def stplot(self, img, fs=None, drawnow=True, **kwargs):
#kwargs['colorbar'] = kwargs.get('colorbar', True)
if img.shape[0] != self.size:
raise ValueError(
"number of rows in image should match number of channels (=%d)"
% self.size)
import SigTools
pylab = SigTools.Plotting.load_pylab()
t = numpy.arange(img.shape[1], dtype=numpy.float64)
if fs == None:
x = None
xlabel = 'time-sample index'
else:
x = t = SigTools.samples2msec(t, fs)
xlabel = 'time (msec)'
x = None
pylab.subplot(121)
h = SigTools.Plotting.imagesc(img,
x=x,
aspect='auto',
drawnow=False,
picker=5,
**kwargs)
ax = pylab.gca()
if x == None and fs != None:
xl = ax.get_xlim()
xt = numpy.array(
[x for x in ax.get_xticks() if min(xl) <= x <= max(xl)])
xtl = ['%g' % x for x in SigTools.samples2msec(xt, fs)]
ax.set(xticks=xt, xticklabels=xtl)
ax.set(
xlabel=xlabel,
yticks=range(img.shape[0]),
yticklabels=['%d: %s' % x for x in enumerate(self.get_labels())])
ax.grid(True)
h.channels = self
h.img = numpy.asarray(img)
h.timebase = t
h.spaceax = pylab.subplot(222)
h.timeax = pylab.subplot(224)
def onpick(evt):
col = int(round(evt.mouseevent.xdata))
row = int(round(evt.mouseevent.ydata))
h = evt.artist
pylab.axes(h.spaceax)
h.channels.plot(h.img[:, col], clim=h.get_clim(), drawnow=False)
pylab.axes(h.timeax)
SigTools.plot(h.timebase, h.img[row], drawnow=False)
pylab.gca().set(ylim=h.get_clim(),
xlim=(h.timebase[0], h.timebase[-1]))
pylab.draw()
pylab.gcf().canvas.mpl_connect('pick_event', onpick)
if drawnow: pylab.draw()
return h
def PlotSCD( files='*.pk' ): import pylab if isinstance( files, basestring ): if os.path.isdir( files ): files = os.path.join( files, '*.pk' ) files = glob.glob( files ) d = DataFiles.load( files ) r = SigTools.correlate( d['x'], d['y'], axis=0 ) SigTools.imagesc( r*numpy.abs(r), y=d['channels'], x=SigTools.samples2msec( range( r.shape[1] ), d['fs'] ), aspect='auto', balance=0.0, colorbar=True ) pylab.title( ', '.join( [ '%d: %d' % ( yi, ( d['y'] == yi ).sum() ) for yi in numpy.unique( d['y'] ) ] ) ) pylab.draw()
def PlotTrials( files='*.pk', channel='Cz' ): import pylab if isinstance( files, basestring ): if os.path.isdir( files ): files = os.path.join( files, '*.pk' ) files = glob.glob( files ) d = DataFiles.load( files ) chind = d[ 'channels' ].index( channel ) v = [ ( d[ 'y' ][ i ], i, vi ) for i, vi in enumerate( d[ 'x' ][ :, chind, : ] ) ] v = numpy.array( [ vi for yi, i, vi in sorted( v ) ] ) SigTools.imagesc( v, x=SigTools.samples2msec( range( v.shape[1] ), d['fs'] ), aspect='auto', balance=0.0, colorbar=True ) pylab.title( ', '.join( [ '%d: %d' % ( yi, ( d['y'] == yi ).sum() ) for yi in numpy.unique( d['y'] ) ] ) + ( ' (channel %s)' % channel ) ) pylab.draw()
def stplot(self, img, fs=None, drawnow=True, **kwargs):
#kwargs['colorbar'] = kwargs.get('colorbar', True)
if img.shape[0] != self.size: raise ValueError("number of rows in image should match number of channels (=%d)" % self.size)
import SigTools
pylab = SigTools.Plotting.load_pylab()
t = numpy.arange(img.shape[1], dtype=numpy.float64)
if fs == None: x = None; xlabel = 'time-sample index'
else: x = t = SigTools.samples2msec(t, fs); xlabel = 'time (msec)'
x = None
pylab.subplot(121)
h = SigTools.Plotting.imagesc(img, x=x, aspect='auto', drawnow=False, picker=5, **kwargs)
ax = pylab.gca()
if x == None and fs != None:
xl = ax.get_xlim()
xt = numpy.array([x for x in ax.get_xticks() if min(xl)<=x<=max(xl)])
