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allow stimuli to be non-threshold based #83

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Nov 20, 2023
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Merged

allow stimuli to be non-threshold based #83

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f7c4722
allow stimuli to be non-threshold based
Nov 20, 2023
f89d62a
Add tests for non-threshold based stimuli
Nov 20, 2023
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22 changes: 13 additions & 9 deletions bluepyemodel/ecode/dehyperpol.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -105,6 +105,8 @@ def depol_amplitude(self):
def instantiate(self, sim=None, icell=None):
"""Run stimulus"""

holding_current = self.holding_current if self.holding_current is not None else 0

icomp = self.location.instantiate(sim=sim, icell=icell)

self.iclamp = sim.neuron.h.IClamp(icomp.x, sec=icomp.sec)
Expand All @@ -114,28 +116,28 @@ def instantiate(self, sim=None, icell=None):
self.time_vec = sim.neuron.h.Vector()

self.time_vec.append(0.0)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.time_vec.append(self.delay)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.time_vec.append(self.delay)
self.current_vec.append(self.holding_current + self.depol_amplitude)
self.current_vec.append(holding_current + self.depol_amplitude)

self.time_vec.append(self.tmid)
self.current_vec.append(self.holding_current + self.depol_amplitude)
self.current_vec.append(holding_current + self.depol_amplitude)

self.time_vec.append(self.tmid)
self.current_vec.append(self.holding_current + self.amplitude)
self.current_vec.append(holding_current + self.amplitude)

self.time_vec.append(self.toff)
self.current_vec.append(self.holding_current + self.amplitude)
self.current_vec.append(holding_current + self.amplitude)

self.time_vec.append(self.toff)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.time_vec.append(self.total_duration)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.iclamp.delay = 0
self.current_vec.play(
Expand All @@ -149,8 +151,10 @@ def generate(self, dt=0.1):
"""Return current time series

WARNING: do not offset ! This is on-top of a holding stimulus."""
holding_current = self.holding_current if self.holding_current is not None else 0

t = numpy.arange(0.0, self.total_duration, dt)
current = numpy.full(t.shape, self.holding_current, dtype="float64")
current = numpy.full(t.shape, holding_current, dtype="float64")

ton = int(self.delay / dt)
tmid = int(self.tmid / dt)
Expand Down
21 changes: 12 additions & 9 deletions bluepyemodel/ecode/hyperdepol.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -106,6 +106,8 @@ def depol_amplitude(self):
def instantiate(self, sim=None, icell=None):
"""Run stimulus"""

holding_current = self.holding_current if self.holding_current is not None else 0

icomp = self.location.instantiate(sim=sim, icell=icell)

self.iclamp = sim.neuron.h.IClamp(icomp.x, sec=icomp.sec)
Expand All @@ -115,28 +117,28 @@ def instantiate(self, sim=None, icell=None):
self.time_vec = sim.neuron.h.Vector()

self.time_vec.append(0.0)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.time_vec.append(self.delay)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.time_vec.append(self.delay)
self.current_vec.append(self.holding_current + self.amplitude)
self.current_vec.append(holding_current + self.amplitude)

self.time_vec.append(self.tmid)
self.current_vec.append(self.holding_current + self.amplitude)
self.current_vec.append(holding_current + self.amplitude)

self.time_vec.append(self.tmid)
self.current_vec.append(self.holding_current + self.depol_amplitude)
self.current_vec.append(holding_current + self.depol_amplitude)

self.time_vec.append(self.toff)
self.current_vec.append(self.holding_current + self.depol_amplitude)
self.current_vec.append(holding_current + self.depol_amplitude)

self.time_vec.append(self.toff)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.time_vec.append(self.total_duration)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.iclamp.delay = 0
self.current_vec.play(
Expand All @@ -150,8 +152,9 @@ def generate(self, dt=0.1):
"""Return current time series

