def CodeSeqItemGenerator(code_value: str, code_meaning: str,
coding_shceme_designator: str) -> Dataset:
output = Dataset()
cv = Dictionary.tag_for_keyword('CodeValue')
cm = Dictionary.tag_for_keyword('CodeMeaning')
cs = Dictionary.tag_for_keyword('CodingSchemeDesignator')
output[cv] = DataElementX(cv, Dictionary.dictionary_VR(cv), code_value)
output[cm] = DataElementX(cm, Dictionary.dictionary_VR(cm), code_meaning)
output[cs] = DataElementX(cs, Dictionary.dictionary_VR(cs),
coding_shceme_designator)
return output
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 generalfix_VM1(ds, log):
fixed = False
elemsTobeCorrected = []
for key, a in ds.items():
a = ds[key]
if key.is_private:
continue
try:
dvr = dictionary_VM(key)
except (BaseException):
return fixed
if dvr != '1':
continue
if a.VM <= 1:
continue
if (a.VR != 'LT' or a.VR != 'LO'):
continue
concat = '/'.join(a.value)
ds[key] = DataElementX(key, a.VR, concat)
fixed = True
err = "<{}> {}".format(a.keyword, validate_vr.tag2str(a.tag))
msg = ErrorInfo(
"General Fix - Value Multiplicity for {} "\
"is not allowed to be more than one".format(err),
"fixed by concatenating all itmes into one {}".format(concat))
log.append(msg.getWholeMessage())
fixed = True
return fixed
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 subfix_AddOrChangeAttrib(ds: Dataset, log: list, error_regexp: str,
fix_message: str, keyword: str, value) -> bool:
fixed = False
t = Dictionary.tag_for_keyword(keyword)
if t is None:
return False
desc = Dictionary.dictionary_description(t)
ErrorOccured = False
log_l = len(log)
for i in range(0, log_l):
if re.match(error_regexp, log[i]) is not None:
msg = mesgtext_cc.ErrorInfo(log[i], fix_message)
log[i] = msg.getWholeMessage()
ErrorOccured = True
if ErrorOccured:
if keyword in ds:
ds[keyword].value = value # just modify
fixed = True
else:
vr = Dictionary.dictionary_VR(t)
vm = 1
elem = DataElementX(t, vr, value)
ds[keyword] = elem
fixed = True
return fixed
def fix_ByAddingEmptyAttrib(ds: Dataset, element: str) -> str:
reason = ''
ttag = tag_for_keyword(element)
if ttag is not None:
vr = Dic.dictionary_VR(ttag)
element = DataElementX(ttag, vr, '')
element.value = element.empty_value
ds[ttag] = element
reason += "fixed by adding empty attribute"
return reason
def fix_ReferencedImageSequence(ds, log: list) -> bool:
# This patch is a prticular fixing procedure to replace SOPInstanceUID
# with ReferencedSOPInstanceUID and SOPClassUID with ReferencedSOPClassUID
fixed = False
kw = 'ReferencedImageSequence'
tg = Dictionary.tag_for_keyword(kw)
if tg not in ds:
return True
val = ds[tg].value
ref_cls_kw = 'ReferencedSOPClassUID'
ref_cls_tg = Dictionary.tag_for_keyword(ref_cls_kw)
ref_inst_kw = 'ReferencedSOPInstanceUID'
ref_inst_tg = Dictionary.tag_for_keyword(ref_inst_kw)
i = 0
while i < len(val):
item = val[i]
if 'SOPInstanceUID' in item:
msg = mesgtext_cc.ErrorInfo()
msg.msg = "Item {}/{} in <ReferencedImageSequence> holds "\
"<SOPInstanceUID> instead of <ReferencedSOPInstanceUID>".format(i + 1, len(val))
msg.fix = "fixed by changing the attribute into <ReferencedSOPInstanceUID>"
log.append(msg.getWholeMessage())
item[ref_inst_tg] = DataElementX(ref_inst_tg, 'UI',
item['SOPInstanceUID'].value)
del item['SOPInstanceUID']
fixed = True
if 'SOPClassUID' in item:
msg = mesgtext_cc.ErrorInfo()
msg.msg = "Item {}/{} in <ReferencedImageSequence> holds "\
"<SOPClassUID> instead of <ReferencedSOPClassUID>".format(i + 1, len(val))
msg.fix = "fixed by changing the attribute into <ReferencedSOPClassUID>"
log.append(msg.getWholeMessage())
item[ref_cls_tg] = DataElementX(ref_cls_tg, 'UI',
item['SOPClassUID'].value)
del item['SOPClassUID']
