def fix_RemoveFOVDimensionsWhenZero(ds: Dataset, log: list) -> bool:
fixed = False
kw = "FieldOfViewDimensions"
Error_regex = ".*Value is zero for.*attribute.*Field.*View.*Dimension.*"
msg = mesgtext_cc.ErrorInfo()
idx = subfix_LookUpRegexInLog(Error_regex, log)
if kw in ds:
if len(idx) == 0:
idx.append(-1)
log.append("Error - bad value (=0) for {}".format(kw))
tag = Dictionary.tag_for_keyword(kw)
elem = ds[tag]
for i in elem.value:
if i == 0:
fixed = True
break
if fixed:
del ds[kw]
for i in idx:
msg.msg = log[i]
msg.fix = "fixed by removing the attribute"
msg1 = msg.getWholeMessage()
log[i] = msg1
else:
for i in idx:
log.pop(i)
return fixed
def fix_PatientPositionAndPatientOrientationCodeSequencePresent(
ds: Dataset, log: list) -> bool:
code_kws = [
'CodeValue', "CodeMeaning", "CodingSchemeDesignator", "LongCodeValue",
"URNCodeValue", "CodingSchemeVersion"
]
msg = mesgtext_cc.ErrorInfo()
fixed = False
pp = 'PatientPosition'
posq = 'PatientOrientationCodeSequence'
Error_regex = ".*May not be present when {} is present.*{}.*".format(
posq, pp)
if posq in ds:
if pp in ds:
seq_elem = ds[posq]
idx = subfix_LookUpRegexInLog(Error_regex, log)
txt = subfix_CodeSeqItem2txt(seq_elem, 0)
if len(idx) == 0:
idx.append(-1)
log.append("{} = {} and {} both are present".format(
pp, ds[pp].value, txt))
for i in idx:
msg.msg = log[i]
if len(seq_elem.value) > 0:
msg.fix = "kept {} but removed {}".format(txt, pp)
del ds[pp]
else:
msg.fix = "kept {} but removed {}".format(pp, txt)
del ds[posq]
log[i] = msg.getWholeMessage()
fixed = True
return fixed
def subfix_ReplaceSlashWithBackslash(attrib: DataElementX, log: list) -> bool:
fixed = False
msg = mesgtext_cc.ErrorInfo('General Fix -', '')
fix = 'fixed attribute <{}> ({}) value by changing slash to backslash {} -> {}'
if type(attrib.value) == MultiValue:
tmp = attrib.value
else:
tmp = [attrib.value]
for idx in range(0, len(tmp)):
old_val = tmp[idx]
if type(tmp[idx]) == str:
tmp[idx] = tmp[idx].replace('/', '\\')
elif type(tmp[idx]) == bytes:
x = bytearray()
for elem in tmp[idx]:
if elem == ord('/'):
x.append(ord('\\'))
else:
x.append(elem)
tmp[idx] = bytes(x)
if old_val != tmp[idx]:
msg.fix = fix.format(attrib.name, idx + 1, old_val, tmp[idx])
log.append(msg.getWholeMessage())
fixed = True
if type(attrib.value) != MultiValue:
attrib.value = tmp[0]
return fixed
def fix_VRForLongitudinalTemporalInformationModified(ds: Dataset,
log: list) -> bool:
fixed = False
msg = mesgtext_cc.ErrorInfo()
kw = "LongitudinalTemporalInformationModified"
Error_regex = ".*Invalid Value Representation SH \(CS Required\)" \
".*{}.*".format(kw)
idx = subfix_LookUpRegexInLog(Error_regex, log)
if len(idx) == 0:
idx.append(-1)
log.append("Error - bad VR for {}".format(kw))
if kw in ds:
tag = Dictionary.tag_for_keyword(kw)
if ds[tag].VR == "SH":
ds[tag].VR = "CS"
for i in idx:
msg.msg = log[i]
msg.fix = "fixed by editing SH to CS"
msg1 = msg.getWholeMessage()
log[i] = msg1
fixed = True
if not fixed:
for i in idx:
log.pop(i)
return fixed
def LoopOverAllAtribsAndRemoveIfConditionIsTrue(ds: Dataset,
cond,
log: list,
err='') -> bool:
fixed = False
elements_to_be_removed = []
for key, a in ds.items():
a = ds[key]
if type(a) == pydicom.dataelem.RawDataElement:
a = pydicom.dataelem.DataElementX_from_raw(a)
if type(a.value) == Sequence:
for item in a.value:
fixed = fixed or LoopOverAllAtribsAndRemoveIfConditionIsTrue(
item, cond, log, err)
elif type(a.value) == Dataset:
fixed = fixed or LoopOverAllAtribsAndRemoveIfConditionIsTrue(
a.value, cond, log, err)
else:
if cond(a):
ttaagg = validate_vr.tag2str(a.tag)
attrib = "<{}> -> {}".format(a.keyword, ttaagg)
tmperr = err.format(attrib)
msg = mesgtext_cc.ErrorInfo()
msg.msg = tmperr
msg.fix = "fixed by removing the attribute"
log.append(msg.getWholeMessage())
fixed = True
elements_to_be_removed.append(a.tag)
for tg in elements_to_be_removed:
del ds[tg]
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 priorfix_RemoveIllegalTags(ds: Dataset, parent_kw: str, log: list) -> bool:
logger = logging.getLogger(__name__)
tags_to_be_removed = []
fixed = False
for k, a in ds.items():
