def test_write_UR_explicit_little(self):
"""Test writing elements with VR of UR works correctly.
Elements with a VR of 'UR' use the newer explicit VR
encoded (see PS3.5 Section 7.1.2).
"""
# Even length URL
elem = DataElement(0x00080120, 'UR', 'ftp://bits')
encoded_elem = self.encode_element(elem, False, True)
# Tag pair (0008, 2001): 08 00 20 01
# VR (UR): \x55\x52
# Reserved: \x00\x00
# Length (4): \x0a\x00\x00\x00
# Value: \x66\x74\x70\x3a\x2f\x2f\x62\x69\x74\x73
ref_bytes = b'\x08\x00\x20\x01\x55\x52\x00\x00\x0a\x00\x00\x00' \
b'\x66\x74\x70\x3a\x2f\x2f\x62\x69\x74\x73'
self.assertEqual(encoded_elem, ref_bytes)
# Odd length URL has trailing \x20 (SPACE) padding
elem.value = 'ftp://bit'
encoded_elem = self.encode_element(elem, False, True)
ref_bytes = b'\x08\x00\x20\x01\x55\x52\x00\x00\x0a\x00\x00\x00' \
b'\x66\x74\x70\x3a\x2f\x2f\x62\x69\x74\x20'
self.assertEqual(encoded_elem, ref_bytes)
# Empty value
elem.value = ''
encoded_elem = self.encode_element(elem, False, True)
ref_bytes = b'\x08\x00\x20\x01\x55\x52\x00\x00\x00\x00\x00\x00'
self.assertEqual(encoded_elem, ref_bytes)
def test_write_UC_implicit_little(self):
"""Test writing elements with VR of UC works correctly."""
# VM 1, even data
elem = DataElement(0x00189908, 'UC', 'Test')
encoded_elem = self.encode_element(elem)
# Tag pair (0018, 9908): 08 00 20 01
# Length (4): 04 00 00 00
# Value: \x54\x65\x73\x74
ref_bytes = b'\x18\x00\x08\x99\x04\x00\x00\x00\x54\x65\x73\x74'
self.assertEqual(encoded_elem, ref_bytes)
# VM 1, odd data - padded to even length
elem.value = 'Test.'
encoded_elem = self.encode_element(elem)
ref_bytes = b'\x18\x00\x08\x99\x06\x00\x00\x00\x54\x65\x73\x74\x2e\x20'
self.assertEqual(encoded_elem, ref_bytes)
# VM 3, even data
elem.value = ['Aa', 'B', 'C']
encoded_elem = self.encode_element(elem)
ref_bytes = b'\x18\x00\x08\x99\x06\x00\x00\x00\x41\x61\x5c\x42\x5c\x43'
self.assertEqual(encoded_elem, ref_bytes)
# VM 3, odd data - padded to even length
elem.value = ['A', 'B', 'C']
encoded_elem = self.encode_element(elem)
ref_bytes = b'\x18\x00\x08\x99\x06\x00\x00\x00\x41\x5c\x42\x5c\x43\x20'
self.assertEqual(encoded_elem, ref_bytes)
# Empty data
elem.value = ''
encoded_elem = self.encode_element(elem)
ref_bytes = b'\x18\x00\x08\x99\x00\x00\x00\x00'
self.assertEqual(encoded_elem, ref_bytes)
def test_write_UR_implicit_little(self):
"""Test writing elements with VR of UR works correctly."""
# Even length URL
elem = DataElement(0x00080120, 'UR',
'http://github.com/darcymason/pydicom')
encoded_elem = self.encode_element(elem)
# Tag pair (0008, 2001): 08 00 20 01
# Length (36): 24 00 00 00
# Value: 68 to 6d
ref_bytes = b'\x08\x00\x20\x01\x24\x00\x00\x00\x68\x74' \
b'\x74\x70\x3a\x2f\x2f\x67\x69\x74\x68\x75' \
b'\x62\x2e\x63\x6f\x6d\x2f\x64\x61\x72\x63' \
b'\x79\x6d\x61\x73\x6f\x6e\x2f\x70\x79\x64' \
b'\x69\x63\x6f\x6d'
self.assertEqual(encoded_elem, ref_bytes)
# Odd length URL has trailing \x20 (SPACE) padding
elem.value = '../test/test.py'
encoded_elem = self.encode_element(elem)
# Tag pair (0008, 2001): 08 00 20 01
# Length (16): 10 00 00 00
# Value: 2e to 20
ref_bytes = b'\x08\x00\x20\x01\x10\x00\x00\x00\x2e\x2e' \
b'\x2f\x74\x65\x73\x74\x2f\x74\x65\x73\x74' \
b'\x2e\x70\x79\x20'
self.assertEqual(encoded_elem, ref_bytes)
# Empty value
elem.value = ''
encoded_elem = self.encode_element(elem)
self.assertEqual(encoded_elem, b'\x08\x00\x20\x01\x00\x00\x00\x00')
def test_str_no_vr(self):
"""Test DataElement.__str__ output with no VR"""
elem = DataElement(0x00100010, 'PN', 'ANON')
assert "(0010, 0010) Patient's Name" in str(elem)
assert "PN: 'ANON'" in str(elem)
elem.showVR = False
assert "(0010, 0010) Patient's Name" in str(elem)
assert 'PN' not in str(elem)
def test_equality_class_members(self):
"""Test equality is correct when ignored class members differ."""
