/usr/lib/python2.7/dist-packages/dicom/valuerep.py is in python-dicom 0.9.9-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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"""Special classes for DICOM value representations (VR)"""
# Copyright (c) 2008-2012 Darcy Mason
# This file is part of pydicom, released under a modified MIT license.
# See the file license.txt included with this distribution, also
# available at http://pydicom.googlecode.com
from decimal import Decimal
import dicom.config
from dicom.multival import MultiValue
from dicom import in_py3
import logging
logger = logging.getLogger('pydicom')
default_encoding = "iso8859" # can't import from charset or get circular import
# For reading/writing data elements, these ones have longer explicit VR format
extra_length_VRs = ('OB', 'OW', 'OF', 'SQ', 'UN', 'UT')
# VRs that can be affected by character repertoire in (0008,0005) Specific Character Set
# See PS-3.5 (2011), section 6.1.2 Graphic Characters
text_VRs = ('SH', 'LO', 'ST', 'LT', 'UT') # and PN, but it is handled separately.
import re
match_string = b''.join([
b'(?P<single_byte>',
b'(?P<family_name>[^=\^]*)',
b'\^?(?P<given_name>[^=\^]*)',
b'\^?(?P<middle_name>[^=\^]*)',
b'\^?(?P<name_prefix>[^=\^]*)',
b'\^?(?P<name_suffix>[^=\^]*)',
b')',
b'=?(?P<ideographic>[^=]*)',
b'=?(?P<phonetic>[^=]*)$'])
match_string_uni = re.compile(match_string.decode('iso8859'))
match_string_bytes = re.compile(match_string)
class DSfloat(float):
"""Store values for DICOM VR of DS (Decimal String) as a float.
If constructed from an empty string, return the empty string,
not an instance of this class.
"""
__slots__ = 'original_string'
def __init__(self, val):
"""Store the original string if one given, for exact write-out of same
value later.
"""
# ... also if user changes a data element value, then will get
# a different object, becuase float is immutable.
if isinstance(val, (str, unicode)):
self.original_string = val
elif isinstance(val, (DSfloat, DSdecimal)) and hasattr(val, 'original_string'):
self.original_string = val.original_string
def __str__(self):
if hasattr(self, 'original_string'):
return self.original_string
else:
return super(DSfloat, self).__str__()
def __repr__(self):
return "'" + str(self) + "'"
class DSdecimal(Decimal):
"""Store values for DICOM VR of DS (Decimal String).
Note: if constructed by an empty string, returns the empty string,
not an instance of this class.
"""
__slots__ = 'original_string'
def __new__(cls, val):
"""Create an instance of DS object, or return a blank string if one is
passed in, e.g. from a type 2 DICOM blank value.
:param val: val must be a string or a number type which can be
converted to a decimal
"""
# Store this value here so that if the input string is actually a valid
# string but decimal.Decimal transforms it to an invalid string it will
# still be initialized properly
enforce_length = dicom.config.enforce_valid_values
# DICOM allows spaces around the string, but python doesn't, so clean it
if isinstance(val, (str, unicode)):
val = val.strip()
# If the input string is actually invalid that we relax the valid
# value constraint for this particular instance
if len(val) <= 16:
enforce_length = False
if val == '':
return val
if isinstance(val, float) and not dicom.config.allow_DS_float:
msg = ("DS cannot be instantiated with a float value, unless "
"config.allow_DS_float is set to True. It is recommended to "
"convert to a string instead, with the desired number of digits, "
"or use Decimal.quantize and pass a Decimal instance.")
raise TypeError(msg)
if not isinstance(val, Decimal):
val = super(DSdecimal, cls).__new__(cls, val)
if len(str(val)) > 16 and enforce_length:
msg = ("DS value representation must be <= 16 characters by DICOM "
"standard. Initialize with a smaller string, or set config.enforce_valid_values "
"to False to override, "
"or use Decimal.quantize() and initialize with a Decimal instance.")
raise OverflowError(msg)
return val
def __init__(self, val):
"""Store the original string if one given, for exact write-out of same
value later. E.g. if set '1.23e2', Decimal would write '123', but DS
will use the original
"""
# ... also if user changes a data element value, then will get
# a different Decimal, as Decimal is immutable.
if isinstance(val, (str, unicode)):
self.original_string = val
elif isinstance(val, (DSfloat, DSdecimal)) and hasattr(val, 'original_string'):
self.original_string = val.original_string
def __str__(self):
if hasattr(self, 'original_string') and len(self.original_string) <= 16:
return self.original_string
else:
return super(DSdecimal, self).__str__()
def __repr__(self):
return "'" + str(self) + "'"
# CHOOSE TYPE OF DS
if dicom.config.use_DS_decimal:
DSclass = DSdecimal
else:
DSclass = DSfloat
def DS(val):
"""Factory function for creating DS class instances.
