def test_9_epochcontainer_for_regionbodies_currentstimulus(self):
no_of_epochs = eg.compute_totalepochs_per_cellregion(
self.ic_stimparameters)
[start_ts, stop_ts] = eg.epoch_times_list(self.ic_stimparameters)
filler = eg.epochcontainer_for_regionbodies(self.chosenmodel,
no_of_epochs, start_ts,
stop_ts)
#print(filler) # how does the epochcontainer metadata look?
# self.chosenmodel.regions ->
# {"soma": ["v", "i_cap"], "axon": ["v"],
# "channels": {"soma": {"hh": ["il", "el"], "pas": ["i"]}, "axon": {"pas": ["i"]}}}
compare1a = filler["epoch0soma"]["v"]["tags"][0] # number of epochs
compare1b = filler["epoch0soma"]["v"]["tags"][1] # epochID
compare1c = filler["epoch0soma"]["v"]["tags"][2].split()[-1] # recsite
compare1d = filler["epoch0soma"]["v"]["tags"][3] # all recsites
compare1e = filler["epoch0soma"]["v"]["tags"][4] # modelname
compare1f = filler["epoch0soma"]["v"]["tags"][5] # modelscale
compare1g = filler["epoch0soma"]["v"]["tags"][6].split()[
-1] # key for recsite
compare2a = filler["epoch0axon"]["v"]["tags"][0]
compare2b = filler["epoch0axon"]["v"]["tags"][1]
compare2c = filler["epoch0axon"]["v"]["tags"][2].split()[-1]
compare2d = filler["epoch1soma"]["v"]["tags"][3] # all recsites
compare2e = filler["epoch0axon"]["v"]["tags"][4]
compare2f = filler["epoch0axon"]["v"]["tags"][5]
compare2g = filler["epoch1soma"]["v"]["tags"][6].split()[-1]
#
compare1 = [
compare1a, compare1b, compare1c, compare1d, compare1e, compare1f,
compare1g
]
compare2 = [
compare2a, compare2b, compare2c, compare2d, compare2e, compare2f,
compare2g
]
a = Counter(compare1) == Counter(compare2)
#
compare3a = filler["epoch0soma"]["v"]["tags"][1] # epochID
compare3b = filler["epoch0soma"]["v"]["tags"][2].split()[
-1] # [ region, recsite ]
compare3c = filler["epoch0soma"]["v"]["tags"][3] # all recsites
compare4a = filler["epoch1soma"]["v"]["tags"][1]
compare4b = filler["epoch1soma"]["i_cap"]["tags"][2].split()[-1]
compare4c = filler["epoch0axon"]["v"]["tags"][3]
#
compare3 = [compare3a, compare3b, compare3c]
compare4 = [compare4a, compare4b, compare4c]
b = Counter(compare3) != Counter(compare4)
#
self.assertEqual([a, b], [True, True])
def test_4_epoch_times_list_epoch1Istimulus(self):
# <---100---> <----50---->
# 0----------10-----------110------------160------------200
# ep0 ep1 ep2 ep3
ic_stimparam = {
"type": ["current", "IClamp"],
"stimlist": [
{
"amp": 0.5,
"dur": 100.0,
"delay": 10
}, # 0, 10.0
{
"amp": 1.0,
"dur": 50.0,
"delay": 10.0 + 100.0
}
],
"tstop":
self.ic_runtimeparam["tstop"]
}
[start_ts, stop_ts] = eg.epoch_times_list(ic_stimparam)
#print(start_ts, stop_ts)
a = Counter(start_ts) == Counter([0, 10, 110, 160])
b = Counter(stop_ts) == Counter([10, 110, 160, 200])
self.assertEqual([a, b], [True, True])
def test_7_epoch_times_list_nostimulus(self):
# 0----------10
# ep0
[start_ts, stop_ts] = eg.epoch_times_list(self.no_runtimeparam)
#print(start_ts, stop_ts)
a = Counter(start_ts) == Counter([0])
b = Counter(stop_ts) == Counter([self.no_runtimeparam["tstop"]])
self.assertEqual([a, b], [True, True])
def test_8_epochcontainer_for_regionbodies_nostimulus(self):
no_of_epochs = eg.compute_totalepochs_per_cellregion(
self.no_runtimeparam)
[start_ts, stop_ts] = eg.epoch_times_list(self.no_runtimeparam)
filler = eg.epochcontainer_for_regionbodies(self.chosenmodel,
no_of_epochs, start_ts,
stop_ts)
compare2 = len(filler)
# self.chosenmodel.regions ->
# {"soma": ["v", "i_cap"], "axon": ["v"],
# "channels": {"soma": {"hh": ["il", "el"], "pas": ["i"]}, "axon": {"pas": ["i"]}}}
no_of_regions = 2
compare1 = no_of_regions * no_of_epochs
a = Counter( [ compare2, filler["epoch0soma"]["v"]["start_time"],
filler["epoch0soma"]["v"]["stop_time"] ] ) \
== Counter( [ compare1, filler["epoch0axon"]["v"]["start_time"],
self.no_runtimeparam["tstop"] ] )
#print filler # how does the epochcontainer metadata look?