xtl = ['%g' % x for x in SigTools.samples2msec(xt, fs)]
ax.set(xticks=xt, xticklabels=xtl)
ax.set(xlabel=xlabel, yticks=range(img.shape[0]), yticklabels=['%d: %s' % x for x in enumerate(self.get_labels())])
ax.grid(True)
h.channels = self
h.img = numpy.asarray(img)
h.timebase = t
h.spaceax = pylab.subplot(222)
h.timeax = pylab.subplot(224)
def onpick(evt):
col = int(round(evt.mouseevent.xdata))
row = int(round(evt.mouseevent.ydata))
h = evt.artist
pylab.axes(h.spaceax)
h.channels.plot(h.img[:,col], clim=h.get_clim(), drawnow=False)
pylab.axes(h.timeax)
SigTools.plot(h.timebase, h.img[row], drawnow=False)
pylab.gca().set(ylim=h.get_clim(), xlim=(h.timebase[0],h.timebase[-1]))
pylab.draw()
pylab.gcf().canvas.mpl_connect('pick_event', onpick)
if drawnow: pylab.draw()
return h
def PlotSCD(files='*.pk'):
import pylab
if isinstance(files, basestring):
if os.path.isdir(files): files = os.path.join(files, '*.pk')
files = glob.glob(files)
d = DataFiles.load(files)
r = SigTools.correlate(d['x'], d['y'], axis=0)
SigTools.imagesc(r * numpy.abs(r),
y=d['channels'],
x=SigTools.samples2msec(range(r.shape[1]), d['fs']),
aspect='auto',
balance=0.0,
colorbar=True)
pylab.title(', '.join([
'%d: %d' % (yi, (d['y'] == yi).sum()) for yi in numpy.unique(d['y'])
]))
pylab.draw()
def PlotTrials(files='*.pk', channel='Cz'):
import pylab
if isinstance(files, basestring):
if os.path.isdir(files): files = os.path.join(files, '*.pk')
files = glob.glob(files)
d = DataFiles.load(files)
chind = d['channels'].index(channel)
v = [(d['y'][i], i, vi) for i, vi in enumerate(d['x'][:, chind, :])]
v = numpy.array([vi for yi, i, vi in sorted(v)])
SigTools.imagesc(v,
x=SigTools.samples2msec(range(v.shape[1]), d['fs']),
aspect='auto',
balance=0.0,
colorbar=True)
pylab.title(', '.join(
['%d: %d' % (yi, (d['y'] == yi).sum())
for yi in numpy.unique(d['y'])]) + (' (channel %s)' % channel))
pylab.draw()
def ClassifyERPs (
featurefiles,
C = (10.0, 1.0, 0.1, 0.01),
gamma = (1.0, 0.8, 0.6, 0.4, 0.2, 0.0),
keepchan = (),
rmchan = (),
rmchan_usualsuspects = ('AUDL','AUDR','LAUD','RAUD','SYNC','VSYNC', 'VMRK', 'OLDREF'),
rebias = True,
save = False,
select = False,
description='ERPs to attended vs unattended events',
maxcount=None,
classes=None,
folds=None,
time_window=None,
keeptrials=None,
):
file_inventory = []
d = DataFiles.load(featurefiles, catdim=0, maxcount=maxcount, return_details=file_inventory)
if isinstance(folds, basestring) and folds.lower() in ['lofo', 'loro', 'leave on run out', 'leave one file out']:
n, folds = 0, []
for each in file_inventory:
neach = each[1]['x']
folds.append(range(n, n+neach))
n += neach
if 'x' not in d: raise ValueError("found no trial data - no 'x' variable - in the specified files")
if 'y' not in d: raise ValueError("found no trial labels - no 'y' variable - in the specified files")
x = d['x']
y = numpy.array(d['y'].flat)
if keeptrials != None:
x = x[numpy.asarray(keeptrials), :, :]
y = y[numpy.asarray(keeptrials)]
if time_window != None:
fs = d['fs']
t = SigTools.samples2msec(numpy.arange(x.shape[2]), fs)
x[:, :, t<min(time_window)] = 0
x[:, :, t>max(time_window)] = 0
if classes != None:
for cl in classes:
if cl not in y: raise ValueError("class %s is not in the dataset" % str(cl))
mask = numpy.array([yi in classes for yi in y])
y = y[mask]
x = x[mask]
discarded = sum(mask==False)
if discarded: print "discarding %d trials that are outside the requested classes %s"%(discarded,str(classes))