dd = DataElement(0x00100010, 'PN', 'ANON')
dd.showVR = False
dd.file_tell = 10
dd.maxBytesToDisplay = 0
dd.descripWidth = 0
ee = DataElement(0x00100010, 'PN', 'ANON')
self.assertTrue(dd == ee)
def test_description_unknown_private(self):
"""Test DataElement.description with an unknown private element"""
elem = DataElement(0x00110010, 'LO', 12345)
elem.private_creator = 'TEST'
assert elem.description() == 'Private tag data'
elem = DataElement(0x00110F00, 'LO', 12345)
assert elem.tag.is_private
assert not hasattr(elem, 'private_creator')
assert elem.description() == 'Private tag data'
def test_inequality_sequence(self):
"""Test DataElement.__ne__ for sequence element"""
dd = DataElement(0x300A00B0, 'SQ', [])
assert not dd != dd
ee = DataElement(0x300A00B0, 'SQ', [])
assert not dd != ee
ee = DataElement(0x300A00B0, 'SQ', [Dataset()])
assert dd != ee
# Check value
dd.value = [Dataset()]
dd[0].PatientName = 'ANON'
ee[0].PatientName = 'ANON'
assert not dd != ee
ee[0].PatientName = 'ANONA'
assert dd != ee
def test_write_OL_implicit_little(self):
"""Test writing elements with VR of OL works correctly."""
# TrackPointIndexList
bytestring = b'\x00\x01\x02\x03\x04\x05\x06\x07' \
b'\x01\x01\x02\x03'
elem = DataElement(0x00660129, 'OL', bytestring)
encoded_elem = self.encode_element(elem)
# Tag pair (0066, 0129): 66 00 29 01
# Length (12): 0c 00 00 00
# | Tag | Length | Value ->
ref_bytes = b'\x66\x00\x29\x01\x0c\x00\x00\x00' + bytestring
self.assertEqual(encoded_elem, ref_bytes)
# Empty data
elem.value = b''
encoded_elem = self.encode_element(elem)
ref_bytes = b'\x66\x00\x29\x01\x00\x00\x00\x00'
self.assertEqual(encoded_elem, ref_bytes)
def testEqualityPrivateElement(self):
"""DataElement: equality returns correct value for private elements"""
dd = DataElement(0x01110001, 'PN', 'ANON')
self.assertTrue(dd == dd)
ee = DataElement(0x01110001, 'PN', 'ANON')
self.assertTrue(dd == ee)
# Check value
ee.value = 'ANAN'
self.assertFalse(dd == ee)
# Check tag
ee = DataElement(0x01110002, 'PN', 'ANON')
self.assertFalse(dd == ee)
# Check VR
ee = DataElement(0x01110001, 'SH', 'ANON')
self.assertFalse(dd == ee)
def test_write_OD_implicit_little(self):
"""Test writing elements with VR of OD works correctly."""
# VolumetricCurvePoints
bytestring = b'\x00\x01\x02\x03\x04\x05\x06\x07' \
b'\x01\x01\x02\x03\x04\x05\x06\x07'
elem = DataElement(0x0070150d, 'OD', bytestring)
encoded_elem = self.encode_element(elem)
# Tag pair (0070, 150d): 70 00 0d 15
# Length (16): 10 00 00 00
# | Tag | Length | Value ->
ref_bytes = b'\x70\x00\x0d\x15\x10\x00\x00\x00' + bytestring
self.assertEqual(encoded_elem, ref_bytes)
# Empty data
elem.value = b''
encoded_elem = self.encode_element(elem)
ref_bytes = b'\x70\x00\x0d\x15\x00\x00\x00\x00'
self.assertEqual(encoded_elem, ref_bytes)
def test_write_UC_explicit_little(self):
"""Test writing elements with VR of UC works correctly.
Elements with a VR of 'UC' use the newer explicit VR
encoding (see PS3.5 Section 7.1.2).
"""
# VM 1, even data
elem = DataElement(0x00189908, 'UC', 'Test')
encoded_elem = self.encode_element(elem, False, True)
# Tag pair (0018, 9908): 08 00 20 01
# VR (UC): \x55\x43
# Reserved: \x00\x00
# Length (4): \x04\x00\x00\x00
# Value: \x54\x65\x73\x74
ref_bytes = b'\x18\x00\x08\x99\x55\x43\x00\x00\x04\x00\x00\x00' \
b'\x54\x65\x73\x74'
self.assertEqual(encoded_elem, ref_bytes)
# VM 1, odd data - padded to even length
elem.value = 'Test.'
