def test_write_tag(self):
string_io = BytesIO()
stream = odil.iostream(string_io)
writer = odil.Writer(stream, odil.registry.ExplicitVRLittleEndian)
writer.write_tag(odil.registry.PatientID)
self.assertEqual(string_io.getvalue(), b"\x10\x00\x20\x00")
def test_read_element(self):
string_io = BytesIO(b"PN\x08\x00Foo^Bar ")
stream = odil.iostream(string_io)
reader = odil.Reader(stream, odil.registry.ExplicitVRLittleEndian)
self.assertEqual(
reader.read_element(odil.registry.PatientName),
odil.Element([b"Foo^Bar"], odil.VR.PN))
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_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 test_constructor_1(self):
stream = odil.iostream(BytesIO())
writer = odil.Writer(stream, odil.ByteOrdering.LittleEndian, False)
self.assertEqual(writer.byte_ordering, odil.ByteOrdering.LittleEndian)
self.assertFalse(writer.explicit_vr)
self.assertEqual(
writer.item_encoding, odil.Writer.ItemEncoding.ExplicitLength)
self.assertFalse(writer.use_group_length)
def test_constructor(self):
stream = odil.iostream(BytesIO())
reader = odil.Reader(stream, odil.registry.ImplicitVRLittleEndian)
self.assertEqual(reader.transfer_syntax,
odil.registry.ImplicitVRLittleEndian)
self.assertEqual(reader.byte_ordering, odil.ByteOrdering.LittleEndian)
self.assertFalse(reader.explicit_vr)
self.assertFalse(reader.keep_group_length)
def test_constructor_2(self):
stream = odil.iostream(BytesIO())
writer = odil.Writer(stream, odil.registry.ExplicitVRBigEndian_Retired)
self.assertEqual(writer.byte_ordering, odil.ByteOrdering.BigEndian)
self.assertTrue(writer.explicit_vr)
self.assertEqual(writer.item_encoding,
odil.Writer.ItemEncoding.ExplicitLength)
self.assertFalse(writer.use_group_length)
def test_constructor_no_default(self):
stream = odil.iostream(BytesIO())
reader = odil.Reader(stream, odil.registry.ExplicitVRBigEndian, True)
self.assertEqual(reader.transfer_syntax.encode(),
odil.registry.ExplicitVRBigEndian)
self.assertEqual(reader.byte_ordering, odil.ByteOrdering.BigEndian)
self.assertTrue(reader.explicit_vr)
self.assertTrue(reader.keep_group_length)
def test_constructor(self):
stream = odil.iostream(BytesIO())
reader = odil.Reader(stream, odil.registry.ImplicitVRLittleEndian)
self.assertEqual(
reader.transfer_syntax.encode(),
odil.registry.ImplicitVRLittleEndian)
self.assertEqual(reader.byte_ordering, odil.ByteOrdering.LittleEndian)
self.assertFalse(reader.explicit_vr)
self.assertFalse(reader.keep_group_length)
def test_default_record_keys(self):
creator = odil.BasicDirectoryCreator(self.root, self.files)
creator()
with open(os.path.join(self.root, "DICOMDIR"), "rb") as fd:
header, dicomdir = odil.Reader.read_file(odil.iostream(fd))
records = dicomdir.as_data_set("DirectoryRecordSequence")
self._test_default_records(records)
def test_constructor_2(self):
stream = odil.iostream(BytesIO())
writer = odil.Writer(
stream, odil.registry.ExplicitVRBigEndian_Retired)
self.assertEqual(writer.byte_ordering, odil.ByteOrdering.BigEndian)
self.assertTrue(writer.explicit_vr)
self.assertEqual(
writer.item_encoding, odil.Writer.ItemEncoding.ExplicitLength)
self.assertFalse(writer.use_group_length)