n = len(y)
uy = numpy.unique(y)
if uy.size != 2: raise ValueError("expected 2 classes in dataset, found %d : %s" % (uy.size, str(uy)))
for uyi in uy:
nyi = sum([yi==uyi for yi in y])
nyi_min = 2
if nyi < nyi_min: raise ValueError('only %d exemplars of class %s - need at least %d' % (nyi,str(uyi),nyi_min))
y = numpy.sign(y - uy.mean())
cov,trchvar = SigTools.spcov(x=x, y=y, balance=False, return_trchvar=True) # NB: symwhitenkern would not be able to balance
starttime = time.time()
chlower = [ch.lower() for ch in d['channels']]
if keepchan in [None,(),'',[]]:
if isinstance(rmchan, basestring): rmchan = rmchan.split()
if isinstance(rmchan_usualsuspects, basestring): rmchan_usualsuspects = rmchan_usualsuspects.split()
allrmchan = [ch.lower() for ch in list(rmchan)+list(rmchan_usualsuspects)]
unwanted = numpy.array([ch in allrmchan for ch in chlower])
notfound = [ch for ch in rmchan if ch.lower() not in chlower]
else:
if isinstance(keepchan, basestring): keepchan = keepchan.split()
lowerkeepchan = [ch.lower() for ch in keepchan]
unwanted = numpy.array([ch not in lowerkeepchan for ch in chlower])
notfound = [ch for ch in keepchan if ch.lower() not in chlower]
wanted = numpy.logical_not(unwanted)
print ' '
if len(notfound): print "WARNING: could not find channel%s %s\n" % ({1:''}.get(len(notfound),'s'), ', '.join(notfound))
removed = [ch for removing,ch in zip(unwanted, d['channels']) if removing]
if len(removed): print "removed %d channel%s (%s)" % (len(removed), {1:''}.get(len(removed),'s'), ', '.join(removed))
print "classification will be based on %d channel%s" % (sum(wanted), {1:''}.get(sum(wanted),'s'))
print "%d negatives + %d positives = %d exemplars" % (sum(y<0), sum(y>0), n)
print ' '
x[:, unwanted, :] = 0
cov[:, unwanted] = 0
cov[unwanted, :] = 0
nu = numpy.asarray(cov).diagonal()[wanted].mean()
for i in range(len(cov)):
if cov[i,i] == 0: cov[i,i] = nu
if not isinstance(C, (tuple,list,numpy.ndarray,type(None))): C = [C]
if not isinstance(gamma, (tuple,list,numpy.ndarray,type(None))): gamma = [gamma]
c = SigTools.klr2class(lossfunc=SigTools.balanced_loss, relcost='balance')
c.varyhyper({})
if c != None: c.hyper.C=list(C)
if gamma == None: c.hyper.kernel.func = SigTools.linkern
else: c.varyhyper({'kernel.func':SigTools.symwhitenkern, 'kernel.cov':[cov], 'kernel.gamma':list(gamma)})
c.cvtrain(x=x, y=y, folds=folds)
if rebias: c.rebias()
c.calibrate()
chosen = c.cv.chosen.hyper
if gamma == None:
Ps = None
Gp = c.featureweight(x=x)
else:
Ps = SigTools.svd(SigTools.shrinkcov(cov, copy=True, gamma=chosen.kernel.gamma)).isqrtm
xp = SigTools.spfilt(x, Ps.H, copy=True)
Gp = c.featureweight(x=xp)
u = SigTools.stfac(Gp, Ps)
u.channels = d['channels']
u.channels_used = wanted
u.fs = d['fs']
u.trchvar = trchvar
try: u.channels = SigTools.ChannelSet(u.channels)
except: print 'WARNING: failed to convert channels to ChannelSet'
elapsed = time.time() - starttime
minutes = int(elapsed/60.0)
seconds = int(round(elapsed - minutes * 60.0))
print '%d min %d sec' % (minutes, seconds)
datestamp = time.strftime('%Y-%m-%d %H:%M:%S')
csummary = '%s (%s) trained on %d (CV %s = %.3f) at %s' % (
c.__class__.__name__,
SigTools.experiment()._shortdesc(chosen),
sum(c.input.istrain),
c.loss.func.__name__,
c.loss.train,
datestamp,
)
description = 'binary classification of %s: %s' % (description, csummary)
u.description = description
