def __setitem__(self, key, value):
if isinstance(key, int):
setattr(self, self._dict[key][4], value)
elif isinstance(key, str):
setattr(self, key, value)
elif isinstance(key, tuple):
tag1, tag2 = key
setattr((self, self._dict[tag1 * (16**4) + tag2][4], value))
else:
raise LightError("This is not valid indexing. Try one of:\n" + \
" 1. dcm[0x10,0x10]\n" + \
" 2. dcm[0x100010]\n" + \
" 3. dcm.PatientName")
def __getitem__(self, tag: Union[str, int, tuple]) -> Any:
if isinstance(tag, str):
return getattr(self, tag)
elif isinstance(tag, int):
field = self._dict[tag][4]
return getattr(self, field)
elif isinstance(tag, tuple):
tag1, tag2 = tag
field = self._dict[tag1 * (16**4) + tag2][4]
return getattr(self, field)
else:
raise LightError("This is not valid indexing. Try one of:\n"+\
" 1. dcm[0x10,0x10]\n"+\
" 2. dcm[0x100010]\n"+\
" 3. dcm.PatientName")
def parseUntilUID(tagClass:Tag, \
file:bin, \
idx=132) -> Tag:
UID = None
while True:
idx = int(idx)
_tag = getTag(file[idx:idx + 4], isLittle=True)
isGroupLengthTag = ifGroupLengthTag(_tag)
idx = idx + 4
vr = file[idx:idx + 2]
# Refer "https://dicom.nema.org/dicom/2013/output/chtml/part05/chapter_7.html" for more details.
if vr in [b'OB', b'OW', b'OF', b'SQ', b'UT', b'UN']:
idx = idx + 2 + 2 # Last 2 is for reserved 2 bytes.
vl = file[idx:idx + 4]
idx = idx + 4
vl = _OBOW_vr(vl, _tag, isLittle=True)
else:
idx = idx + 2 # There are no reseved bytes.
vl = file[idx:idx + 2]
vl = _get_vr_length(vl, isLittle=True)
idx = idx + 2
value = file[idx:idx + vl]
if isGroupLengthTag:
assert vr == b'UL', "Value Representation (VR) should be type of UL (Unsigned Long) for Group Length Tag."+\
f"Current VR : {vr}. Check your DICOM sanity."
value = parseUL(value, isLittle=True)
idx = idx + vl
tagClass[_tag] = [vr, vl, value]
if _tag == 131088:
UID = hex(_tag)
print(hex(_tag), vr, vl, value)
if UID is not None:
return tagClass, idx, UID
if idx > len(file):
raise LightError(
"This file does not follow DICOM standard protocol. Check your DICOM sanity."
)
def _exam_file(self, file, force):
preamble = bytes([0]) * 128
if file[:128] != preamble:
if self.print_warning == True:
print(
f"For {self.path}, first 128 bytes are not zeros. This is not usual DICOM type. Handle this file carefully."
)
else:
pass
if file[128:132] != b'DICM':
if force is False:
raise LightError(f"For {self.path}, 129-th~133-th bytes should be 'DICM'. This is not valid DICOM file.\n"\
+"If you want to read this file anyway, try 'LightDCMClass(force=True)'")
else:
if self.print_warning is True:
print(
f"For {self.path}, 129-th~133-th bytes are not 'DICM'. This is not usual DICOM type. Handle this file carefully."
)
else:
pass
def parseImplicitVRLittleEndian(tagClass:Tag, \
file:bin, \
isLittle:bool,\
idx=132) -> Tag:
while True:
idx = int(idx)
_tag = getTag(file[idx:idx + 4], isLittle=isLittle)
isGroupLengthTag = ifGroupLengthTag(_tag)
idx = idx + 4
# Refer "https://dicom.nema.org/dicom/2013/output/chtml/part05/chapter_7.html" for more details.
print(hex(_tag))
vr = DicomDictionary[_tag][0]
vl = file[idx:idx + 4]
idx = idx + 4
vl = _get_vr_length(vl, isLittle=isLittle)
value = file[idx:idx + vl]
if isGroupLengthTag:
assert vr == b'UL', "Value Representation (VR) should be type of UL (Unsigned Long) for Group Length Tag."+\
f"Current VR : {vr}. Check your DICOM sanity."
value = parseUL(value, isLittle=isLittle)
idx = idx + vl
tagClass[_tag] = [vr, vl, value]
print(hex(_tag), vr, vl, value)
if idx == len(file):
return tagClass
if idx > len(file):
raise LightError(
"This file does not follow DICOM standard protocol. Check your DICOM sanity."