def test_default_record_keys(self):
creator = odil.BasicDirectoryCreator(self.root, self.files)
creator()
with open(os.path.join(self.root, "DICOMDIR"), "rb") as fd:
header, dicomdir = odil.Reader.read_file(odil.iostream(fd))
records = dicomdir.as_data_set("DirectoryRecordSequence")
self._test_default_records(records)
def test_read_data_set(self):
string_io = BytesIO(b"\x10\x00\x10\x00PN\x07\x00Foo^Bar"
b"\x10\x00\x20\x00CS\x03\x00FOO")
stream = odil.iostream(string_io)
reader = odil.Reader(stream, odil.registry.ExplicitVRLittleEndian)
data_set = reader.read_data_set()
self.assertEqual(data_set.size(), 2)
self.assertSequenceEqual(data_set.as_string("PatientName"),
["Foo^Bar"])
self.assertSequenceEqual(data_set.as_string("PatientID"), ["FOO"])
def test_constructor_no_default(self):
stream = odil.iostream(BytesIO())
reader = odil.Reader(
stream, odil.registry.ExplicitVRBigEndian_Retired, True)
self.assertEqual(
reader.transfer_syntax.encode(),
odil.registry.ExplicitVRBigEndian_Retired)
self.assertEqual(reader.byte_ordering, odil.ByteOrdering.BigEndian)
self.assertTrue(reader.explicit_vr)
self.assertTrue(reader.keep_group_length)
def test_read_data_set_halt_condition(self):
string_io = BytesIO(
b"\x10\x00\x10\x00" b"PN" b"\x08\x00" b"Foo^Bar "
b"\x10\x00\x20\x00" b"LO" b"\x04\x00" b"FOO "
)
stream = odil.iostream(string_io)
reader = odil.Reader(stream, odil.registry.ExplicitVRLittleEndian)
data_set = reader.read_data_set(lambda x: x==odil.registry.PatientID)
self.assertEqual(data_set.size(), 1)
self.assertSequenceEqual(data_set.as_string("PatientName"), [b"Foo^Bar"])
def setUp(self):
self.root = tempfile.mkdtemp()
data_set_1 = odil.DataSet()
data_set_1.add("PatientID", ["DJ123"])
data_set_1.add("StudyDate", ["19100110"])
data_set_1.add("StudyTime", ["1234"])
data_set_1.add("StudyDescription", ["Study"])
data_set_1.add("StudyInstanceUID", ["1.2.3.4"])
data_set_1.add("StudyID", ["FOO"])
data_set_1.add("Modality", ["OT"])
data_set_1.add("SeriesInstanceUID", ["1.2.3.4.1"])
data_set_1.add("SeriesNumber", [1])
data_set_1.add("SeriesDescription", ["Series"])
data_set_1.add("InstanceNumber", [1])
data_set_1.add("SOPInstanceUID", ["1.2.3.4.1.1"])
data_set_1.add("SOPClassUID", [odil.registry.RawDataStorage])
with open(os.path.join(self.root, "a.dcm"), "wb") as fd:
stream_1 = odil.iostream(fd)
odil.Writer.write_file(data_set_1, stream_1)
data_set_2 = odil.DataSet()
data_set_2.add("PatientID", ["DJ123"])
data_set_2.add("StudyDate", ["19100110"])
data_set_2.add("StudyTime", ["1234"])
data_set_2.add("StudyDescription", ["Study"])
data_set_2.add("StudyInstanceUID", ["1.2.3.4"])
data_set_2.add("StudyID", ["FOO"])
data_set_2.add("Modality", ["OT"])
data_set_2.add("SeriesInstanceUID", ["1.2.3.4.1"])
data_set_2.add("SeriesNumber", [1])
data_set_2.add("SeriesDescription", ["Series"])
data_set_2.add("InstanceNumber", [2])
data_set_2.add("SOPInstanceUID", ["1.2.3.4.1.2"])
data_set_2.add("SOPClassUID", [odil.registry.RawDataStorage])
with open(os.path.join(self.root, "b.dcm"), "wb") as fd:
stream_2 = odil.iostream(fd)
odil.Writer.write_file(data_set_2, stream_2)
self.files = ["a.dcm", "b.dcm"]
