def generalfix_TrailingNulls(ds: Dataset, log: list) -> bool:
fixed = False
elemsTobeCorrected = []
for key, a in ds.items():
a = ds[key]
if key.is_private:
continue
if a.VR == 'UI' or a.VR == 'OB' or a.VR == 'OW' or a.VR == 'UN':
continue
if type(a) == pydicom.dataelem.RawDataElement:
a = pydicom.dataelem.DataElement_from_raw(a)
if type(a.value) == Sequence:
for item in a.value:
fixed = fixed or generalfix_TrailingNulls(item, log)
elif type(a.value) == Dataset:
fixed = fixed or generalfix_TrailingNulls(a.value, log)
else:
partial_fixed = subfix_HasTrailingNulls(a)
if partial_fixed:
msg = mesgtext_cc.ErrorInfo("<{}> {}".format(
a.description(), validate_vr.tag2str(a.tag)))
err = "<{}> {}".format(a.description(),
validate_vr.tag2str(a.tag))
msg = mesgtext_cc.ErrorInfo(
"General Fix - Trailing null bytesz",
"fixed by removing the trailing null bytes for {}".format(
err))
log.append(msg.getWholeMessage())
elemsTobeCorrected.append(a)
fixed = True
return fixed
def subfix_ReplaceSlashWithBackslash(attrib: DataElement, 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 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 = DataElement(t, vr, value)
ds[keyword] = elem
fixed = True
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
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 = mesgtext_cc.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
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.DataElement_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 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 priorfix_RemoveIllegalTags(ds: Dataset, parent_kw: str, log: list) -> bool:
tags_to_be_removed = []
fixed = False
for k, a in ds.items():
try:
a = ds[k]
except KeyError as err:
if not k.is_private:
if not Dictionary.dictionary_has_tag(k):
ttaagg = validate_vr.tag2str(a.tag)
eerr = mesgtext_cc.ErrorInfo(
"General Fix - tag {} in {}is not a standard dicom tag"
.format(ttaagg,
parent_kw), 'fixed by removing the attribute')
log.append(eerr.getWholeMessage())
tags_to_be_removed.append(a.tag)
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_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 len(idx) == 0:
idx.append(-1)
log.append("Error - bad value (=0) for {}".format(kw))
if kw in ds:
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
return fixed
def fix_BitsAllocated8ToBitsAllocated16(ds: Dataset, log: list):
log_l = len(log)
ErrorPattern = "Error - Unrecognized enumerated value <{}> for value 1 of " \
"attribute {} BinaryValueDescription_BitsAre{}"
convert = False
for i in range(0, log_l):
if log[i] == ErrorPattern.format(8, "Bits Allocated", 16) or\
log[i] == ErrorPattern.format(8, "Bits Stored", 16) or\
log[i] == ErrorPattern.format(7, "High Bit", 15) :
x = "fixed by conversion of PixelData to 16 bits"
msg = mesgtext_cc.ErrorInfo(log[i], x)
log[i] += msg.getWholeMessage()
convert = True
if convert:
subfix_ConvertImageData16(ds, log)
def subfix_checkandfixBasicCodeSeq(seqelem: DataElement, 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"] = '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 = DataElement(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: DataElement, 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