def setUp(self):
super(DicomTests, self).setUp()
self.libs = Mock()
self.dependencies.getLibraries.return_value = self.libs
self.setupPydicom()
from niprov.dcm import DicomFile
self.constructor = DicomFile
self.file = DicomFile(self.path, dependencies=self.dependencies)
def setUp(self):
super(DicomTests, self).setUp()
self.libs = Mock()
self.dependencies.getLibraries.return_value = self.libs
self.setupPydicom()
from niprov.dcm import DicomFile
self.constructor = DicomFile
self.file = DicomFile(self.path, dependencies=self.dependencies)
class DicomTests(BaseFileTests):
def setUp(self):
super(DicomTests, self).setUp()
self.libs = Mock()
self.dependencies.getLibraries.return_value = self.libs
self.setupPydicom()
from niprov.dcm import DicomFile
self.constructor = DicomFile
self.file = DicomFile(self.path, dependencies=self.dependencies)
def test_Gets_basic_info_from_pydicom_and_returns_it(self):
out = self.file.inspect()
self.assertEqual(out['subject'], 'John Doeish')
self.assertEqual(out['protocol'], 'T1 SENSE')
self.assertEqual(out['acquired'], datetime(2014, 8, 5, 12, 19, 14))
def test_if_doesnt_have_acqDateTime_get_seriesDatetime(self):
del (self.img.AcquisitionDateTime)
self.img.SeriesDate = '20120416'
self.img.SeriesTime = '101330.60000'
h = datetime.fromtimestamp(101330.60000).hour
out = self.file.inspect()
self.assertEqual(out['acquired'], datetime(2012, 4, 16, h, 8, 50))
def test_Series_interface(self):
self.assertEqual(self.file.getSeriesId(), self.img.SeriesInstanceUID)
self.assertIn(self.file.path, self.file.provenance['filesInSeries'])
newFile = Mock()
otherFile = Mock()
out = self.file.mergeWith(newFile)
self.assertIn(newFile.path, self.file.provenance['filesInSeries'])
self.assertEqual(self.file, out)
self.assertEqual('series-new-file', self.file.status)
self.assertTrue(self.file.hasFile(newFile))
self.assertFalse(self.file.hasFile(otherFile))
def test_Gets_dimensions(self):
out = self.file.inspect()
self.assertEqual(out['dimensions'], [11, 12, 13])
del (self.img.NumberOfFrames)
out = self.file.inspect()
self.assertEqual(out['dimensions'], [11, 12, 1])
self.file.mergeWith(Mock())
self.assertEqual(out['dimensions'], [11, 12, 2])
def test_Gets_other_fields(self):
out = self.file.inspect()
self.assertEqual(out['duration'], 65.04713439941406)
self.assertEqual(out['subject-position'], 'HFS')
self.assertEqual(out['water-fat-shift'], 1.1173381805419922)
def test_File_without_Rows(self):
del (self.img.Rows)
out = self.file.inspect()
assert not self.listener.fileError.called
self.assertNotIn('dimensions', out)
del (self.img.NumberOfFrames)
out = self.file.inspect()
self.file.mergeWith(Mock())
assert not self.listener.fileError.called
def test_Determines_modality(self):
out = self.file.inspect()
self.assertEqual(out['modality'], 'MRI')
def test_Preserves_modality_if_inherited(self):
pass # Doesn't have to preserve
def setupPydicom(self):
self.img = Mock()
self.img.AcquisitionDateTime = '20140805121914.59000'
self.img.AcquisitionDuration = 65.04713439941406
self.img.SeriesDescription = 'T1 SENSE'
self.img.PatientID = 'John Doeish'
self.img.PatientPosition = 'HFS'
self.img.SeriesInstanceUID = '1.3.46.670589.11.17388.5.0.6340.2011121308140690488'
self.img.Rows = 11
