def testHistValues(self):
# Simple example
# Two triggers: n=10, 20
# Trial 1 extends from -2 to +1 (centered at first trigger)
# Trial 2 extends from -1 to +2 (centered at second trigger)
# Spikes occurred at centered times +1 and +2
# Initialize PSTH with this info
psth = PSTH(F_SAMP=1000.,
adjusted_spike_times=[1, 2],
t_starts=[8, 19],
t_stops=[12, 23],
t_centers=[10, 20],
nbins=5)
# Check that range was set based on trial extents
self.assertTrue(np.all(psth.range == [-2, 3]))
# Calculate histogram values
t, counts = psth.hist_values(style='elastic')
# Bin edges were auto set to include all trials
self.assertTrue(np.all(psth._bin_edges == np.arange(-2, 4)))
# The first and last bins contain only one trial
self.assertTrue(np.all(psth._trials == np.array([1, 2, 2, 2, 1])))
# Time +1 includes two trials, so that count is divided by 2.
# Time +2 includes only one trial, so that count is divided by 1.
self.assertTrue(np.all(counts == np.array([0, 0, 0, 0.5, 1.0])))
def testHistValues(self):
# Simple example
# Two triggers: n=10, 20
# Trial 1 extends from -2 to +1 (centered at first trigger)
# Trial 2 extends from -1 to +2 (centered at second trigger)
# Spikes occurred at centered times +1 and +2
# Initialize PSTH with this info
psth = PSTH(F_SAMP=1000.,
adjusted_spike_times=[1, 2],
t_starts=[8, 19], t_stops=[12, 23], t_centers=[10, 20],
nbins=5)
# Check that range was set based on trial extents
self.assertTrue(np.all(psth.range == [-2, 3]))
# Calculate histogram values
t, counts = psth.hist_values(style='elastic')
# Bin edges were auto set to include all trials
self.assertTrue(np.all(psth._bin_edges == np.arange(-2, 4)))
# The first and last bins contain only one trial
self.assertTrue(np.all(psth._trials == np.array([1, 2, 2, 2, 1])))
# Time +1 includes two trials, so that count is divided by 2.
# Time +2 includes only one trial, so that count is divided by 1.
self.assertTrue(np.all(counts == np.array([0, 0, 0, 0.5, 1.0])))
def testElasticWiderBins(self):
# Now bins are specified to be 2ms wide.
# Trial 1: -2 to 1 (closed)
# Trial 2: -1 to 2 (closed)
# Spikes: +1, +2
# Thus the bins are [-2,0), [0, 2), [2, 4]
# The middle bin includes one spike and two trials, so
# 0.5 spike/trial/bin.
# The last bin includes one spike and only half a trial, because
# one trial extends through half of it, so
# 2 spike/trial/bin
psth = PSTH(F_SAMP=1000.,
adjusted_spike_times=[1, 2],
t_starts=[8, 19],
t_stops=[12, 23],
t_centers=[10, 20],
binwidth=.002)
self.assertTrue(np.all(psth.range == [-2, 4]))
t, counts = psth.hist_values(style='elastic')
self.assertTrue(np.all(psth.range == [-2, 4]))
self.assertTrue(np.all(psth._bin_edges == np.array([-2, 0, 2, 4])))
self.assertTrue(np.all(psth._trials == np.array([3, 4, 1])))
self.assertTrue(np.all(counts == np.array([0, 0.5, 2.])))
def testElastic(self):
psth = PSTH(F_SAMP=1000.,
adjusted_spike_times=[1, 2, 4],
t_starts=[8, 19], t_stops=[12, 23], t_centers=[10, 20],
binwidth=.001)
self.assertTrue(np.all(psth.range == [-2, 3]))
t, counts = psth.hist_values(style='elastic')
self.assertTrue(np.all(psth._bin_edges == np.arange(-2, 4)))
self.assertTrue(np.all(psth._trials == np.array([1, 2, 2, 2, 1])))
self.assertTrue(np.all(counts == np.array([0, 0, 0, 0.5, 1.0])))
def testWithSpuriousSpike(self):
# Same as testHistValues, but with an extra spike that is outside
# of any trial, so the results should be the same.
# Note that a spike at time 3 would be included in the last bin,
# which is not strictly correct because the t_stop is not inclusive.
psth = PSTH(F_SAMP=1000.,
adjusted_spike_times=[1, 2, 4],
t_starts=[8, 19], t_stops=[12, 23], t_centers=[10, 20],
nbins=5)
self.assertTrue(np.all(psth.range == [-2, 3]))
t, counts = psth.hist_values(style='elastic')
self.assertTrue(np.all(psth._bin_edges == np.arange(-2, 4)))
self.assertTrue(np.all(psth._trials == np.array([1, 2, 2, 2, 1])))
self.assertTrue(np.all(counts == np.array([0, 0, 0, 0.5, 1.0])))
def testElastic(self):
psth = PSTH(F_SAMP=1000.,
adjusted_spike_times=[1, 2, 4],
t_starts=[8, 19],
t_stops=[12, 23],
t_centers=[10, 20],
binwidth=.001)
self.assertTrue(np.all(psth.range == [-2, 3]))
t, counts = psth.hist_values(style='elastic')
self.assertTrue(np.all(psth._bin_edges == np.arange(-2, 4)))
self.assertTrue(np.all(psth._trials == np.array([1, 2, 2, 2, 1])))
self.assertTrue(np.all(counts == np.array([0, 0, 0, 0.5, 1.0])))
def testWithSpuriousSpike(self):
