def test_4_save_nwbfile_voltagestimulus(self):
os.chdir("..") # move up to ~/cerebmodels
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()
fullname = tm.save_nwbfile()
#
io = NWBHDF5IO(fullname, mode="r")
nwbfile = io.read()
stimulus = nwbfile.get_stimulus(self.chosenmodel.modelname+"_stimulus")
#
#print(type(stimulus.data)) # <class 'h5py._hl.dataset.Dataset'>
#print(type(self.recordings_stimulus['stimulus'])) # <type 'numpy.ndarray'>
#print(len(stimulus.data))
#print(len(numpy.array(stimulus.data)))
#breakpoint()
#
a = all(boolean == True for boolean in
numpy.array(stimulus.data) == self.sec_recordings['stimulus'])
b = all(boolean == False for boolean in
numpy.array(stimulus.timestamps) == self.sec_recordings['time'])
self.assertTrue( a is True and b is False)
io.close()
#
path = os.getcwd() + os.sep + "responses" + os.sep + self.chosenmodel.modelscale + os.sep + self.chosenmodel.modelname
shutil.rmtree( path )
os.chdir(pwd) # reset to the location of this managerTranscriberTest.py
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 test_1_load_metadata_nostimulus(self):
# self.chosenmodel.regions ->
# {"soma": ["v", "i_cap"], "axon": ["v"],
# "channels": {"soma": {"hh": ["il", "el"], "pas": ["i"]}, "axon": {"pas": ["i"]}}}
tm = TranscribeManager()
tm.load_metadata( chosenmodel = self.chosenmodel, simtime = self.simtime,
recordings = self.no_recordings,
runtimeparameters = self.no_runtimeparam )
compare1 = [ tm.filemd["identifier"], tm.filemd["experimenter"],
tm.respmd["soma"][0]["name"],
tm.epochmd["epoch0soma"]["v"]["stop_time"] ]
compare2 = [ "no_model_uuid", "anonymous",
"DummyTest_soma_v",
tm.epochmd["epoch0axon"]["v"]["stop_time"] ]
a = Counter( compare1 ) == Counter( compare2 )
b = all(boolean == True for boolean in tm.respmd["axon"][0]["data"] ==
self.no_recordings["response"]["axon"][0])
self.assertTrue( a and b is True )
def test_3_save_nwbfile_nostimulus(self):
os.chdir("..") # move up to ~/cerebmodels
tm = TranscribeManager()
tm.load_metadata( chosenmodel = self.chosenmodel, simtime = self.simtime,
recordings = self.no_recordings,
runtimeparameters = self.no_runtimeparam )
tm.compile_nwbfile()
fullname = tm.save_nwbfile()
#
sesstime = str(tm.nwbfile.session_start_time).replace(" ", "_")[0:-6]
filename_shouldbe = tm.nwbfile.session_id + "_" + sesstime.replace(":", "-") + ".h5"
#
path = os.getcwd() + os.sep + "responses" + os.sep + self.chosenmodel.modelscale + os.sep + self.chosenmodel.modelname
shutil.rmtree( path )
os.chdir(pwd) # reset to the location of this managerTranscriberTest.py
#
fullname_shouldbe = path + os.sep + filename_shouldbe
#print(fullname_shouldbe)
#breakpoint()
self.assertEqual( fullname, fullname_shouldbe )
def test_2_compile_nwbfile_currentstimulus(self):
tm = TranscribeManager()
tm.load_metadata( chosenmodel = self.chosenmodel, simtime = self.simtime,
recordings = self.recordings_nostimulus,
runtimeparameters = self.runtimeparam,
stimparameters = self.stimparameters )
tm.compile_nwbfile()
#
compare1 = tm.nwbfile.epochs[0][3][0] # 4_no_of_epochs
compare2 = tm.nwbfile.epochs[1][3][0] # 4_no_of_epochs
#
compare3 = tm.nwbfile.epochs[0][1] # start_time
compare4 = tm.nwbfile.epochs[1][1] # start_time
#
compare5 = tm.nwbfile.epochs[0][3][1] # epochID
compare6 = tm.nwbfile.epochs[1][3][1] # epochID
#
a = compare1 == compare2
b = compare3 != compare4
c = compaer5 != compare6
self.assertTrue( a and b and c is True )
class ExecutiveControl(object):
"""
**Available Methods:**
+------------------------------+---------------------+
| Method name | Method type |
+==============================+=====================+
| :py:meth:`.list_modelscales` | static method |
+------------------------------+---------------------+
| :py:meth:`.list_models` | static method |
+------------------------------+---------------------+
| :py:meth:`.choose_model` | static method |
+------------------------------+---------------------+
| :py:meth:`.launch_model` | instance method |
+------------------------------+---------------------+
| :py:meth:`.save_response` | instance method |
+------------------------------+---------------------+
| :py:meth:`.load_response` | instance method |
+------------------------------+---------------------+
"""
def __init__(self):
self.recordings = {"time": None, "response": None, "stimulus": None}
self.simtime = None
self.tm = TranscribeManager()
self.fullname = ""
@staticmethod
def list_modelscales():
"""Directs :ref:`FilingManager` to return available model scales.
