def l5pc_specific_modifications(tests):
tests = TSD(tests)
tests.pop('InputResistanceTest', None)
tests.pop('CapacitanceTest', None)
tests.pop('TimeConstantTest', None)
#tests.pop('RestingPotentialTest',None)
return tests
def glif_specific_modifications(tests):
'''
Now appropriate for all tests
'''
tests = TSD(tests)
#tests.pop('RheobaseTest',None)
tests.pop('InjectedCurrentAPAmplitudeTest', None)
tests.pop('InjectedCurrentAPThresholdTest', None)
tests.pop('InjectedCurrentAPWidthTest', None)
#tests.pop('InputResistanceTest',None)
#tests.pop('CapacitanceTest',None)
#tests.pop('TimeConstantTest',None)
return tests
from neuronunit.optimization.optimization_management import TSD
from neuronunit.optimization.model_parameters import MODEL_PARAMS, BPO_PARAMS
from neuronunit.optimization.optimization_management import inject_and_not_plot_model, plot_as_normal
from neuronunit.optimization.optimization_management import inject_and_plot_model, plot_as_normal
from neuronunit.tests import *
import quantities as qt
from sciunit.scores import RelativeDifferenceScore, ZScore
from sciunit import TestSuite
from quantities import Hz, pA
cells = pickle.load(open("processed_multicellular_constraints.p", "rb"))
#purk = TSD(cells['Cerebellum Purkinje cell'])#.tests
#purk_vr = purk["RestingPotentialTest"].observation['mean']
ncl5 = TSD(cells["Neocortex pyramidal cell layer 5-6"])
ncl5.name = str("Neocortex pyramidal cell layer 5-6")
ncl5_vr = ncl5["RestingPotentialTest"].observation['mean']
ca1 = TSD(cells["Hippocampus CA1 pyramidal cell"])
ca1.name = str("Hippocampus CA1 pyramidal cell")
ca1_vr = ca1["RestingPotentialTest"].observation['mean']
experimental_constraints = cells
'''
def make_observations_frame():
list_of_dicts = []
for k,v in cells.items():
observations = {}
for k1 in ca1.keys():
def make_allen():
rt = RheobaseTest(observation={'mean': 70 * qt.pA, 'std': 70 * qt.pA})
tc = TimeConstantTest(observation={
'mean': 24.4 * qt.ms,
'std': 24.4 * qt.ms
})
ir = InputResistanceTest(observation={
'mean': 132 * qt.MOhm,
'std': 132 * qt.MOhm
})
rp = RestingPotentialTest(observation={
'mean': -71.6 * qt.mV,
'std': 77.5 * qt.mV
})
allen_tests = [rt, tc, rp, ir]
for t in allen_tests:
t.score_type = RelativeDifferenceScore
allen_suite482493761 = TestSuite(allen_tests)
allen_suite482493761.name = "http://celltypes.brain-map.org/mouse/experiment/electrophysiology/482493761"
rt = RheobaseTest(observation={'mean': 190 * qt.pA, 'std': 190 * qt.pA})
tc = TimeConstantTest(observation={
'mean': 13.8 * qt.ms,
'std': 13.8 * qt.ms
})
ir = InputResistanceTest(observation={
'mean': 132 * qt.MOhm,
'std': 132 * qt.MOhm
})
rp = RestingPotentialTest(observation={
'mean': -77.5 * qt.mV,
'std': 77.5 * qt.mV
})
fi = FITest(observation={'mean': 0.09 * Hz / pA}) #'std':77.5*qt.mV})
allen_tests = [rt, tc, rp, ir] #,fi]
for t in allen_tests:
t.score_type = RelativeDifferenceScore
#allen_tests[-1].score_type = ZScore
allen_suite471819401 = TestSuite(allen_tests)
allen_suite471819401.name = "http://celltypes.brain-map.org/mouse/experiment/electrophysiology/471819401"
list_of_dicts = []
cells = {}
cells['471819401'] = TSD(allen_suite471819401)
cells['482493761'] = TSD(allen_suite482493761)
allen_tests = [rt, fi]
for t in allen_tests:
t.score_type = RelativeDifferenceScore
allen_suite3 = TestSuite(allen_tests)
cells['3'] = TSD(allen_suite3)
for k, v in cells.items():
observations = {}
for k1 in cells['482493761'].keys():
vsd = TSD(v)
if k1 in vsd.keys():
vsd[k1].observation['mean']
observations[k1] = np.round(vsd[k1].observation['mean'], 2)
observations['name'] = k
list_of_dicts.append(observations)
df = pd.DataFrame(list_of_dicts)
df
return allen_suite471819401, allen_suite482493761, df, cells
def glif_specific_modifications(tests):
tests = TSD(tests)
tests.pop('InjectedCurrentAPAmplitudeTest', None)
tests.pop('InjectedCurrentAPThresholdTest', None)
tests.pop('InjectedCurrentAPWidthTest', None)
return tests