def setUp(self):
super(FifTests, self).setUp()
self.libs = Mock()
self.libs.hasDependency.return_value = True
self.libs.mne.io.read_raw_fif.side_effect = ValueError
self.libs.mne.read_cov.side_effect = ValueError
self.libs.mne.read_epochs.side_effect = ValueError
self.libs.mne.read_evokeds.side_effect = ValueError
self.libs.mne.read_forward_solution.side_effect = ValueError
self.libs.mne.read_trans.side_effect = ValueError
self.libs.mne.read_proj.side_effect = ValueError
self.dependencies.getLibraries.return_value = self.libs
from niprov.fif import FifFile
self.constructor = FifFile
self.file = FifFile(self.path, dependencies=self.dependencies)
def setUp(self):
super(FifTests, self).setUp()
self.libs = Mock()
self.libs.hasDependency.return_value = True
self.libs.mne.io.read_raw_fif.side_effect = ValueError
self.libs.mne.read_cov.side_effect = ValueError
self.libs.mne.read_epochs.side_effect = ValueError
self.libs.mne.read_evokeds.side_effect = ValueError
self.libs.mne.read_forward_solution.side_effect = ValueError
self.libs.mne.read_trans.side_effect = ValueError
self.libs.mne.read_proj.side_effect = ValueError
self.dependencies.getLibraries.return_value = self.libs
from niprov.fif import FifFile
self.constructor = FifFile
self.file = FifFile(self.path, dependencies=self.dependencies)
class FifTests(BaseFileTests):
def setUp(self):
super(FifTests, self).setUp()
self.libs = Mock()
self.libs.hasDependency.return_value = True
self.libs.mne.io.read_raw_fif.side_effect = ValueError
self.libs.mne.read_cov.side_effect = ValueError
self.libs.mne.read_epochs.side_effect = ValueError
self.libs.mne.read_evokeds.side_effect = ValueError
self.libs.mne.read_forward_solution.side_effect = ValueError
self.libs.mne.read_trans.side_effect = ValueError
self.libs.mne.read_proj.side_effect = ValueError
self.dependencies.getLibraries.return_value = self.libs
from niprov.fif import FifFile
self.constructor = FifFile
self.file = FifFile(self.path, dependencies=self.dependencies)
def test_Gets_basic_info_from_mne_and_returns_it(self):
self.setupRawFile()
out = self.file.inspect()
self.assertEqual(out["subject"], "John Doeish")
self.assertEqual(out["project"], "worlddom")
self.assertEqual(out["acquired"], self.acquired)
def test_Gets_dimensions(self):
self.setupRawFile()
out = self.file.inspect()
self.assertEqual(out["dimensions"], [123, 91])
self.assertEqual(out["sampling-frequency"], 200)
self.assertEqual(out["duration"], 91 / 200.0)
def test_Attach_method(self):
self.setupRawFile()
self.file.inspect()
self.file.getProvenance = Mock()
self.file.getProvenance.return_value = "serial prov"
self.file.attach("json")
self.file.getProvenance.assert_called_with("json")
self.assertIn("existing bla bla ", self.img.info["description"]) # original string+added space
self.assertIn("NIPROV:" + "serial prov", self.img.info["description"])
self.libs.mne.io.write_info.assert_called_with(self.file.path, self.img.info)
def test_Attach_method_doesnt_do_anything_on_non_raw_files(self):
self.setupEpochsFile()
self.file.getProvenance = Mock()
self.file.attach("json")
assert not self.libs.mne.io.read_info.called
assert not self.file.getProvenance.called
assert not self.libs.mne.io.write_info.called
def test_Determines_modality(self):
out = self.file.inspect()
self.assertEqual(out["modality"], "MEG")
def test_Preserves_modality_if_inherited(self):
pass # Doesn't have to preserve
def test_Tries_different_mne_access_functions_or_fails_silently(self):
out = self.file.inspect()
self.libs.mne.io.read_raw_fif.assert_called_with(self.path, allow_maxshield=True)
self.libs.mne.read_cov.assert_called_with(self.path)
self.libs.mne.read_epochs.assert_called_with(self.path)
self.libs.mne.read_evokeds.assert_called_with(self.path)
self.libs.mne.read_forward_solution.assert_called_with(self.path)
self.libs.mne.read_trans.assert_called_with(self.path)
self.libs.mne.read_proj.assert_called_with(self.path)
self.assertEqual(out["fif-type"], "other")
def test_epochs(self):
self.setupEpochsFile()
out = self.file.inspect()
self.assertEqual(out["fif-type"], "epo")