encoded_elem = self.encode_element(elem, False, True)
ref_bytes = b'\x18\x00\x08\x99\x55\x43\x00\x00\x06\x00\x00\x00' \
b'\x54\x65\x73\x74\x2e\x20'
self.assertEqual(encoded_elem, ref_bytes)
# VM 3, even data
elem.value = ['Aa', 'B', 'C']
encoded_elem = self.encode_element(elem, False, True)
ref_bytes = b'\x18\x00\x08\x99\x55\x43\x00\x00\x06\x00\x00\x00' \
b'\x41\x61\x5c\x42\x5c\x43'
self.assertEqual(encoded_elem, ref_bytes)
# VM 3, odd data - padded to even length
elem.value = ['A', 'B', 'C']
encoded_elem = self.encode_element(elem, False, True)
ref_bytes = b'\x18\x00\x08\x99\x55\x43\x00\x00\x06\x00\x00\x00' \
b'\x41\x5c\x42\x5c\x43\x20'
self.assertEqual(encoded_elem, ref_bytes)
# Empty data
elem.value = ''
encoded_elem = self.encode_element(elem, False, True)
ref_bytes = b'\x18\x00\x08\x99\x55\x43\x00\x00\x00\x00\x00\x00'
self.assertEqual(encoded_elem, ref_bytes)
def __setattr__(self, name, value):
"""Intercept any attempts to set a value for an instance attribute.
If name is a dicom descriptive string (cleaned with CleanName),
then set the corresponding tag and data_element.
Else, set an instance (python) attribute as any other class would do.
"""
tag = tag_for_name(name)
if tag is not None: # successfully mapped name to a tag
if tag not in self: # don't have this tag yet->create the data_element instance
VR = dictionaryVR(tag)
data_element = DataElement(tag, VR, value)
else: # already have this data_element, just changing its value
data_element = self[tag]
data_element.value = value
# Now have data_element - store it in this dict
self[tag] = data_element
else: # name not in dicom dictionary - setting a non-dicom instance attribute
# XXX note if user mis-spells a dicom data_element - no error!!!
self.__dict__[name] = value
def testEqualityStandardElement(self):
"""DataElement: equality returns correct value for simple elements"""
dd = DataElement(0x00100010, 'PN', 'ANON')
self.assertTrue(dd == dd)
ee = DataElement(0x00100010, 'PN', 'ANON')
self.assertTrue(dd == ee)
# Check value
ee.value = 'ANAN'
self.assertFalse(dd == ee)
# Check tag
ee = DataElement(0x00100011, 'PN', 'ANON')
self.assertFalse(dd == ee)
# Check VR
ee = DataElement(0x00100010, 'SH', 'ANON')
self.assertFalse(dd == ee)
dd = DataElement(0x00080018, 'UI', '1.2.3.4')
ee = DataElement(0x00080018, 'UI', '1.2.3.4')
self.assertTrue(dd == ee)
ee = DataElement(0x00080018, 'PN', '1.2.3.4')
self.assertFalse(dd == ee)
def testEqualitySequenceElement(self):
"""DataElement: equality returns correct value for sequence elements"""
dd = DataElement(0x300A00B0, 'SQ', [])
self.assertTrue(dd == dd)
ee = DataElement(0x300A00B0, 'SQ', [])
self.assertTrue(dd == ee)
# Check value
e = Dataset()
e.PatientName = 'ANON'
ee.value = [e]
self.assertFalse(dd == ee)
# Check tag
ee = DataElement(0x01110002, 'SQ', [])
self.assertFalse(dd == ee)
# Check VR
ee = DataElement(0x300A00B0, 'SH', [])
self.assertFalse(dd == ee)
# Check with dataset
dd = DataElement(0x300A00B0, 'SQ', [Dataset()])
dd.value[0].PatientName = 'ANON'
ee = DataElement(0x300A00B0, 'SQ', [Dataset()])
ee.value[0].PatientName = 'ANON'
self.assertTrue(dd == ee)
# Check uneven sequences
dd.value.append(Dataset())
dd.value[1].PatientName = 'ANON'
self.assertFalse(dd == ee)
ee.value.append(Dataset())
ee.value[1].PatientName = 'ANON'
self.assertTrue(dd == ee)
ee.value.append(Dataset())
ee.value[2].PatientName = 'ANON'
self.assertFalse(dd == ee)
def __setattr__(self, name, value):
"""Intercept any attempts to set a value for an instance attribute.
If name is a DICOM keyword, set the corresponding tag and DataElement.
Else, set an instance (python) attribute as any other class would do.
Parameters
----------
name : str
The element keyword for the DataElement you wish to add/change. If
`name` is not a DICOM element keyword then this will be the
name of the attribute to be added/changed.
value
The value for the attribute to be added/changed.
"""
tag = tag_for_keyword(name)
if tag is not None: # successfully mapped name to a tag
if tag not in self:
# don't have this tag yet->create the data_element instance
VR = dictionary_VR(tag)
data_element = DataElement(tag, VR, value)
else:
# already have this data_element, just changing its value
data_element = self[tag]
data_element.value = value
# Now have data_element - store it in this dict
self[tag] = data_element
elif repeater_has_keyword(name):
# Check if `name` is repeaters element
raise ValueError('{} is a DICOM repeating group '
'element and must be added using '
'the add() or add_new() methods.'
