def test_request_data_set(self):
# Selector
selector = odil.webservices.Selector()
selector.set_study("1.2").set_instance("")
# DataSet
dataset = odil.DataSet()
dataset.add(odil.Tag("PatientName"), ["TOTO"])
dataset.add(odil.Tag("00200020"))
shared = odil.DataSet()
shared.add(odil.Tag("StudyDate"), [20130509])
shared.add(odil.Tag("00200035"))
dataset.add(odil.Tag("SharedFunctionalGroupsSequence"), [shared])
request = odil.webservices.QIDORSRequest(self.base_url_http)
request.request_datasets(
odil.webservices.Utils.Representation.DICOM_XML, selector, dataset)
full_url_alphabetic_tags = odil.webservices.URL(
"http", "example.com", "/dicom/studies/1.2/instances",
"PatientName=TOTO&"
"SharedFunctionalGroupsSequence.StudyDate=20130509&"
"includefield=PatientOrientation&"
"includefield=SharedFunctionalGroupsSequence.ImageOrientation&"
"fuzzymatching=false", "")
self.assertEqual(request.get_http_request().get_target(),
full_url_alphabetic_tags)
self.assertEqual(request.get_http_request().get_method(), "GET")
def test_write_file_path(self):
data_set = odil.DataSet()
data_set.add("SOPClassUID", ["1.2.3.4"])
data_set.add("SOPInstanceUID", ["1.2.3.4.5"])
data_set.add("PatientName", ["Foo^Bar"])
fd, path = tempfile.mkstemp()
os.close(fd)
string_io = BytesIO()
stream = odil.iostream(string_io)
odil.Writer.write_file(
data_set, path, odil.DataSet(),
odil.registry.ExplicitVRLittleEndian)
data = (
128*b"\0"+b"DICM"+
b"\x02\x00\x00\x00" b"UL" b"\x04\x00" b"\x80\x00\x00\x00"
b"\x02\x00\x01\x00" b"OB" b"\x00\x00" b"\x02\x00\x00\x00" b"\x00\x01"
b"\x02\x00\x02\x00" b"UI" b"\x08\x00" b"1.2.3.4\x00"
b"\x02\x00\x03\x00" b"UI" b"\x0a\x00" b"1.2.3.4.5\x00"
b"\x02\x00\x10\x00" b"UI" b"\x14\x00" b"1.2.840.10008.1.2.1\x00"
b"\x02\x00\x12\x00" b"UI" b"\x1e\x00" b"1.2.826.0.1.3680043.9.55600.0\x00"
b"\x02\x00\x13\x00" b"SH" b"\x06\x00" b"Odil 0"
b"\x08\x00\x16\x00" b"UI" b"\x08\x00" b"1.2.3.4\x00"
b"\x08\x00\x18\x00" b"UI" b"\x0a\x00" b"1.2.3.4.5\x00"
b"\x10\x00\x10\x00" b"PN" b"\x08\x00" b"Foo^Bar ")
with open(path, "rb") as fd:
contents = fd.read()
os.remove(path)
self.assertEqual(contents, data)
def setUp(self):
data_set_1 = odil.DataSet()
data_set_1.add("SOPClassUID", [odil.registry.RawDataStorage])
data_set_1.add("SOPInstanceUID", ["1.2.3.4"])
data_set_1.add("PatientID", ["DJ1234"])
data_set_1.add("PixelSpacing", [1.5, 2.5])
data_set_2 = odil.DataSet()
data_set_2.add("SOPClassUID", [odil.registry.MRImageStorage])
data_set_2.add("SOPInstanceUID", ["1.2.3.5"])
data_set_2.add("PatientName", ["Doe^John"])
data_set_2.add("PatientAge", ["042Y"])
self.data_sets = [data_set_1, data_set_2]
bin = odil.Value.BinaryItem()
bin.append(0x01)
bin.append(0x02)
bulk_data_1 = odil.webservices.BulkData(bin, "foo/bar", "here")
bin = odil.Value.BinaryItem()
bin.append(0x03)
bin.append(0x04)
bulk_data_2 = odil.webservices.BulkData(bin, "plip/plop", "not/here")
self.bulk_data = [bulk_data_1, bulk_data_2]
def test_kwargs_constructor(self):
data_set = odil.DataSet(
odil.registry.ImplicitVRLittleEndian,