self.assertEqual(out["lowpass"], 40.0)
self.assertEqual(out["highpass"], 0.10000000149)
self.assertEqual(out["bad-channels"], ["MEG666", "ECG999"])
self.assertEqual(out["dimensions"], [7, 455])
def test_evokeds(self):
self.setupEvokedsFile()
out = self.file.inspect()
self.assertEqual(out["fif-type"], "ave")
self.assertEqual(out["dimensions"], [3, 306, 455])
def test_covariance(self):
self.setupCovarianceFile()
out = self.file.inspect()
self.assertEqual(out["fif-type"], "cov")
self.assertEqual(out["dimensions"], [365, 365])
def test_forward(self):
self.setupForwardFile()
out = self.file.inspect()
self.assertEqual(out["fif-type"], "fwd")
def test_trans(self):
self.setupTransFile()
out = self.file.inspect()
self.assertEqual(out["fif-type"], "trans")
def test_proj(self):
self.setupProjFile()
out = self.file.inspect()
self.assertEqual(out["fif-type"], "proj")
self.assertEqual(out["projection-description"], "Mars")
def test_mnepy_read_funcs_throw_ioerror(self):
self.libs.mne.read_trans.side_effect = IOError
out = self.file.inspect()
self.libs.mne.read_trans.assert_called_with(self.path)
def test_inspect_right_reader_for_evoked_fiftype(self):
self.libs.mne.read_proj.side_effect = None
self.setupEvokedsFile()
out = self.file.inspect()
self.assertEqual(out["fif-type"], "ave")
def setupRawFile(self):
TS = 1422522595.76096
self.acquired = datetime.fromtimestamp(TS)
self.img = Mock()
self.img.info = {
"meas_date": (TS,),
"proj_name": "worlddom",
"subject_info": {"first_name": "John", "last_name": "Doeish"},
"nchan": 123,
"sfreq": 200,
"description": "existing bla bla",
}
self.img.first_samp = 10
self.img.last_samp = 100
self.libs.mne.io.read_raw_fif.side_effect = None
self.libs.mne.io.read_raw_fif.return_value = self.img
self.libs.mne.io.read_info.return_value = self.img.info
def setupEpochsFile(self):
self.img = Mock()
self.img.info = {"lowpass": 40.0, "highpass": 0.10000000149, "bads": ["MEG666", "ECG999"]}
self.img.events = numpy.zeros((7, 3))
self.img.times = numpy.zeros((455, 1))
self.libs.mne.read_epochs.side_effect = None
self.libs.mne.read_epochs.return_value = self.img
def setupEvokedsFile(self):
self.img = Mock()
self.img.info = {}
self.img.data = numpy.zeros((306, 455))
self.libs.mne.read_evokeds.side_effect = None
self.libs.mne.read_evokeds.return_value = [self.img, self.img, self.img]
def setupCovarianceFile(self):
self.img = Mock()
self.img.data = numpy.zeros((365, 365))
self.libs.mne.read_cov.side_effect = None
self.libs.mne.read_cov.return_value = self.img
def setupForwardFile(self):
self.img = Mock()
self.libs.mne.read_forward_solution.side_effect = None
self.libs.mne.read_forward_solution.return_value = self.img
def setupTransFile(self):
self.img = Mock()
self.libs.mne.read_trans.side_effect = None
self.libs.mne.read_trans.return_value = self.img
def setupProjFile(self):
self.img = [{"desc": "Mars"}]
self.libs.mne.read_proj.side_effect = None
self.libs.mne.read_proj.return_value = self.img
class FifTests(BaseFileTests):
def setUp(self):
super(FifTests, self).setUp()
self.libs = Mock()
self.libs.hasDependency.return_value = True
self.libs.mne.io.read_raw_fif.side_effect = ValueError
self.libs.mne.read_cov.side_effect = ValueError
self.libs.mne.read_epochs.side_effect = ValueError
self.libs.mne.read_evokeds.side_effect = ValueError
self.libs.mne.read_forward_solution.side_effect = ValueError
self.libs.mne.read_trans.side_effect = ValueError
self.libs.mne.read_proj.side_effect = ValueError
self.dependencies.getLibraries.return_value = self.libs
from niprov.fif import FifFile
self.constructor = FifFile
self.file = FifFile(self.path, dependencies=self.dependencies)
def test_Gets_basic_info_from_mne_and_returns_it(self):
self.setupRawFile()
out = self.file.inspect()
self.assertEqual(out['subject'], 'John Doeish')
self.assertEqual(out['project'], 'worlddom')
self.assertEqual(out['acquired'], self.acquired)
def test_Gets_dimensions(self):
self.setupRawFile()
out = self.file.inspect()
self.assertEqual(out['dimensions'], [123, 91])
self.assertEqual(out['sampling-frequency'], 200)
self.assertEqual(out['duration'], 91 / 200.)
