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Fixed bug where treeChange update to ERev always uses T=37 #7

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Fixed bug where treeChange update to ERev always uses T=37 #7

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5de257a
Add readout of cursor values
tomjhou Feb 13, 2025
8225666
Fixed bug where treeChange update to ERev always uses T=37
tomjhou Feb 13, 2025
addbc8d
Delete unneeded test files.
tomjhou Feb 13, 2025
be8e178
Merge branch 'Add_cursor_values' into masterJhouLab2
tomjhou Feb 13, 2025
a7b7f01
Now removes all channel-associated plots if that ion channel is remov…
tomjhou Feb 13, 2025
9a4e9bb
Update so that command value display at cursor switches units accordi…
tomjhou Feb 13, 2025
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10 changes: 6 additions & 4 deletions neurodemo/channelparam.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,6 +54,7 @@ def __init__(self, ion: IonClass):
dict(name='[C]out', type='float', value=ion.Cout, suffix='mM', siPrefix=True, step=1),
dict(name='[C]in', type='float', value=ion.Cin, suffix='mM', siPrefix=True, step=1),
]
self.temperatureC = 37.
self.ion.Erev = self.Nernst(ion)
self.ion_params.append(dict(name="Erev", type='float', value=self.ion.Erev, suffix='V', siPrefix=True, readonly=True))
pt.parameterTypes.GroupParameter.__init__(self, name=name, type='group',
Expand All @@ -72,12 +73,13 @@ def treeChange(self, root, changes: list[tuple[pt.Parameter, str, typing.Any]]):
self.ion.Cin = val
self['Erev'] = self.Nernst(self.ion)

def updateErev(self, temp:float=37.):
self['Erev']=self.Nernst(self.ion, temp=temp)
def updateTemperature(self, temp:float=37.):
self.temperatureC = temp
self['Erev']=self.Nernst(self.ion)

def Nernst(self, ion, temp:float=37.):
def Nernst(self, ion):
R = 8.135 # J/K/M
F = 96840 # C/M
RTF = R*(273.16+temp)/F
RTF = R*(273.16+self.temperatureC)/F
Er = (2.303*RTF/ion.valence)*np.log10(ion.Cout/ion.Cin)
return Er
10 changes: 10 additions & 0 deletions neurodemo/clampparam.py
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Original file line number Diff line number Diff line change
Expand Up @@ -86,6 +86,13 @@ def __init__(self, clamp: neurodemo.neuronsim.PatchClamp, sim: neurodemo.main_wi
dict(name="Plot Current", type="bool", value=False),
dict(name="Plot Voltage", type="bool", value=False),
dict(name="Plot Command", type="bool", value=False),
dict(name="Cursor values",
type="group",
children=[
dict(name="Relative time", type="float", value=0.0, suffix="s", siPrefix=True, step=0.0001),
dict(name="Memb voltage", type="float", value=0.0, suffix="V", siPrefix=True),
dict(name="Command", type="float", value=0.0, suffix="A", siPrefix=True),
]),
dict(
name="Pulse",
type="group",
Expand Down Expand Up @@ -243,6 +250,9 @@ def set_mode(self, mode):
self.child("Holding").setOpts(
suffix=suff, value=self.clamp.holding[mode], step=step
)

self.child("Cursor values", "Command").setOpts(suffix=suff)

self.child("Pulse", "Pre-amplitude").setOpts(suffix=suff, value=pre_amp, step=step)
self.child("Pulse", "Post-amplitude").setOpts(suffix=suff, value=post_amp, step=step)
self.child("Pulse", "Amplitude").setOpts(suffix=suff, value=amp, step=step)
Expand Down
64 changes: 31 additions & 33 deletions neurodemo/main_window.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,12 +127,15 @@ def __init__(self, multiprocessing=False):
]

for ch in self.channel_params:
# These will use default Erev values defined in neuronsim.py, Section(SimObject) class, which
# are INDEPENDENT of values defined in self.use_default_erev(). Consider replacing both with
# calculated Erev.
ch.plots_changed.connect(self.plots_changed)

self.ion_concentrations = [IonConcentrations(ion) for ion in ions.all_ions]
for ion in self.ion_concentrations:
ion.updateErev(self.sim.temp) # match temperature with an update
ion.updateTemperature(self.sim.temp) # match temperature with an update

self.params = pt.Parameter.create(name='Parameters', type='group', children=[
dict(name='Preset', type='list', value='HH AP', limits=['Passive', 'HH AP', 'LG AP']),
dict(name='Run/Stop', type='action', value=False),
Expand All @@ -145,14 +148,16 @@ def __init__(self, multiprocessing=False):
dict(name='Capacitance', type='float', value=self.neuron.cap, limits=[0.1e-12, 1000.e-12], suffix='F', siPrefix=True, dec=True, children=[
dict(name='Plot Current', type='bool', value=False),
]),
dict(name='Ions', type='bool', children=self.ion_concentrations),
dict(name='Ions', type='group', children=self.ion_concentrations),
dict(name='Cell Schematic', type='bool', value=True, children=[
dict(name='Show Circuit', type='bool', value=False),
]),
# self.clamp_param, # now in the adjacent window
dict(name='Ion Channels', type='group', children=self.channel_params),
])

self.use_calculated_erev()