PatientName=["Doe^John"],
PatientWeight=[70],
ReferencedStudySequence=[odil.DataSet(StudyInstanceUID=["1.2.3"])],
PixelData=[odil.Value.BinaryItem([1, 2, 3])])
self.assertEqual(data_set.size(), 4)
self._test_element_value(data_set, "PatientName", [b"Doe^John"],
odil.VR.PN, odil.DataSet.is_string,
odil.DataSet.as_string)
self._test_element_value(data_set, "PatientWeight", [70], odil.VR.DS,
odil.DataSet.is_int, odil.DataSet.as_int)
self._test_element_value(data_set, "ReferencedStudySequence",
[odil.DataSet(StudyInstanceUID=["1.2.3"])],
odil.VR.SQ, odil.DataSet.is_data_set,
odil.DataSet.as_data_set)
self._test_element_value(data_set, "PixelData",
[odil.Value.BinaryItem([1, 2, 3])],
odil.VR.OW, odil.DataSet.is_binary,
odil.DataSet.as_binary)
with self.assertRaises(odil.Exception):
odil.DataSet(FooBar=["foo"])
def setUp(self):
data_set_1 = odil.DataSet()
data_set_1.add("RetrieveURL",
["http://example.com/dicom/studies/7.8.9"])
data_set_1.add("FailedSOPSequence", [odil.DataSet()], odil.VR.SQ)
referenceSOPSequence_item1 = odil.DataSet()
referenceSOPSequence_item1.add("ReferencedSOPClassUID",
[odil.registry.MRImageStorage])
referenceSOPSequence_item1.add("ReferencedSOPInstanceUID",
["1.2.3.6.1"])
referenceSOPSequence_item1.add("RetrieveURL", [
"http://example.com/dicom/studies/7.8.9/series/4.5/instances/1.2.3.6.1"
])
referenceSOPSequence_item2 = odil.DataSet()
referenceSOPSequence_item2.add("ReferencedSOPClassUID",
[odil.registry.RawDataStorage])
referenceSOPSequence_item2.add("ReferencedSOPInstanceUID",
["1.2.3.6.2"])
referenceSOPSequence_item2.add("RetrieveURL", [
"http://example.com/dicom/studies/7.8.9/series/4.5/instances/1.2.3.6.2"
])
data_set_1.add(
"ReferencedSOPSequence",
[referenceSOPSequence_item1, referenceSOPSequence_item2])
self.data_set = data_set_1
def test_write_file(self):
data_set = odil.DataSet()
data_set.add("SOPClassUID", ["1.2.3.4"])
data_set.add("SOPInstanceUID", ["1.2.3.4.5"])
data_set.add("PatientName", ["Foo^Bar"])
string_io = BytesIO()
stream = odil.iostream(string_io)
odil.Writer.write_file(
data_set, stream, odil.DataSet(),
odil.registry.ExplicitVRLittleEndian)
data = (
128*b"\0"+b"DICM"+
b"\x02\x00\x00\x00" b"UL" b"\x04\x00" b"\x80\x00\x00\x00"
b"\x02\x00\x01\x00" b"OB" b"\x00\x00" b"\x02\x00\x00\x00" b"\x00\x01"
b"\x02\x00\x02\x00" b"UI" b"\x08\x00" b"1.2.3.4\x00"
b"\x02\x00\x03\x00" b"UI" b"\x0a\x00" b"1.2.3.4.5\x00"
b"\x02\x00\x10\x00" b"UI" b"\x14\x00" b"1.2.840.10008.1.2.1\x00"
b"\x02\x00\x12\x00" b"UI" b"\x1e\x00" b"1.2.826.0.1.3680043.9.55600.0\x00"
b"\x02\x00\x13\x00" b"SH" b"\x06\x00" b"Odil 0"
b"\x08\x00\x16\x00" b"UI" b"\x08\x00" b"1.2.3.4\x00"
b"\x08\x00\x18\x00" b"UI" b"\x0a\x00" b"1.2.3.4.5\x00"
b"\x10\x00\x10\x00" b"PN" b"\x08\x00" b"Foo^Bar ")
self.assertEqual(string_io.getvalue(), data)
def test_data_sets(self):
data_set_1 = odil.DataSet(PatientID=["DJ1234"])
data_set_2 = odil.DataSet(EchoTime=[100])
data_set_3 = odil.DataSet(PixelSpacing=[2.3, 4.5])
self._test(odil.Value.DataSets(), [data_set_1, data_set_2, data_set_3],
