def setUp(self):
os.chdir(rootwd)
self.chosenmodel = DummyCell(
) #for alternative approach see managerSimulationTest.py
os.chdir(pwd)
self.rec = {"time": None, "response": None, "stimulus": None}
self.regionslist_str = list(self.chosenmodel.regions.keys())
def setUp(self):
os.chdir(rootwd)
self.chosenmodel = DummyCell()
self.simtime = datetime.datetime.now()
os.chdir(pwd)
# self.chosenmodel.regions ->
# {"soma": ["v", "i_cap"], "axon": ["v"],
# "channels": {"soma": {"hh": ["il", "el"], "pas": ["i"]}, "axon": {"pas": ["i"]}}}
# Voltage clamp
self.sec_runtimeparam = {
"dt": 0.1,
"celsius": 30,
"tstop": 35,
"v_init": 65
}
self.sec_stimparameters = {
"type": ["voltage", "SEClamp"],
"stimlist": [{
'amp1': 0.,
'dur1': 10.0
}, {
'amp2': -70.0,
'dur2': 20.0
}],
"tstop": self.sec_runtimeparam["tstop"]
}
self.sec_rec_t = [
t * self.sec_runtimeparam["dt"] for t in range(
int(self.sec_runtimeparam["tstop"] /
self.sec_runtimeparam["dt"]))
]
self.sec_rec_stim = numpy.random.rand(1, len(self.sec_rec_t))[0]
self.sec_rec_resp = numpy.random.rand(7, len(self.sec_rec_t))
self.sec_recordings = {
"time": self.sec_rec_t,
"response": {
"soma": [self.sec_rec_resp[0], self.sec_rec_resp[1]],
"axon": [self.sec_rec_resp[2]],
"channels": {
"soma": {
"hh": [self.sec_rec_resp[3], self.sec_rec_resp[4]],
"pas": [self.sec_rec_resp[5]]
},
"axon": {
"pas": [self.sec_rec_resp[3]]
}
}
},
"stimulus": self.sec_rec_stim
}
#
tm = TranscribeManager()
tm.load_metadata(chosenmodel=self.chosenmodel,
simtime=self.simtime,
recordings=self.sec_recordings,
runtimeparameters=self.sec_runtimeparam,
stimparameters=self.sec_stimparameters)
tm.compile_nwbfile()
self.fullname = tm.save_nwbfile()
def setUp(self):
self.pwd = os.getcwd()
# Create two files with/without stimulus
#fab = Fabricator() # NOTE: Reader() is an exception for not instantiating
os.chdir(rootwd)
self.chosenmodel = DummyCell()
os.chdir(pwd)
#
self.ec = ExecutiveControl()
#
if os.path.isdir(pwd + os.sep + "responses"):
shutil.rmtree("responses")
#
runtimeparam = {"dt": 0.1, "celsius": 30, "tstop": 200.0, "v_init": 65}
stimparam = {
"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":
runtimeparam["tstop"]
}
#
# Write for stimulus
self.ec.launch_model(parameters=runtimeparam,
stimparameters=stimparam,
stimloc=self.chosenmodel.cell.soma,
onmodel=self.chosenmodel)
self.ec.save_response()
# Get filename
self.file_stim = fm.show_filenames_with_path(
["responses", "cells", "DummyTest"])
# save for comparison
self.stimulus_for_comparison = numpy.array(
self.ec.recordings["stimulus"])
#
# Write for nostimulus
self.ec.launch_model(parameters=runtimeparam, onmodel=self.chosenmodel)
self.ec.save_response()
# Get filename
self.file_nostim = fm.show_filenames_with_path(
["responses", "cells", "DummyTest"])
for key in self.file_stim:
