek(location) # ready for next data_element
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, encoding=default_encoding):
"""Write the data_element to file fp according to dicom media storage rules.
"""
fp.write_tag(data_element.tag)
VR = data_element.VR
if not fp.is_implicit_VR:
if len(VR) != 2:
msg = "Cannot write ambiguous VR of '%s' for data element with tag %r." % (VR, data_element.tag)
msg += "\nSet the correct VR before writing, or use an implicit VR transfer syntax"
raise ValueError(msg)
if in_py3:
fp.write(bytes(VR, default_encoding))
else:
fp.write(VR)
if VR in extra_length_VRs:
fp.write_US(0) # reserved 2 bytes
if VR not in writers:
raise NotImplementedError("write_data_element: unknown Value Representation '{0}'".format(VR))
length_location = fp.tell() # save location for later.
if not fp.is_implicit_VR and VR not in ['OB', 'OW', 'OF', 'SQ', 'UT', 'UN']:
fp.write_US(0) # Explicit VR length field is only 2 bytes
else:
fp.write_UL(0xFFFFFFFF) # will fill in real length value later if not undefined length item
encoding = convert_encodings(encoding)
writer_function, writer_param = writers[VR]
if VR in text_VRs:
writer_function(fp, data_element, encoding=encoding[1])
elif VR in ('PN', 'SQ'):
writer_function(fp, data_element, encoding=encoding)
else:
# Many numeric types use the same writer but with numeric format parameter
if writer_param is not None:
writer_function(fp, data_element, writer_param)
else:
writer_function(fp, data_element)
# print DataElement(tag, VR, value)
is_undefined_length = False
if hasattr(data_element, "is_undefined_length") and data_element.is_undefined_length:
is_undefined_length = True
location = fp.tell()
fp.seek(length_location)
if not fp.is_implicit_VR and VR not in ['OB', 'OW', 'OF', 'SQ', 'UT', 'UN']:
fp.write_US(location - length_location - 2) # 2 is length of US
else:
# write the proper length of the data_element back in the length slot, unless is SQ with undefined length.
if not is_undefined_length:
fp.write_UL(location - length_location - 4) # 4 is length of UL
fp.seek(location) # ready for next data_element
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, encoding=default_encoding):
"""Write the data_element to file fp according to dicom media storage rules."""
fp.write_tag(data_element.tag)
VR = data_element.VR
if not fp.is_implicit_VR:
if len(VR) != 2:
msg = "Cannot write ambiguous VR of '%s' for data element with tag %r." % (VR, data_element.tag)
msg += "\nSet the correct VR before writing, or use an implicit VR transfer syntax"
raise ValueError(msg)
if in_py3:
fp.write(bytes(VR, default_encoding))
else:
fp.write(VR)
if VR in extra_length_VRs:
fp.write_US(0) # reserved 2 bytes
if VR not in writers:
raise NotImplementedError("write_data_element: unknown Value Representation '{0}'".format(VR))
length_location = fp.tell() # save location for later.
if not fp.is_implicit_VR and VR not in ["OB", "OW", "OF", "SQ", "UT", "UN"]:
fp.write_US(0) # Explicit VR length field is only 2 bytes
else:
fp.write_UL(0xFFFFFFFFL) # will fill in real length value later if not undefined length item
encoding = convert_encodings(encoding)
if VR in text_VRs:
writers[VR](fp, data_element, encoding=encoding[1])
elif VR in ("PN", "SQ"):
writers[VR](fp, data_element, encoding=encoding)
else:
try:
writers[VR][0] # if writer is a tuple, then need to pass a number format
except TypeError:
writers[VR](fp, data_element) # call the function to write that kind of item
else:
writers[VR][0](fp, data_element, writers[VR][1])
# print DataElement(tag, VR, value)
is_undefined_length = False
if hasattr(data_element, "is_undefined_length") and data_element.is_undefined_length:
is_undefined_length = True
location = fp.tell()
fp.seek(length_location)
if not fp.is_implicit_VR and VR not in ["OB", "OW", "OF", "SQ", "UT", "UN"]:
fp.write_US(location - length_location - 2) # 2 is length of US
else:
# write the proper length of the data_element back in the length slot, unless is SQ with undefined length.
if not is_undefined_length:
fp.write_UL(location - length_location - 4) # 4 is length of UL
fp.seek(location) # ready for next data_element
if is_undefined_length:
fp.write_tag(SequenceDelimiterTag)
fp.write_UL(0) # 4-byte 'length' of delimiter data item
def _character_set(self):
"""
:return:
"""
char_set = self.get('SpecificCharacterSet', None)
if not char_set:
char_set = self._parent_encoding
else:
char_set = convert_encodings(char_set)
return char_set
def _character_set(self):
"""
:return:
"""
char_set = self.get('SpecificCharacterSet', None)
if not char_set:
char_set = self._parent_encoding
else:
char_set = convert_encodings(char_set)
return char_set
def data_element_generator(fp, is_implicit_VR, is_little_endian,
stop_when=None, defer_size=None, encoding=default_encoding):
"""Create a generator to efficiently return the raw data elements
Returns (VR, length, raw_bytes, value_tell, is_little_endian),
where:
VR -- None if implicit VR, otherwise the VR read from the file
length -- the length as in the DICOM data element (could be
DICOM "undefined length" 0xffffffffL),
value_bytes -- the raw bytes from the DICOM file
(not parsed into python types)
is_little_endian -- True if transfer syntax is little endian; else False
"""