[data_set_2, data_set_1], odil.VR.SQ, odil.VR.UN,
odil.Element.is_data_set, odil.Element.as_data_set)
def test_get_position_single_frame(self):
data_set = odil.DataSet()
planePositionSeq = odil.DataSet()
position = [0.0, 0.0, 1.0]
planePositionSeq.add("ImagePositionPatient", position)
data_set.add("PlanePositionSequence", [planePositionSeq])
val = dicomifier.dicom_to_nifti.odil_getter._get_position(data_set, 0)
self.assertEqual(None, val)
def test_getter_data_set(self):
data_set = odil.DataSet()
planePositionSeq = odil.DataSet()
position = [0.0, 0.0, 1.0]
planePositionSeq.add("ImagePositionPatient", position)
data_set.add("PlanePositionSequence", [planePositionSeq])
val = dicomifier.dicom_to_nifti.odil_getter._getter(
data_set, odil.registry.PlanePositionSequence)
self.assertEqual((planePositionSeq, ), val)
def test_diffusion_getter_directionality_iso_none(self):
data_set = odil.DataSet()
mr_diff_seq = odil.DataSet()
mr_diff_seq.add("DiffusionBValue", [1000.])
mr_diff_seq.add("DiffusionDirectionality", ["ISOTROPIC"])
data_set.add("MRDiffusionSequence", [mr_diff_seq])
val = dicomifier.dicom_to_nifti.odil_getter._diffusion_getter(
data_set, odil.registry.MRDiffusionSequence)
self.assertEqual(val, None)
def test_data_sets(self):
data_set_1 = odil.DataSet()
data_set_1.add("PatientID", ["DJ1234"])
data_set_2 = odil.DataSet()
data_set_2.add("EchoTime", [100])
self._test(odil.Value.DataSets(), [data_set_1, data_set_2],
[data_set_2, data_set_1], odil.VR.SQ, odil.VR.UN,
odil.Element.is_data_set, odil.Element.as_data_set)
def test_delitem(self):
data_set = odil.DataSet()
data_set.add("PatientName", ["Doe^John"])
del data_set[odil.registry.PatientName]
self.assertTrue(data_set.empty())
data_set = odil.DataSet()
data_set.add("PatientName", ["Doe^John"])
del data_set["PatientName"]
self.assertTrue(data_set.empty())
def test_data_sets(self):
data_set_1 = odil.DataSet()
data_set_1.add("PatientID", ["DJ1234"])
data_set_2 = odil.DataSet()
data_set_2.add("EchoTime", [100])
self._test(
odil.Value.DataSets(),
[data_set_1, data_set_2], [data_set_2, data_set_1],
odil.Value.Type.DataSets, odil.Value.as_data_sets)
def test_data_set(self):
data_set_1 = odil.DataSet()
data_set_1.add("PatientID", ["DJ1234"])
data_set_2 = odil.DataSet()
data_set_2.add("EchoTime", [100])
self._test_element(odil.registry.ReferencedStudySequence,
odil.Value.DataSets(), [data_set_1, data_set_2],
odil.VR.SQ, odil.DataSet.is_data_set,
odil.DataSet.as_data_set)
def test_get_in_stack_position_index_none(self):
data_set = odil.DataSet()
dimension_index_seq = odil.DataSet()
data_set.add("DimensionIndexSequence", [dimension_index_seq])
idx = dicomifier.dicom_to_nifti.odil_getter.get_in_stack_position_index(
data_set)
self.assertEqual(idx, None)
data_set_empty = odil.DataSet()
idx = dicomifier.dicom_to_nifti.odil_getter.get_in_stack_position_index(
data_set_empty)
self.assertEqual(idx, None)
def test_orientation_getter_differents(self):
d1 = odil.DataSet()
d1.add("ImageOrientationPatient", [1., 0., 0., 0., 1., 0.])
