def fix_SOPReferencedMacro(ds: Dataset,
log: list,
suggested_SOPClassUID: dict = {}):
kw = 'ReferencedStudySequence'
tg = tag_for_keyword(kw)
if tg not in ds:
return
val = ds[tg].value
if len(val) == 0:
del ds[tg]
return
i = 0
while i < len(val):
item = val[i]
msg = ErrorInfo()
if 'ReferencedSOPInstanceUID' not in item:
msg.msg = 'General Fix - item {}/{} <ReferencedStudySequence>'\
' lacks <ReferencedSOPInstanceUID> attribute'.format(i + 1, len(val))
msg.fix = 'fixed by removint the item'
log.append(msg.getWholeMessage())
val.pop(i)
continue
if item['ReferencedSOPInstanceUID'].is_empty:
msg.msg = 'General Fix - item {}/{} <ReferencedStudySequence>'\
' holds an empty <ReferencedSOPInstanceUID> attribute'.format(i + 1, len(val))
msg.fix = 'fixed by removint the item'
log.append(msg.getWholeMessage())
val.pop(i)
continue
if 'ReferencedSOPClassUID' not in item or\
item['ReferencedSOPClassUID'].is_empty:
uid = item['ReferencedSOPInstanceUID'].value
msg.msg = 'General Fix - item {}/{} <ReferencedStudySequence>'\
' lacks <ReferencedSOPClassUID> attribute'.format(i + 1, len(val))
if uid not in suggested_SOPClassUID:
msg.fix = 'fixed by removint the item'
log.append(msg.getWholeMessage())
val.pop(i)
continue
else:
msg.fix = 'fixed by querying the attribute '\
'ReferencedSOPClassUID filling it with {}'.format(
suggested_SOPClassUID[uid]
)
log.append(msg.getWholeMessage())
item['ReferencedSOPClassUID'].value = suggested_SOPClassUID[
uid]
i += 1
if len(val) == 0:
msg = ErrorInfo()
msg.msg = 'General Fix - Attribute <{}> is empty '.format(kw)
msg.fix = 'fixed by removint the attribute'
log.append(msg.getWholeMessage())
del ds[tg]
return
def add_anatomy(ds: Dataset,
BodyPartExamined_value: str,
AnatomicRegionSequence_value: tuple,
log: list,
check_consistency: bool = True):
bpe = tag_for_keyword('BodyPartExamined')
ars = tag_for_keyword('AnatomicRegionSequence')
old_bpe, old_ars = get_old_anatomy(ds)
if old_bpe is None:
if check_consistency:
new_bpe, new_ars = \
CorrectAnatomicInfo(
BodyPartExamined_value, AnatomicRegionSequence_value)
else:
new_bpe, new_ars = (BodyPartExamined_value,
AnatomicRegionSequence_value)
else:
new_bpe, new_ars = CorrectAnatomicInfo(old_bpe, old_ars)
if old_bpe != new_bpe and new_bpe is not None:
bpe_a = DataElementX(bpe, dictionary_VR(bpe), new_bpe)
old_bpe_txt = old_bpe if bpe not in ds else ds[bpe].value
ds[bpe] = bpe_a
msg = ErrorInfo()
msg.msg = 'General Fix - {}'.format("<BodyPartExamined> is absent")
msg.fix = "fixed by setting the <BodyPartExamined>"\
"from {} to '{}'".format(old_bpe_txt, new_bpe)
log.append(msg.getWholeMessage())
if is_accurate_code_seq(new_ars) and not is_code_equal(old_ars, new_ars):
code_value, code_meaning, coding_scheme_designator = new_ars
if ars in ds:
old_item_text = subfix_CodeSeqItem2txt(ds[ars], 0)
else:
old_item_text = 'None'
new_item = CodeSeqItemGenerator(str(code_value), code_meaning,
coding_scheme_designator)
ars_a = DataElementX(ars, 'SQ', DicomSequence([
new_item,
]))
ds[ars] = ars_a
msg = ErrorInfo()
msg.msg = 'General Fix - {}'.format(
"<AnatomicRegionSequence> is absent")
msg.fix = "fixed by setting the <AnatomicRegionSequence>"\
"from {} to '{}'".format(
old_item_text,
subfix_CodeSeqItem2txt(ars_a, 0))
log.append(msg.getWholeMessage())
AddLaterality(ds, log)
def AddLaterality(ds: Dataset, log: list):
needlaterality = checkLaterality(ds, 0, ds)
old_laterality = None if "Laterality" not in ds else ds['Laterality'].value
AddImageLateralityForBoth = False
if needlaterality:
if old_laterality is None:
AddImageLateralityForBoth = True
if old_laterality is not None:
if old_laterality not in ['L', 'R']:
if old_laterality.lower() == 'left':