if save or select:
if not isinstance(save, basestring):
save = featurefiles
if isinstance(save, (tuple,list)): save = save[-1]
if save.lower().endswith('.gz'): save = save[:-3]
if save.lower().endswith('.pk'): save = save[:-3]
save = save + '_weights.prm'
print "\nsaving %s\n" % save
Parameters.Param(u.G.A, Name='ERPClassifierWeights', Section='PythonSig', Subsection='Epoch', Comment=csummary).write_to(save)
Parameters.Param(c.model.bias, Name='ERPClassifierBias', Section='PythonSig', Subsection='Epoch', Comment=csummary).append_to(save)
Parameters.Param(description, Name='SignalProcessingDescription', Section='PythonSig').append_to(save)
if select:
if not isinstance(select, basestring): select = 'ChosenWeights.prm'
if not os.path.isabs(select): select = os.path.join(os.path.split(save)[0], select)
print "saving %s\n" % select
import shutil; shutil.copyfile(save, select)
print description
return u,c
def ClassifyERPs(
featurefiles,
C=(10.0, 1.0, 0.1, 0.01),
gamma=(1.0, 0.8, 0.6, 0.4, 0.2, 0.0),
keepchan=(),
rmchan=(),
rmchan_usualsuspects=('AUDL', 'AUDR', 'LAUD', 'RAUD', 'SYNC', 'VSYNC',
'VMRK', 'OLDREF'),
rebias=True,
save=False,
select=False,
description='ERPs to attended vs unattended events',
maxcount=None,
classes=None,
folds=None,
time_window=None,
keeptrials=None,
):
file_inventory = []
d = DataFiles.load(featurefiles,
catdim=0,
maxcount=maxcount,
return_details=file_inventory)
if isinstance(folds, basestring) and folds.lower() in [
'lofo', 'loro', 'leave on run out', 'leave one file out'
]:
n, folds = 0, []
for each in file_inventory:
neach = each[1]['x']
folds.append(range(n, n + neach))
n += neach
if 'x' not in d:
raise ValueError(
"found no trial data - no 'x' variable - in the specified files")
if 'y' not in d:
raise ValueError(
"found no trial labels - no 'y' variable - in the specified files")
x = d['x']
y = numpy.array(d['y'].flat)
if keeptrials != None:
x = x[numpy.asarray(keeptrials), :, :]
y = y[numpy.asarray(keeptrials)]
if time_window != None:
fs = d['fs']
t = SigTools.samples2msec(numpy.arange(x.shape[2]), fs)
x[:, :, t < min(time_window)] = 0
x[:, :, t > max(time_window)] = 0
if classes != None:
for cl in classes:
if cl not in y:
raise ValueError("class %s is not in the dataset" % str(cl))
mask = numpy.array([yi in classes for yi in y])
y = y[mask]
x = x[mask]
discarded = sum(mask == False)
if discarded:
print "discarding %d trials that are outside the requested classes %s" % (
discarded, str(classes))
n = len(y)
uy = numpy.unique(y)
if uy.size != 2:
raise ValueError("expected 2 classes in dataset, found %d : %s" %
(uy.size, str(uy)))
for uyi in uy:
nyi = sum([yi == uyi for yi in y])
nyi_min = 2
if nyi < nyi_min:
raise ValueError(
'only %d exemplars of class %s - need at least %d' %
(nyi, str(uyi), nyi_min))
y = numpy.sign(y - uy.mean())
cov, trchvar = SigTools.spcov(
x=x, y=y, balance=False,
return_trchvar=True) # NB: symwhitenkern would not be able to balance
starttime = time.time()
chlower = [ch.lower() for ch in d['channels']]
if keepchan in [None, (), '', []]:
if isinstance(rmchan, basestring): rmchan = rmchan.split()
if isinstance(rmchan_usualsuspects, basestring):
rmchan_usualsuspects = rmchan_usualsuspects.split()
allrmchan = [
ch.lower() for ch in list(rmchan) + list(rmchan_usualsuspects)
]
unwanted = numpy.array([ch in allrmchan for ch in chlower])
notfound = [ch for ch in rmchan if ch.lower() not in chlower]