.format(name))
else:
# name not in dicom dictionary - setting a non-dicom instance
# attribute
# XXX note if user mis-spells a dicom data_element - no error!!!
super(Dataset, self).__setattr__(name, value)
def apply_rules(self, rules: RuleSet, dataset: Dataset) -> Dataset:
"""Apply rules to each element in dataset, recursing into sequence elements
This creates a deep copy of the input dataset. Except for PixelData, which
will be a reference. PixelData is not copied because it can take up a lot
of memory
"""
deidentified = Dataset()
pixel_data_tag = 0x7FE00010
for element in dataset:
if element.tag == pixel_data_tag:
deidentified.add(
element) # add pixel data as reference to save mem
elif element.VR == VRs.Sequence.short_name: # recurse into sequences
deidentified.add(
DataElement(
tag=element.tag,
VR=element.VR,
value=Sequence([
self.apply_rules(rules, sub_dataset)
for sub_dataset in element
]),
))
elif rule := rules.get_rule(element):
if type(rule.operation) == Remove:
continue # special handling. should be removed, do not add
try:
new = rule.operation.apply(element, dataset)
deidentified.add(new)
except ElementShouldBeRemoved: # Operators signals removal
continue
else: # no rule found. Just copy the element over
deidentified.add(
DataElement(tag=element.tag,
VR=element.VR,
value=element.value))
def __setattr__(self, name, value):
"""Intercept any attempts to set a value for an instance attribute.
If name is a DICOM keyword, set the corresponding tag and DataElement.
Else, set an instance (python) attribute as any other class would do.
Parameters
----------
name : str
The element keyword for the DataElement you wish to add/change. If
`name` is not a DICOM element keyword then this will be the
name of the attribute to be added/changed.
value
The value for the attribute to be added/changed.
"""
tag = tag_for_keyword(name)
if tag is not None: # successfully mapped name to a tag
if tag not in self:
# don't have this tag yet->create the data_element instance
VR = dictionary_VR(tag)
data_element = DataElement(tag, VR, value)
else:
# already have this data_element, just changing its value
data_element = self[tag]
data_element.value = value
# Now have data_element - store it in this dict
self[tag] = data_element
elif repeater_has_keyword(name):
# Check if `name` is repeaters element
raise ValueError('{} is a DICOM repeating group '
'element and must be added using '
'the add() or add_new() methods.'.format(name))
else:
# name not in dicom dictionary - setting a non-dicom instance
# attribute
# XXX note if user mis-spells a dicom data_element - no error!!!
super(Dataset, self).__setattr__(name, value)
def get_idis_code_sequence(ruleset_names: List[str]) -> DataElement:
"""Create the element (0012,0064) - DeIdentificationMethodCodeSequence
This sequence specifies what kind of anonymization has been performed. It is
quite free form. This implementation uses the following format:
DeIdentificationMethodCodeSequence will contain the code of each official
DICOM deidentification profile that was used. Codes are taken from
Table CID 7050
Parameters
----------
ruleset_names: List[str]
list of names as defined in nema.E1_1_METHOD_INFO
Returns
-------
DataElement
Sequence element (0012,0064) - DeIdentificationMethodCodeSequence. Will
contain the code of each official DICOM deidentification profile passed
Raises
------
ValueError
When any name in ruleset_names is not recognized as a standard DICOM
rule set
"""
code_per_name = {x.full_name: x for x in E1_1_METHOD_INFO}
codes = []
for name in ruleset_names:
try: # check whether we know this ruleset as a standard DICOM one
ruleset_info = code_per_name[name]
except KeyError:
raise ValueError(
f'Could not find the code for rule set "{name}". I do'
f" not know this ruleset")
# Create the required designation for this dataset
code_dataset = Dataset()
code_dataset.CodeValue = ruleset_info.code
code_dataset.CodingSchemeDesignator = "DCM"
code_dataset.CodeMeaning = ruleset_info.full_name
codes.append(code_dataset)
element = DataElement(
tag=Tag("DeidentificationMethodCodeSequence"),
VR=VRs.Sequence.short_name,
value=Sequence(codes),
)
return element
def test_write_OD_explicit_little(self):
"""Test writing elements with VR of OD works correctly.
Elements with a VR of 'OD' use the newer explicit VR
encoding (see PS3.5 Section 7.1.2).