d2 = odil.DataSet()
d2.add("ImageOrientationPatient", [-1., 0.5, 0.2, 0., 1., -0.5])
orientationGetter = dicomifier.dicom_to_nifti.odil_getter.OrientationGetter(
)
orientationGetter(d1, "ImageOrientationPatient")
orientationGetter(d2, "ImageOrientationPatient")
orientations = orientationGetter._orientations
self.assertEqual(2, len(orientations))
def initialize(self, message):
data_set_1 = odil.DataSet()
data_set_1.add("PatientName", ["Hello^World"])
data_set_1.add("PatientID", ["1234"])
self._responses.append(data_set_1)
data_set_2 = odil.DataSet()
data_set_2.add("PatientName", ["Doe^John"])
data_set_2.add("PatientID", ["5678"])
self._responses.append(data_set_2)
self._response_index = 0
def test_query_dataset(self):
http_request = odil.webservices.HTTPRequest("GET", self.full_url)
http_request.set_header("Accept", "application/dicom+json")
request = odil.webservices.QIDORSRequest(http_request)
# Check For DataSet
dataset = odil.DataSet()
dataset.add(odil.Tag("PatientName"), ["TOTO"])
dataset.add(odil.Tag("00200020"))
shared = odil.DataSet()
shared.add(odil.Tag("EffectiveEchoTime"), [10.5])
shared.add(odil.Tag("00200035"))
dataset.add(odil.Tag("SharedFunctionalGroupsSequence"), [shared])
self.assertEqual(request.get_query_data_set(), dataset)
def test_get_position(self):
data_set = odil.DataSet()
first_frame = odil.DataSet()
planePositionSeq = odil.DataSet()
position = [0.0, 0.0, 1.0]
planePositionSeq.add("ImagePositionPatient", position)
first_frame.add("PlanePositionSequence", [planePositionSeq])
per_frame = [first_frame]
data_set.add("PerFrameFunctionalGroupsSequence", per_frame)
data_set.add("NumberOfFrames", [1])
val = list(
dicomifier.dicom_to_nifti.odil_getter._get_position(data_set, 0))
self.assertEqual([0.0, 0.0, 1.0], val)
def test_get_spacing_with_index(self):
data_set = odil.DataSet()
first_frame = odil.DataSet()
pixelMeasuresSeq = odil.DataSet()
spacing = [0.2, 0.2]
pixelMeasuresSeq.add("PixelSpacing", spacing)
first_frame.add("PixelMeasuresSequence", [pixelMeasuresSeq])
per_frame = [first_frame]
data_set.add("PerFrameFunctionalGroupsSequence", per_frame)
data_set.add("NumberOfFrames", [1])
val = list(
dicomifier.dicom_to_nifti.odil_getter._get_spacing(data_set, 0))
self.assertEqual([0.2, 0.2], val)
def test_check_frame_idx_out_of_bounds(self):
data_set = odil.DataSet()
first_frame = odil.DataSet()
per_frame = [first_frame]
data_set.add("PerFrameFunctionalGroupsSequence", per_frame)
data_set.add("NumberOfFrames", [1])
frame_idx = 1
numberOfFrames = data_set.as_int("NumberOfFrames")[0]
with self.assertRaises(Exception) as context:
val = list(
dicomifier.dicom_to_nifti.odil_getter.check_frame_index(
data_set, 1))
self.assertTrue("Frame index out of bound ({}/{})".format(
frame_idx, numberOfFrames) in context.exception)
def test_orientation_getter_equal(self):
d1 = odil.DataSet()
d1.add("ImageOrientationPatient", [1., 0., 0., 0., 1., 0.])
d2 = odil.DataSet()
d2.add("ImageOrientationPatient", [1., 0., 0., 0., 1., 0.])
orientationGetter = dicomifier.dicom_to_nifti.odil_getter.OrientationGetter(
)
orientationGetter(d1, "ImageOrientationPatient")
orientationGetter(d2, "ImageOrientationPatient")
orientations = orientationGetter._orientations
self.assertEqual(1, len(orientations))
self.assertEqual(list(orientations.values()[0]),
[1., 0., 0., 0., 1., 0.])