WARNING: do not offset ! This is on-top of a holding stimulus."""
holding_current = self.holding_current if self.holding_current is not None else 0
t = numpy.arange(0.0, self.total_duration, dt)
current = numpy.full(t.shape, self.holding_current, dtype="float64")
current = numpy.full(t.shape, holding_current, dtype="float64")

ton = int(self.delay / dt)
tmid = int(self.tmid / dt)
Expand Down
17 changes: 10 additions & 7 deletions bluepyemodel/ecode/idrest.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -88,6 +88,8 @@ def amplitude(self):
def instantiate(self, sim=None, icell=None):
"""Run stimulus"""

holding_current = self.holding_current if self.holding_current is not None else 0

icomp = self.location.instantiate(sim=sim, icell=icell)

self.iclamp = sim.neuron.h.IClamp(icomp.x, sec=icomp.sec)
Expand All @@ -97,22 +99,22 @@ def instantiate(self, sim=None, icell=None):
self.time_vec = sim.neuron.h.Vector()

self.time_vec.append(0.0)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.time_vec.append(self.delay)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.time_vec.append(self.delay)
self.current_vec.append(self.holding_current + self.amplitude)
self.current_vec.append(holding_current + self.amplitude)

self.time_vec.append(self.stim_end)
self.current_vec.append(self.holding_current + self.amplitude)
self.current_vec.append(holding_current + self.amplitude)

self.time_vec.append(self.stim_end)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.time_vec.append(self.total_duration)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.iclamp.delay = 0
self.current_vec.play(
Expand All @@ -124,9 +126,10 @@ def instantiate(self, sim=None, icell=None):

def generate(self, dt=0.1):
"""Return current time series"""
holding_current = self.holding_current if self.holding_current is not None else 0

t = numpy.arange(0.0, self.total_duration, dt)
current = numpy.full(t.shape, self.holding_current, dtype="float64")
current = numpy.full(t.shape, holding_current, dtype="float64")

ton_idx = int(self.stim_start / dt)
toff_idx = int(self.stim_end / dt)
Expand Down
27 changes: 15 additions & 12 deletions bluepyemodel/ecode/negcheops.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -111,6 +111,8 @@ def amplitude(self):
def instantiate(self, sim=None, icell=None):
"""Run stimulus"""

holding_current = self.holding_current if self.holding_current is not None else 0

icomp = self.location.instantiate(sim=sim, icell=icell)

self.iclamp = sim.neuron.h.IClamp(icomp.x, sec=icomp.sec)
Expand All @@ -120,33 +122,33 @@ def instantiate(self, sim=None, icell=None):
self.time_vec = sim.neuron.h.Vector()

self.time_vec.append(0.0)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.time_vec.append(self.delay)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)
self.time_vec.append(self.delay + self.ramp1_duration)
self.current_vec.append(self.holding_current + self.amplitude)
self.current_vec.append(holding_current + self.amplitude)
self.time_vec.append(self.delay + 2.0 * self.ramp1_duration)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

start_cheops2 = self.delay + 2.0 * self.ramp1_duration + self.inter_delay
self.time_vec.append(start_cheops2)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)
self.time_vec.append(start_cheops2 + self.ramp2_duration)
self.current_vec.append(self.holding_current + self.amplitude)
self.current_vec.append(holding_current + self.amplitude)
self.time_vec.append(start_cheops2 + 2.0 * self.ramp2_duration)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

start_cheops3 = start_cheops2 + 2.0 * self.ramp2_duration + self.inter_delay
self.time_vec.append(start_cheops3)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)
self.time_vec.append(start_cheops3 + self.ramp3_duration)
self.current_vec.append(self.holding_current + self.amplitude)
self.current_vec.append(holding_current + self.amplitude)
self.time_vec.append(start_cheops3 + 2.0 * self.ramp3_duration)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.time_vec.append(self.total_duration)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.iclamp.delay = 0
self.current_vec.play(
Expand All @@ -160,9 +162,10 @@ def generate(self, dt=0.1):
"""Return current time series

WARNING: do not offset ! This is on-top of a holding stimulus."""
holding_current = self.holding_current if self.holding_current is not None else 0

t = numpy.arange(0.0, self.total_duration, dt)
current = numpy.full(t.shape, self.holding_current, dtype="float64")
current = numpy.full(t.shape, holding_current, dtype="float64")

idx_ton = int(self.delay / dt)
idx_inter_delay = int(self.inter_delay / dt)
Expand Down
3 changes: 2 additions & 1 deletion bluepyemodel/ecode/noise.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -53,10 +53,11 @@ def stim_end(self):

def generate(self, dt=0.1):
"""Return current time series"""
holding_current = self.holding_current if self.holding_current is not None else 0

if dt != 0.1:
raise ValueError(f"For eCode {self.name}, dt has to be 0.1ms.")

