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amplitude based stimuli in apply_multiple_stimuli (#182)
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* amplitude based stimuli in apply_multiple_stimuli

* threshold_current = 0 edge case

* improve test with error raising check

* add logging in stimulus factory

---------

Co-authored-by: Jaquier Aurélien Tristan <[email protected]>
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@AurelienJaquier
AurelienJaquier and Jaquier Aurélien Tristan authored May 8, 2024
1 parent 62947a9 commit 2de98ed
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Showing 4 changed files with 241 additions and 54 deletions.
34 changes: 28 additions & 6 deletions bluecellulab/analysis/inject_sequence.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -74,6 +74,7 @@ def apply_multiple_stimuli(
cell: Cell,
stimulus_name: StimulusName,
amplitudes: Sequence[float],
threshold_based: bool = True,
section_name: str | None = None,
segment: float = 0.5,
n_processes: int | None = None,
Expand All @@ -84,6 +85,8 @@ def apply_multiple_stimuli(
cell: The cell to which the stimuli are applied.
stimulus_name: The name of the stimulus to apply.
amplitudes: The amplitudes of the stimuli to apply.
threshold_based: Whether to consider amplitudes to be
threshold percentages or to be raw amplitudes.
section_name: Section name of the cell where the stimuli are applied.
If None, the stimuli are applied at the soma[0] of the cell.
segment: The segment of the section where the stimuli are applied.
Expand All @@ -103,18 +106,37 @@ def apply_multiple_stimuli(

# Prepare arguments for each stimulus
for amplitude in amplitudes:
if threshold_based:
thres_perc = amplitude
amp = None
else:
thres_perc = None
amp = amplitude

if stimulus_name == StimulusName.AP_WAVEFORM:
stimulus = stim_factory.ap_waveform(threshold_current=cell.threshold, threshold_percentage=amplitude)
stimulus = stim_factory.ap_waveform(
threshold_current=cell.threshold, threshold_percentage=thres_perc, amplitude=amp
)
elif stimulus_name == StimulusName.IDREST:
stimulus = stim_factory.idrest(threshold_current=cell.threshold, threshold_percentage=amplitude)
stimulus = stim_factory.idrest(
threshold_current=cell.threshold, threshold_percentage=thres_perc, amplitude=amp
)
elif stimulus_name == StimulusName.IV:
stimulus = stim_factory.iv(threshold_current=cell.threshold, threshold_percentage=amplitude)
stimulus = stim_factory.iv(
threshold_current=cell.threshold, threshold_percentage=thres_perc, amplitude=amp
)
elif stimulus_name == StimulusName.FIRE_PATTERN:
stimulus = stim_factory.fire_pattern(threshold_current=cell.threshold, threshold_percentage=amplitude)
stimulus = stim_factory.fire_pattern(
threshold_current=cell.threshold, threshold_percentage=thres_perc, amplitude=amp
)
elif stimulus_name == StimulusName.POS_CHEOPS:
stimulus = stim_factory.pos_cheops(threshold_current=cell.threshold, threshold_percentage=amplitude)
stimulus = stim_factory.pos_cheops(
threshold_current=cell.threshold, threshold_percentage=thres_perc, amplitude=amp
)
elif stimulus_name == StimulusName.NEG_CHEOPS:
stimulus = stim_factory.neg_cheops(threshold_current=cell.threshold, threshold_percentage=amplitude)
stimulus = stim_factory.neg_cheops(
threshold_current=cell.threshold, threshold_percentage=thres_perc, amplitude=amp
)
else:
raise ValueError("Unknown stimulus name.")

Expand Down
196 changes: 151 additions & 45 deletions bluecellulab/stimulus/factory.py
View file
Original file line number Diff line number Diff line change
@@ -1,8 +1,12 @@
from __future__ import annotations
from abc import ABC, abstractmethod
from typing import Optional
import logging
import matplotlib.pyplot as plt
import numpy as np

logger = logging.getLogger(__name__)


class Stimulus(ABC):
def __init__(self, dt: float) -> None:
Expand Down Expand Up @@ -299,106 +303,190 @@ def ramp(
)

def ap_waveform(
self, threshold_current: float, threshold_percentage: float = 220.0
self,
threshold_current: Optional[float] = None,
threshold_percentage: Optional[float] = 220.0,
amplitude: Optional[float] = None,
) -> Stimulus:
"""Returns the APWaveform Stimulus object, a type of Step stimulus.
Args:
threshold_current: The threshold current of the Cell.
threshold_percentage: Percentage of desired threshold_current amplification.
amplitude: Raw amplitude of input current.
"""
pre_delay = 250.0
duration = 50.0
post_delay = 250.0
return Step.threshold_based(
self.dt,
pre_delay=pre_delay,
duration=duration,
post_delay=post_delay,
threshold_current=threshold_current,
threshold_percentage=threshold_percentage,
)