self.assertEqual(a, True)
def test_11_epochcontainer_without_stimulus(self):
filler = eg.epochcontainer(chosenmodel=self.chosenmodel,
parameters=self.no_runtimeparam)
no_of_epochs = filler["epoch0soma"]["v"]["tags"][0]
a = Counter( [ int(no_of_epochs[0]),
filler["epoch0soma"]["v"]["start_time"],
filler["epoch0soma"]["v"]["stop_time"] ] ) \
== Counter( [ 1, filler["epoch0axon"]["v"]["start_time"],
self.no_runtimeparam["tstop"] ] )
#print filler # how does the epochcontainer metadata look?
self.assertEqual(a, True)
def test_12_forepoch_without_stimulus(self):
runtimeparam = {"dt": 0.01, "celsius": 30, "tstop": 100, "v_init": 65}
epochmd = eg.forepoch(chosenmodel=self.chosenmodel,
parameters=runtimeparam)
# self.chosenmodel.regions = {'soma':0.0, 'axon':0.0}
no_of_stimulus_epochs_per_region = 0
compare2 = epochmd["epoch" + str(no_of_stimulus_epochs_per_region) +
"soma"]["stop_time"]
compare1 = epochmd["epoch" + str(no_of_stimulus_epochs_per_region) +
"axon"]["stop_time"]
#print epochmd # hows does the main epoch metadata look?
self.assertEqual(compare2, compare1)
def test_14_forepoch_with_stimulus_laststimulus_notequals_tstop(self):
stimparameters = {
"type": ["current", "IRamp"],
"stimlist": [{
"amp_initial": 0.0,
"amp_final": 0.5,
"dur": 5.0,
"delay": 5.0
}, {
"amp_initial": 0.5,
"amp_final": 1.0,
"dur": 5.0,
"delay": 10.0
}, {
"amp_initial": 1.0,
"amp_final": 0.5,
"dur": 5.0,
"delay": 15.0
}, {
"amp_initial": 0.5,
"amp_final": 0.0,
"dur": 5.0,
"delay": 20.0
}],
"tstop":
20.0 + 10.0
}
epochmd = eg.forepoch(chosenmodel=self.chosenmodel,
parameters=stimparameters)
# self.chosenmodel.regions = {'soma':0.0, 'axon':0.0}
no_of_stimulus_epochs_per_region = len(stimparameters["stimlist"])
compare2 = [
epochmd["epoch" + str(0) + "soma"]["stop_time"],
epochmd["epoch" + str(no_of_stimulus_epochs_per_region) +
"soma"]["stop_time"],
epochmd["epoch" + str(no_of_stimulus_epochs_per_region + 1) +
"soma"]["stop_time"]
]
compare1 = [
epochmd["epoch" + str(0) + "axon"]["stop_time"],
epochmd["epoch" + str(no_of_stimulus_epochs_per_region) +
"axon"]["stop_time"], stimparameters["tstop"]
]
#print epochmd # how does the main epoch metadata look?
self.assertEqual(compare2, compare1)
def test_11_an_epoch_poststimulus(self):
stimparameters = {
"type": ["current", "IClamp"],
"stimlist": [{
"amp": 0.5,
"dur": 100.0,
"delay": 10.0
}, {
"amp": 1.0,
"dur": 50.0,
"delay": 10.0 + 100.0
}],
"tstop":
200.0
}
epoch_value = eg.an_epoch(3, "axon", stimparameters)
compare2 = epoch_value["description"]
compare1 = "last, no stimulus"
#print epoch_value # hows does an epoch metadata look?