# Same as testHistValues, but with an extra spike that is outside
# of any trial, so the results should be the same.
# Create a PSTH
psth = PSTH(F_SAMP=1000.,
adjusted_spike_times=[1, 2, 3],
n_trials=2, range=(-2, 2),
nbins=4)
t, counts = psth.hist_values(style='rigid')
# Bin edges stretch across range, inclusively
self.assertTrue(np.all(psth._bin_edges == np.arange(-2, 3)))
self.assertTrue(np.all(counts == np.array([0, 0, 0, 1.0])))
def testHistValues(self):
# Simple example
# Two trials, extending from -2 to +2 (centered, inclusive)
# Two spikes, at +1 and +2 (centered)
# Create a PSTH
psth = PSTH(F_SAMP=1000.,
adjusted_spike_times=[1, 2],
n_trials=2, range=(-2, 2),
nbins=4)
t, counts = psth.hist_values(style='rigid')
# Bin edges stretch across range, inclusively
self.assertTrue(np.all(psth._bin_edges == np.arange(-2, 3)))
self.assertTrue(np.all(counts == np.array([0, 0, 0, 1.0])))
def testWiderBins(self):
# Same as testHistValues, but now the bins are wider so that
# a trial might cover only half of it.
psth = PSTH(F_SAMP=1000.,
adjusted_spike_times=[1, 2, 4],
t_starts=[8, 19], t_stops=[12, 23], t_centers=[10, 20],
nbins=2)
self.assertTrue(np.all(psth.range == [-2, 3]))
t, counts = psth.hist_values(style='elastic')
# Wider bins covering the same range
self.assertTrue(np.all(psth._bin_edges == np.array([-2, .5, 3])))
# Each trial is only partly contained by one of the bins
self.assertTrue(np.all(psth._trials == np.array([5, 3])))
self.assertTrue(np.all(counts == np.array([0., 5/3.])))
def testWithSpuriousSpike(self):
# Same as testHistValues, but with an extra spike that is outside
# of any trial, so the results should be the same.
# Note that a spike at time 3 would be included in the last bin,
# which is not strictly correct because the t_stop is not inclusive.
psth = PSTH(F_SAMP=1000.,
adjusted_spike_times=[1, 2, 4],
t_starts=[8, 19],
t_stops=[12, 23],
t_centers=[10, 20],
nbins=5)
self.assertTrue(np.all(psth.range == [-2, 3]))
t, counts = psth.hist_values(style='elastic')
self.assertTrue(np.all(psth._bin_edges == np.arange(-2, 4)))
self.assertTrue(np.all(psth._trials == np.array([1, 2, 2, 2, 1])))
self.assertTrue(np.all(counts == np.array([0, 0, 0, 0.5, 1.0])))
def testWithSpuriousSpike(self):
# Same as testHistValues, but with an extra spike that is outside
# of any trial, so the results should be the same.
# Create a PSTH
psth = PSTH(F_SAMP=1000.,
adjusted_spike_times=[1, 2, 3],
n_trials=2,
range=(-2, 2),
nbins=4)
t, counts = psth.hist_values(style='rigid')
# Bin edges stretch across range, inclusively
self.assertTrue(np.all(psth._bin_edges == np.arange(-2, 3)))
self.assertTrue(np.all(counts == np.array([0, 0, 0, 1.0])))
def testHistValues(self):
# Simple example
# Two trials, extending from -2 to +2 (centered, inclusive)
# Two spikes, at +1 and +2 (centered)
# Create a PSTH
psth = PSTH(F_SAMP=1000.,
adjusted_spike_times=[1, 2],
n_trials=2,
range=(-2, 2),
nbins=4)
t, counts = psth.hist_values(style='rigid')
# Bin edges stretch across range, inclusively
self.assertTrue(np.all(psth._bin_edges == np.arange(-2, 3)))
self.assertTrue(np.all(counts == np.array([0, 0, 0, 1.0])))
def testWiderBins(self):
# Same as testHistValues, but now the bins are wider so that
# a trial might cover only half of it.
psth = PSTH(F_SAMP=1000.,
adjusted_spike_times=[1, 2, 4],
t_starts=[8, 19],
t_stops=[12, 23],
t_centers=[10, 20],
nbins=2)
self.assertTrue(np.all(psth.range == [-2, 3]))
t, counts = psth.hist_values(style='elastic')
# Wider bins covering the same range
self.assertTrue(np.all(psth._bin_edges == np.array([-2, .5, 3])))
# Each trial is only partly contained by one of the bins
self.assertTrue(np.all(psth._trials == np.array([5, 3])))
self.assertTrue(np.all(counts == np.array([0., 5 / 3.])))
def testElasticWiderBins(self):
# Now bins are specified to be 2ms wide.
# Trial 1: -2 to 1 (closed)
# Trial 2: -1 to 2 (closed)
# Spikes: +1, +2
# Thus the bins are [-2,0), [0, 2), [2, 4]
# The middle bin includes one spike and two trials, so
# 0.5 spike/trial/bin.
# The last bin includes one spike and only half a trial, because
# one trial extends through half of it, so
# 2 spike/trial/bin
psth = PSTH(F_SAMP=1000.,
adjusted_spike_times=[1, 2],
t_starts=[8, 19], t_stops=[12, 23], t_centers=[10, 20],
binwidth=.002)
self.assertTrue(np.all(psth.range == [-2, 4]))
t, counts = psth.hist_values(style='elastic')
self.assertTrue(np.all(psth.range == [-2, 4]))
self.assertTrue(np.all(psth._bin_edges == np.array([-2, 0, 2, 4])))
self.assertTrue(np.all(psth._trials == np.array([3, 4, 1])))
self.assertTrue(np.all(counts == np.array([0, 0.5, 2.])))