try:
a = ds[k]
except BaseException as err:
ttaagg = validate_vr.tag2str(k)
eerr = mesgtext_cc.ErrorInfo(
"General Fix - attribute with tag {} in {} is not"
" readable by pydicom".format(ttaagg, parent_kw),
'fixed by removing the attribute')
log.append(eerr.getWholeMessage())
loggermsg = 'attribute with tag {} in {} is not '\
'readable by pydicom because {}'.format(ttaagg, parent_kw, err)
logger.error(loggermsg, stack_info=True)
tags_to_be_removed.append(k)
continue
if type(a.value) == Sequence:
for item in a.value:
fixed = fixed or priorfix_RemoveIllegalTags(
item, a.keyword, log)
elif type(a.value) == Dataset:
fixed = fixed or priorfix_RemoveIllegalTags(
a.value, a.keyword, log)
for tg in tags_to_be_removed:
del ds[tg]
return fixed
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 fix_PatientSex(ds: Dataset, log: list) -> bool:
fixed = False
msg = mesgtext_cc.ErrorInfo()
kw = "PatientSex"
error_regex = r".*Unrecognized enumerated value .* for .* of attribute .*Patient.*Sex"
if kw in ds:
old_value = ds[kw].value
else:
old_value = ''
new_value = ""
fix_m = "fixed by modifying the {} from {} to empty string".format(
kw, old_value)
return subfix_AddOrChangeAttrib(ds, log, error_regex, fix_m, kw, new_value)
def subfix_RemoveAttrib(ds: Dataset, log: list, error_regexp: str,
keyword: str) -> 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],
"fixed by removing the attribute")
log[i] = msg.getWholeMessage()
ErrorOccured = True
if ErrorOccured:
del ds[keyword]
fixed = True
return fixed
def generalfix_CT_RescaleType(ds, log):
fixed = False
modality = None if "Modality" not in ds else ds['Modality'].value
if modality == 'CT':
if 'RescaleType' not in ds:
return fixed
if ds['RescaleType'] == 'HU':
return fixed
contains_localizer = False
ImageType_v = [] if 'ImageType' not in ds else ds['ImageType'].value
for i in ImageType_v:
if i == 'LOCALIZER':
contains_localizer = True
break
if not contains_localizer:
oldval = ds['RescaleType'].value
ds['RescaleType'].value = "HU"
msg = mesgtext_cc.ErrorInfo()
msg.msg = "General Fix - <RescaletType> is not HU (Hounsfield Units) "
msg.fix = "fixed by changing the attribute from {} to {}".format(
oldval, 'HU')
log.append(msg.getWholeMessage())
fixed = True
return fixed
def fix_PregnancyStatus(ds: Dataset, log: list) -> bool:
fixed = False
msg = mesgtext_cc.ErrorInfo()
kw = "PregnancyStatus"
error_regex = r".*Unrecognized enumerated value .* attribute .*Pregnancy.*Status.*"
return subfix_RemoveAttrib(ds, log, error_regex, kw)
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)
def subfix_UpdateSRTCodes(seqelem: DataElementX, log: list) -> bool:
fixed = False
msg = mesgtext_cc.ErrorInfo(
"General Fix - Upadate old snomed codes to SCT")
items_to_be_deleted = []
text_fun = lambda ds, att: '{}: {}\t'.format(att, ds[att])
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)
isSRT = False
if hasCodingSchemeDesignator:
v = item["CodingSchemeDesignator"].value
if v == "SNM3" or v == "99SDM" or v == "SRT":
isSRT = True
else:
if hasCodeValue:
v = item["CodeValue"].value
if re.match("[A-Z][A-Z0-9]{0,2}-[0-9A-Z]{4,5}", v) is not None:
isSRT = True
if not isSRT or not hasCodeValue:
return False
value = item["CodeValue"].value
first_dict = srt.mapping['SRT']
second_dict = sctsrt.replaced_entries
replacing_value = ''
if value in first_dict:
replacing_value = first_dict[value]
elif value in second_dict:
replacingvalue = second_dict[value]
if len(replacing_value) == 0:
return False
replacing_meaning = ''
if replacing_value in sctsrt.sct_meaning:
replacing_meaning = sctsrt.sct_meaning[replacing_value]
msg1 = "item {} of {}:\t".format(i, seqelem.keyword)
msg1 += "({}-{})".format(i, 1) + subfix_UpdateOrInsertCodeAttribute(
seqelem, i - 1, "CodeValue", replacing_value)
msg1 += "({}-{})".format(i, 2) + subfix_UpdateOrInsertCodeAttribute(
seqelem, i - 1, "CodeMeaning", replacing_meaning)
msg1 += "({}-{})".format(i, 3) + subfix_UpdateOrInsertCodeAttribute(
seqelem, i - 1, "CodingSchemeDesignator", 'SCT')
msg.fix = msg1
msg2 = msg.getWholeMessage()
log.append(msg2)
fixed = True
return fixed