del self.file_nostim[key]
def setUp(self):
os.chdir(rootwd)
self.chosenmodel = DummyCell()
os.chdir(pwd)
# No stimulus
self.no_runtimeparam = {
"dt": 0.01,
"celsius": 30,
"tstop": 10,
"v_init": 65
}
# IClamp
self.ic_runtimeparam = {
"dt": 0.01,
"celsius": 30,
"tstop": 200,
"v_init": 65
}
self.ic_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":
self.ic_runtimeparam["tstop"]
}
# SEClamp
self.sec_runtimeparam = {
"dt": 0.01,
"celsius": 30,
"tstop": 35,
"v_init": 65
}
self.sec_stimparameters = {
"type": ["voltage", "SEClamp"],
"stimlist": [{
'amp1': 0.,
'dur1': 10.0
}, {
'amp2': -70.0,
'dur2': 20.0
}],
"tstop": self.sec_runtimeparam["tstop"]
}
def setUp(self):
os.chdir(rootwd)
self.chosenmodel = DummyCell()
self.simtime = datetime.datetime.now()
os.chdir(pwd)
# self.chosenmodel.regions ->
# {"soma": ["v", "i_cap"], "axon": ["v"],
# "channels": {"soma": {"hh": ["il", "el"], "pas": ["i"]}, "axon": {"pas": ["i"]}}}
# No stimulus
self.no_runtimeparam = {"dt": 0.01, "celsius": 30, "tstop": 10, "v_init": 65}
self.no_rec_t = [ t*self.no_runtimeparam["dt"] for t in
range( int( self.no_runtimeparam["tstop"]/self.no_runtimeparam["dt"] ) ) ]
self.no_rec_resp = numpy.random.rand(7,len(self.no_rec_t))
self.no_rec_stim = "Model is not stimulated" # response["stimulus"]
#self.no_stimtype = None # stimparameters["type"] = ["current", "IClamp"]
self.no_recordings = {"time": self.no_rec_t,
"response": {"soma": [self.no_rec_resp[0], self.no_rec_resp[1]],
"axon": [ self.no_rec_resp[2] ],
"channels": {"soma": {"hh": [self.no_rec_resp[3], self.no_rec_resp[4]],
"pas":[ self.no_rec_resp[5] ]},
"axon": {"pas":[ self.no_rec_resp[3] ]}}},
"stimulus": "Model is not stimulated"}
#self.no_respmd = tg.forrecording( chosenmodel = self.chosenmodel,
# recordings = self.no_recordings,
# runtimeparameters = self.no_runtimeparam )
#self.no_epochmd = eg.epochcontainer( chosenmodel = self.chosenmodel,
# parameters = self.no_runtimeparam )
# IClamp
self.ic_runtimeparam = {"dt": 0.01, "celsius": 30, "tstop": 10, "v_init": 65}
self.ic_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": self.ic_runtimeparam["tstop"]}
self.ic_rec_t = [ t*self.ic_runtimeparam["dt"] for t in
range( int( self.ic_runtimeparam["tstop"]/self.ic_runtimeparam["dt"] ) ) ]
self.ic_rec_stim = numpy.random.rand(1,len(self.ic_rec_t))[0]
self.ic_rec_resp = numpy.random.rand(7,len(self.ic_rec_t))
self.ic_recordings = {"time": self.ic_rec_t,
"response": {"soma": [self.ic_rec_resp[0], self.ic_rec_resp[1]],
"axon": [ self.ic_rec_resp[2] ],
"channels": {"soma": {"hh": [self.ic_rec_resp[3], self.ic_rec_resp[4]],
"pas":[ self.ic_rec_resp[5] ]},
"axon": {"pas":[ self.ic_rec_resp[6] ]}}},
"stimulus": self.ic_rec_stim}
#self.ic_respmd = tg.forrecording( chosenmodel = self.chosenmodel,