"""
# VolumetricCurvePoints
bytestring = b'\x00\x01\x02\x03\x04\x05\x06\x07' \
b'\x01\x01\x02\x03\x04\x05\x06\x07'
elem = DataElement(0x0070150d, 'OD', bytestring)
encoded_elem = self.encode_element(elem, False, True)
# Tag pair (0070, 150d): 70 00 0d 15
# VR (OD): \x4f\x44
# Reserved: \x00\x00
# Length (16): \x10\x00\x00\x00
# | Tag | VR | Rsrvd | Length | Value ->
ref_bytes = b'\x70\x00\x0d\x15\x4f\x44\x00\x00\x10\x00\x00\x00' + bytestring
self.assertEqual(encoded_elem, ref_bytes)
# Empty data
elem.value = b''
encoded_elem = self.encode_element(elem, False, True)
ref_bytes = b'\x70\x00\x0d\x15\x4f\x44\x00\x00\x00\x00\x00\x00'
self.assertEqual(encoded_elem, ref_bytes)
def testEqualityInheritance(self):
"""DataElement: equality returns correct value for subclasses"""
class DataElementPlus(DataElement):
pass
dd = DataElement(0x00100010, 'PN', 'ANON')
ee = DataElementPlus(0x00100010, 'PN', 'ANON')
self.assertTrue(ee == ee)
self.assertTrue(dd == ee)
self.assertTrue(ee == dd)
ee = DataElementPlus(0x00100010, 'PN', 'ANONY')
self.assertFalse(dd == ee)
self.assertFalse(ee == dd)
def test_overlay(self):
"""Test correcting OverlayData"""
# Implicit VR must be 'OW'
ref_ds = Dataset()
ref_ds.is_implicit_VR = True
ref_ds.add(DataElement(0x60003000, 'OB or OW', b'\x00'))
ref_ds.add(DataElement(0x601E3000, 'OB or OW', b'\x00'))
ds = correct_ambiguous_vr(deepcopy(ref_ds), True)
self.assertTrue(ds[0x60003000].VR == 'OW')
self.assertTrue(ds[0x601E3000].VR == 'OW')
self.assertTrue(ref_ds[0x60003000].VR == 'OB or OW')
self.assertTrue(ref_ds[0x601E3000].VR == 'OB or OW')
# Explicit VR may be 'OB' or 'OW' (leave unchanged)
ref_ds.is_implicit_VR = False
ds = correct_ambiguous_vr(deepcopy(ref_ds), True)
self.assertTrue(ds[0x60003000].VR == 'OB or OW')
self.assertTrue(ref_ds[0x60003000].VR == 'OB or OW')
# Missing is_implicit_VR (leave unchanged)
del ref_ds.is_implicit_VR
ds = correct_ambiguous_vr(deepcopy(ref_ds), True)
self.assertTrue(ds[0x60003000].VR == 'OB or OW')
self.assertTrue(ref_ds[0x60003000].VR == 'OB or OW')
def get_deidentification_method(
method: str = DEFAULT_DEIDENTIFICATION_METHOD, ) -> DataElement:
"""Create the element (0012,0063) - DeIdentificationMethod
A string description of the deidentification method used
Parameters
----------
method: str, optional
String representing the deidentification method used. Defaults to
'idiscore <version>'
"""
return DataElement(tag=Tag("DeidentificationMethod"),
VR=VRs.LongString.short_name,
value=method)
def test_empty_AT(self):
"""Write empty AT correctly.........."""
# Was issue 74
data_elem = DataElement(0x00280009, "AT", [])
expected = hex2bytes((
" 28 00 09 00" # (0028,0009) Frame Increment Pointer
" 00 00 00 00" # length 0
))
write_data_element(self.f1, data_elem)
got = self.f1.parent.getvalue()
msg = ("Did not write zero-length AT value correctly. "
"Expected %r, got %r") % (bytes2hex(expected), bytes2hex(got))
msg = "%r %r" % (type(expected), type(got))
msg = "'%r' '%r'" % (expected, got)
self.assertEqual(expected, got, msg)
def test_write_OL_explicit_little(self):
"""Test writing elements with VR of OL works correctly.
Elements with a VR of 'OL' use the newer explicit VR
encoding (see PS3.5 Section 7.1.2).
"""
# TrackPointIndexList
bytestring = b'\x00\x01\x02\x03\x04\x05\x06\x07' \
b'\x01\x01\x02\x03'
elem = DataElement(0x00660129, 'OL', bytestring)
encoded_elem = self.encode_element(elem, False, True)
# Tag pair (0066, 0129): 66 00 29 01
# VR (OL): \x4f\x4c
# Reserved: \x00\x00
# Length (12): 0c 00 00 00
# | Tag | VR | Rsrvd | Length | Value ->
ref_bytes = b'\x66\x00\x29\x01\x4f\x4c\x00\x00\x0c\x00\x00\x00' + bytestring
self.assertEqual(encoded_elem, ref_bytes)
# Empty data
elem.value = b''
encoded_elem = self.encode_element(elem, False, True)
ref_bytes = b'\x66\x00\x29\x01\x4f\x4c\x00\x00\x00\x00\x00\x00'
self.assertEqual(encoded_elem, ref_bytes)
def test_write_OD_explicit_little(self):
"""Test writing elements with VR of OD works correctly.
Elements with a VR of 'OD' use the newer explicit VR
encoding (see PS3.5 Section 7.1.2).
"""
# VolumetricCurvePoints
bytestring = b'\x00\x01\x02\x03\x04\x05\x06\x07' \
b'\x01\x01\x02\x03\x04\x05\x06\x07'
elem = DataElement(0x0070150d, 'OD', bytestring)
encoded_elem = self.encode_element(elem, False, True)
# Tag pair (0070, 150d): 70 00 0d 15
# VR (OD): \x4f\x44
# Reserved: \x00\x00
# Length (16): \x10\x00\x00\x00
# | Tag | VR | Rsrvd | Length | Value ->
ref_bytes = b'\x70\x00\x0d\x15\x4f\x44\x00\x00\x10\x00\x00\x00' + bytestring
self.assertEqual(encoded_elem, ref_bytes)
# Empty data
elem.value = b''
encoded_elem = self.encode_element(elem, False, True)
ref_bytes = b'\x70\x00\x0d\x15\x4f\x44\x00\x00\x00\x00\x00\x00'
self.assertEqual(encoded_elem, ref_bytes)
def test_equality_inheritance(self):
"""DataElement: equality returns correct value for subclasses"""
class DataElementPlus(DataElement):
pass
dd = DataElement(0x00100010, 'PN', 'ANON')
ee = DataElementPlus(0x00100010, 'PN', 'ANON')
assert ee == ee
assert dd == ee
assert ee == dd
ee = DataElementPlus(0x00100010, 'PN', 'ANONY')
assert not dd == ee
assert not ee == dd
def convert_to_dataset(json_obj):
ds = Dataset()
for key in json_obj:
obj = json_obj[key]
#print "*" , key, obj
val = ''
if 'Value' in obj:
val = obj['Value']
if obj['vr'] == 'SQ' and val != '':
child_ds_list = []
for val_item in val:
child_ds = convert_to_dataset(val_item)
child_ds_list.append(child_ds)
#print (child_ds_list)
#print "Creating SQ Element....."