new_laterality = 'L'
elif old_laterality.lower() == 'right':
new_laterality = 'R'
else:
new_laterality = None
if new_laterality is not None:
msg = ErrorInfo()
msg.msg = 'General Fix - {}'.format(
"<Laterality> holds wrong value")
msg.fix = "fixed by setting the <Laterality>"\
"from {} to '{}'".format(old_laterality, new_laterality)
log.append(msg.getWholeMessage())
ds['Laterlaity'].value = new_laterality
return
else:
AddImageLateralityForBoth = True
else:
return
elif 'Laterality' in ds:
del ds['Laterality']
def verifyType2C(ds: Dataset, module: str, element: str, verbose: bool,
log: list, fix_trivials: bool, condition_function, mbpo: bool,
parent_ds: Dataset, root_ds: Dataset, multiplicityMin: uint32,
multiplicityMax: uint32) -> bool:
# Type 2C - Conditional Data Element (May be Empty)
err_not_exists = False
err_vr = False
err_vm = False
reason = ""
if condition_function == 0:
conditionNotSatisfied = True
else:
conditionNotSatisfied = not condition_function(ds, parent_ds, root_ds)
if element in ds:
elem = ds[element]
else:
if not conditionNotSatisfied:
reason = "Error - T<{}> {}"
reason = reason.format(ErrorType.Type2CAbsent.value,
MMsgDC("MissingAttribute"))
err_not_exists = True
if not err_not_exists:
if condition_function != 0 and conditionNotSatisfied and not mbpo:
reason = "Error - T<{}> {}"
reason = reason.format(
ErrorType.Type2CPresent.value,
MMsgDC(
"AttributePresentWhenConditionUnsatisfiedWithoutMayBePresentOtherwise"
))
if fix_trivials:
tmp = ErrorInfo(reason + "{} {}", fix_by_removing(ds, element))
reason = tmp.getWholeMessage()
if elem.is_empty:
if not verifyVR(elem, module, element, verbose, log):
reason = "Error - T<{}> {}"
reason = reason.format(ErrorType.Type2CVR.value,
MMsgDC("BadValueRepresentation"))
err_vr = True
else:
if not verifyVM(elem, module, element, verbose, log,
multiplicityMin, multiplicityMax, "source"):
reason = "Error - T<{}> {}"
reason = reason.format(
ErrorType.Type2CVM.value,
MMsgDC("BadAttributeValueMultiplicity"))
err_vm = True
if len(reason) != 0:
if fix_trivials:
ViolationMessage(reason, MMsgDC("Type2C"), module, element, log,
verbose, True)
else:
ViolationMessage(reason, MMsgDC("Type2C"), module, element, log,
verbose)
else:
ValidMessage(MMsgDC("Type2C"), module, element, log, verbose)
return len(reason) == 0
def verifyType2(ds: Dataset, module: str, element: str, verbose: bool,
log: list, fix_trivials: bool, multiplicityMin: uint32,
multiplicityMax: uint32) -> bool:
# Type 2 - Required Data Element (May be Empty)
err_vr = False
err_vm = False
err_not_exists = False
reason = ""
if element in ds:
elem = ds[element]
else:
reason = "Error - T<{}> {}"
reason = reason.format(ErrorType.Type2.value,
MMsgDC("MissingAttribute"))
err_not_exists = True
if fix_trivials: # add an empty attrib
tmp = ErrorInfo(reason + "{} {}",
fix_ByAddingEmptyAttrib(ds, element))
reason = tmp.getWholeMessage()
if not err_not_exists:
# do not check emptiness
if not elem.is_empty:
if not verifyVR(elem, module, element, verbose, log):
reason = "Error - T<{}> {}"
reason = reason.format(ErrorType.Type2VR.value,
MMsgDC("BadValueRepresentation"))
err_vr = True
else:
if not verifyVM(elem, module, element, verbose, log,
multiplicityMin, multiplicityMax):
reason = "Error - T<{}> {}"
reason = reason.format(
ErrorType.Type2VM.value,
MMsgDC("BadAttributeValueMultiplicity"))
err_vm = True
if len(reason) != 0:
if fix_trivials:
ViolationMessage(reason, MMsgDC("Type2"), module, element, log,
verbose, True)
else:
ViolationMessage(reason, MMsgDC("Type2"), module, element, log,
verbose)
else:
ValidMessage(MMsgDC("Type2"), module, element, log, verbose)
return len(reason) == 0