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feat(stimuli): add input validation to stimulus classes #17

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37 changes: 35 additions & 2 deletions neuroanalysis/stimuli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -379,6 +379,8 @@ class SquarePulse(Stimulus):
_attributes = Stimulus._attributes + ['duration', 'amplitude']

def __init__(self, start_time, duration, amplitude, description="square pulse", units=None, parent=None):
if duration < 0:
raise ValueError("duration must be non-negative")
self.duration = duration
self.amplitude = amplitude
Stimulus.__init__(self, description=description, start_time=start_time, units=units, parent=parent)
Expand Down Expand Up @@ -518,6 +520,12 @@ class SquarePulseTrain(Stimulus):
_attributes = Stimulus._attributes + ['n_pulses', 'pulse_duration', 'amplitude', 'interval']

def __init__(self, start_time, n_pulses, pulse_duration, amplitude, interval, description="square pulse train", units=None, parent=None):
if not isinstance(n_pulses, int):
raise TypeError("n_pulses must be an integer")
if n_pulses < 1:
raise ValueError("n_pulses must be a positive integer")
if interval < pulse_duration:
raise ValueError("interval must be >= pulse_duration (pulses would overlap)")
self.n_pulses = n_pulses
self.pulse_duration = pulse_duration
self.amplitude = amplitude
Expand Down Expand Up @@ -572,7 +580,8 @@ def __init__(self, start_time, pulse_times, pulse_durations, amplitudes, descrip
self.pulse_times = pulse_times
self.pulse_durations = pulse_durations
self.amplitudes = amplitudes
assert len(pulse_times) == len(pulse_durations) == len(amplitudes)
if not (len(pulse_times) == len(pulse_durations) == len(amplitudes)):
raise ValueError("pulse_times, pulse_durations, and amplitudes must all have the same length")
Stimulus.__init__(self, description=description, start_time=start_time, units=units, parent=parent)

for i,t in enumerate(pulse_times):
Expand Down Expand Up @@ -613,6 +622,8 @@ class Ramp(Stimulus):
_attributes = Stimulus._attributes + ['duration', 'slope', 'initial_amplitude']

def __init__(self, start_time, duration, slope, offset=0, description="linear ramp", units=None, parent=None):
if duration < 0:
raise ValueError("duration must be non-negative")
self.duration = duration
self.slope = slope
self.offset = offset
Expand Down Expand Up @@ -659,6 +670,10 @@ class Sine(Stimulus):
_attributes = Stimulus._attributes + ['duration', 'frequency', 'amplitude', 'phase']

def __init__(self, start_time, duration, frequency, amplitude, phase=0, offset=0, description="sine wave", units=None, parent=None):
if duration < 0:
raise ValueError("duration must be non-negative")
if frequency <= 0:
raise ValueError("frequency must be positive")
self.duration = duration
self.frequency = frequency
self.amplitude = amplitude
Expand All @@ -667,11 +682,14 @@ def __init__(self, start_time, duration, frequency, amplitude, phase=0, offset=0
Stimulus.__init__(self, description=description, start_time=start_time, parent=parent, units=units)

def eval(self, **kwds):
if kwds.get("sample_rate") is not None:
if self.frequency > kwds["sample_rate"] / 2:
raise ValueError("Sample rate must be at least twice the frequency of the sine wave.")
trace = Stimulus.eval(self, **kwds)
start = self.global_start_time
chunk = trace.time_slice(start, start+self.duration, index_mode=kwds.get('index_mode'))
chunk.data[:] += self.offset

t = chunk.time_values - start
phase = self.phase_at(t)
chunk.data[:] += self.amplitude * np.sin(phase)
Expand Down Expand Up @@ -759,6 +777,12 @@ class Chirp(Stimulus):
_attributes = Stimulus._attributes + ['duration', 'start_frequency', 'end_frequency', 'amplitude', 'phase', 'offset']

def __init__(self, start_time, duration, start_frequency, end_frequency, amplitude, phase=0, offset=0, description="frequency chirp", units=None, parent=None):
if duration <= 0:
raise ValueError("duration must be positive")
if start_frequency <= 0:
raise ValueError("start_frequency must be positive")
if end_frequency <= 0:
raise ValueError("end_frequency must be positive")
self.duration = duration
self.start_frequency = start_frequency
self.end_frequency = end_frequency
Expand All @@ -768,6 +792,9 @@ def __init__(self, start_time, duration, start_frequency, end_frequency, amplitu
Stimulus.__init__(self, description=description, start_time=start_time, parent=parent, units=units)

def eval(self, **kwds):
if kwds.get("sample_rate") is not None:
if self.start_frequency > kwds["sample_rate"] / 2 or self.end_frequency > kwds["sample_rate"] / 2:
raise ValueError("Sample rate must be at least twice the maximum frequency in the chirp.")
trace = Stimulus.eval(self, **kwds)
start = self.global_start_time
chunk = trace.time_slice(start, start + self.duration, index_mode=kwds.get('index_mode'))
Expand Down Expand Up @@ -837,6 +864,12 @@ class Psp(Stimulus):
_attributes = Stimulus._attributes + ['rise_time', 'decay_tau', 'amplitude', 'rise_power']