# Summary of DICOM standard PS3.5-2008 chapter 7:
# If Implicit VR, data element is:
# tag, 4-byte length, value.
# The 4-byte length can be FFFFFFFF (undefined length)*
# If Explicit VR:
# if OB, OW, OF, SQ, UN, or UT:
# tag, VR, 2-bytes reserved (both zero), 4-byte length, value
# For all but UT, the length can be FFFFFFFF (undefined length)*
# else: (any other VR)
# tag, VR, (2 byte length), value
# * for undefined length, a Sequence Delimitation Item marks the end
# of the Value Field.
# Note, except for the special_VRs, both impl and expl VR use 8 bytes;
# the special VRs follow the 8 bytes with a 4-byte length
# With a generator, state is stored, so we can break down
# into the individual cases, and not have to check them again for each
# data element
if is_little_endian:
endian_chr = "<"
else:
endian_chr = ">"
if is_implicit_VR:
element_struct = Struct(endian_chr + "HHL")
else: # Explicit VR
# tag, VR, 2-byte length (or 0 if special VRs)
element_struct = Struct(endian_chr + "HH2sH")
extra_length_struct = Struct(endian_chr + "L") # for special VRs
extra_length_unpack = extra_length_struct.unpack # for lookup speed
# Make local variables so have faster lookup
fp_read = fp.read
fp_tell = fp.tell
logger_debug = logger.debug
debugging = dicom.debugging
element_struct_unpack = element_struct.unpack
while True:
# Read tag, VR, length, get ready to read value
bytes_read = fp_read(8)
if len(bytes_read) < 8:
raise StopIteration # at end of file
if debugging:
debug_msg = "{0:08x}: {1}".format(fp.tell() - 8,
bytes2hex(bytes_read))
if is_implicit_VR:
# must reset VR each time; could have set last iteration (e.g. SQ)
VR = None
group, elem, length = element_struct_unpack(bytes_read)
else: # explicit VR
group, elem, VR, length = element_struct_unpack(bytes_read)
if in_py3:
VR = VR.decode(default_encoding)
if VR in extra_length_VRs:
bytes_read = fp_read(4)
length = extra_length_unpack(bytes_read)[0]
if debugging:
debug_msg += " " + bytes2hex(bytes_read)
if debugging:
debug_msg = "%-47s (%04x, %04x)" % (debug_msg, group, elem)
if not is_implicit_VR:
debug_msg += " %s " % VR
if length != 0xFFFFFFFFL:
debug_msg += "Length: %d" % length
else:
debug_msg += "Length: Undefined length (FFFFFFFF)"
logger_debug(debug_msg)
# Positioned to read the value, but may not want to -- check stop_when
value_tell = fp_tell()
tag = TupleTag((group, elem))
if stop_when is not None:
# XXX VR may be None here!! Should stop_when just take tag?
if stop_when(tag, VR, length):
if debugging:
logger_debug("Reading ended by stop_when callback. "
"Rewinding to start of data element.")
rewind_length = 8
if not is_implicit_VR and VR in extra_length_VRs:
rewind_length += 4
fp.seek(value_tell - rewind_length)
raise StopIteration
# Reading the value
# First case (most common): reading a value with a defined length
if length != 0xFFFFFFFFL:
if defer_size is not None and length > defer_size:
# Flag as deferred by setting value to None, and skip bytes
value = None
logger_debug("Defer size exceeded."
"Skipping forward to next data element.")
fp.seek(fp_tell() + length)
else:
value = fp_read(length)
if debugging:
dotdot = " "
if length > 12:
dotdot = "..."
logger_debug("%08x: %-34s %s %r %s" % (value_tell,
bytes2hex(value[:12]), dotdot, value[:12], dotdot))
# If the tag is (0008,0005) Specific Character Set, then store it
if tag == (0x08, 0x05):
from dicom.values import convert_string
encoding = convert_string(value, is_little_endian, encoding=default_encoding)
# Store the encoding value in the generator for use with future elements (SQs)
encoding = convert_encodings(encoding)
yield RawDataElement(tag, VR, length, value, value_tell,
is_implicit_VR, is_little_endian)
# Second case: undefined length - must seek to delimiter,
# unless is SQ type, in which case is easier to parse it, because
# undefined length SQs and items of undefined lengths can be nested
# and it would be error-prone to read to the correct outer delimiter
else:
# Try to look up type to see if is a SQ
# if private tag, won't be able to look it up in dictionary,
# in which case just ignore it and read the bytes unless it is
# identified as a Sequence
if VR is None:
try:
VR = dictionaryVR(tag)
except KeyError:
# Look ahead to see if it consists of items and is thus a SQ
next_tag = TupleTag(unpack(endian_chr + "HH", fp_read(4)))
# Rewind the file
fp.seek(fp_tell() - 4)
if next_tag == ItemTag:
VR = 'SQ'
if VR == 'SQ':
if debugging:
msg = "{0:08x}: Reading/parsing undefined length sequence"
logger_debug(msg.format(fp_tell()))
seq = read_sequence(fp, is_implicit_VR,
is_little_endian, length, encoding)
yield DataElement(tag, VR, seq, value_tell,
is_undefined_length=True)
else:
delimiter = SequenceDelimiterTag
if debugging:
logger_debug("Reading undefined length data element")
value = read_undefined_length_value(fp, is_little_endian,
delimiter, defer_size)
# If the tag is (0008,0005) Specific Character Set, then store it
if tag == (0x08, 0x05):
from dicom.values import convert_string
encoding = convert_string(value, is_little_endian, encoding=default_encoding)
# Store the encoding value in the generator for use with future elements (SQs)
encoding = convert_encodings(encoding)
yield RawDataElement(tag, VR, length, value, value_tell,
is_implicit_VR, is_little_endian)