delem = DataElement(key, obj['vr'], child_ds_list)
ds.add(delem)
else:
if val != '':
val = val[0]
delem = DataElement(key, obj['vr'], val)
ds.add(delem)
#print delem
return ds
def test_write_OL_explicit_little(self):
"""Test writing elements with VR of OL works correctly.
Elements with a VR of 'OL' use the newer explicit VR
encoding (see PS3.5 Section 7.1.2).
"""
# TrackPointIndexList
bytestring = b'\x00\x01\x02\x03\x04\x05\x06\x07' \
b'\x01\x01\x02\x03'
elem = DataElement(0x00660129, 'OL', bytestring)
encoded_elem = self.encode_element(elem, False, True)
# Tag pair (0066, 0129): 66 00 29 01
# VR (OL): \x4f\x4c
# Reserved: \x00\x00
# Length (12): 0c 00 00 00
# | Tag | VR | Rsrvd | Length | Value ->
ref_bytes = b'\x66\x00\x29\x01\x4f\x4c\x00\x00\x0c\x00\x00\x00' + bytestring
self.assertEqual(encoded_elem, ref_bytes)
# Empty data
elem.value = b''
encoded_elem = self.encode_element(elem, False, True)
ref_bytes = b'\x66\x00\x29\x01\x4f\x4c\x00\x00\x00\x00\x00\x00'
self.assertEqual(encoded_elem, ref_bytes)
def test_data_element_factory_init():
"""Check different init methods
"""
# factory casts tag init argument to Tag(). Verify that this works.
assert type(DataElementFactory().tag) == BaseTag
assert type(DataElement(tag="Modality", VR="SH",
value="kees").tag) == BaseTag
assert type(DataElementFactory(tag="Modality").tag) == BaseTag
assert type(DataElementFactory(tag=(0x0010, 0x0020)).tag) == BaseTag
# For unknown tags, just give a default VR. Assuming the default position
# for users of DataElementFactory will be 'Don't care, just give me the Element'
assert DataElementFactory(tag=(0xee30,
0xf120)).VR == VRs.LongString.short_name
assert DataElementFactory.create(tag=(0xee30, 0xf120),
value=100).VR == VRs.LongString.short_name
def subfix_UpdateOrInsertCodeAttribute(seqelem: DataElement, 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 = DataElement(newtag, newvr, value)
seqelem.value[index].add(elem)
return out_msg
def test_write_invalid_length_non_ascii_text(
self, enforce_writing_invalid_values):
fp = DicomBytesIO()
ds = Dataset()
ds.is_implicit_VR = True
ds.is_little_endian = True
ds.SpecificCharacterSet = "ISO_IR 192" # UTF-8
# the string length is 9, so constructing the data element
# is possible
ds.add(DataElement(0x00080050, "SH", "洪^吉洞=홍^길동"))
# encoding the element during writing shall fail,
# as the encoded length is 21, while only 16 bytes are allowed for SH
msg = r"The value length \(21\) exceeds the maximum length of 16 *"
with pytest.raises(ValueError, match=msg):
ds.save_as(fp)
def testEqualityPrivateElement(self):
"""DataElement: equality returns correct value for private elements"""
dd = DataElement(0x01110001, 'PN', 'ANON')
self.assertTrue(dd == dd)
ee = DataElement(0x01110001, 'PN', 'ANON')
self.assertTrue(dd == ee)
# Check value
ee.value = 'ANAN'
self.assertFalse(dd == ee)
# Check tag
ee = DataElement(0x01110002, 'PN', 'ANON')
self.assertFalse(dd == ee)
# Check VR
ee = DataElement(0x01110001, 'SH', 'ANON')
self.assertFalse(dd == ee)
def test_equality_private_element(self):
"""DataElement: equality returns correct value for private elements"""
dd = DataElement(0x01110001, 'PN', 'ANON')
assert dd == dd
ee = DataElement(0x01110001, 'PN', 'ANON')
assert dd == ee
# Check value
ee.value = 'ANAN'
assert not dd == ee
# Check tag
ee = DataElement(0x01110002, 'PN', 'ANON')
assert not dd == ee
# Check VR
ee = DataElement(0x01110001, 'SH', 'ANON')
assert not dd == ee
def test_code_sequence(self):
"""Test utils.codify.code_dataelem"""
# ControlPointSequence
elem = DataElement(0x300A0111, 'SQ', [])
elem.value.append(Dataset())
elem[0].PatientID = '1234'
out = "\n"
out += "# Control Point Sequence\n"
out += "cp_sequence = Sequence()\n"
out += "ds.ControlPointSequence = cp_sequence\n"
out += "\n"
out += "# Control Point Sequence: Control Point 1\n"