def __init__(self, start_time, rise_time, decay_tau, amplitude, rise_power=2, description="frequency chirp", units=None, parent=None):
if rise_time <= 0:
raise ValueError("rise_time must be positive")
if decay_tau <= 0:
raise ValueError("decay_tau must be positive")
if rise_power <= 0:
raise ValueError("rise_power must be positive")
self.rise_time = rise_time
self.decay_tau = decay_tau
self.amplitude = amplitude
Expand Down
79 changes: 79 additions & 0 deletions neuroanalysis/tests/test_stimuli.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
from collections import OrderedDict

import numpy as np
import pytest

import neuroanalysis.stimuli as stimuli
from neuroanalysis.data.dataset import TSeries
Expand Down Expand Up @@ -296,6 +297,84 @@ def test_chirp():
freqs = f0 ** np.linspace(1, np.log(f1) / np.log(f0), len(t)+1)[:-1]
assert np.allclose(freqs, stim.frequency_at(t))

def test_validation():
# Sine: Nyquist check in eval
sine = stimuli.Sine(start_time=0, duration=0.1, frequency=100, amplitude=1)
with pytest.raises(ValueError):
sine.eval(n_pts=100, sample_rate=150) # 150 < 2*100
sine.eval(n_pts=100, sample_rate=300) # should be fine

# Sine: frequency must be positive
with pytest.raises(ValueError):
stimuli.Sine(start_time=0, duration=0.1, frequency=0, amplitude=1)
with pytest.raises(ValueError):
stimuli.Sine(start_time=0, duration=0.1, frequency=-5, amplitude=1)

# Sine: duration must be non-negative
with pytest.raises(ValueError):
stimuli.Sine(start_time=0, duration=-1, frequency=10, amplitude=1)

# Chirp: Nyquist check in eval (restore original check)
chirp = stimuli.Chirp(start_time=0, duration=0.1, start_frequency=10, end_frequency=100, amplitude=1)
with pytest.raises(ValueError):
chirp.eval(n_pts=100, sample_rate=150) # 150 < 2*100
chirp.eval(n_pts=100, sample_rate=300) # should be fine

# Chirp: frequencies must be positive
with pytest.raises(ValueError):
stimuli.Chirp(start_time=0, duration=0.1, start_frequency=0, end_frequency=100, amplitude=1)
with pytest.raises(ValueError):
stimuli.Chirp(start_time=0, duration=0.1, start_frequency=10, end_frequency=-1, amplitude=1)

# Chirp: duration must be positive
with pytest.raises(ValueError):
stimuli.Chirp(start_time=0, duration=0, start_frequency=10, end_frequency=100, amplitude=1)
with pytest.raises(ValueError):
stimuli.Chirp(start_time=0, duration=-1, start_frequency=10, end_frequency=100, amplitude=1)

# SquarePulse: duration must be non-negative
with pytest.raises(ValueError):
stimuli.SquarePulse(start_time=0, duration=-0.1, amplitude=1)

# SquarePulseTrain: n_pulses must be a positive integer
with pytest.raises(ValueError):
stimuli.SquarePulseTrain(start_time=0, n_pulses=0, pulse_duration=0.01, amplitude=1, interval=0.1)
with pytest.raises(ValueError):
stimuli.SquarePulseTrain(start_time=0, n_pulses=-3, pulse_duration=0.01, amplitude=1, interval=0.1)
with pytest.raises(TypeError):
stimuli.SquarePulseTrain(start_time=0, n_pulses=1.5, pulse_duration=0.01, amplitude=1, interval=0.1)

# SquarePulseTrain: interval must be >= pulse_duration
with pytest.raises(ValueError):
stimuli.SquarePulseTrain(start_time=0, n_pulses=3, pulse_duration=0.1, amplitude=1, interval=0.05)

# Ramp: duration must be non-negative
with pytest.raises(ValueError):
stimuli.Ramp(start_time=0, duration=-1, slope=1)

# Psp: rise_time must be positive
with pytest.raises(ValueError):
stimuli.Psp(start_time=0, rise_time=0, decay_tau=0.01, amplitude=1)
with pytest.raises(ValueError):
stimuli.Psp(start_time=0, rise_time=-0.01, decay_tau=0.01, amplitude=1)

# Psp: decay_tau must be positive
with pytest.raises(ValueError):
stimuli.Psp(start_time=0, rise_time=0.01, decay_tau=0, amplitude=1)
with pytest.raises(ValueError):
stimuli.Psp(start_time=0, rise_time=0.01, decay_tau=-0.01, amplitude=1)

# Psp: rise_power must be positive
with pytest.raises(ValueError):
stimuli.Psp(start_time=0, rise_time=0.01, decay_tau=0.01, amplitude=1, rise_power=0)
with pytest.raises(ValueError):
stimuli.Psp(start_time=0, rise_time=0.01, decay_tau=0.01, amplitude=1, rise_power=-1)

# SquarePulseSeries: mismatched array lengths should raise ValueError (not AssertionError)
with pytest.raises(ValueError):
stimuli.SquarePulseSeries(start_time=0, pulse_times=[0, 0.1], pulse_durations=[0.01], amplitudes=[1, 1])


def test_find_noisy_square_pulses():
dt = 0.0002
np.random.seed(54321)
Expand Down
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