def stp_magnitude(tau,
u,
u2=None,
tau2=None,
urat=0.5,
fs=100,
A=0.5,
quick_eval=False):
""" compute effect of stp (tau,u) on a dummy signal and computer effect magnitude
"""
c = len(tau)
seg = np.int(fs * 0.05)
pred = np.concatenate([
np.zeros([c, seg * 2]),
np.ones([c, seg * 4]) * A / 2,
np.zeros([c, seg * 4]),
np.ones([c, seg]) * A,
np.zeros([c, seg]),
np.ones([c, seg]) * A,
np.zeros([c, seg]),
np.ones([c, seg]) * A,
np.zeros([c, seg * 2])
],
axis=1)
kwargs = {
'data': pred,
'name': 'pred',
'recording': 'rec',
'chans': ['chan' + str(n) for n in range(c)],
'fs': fs,
'meta': {},
}
pred = signal.RasterizedSignal(**kwargs)
r = recording.Recording({'pred': pred})
if tau2 is None:
r = stp.short_term_plasticity(r,
'pred',
'pred_out',
u=u,
tau=tau,
quick_eval=quick_eval)
else:
r = stp.short_term_plasticity2(r,
'pred',
'pred_out',
u=u,
tau=tau,
u2=u2,
tau2=tau2,
urat=urat,
quick_eval=quick_eval)
pred_out = r[0]
stp_mag = (
np.sum(pred.as_continuous() - pred_out.as_continuous(), axis=1) /
np.sum(pred.as_continuous()))
return (stp_mag, pred, pred_out)
def test_stp():
nchans = 1
fs = 100
data = np.concatenate([np.zeros([1, 10]), np.ones([1, 20]),
np.zeros([1, 20]), np.ones([1, 5]), np.zeros([1, 5]),
np.ones([1, 5]), np.zeros([1, 5]),
np.ones([1, 5]), np.zeros([1, 10])], axis=1)
kwargs = {
'data': data,
'name': 'pred',
'recording': 'rec',
'chans': ['chan' + str(n) for n in range(nchans)],
'fs': fs,
'meta': {
'for_testing': True,
'date': "2018-01-10",
'animal': "Donkey Hotey",
'windmills': 'tilting'
},
}
pred = signal.RasterizedSignal(**kwargs)
rec = recording.Recording({'pred': pred})
u = np.array([5.0])
tau = np.array([8.0])
r = stp.short_term_plasticity(rec, 'pred', 'pred_out', u=u, tau=tau)
pred_out = r[0]
def load_sadagopan(cellid='MS_u0004_f0025',
recname='MS_u0004',
stimfile=None,
respfile=None,
epochsfile=None,
fs=50,
channel_num=0,
**context):
"""
example file from Sadagopan lab
"""
if stimfile is None:
stimfile = signals_dir / (cellid + '_stim.csv.gz')
if respfile is None:
respfile = signals_dir / (cellid + '_resp.csv.gz')
if epochsfile is None:
epochsfile = signals_dir / (cellid + '_epochs.csv')
X = np.loadtxt(gzip.open(stimfile, mode='rb'), delimiter=",", skiprows=0)
Y = np.loadtxt(gzip.open(respfile, mode='rb'), delimiter=",", skiprows=0)
# get list of stimuli with start and stop times (in sec)
epochs = pd.read_csv(epochsfile)
# create NEMS-format recording objects from the raw data
resp = RasterizedSignal(fs,
Y,
'resp',
recname,
chans=[cellid],
epochs=epochs.loc[:])
stim = RasterizedSignal(fs, X, 'stim', recname, epochs=epochs.loc[:])
# create the recording object from the signals
signals = {'resp': resp, 'stim': stim}
rec = recording.Recording(signals)
return {'rec': rec}
# download demo data
recording.get_demo_recordings(signals_dir)
datafile = signals_dir / 'TAR010c-18-1.pkl'
# LOAD AND FORMAT RECORDING DATA
with open(datafile, 'rb') as f:
#cellid, recname, fs, X, Y, X_val, Y_val = pickle.load(f)
cellid, recname, fs, X, Y, epochs = pickle.load(f)
# create NEMS-format recording objects from the raw data
resp = RasterizedSignal(fs, Y, 'resp', recname, chans=[cellid])
stim = RasterizedSignal(fs, X, 'stim', recname)
# create the recording object from the signals
signals = {'resp': resp, 'stim': stim}
est = recording.Recording(signals)
val_signals = {
'resp': RasterizedSignal(fs, Y_val, 'resp', recname, chans=[cellid]),
'stim': RasterizedSignal(fs, X_val, 'stim', recname)
}
val = recording.Recording(val_signals)
# INITIALIZE MODELSPEC
log.info('Initializing modelspec...')