**Arguments:** no argument is passed to get the list of model scales.
"""
x = fm.available_modelscales()
if "__pycache__" in x:
x.remove("__pycache__")
return x
@staticmethod
def list_models(modelscale=None):
"""Directs :ref:`FilingManager` to return available model names for a given model scale.
**Keyword Argument:**
+----------------+---------------------------------------------------+
| Key | Value type |
+================+===================================================+
| ``modelscale`` | string; egs. "cells", "microcircuits", "networks" |
+----------------+---------------------------------------------------+
*NOTE:* The string value will depend on the availability of model scales which can be checked using :py:meth:`.list_modelscales()`.
"""
x = fm.modelscale_inventory(model_scale=modelscale)
return [
model for model in x if model not in ["__pycache__", "DummyTest"]
]
@staticmethod
def choose_model(modelscale=None, modelname=None):
"""Returns instantiated model for a desired model name available in the specified model scale.
**Keyword Arguments:**
+----------------+-------------+
| Key | Value type |
+================+=============+
| ``modelscale`` | string |
+----------------+-------------+
| ``modelname`` | string |
+----------------+-------------+
*NOTE*: Currently only ``modelscale="cells"`` are supported. Future releases will include other model scales.
"""
sm.lock_and_load_model_libraries(modelscale=modelscale,
modelname=modelname)
modelmodule = importlib.import_module("models." + modelscale +
".model" + modelname)
chosenmodel = getattr(modelmodule,
uu.classesinmodule(modelmodule)[0].__name__)
return chosenmodel()
#return self.chosenmodel # the picked model is available as attribute
# NOTE: all model __init__ method will have the attributes
# modelscale and modelname => self.chosenmodel.modelscale/modelname
def launch_model(self,
parameters=None,
onmodel=None,
stimparameters=None,
stimloc=None,
capabilities={
'model': None,
'vtest': None
},
mode="raw"):
"""Directs the :ref:`SimulationManager` to launch simulation on an instantiated model.
**Keyword Arguments:**
+-------------------------------+----------------------------------------------+
| Key | Value type |
+===============================+==============================================+
| ``parameters`` | dictionary |
+-------------------------------+----------------------------------------------+
| ``onmodel`` | instantiated model |
+-------------------------------+----------------------------------------------+
| ``stimparameters`` (optional) | dictionary |
+-------------------------------+----------------------------------------------+
| ``stimloc`` (optional) | string; attribute name of instantiated model |
+-------------------------------+----------------------------------------------+
| ``capabilities`` (optional) | dictionary |
+-------------------------------+----------------------------------------------+
| ``mode`` (optional) | string; |
| |- "raw" (default), "capability" |
+-------------------------------+----------------------------------------------+
* ``parameters``- *mandatory* whose value is a dictionary. For example, ``parameters = {"dt": 0.01, "celsius": 30, "tstop": 100, "v_init": 65}``
* ``onmodel``- *mandatory* whose value is the instantiated model using :py:meth:`.choose_model()`. For example, ``onmodel = <instance>.choose_model(modelscale="a_chosen_scale", modelname="a_chosen_name")``.
* ``stimparameters``- optional whose value is a dictionary. For example, ``{"type": ["current", "IClamp"], "stimlist": [ {'amp': 0.5, 'dur': 100.0, 'delay': 10.0}, {'amp': 1.0, 'dur': 50.0, 'delay': 10.0+100.0} ] }``.
* ``stimloc``- optional (mandatory only if ``stimparameters`` argument is provided). Its value is string representing the namse of an attribute of the instantiated model. Note that this instantiated model is the value for the mandatory keyword argument ``onmodel``.
* ``capabilties``- optional whose value is a dictionary. The dictionary **must** have the keys ``model`` and ``vtest``. The value for ``model`` key is a string representing the models method. For example, ``model: "produce_voltage_response"``. The value for ``vtest`` key is a class imported from the installed ``CerebUnit``.
*NOTE*: Calling this function returns the model as the attribute ``ExecutiveControl.chosenmodel``.