# recordings = self.ic_recordings,
# runtimeparameters = self.ic_runtimeparam,
# stimparameters = self.ic_stimparameters )
#self.ic_epochmd = eg.epochcontainer( chosenmodel = self.chosenmodel,
# parameters = self.ic_stimparameters )
# Voltage clamp
self.sec_runtimeparam = {"dt": 0.1, "celsius": 30, "tstop": 35, "v_init": 65}
self.sec_stimparameters = {"type": ["voltage", "SEClamp"],
"stimlist": [ {'amp1': 0., 'dur1': 10.0},
{'amp2': -70.0, 'dur2': 20.0} ],
"tstop": self.sec_runtimeparam["tstop"]}
self.sec_rec_t = [ t*self.sec_runtimeparam["dt"] for t in
range( int( self.sec_runtimeparam["tstop"]/self.sec_runtimeparam["dt"] ) ) ]
self.sec_rec_stim = numpy.random.rand(1,len(self.sec_rec_t))[0]
self.sec_rec_resp = numpy.random.rand(7,len(self.sec_rec_t))
self.sec_recordings = {"time": self.sec_rec_t,
"response": {"soma": [self.sec_rec_resp[0], self.sec_rec_resp[1]],
"axon": [ self.sec_rec_resp[2] ],
"channels": {"soma": {"hh": [self.sec_rec_resp[3], self.sec_rec_resp[4]],
"pas":[ self.sec_rec_resp[5] ]},
"axon": {"pas":[ self.sec_rec_resp[3] ]}}},
"stimulus": self.sec_rec_stim}
def setUp(self):
os.chdir(rootwd)
self.chosenmodel = DummyCell()
self.simtime = datetime.datetime.now()
os.chdir(pwd)
def setUp(self):
os.chdir(rootwd)
self.chosenmodel = DummyCell(
) #for alternative approach see managerSimulationTest.py
os.chdir(pwd)
#self.regionslist_str = list(self.chosenmodel.regions.keys())
self.no_parameters = {
"dt": 0.1,
"celsius": 30,
"tstop": 10,
"v_init": 65
}
self.ic_parameters = {
"dt": 0.1,
"celsius": 30,
"tstop": 35,
"v_init": 65
}
self.ic_stimparam = {
"type": ["current", "IClamp"],
"stimlist": [{
'amp': 0.5,
'dur': 10.0,
'delay': 5.0
}, {
'amp': 1.0,
'dur': 20.0,
'delay': 5.0 + 10.0
}],
"tstop":
self.ic_parameters["tstop"]
}
self.sec_parameters = {
"dt": 0.1,
"celsius": 30,
"tstop": 35,
"v_init": 65
}
self.sec_stimparam = {
"type": ["voltage", "SEClamp"],
"stimlist": [{
'amp1': 0.,
'dur1': 10.0
}, {
'amp2': -70.0,
'dur2': 20.0
}],
"tstop": self.sec_parameters["tstop"]
}
self.ir_parameters = {
"dt": 0.1,
"celsius": 30,
"tstop": 35,
"v_init": 65
}
self.ir_stimparam = {
"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":
self.ir_parameters["tstop"]
}
def setUp(self):
os.chdir(rootwd)
self.chosenmodel = DummyCell()
os.chdir(pwd)
#
self.parameters = {"dt": 0.1, "celsius": 20, "tstop": 10, "v_init": 65}
def setUp(self):
os.chdir(rootwd)
self.chosenmodel = DummyCell()
os.chdir(pwd)
def setUp(self):
os.chdir(rootwd)
self.chosenmodel = DummyCell()
os.chdir(pwd)
self.rec = {"time": None, "response": None, "stimulus": None}
self.regionslist_str = list(self.chosenmodel.regions.keys())
def setUp(self):
self.st = Stimulator()
os.chdir(rootwd)
self.chosenmodel = DummyCell()
os.chdir(pwd)
def setUp(self):
#self.fm = FilingManager() #instance for non: static & class methods.