def _test_implicit_container(self, tag, empty_content, vr, type_check,
accessor):
# Implicit empty content
data_set = odil.DataSet()
data_set.add(tag)
self._test_element_value(data_set, tag, empty_content, vr, type_check,
accessor)
# Explicit empty content
data_set = odil.DataSet()
data_set.add(tag, empty_content)
self._test_element_value(data_set, tag, empty_content, vr, type_check,
accessor)
def test_get_geometry_single_normal(self): #normal test single_frame
data_set = odil.DataSet()
data_set.add("ImageOrientationPatient", [1.0, 0.0, 0.0, 0.0, 1.0, 0.0])
data_set.add("ImagePositionPatient", [-20., -14., -4.5])
data_set.add("PixelSpacing", [0.2, 0.2])
val = dicomifier.dicom_to_nifti.image.get_geometry([(data_set, None)])
data_set_2 = odil.DataSet()
data_set_2.add("ImageOrientationPatient", [1.0, 0.0, 0.0, 0.0, 1.0, 0.0])
data_set_2.add("ImagePositionPatient", [-20., -14., -4.])
data_set_2.add("PixelSpacing", [0.2, 0.2])
val = dicomifier.dicom_to_nifti.image.get_geometry([(data_set, None), (data_set_2, None)])
self.assertEqual(list(val[0]), [-20., -14., -4.5])
self.assertEqual(val[1], [0.2, 0.2, 0.5])
direction = numpy.identity(3)
numpy.testing.assert_array_equal(val[2], direction)
def test_get_geometry_no_orientation (self):
data_set = odil.DataSet()
shared = odil.DataSet()
per_frame = []
first_frame = odil.DataSet()
plane_position_seq = odil.DataSet()
plane_position_seq.add("ImagePositionPatient", [-20., -14., -4.5])
first_frame.add("PlanePositionSequence", [plane_position_seq])
per_frame.append(first_frame)
data_set.add("SharedFunctionalGroupsSequence", [shared])
data_set.add("PerFrameFunctionalGroupsSequence", per_frame)
val = dicomifier.dicom_to_nifti.image.get_geometry([(data_set, 0)])
self.assertEqual(list(val[0]), [-20., -14., -4.5])
self.assertEqual(val[1], self.default_spacing)
numpy.testing.assert_array_equal(val[2], self.default_direction)
def test_sort_position_no_position(self):
ds = odil.DataSet()
shared = odil.DataSet()
plane_ori_seq = odil.DataSet()
plane_ori_seq.add("ImageOrientationPatient",
[1.0, 0.0, 0.0, 0.0, 1.0, 0.0])
shared.add("PlaneOrientationSequence", [plane_ori_seq])
ds.add("SharedFunctionalGroupsSequence", [shared])
per_frame = [odil.DataSet(), odil.DataSet()]
ds.add("PerFrameFunctionalGroupsSequence", per_frame)
ds.add("NumberOfFrames", [len(per_frame)])
data_sets_frame_index = [(ds, 0), (ds, 1)]
sort_return = sort_position(data_sets_frame_index,
[1.0, 0.0, 0.0, 0.0, 1.0, 0.0])
self.assertFalse(sort_return)
def test_get_stacks_orientation(self):
# Test with multi_frame dataSets (one dataSet will have the orientation stored in the
# shared and the second in the per_frame)
# This example is only here to show the importance of the tag location (per_frame or shared)
ds = odil.DataSet()
ds.add("SOPClassUID", [odil.registry.EnhancedMRImageStorage])
shared = odil.DataSet()
plane_ori_seq = odil.DataSet()
plane_ori_seq.add("ImageOrientationPatient",
[1.0, 0.0, 0.0, 0.0, 1.0, 0.0])
shared.add("PlaneOrientationSequence", [plane_ori_seq])
per_frame = [odil.DataSet(), odil.DataSet()] # two frames both empty
ds.add("SharedFunctionalGroupsSequence", [shared])
ds.add("PerFrameFunctionalGroupsSequence", per_frame)
ds.add("NumberOfFrames", [len(per_frame)])
ds2 = odil.DataSet()
ds2.add("SOPClassUID", [odil.registry.EnhancedMRImageStorage])
ds2.add("SharedFunctionalGroupsSequence", [odil.DataSet()])