if amplitude is not None:
if threshold_current is not None and threshold_current != 0 and threshold_percentage is not None:
logger.info(
"amplitude, threshold_current and threshold_percentage are all set in ap_waveform."
" Will only keep amplitude value."
)
return Step.amplitude_based(
self.dt,
pre_delay=pre_delay,
duration=duration,
post_delay=post_delay,
amplitude=amplitude,
)

if threshold_current is not None and threshold_current != 0 and threshold_percentage is not None:
return Step.threshold_based(
self.dt,
pre_delay=pre_delay,
duration=duration,
post_delay=post_delay,
threshold_current=threshold_current,
threshold_percentage=threshold_percentage,
)

raise TypeError("You have to give either threshold_current or amplitude")

def idrest(
self,
threshold_current: float,
threshold_percentage: float = 200.0,
threshold_current: Optional[float] = None,
threshold_percentage: Optional[float] = 200.0,
amplitude: Optional[float] = None,
) -> Stimulus:
"""Returns the IDRest Stimulus object, a type of Step stimulus.
Args:
threshold_current: The threshold current of the Cell.
threshold_percentage: Percentage of desired threshold_current amplification.
amplitude: Raw amplitude of input current.
"""
pre_delay = 250.0
duration = 1350.0
post_delay = 250.0
return Step.threshold_based(
self.dt,
pre_delay=pre_delay,
duration=duration,
post_delay=post_delay,
threshold_current=threshold_current,
threshold_percentage=threshold_percentage,
)

if amplitude is not None:
if threshold_current is not None and threshold_current != 0 and threshold_percentage is not None:
logger.info(
"amplitude, threshold_current and threshold_percentage are all set in idrest."
" Will only keep amplitude value."
)
return Step.amplitude_based(
self.dt,
pre_delay=pre_delay,
duration=duration,
post_delay=post_delay,
amplitude=amplitude,
)

if threshold_current is not None and threshold_current != 0 and threshold_percentage is not None:
return Step.threshold_based(
self.dt,
pre_delay=pre_delay,
duration=duration,
post_delay=post_delay,
threshold_current=threshold_current,
threshold_percentage=threshold_percentage,
)

raise TypeError("You have to give either threshold_current or amplitude")

def iv(
self,
threshold_current: float,
threshold_percentage: float = -40.0,
threshold_current: Optional[float] = None,
threshold_percentage: Optional[float] = -40.0,
amplitude: Optional[float] = None,
) -> Stimulus:
"""Returns the IV Stimulus object, a type of Step stimulus.
Args:
threshold_current: The threshold current of the Cell.
threshold_percentage: Percentage of desired threshold_current amplification.
amplitude: Raw amplitude of input current.
"""
pre_delay = 250.0
duration = 3000.0
post_delay = 250.0
return Step.threshold_based(
self.dt,
pre_delay=pre_delay,
duration=duration,
post_delay=post_delay,
threshold_current=threshold_current,
threshold_percentage=threshold_percentage,
)

if amplitude is not None:
if threshold_current is not None and threshold_current != 0 and threshold_percentage is not None:
logger.info(
"amplitude, threshold_current and threshold_percentage are all set in iv."
" Will only keep amplitude value."
)
return Step.amplitude_based(
self.dt,
pre_delay=pre_delay,
duration=duration,
post_delay=post_delay,
amplitude=amplitude,
)

if threshold_current is not None and threshold_current != 0 and threshold_percentage is not None:
return Step.threshold_based(
self.dt,
pre_delay=pre_delay,
duration=duration,
post_delay=post_delay,
threshold_current=threshold_current,
threshold_percentage=threshold_percentage,
)

raise TypeError("You have to give either threshold_current or amplitude")

def fire_pattern(
self,
threshold_current: float,
threshold_percentage: float = 200.0,
threshold_current: Optional[float] = None,
threshold_percentage: Optional[float] = 200.0,
amplitude: Optional[float] = None,
) -> Stimulus:
"""Returns the FirePattern Stimulus object, a type of Step stimulus.
Args:
threshold_current: The threshold current of the Cell.
threshold_percentage: Percentage of desired threshold_current amplification.
amplitude: Raw amplitude of input current.
"""
pre_delay = 250.0
duration = 3600.0
post_delay = 250.0
return Step.threshold_based(
self.dt,
pre_delay=pre_delay,
duration=duration,
post_delay=post_delay,
threshold_current=threshold_current,
threshold_percentage=threshold_percentage,
)

if amplitude is not None:
if threshold_current is not None and threshold_current != 0 and threshold_percentage is not None:
logger.info(
"amplitude, threshold_current and threshold_percentage are all set in fire_pattern."
" Will only keep amplitude value."
)
return Step.amplitude_based(
self.dt,
pre_delay=pre_delay,
duration=duration,
post_delay=post_delay,
amplitude=amplitude,
)

if threshold_current is not None and threshold_current != 0 and threshold_percentage is not None:
return Step.threshold_based(
self.dt,
pre_delay=pre_delay,
duration=duration,
post_delay=post_delay,
threshold_current=threshold_current,
threshold_percentage=threshold_percentage,
)

raise TypeError("You have to give either threshold_current or amplitude")