self.assertEqual(compare2, compare1)
def test_7_an_epoch_prestimulus(self):
stimparameters = {
"type": ["current", "IClamp"],
"stimlist": [{
"amp": 0.5,
"dur": 100.0,
"delay": 10.0
}, {
"amp": 1.0,
"dur": 50.0,
"delay": 10.0 + 100.0
}],
"tstop":
10.0 + 100.0 + 50.0
}
epoch_value = eg.an_epoch(0, "soma", stimparameters)
compare2 = epoch_value["start_time"] + epoch_value["stop_time"]
compare1 = 0.0 + stimparameters["stimlist"][0]["delay"]
#print epoch_value # how does an epoch metadata look?
self.assertEqual(compare2, compare1)
def test_6_epoch_times_list_Vstimulus(self):
# <---10---> <----20---->
# 0----------10-----------20------------35
# ep0 ep1 ep2
sec_stimparam = {
"type": ["voltage", "SEClamp"],
"stimlist": [{
'amp1': 0.,
'dur1': 10.0
}, {
'amp2': -70.0,
'dur2': 20.0
}],
"tstop": self.sec_runtimeparam["tstop"]
}
[start_ts, stop_ts] = eg.epoch_times_list(sec_stimparam)
#print(start_ts, stop_ts)
a = Counter(start_ts) == Counter([0, 10, 20])
b = Counter(stop_ts) == Counter([10, 20, 35])
self.assertEqual([a, b], [True, True])
def test_10_an_epoch_laststimulus_notequals_tstop(self):
stimparameters = {
"type": ["current", "IClamp"],
"stimlist": [{
"amp": 0.5,
"dur": 100.0,
"delay": 10.0
}, {
"amp": 1.0,
"dur": 50.0,
"delay": 10.0 + 100.0
}],
"tstop":
200.0
}
epoch_value = eg.an_epoch(2, "axon", stimparameters)
compare2 = epoch_value["description"]
compare1 = "IClamp stimulation of model with amplitude = " + \
str(stimparameters["stimlist"][1]["amp"]) + " nA"
#print epoch_value # hows does an epoch metadata look?
self.assertEqual(compare2, compare1)
def test_3_compute_totalepochs_per_cellregion_with_voltagestimulus(self):
self.assertEqual(
eg.compute_totalepochs_per_cellregion(self.sec_stimparameters),
1 + len(self.sec_stimparameters["stimlist"]))
def test_2_compute_totalepochs_per_cellregion_with_currentstimulus(self):
self.assertEqual(
eg.compute_totalepochs_per_cellregion(self.ic_stimparameters),
1 + len(self.ic_stimparameters["stimlist"]))
def test_1_compute_totalepochs_per_cellregion_without_stimulus(self):
self.assertEqual(
eg.compute_totalepochs_per_cellregion(self.no_runtimeparam), 1)
def test_8_epochcontainer_with_voltagestimulus(self):
filler = eg.epochcontainer(chosenmodel=self.chosenmodel,
parameters=self.sec_stimparameters)
#print(filler) # how does the epochcontainer metadata look?
#print(filler.keys())
#print(filler["epoch0soma"].keys())
# self.chosenmodel.regions ->
# {"soma": ["v", "i_cap"], "axon": ["v"],
# "channels": {"soma": {"hh": ["il", "el"], "pas": ["i"]}, "axon": {"pas": ["i"]}}}
compare1a = filler["epoch0soma"]["v"]["tags"][0] # number of epochs
compare1b = filler["epoch0soma"]["v"]["tags"][1] # epochID
compare1c = filler["epoch0soma"]["v"]["tags"][2].split()[-1] # recsite
compare1d = filler["epoch0soma"]["v"]["tags"][3] # all recsites
compare1e = filler["epoch0soma"]["v"]["tags"][4] # modelname
compare1f = filler["epoch0soma"]["v"]["tags"][5] # modelscale
compare1g = filler["epoch0soma"]["v"]["tags"][6].split()[
-1] # key for recsite
compare2a = filler["epoch0axon"]["v"]["tags"][0]
compare2b = filler["epoch0axon"]["v"]["tags"][1]
compare2c = filler["epoch0axon"]["v"]["tags"][2].split()[-1]
compare2d = filler["epoch1soma"]["v"]["tags"][3] # all recsites
compare2e = filler["epoch0axon"]["v"]["tags"][4]
compare2f = filler["epoch0axon"]["v"]["tags"][5]
