def test_fmt_docval_args_no_docval(self):
""" Test that fmt_docval_args raises an error when run on function without docval """
def method1(self, **kwargs):
pass
with self.assertRaisesRegex(ValueError, r"no docval found on .*method1.*"):
fmt_docval_args(method1, {})
def __init__(self, **kwargs):
description, emission_lambda = popargs("description",
"emission_lambda", kwargs)
pargs, pkwargs = fmt_docval_args(
super(OpticalChannel, self).__init__, kwargs)
super(OpticalChannel, self).__init__(*pargs, **pkwargs)
self.description = description
self.emission_lambda = emission_lambda
def __init__(self, **kwargs):
"""Create a TimeSeries object
"""
pargs, pkwargs = fmt_docval_args(super(TimeSeries, self).__init__, kwargs)
super(TimeSeries, self).__init__(*pargs, **pkwargs)
keys = ("resolution",
"comments",
"description",
"conversion",
"unit",
"control",
"control_description")
for key in keys:
val = kwargs.get(key)
if val is not None:
setattr(self, key, val)
data = getargs('data', kwargs)
self.fields['data'] = data
if isinstance(data, TimeSeries):
data.__add_link('data_link', self)
self.fields['num_samples'] = data.num_samples
elif isinstance(data, AbstractDataChunkIterator):
self.fields['num_samples'] = -1
elif isinstance(data, DataIO):
this_data = data.data
if isinstance(this_data, AbstractDataChunkIterator):
self.fields['num_samples'] = -1
else:
self.fields['num_samples'] = len(this_data)
elif data is None:
self.fields['num_samples'] = 0
else:
self.fields['num_samples'] = len(data)
timestamps = kwargs.get('timestamps')
starting_time = kwargs.get('starting_time')
rate = kwargs.get('rate')
if timestamps is not None:
if rate is not None:
raise ValueError('Specifying rate and timestamps is not supported.')
if starting_time is not None:
raise ValueError('Specifying starting_time and timestamps is not supported.')
self.fields['timestamps'] = timestamps
self.timestamps_unit = 'Seconds'
self.interval = 1
if isinstance(timestamps, TimeSeries):
timestamps.__add_link('timestamp_link', self)
elif rate is not None:
self.rate = rate
if starting_time is not None:
self.starting_time = starting_time
self.starting_time_unit = 'Seconds'
else:
self.starting_time = 0.0
else:
raise TypeError("either 'timestamps' or 'rate' must be specified")
def __init__(self, **kwargs):
device, description, excitation_lambda, location = popargs(
'device', 'description', 'excitation_lambda', 'location', kwargs)
pargs, pkwargs = fmt_docval_args(super(OptogeneticStimulusSite, self).__init__, kwargs)
super(OptogeneticStimulusSite, self).__init__(*pargs, **pkwargs)
self.device = device
self.description = description
self.excitation_lambda = excitation_lambda
self.location = location
def __init__(self, **kwargs):
data, field_of_view, unit, dimension = popargs('data', 'field_of_view',
'unit', 'dimension',
kwargs)
pargs, pkwargs = fmt_docval_args(super(AxisMap, self).__init__, kwargs)
super(AxisMap, self).__init__(*pargs, **pkwargs)
self.data = data
self.field_of_view = field_of_view
self.unit = unit
self.dimension = dimension
def __init__(self, **kwargs):
data, bits_per_pixel, dimension, format, field_of_view = popargs(
'data', 'bits_per_pixel', 'dimension', 'format', 'field_of_view',
kwargs)
pargs, pkwargs = fmt_docval_args(super(AImage, self).__init__, kwargs)
super(AImage, self).__init__(*pargs, **pkwargs)
