def _transform(self,
var,
model='spm',
derivative=False,
dispersion=False,
fir_delays=None):
model = model.lower()
if isinstance(var, SparseRunVariable):
sr = self.collection.sampling_rate
var = var.to_dense(sr)
df = var.to_df(entities=False)
onsets = df['onset'].values
vals = df[['onset', 'duration', 'amplitude']].values.T
if model in ['spm', 'glover']:
if derivative:
model += ' + derivative'
if dispersion:
model += ' + dispersion'
elif model != 'fir':
raise ValueError("Model must be one of 'spm', 'glover', or 'fir'.")
convolved = hrf.compute_regressor(vals,
model,
onsets,
fir_delays=fir_delays,
min_onset=0)
return DenseRunVariable(var.name, convolved[0], var.run_info,
var.source, var.sampling_rate)
def _transform(self,
var,
model='spm',
derivative=False,
dispersion=False,
fir_delays=None):
model = model.lower()
df = var.to_df(entities=False)
if isinstance(var, SparseRunVariable):
sampling_rate = self.collection.sampling_rate
dur = var.get_duration()
resample_frames = np.linspace(0,
dur,
int(math.ceil(dur * sampling_rate)),
endpoint=False)
else:
resample_frames = df['onset'].values
sampling_rate = var.sampling_rate
vals = df[['onset', 'duration', 'amplitude']].values.T
if model in ['spm', 'glover']:
if derivative:
model += ' + derivative'
if dispersion:
model += ' + dispersion'
elif model != 'fir':
raise ValueError("Model must be one of 'spm', 'glover', or 'fir'.")
# Minimum interval between event onsets/duration
# Used to compute oversampling factor to prevent information loss
unique_onsets = np.unique(np.sort(df.onset))
if len(unique_onsets) > 1:
min_interval = min(
np.ediff1d(unique_onsets).min(), df.duration.min())
oversampling = np.ceil(2 * (1 / (min_interval * sampling_rate)))
else:
oversampling = 2
convolved = hrf.compute_regressor(vals,
model,
resample_frames,
fir_delays=fir_delays,
min_onset=0,
oversampling=oversampling)
return DenseRunVariable(name=var.name,
values=convolved[0],
run_info=var.run_info,
source=var.source,
sampling_rate=sampling_rate)
def _transform(self,
var,
model='spm',
derivative=False,
dispersion=False,
fir_delays=None):
model = model.lower()
df = var.to_df(entities=False)
if isinstance(var, SparseRunVariable):
sampling_rate = self.collection.sampling_rate
dur = var.get_duration()
resample_frames = np.linspace(0,
dur,
int(math.ceil(dur * sampling_rate)),
endpoint=False)
safety = 2 # Double frequency to resolve events
else:
resample_frames = df['onset'].values
sampling_rate = var.sampling_rate
safety = 1 # Maximum signal resolution is already 0.5 * SR
vals = df[['onset', 'duration', 'amplitude']].values.T
if model in ['spm', 'glover']:
if derivative:
model += ' + derivative'
if dispersion:
model += ' + dispersion'
elif model != 'fir':
raise ValueError("Model must be one of 'spm', 'glover', or 'fir'.")
# Sampling at >100Hz will never be useful, but can be wildly expensive
max_freq, min_interval = 100, 0.01
# Sampling at <1Hz can degrade signals
min_freq, max_interval = 1, 1
# Given the sampling rate, determine an oversampling factor to ensure that
# events can be modeled with reasonable precision
unique_onsets = np.unique(df.onset)
unique_durations = np.unique(df.duration)
# Align existing data ticks with, event onsets and offsets, up to ms resolution
# Note that GCD ignores zeros, so 0 onsets and impulse responses (0 durations) do
# not harm this.
required_resolution = _fractional_gcd(np.concatenate(
(unique_onsets, unique_durations)),
res=min_interval)
# Bound the effective sampling rate between min_freq and max_freq
effective_sr = max(min_freq, min(safety / required_resolution,
max_freq))
convolved = hrf.compute_regressor(vals,
model,
resample_frames,
fir_delays=fir_delays,
min_onset=0,
oversampling=np.ceil(effective_sr /
sampling_rate))
return DenseRunVariable(name=var.name,
values=convolved[0],
run_info=var.run_info,
source=var.source,
sampling_rate=sampling_rate)