def __init__(self, observation = {'mean_Ith':None, 'Ith_std':None, 'mean_Veq': None, 'Veq_std': None} , name="Depolarization block test" , force_run=False, base_directory= None, show_plot=True, save_all=True): observation = self.format_data(observation) Test.__init__(self,observation,name) self.required_capabilities += (cap.ReceivesSquareCurrent_ProvidesResponse,) self.force_run = force_run self.base_directory = base_directory self.save_all = save_all self.show_plot = show_plot self.path_temp_data = None #added later, because model name is needed self.path_figs = None self.path_results = None self.figures = [] self.npool = multiprocessing.cpu_count() - 1 self.logFile = None self.test_log_filename = 'test_log.txt' description = "Tests if the model enters depolarization block under current injection of increasing amplitudes."
def test_ObservationValidator(self): import random from sciunit import Test from sciunit.validators import ObservationValidator long_test_list = [None] * 100 for index in range(100): long_test_list[index] = random.randint(1, 1000) q = pq.Quantity([1, 2, 3], "ft") units = q.simplified.units units.name = "UnitName" testObj = Test(long_test_list) testObj.units = units obsVal = ObservationValidator(test=testObj) # test constructor self.assertRaises(BaseException, ObservationValidator) self.assertIsInstance(obsVal, ObservationValidator) # test _validate_iterable obsVal._validate_iterable(True, "key", long_test_list) self.assertRaises( BaseException, obsVal._validate_iterable, is_iterable=True, key="Test key", value=0, ) # test _validate_units self.assertRaises( BaseException, obsVal._validate_units, has_units=True, key="Test Key", value="I am not units", ) # units in test object is q.simplified.units obsVal._validate_units(has_units=True, key="TestKey", value=q) # units in test object is a dict testObj.units = {"TestKey": units} obsVal._validate_units(has_units=True, key="TestKey", value=q) print( "debug here..............................................................................." ) # Units dismatch q2 = pq.Quantity([1], "J") self.assertRaises( BaseException, obsVal._validate_units, has_units=True, key="TestKey", value=q2, )
def __init__(self, observation={'mean':None,'std':None}, name="Resting potential test"): """Takes the mean and standard deviation of reference membrane potentials.""" Test.__init__(self,observation,name) self.required_capabilities += (ProducesMembranePotential, ReceivesCurrent,)
def __init__(self, config = {}, observation = {"mean_AP1_amp_at_50um" : None, "std_AP1_amp_at_50um" : None, "mean_AP1_amp_at_150um" : None, "std_AP1_amp_at_150um" : None, "mean_AP1_amp_at_250um" : None, "std_AP1_amp_at_250um" : None, "mean_AP1_amp_strong_propagating_at_350um" : None, "std_AP1_amp_strong_propagating_at_350um" : None, "mean_AP1_amp_weak_propagating_at_350um" : None, "std_AP1_amp_weak_propagating_at_350um" : None, "mean_APlast_amp_at_50um" : None, "std_APlast_amp_at_50um" : None, "mean_APlast_amp_at_150um" : None, "std_APlast_amp_at_150um" : None, "mean_APlast_amp_at_250um" : None, "std_APlast_amp_at_250um" : None, "mean_APlast_amp_at_350um" : None, "std_APlast_amp_at_350um" : None}, name="Back-propagating action potential test" , force_run=False, force_run_FindCurrentStim=False, base_directory= None, show_plot=True, save_all = True, trunk_origin = None): observation = self.format_data(observation) Test.__init__(self, observation, name) self.required_capabilities += (cap.ReceivesSquareCurrent_ProvidesResponse_MultipleLocations, cap.ProvidesRecordingLocationsOnTrunk, cap.ReceivesSquareCurrent_ProvidesResponse,) self.force_run = force_run self.force_run_FindCurrentStim = force_run_FindCurrentStim self.show_plot = show_plot self.save_all = save_all self.base_directory = base_directory self.path_temp_data = None #added later, because model name is needed self.path_figs = None self.path_results = None self.trunk_origin = trunk_origin self.logFile = None self.test_log_filename = 'test_log.txt' self.npool = multiprocessing.cpu_count() - 1 self.config = config description = "Tests the mode and efficacy of back-propagating action potentials on the apical trunk."
def __init__(self, config={}, observation={}, name="PSP attenuation test", force_run=False, base_directory=None, show_plot=True, num_of_dend_locations=15, random_seed=1, save_all=True, trunk_origin=None): observation = self.format_data(observation) Test.__init__(self, observation, name) self.required_capabilities += (cap.ProvidesRandomDendriticLocations, cap.ReceivesEPSCstim) self.force_run = force_run self.show_plot = show_plot self.save_all = save_all self.base_directory = base_directory self.path_temp_data = None #added later, because model name is needed self.path_figs = None self.path_results = None self.trunk_origin = trunk_origin self.logFile = None self.test_log_filename = 'test_log.txt' self.npool = multiprocessing.cpu_count() - 1 self.config = config self.num_of_dend_locations = num_of_dend_locations self.random_seed = random_seed description = "Tests how much synaptic potential attenuates from the dendrite (different distances) to the soma."
def __init__(self, observation={}, config={}, name="Somatic features test", force_run=False, base_directory=None, show_plot=True, save_all=True, specify_data_set=''): Test.__init__(self, observation, name) self.required_capabilities += ( cap.ReceivesSquareCurrent_ProvidesResponse, ) self.force_run = force_run self.show_plot = show_plot self.save_all = save_all self.config = config self.base_directory = base_directory self.path_temp_data = None #added later, because model name is needed self.path_figs = None self.path_results = None self.npool = multiprocessing.cpu_count() - 1 self.logFile = None self.test_log_filename = 'test_log.txt' self.specify_data_set = specify_data_set #this is added to the name of the directory (somaticfeat), so tests runs using different data sets can be saved into different directories plt.close( 'all' ) #needed to avoid overlapping of saved images when the test is run on multiple models in a for loop #with open('./stimfeat/PC_newfeat_No14112401_15012303-m990803_stimfeat.json') as f: #self.config = json.load(f, object_pairs_hook=collections.OrderedDict) description = "Tests some somatic features under current injection of increasing amplitudes."
def __init__(self, observation=None, name=None): Test.__init__(self, observation, name)
def __init__(self, observation={'mean':None,'std':None}, name="Action potential width"): """Takes the mean and standard deviation of observed spike widths""" Test.__init__(self,observation,name)
def __init__(self, observation=None, name=None): Test.__init__(self, observation, name)