self.data = data
self.bits_per_pixel = bits_per_pixel
self.dimension = format
self.field_of_view = field_of_view
def __init__(self, **kwargs):
field_of_view, imaging_plane, pmt_gain, scan_line_rate = popargs(
'field_of_view', 'imaging_plane', 'pmt_gain', 'scan_line_rate',
kwargs)
pargs, pkwargs = fmt_docval_args(
super(TwoPhotonSeries, self).__init__, kwargs)
super(TwoPhotonSeries, self).__init__(*pargs, **pkwargs)
self.field_of_view = field_of_view
self.imaging_plane = imaging_plane
self.pmt_gain = pmt_gain
self.scan_line_rate = scan_line_rate
def test_fmt_docval_args(self):
""" Test that fmt_docval_args works """
test_kwargs = {
'arg1': 'a string',
'arg2': 1,
'arg3': True,
}
rec_args, rec_kwargs = fmt_docval_args(self.test_obj.basic_add2_kw, test_kwargs)
exp_args = ['a string', 1]
self.assertListEqual(rec_args, exp_args)
exp_kwargs = {'arg3': True}
self.assertDictEqual(rec_kwargs, exp_kwargs)
def __init__(self, **kwargs):
imaging_plane, reference_images = popargs('imaging_plane',
'reference_images', kwargs)
if kwargs.get('name') is None:
kwargs['name'] = imaging_plane.name
columns, colnames = getargs('columns', 'colnames', kwargs)
pargs, pkwargs = fmt_docval_args(
super(PlaneSegmentation, self).__init__, kwargs)
super(PlaneSegmentation, self).__init__(*pargs, **pkwargs)
self.imaging_plane = imaging_plane
if isinstance(reference_images, ImageSeries):
reference_images = (reference_images, )
self.reference_images = reference_images
def test_fmt_docval_args_allow_extra(self):
""" Test that fmt_docval_args works """
test_kwargs = {
'arg1': 'a string',
'arg2': 1,
'arg3': True,
'hello': 'abc',
'list': ['abc', 1, 2, 3]
}
rec_args, rec_kwargs = fmt_docval_args(self.test_obj.basic_add2_kw_allow_extra, test_kwargs)
exp_args = ['a string', 1]
self.assertListEqual(rec_args, exp_args)
exp_kwargs = {'arg3': True, 'hello': 'abc', 'list': ['abc', 1, 2, 3]}
self.assertDictEqual(rec_kwargs, exp_kwargs)
def __init__(self, **kwargs):
slice, seal, description, location, resistance, filtering, initial_access_resistance, device = popargs(
'slice', 'seal', 'description', 'location', 'resistance',
'filtering', 'initial_access_resistance', 'device', kwargs)
pargs, pkwargs = fmt_docval_args(
super(IntracellularElectrode, self).__init__, kwargs)
super(IntracellularElectrode, self).__init__(*pargs, **pkwargs)
self.slice = slice
self.seal = seal
self.description = description
self.location = location
self.resistance = resistance
self.filtering = filtering
self.initial_access_resistance = initial_access_resistance
self.device = device
def __init__(self, **kwargs):
axis_1_phase_map, axis_1_power_map, axis_2_phase_map, axis_2_power_map, axis_descriptions, \
focal_depth_image, sign_map, vasculature_image = popargs(
'axis_1_phase_map', 'axis_1_power_map', 'axis_2_phase_map', 'axis_2_power_map',
'axis_descriptions', 'focal_depth_image', 'sign_map', 'vasculature_image', kwargs)
pargs, pkwargs = fmt_docval_args(
super(ImagingRetinotopy, self).__init__, kwargs)
super(ImagingRetinotopy, self).__init__(*pargs, **pkwargs)
self.axis_1_phase_map = axis_1_phase_map
self.axis_1_power_map = axis_1_power_map
self.axis_2_phase_map = axis_2_phase_map
self.axis_2_power_map = axis_2_power_map
self.axis_descriptions = axis_descriptions
self.focal_depth_image = focal_depth_image
self.sign_map = sign_map