else:
if isinstance(keepchan, basestring): keepchan = keepchan.split()
lowerkeepchan = [ch.lower() for ch in keepchan]
unwanted = numpy.array([ch not in lowerkeepchan for ch in chlower])
notfound = [ch for ch in keepchan if ch.lower() not in chlower]
wanted = numpy.logical_not(unwanted)
print ' '
if len(notfound):
print "WARNING: could not find channel%s %s\n" % ({
1: ''
}.get(len(notfound), 's'), ', '.join(notfound))
removed = [ch for removing, ch in zip(unwanted, d['channels']) if removing]
if len(removed):
print "removed %d channel%s (%s)" % (len(removed), {
1: ''
}.get(len(removed), 's'), ', '.join(removed))
print "classification will be based on %d channel%s" % (sum(wanted), {
1: ''
}.get(sum(wanted), 's'))
print "%d negatives + %d positives = %d exemplars" % (sum(y < 0),
sum(y > 0), n)
print ' '
x[:, unwanted, :] = 0
cov[:, unwanted] = 0
cov[unwanted, :] = 0
nu = numpy.asarray(cov).diagonal()[wanted].mean()
for i in range(len(cov)):
if cov[i, i] == 0: cov[i, i] = nu
if not isinstance(C, (tuple, list, numpy.ndarray, type(None))): C = [C]
if not isinstance(gamma, (tuple, list, numpy.ndarray, type(None))):
gamma = [gamma]
c = SigTools.klr2class(lossfunc=SigTools.balanced_loss, relcost='balance')
c.varyhyper({})
if c != None: c.hyper.C = list(C)
if gamma == None: c.hyper.kernel.func = SigTools.linkern
else:
c.varyhyper({
'kernel.func': SigTools.symwhitenkern,
'kernel.cov': [cov],
'kernel.gamma': list(gamma)
})
c.cvtrain(x=x, y=y, folds=folds)
if rebias: c.rebias()
c.calibrate()
chosen = c.cv.chosen.hyper
if gamma == None:
Ps = None
Gp = c.featureweight(x=x)
else:
Ps = SigTools.svd(
SigTools.shrinkcov(cov, copy=True,
gamma=chosen.kernel.gamma)).isqrtm
xp = SigTools.spfilt(x, Ps.H, copy=True)
Gp = c.featureweight(x=xp)
u = SigTools.stfac(Gp, Ps)
u.channels = d['channels']
u.channels_used = wanted
u.fs = d['fs']
u.trchvar = trchvar
try:
u.channels = SigTools.ChannelSet(u.channels)
except:
print 'WARNING: failed to convert channels to ChannelSet'
elapsed = time.time() - starttime
minutes = int(elapsed / 60.0)
seconds = int(round(elapsed - minutes * 60.0))
print '%d min %d sec' % (minutes, seconds)
datestamp = time.strftime('%Y-%m-%d %H:%M:%S')
csummary = '%s (%s) trained on %d (CV %s = %.3f) at %s' % (
c.__class__.__name__,
SigTools.experiment()._shortdesc(chosen),
sum(c.input.istrain),
c.loss.func.__name__,
c.loss.train,
datestamp,
)
description = 'binary classification of %s: %s' % (description, csummary)
u.description = description
if save or select:
if not isinstance(save, basestring):
save = featurefiles
if isinstance(save, (tuple, list)): save = save[-1]
if save.lower().endswith('.gz'): save = save[:-3]
if save.lower().endswith('.pk'): save = save[:-3]
save = save + '_weights.prm'
print "\nsaving %s\n" % save
Parameters.Param(u.G.A,
Name='ERPClassifierWeights',
Section='PythonSig',
Subsection='Epoch',
Comment=csummary).write_to(save)
Parameters.Param(c.model.bias,
Name='ERPClassifierBias',
Section='PythonSig',
Subsection='Epoch',
Comment=csummary).append_to(save)
Parameters.Param(description,
Name='SignalProcessingDescription',
Section='PythonSig').append_to(save)
if select:
if not isinstance(select, basestring): select = 'ChosenWeights.prm'
if not os.path.isabs(select):
select = os.path.join(os.path.split(save)[0], select)
print "saving %s\n" % select
import shutil
shutil.copyfile(save, select)
print description
return u, c