fixed = True
i += 1
return fixed
def subfix_UpdateOrInsertCodeAttribute(seqelem: DataElementX, index: int,
kw: str, value: str) -> str:
text_fun = lambda ds, att: '{}: {}\t'.format(att, ds[att])
out_msg = ''
if kw in seqelem.value[index]:
out_msg = " {} modified <{}> -> <{}>".format(
kw, seqelem.value[index][kw].value, value)
seqelem.value[index][kw].value = value
else:
out_msg = "{} = <{}> was added".format(kw, value)
newtag = Dictionary.tag_for_keyword(kw)
newvr = Dictionary.dictionary_VR(newtag)
elem = DataElementX(newtag, newvr, value)
seqelem.value[index].add(elem)
return out_msg
def generalfix_RealWorldValueMappingSequence(ds, log):
kw = 'RealWorldValueMappingSequence'
tg = tag_for_keyword(kw)
if tg in ds:
v = ds[tg].value
for i, item in enumerate(v):
in_key = 'LUTLabel'
in_tg = tag_for_keyword(in_key)
if in_tg not in item:
new_el = DataElementX(in_tg, 'SH', 'Unknown')
item[in_tg] = new_el
err = "<{}> {}".format(in_key, validate_vr.tag2str(in_tg))
msg = ErrorInfo(
"General Fix - The item number {} lacks {}".format(i, err),
"fixed by adding a new element with value <{}>".format(
new_el.value))
log.append(msg.getWholeMessage())
def put_attribute_in_path(ds: Dataset, path: list, a: DataElementX):
if not path:
if a.tag not in ds:
ds[a.tag] = a
else:
kw = path.pop(0)
tg = Dictionary.tag_for_keyword(kw)
vr = Dictionary.dictionary_VR(tg)
if vr == 'SQ':
if tg in ds and ds[tg].VM > 0:
inner_sq = ds[tg]
item = inner_sq.value[0]
else:
item = Dataset()
new_element = DataElementX(tg, vr, Sequence([item]))
ds[tg] = new_element
put_attribute_in_path(item, path, a)
def generalfix_MisplacedAttributes(ds: Dataset, log: list):
paths = {}
current_folder = os.path.dirname(__file__)
with open(os.path.join(current_folder, 'config.json')) as json_file:
fix_config = json.load(json_file)
get_all_kw_paths(ds, [], paths)
standard_ds = get_full_attrib_list(ds)
not_in_std = {}
misplaced = {}
for kw, pp in paths.items():
tg = tag_for_keyword(kw)
if kw not in standard_ds:
not_in_std[kw] = pp
else:
std__ = standard_ds[kw]
if len(std__) > 1:
continue
for parent, path in pp:
correct_path = std__[0]['path']
if path != correct_path:
if kw not in misplaced:
misplaced[kw] = [(parent, path, correct_path)]
else:
misplaced[kw].append((parent, path, correct_path))
for kw, val in misplaced.items():
if not fix_config["MisplacedAttributes"][
"DisplaceIfAttributeIsInWrongPath"]:
break
for parent, path, correct_path in val:
# print(parent, path, correct_path)
delem = parent[kw]
del parent[kw]
new_paretn = ds
inner_kw = kw
parent_ds = ds
for p in correct_path:
if p not in parent_ds:
new_ds = Dataset()
parent_ds[p] = DataElementX(tag_for_keyword(p), 'SQ',
DataElementSequence([new_ds]))
elif parent_ds[p].is_empty:
new_ds = Dataset()
parent_ds[p].value = DataElementSequence([new_ds])
parent_ds = parent_ds[p].value[0]
if kw not in parent_ds:
parent_ds[kw] = delem
msg = ErrorInfo(
"General Fix - The DICOM attribute <{}> is not in "
"correct place. "
"current-path = {} vs. correct-path = {}".format(
kw, path, correct_path),
"fixed by attribute displacement")
else:
msg = ErrorInfo(
"General Fix - The DICOM attribute <{}> is not in "
"correct place. "
"current-path = {} vs. correct-path = {}".format(
kw, path, correct_path),
"couldn't fix because there is already "
"an attribute in correct place")
log.append(msg.getWholeMessage())
for kw, val in not_in_std.items():
if not fix_config["MisplacedAttributes"]["RemoveIfAttributeIsNotInIOD"]:
break
for parent, path in val:
if kw in parent:
del parent[kw]
msg = ErrorInfo(
"General Fix - The keyword <{}> is not in "
"standard DICOM IOD".format(kw),
"fixed by removing the attribute")
