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)