def pos_cheops(
self,
threshold_current: float,
threshold_percentage: float = 300.0,
threshold_current: Optional[float] = None,
threshold_percentage: Optional[float] = 300.0,
amplitude: Optional[float] = None,
) -> Stimulus:
"""A combination of pyramid shaped Ramp stimuli with a positive
amplitude.
Args:
threshold_current: The threshold current of the Cell.
threshold_percentage: Percentage of desired threshold_current amplification.
amplitude: Raw amplitude of input current.
"""
delay = 250.0
ramp1_duration = 4000.0
Expand All @@ -407,7 +495,15 @@ def pos_cheops(
inter_delay = 2000.0
post_delay = 250.0

amplitude = threshold_current * threshold_percentage / 100
if amplitude is None:
if threshold_current is None or threshold_current == 0 or threshold_percentage is None:
raise TypeError("You have to give either threshold_current or amplitude")
amplitude = threshold_current * threshold_percentage / 100
elif threshold_current is not None and threshold_current != 0 and threshold_percentage is not None:
logger.info(
"amplitude, threshold_current and threshold_percentage are all set in pos_cheops."
" Will only keep amplitude value."
)
result = (
Empty(self.dt, duration=delay)
+ Slope(self.dt, duration=ramp1_duration, amplitude_start=0.0, amplitude_end=amplitude)
Expand All @@ -424,15 +520,17 @@ def pos_cheops(

def neg_cheops(
self,
threshold_current: float,
threshold_percentage: float = 300.0,
threshold_current: Optional[float] = None,
threshold_percentage: Optional[float] = 300.0,
amplitude: Optional[float] = None,
) -> Stimulus:
"""A combination of pyramid shaped Ramp stimuli with a negative
amplitude.
Args:
threshold_current: The threshold current of the Cell.
threshold_percentage: Percentage of desired threshold_current amplification.
amplitude: Raw amplitude of input current.
"""
delay = 1750.0
ramp1_duration = 3333.0
Expand All @@ -441,7 +539,15 @@ def neg_cheops(
inter_delay = 2000.0
post_delay = 250.0

amplitude = - threshold_current * threshold_percentage / 100
if amplitude is None:
if threshold_current is None or threshold_current == 0 or threshold_percentage is None:
raise TypeError("You have to give either threshold_current or amplitude")
amplitude = - threshold_current * threshold_percentage / 100
elif threshold_current is not None and threshold_current != 0 and threshold_percentage is not None:
logger.info(
"amplitude, threshold_current and threshold_percentage are all set in neg_cheops."
" Will only keep amplitude value."
)
result = (
Empty(self.dt, duration=delay)
+ Slope(self.dt, duration=ramp1_duration, amplitude_start=0.0, amplitude_end=amplitude)
Expand Down
12 changes: 9 additions & 3 deletions tests/test_analysis/test_inject_sequence.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,16 +32,19 @@ def mock_run_stimulus():
def test_apply_multiple_step_stimuli(mock_run_stimulus):
"""Do not run the code in parallel, mock the return value via MockRecording."""
amplitudes = [80, 100, 120, 140]
thres_perc = [0.08]
cell = create_ball_stick()

with patch('bluecellulab.analysis.inject_sequence.IsolatedProcess') as mock_isolated_process, \
patch('bluecellulab.analysis.inject_sequence.run_stimulus', mock_run_stimulus):
# the mock process pool to return a list of MockRecordings
mock_isolated_process.return_value.__enter__.return_value.starmap.return_value = [MockRecording() for _ in amplitudes]

recordings = apply_multiple_stimuli(cell, StimulusName.FIRE_PATTERN, amplitudes, n_processes=4)
recordings = apply_multiple_stimuli(cell, StimulusName.FIRE_PATTERN, amplitudes, threshold_based=False, n_processes=4)
recordings_thres = apply_multiple_stimuli(cell, StimulusName.FIRE_PATTERN, thres_perc, n_processes=4)
assert len(recordings) == len(amplitudes)
for recording in recordings.values():
assert len(recordings_thres) == len(thres_perc)
for recording in list(recordings.values()) + list(recordings_thres.values()):
assert len(recording.time) > 0
assert len(recording.time) == len(recording.voltage)
assert len(recording.time) == len(recording.current)
Expand All @@ -52,7 +55,10 @@ def test_apply_multiple_step_stimuli(mock_run_stimulus):
assert "Unknown stimulus name" in str(exc_info.value)

short_amplitudes = [80]
short_thres = [0.08]
other_stim = [StimulusName.AP_WAVEFORM, StimulusName.IV, StimulusName.IDREST, StimulusName.POS_CHEOPS, StimulusName.NEG_CHEOPS]
for stim in other_stim:
res = apply_multiple_stimuli(cell, stim, short_amplitudes, n_processes=1)
res = apply_multiple_stimuli(cell, stim, short_amplitudes, threshold_based=False, n_processes=1)
res_thres = apply_multiple_stimuli(cell, stim, short_thres, n_processes=1)
assert len(res) == len(short_amplitudes)
assert len(res_thres) == len(short_thres)
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