def setUp(self):
self.root = tempfile.mkdtemp()
data_set_1 = odil.DataSet()
data_set_1.add("PatientID", ["DJ123"])
data_set_1.add("StudyDate", ["19100110"])
data_set_1.add("StudyTime", ["1234"])
data_set_1.add("StudyDescription", ["Study"])
data_set_1.add("StudyInstanceUID", ["1.2.3.4"])
data_set_1.add("StudyID", ["FOO"])
data_set_1.add("Modality", ["OT"])
data_set_1.add("SeriesInstanceUID", ["1.2.3.4.1"])
data_set_1.add("SeriesNumber", [1])
data_set_1.add("SeriesDescription", ["Series"])
data_set_1.add("InstanceNumber", [1])
data_set_1.add("SOPInstanceUID", ["1.2.3.4.1.1"])
data_set_1.add("SOPClassUID", [odil.registry.RawDataStorage])
with open(os.path.join(self.root, "a.dcm"), "wb") as fd:
stream_1 = odil.iostream(fd)
odil.Writer.write_file(data_set_1, stream_1)
data_set_2 = odil.DataSet()
data_set_2.add("PatientID", ["DJ123"])
data_set_2.add("StudyDate", ["19100110"])
data_set_2.add("StudyTime", ["1234"])
data_set_2.add("StudyDescription", ["Study"])
data_set_2.add("StudyInstanceUID", ["1.2.3.4"])
data_set_2.add("StudyID", ["FOO"])
data_set_2.add("Modality", ["OT"])
data_set_2.add("SeriesInstanceUID", ["1.2.3.4.1"])
data_set_2.add("SeriesNumber", [1])
data_set_2.add("SeriesDescription", ["Series"])
data_set_2.add("InstanceNumber", [2])
data_set_2.add("SOPInstanceUID", ["1.2.3.4.1.2"])
data_set_2.add("SOPClassUID", [odil.registry.RawDataStorage])
with open(os.path.join(self.root, "b.dcm"), "wb") as fd:
stream_2 = odil.iostream(fd)
odil.Writer.write_file(data_set_2, stream_2)
self.files = ["a.dcm", "b.dcm"]
def test_read_data_set(self):
string_io = BytesIO(
b"\x10\x00\x10\x00PN\x07\x00Foo^Bar"
b"\x10\x00\x20\x00CS\x03\x00FOO"
)
stream = odil.iostream(string_io)
reader = odil.Reader(stream, odil.registry.ExplicitVRLittleEndian)
data_set = reader.read_data_set()
self.assertEqual(data_set.size(), 2)
self.assertSequenceEqual(data_set.as_string("PatientName"), [b"Foo^Bar"])
self.assertSequenceEqual(data_set.as_string("PatientID"), [b"FOO"])
def test_extra_record_keys_tuple(self):
creator = odil.BasicDirectoryCreator(
self.root, self.files, {"SERIES": (("SeriesDescription", 1), )})
creator()
with open(os.path.join(self.root, "DICOMDIR"), "rb") as fd:
header, dicomdir = odil.Reader.read_file(odil.iostream(fd))
records = dicomdir.as_data_set("DirectoryRecordSequence")
self._test_default_records(records)
self.assertSequenceEqual(records[2].as_string("SeriesDescription"),
[b"Series"])
def test_extra_record_keys_tuple(self):
creator = odil.BasicDirectoryCreator(
self.root, self.files,
{ "SERIES": (("SeriesDescription", 1), )})
creator()
with open(os.path.join(self.root, "DICOMDIR"), "rb") as fd:
header, dicomdir = odil.Reader.read_file(odil.iostream(fd))
records = dicomdir.as_data_set("DirectoryRecordSequence")
self._test_default_records(records)
self.assertSequenceEqual(
records[2].as_string("SeriesDescription"), [b"Series"])
def test_write_data_set(self):
data_set = odil.DataSet()
data_set.add("PatientName", ["Foo^Bar"])
data_set.add("PatientID", ["FOO"])
string_io = BytesIO()
stream = odil.iostream(string_io)
writer = odil.Writer(stream, odil.registry.ExplicitVRLittleEndian)