Checks for blank string; if so, return that. Else calls DSfloat or DSdecimal
to create the class instance. This avoids overriding __new__ in DSfloat
(which carries a time penalty for large arrays of DS).
Similarly the string clean and check can be avoided and DSfloat called
directly if a string has already been processed.
"""
if isinstance(val, (str, unicode)):
val = val.strip()
if val == '':
return val
return DSclass(val)
class IS(int):
"""Derived class of int. Stores original integer string for exact rewriting
of the string originally read or stored.
"""
if not in_py3:
__slots__ = 'original_string'
# Unlikely that str(int) will not be the same as the original, but could happen
# with leading zeros.
def __new__(cls, val):
"""Create instance if new integer string"""
if isinstance(val, (str, unicode)) and val.strip() == '':
return ''
newval = super(IS, cls).__new__(cls, val)
# check if a float or Decimal passed in, then could have lost info,
# and will raise error. E.g. IS(Decimal('1')) is ok, but not IS(1.23)
if isinstance(val, (float, Decimal)) and newval != val:
raise TypeError("Could not convert value to integer without loss")
# Checks in case underlying int is >32 bits, DICOM does not allow this
if (newval < -2 ** 31 or newval >= 2 ** 31) and dicom.config.enforce_valid_values:
message = "Value exceeds DICOM limits of -2**31 to (2**31 - 1) for IS"
raise OverflowError(message)
return newval
def __init__(self, val):
# If a string passed, then store it
if isinstance(val, (str, unicode)):
self.original_string = val
elif isinstance(val, IS) and hasattr(val, 'original_string'):
self.original_string = val.original_string
def __repr__(self):
if hasattr(self, 'original_string'):
return "'" + self.original_string + "'"
else:
return "'" + int.__str__(self) + "'"
def MultiString(val, valtype=str):
"""Split a bytestring by delimiters if there are any
val -- DICOM bytestring to split up
valtype -- default str, but can be e.g. UID to overwrite to a specific type
"""
# Remove trailing blank used to pad to even length
# 2005.05.25: also check for trailing 0, error made in PET files we are converting
if val and (val.endswith(' ') or val.endswith('\x00')):
val = val[:-1]
splitup = val.split("\\")
if len(splitup) == 1:
val = splitup[0]
return valtype(val) if val else val
else:
return MultiValue(valtype, splitup)
class PersonName3(object):
def __init__(self, val, encodings=default_encoding):
if isinstance(val, PersonName3):
val = val.original_string
self.original_string = val
self.encodings = self._verify_encodings(encodings)
self.parse(val)
def parse(self, val):
if isinstance(val, bytes):
matchstr = match_string_bytes
else:
matchstr = match_string_uni
matchobj = re.match(matchstr, val)
self.__dict__.update(matchobj.groupdict())
groups = matchobj.groups()
self.components = [groups[i] for i in (0, -2, -1)]
def __eq__(self, other):
return self.original_string == other
def __ne__(self, other):
return not self == other
def __str__(self):
return self.original_string.__str__()
def __repr__(self):
return self.original_string.__repr__()
def decode(self, encodings=None):
encodings = self._verify_encodings(encodings)
from dicom.charset import clean_escseq
if not isinstance(self.components[0], bytes):
comps = self.components
else:
comps = [clean_escseq(comp.decode(enc), encodings)
for comp, enc in zip(self.components, encodings)]
while len(comps) and not comps[-1]:
comps.pop()
return PersonName3('='.join(comps), encodings)
def encode(self, encodings=None):
encodings = self._verify_encodings(encodings)
if isinstance(self.components[0], bytes):
comps = self.components
else:
comps = [C.encode(enc) for C, enc in zip(self.components, encodings)]
# Remove empty elements from the end
while len(comps) and not comps[-1]:
comps.pop()
return b'='.join(comps)
def family_comma_given(self):
return self.formatted('%(family_name)s, %(given_name)s')
def formatted(self, format_str):
if isinstance(self.original_string, bytes):
return format_str % self.decode(default_encoding).__dict__
else:
return format_str % self.__dict__
def _verify_encodings(self, encodings):
if encodings is None:
return self.encodings
if not isinstance(encodings, list):
encodings = [encodings] * 3
if len(encodings) == 2:
encodings.append(encodings[1])