# Now that add_plot() sets x-axis limits, it must be called AFTER defining self.params,
# rather than before, since it uses "Plot Duration" field in self.params.
self.vm_plot = self.add_plot('soma.V', 'Membrane Potential', 'V')
Expand Down Expand Up @@ -217,7 +222,7 @@ def params_changed(self, root, changes):
self.sim.temp = val
# also update the ion channel values = specifically Erev
for ion in self.ion_concentrations:
ion.updateErev(self.sim.temp)
ion.updateTemperature(self.sim.temp)
elif param is self.params.child('Capacitance'):
self.neuron.cap = val
elif param is self.params.child('Capacitance', 'Plot Current'):
Expand All @@ -231,20 +236,22 @@ def params_changed(self, root, changes):
self.neuronview.setVisible(val)
elif param is self.params.child('Cell Schematic', 'Show Circuit'):
self.neuronview.show_circuit(val)
elif param is self.params.child('Ions'):
if val: # checkbox checked
self.use_calculated_erev()
else: # not checked
self.use_default_erev()
elif param in [ # change in ion concentrations and erev...
elif param in [ # change in ion concentrations and erev...
self.params.child('Ions', "Na", "[C]in"),
self.params.child('Ions', "Na", "[C]out"),
self.params.child('Ions', "K", "[C]in"),
self.params.child('Ions', "K", "[C]out"),
self.params.child('Ions', "Cl", "[C]in"),
self.params.child('Ions', "Cl", "[C]out"),
] and self.params.child('Ions').value():
]:
self.use_calculated_erev() # force update of erevs
elif param in self.params.child('Ion Channels'):
if not param.value():
# When turning ion off, also remove any plots associated with this ion
for p in param.children():
if p.name().startswith('Plot') and p.value():
# Turn off any plots that are currently ON
p.setValue(False)

def plots_changed(self, param, channel, name, plot):
key = channel.name + '.' + name
Expand Down Expand Up @@ -353,7 +360,19 @@ def set_hover_time(self, t):
plt.hover_line.setPos(t)
state = self.result_buffer.get_state_at_time(t)
if state is not None:
self.neuronview.update_state(state)
self.clamp_param['Cursor values', 'Relative time'] = t
if 'soma.V' in self.clamp_param.plot_keys:
self.clamp_param['Cursor values', 'Memb voltage'] = state['soma.V']
if 'soma.PatchClamp.cmd' in self.channel_plots.keys():
# Command values are not in the state variable, so we grab them out of the actual plot object
plt: ScrollingPlot = self.channel_plots['soma.PatchClamp.cmd']
dc: pg.PlotDataItem = plt.data_curve
[x, y] = [dc.xData, dc.yData]
dx = x[1] - x[0]
idx = int(t / dx) # Note that t will be negative, since it represents time before present. This will make idx negative, so index will count from end
if idx >= -len(y):
self.clamp_param['Cursor values', 'Command'] = y[idx]
self.neuronview.update_state(state)

def running(self):
return self.runner.running()
Expand Down Expand Up @@ -492,20 +511,6 @@ def use_calculated_erev(self):
self.set_hh_erev(ENa_erev, EK_erev, Eleak_erev, Eh_erev)
self.set_lg_erev(ENa_erev, EK_erev, EK_erev, -55*NU.mV)

def use_default_erev(self):
chans: pt.Parameter = self.params.child('Ion Channels')
ENa_revs = {"INa": 50*NU.mV, "INa1": 74*NU.mV}
for ch in ["INa", "INa1"]:
chans[f"soma.{ch:s}", 'Erev'] = ENa_revs[ch]
EK_revs = {"IK": -74*NU.mV, "IKf": -90*NU.mV, "IKs": -90*NU.mV}
for ch in ["IK", "IKf", "IKs"]:
chans[f"soma.{ch:s}", 'Erev'] = EK_revs[ch]
Eh_revs = {"IH": -43*NU.mV,}
for ch in ["IH"]:
chans[f"soma.{ch:s}", 'Erev'] = Eh_revs[ch]
self.set_hh_erev(ENa_revs["INa"], EK_revs["IK"], -55*NU.mV, Eh_revs["IH"])
self.set_lg_erev(ENa_revs["INa1"], EK_revs["IKf"], EK_revs["IKs"], -55*NU.mV, )

def set_hh_erev(self, ENa_erev=50*NU.mV, EK_erev=-74*NU.mV,
Eleak_erev=-55*NU.mV, Eh_erev=-43*NU.mV):
"""Set new reversal potentials for the HH currents
Expand Down Expand Up @@ -536,13 +541,6 @@ def set_lg_erev(self, ENa_erev=74*NU.mV, EKf_erev=-90*NU.mV,
self.lgks.set_erev(EKs_erev)
self.leak.set_erev(Eleak_erev)

def set_ions_off(self):
"""Turn off use of ion concentrations, and reset
all of the checkboxes associated with those.
"""
self.params.child('Ions', 'Na').setValue(False)
self.params.child('Ions', 'K').setValue(False)
self.params.child('Ions', 'Cl').setValue(False)

def load_preset(self, preset):
"""Load preset configurations for the simulations.
Expand Down
95 changes: 0 additions & 95 deletions pgtest.py
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60 changes: 0 additions & 60 deletions setup_win.spec
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