)
def read_all(self, with_pixel=True, resize_pixel=True):
if not os.path.isfile(self.path):
raise LightError(
f"{self.path} does not exist. Check your file path")
if self.file == None:
self.lightRead(self.path)
idx = 132
self._check_endian()
all_dict = {}
while idx < len(self.file) - 4:
find_tag = self._maketag(self.file[idx:idx + 4], idx)
if 'Explicit' in self.endian:
dtype = self.file[idx + 4:idx + 6]
if find_tag == '0008,1140':
vl = self.file[idx + 8:idx + 12]
all_dict[find_tag] = self.file[idx + 12:idx + 12 + 8]
idx = idx + 20
else:
if dtype in [b'OB', b'OW', b'SQ', b'UN']:
reserved = self.file[idx + 6:idx + 8]
vl = self.file[idx + 8:idx + 12]
if dtype in [b'OB', b'OW']:
vl = self._OBOW_vr(vl, find_tag)
else:
vl = self._get_vr_length(vl)
if find_tag == '7fe0,0010':
if with_pixel:
all_dict[find_tag] = self.file[idx + 12:idx +
12 + vl]
idx = idx + 12 + vl
else:
all_dict[find_tag] = b''
idx = idx + 12 + vl
else:
all_dict[find_tag] = self.file[idx + 12:idx + 12 +
vl]
idx = idx + 12 + vl
else:
vl = self.file[idx + 6:idx + 8]
vl = self._get_vr_length(vl)
all_dict[find_tag] = self.file[idx + 8:idx + 8 + vl]
idx = idx + 8 + vl
if 'Implicit' in self.endian:
if find_tag == '0008,1140':
vl = self.file[idx + 8:idx + 12]
all_dict[find_tag] = self.file[idx + 12:idx + 12 + 8]
idx = idx + 20
else:
try:
if int(find_tag[:4]) < 8:
dummy = 0
vl = self.file[idx + 6:idx + 8 + dummy]
else:
dummy = 2
vl = self.file[idx + 4:idx + 6 + dummy]
except:
dummy = 2
vl = self.file[idx + 4:idx + 6 + dummy]
if find_tag == '7fe0,0010':
if with_pixel:
if resize_pixel:
vl = self._OBOW_vr(vl, find_tag)
all_dict[find_tag] = self.read_pixel()
else:
vl = self._OBOW_vr(vl, find_tag)
value = self.file[idx + 8:idx + 8 + vl]
all_dict[find_tag] = np.frombuffer(
value, np.int16)
else:
vl = self._OBOW_vr(vl, find_tag)
all_dict[find_tag] = ''
else:
vl = self._get_vr_length(vl)
all_dict[find_tag] = self.file[idx + 8:idx + 8 + vl]
try:
if int(find_tag[:4]) < 8:
idx = idx + 8 + vl + dummy
else:
idx = idx + 6 + vl + dummy
except:
idx = idx + 6 + dummy + vl
return all_dict
def get_data(self, tag, path=None):
if not os.path.isfile(self.path):
raise LightError(
f"{self.path} does not exist. Check your file path")
if self.file == None:
self.lightRead(path)
tag = tag.replace(' ', '')
idx = 132
self._check_endian()
while True:
find_tag = self._maketag(self.file[idx:idx + 4], idx)
if 'Explicit' in self.endian:
dtype = self.file[idx + 4:idx + 6]
if find_tag == '0008,1140':
if tag == '0008,1140':
vl = self.file[idx + 8:idx + 12]
return {
'tag': tag,
'dtype': dtype,
'length': vl,
'value': self.file[idx + 12:idx + 12 + 8]
}
else:
idx = idx + 20
else:
if dtype in [b'OB', b'OW', b'SQ', b'UN']:
reserved = self.file[idx + 6:idx + 8]
vl = self.file[idx + 8:idx + 12]
if dtype in [b'OB', b'OW']:
vl = self._OBOW_vr(vl, find_tag)
else:
vl = self._get_vr_length(vl)
if find_tag == tag:
return {
'tag': tag,
'dtype': dtype,
'reserved': reserved,
'length': vl,
'value': self.file[idx + 12:idx + 12 + vl]
}
else:
idx = idx + 12 + vl
else:
vl = self.file[idx + 6:idx + 8]
vl = self._get_vr_length(vl)
if find_tag == tag:
return {
'tag': tag,
'dtype': dtype,
'length': vl,
'value': self.file[idx + 8:idx + 8 + vl]
}
else:
idx = idx + 8 + vl
if 'Implicit' in self.endian:
if find_tag == '0008,1140':
if tag == '0008,1140':
vl = self.file[idx + 8:idx + 12]
return {
'tag': tag,
'dtype': dtype,
'length': vl,
'value': self.file[idx + 12:idx + 12 + 8]
}
else:
idx = idx + 20
else:
try:
if int(find_tag[:4]) < 8:
dummy = 0
vl = self.file[idx + 6:idx + 8 + dummy]
else:
dummy = 2
vl = self.file[idx + 4:idx + 6 + dummy]
except:
dummy = 2
vl = self.file[idx + 4:idx + 6 + dummy]
if find_tag == '7fe0,0010':
vl = self._OBOW_vr(vl, find_tag)
value = self.file[idx + 8:idx + 8 + vl]
return {
'tag': tag,
'length': vl,
'value': np.frombuffer(value, np.int16)
}
else:
vl = self._get_vr_length(vl)
if find_tag == tag:
return {
'tag': tag,
'length': vl,
'value': self.file[idx + 8:idx + 8 + vl]
}
else:
try:
if int(find_tag[:4]) < 8:
idx = idx + 8 + vl + dummy
else:
idx = idx + 6 + vl + dummy
except:
idx = idx + 6 + dummy + vl
if idx >= len(self.file) - 4:
raise LightError(
f"No matching tag was founded for tag ({tag}) in file {self.path}."
)