"""
# NOTE: although it is convenient to use self.chosenmodel
# to the user having explicitly choose onmodel as an argument is clearer
uu.check_not_None_in_arg({
'parameters': parameters,
'onmodel': onmodel
})
get_stimtype = (lambda stimpar: None
if stimpar is None else stimpar["type"])
self.simtime = datetime.datetime.now()
if onmodel.modelscale is "cells":
get_stimloc = (
lambda stimloc: None
if stimloc is None else getattr(onmodel.cell, stimloc))
sm.prepare_model_NEURON(parameters=parameters,
chosenmodel=onmodel,
modelcapability=capabilities['model'],
cerebunitcapability=capabilities['vtest'])
stimuli_clamp = sm.stimulate_model_NEURON(
stimparameters=stimparameters, modelsite=get_stimloc(stimloc))
self.recordings["time"], self.recordings["response"], rec_clamp_indivs = \
rm.prepare_recording_NEURON( onmodel,
stimuli = stimuli_clamp,
stimtype = get_stimtype(stimparameters) )
if mode == "raw":
sm.trigger_NEURON(onmodel)
elif mode == "capability":
sm.trigger_NEURON(
onmodel,
modelcapability=capabilities['model'],
# Below are the **kwargs for lock_and_load_capability
parameters=parameters,
stimparameters=stimparameters,
stimloc=stimloc,
onmodel=onmodel,
mode="capability")
self.recordings["stimulus"] = \
rm.postrun_record_NEURON( injectedstimuli = rec_clamp_indivs,
stimtype = get_stimtype(stimparameters) )
# save the parameters as attributes
self.chosenmodel = onmodel
self.parameters = parameters
self.stimparameters = stimparameters
return self.chosenmodel
#return "model was successfully simulated" # for executiveTest.py
def save_response(self):
"""Returns filename after saving the model response into a `NWB <https://www.nwb.org/>`_ formated ``.h5`` file located in ``~/response/<modelscale>/<modelname>/`` in root directory of ``cerebmodels``.
**Arguments:** no argument is passed.
"""
self.tm.load_metadata(chosenmodel=self.chosenmodel,
simtime=self.simtime,
recordings=self.recordings,
runtimeparameters=self.parameters,
stimparameters=self.stimparameters)
self.tm.compile_nwbfile()
# saves and returns fullfilename (filepath+filename)
self.fullfilename = self.tm.save_nwbfile()
return self.fullfilename
@classmethod
def list_regions(cls, modelregions, reglist, oldstr):
# initiate with list_regions(modelregions, [], 0)
for key, value in modelregions.items():
if oldstr == 0:
oldstr = key
else:
oldstr = oldstr + " " + key
if type(value) is list:
for its_v in value:
reglist.append(oldstr + " " + its_v)
else:
cls.list_regions(value, reglist, key)
return reglist
def list_modelregions(self, chosenmodel=None):
return self.list_regions(chosenmodel.regions, [], 0)
@staticmethod
def visualize_all(chosenmodel=None, roi=None):
nwbfile = rdm.load_nwbfile(chosenmodel.fullfilename)
orderedepochs = rdm.order_all_epochs_for_region(nwbfile=nwbfile,
region=roi)
#
n_epochs = len(orderedepochs)
#if n_epochs == 1:
# plt.plot( orderedepochs[0][4][0][2].timestamps, orderedepochs[0][4][0][2].data )
#else:
timestamps_over_epochs = [
rdm.timestamps_for_epoch(orderedepochs[i])
for i in range(len(orderedepochs))
]
data_over_epochs = [
rdm.data_for_epoch(orderedepochs[i])
for i in range(len(orderedepochs))
]
#
cols = 2
rows = math.ceil(n_epochs / cols)
axes = []
try:
stim = nwbfile.get_stimulus()
axes.append(plt.subplot(rows + 1, 1, 1))
axes[0].plot(stim.timestamps, stim.data)
for i in range(n_epochs):
axes.append(plt.subplot(rows + 1, cols, i + 3))
axes[i + 1].plot(timestamps_over_epochs[i],
data_over_epochs[i])
except:
axes = []
for i in range(n_epochs):
axes.append(plt.subplot(rows, cols, i + 1))
axes[i].plot(timestamps_over_epochs[i], data_over_epochs[i])
@staticmethod
def visualize_aio(chosenmodel=None, roi=None):
nwbfile = rdm.load_nwbfile(chosenmodel.fullfilename)
orderedepochs = rdm.order_all_epochs_for_region(nwbfile=nwbfile,
region=roi)
#
n_epochs = len(orderedepochs)
#if n_epochs == 1:
# plt.plot( orderedepochs[0][4][0][2].timestamps, orderedepochs[0][4][0][2].data )
#else:
timestamps_over_epochs = [
rdm.timestamps_for_epoch(orderedepochs[i])
for i in range(len(orderedepochs))
]
data_over_epochs = [
rdm.data_for_epoch(orderedepochs[i])
for i in range(len(orderedepochs))
]
#
t_axis = timestamps_over_epochs[0]
y_axis = data_over_epochs[0]
for i in range(1, n_epochs):
t_axis = t_axis + timestamps_over_epochs[i]
y_axis = y_axis + data_over_epochs[i]
try:
axes = []
stim = nwbfile.get_stimulus()
axes.append(plt.subplot(2, 1, 1))
axes[0].plot(stim.timestamps, stim.data)
axes.append(plt.subplot(2, 1, 2))
axes[1].plot(t_axis, y_axis)
except:
plt.plot(t_axis, y_axis)