/usr/lib/python2.7/dist-packages/dicom/dataelem.py is in python-dicom 0.9.7-1.1ubuntu1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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"""Define the DataElement class - elements within a dataset.
DataElements have a DICOM value representation VR, a value multiplicity VM,
and a value.
"""
#
# 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
#
import logging
logger = logging.getLogger('pydicom')
from dicom.datadict import dictionary_has_tag, dictionary_description
from dicom.datadict import private_dictionary_description, dictionaryVR
from dicom.tag import Tag
from dicom.UID import UID
from dicom.valuerep import IS, DS, PersonName
from decimal import Decimal
try:
from collections import namedtuple
except ImportError: # for python <2.6
from dicom.util.namedtup import namedtuple
# os.stat is only available on Unix and Windows
# Not sure if on other platforms the import fails, or the call to it??
stat_available = True
try:
from os import stat
except:
stat_available = False
import os.path
from dicom.filebase import DicomFile
import warnings
# Helper functions:
def isMultiValue(value):
"""Helper function: return True if 'value' is 'list-like'."""
if isString(value):
return False
try:
iter(value)
except TypeError:
return False
return True
def isString(val):
"""Helper function: return True if val is a string."""
try:
val + ""
except:
return False
return True
def isStringOrStringList(val):
"""Return true if val consists only of strings. val may be a list/tuple."""
if isMultiValue(val):
for item in val:
if not isString(item):
return False
return True
else: # single value - test for a string
return isString(val)
_backslash = "\\" # double '\' because it is used as escape chr in Python
class DataElement(object):
"""Contain and manipulate a Dicom data element, having a tag, VR, VM and value.
Most user code will not create data elements using this class directly,
but rather through 'named tags' in Dataset objects.
See the Dataset class for a description of how Datasets, Sequences,
and DataElements work.
Class Data
----------
For string display (via __str__), the following are used:
descripWidth -- maximum width of description field (default 35).
maxBytesToDisplay -- longer data will display "array of # bytes" (default 16).
showVR -- True (default) to include the dicom VR just before the value.
"""
descripWidth = 35
maxBytesToDisplay = 16
showVR = 1
def __init__(self, tag, VR, value, file_value_tell=None,
is_undefined_length=False):
"""Create a data element instance.
Most user code should instead use DICOM keywords, (formerly 'Named tags'
in pydicom) to create data_elements, for which only the value is supplied,
and the VR and tag are determined from the dicom dictionary.
tag -- dicom (group, element) tag in any form accepted by Tag().
VR -- dicom value representation (see DICOM standard part 6)
value -- the value of the data element. One of the following:
- a single string value
- a number
- a list or tuple with all strings or all numbers
- a multi-value string with backslash separator
file_value_tell -- used internally by Dataset, to store the write
position for ReplaceDataElementValue method
is_undefined_length -- used internally to store whether the length
field in this data element was 0xFFFFFFFFL, i.e. "undefined length"
"""
self.tag = Tag(tag)
self.VR = VR # Note!: you must set VR before setting value
self.value = value
self.file_tell = file_value_tell
self.is_undefined_length = is_undefined_length
def _getvalue(self):
"""Get method for 'value' property"""
return self._value
def _setvalue(self, val):
"""Set method for 'value' property"""
# Check if is a string with multiple values separated by '\'
# If so, turn them into a list of separate strings
if isString(val) and self.VR not in \
['UT','ST','LT', 'FL','FD','AT','OB','OW','OF','SL','SQ','SS',
'UL', 'OB/OW', 'OW/OB', 'OB or OW', 'OW or OB', 'UN'] and 'US' not in self.VR: # latter covers 'US or SS' etc
if _backslash in val:
val = val.split(_backslash)
self._value = self._convert_value(val)
value = property(_getvalue, _setvalue, doc=
"""The value (possibly multiple values) of this data_element.""")