out += "cp1 = Dataset()\n"
out += "cp1.PatientID = '1234'\n"
out += "cp_sequence.append(cp1)"
assert code_dataelem(elem) == out
def write_PN(fp: DicomIO,
elem: DataElement,
encodings: Optional[List[str]] = None) -> None:
if not encodings:
encodings = [default_encoding]
val: List[PersonName]
if elem.VM == 1:
val = [cast(PersonName, elem.value)]
else:
val = cast(List[PersonName], elem.value)
enc = b'\\'.join([elem.encode(encodings) for elem in val])
if len(enc) % 2 != 0:
enc += b' '
fp.write(enc)
def apply(self,
element: DataElement,
dataset: Optional[Dataset] = None) -> DataElement:
vr = VRs.short_name_to_vr(element.VR)
if element.tag.is_private:
return self.clean_private(element, dataset)
elif vr in VRs.date_like:
return self.clean_date_time(element, dataset)
elif vr in VRs.string_like:
return DataElement(tag=element.tag, VR=element.VR, value="CLEANED")
elif vr == VRs.Sequence:
return copy(element) # sequence elements are processed later. pass
else:
# too difficult. Cannot do it
raise ValueError(
f"Cannot clean {element}. I don't know how to handle "
f"tags of type '{vr}'")
def test_long_specific_char_set(self):
"""Test that specific character set is read even if it is longer
than defer_size"""
ds = Dataset()
long_specific_char_set_value = ['ISO 2022IR 100'] * 9
ds.add(DataElement(0x00080005, 'CS', long_specific_char_set_value))
msg = (r"Unknown encoding 'ISO 2022IR 100' - using default encoding "
r"instead")
fp = BytesIO()
file_ds = FileDataset(fp, ds)
with pytest.warns(UserWarning, match=msg):
file_ds.save_as(fp, write_like_original=True)
with pytest.warns(UserWarning, match=msg):
ds = dcmread(fp, defer_size=65, force=True)
assert long_specific_char_set_value == ds[0x00080005].value
def add_field(self, field, value):
"""add a field to the dicom. If it's already present, update the value.
"""
value = parse_value(item=self.lookup,
value=value,
field=field,
dicom=self.dicom)
# Assume we don't want to add an empty value
if value is not None:
# If provided a field object, create based on keyword or tag identifer
name = field
if isinstance(field, DicomField):
name = field.element.keyword or field.stripped_tag
# Generate a tag item, add if it's a name found in the dicom dictionary
tag = get_tag(name)
# Second try, it might be a private (or other numerical) string identifier
if not tag:
tag = add_tag(name)
if tag:
uid = getattr(field, "uid", None) or str(tag["tag"])
# For a replacement, this is likely
if uid in self.fields:
element = self.fields[uid]
# Nested fields
while not hasattr(element, "value"):
element = element.element
element.value = value
else:
element = DataElement(tag["tag"], tag["VR"], value)
self.dicom.add(element)
self.fields[uid] = DicomField(element, name, uid)
else:
bot.warning("Cannot find tag for field %s, skipping." % name)
def testEqualityNoSequence(self):
"""Dataset: equality returns correct value with simple dataset"""
# Test empty dataset
assert Dataset() == Dataset()
d = Dataset()
d.SOPInstanceUID = '1.2.3.4'
d.PatientName = 'Test'
assert d == d
e = Dataset()
e.PatientName = 'Test'
e.SOPInstanceUID = '1.2.3.4'
assert d == e
e.SOPInstanceUID = '1.2.3.5'
assert not d == e
# Check VR
del e.SOPInstanceUID
e.add(DataElement(0x00080018, 'PN', '1.2.3.4'))
assert not d == e
# Check Tag
del e.SOPInstanceUID
e.StudyInstanceUID = '1.2.3.4'
assert not d == e
# Check missing Element in self
e.SOPInstanceUID = '1.2.3.4'
assert not d == e
# Check missing Element in other
d = Dataset()
d.SOPInstanceUID = '1.2.3.4'
d.StudyInstanceUID = '1.2.3.4.5'
e = Dataset()
e.SOPInstanceUID = '1.2.3.4'
assert not d == e
def add_new(self, tag, VR, value):
"""Add a DataElement to the Dataset.
Parameters
----------
tag
The DICOM (group, element) tag in any form accepted by
pydicom.tag.Tag such as [0x0010, 0x0010], (0x10, 0x10), 0x00100010,
etc.
