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 generalfix_AddPresentationLUTShape(ds: Dataset, log: list) -> bool:
fixed = False
photo_in_tg = tag_for_keyword('PhotometricInterpretation')
if photo_in_tg not in ds:
return fixed
photo_in_v = ds[photo_in_tg].value
pres_lut_shape_tg = tag_for_keyword('PresentationLUTShape')
if pres_lut_shape_tg in ds:
pres_lut_shape_a = ds[pres_lut_shape_tg]
else:
pres_lut_shape_a = DataElementX(pres_lut_shape_tg,
dictionary_VR(pres_lut_shape_tg), '')
old_pls = pres_lut_shape_a.value
if photo_in_v == 'MONOCHROME2' and old_pls != 'IDENTITY':
new_pls = 'IDENTITY'
pres_lut_shape_a.value = new_pls
fixed = True
elif photo_in_v == 'MONOCHROME1' and old_pls != 'INVERSE':
new_pls = 'INVERSE'
pres_lut_shape_a.value = new_pls
fixed = True
if fixed:
ds[pres_lut_shape_tg] = pres_lut_shape_a
msg = ErrorInfo()
msg.msg = 'General Fix - {}'.format(
"<PresentationLUTShape> is wrong or absent")
msg.fix = "fixed by setting the <PresentationLUTShape>"\
" from '{}' to '{}'".format(old_pls, new_pls)
log.append(msg.getWholeMessage())
return fixed
def generalfix_CheckAndFixModality(ds: Dataset, log: list) -> bool:
fixed = False
modality_sop = {
CTImageStorageSOPClassUID: 'CT',
MRImageStorageSOPClassUID: 'MR',
PETImageStorageSOPClassUID: 'PT',
}
if 'SOPClassUID' in ds:
sop_class = ds['SOPClassUID'].value
else:
return False
if sop_class not in modality_sop:
return False
mod_tg = tag_for_keyword('Modality')
if mod_tg in ds:
modality = ds[mod_tg].value
else:
modality = ''
if modality == '' or modality != modality_sop[sop_class]:
ds[mod_tg] = DataElementX(mod_tg, dictionary_VR(mod_tg),
modality_sop[sop_class])
msg = ErrorInfo()
msg.msg = 'General Fix - {}'.format("<Modality> is wrong or absent")
msg.fix = "fixed by reading the <SOPClassUID> and setting <Modality>"\
" from '{}' to '{}'".format(modality, modality_sop[sop_class])
log.append(msg.getWholeMessage())
fixed = True
return fixed
def generalfix_RemoveUnwanterPixelAspctRatio(ds: Dataset, log: list) -> bool:
fixed = False
kw = "PixelAspectRatio"
is_one_to_one = False
if kw in ds:
elem = ds[kw]
if type(elem) == MultiValue:
if len(elem) == 2:
is_one_to_one = (elem.value[0] == elem.value[2])
if (Condition_UnwantedPixelAspectRatioWhenPixelSpacingPresent(
ds, ds, ds
) or Condition_UnwantedPixelAspectRatioWhenImagerPixelSpacingPresent(
ds, ds, ds
) or Condition_UnwantedPixelAspectRatioWhenNominalScannedPixelSpacingPresent(
ds, ds, ds
) or Condition_UnwantedPixelAspectRatioWhenSharedPixelMeasuresMacro(
ds, ds, ds
) or Condition_UnwantedPixelAspectRatioWhenPerFramePixelMeasuresMacro(
ds, ds, ds) or
Condition_UnwantedPixelAspectRatioWhenMPEG2MPHLTransferSyntax(
ds, ds, ds) or is_one_to_one):
msg = ErrorInfo()
msg.msg = '{} Error - {}'.format(
ErrorType.BadValue.value,
"<PixelAspectRatio> is 1:1 or redundant")
msg.fix = "fixed by removing the attribute"
log.append(msg.getWholeMessage())
del ds["PixelAspectRatio"]
fixed = True
return fixed