per_frame = []
first_frame = odil.DataSet()
plane_ori_seq = odil.DataSet()
plane_ori_seq.add("ImageOrientationPatient",
[1.0, 0.0, 0.0, 0.0, 1.0, 0.0])
first_frame.add("PlaneOrientationSequence", [plane_ori_seq])
per_frame.append(first_frame)
second_frame = odil.DataSet()
plane_ori_seq.add("ImageOrientationPatient",
[1.0, 0.0, 0.0, 0.0, -1.0, 0.0])
second_frame.add("PlaneOrientationSequence", [plane_ori_seq])
per_frame.append(second_frame)
ds2.add("PerFrameFunctionalGroupsSequence", per_frame)
ds2.add("NumberOfFrames", [len(per_frame)])
stacks = get_stacks([ds, ds2])
imageOrientationTag = str(odil.Tag("ImageOrientationPatient"))
plane_ori_seq_tag = str(odil.Tag("PlaneOrientationSequence"))
per_frame_tag = str(odil.Tag("PerFrameFunctionalGroupsSequence"))
shared_tag = str(odil.Tag("SharedFunctionalGroupsSequence"))
wanted_stacks = {
(((shared_tag, plane_ori_seq_tag, imageOrientationTag), (1.0, 0.0, 0.0, 0.0, 1.0, 0.0)), ):
[(ds, 0), (ds, 1)],
(((per_frame_tag, plane_ori_seq_tag, imageOrientationTag), (1.0, 0.0, 0.0, 0.0, 1.0, 0.0)), ):
[(ds2, 0)],
(((per_frame_tag, plane_ori_seq_tag, imageOrientationTag), (1.0, 0.0, 0.0, 0.0, -1.0, 0.0)), ):
[(ds2, 1)],
}
self.assertEqual(stacks, wanted_stacks)
def test_values(self):
data_set = odil.DataSet()
data_set.add("PatientName", ["Doe^John"])
data_set.add("PatientID", ["DJ123"])
self.assertEqual([[item for item in element.as_string()]
for element in data_set.values()],
[[b"Doe^John"], [b"DJ123"]])
def test_contains(self):
data_set = odil.DataSet()
data_set.add("PatientName", ["Doe^John"])
self.assertTrue("PatientName" in data_set)
self.assertTrue(odil.registry.PatientName in data_set)
self.assertTrue("PatientID" not in data_set)
self.assertTrue(odil.registry.PatientID not in data_set)
def find(host, port, calling_ae_title, called_ae_title, level, keys,
decode_uids):
query = odil.DataSet()
for key in keys:
if "=" in key:
key, value = key.split("=", 1)
value = value.split("\\")
else:
value = None
tag = getattr(odil.registry, key)
if value is not None:
vr = odil.registry.public_dictionary[tag].vr
if vr in ["DS", "FL", "FD"]:
value = [float(x) for x in value]
elif vr in ["IS", "SL", "SS", "UL", "US"]:
value = [int(x) for x in value]
query.add(tag, value)
else:
query.add(tag)
sop_class = getattr(
odil.registry,
"{}RootQueryRetrieveInformationModelFind".format(level.capitalize()))
find_pc = odil.AssociationParameters.PresentationContext(
1, sop_class, [
odil.registry.ImplicitVRLittleEndian,
odil.registry.ExplicitVRLittleEndian
], odil.AssociationParameters.PresentationContext.Role.SCU)
association = odil.Association()
association.set_peer_host(host)
association.set_peer_port(port)
association.update_parameters()\
.set_calling_ae_title(calling_ae_title)\
.set_called_ae_title(called_ae_title) \
.set_presentation_contexts([find_pc])
association.associate()
logging.info("Association established")
find = odil.FindSCU(association)
find.set_affected_sop_class(sop_class)
data_sets = find.find(query)
print("{} answer{}".format(len(data_sets),
"s" if len(data_sets) > 1 else ""))
max_length = 0
for data_set in data_sets:
max_length = max(max_length, find_max_name_length(data_set))
for data_set in data_sets:
print_data_set(data_set, decode_uids, "", max_length,
odil.Value.Strings())
print()
association.release()
logging.info("Association released")