self.vasculature_image = vasculature_image
def __init__(self, **kwargs):
kwargs['name'] = 'subject'
pargs, pkwargs = fmt_docval_args(super(Subject, self).__init__, kwargs)
super(Subject, self).__init__(*pargs, **pkwargs)
self.age = getargs('age', kwargs)
self.description = getargs('description', kwargs)
self.genotype = getargs('genotype', kwargs)
self.sex = getargs('sex', kwargs)
self.species = getargs('species', kwargs)
self.subject_id = getargs('subject_id', kwargs)
self.weight = getargs('weight', kwargs)
date_of_birth = getargs('date_of_birth', kwargs)
if date_of_birth and date_of_birth.tzinfo is None:
self.date_of_birth = _add_missing_timezone(date_of_birth)
else:
self.date_of_birth = date_of_birth
def __init__(self, **kwargs):
optical_channel, description, device, excitation_lambda, imaging_rate, \
indicator, location, manifold, conversion, unit, reference_frame = popargs(
'optical_channel', 'description', 'device', 'excitation_lambda',
'imaging_rate', 'indicator', 'location', 'manifold', 'conversion',
'unit', 'reference_frame', kwargs)
pargs, pkwargs = fmt_docval_args(
super(ImagingPlane, self).__init__, kwargs)
super(ImagingPlane, self).__init__(*pargs, **pkwargs)
self.optical_channel = optical_channel if isinstance(
optical_channel, list) else [optical_channel]
self.description = description
self.device = device
self.excitation_lambda = excitation_lambda
self.imaging_rate = imaging_rate
self.indicator = indicator
self.location = location
self.manifold = manifold
self.conversion = conversion
self.unit = unit
self.reference_frame = reference_frame
def _func(self, **kwargs):
cargs, ckwargs = fmt_docval_args(container_type.__init__, kwargs)
ret = container_type(*cargs, **ckwargs)
getattr(self, add_name)(ret)
return ret
def __init__(self, **kwargs):
args, kwargs = fmt_docval_args(LinkSpec.__init__, kwargs)
super(NWBLinkSpec, self).__init__(*args, **kwargs)
def __init__(self, **kwargs):
args, kwargs = fmt_docval_args(AttributeSpec.__init__, kwargs)
super(NWBAttributeSpec, self).__init__(*args, **kwargs)
def __init__(self, **kwargs):
''' Create a NWBNamespaceBuilder '''
args, vargs = fmt_docval_args(NamespaceBuilder.__init__, kwargs)
kwargs['namespace_cls'] = NWBNamespace
super(NWBNamespaceBuilder, self).__init__(*args, **kwargs)
self.include_namespace(CORE_NAMESPACE)
def __init__(self, **kwargs):
rois = popargs('rois', kwargs)
pargs, pkwargs = fmt_docval_args(
super(RoiResponseSeries, self).__init__, kwargs)
super(RoiResponseSeries, self).__init__(*pargs, **pkwargs)
self.rois = rois
def __init__(self, **kwargs):
pargs, pkwargs = fmt_docval_args(super(NWBFile, self).__init__, kwargs)
pkwargs['name'] = 'root'
super(NWBFile, self).__init__(*pargs, **pkwargs)
self.__session_description = getargs('session_description', kwargs)
self.__identifier = getargs('identifier', kwargs)
self.__session_start_time = getargs('session_start_time', kwargs)
if self.__session_start_time.tzinfo is None:
self.__session_start_time = _add_missing_timezone(
self.__session_start_time)
self.__timestamps_reference_time = getargs('timestamps_reference_time',
kwargs)
if self.__timestamps_reference_time is None:
self.__timestamps_reference_time = self.__session_start_time
elif self.__timestamps_reference_time.tzinfo is None:
raise ValueError(
"'timestamps_reference_time' must be a timezone-aware datetime object."