return encodings
class PersonNameBase(object):
"""Base class for Person Name classes"""
def __init__(self, val):
"""Initialize the PN properties"""
# Note normally use __new__ on subclassing an immutable, but here we just want
# to do some pre-processing for properties
# PS 3.5-2008 section 6.2 (p.28) and 6.2.1 describes PN. Briefly:
# single-byte-characters=ideographic characters=phonetic-characters
# (each with?):
# family-name-complex^Given-name-complex^Middle-name^name-prefix^name-suffix
self.parse()
def formatted(self, format_str):
"""Return a formatted string according to the format pattern
Use "...%(property)...%(property)..." where property is one of
family_name, given_name, middle_name, name_prefix, name_suffix
"""
return format_str % self.__dict__
def parse(self):
"""Break down the components and name parts"""
self.components = self.split("=")
nComponents = len(self.components)
self.single_byte = self.components[0]
self.ideographic = ''
self.phonetic = ''
if nComponents > 1:
self.ideographic = self.components[1]
if nComponents > 2:
self.phonetic = self.components[2]
if self.single_byte:
name_string = self.single_byte + "^^^^" # in case missing trailing items are left out
parts = name_string.split("^")[:5]
self.family_name, self.given_name, self.middle_name = parts[:3]
self.name_prefix, self.name_suffix = parts[3:]
else:
(self.family_name, self.given_name, self.middle_name,
self.name_prefix, self.name_suffix) = ('', '', '', '', '')
class PersonName(PersonNameBase, bytes):
"""Human-friendly class to hold VR of Person Name (PN)
Name is parsed into the following properties:
single-byte, ideographic, and phonetic components (PS3.5-2008 6.2.1)
family_name,
given_name,
middle_name,
name_prefix,
name_suffix
"""
def __new__(cls, val):
"""Return instance of the new class"""
# Check if trying to convert a string that has already been converted
if isinstance(val, PersonName):
return val
return super(PersonName, cls).__new__(cls, val)
def encode(self, *args):
"""Dummy method to mimic py2 str behavior in py3 bytes subclass"""
# This greatly simplifies the write process so all objects have the
# "encode" method
return self
def family_comma_given(self):
"""Return name as 'Family-name, Given-name'"""
return self.formatted("%(family_name)s, %(given_name)s")
# def __str__(self):
# return str(self.byte_string)
# XXX need to process the ideographic or phonetic components?
# def __len__(self):
# return len(self.byte_string)
class PersonNameUnicode(PersonNameBase, unicode):
"""Unicode version of Person Name"""
def __new__(cls, val, encodings):
"""Return unicode string after conversion of each part
val -- the PN value to store
encodings -- a list of python encodings, generally found
from dicom.charset.python_encodings mapping
of values in DICOM data element (0008,0005).
"""
from dicom.charset import clean_escseq # in here to avoid circular import
# Make the possible three character encodings explicit:
if not isinstance(encodings, list):
encodings = [encodings] * 3
if len(encodings) == 2:
encodings.append(encodings[1])
components = val.split(b"=")
# Remove the first encoding if only one component is present
if (len(components) == 1):
del encodings[0]
comps = [clean_escseq(C.decode(enc), encodings)
for C, enc in zip(components, encodings)]
new_val = u"=".join(comps)
return unicode.__new__(cls, new_val)
def __init__(self, val, encodings):
self.encodings = self._verify_encodings(encodings)
PersonNameBase.__init__(self, val)
def _verify_encodings(self, encodings):
"""Checks the encoding to ensure proper format"""
if encodings is None:
return self.encodings
if not isinstance(encodings, list):
encodings = [encodings] * 3
if len(encodings) == 2:
encodings.append(encodings[1])
return encodings
def encode(self, encodings):
"""Encode the unicode using the specified encoding"""
encodings = self._verify_encodings(encodings)
components = self.split('=')
comps = [C.encode(enc) for C, enc in zip(components, encodings)]
# Remove empty elements from the end
while len(comps) and not comps[-1]:
comps.pop()
return '='.join(comps)
def family_comma_given(self):
"""Return name as 'Family-name, Given-name'"""
return self.formatted("%(family_name)u, %(given_name)u")
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