compare2g = filler["epoch1soma"]["v"]["tags"][6].split()[-1]
#
compare1 = [
compare1a, compare1b, compare1c, compare1d, compare1e, compare1f,
compare1g
]
compare2 = [
compare2a, compare2b, compare2c, compare2d, compare2e, compare2f,
compare2g
]
a = Counter(compare1) == Counter(compare2)
#
compare3a = filler["epoch0soma"]["v"]["tags"][1] # epochID
compare3b = filler["epoch0soma"]["v"]["tags"][2].split()[
-1] # [ region, recsite ]
compare3c = filler["epoch0soma"]["v"]["tags"][3] # all recsites
compare4a = filler["epoch1soma"]["v"]["tags"][1]
compare4b = filler["epoch1soma"]["i_cap"]["tags"][2].split()[-1]
compare4c = filler["epoch0axon"]["v"]["tags"][3]
#
compare3 = [compare3a, compare3b, compare3c]
compare4 = [compare4a, compare4b, compare4c]
b = Counter(compare3) != Counter(compare4)
#
compare5a = filler["epoch0channels"]["soma"]["pas"]["i"]["tags"][
0] # number of epochs
compare5b = filler["epoch0channels"]["soma"]["pas"]["i"]["tags"][
1] # epochID
compare5c = filler["epoch0channels"]["soma"]["pas"]["i"]["tags"][
2].split()[-1] # recsite
compare5d = filler["epoch0channels"]["soma"]["pas"]["i"]["tags"][
3] # all recsites
compare5e = filler["epoch0channels"]["soma"]["pas"]["i"]["tags"][
4] # modelname
compare5f = filler["epoch0channels"]["soma"]["pas"]["i"]["tags"][
5] # modelscale
compare5g = filler["epoch0channels"]["soma"]["pas"]["i"]["tags"][
6].split()[-1] # key for recsite
compare6a = filler["epoch0channels"]["axon"]["pas"]["i"]["tags"][
0] # number of epochs
compare6b = filler["epoch0channels"]["axon"]["pas"]["i"]["tags"][
1] # epochID
compare6c = filler["epoch0channels"]["axon"]["pas"]["i"]["tags"][
2].split()[-1] # recsite
compare6d = filler["epoch0channels"]["axon"]["pas"]["i"]["tags"][
3] # all recsites
compare6e = filler["epoch0channels"]["axon"]["pas"]["i"]["tags"][
4] # modelname
compare6f = filler["epoch0channels"]["axon"]["pas"]["i"]["tags"][
5] # modelscale
compare6g = filler["epoch0channels"]["axon"]["pas"]["i"]["tags"][
6].split()[-1] # key for recsite
#
compare5 = [
compare5a, compare5b, compare5c, compare5d, compare5e, compare5f,
compare5g
]
compare6 = [
compare6a, compare6b, compare6c, compare6d, compare6e, compare6f,
compare6g
]
c = Counter(compare5) == Counter(compare6)
#
compare7a = filler["epoch0channels"]["soma"]["hh"]["il"]["tags"][
0] # number of epochs
compare7b = filler["epoch0channels"]["soma"]["hh"]["il"]["tags"][
1] # epochID
compare7c = filler["epoch0channels"]["soma"]["hh"]["il"]["tags"][
2].split()[-1] # recsite
compare7d = filler["epoch0channels"]["soma"]["hh"]["il"]["tags"][
3] # all recsites
compare7e = filler["epoch0channels"]["soma"]["hh"]["il"]["tags"][
6].split()[-1] # key for recsite
compare8a = filler["epoch1channels"]["axon"]["pas"]["i"]["tags"][
0] # number of epochs
compare8b = filler["epoch1channels"]["soma"]["hh"]["il"]["tags"][
1] # epochID
compare8c = filler["epoch0channels"]["axon"]["pas"]["i"]["tags"][
2].split()[-1] # recsite
compare8d = filler["epoch0channels"]["soma"]["pas"]["i"]["tags"][
3] # all recsites
compare8e = filler["epoch0channels"]["soma"]["hh"]["el"]["tags"][
6].split()[-1] # key for recsite
#
compare7 = [compare7a, compare7b, compare7c, compare7d, compare7e]
compare8 = [compare8a, compare8b, compare8c, compare8d, compare8e]
d = Counter(compare7) != Counter(compare8)
#
self.assertEqual([a, b, c, d], [True, True, True, True])