writer.write_data_set(data_set)
self.assertEqual(
string_io.getvalue(),
b"\x10\x00\x10\x00" b"PN" b"\x08\x00" b"Foo^Bar "
b"\x10\x00\x20\x00" b"LO" b"\x04\x00" b"FOO "
)
def test_read_data_set_halt_condition(self):
string_io = BytesIO(b"\x10\x00\x10\x00"
b"PN"
b"\x08\x00"
b"Foo^Bar "
b"\x10\x00\x20\x00"
b"LO"
b"\x04\x00"
b"FOO ")
stream = odil.iostream(string_io)
reader = odil.Reader(stream, odil.registry.ExplicitVRLittleEndian)
data_set = reader.read_data_set(lambda x: x == odil.registry.PatientID)
self.assertEqual(data_set.size(), 1)
self.assertSequenceEqual(data_set.as_string("PatientName"),
["Foo^Bar"])
def test_read_file(self):
data = (
128*b"\x00"+b"DICM"+
b"\x02\x00\x10\x00" b"UI" b"\x14\x00" b"1.2.840.10008.1.2.1\x00"
b"\x10\x00\x10\x00" b"PN" b"\x08\x00" b"Foo^Bar "
)
string_io = BytesIO(data)
stream = odil.iostream(string_io)
header, data_set = odil.Reader.read_file(stream)
self.assertEqual(len(header), 1)
self.assertSequenceEqual(
header.as_string("TransferSyntaxUID"),
[odil.registry.ExplicitVRLittleEndian])
self.assertEqual(len(data_set), 1)
self.assertSequenceEqual(data_set.as_string("PatientName"), [b"Foo^Bar"])
def test_read_file(self):
data = (128 * b"\x00" + b"DICM" + b"\x02\x00\x10\x00"
b"UI"
b"\x14\x00"
b"1.2.840.10008.1.2.1\x00"
b"\x10\x00\x10\x00"
b"PN"
b"\x08\x00"
b"Foo^Bar ")
string_io = BytesIO(data)
stream = odil.iostream(string_io)
header, data_set = odil.Reader.read_file(stream)
self.assertEqual(len(header), 1)
self.assertSequenceEqual(header.as_string("TransferSyntaxUID"),
[odil.registry.ExplicitVRLittleEndian])
self.assertEqual(len(data_set), 1)
self.assertSequenceEqual(data_set.as_string("PatientName"),
["Foo^Bar"])
def test_read_tag(self):
string_io = BytesIO(b"\x10\x00\x20\x00")
stream = odil.iostream(string_io)
reader = odil.Reader(stream, odil.registry.ExplicitVRLittleEndian)
self.assertEqual(reader.read_tag(), odil.registry.PatientID)
def test_read_length(self):
string_io = BytesIO(b"\x34\x12")
stream = odil.iostream(string_io)
reader = odil.Reader(stream, odil.registry.ExplicitVRLittleEndian)
self.assertEqual(reader.read_length(odil.VR.CS), 0x1234)
def test_write_element(self):
string_io = BytesIO()
stream = odil.iostream(string_io)
writer = odil.Writer(stream, odil.registry.ExplicitVRLittleEndian)
writer.write_element(odil.Element(["Foo^Bar"], odil.VR.PN))
self.assertEqual(string_io.getvalue(), b"PN\x08\x00Foo^Bar ")
def test_read_length(self):
string_io = BytesIO(b"\x34\x12")
stream = odil.iostream(string_io)
reader = odil.Reader(stream, odil.registry.ExplicitVRLittleEndian)
self.assertEqual(reader.read_length(odil.VR.CS), 0x1234)
def test_read_tag(self):
string_io = BytesIO(b"\x10\x00\x20\x00")
stream = odil.iostream(string_io)
reader = odil.Reader(stream, odil.registry.ExplicitVRLittleEndian)
self.assertEqual(reader.read_tag(), odil.registry.PatientID)
def test_read_element(self):
string_io = BytesIO(b"PN\x08\x00Foo^Bar ")
stream = odil.iostream(string_io)
reader = odil.Reader(stream, odil.registry.ExplicitVRLittleEndian)
self.assertEqual(reader.read_element(odil.registry.PatientName),
odil.Element(["Foo^Bar"], odil.VR.PN))