self.img.Columns = 12
self.img.NumberOfFrames = 13
wfs = Mock()
wfs.value = 1.1173381805419922
self.img.__getitem__ = Mock(
side_effect=lambda x: {(0x2001, 0x1022): wfs}[x])
self.libs.dicom.read_file.return_value = self.img
self.libs.hasDependency.return_value = True
class DicomTests(BaseFileTests):
def setUp(self):
super(DicomTests, self).setUp()
self.libs = Mock()
self.dependencies.getLibraries.return_value = self.libs
self.setupPydicom()
from niprov.dcm import DicomFile
self.constructor = DicomFile
self.file = DicomFile(self.path, dependencies=self.dependencies)
def test_Gets_basic_info_from_pydicom_and_returns_it(self):
out = self.file.inspect()
self.assertEqual(out['subject'], 'John Doeish')
self.assertEqual(out['protocol'], 'T1 SENSE')
self.assertEqual(out['acquired'], datetime(2014, 8, 5, 12, 19, 14))
def test_if_doesnt_have_acqDateTime_get_seriesDatetime(self):
del(self.img.AcquisitionDateTime)
self.img.SeriesDate = '20120416'
self.img.SeriesTime = '101330.60000'
h = datetime.fromtimestamp(101330.60000).hour
out = self.file.inspect()
self.assertEqual(out['acquired'],
datetime(2012, 4, 16, h, 8, 50))
def test_Series_interface(self):
self.assertEqual(self.file.getSeriesId(), self.img.SeriesInstanceUID)
self.assertIn(self.file.path, self.file.provenance['filesInSeries'])
newFile = Mock()
otherFile = Mock()
out = self.file.mergeWith(newFile)
self.assertIn(newFile.path, self.file.provenance['filesInSeries'])
self.assertEqual(self.file, out)
self.assertEqual('series-new-file', self.file.status)
self.assertTrue(self.file.hasFile(newFile))
self.assertFalse(self.file.hasFile(otherFile))
def test_Gets_dimensions(self):
out = self.file.inspect()
self.assertEqual(out['dimensions'], [11, 12, 13])
del(self.img.NumberOfFrames)
out = self.file.inspect()
self.assertEqual(out['dimensions'], [11, 12, 1])
self.file.mergeWith(Mock())
self.assertEqual(out['dimensions'], [11, 12, 2])
def test_Gets_other_fields(self):
out = self.file.inspect()
self.assertEqual(out['duration'], 65.04713439941406)
self.assertEqual(out['subject-position'], 'HFS')
self.assertEqual(out['water-fat-shift'], 1.1173381805419922)
def test_File_without_Rows(self):
del(self.img.Rows)
out = self.file.inspect()
assert not self.listener.fileError.called
self.assertNotIn('dimensions', out)
del(self.img.NumberOfFrames)
out = self.file.inspect()
self.file.mergeWith(Mock())
assert not self.listener.fileError.called
def test_Determines_modality(self):
out = self.file.inspect()
self.assertEqual(out['modality'], 'MRI')
def test_Preserves_modality_if_inherited(self):
pass # Doesn't have to preserve
def setupPydicom(self):
self.img = Mock()
self.img.AcquisitionDateTime = '20140805121914.59000'
self.img.AcquisitionDuration = 65.04713439941406
self.img.SeriesDescription = 'T1 SENSE'
self.img.PatientID = 'John Doeish'
self.img.PatientPosition = 'HFS'
self.img.SeriesInstanceUID = '1.3.46.670589.11.17388.5.0.6340.2011121308140690488'
self.img.Rows = 11
self.img.Columns = 12
self.img.NumberOfFrames = 13
wfs = Mock()
wfs.value = 1.1173381805419922
self.img.__getitem__ = Mock(side_effect=lambda x: {(0x2001, 0x1022):wfs}[x])
self.libs.dicom.read_file.return_value = self.img
self.libs.hasDependency.return_value = True