current = self.holding_current + self.current_series * (self.mu / 2.0) + self.mu
current = holding_current + self.current_series * (self.mu / 2.0) + self.mu

return self.time_series, current
27 changes: 15 additions & 12 deletions bluepyemodel/ecode/poscheops.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -114,6 +114,8 @@ def amplitude(self):
def instantiate(self, sim=None, icell=None):
"""Run stimulus"""

holding_current = self.holding_current if self.holding_current is not None else 0

icomp = self.location.instantiate(sim=sim, icell=icell)

self.iclamp = sim.neuron.h.IClamp(icomp.x, sec=icomp.sec)
Expand All @@ -123,33 +125,33 @@ def instantiate(self, sim=None, icell=None):
self.time_vec = sim.neuron.h.Vector()

self.time_vec.append(0.0)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.time_vec.append(self.delay)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)
self.time_vec.append(self.delay + self.ramp1_duration)
self.current_vec.append(self.holding_current + self.amplitude)
self.current_vec.append(holding_current + self.amplitude)
self.time_vec.append(self.delay + 2.0 * self.ramp1_duration)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

start_cheops2 = self.delay + 2.0 * self.ramp1_duration + self.inter_delay
self.time_vec.append(start_cheops2)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)
self.time_vec.append(start_cheops2 + self.ramp2_duration)
self.current_vec.append(self.holding_current + self.amplitude)
self.current_vec.append(holding_current + self.amplitude)
self.time_vec.append(start_cheops2 + 2.0 * self.ramp2_duration)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

start_cheops3 = start_cheops2 + 2.0 * self.ramp2_duration + self.inter_delay
self.time_vec.append(start_cheops3)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)
self.time_vec.append(start_cheops3 + self.ramp3_duration)
self.current_vec.append(self.holding_current + self.amplitude)
self.current_vec.append(holding_current + self.amplitude)
self.time_vec.append(start_cheops3 + 2.0 * self.ramp3_duration)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.time_vec.append(self.total_duration)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.iclamp.delay = 0
self.current_vec.play(
Expand All @@ -163,9 +165,10 @@ def generate(self, dt=0.1):
"""Return current time series

WARNING: do not offset ! This is on-top of a holding stimulus."""
holding_current = self.holding_current if self.holding_current is not None else 0

t = numpy.arange(0.0, self.total_duration, dt)
current = numpy.full(t.shape, self.holding_current, dtype="float64")
current = numpy.full(t.shape, holding_current, dtype="float64")

idx_ton = int(self.delay / dt)
idx_inter_delay = int(self.inter_delay / dt)
Expand Down
15 changes: 9 additions & 6 deletions bluepyemodel/ecode/ramp.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -92,6 +92,8 @@ def amplitude(self):
def instantiate(self, sim=None, icell=None):
"""Run stimulus"""

holding_current = self.holding_current if self.holding_current is not None else 0

icomp = self.location.instantiate(sim=sim, icell=icell)

self.iclamp = sim.neuron.h.IClamp(icomp.x, sec=icomp.sec)
Expand All @@ -101,19 +103,19 @@ def instantiate(self, sim=None, icell=None):
self.time_vec = sim.neuron.h.Vector()

self.time_vec.append(0.0)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.time_vec.append(self.delay)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.time_vec.append(self.stim_end)
self.current_vec.append(self.holding_current + self.amplitude)
self.current_vec.append(holding_current + self.amplitude)

self.time_vec.append(self.stim_end)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.time_vec.append(self.total_duration)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.iclamp.delay = 0
self.current_vec.play(
Expand All @@ -125,9 +127,10 @@ def instantiate(self, sim=None, icell=None):

def generate(self, dt=0.1):
"""Return current time series"""
holding_current = self.holding_current if self.holding_current is not None else 0

t = numpy.arange(0.0, self.total_duration, dt)
current = numpy.full(t.shape, self.holding_current, dtype="float64")
current = numpy.full(t.shape, holding_current, dtype="float64")

ton_idx = int(self.stim_start / dt)
toff_idx = int((self.stim_end) / dt)
Expand Down
6 changes: 4 additions & 2 deletions bluepyemodel/ecode/random_square_inputs.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -97,6 +97,8 @@ def amplitude(self):
def instantiate(self, sim=None, icell=None):
"""Run stimulus"""

holding_current = self.holding_current if self.holding_current is not None else 0

# Holding current
icomp = self.location.instantiate(sim=sim, icell=icell)

Expand All @@ -107,10 +109,10 @@ def instantiate(self, sim=None, icell=None):
self.time_vec = sim.neuron.h.Vector()

self.time_vec.append(0.0)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.time_vec.append(self.total_duration)
self.current_vec.append(self.holding_current)
self.current_vec.append(holding_current)

self.iclamp.delay = 0
self.current_vec.play(
Expand Down
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