log.append(msg.getWholeMessage())
def subfix_checkandfixBasicCodeSeq(seqelem: DataElementX, log: list) -> bool:
fixed = False
msg = mesgtext_cc.ErrorInfo("General Fix - Remove empty code seq ")
items_to_be_deleted = []
text_fun = lambda ds, att: '{}: <{}>\t'.format(att, ds[att].value)
subfix_UpdateSRTCodes(seqelem, log)
for i, item in enumerate(seqelem.value, 1):
hasCodeValue = True if "CodeValue" in item else False
emptyCodeValue = True if not hasCodeValue else item[
"CodeValue"].is_empty
textCodeValue = '' if not hasCodeValue else text_fun(item, "CodeValue")
hasCodeMeaning = True if "CodeMeaning" in item else False
emptyCodeMeaning = True if not hasCodeMeaning else item[
"CodeMeaning"].is_empty
textCodeMeaning = '' if not hasCodeMeaning else text_fun(
item, "CodeMeaning")
hasLongCodeValue = True if "LongCodeValue" in item else False
emptyLongCodeValue = True if not hasLongCodeValue else item[
"LongCodeValue"].is_empty
textLongCodeValue = '' if not hasLongCodeValue else text_fun(
item, "LongCodeValue")
hasURNCodeValue = True if "URNCodeValue" in item else False
emptyURNCodeValue = True if not hasURNCodeValue else item[
"CodURNCodeValue"].is_empty
textURNCodeValue = '' if not hasURNCodeValue else text_fun(
item, "CodURNCodeValue")
hasCodingSchemeDesignator = True if "CodingSchemeDesignator" in item else False
emptyCodingSchemeDesignator = True if not hasCodingSchemeDesignator else item[
"CodingSchemeDesignator"].is_empty
textCodingSchemeDesignator = '' if not hasCodingSchemeDesignator else text_fun(
item, "CodingSchemeDesignator")
hasCodingSchemeVersion = True if "CodingSchemeVersion" in item else False
emptyCodingSchemeVersion = True if not hasCodingSchemeVersion else item[
"CodingSchemeVersion"].is_empty
textCodingSchemeVersion = '' if not hasCodingSchemeVersion else text_fun(
item, "CodingSchemeVersion")
hasCodeValue = hasCodeValue or hasLongCodeValue or hasURNCodeValue
emptyCodeValue = not (not emptyCodeValue or not emptyLongCodeValue
or not emptyURNCodeValue)
textCodeValue = (textCodeValue + textLongCodeValue + textURNCodeValue)
bit_code = numpy.uint8(0)
if emptyCodeValue:
bit_code = bit_code | 0x1
if emptyCodeMeaning:
bit_code = bit_code | 0x10
if emptyCodingSchemeDesignator:
bit_code = bit_code | 0x100
state_text = subfix_CodeSeqItem2txt(seqelem, i - 1)
state_text = ". Item current value is: " + state_text if state_text != '' else ''
if hasCodingSchemeVersion and emptyCodingSchemeVersion:
del item["CodingSchemeVersion"]
msg.fix = "Empty CodingSchemeVersion in item {} of {} was deleted".format(
i, seqelem.name) + state_text
del_msg = msg.getWholeMessage()
log.append(del_msg)
if bit_code == 0x111 or bit_code == 0x110 or bit_code == 0x011 or \
bit_code == 0x101 or bit_code == 0x001 or bit_code == 0x010:
items_to_be_deleted.append(item)
msg.fix = "Item {} of {} was deleted".format(i, seqelem.keyword)
del_msg = msg.getWholeMessage()
log.append(del_msg)
fixed = True
if bit_code == 0x100:
if hasCodingSchemeDesignator:
item["CodingSchemeDesignator"].value = '99LOCAL'
msg.fix = "The value for CodingSchemeDesignator in "\
"item {} of {} was modified to 99LOCAL".format(
i, seqelem.keyword
) + state_text
del_msg = msg.getWholeMessage()
log.append(del_msg)
else:
kw = "CodingSchemeDesignator"
new_tag = Dictionary.tag_for_keyword(kw)
new_vr = Dictionary.dictionary_VR(new_tag)
new_elem = DataElementX(new_tag, new_vr, "99LOCAL")
item[kw] = new_elem
msg.fix = "An element of CodingSchemeDesignator with value "\
"<99LOCAL> in item {} of {} was added".format(
i, seqelem.keyword
) + state_text
del_msg = msg.getWholeMessage()
log.append(del_msg)
fixed = True
for el in items_to_be_deleted:
seqelem.value.remove(el)