os.chdir(rootwd)
self.chosenmodel = DummyCell()
os.chdir(pwd)
def setUp(self):
#self.tg = TimeseriesGenerator()
#self.pwd = os.getcwd()
os.chdir(rootwd)
self.chosenmodel = DummyCell()
os.chdir(pwd)
#
# self.chosenmodel.regions ->
# {"soma": ["v", "i_cap"], "axon": ["v"],
# "channels": {"soma": {"hh": ["il", "el"], "pas": ["i"]}, "axon": {"pas": ["i"]}}}
#
# The following are generated via RegionParser in operatorsTranscribe/regionparser.py
#self.regionlist = ["soma", "axon"]
#self.componentgrouplist = ["channels"]
#self.regionlist_of_of_componentgroup = ["soma", "axon"]
#self.soma_componentlist = ["hh", "pas"]
#self.axon_componentlist = ["pas"]
# No stimulus
self.no_runtimeparam = {
"dt": 0.01,
"celsius": 30,
"tstop": 10,
"v_init": 65
}
self.no_rec_t = [
t * self.no_runtimeparam["dt"] for t in range(
int(self.no_runtimeparam["tstop"] /
self.no_runtimeparam["dt"]))
]
self.no_rec_resp = numpy.random.rand(7, len(self.no_rec_t))
self.no_rec_stim = "Model is not stimulated" # response["stimulus"]
#self.no_stimtype = None # stimparameters["type"] = ["current", "IClamp"]
self.no_recordings = {
"time": self.no_rec_t,
"response": {
"soma": [self.no_rec_resp[0], self.no_rec_resp[1]],
"axon": [self.no_rec_resp[2]],
"channels": {
"soma": {
"hh": [self.no_rec_resp[3], self.no_rec_resp[4]],
"pas": [self.no_rec_resp[5]]
},
"axon": {
"pas": [self.no_rec_resp[3]]
}
}
},
"stimulus": "Model is not stimulated"
}
# IClamp
self.ic_runtimeparam = {
"dt": 0.01,
"celsius": 30,
"tstop": 10,
"v_init": 65
}
self.ic_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":
self.ic_runtimeparam["tstop"]
}
self.ic_rec_t = [
t * self.ic_runtimeparam["dt"] for t in range(
int(self.ic_runtimeparam["tstop"] /
self.ic_runtimeparam["dt"]))
]
self.ic_rec_stim = numpy.random.rand(1, len(self.ic_rec_t))[0]
self.ic_rec_resp = numpy.random.rand(7, len(self.ic_rec_t))
self.ic_recordings = {
"time": self.ic_rec_t,
"response": {
"soma": [self.ic_rec_resp[0], self.ic_rec_resp[1]],
"axon": [self.ic_rec_resp[2]],
"channels": {
"soma": {
"hh": [self.ic_rec_resp[3], self.ic_rec_resp[4]],
"pas": [self.ic_rec_resp[5]]
},
"axon": {
"pas": [self.ic_rec_resp[3]]
}
}
},
"stimulus": self.ic_rec_stim
}
# Voltage clamp
self.sec_runtimeparam = {
"dt": 0.1,
"celsius": 30,
"tstop": 35,
"v_init": 65
}
self.sec_stimparameters = {
"type": ["voltage", "SEClamp"],
"stimlist": [{
'amp1': 0.,
'dur1': 10.0
}, {
'amp2': -70.0,
'dur2': 20.0
}],
"tstop": self.sec_runtimeparam["tstop"]
}
self.sec_rec_t = [
t * self.sec_runtimeparam["dt"] for t in range(
int(self.sec_runtimeparam["tstop"] /
self.sec_runtimeparam["dt"]))
]
self.sec_rec_stim = numpy.random.rand(1, len(self.sec_rec_t))[0]
self.sec_rec_resp = numpy.random.rand(7, len(self.sec_rec_t))
self.sec_recordings = {
"time": self.sec_rec_t,
"response": {
"soma": [self.sec_rec_resp[0], self.sec_rec_resp[1]],
"axon": [self.sec_rec_resp[2]],
"channels": {
"soma": {
"hh": [self.sec_rec_resp[3], self.sec_rec_resp[4]],
"pas": [self.sec_rec_resp[5]]
},
"axon": {
"pas": [self.sec_rec_resp[3]]
}
}
},
"stimulus": self.sec_rec_stim
}