VR : str
The 2 character DICOM value representation (see DICOM standard part
5, Section 6.2).
value
The value of the data element. One of the following:
* a single string or number
* a list or tuple with all strings or all numbers
* a multi-value string with backslash separator
* for a sequence DataElement, an empty list or list of Dataset
"""
data_element = DataElement(tag, VR, value)
# use data_element.tag since DataElement verified it
self[data_element.tag] = data_element
def testEqualityNoSequence(self):
"""Dataset: equality returns correct value with simple dataset"""
d = Dataset()
d.SOPInstanceUID = '1.2.3.4'
d.PatientName = 'Test'
self.assertTrue(d == d)
e = Dataset()
e.PatientName = 'Test'
e.SOPInstanceUID = '1.2.3.4'
self.assertTrue(d == e)
e.SOPInstanceUID = '1.2.3.5'
self.assertFalse(d == e)
# Check VR
del e.SOPInstanceUID
e.add(DataElement(0x00080018, 'PN', '1.2.3.4'))
self.assertFalse(d == e)
# Check Tag
del e.SOPInstanceUID
e.StudyInstanceUID = '1.2.3.4'
self.assertFalse(d == e)
# Check missing Element in self
e.SOPInstanceUID = '1.2.3.4'
self.assertFalse(d == e)
# Check missing Element in other
d = Dataset()
d.SOPInstanceUID = '1.2.3.4'
d.StudyInstanceUID = '1.2.3.4.5'
e = Dataset()
e.SOPInstanceUID = '1.2.3.4'
self.assertFalse(d == e)
def test_write_UC_explicit_little(self):
"""Test writing elements with VR of UC works correctly.
Elements with a VR of 'UC' use the newer explicit VR
encoding (see PS3.5 Section 7.1.2).
"""
# VM 1, even data
elem = DataElement(0x00189908, 'UC', 'Test')
encoded_elem = self.encode_element(elem, False, True)
# Tag pair (0018, 9908): 08 00 20 01
# VR (UC): \x55\x43
# Reserved: \x00\x00
# Length (4): \x04\x00\x00\x00
# Value: \x54\x65\x73\x74
ref_bytes = b'\x18\x00\x08\x99\x55\x43\x00\x00\x04\x00\x00\x00' \
b'\x54\x65\x73\x74'
self.assertEqual(encoded_elem, ref_bytes)
# VM 1, odd data - padded to even length
elem.value = 'Test.'
encoded_elem = self.encode_element(elem, False, True)
ref_bytes = b'\x18\x00\x08\x99\x55\x43\x00\x00\x06\x00\x00\x00' \
b'\x54\x65\x73\x74\x2e\x20'
self.assertEqual(encoded_elem, ref_bytes)
# VM 3, even data
elem.value = ['Aa', 'B', 'C']
encoded_elem = self.encode_element(elem, False, True)
ref_bytes = b'\x18\x00\x08\x99\x55\x43\x00\x00\x06\x00\x00\x00' \
b'\x41\x61\x5c\x42\x5c\x43'
self.assertEqual(encoded_elem, ref_bytes)
# VM 3, odd data - padded to even length
elem.value = ['A', 'B', 'C']
encoded_elem = self.encode_element(elem, False, True)
ref_bytes = b'\x18\x00\x08\x99\x55\x43\x00\x00\x06\x00\x00\x00' \
b'\x41\x5c\x42\x5c\x43\x20'
self.assertEqual(encoded_elem, ref_bytes)
# Empty data
elem.value = ''
encoded_elem = self.encode_element(elem, False, True)
ref_bytes = b'\x18\x00\x08\x99\x55\x43\x00\x00\x00\x00\x00\x00'
self.assertEqual(encoded_elem, ref_bytes)
def test_repeater_str(self):
"""Test a repeater group element displays the element name."""
elem = DataElement(0x60023000, 'OB', b'\x00')
self.assertTrue('Overlay Data' in elem.__str__())
def test_description_group_length(self):
"""Test DataElement.description for Group Length element"""
elem = DataElement(0x00100000, 'LO', 12345)
assert 'Group Length' == elem.description()
def test_backslash(self):
"""DataElement: String with '\\' sets multi-valued data_element."""
data_element = DataElement((1, 2), "DS", r"42.1\42.2\42.3")
assert 3 == data_element.VM
def test_repval_strange_type(self):
"""Test DataElement.repval doesn't break with bad types"""
elem = DataElement(0x00020001, 'OB', 0)
assert len(elem.repval) < 100
def test_repval_large_vm(self):
"""Test DataElement.repval doesn't return a huge string for a large
vm"""
elem = DataElement(0x00080054, 'AE', 'a\\' * 1000 + 'a')
assert len(elem.repval) < 100
def test_repval_large_elem(self):
"""Test DataElement.repval doesn't return a huge string for a large
value"""
elem = DataElement(0x00820003, 'UT', 'a' * 1000)
assert len(elem.repval) < 100
def test_repval_original_string(self):
"""Test DataElement.repval when original_string is present"""
elem = DataElement(0x00100010, 'PN', 'ANON')
elem.original_string = 'foo'
assert "(0010, 0010) Patient's Name" in str(elem)
assert "PN: 'foo'" in str(elem)
def test_description_group_length(self):
"""Test DataElement.description for Group Length element"""
elem = DataElement(0x00100000, 'LO', 12345)
assert elem.description() == 'Group Length'
def test_description_unknown(self):
"""Test DataElement.description with an unknown element"""
elem = DataElement(0x00000004, 'LO', 12345)
assert elem.description() == ''