)
self.__file_create_date = getargs('file_create_date', kwargs)
if self.__file_create_date is None:
self.__file_create_date = datetime.now(tzlocal())
if isinstance(self.__file_create_date, datetime):
self.__file_create_date = [self.__file_create_date]
self.__file_create_date = list(
map(_add_missing_timezone, self.__file_create_date))
self.acquisition = getargs('acquisition', kwargs)
self.analysis = getargs('analysis', kwargs)
self.stimulus = getargs('stimulus', kwargs)
self.stimulus_template = getargs('stimulus_template', kwargs)
self.keywords = getargs('keywords', kwargs)
self.processing = getargs('processing', kwargs)
epochs = getargs('epochs', kwargs)
if epochs is not None:
if epochs.name != 'epochs':
raise ValueError("NWBFile.epochs must be named 'epochs'")
self.epochs = epochs
self.epoch_tags = getargs('epoch_tags', kwargs)
trials = getargs('trials', kwargs)
if trials is not None:
self.trials = trials
invalid_times = getargs('invalid_times', kwargs)
if invalid_times is not None:
self.invalid_times = invalid_times
units = getargs('units', kwargs)
if units is not None:
self.units = units
self.electrodes = getargs('electrodes', kwargs)
self.electrode_groups = getargs('electrode_groups', kwargs)
self.devices = getargs('devices', kwargs)
self.ic_electrodes = getargs('ic_electrodes', kwargs)
self.imaging_planes = getargs('imaging_planes', kwargs)
self.ogen_sites = getargs('ogen_sites', kwargs)
self.intervals = getargs('intervals', kwargs)
self.subject = getargs('subject', kwargs)
self.sweep_table = getargs('sweep_table', kwargs)
self.lab_meta_data = getargs('lab_meta_data', kwargs)
recommended = [
'experimenter',
'experiment_description',
'session_id',
'lab',
'institution',
'data_collection',
'notes',
'pharmacology',
'protocol',
'related_publications',
'slices',
'source_script',
'source_script_file_name',
'surgery',
'virus',
'stimulus_notes',
]
for attr in recommended:
setattr(self, attr, kwargs.get(attr, None))
if getargs('source_script', kwargs) is None and getargs(
'source_script_file_name', kwargs) is not None:
raise ValueError(
"'source_script' cannot be None when 'source_script_file_name' is set"
)
def __init__(self, **kwargs):
site = popargs('site', kwargs)
pargs, pkwargs = fmt_docval_args(
super(OptogeneticSeries, self).__init__, kwargs)
super(OptogeneticSeries, self).__init__(*pargs, **pkwargs)
self.site = site
def __init__(self, **kwargs):
pargs, pkwargs = fmt_docval_args(super(NWBFile, self).__init__, kwargs)
pkwargs['name'] = 'root'
super(NWBFile, self).__init__(*pargs, **pkwargs)
self.fields['session_description'] = getargs('session_description',
kwargs)
self.fields['identifier'] = getargs('identifier', kwargs)
self.fields['session_start_time'] = getargs('session_start_time',
kwargs)
if self.fields['session_start_time'].tzinfo is None:
self.fields['session_start_time'] = _add_missing_timezone(
self.fields['session_start_time'])
self.fields['timestamps_reference_time'] = getargs(
'timestamps_reference_time', kwargs)
if self.fields['timestamps_reference_time'] is None:
self.fields['timestamps_reference_time'] = self.fields[
'session_start_time']
elif self.fields['timestamps_reference_time'].tzinfo is None:
raise ValueError(
"'timestamps_reference_time' must be a timezone-aware datetime object."
)
self.fields['file_create_date'] = getargs('file_create_date', kwargs)
if self.fields['file_create_date'] is None:
self.fields['file_create_date'] = datetime.now(tzlocal())
if isinstance(self.fields['file_create_date'], datetime):
self.fields['file_create_date'] = [self.fields['file_create_date']]
self.fields['file_create_date'] = list(
map(_add_missing_timezone, self.fields['file_create_date']))
fieldnames = [
'acquisition',
'analysis',
'stimulus',
'stimulus_template',
'keywords',
'processing',
'epoch_tags',
'electrodes',
'electrode_groups',
'devices',
'ic_electrodes',
'imaging_planes',
'ogen_sites',
'intervals',
'subject',
'sweep_table',
'lab_meta_data',
'epochs',
'trials',
'invalid_times',
'units',
'scratch',
'experimenter',
'experiment_description',
'session_id',
'lab',
'institution',
'data_collection',
'notes',
'pharmacology',
'protocol',
'related_publications',
'slices',
'source_script',
'source_script_file_name',
'surgery',
'virus',
'stimulus_notes',
]
for attr in fieldnames:
setattr(self, attr, kwargs.get(attr, None))
if getargs('source_script', kwargs) is None and getargs(
'source_script_file_name', kwargs) is not None:
raise ValueError(
"'source_script' cannot be None when 'source_script_file_name' is set"
)
self.__obj = None