def load_sound_stims(files,
root="",
windowtime=0.016,
ovl=0.0016,
f_min=500,
f_max=8000,
gammatone=False,
dsample=10,
sres=15,
compress=0):
stims = []
durations = []
for f in files:
Fs, wave = read(root + f)
duration = int(1000 * len(wave) / Fs)
durations.append(duration)
if gammatone:
Pxx = gg.gtgram(wave, Fs, windowtime, ovl, sres, f_min)
Pxx = np.log10(Pxx)
else:
w = np.hanning(int(windowtime * Fs))
Pxx = libtfr.stft(wave, w, int(w.size * .1))
freqs, ind = libtfr.fgrid(Fs, w.size, [f_min, f_max])
Pxx = Pxx[ind, :]
Pxx = np.log10(Pxx + compress)
Pxx = resample(Pxx, sres)
Pxx = resample(Pxx, duration / dsample, axis=1)
stims.append(Pxx)
return stims, durations
def __init__(self,
dataset,
t_step_ms=1,
win_size=512,
window_name='Hann',
freq_min=0,
freq_max=10000,
*args,
**kwargs):
super(spectrogram, self).__init__(*args, **kwargs)
self.dataset = dataset
self.selection = None #contains pg.LinearRegionItem representing selection if not None
#getting spectrogram settings
sr = float(dataset.attrs['sampling_rate'])
t_step = int(float(t_step_ms) * sr / 1000.) #time step in samples
if window_name == "Hann":
window = scipy.signal.hann(win_size)
elif window_name == "Bartlett":
window = scipy.signal.bartlett(win_size)
elif window_name == "Blackman":
window = scipy.signal.blackman(win_size)
elif window_name == "Boxcar":
window = scipy.signal.boxcar(win_size)
elif window_name == "Hamming":
window = scipy.signal.hamming(win_size)
elif window_name == "Parzen":
window = scipy.signal.parzen(win_size)
#computing and interpolating image
Pxx = libtfr.stft(dataset, w=window, step=t_step)
Pxx[Pxx == 0] = np.min(
Pxx[Pxx != 0]) #ensures that log won't give -inf
spec = np.log(Pxx.T)
res_factor = 1.0 #factor by which resolution is increased
# spec = interpolate_spectrogram(spec, res_factor=res_factor)
#making color lookup table
pos = np.linspace(0, 1, 6)
color = np.array(
[[0, 0, 255, 255], [0, 255, 255, 255], [0, 255, 0, 255],
[255, 255, 0, 255], [255, 0, 0, 255], [100, 0, 0, 255]],
dtype=np.ubyte)
color_map = pg.ColorMap(pos, color)
lut = color_map.getLookupTable(0.0, 1.0, 256)
self.img = pg.ImageItem(spec, lut=lut)
#img.setLevels((-5, 10))
self.addItem(self.img)
image_scale = t_step / sr / res_factor
self.img.setScale(image_scale)
df = sr / float(win_size)
plot_scale = df / res_factor / image_scale
self.getAxis('left').setScale(plot_scale)
xmax = float(dataset.size) / dataset.attrs['sampling_rate']
self.setXRange(0, xmax)
self.setYRange(freq_min / plot_scale, freq_max / plot_scale)
self.setMouseEnabled(x=True, y=False)
self.win_size = win_size #saving values for export selection function
self.t_step = t_step
def specgram(x, NFFT=256, shift=128, Fs=1.0, drange=60,
ax=None, cmap=mplt.cm.gray_r, **kwargs):
from numpy import hanning
from libtfr import stft, fgrid, tgrid, dynamic_range
w = hanning(NFFT)
S = stft(x, w, shift)
F,ind = fgrid(Fs,NFFT,(0,Fs/2))
T = tgrid(x.size, Fs, shift)
S = nx.log10(dynamic_range(S, drange))
if ax is None: ax = mplt.gca()
ax.imshow(S, extent = (T[0],T[-1],F[0]-0.01,F[-1]), cmap=cmap, **kwargs)
return S
def specgram(x, NFFT=256, shift=128, Fs=1.0, drange=60,
ax=None, cmap=mplt.cm.gray_r, **kwargs):
from numpy import hanning
from libtfr import stft, fgrid, tgrid, dynamic_range
w = hanning(NFFT)
S = stft(x, w, shift)
F,ind = fgrid(Fs,NFFT,(0,Fs/2))
T = tgrid(x.size, Fs, shift)
S = nx.log10(dynamic_range(S, drange))
if ax is None: ax = mplt.gca()
ax.imshow(S, extent = (T[0],T[-1],F[0]-0.01,F[-1]), cmap=cmap, **kwargs)
return S
def __init__(self, dataset, t_step_ms=1, win_size=512, window_name='Hann', freq_min=0,
freq_max=10000, *args, **kwargs):