# Method #1: create from "shorthand" keyword string
#modelspec_name = 'wc.18x1.g-fir.1x15-lvl.1' # very simple linear model
#modelspec_name = 'wc.18x2.g-fir.2x15-lvl.1' # another simple model
modelspec_name = 'wc.18x2.g-fir.2x15-lvl.1-dexp.1' # constrain spectral tuning to be gaussian, add static output NL
Y = np.loadtxt(gzip.open(respfile, mode='rb'), delimiter=",", skiprows=0)
# get list of stimuli with start and stop times (in sec)
epochs = pd.read_csv(epochsfile)
# create NEMS-format recording objects from the raw data
resp = RasterizedSignal(fs,
Y,
'resp',
recname,
chans=[cellid],
epochs=epochs.loc[:])
stim = RasterizedSignal(fs, X, 'stim', recname, epochs=epochs.loc[:])
# create the recording object from the signals
signals = {'resp': resp, 'stim': stim}
rec = recording.Recording(signals)
#generate est/val set_sets
#nfolds=10
#est = rec.jackknife_masks_by_time(njacks=nfolds, invert=False) #VATSUN - doesnt work
#val = rec.jackknife_masks_by_time(njacks=nfolds, invert=True)
est, val = rec.split_at_time(
fraction=0.1) # VATSUN: Fraction=0.1 I think specifies the validation set
# INITIALIZE MODELSPEC
log.info('Initializing modelspec...')
# Method #1: create from "shorthand" keyword string
modelspec_name = 'fir.18x10-lvl.1-dexp.1' # "canonical" linear STRF + nonlinearity
def test_cell_fit_cellwise():
# gets test recording, as would be the output of CPP preprocesing
testfile = '/home/mateo/code/context_probe_analysis/pickles/BRT037b'
# testfile = 'C:\\Users\\Mateo\\Science\\David_lab\\code\\context_probe_analysis\\pickles\\BRT037b' # path for blade
rec = jl.load(testfile)
# ToDo split into estimation validation sets
subsets = {'est': rec, 'val': rec}
# basic modelspec, weighted channels, linear filter and DC shift
modelspec_name = 'wc.2x2.g-fir.2x15-lvl.1'
modelspec_name = 'fir.2x15-lvl.1'
# iterates over each cell, creating a new stim recording containing the response of all other cells in the population
ntime_modspecs = list()
for ii, cellid in enumerate(rec.meta['cellid']):
print('working on cell {}/{}, {}'.format(ii + 1,
len(rec.meta['cellid']),
cellid))
working_sets = dict()
# does the recording construction for each data set
for key, subset in subsets.items():
stim = subset['stim'].rasterize()
resp = subset['resp'].rasterize()
# splits the response into the cell to be fitted and the cells to use as predictors
this_cell_resp = np.expand_dims(resp._data[ii, :], 0)
other_cells_resp = np.delete(resp._data, ii, axis=0)
# build signals with modified _data
resp = resp._modified_copy(data=this_cell_resp)
signals = {'stim': stim, 'resp': resp}
# makes into a recording
mod_rec = recording.Recording(signals)
# adds metadata, e
this_cell_meta = rec.meta.copy()
this_cell_meta['cellid'] = [cellid]
mod_rec.meta = this_cell_meta
# orders in etimation validation sets
working_sets[key] = mod_rec
est = working_sets['est']
val = working_sets['val']
# parses some data from rec meta into the analysis meta
analysis_meta = {
'modelspec_name': modelspec_name,
'recording': None,
**this_cell_meta
}
modelspec = nems.initializers.from_keywords(modelspec_name,
meta=analysis_meta)
# prefits the dc_shift
modelspec = nems.initializers.prefit_to_target(
est,
modelspec,
nems.analysis.api.fit_basic,
target_module='levelshift',
fitter=scipy_minimize,
fit_kwargs={'options': {
'ftol': 1e-4,
'maxiter': 500
}})
# then fit full nonlinear model
modelspecs = nems.analysis.api.fit_basic(est,
modelspec,
fitter=scipy_minimize)
# ----------------------------------------------------------------------------
# GENERATE SUMMARY STATISTICS
# generate predictions
est, val = nems.analysis.api.generate_prediction(est, val, modelspecs)
# evaluate prediction accuracy
modelspecs = nems.analysis.api.standard_correlation(
est, val, modelspecs)
ntime_modspecs.append(modelspecs)
print("Performance: r_fit={0:.3f} r_test={1:.3f}".format(
modelspecs[0][0]['meta']['r_fit'][0],
modelspecs[0][0]['meta']['r_test'][0]))
return ntime_modspecs