def test_Attach_method(self):
self.setupRawFile()
self.file.inspect()
self.file.getProvenance = Mock()
self.file.getProvenance.return_value = 'serial prov'
self.file.attach('json')
self.file.getProvenance.assert_called_with('json')
self.assertIn('existing bla bla ', # original string+added space
self.img.info['description'])
self.assertIn('NIPROV:' + 'serial prov',
self.img.info['description'])
self.libs.mne.io.write_info.assert_called_with(self.file.path,
self.img.info)
def test_Attach_method_doesnt_do_anything_on_non_raw_files(self):
self.setupEpochsFile()
self.file.getProvenance = Mock()
self.file.attach('json')
assert not self.libs.mne.io.read_info.called
assert not self.file.getProvenance.called
assert not self.libs.mne.io.write_info.called
def test_Determines_modality(self):
out = self.file.inspect()
self.assertEqual(out['modality'], 'MEG')
def test_Preserves_modality_if_inherited(self):
pass # Doesn't have to preserve
def test_Tries_different_mne_access_functions_or_fails_silently(self):
out = self.file.inspect()
self.libs.mne.io.read_raw_fif.assert_called_with(self.path,
allow_maxshield=True)
self.libs.mne.read_cov.assert_called_with(self.path)
self.libs.mne.read_epochs.assert_called_with(self.path)
self.libs.mne.read_evokeds.assert_called_with(self.path)
self.libs.mne.read_forward_solution.assert_called_with(self.path)
self.libs.mne.read_trans.assert_called_with(self.path)
self.libs.mne.read_proj.assert_called_with(self.path)
self.assertEqual(out['fif-type'], 'other')
def test_epochs(self):
self.setupEpochsFile()
out = self.file.inspect()
self.assertEqual(out['fif-type'], 'epo')
self.assertEqual(out['lowpass'], 40.0)
self.assertEqual(out['highpass'], 0.10000000149)
self.assertEqual(out['bad-channels'], ['MEG666', 'ECG999'])
self.assertEqual(out['dimensions'], [7, 455])
def test_evokeds(self):
self.setupEvokedsFile()
out = self.file.inspect()
self.assertEqual(out['fif-type'], 'ave')
self.assertEqual(out['dimensions'], [3, 306, 455])
def test_covariance(self):
self.setupCovarianceFile()
out = self.file.inspect()
self.assertEqual(out['fif-type'], 'cov')
self.assertEqual(out['dimensions'], [365, 365])
def test_forward(self):
self.setupForwardFile()
out = self.file.inspect()
self.assertEqual(out['fif-type'], 'fwd')
def test_trans(self):
self.setupTransFile()
out = self.file.inspect()
self.assertEqual(out['fif-type'], 'trans')
def test_proj(self):
self.setupProjFile()
out = self.file.inspect()
self.assertEqual(out['fif-type'], 'proj')
self.assertEqual(out['projection-description'], 'Mars')
def test_mnepy_read_funcs_throw_ioerror(self):
self.libs.mne.read_trans.side_effect = IOError
out = self.file.inspect()
self.libs.mne.read_trans.assert_called_with(self.path)
def test_inspect_right_reader_for_evoked_fiftype(self):
self.libs.mne.read_proj.side_effect = None
self.setupEvokedsFile()
out = self.file.inspect()
self.assertEqual(out['fif-type'], 'ave')
def setupRawFile(self):
TS = 1422522595.76096
self.acquired = datetime.fromtimestamp(TS)
self.img = Mock()
self.img.info = {
'meas_date': (TS,),
'proj_name': 'worlddom',
'subject_info': {'first_name': 'John', 'last_name': 'Doeish'},
'nchan': 123,
'sfreq': 200,
'description': 'existing bla bla'}
self.img.first_samp = 10
self.img.last_samp = 100
self.libs.mne.io.read_raw_fif.side_effect = None
self.libs.mne.io.read_raw_fif.return_value = self.img
self.libs.mne.io.read_info.return_value = self.img.info
def setupEpochsFile(self):
self.img = Mock()
self.img.info = {
'lowpass': 40.0,
'highpass': 0.10000000149,
'bads': ['MEG666', 'ECG999']}
self.img.events = numpy.zeros((7, 3))
self.img.times = numpy.zeros((455, 1))
self.libs.mne.read_epochs.side_effect = None
self.libs.mne.read_epochs.return_value = self.img
def setupEvokedsFile(self):
self.img = Mock()
self.img.info = {}
self.img.data = numpy.zeros((306, 455))
self.libs.mne.read_evokeds.side_effect = None
self.libs.mne.read_evokeds.return_value = [self.img, self.img, self.img]
def setupCovarianceFile(self):
self.img = Mock()
self.img.data = numpy.zeros((365, 365))
self.libs.mne.read_cov.side_effect = None
self.libs.mne.read_cov.return_value = self.img
def setupForwardFile(self):
self.img = Mock()
self.libs.mne.read_forward_solution.side_effect = None
self.libs.mne.read_forward_solution.return_value = self.img
def setupTransFile(self):
self.img = Mock()
self.libs.mne.read_trans.side_effect = None
self.libs.mne.read_trans.return_value = self.img
def setupProjFile(self):
self.img = [{'desc': 'Mars'}]
self.libs.mne.read_proj.side_effect = None
self.libs.mne.read_proj.return_value = self.img