def _getVM(self):
"""Get method for VM property"""
if isMultiValue(self.value):
return len(self.value)
else:
return 1
VM = property(_getVM, doc =
"""The number of values in the data_element's 'value'""")
def _convert_value(self, val):
"""Convert Dicom string values if possible to e.g. numbers. Handle the case
of multiple value data_elements"""
if self.VR=='SQ': # a sequence - leave it alone
from dicom.sequence import Sequence
if isinstance(val,Sequence):
return val
else:
return Sequence(val)
# if the value is a list, convert each element
try:
val.append
except AttributeError: # not a list
return self._convert(val)
else:
returnvalue = []
for subval in val:
returnvalue.append(self._convert(subval))
return returnvalue
def _convert(self, val):
"""Take the value and convert to number, etc if possible"""
if self.VR == 'IS':
return IS(val)
elif self.VR == 'DS':
return DS(val)
elif self.VR == "UI":
return UID(val)
# Later may need this for PersonName as for UI,
# but needs more thought
# elif self.VR == "PN":
# return PersonName(val)
else: # is either a string or a type 2 optionally blank string
return val # this means a "numeric" value could be empty string ""
#except TypeError:
#print "Could not convert value '%s' to VR '%s' in tag %s" \
# % (repr(val), self.VR, self.tag)
#except ValueError:
#print "Could not convert value '%s' to VR '%s' in tag %s" \
# % (repr(val), self.VR, self.tag)
def __str__(self):
"""Return str representation of this data_element"""
repVal = self.repval
if self.showVR:
s = "%s %-*s %s: %s" % (str(self.tag), self.descripWidth,
self.description()[:self.descripWidth], self.VR, repVal)
else:
s = "%s %-*s %s" % (str(self.tag), self.descripWidth,
self.description()[:self.descripWidth], repVal)
return s
def _get_repval(self):
"""Return a str representation of the current value for use in __str__"""
if (self.VR in ['OB', 'OW', 'OW/OB', 'OW or OB', 'OB or OW', 'US or SS or OW', 'US or SS']
and len(self.value) > self.maxBytesToDisplay):
repVal = "Array of %d bytes" % len(self.value)
elif hasattr(self, 'original_string'): # for VR of IS or DS
repVal = repr(self.original_string)
elif isinstance(self.value, Decimal):
repVal = repr(self.value)
elif isinstance(self.value, UID):
repVal = self.value.name
else:
repVal = repr(self.value) # will tolerate unicode too
return repVal
repval = property(_get_repval)
def __unicode__(self):
"""Return unicode representation of this data_element"""
if isinstance(self.value, unicode):
# start with the string rep then replace the value part with the unicode
strVal = str(self)
uniVal = unicode(strVal.replace(self.repval, "")) + self.value
return uniVal
else:
return unicode(str(self))
def __getitem__(self, key):
"""Returns the item from my value's Sequence, if it is one."""
try:
return self.value[key]
except TypeError:
raise TypeError, "DataElement value is unscriptable (not a Sequence)"
def _get_name(self):
return self.description()
name = property(_get_name)
def description(self):
"""Return the DICOM dictionary description for this dicom tag."""
if dictionary_has_tag(self.tag):
name = dictionary_description(self.tag)
elif self.tag.is_private:
name = "Private tag data" # default
if hasattr(self, 'private_creator'):
try:
# If have name from private dictionary, use it, but
# but put in square brackets so is differentiated,
# and clear that cannot access it by name
name = "[" + private_dictionary_description(self.tag, self.private_creator) + "]"
except KeyError:
pass
elif self.tag.elem >> 8 == 0:
name = "Private Creator"
elif self.tag.element == 0: # implied Group Length dicom versions < 3
name = "Group Length"
else:
name = ""
return name
def __repr__(self):
"""Handle repr(data_element)"""
if self.VR == "SQ":
return repr(self.value)
else:
return str(self)
class DeferredDataElement(DataElement):
"""Subclass of DataElement where value is not read into memory until needed"""
def __init__(self, tag, VR, fp, file_mtime, data_element_tell, length):
"""Store basic info for the data element but value will be read later
fp -- DicomFile object representing the dicom file being read
file_mtime -- last modification time on file, used to make sure
it has not changed since original read
data_element_tell -- file position at start of data element,
(not the start of the value part, but start of whole element)
"""
self.tag = Tag(tag)
self.VR = VR
self._value = None # flag as unread
# Check current file object and save info needed for read later
# if not isinstance(fp, DicomFile):
# raise NotImplementedError, "Deferred read is only available for DicomFile objects"
self.fp_is_implicit_VR = fp.is_implicit_VR
self.fp_is_little_endian = fp.is_little_endian
self.filepath = fp.name
self.file_mtime = file_mtime
self.data_element_tell = data_element_tell
self.length = length
def _get_repval(self):
if self._value is None:
return "Deferred read: length %d" % self.length
else:
return DataElement._get_repval(self)
repval = property(_get_repval)
def _getvalue(self):
"""Get method for 'value' property"""
# Must now read the value if haven't already
if self._value is None:
self.read_value()
return DataElement._getvalue(self)
def _setvalue(self, val):
DataElement._setvalue(self, val)
value = property(_getvalue, _setvalue)
RawDataElement = namedtuple('RawDataElement',
'tag VR length value value_tell is_implicit_VR is_little_endian')
def DataElement_from_raw(raw_data_element):
"""Return a DataElement from a RawDataElement"""
from dicom.values import convert_value # XXX buried here to avoid circular import filereader->Dataset->convert_value->filereader (for SQ parsing)
raw = raw_data_element
VR = raw.VR
if VR is None: # Can be if was implicit VR
try:
VR = dictionaryVR(raw.tag)
except KeyError:
if raw.tag.is_private:
VR = 'OB' # just read the bytes, no way to know what they mean
elif raw.tag.element == 0: # group length tag implied in versions < 3.0
VR = 'UL'
else:
raise KeyError, "Unknown DICOM tag %s - can't look up VR" % str(raw.tag)
try:
value = convert_value(VR, raw)
except NotImplementedError, e:
raise NotImplementedError, "%s in tag %r" % (str(e), raw.tag)
return DataElement(raw.tag, VR, value, raw.value_tell, raw.length==0xFFFFFFFFL)
class Attribute(DataElement):
"""Deprecated -- use DataElement instead"""
def __init__(self, tag, VR, value, file_value_tell=None):
warnings.warn("The Attribute class is deprecated and will be removed in pydicom 1.0. Use DataElement", DeprecationWarning)
DataElement.__init__(self, tag, VR, value, file_value_tell)
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