super(spectrogram, self).__init__(*args, **kwargs)
self.dataset = dataset
self.selection = None #contains pg.LinearRegionItem representing selection if not None
#getting spectrogram settings
sr = float(dataset.attrs['sampling_rate'])
t_step = int(float(t_step_ms) * sr/1000.) #time step in samples
if window_name == "Hann":
window = scipy.signal.hann(win_size)
elif window_name == "Bartlett":
window = scipy.signal.bartlett(win_size)
elif window_name == "Blackman":
window = scipy.signal.blackman(win_size)
elif window_name == "Boxcar":
window = scipy.signal.boxcar(win_size)
elif window_name == "Hamming":
window = scipy.signal.hamming(win_size)
elif window_name == "Parzen":
window = scipy.signal.parzen(win_size)
#computing and interpolating image
Pxx = libtfr.stft(dataset,w=window,step=t_step)
Pxx[Pxx==0] = np.min(Pxx[Pxx!=0]) #ensures that log won't give -inf
spec = np.log(Pxx.T)
res_factor = 1.0 #factor by which resolution is increased
# spec = interpolate_spectrogram(spec, res_factor=res_factor)
#making color lookup table
pos = np.linspace(0,1,6)
color = np.array([[0,0,255,255],[0,255,255,255],[0,255,0,255],
[255,255,0,255],[255,0,0,255],[100,0,0,255]], dtype=np.ubyte)
color_map = pg.ColorMap(pos,color)
lut = color_map.getLookupTable(0.0,1.0,256)
self.img = pg.ImageItem(spec,lut=lut)
#img.setLevels((-5, 10))
self.addItem(self.img)
image_scale = t_step/sr/res_factor
self.img.setScale(image_scale)
df = sr/float(win_size)
plot_scale = df/res_factor/image_scale
self.getAxis('left').setScale(plot_scale)
xmax = float(dataset.size)/dataset.attrs['sampling_rate']
self.setXRange(0, xmax)
self.setYRange(freq_min/plot_scale, freq_max/plot_scale)
self.setMouseEnabled(x=True, y=False)
self.win_size = win_size #saving values for export selection function
self.t_step = t_step
def linspect(self, signal, Fs, nfft=None):
""" Calculate the spectrogram on a linear power scale. """
import numpy as nx
from libtfr import stft, tfr_spec, tgrid
shift = int(self.options['window_shift'] * Fs)
if not nfft:
Np = int(Fs * self.options['window_len'])
nfft = int(2 ** nx.ceil(nx.log2(Np)))
else:
Np = nfft
if self.options['spec_method'] == 'tfr':
S = tfr_spec(signal, nfft, shift, Np,
K=self.options['tfr_order'], tm=self.options['tfr_tm'],
flock=self.options['tfr_flock'], tlock=self.options['tfr_tlock'])
else:
try:
wfun = getattr(nx, self.options['spec_method'])
w = wfun(Np)
except Exception, e:
raise Error("invalid window function {}: {}".format(self.options['spec_method'], e))
S = stft(signal, w, shift, nfft)
def plot_dataset_list(self, dataset_list, data_layout, append=False):
''' plots a list of datasets to a data layout'''
data_layout.clear()
if not append:
self.subplots = []
# rasterQPainterPath = QtGui.QPainterPath().addRect(-.1,-5,.2,1) # TODO make a better raster
# shape that works
toes = []
for dataset in dataset_list:
print(dataset)
if 'datatype' not in dataset.attrs.keys():
print('{} is not an arf dataset'.format(repr(dataset)))
if os.path.basename(dataset.name) == 'jill_log':
print(dataset.value)
continue
'''sampled data'''
if dataset.attrs['datatype'] < 1000: # sampled data
if (self.settings_panel.oscillogram_check.checkState()
==QtCore.Qt.Checked):
pl = downsamplePlot(dataset, title=dataset.name,
name=str(len(self.subplots)))
data_layout.addItem(pl,row=len(self.subplots), col=0)
pl.setXRange(0, dataset.size/float(dataset.attrs['sampling_rate']))
pl.setYRange(np.min(dataset), np.max(dataset))
self.subplots.append(pl)
pl.showGrid(x=True, y=True)
''' simple events '''
elif utils.is_simple_event(dataset):
if dataset.attrs['units'] == 'ms':
data = dataset.value / 1000.
elif dataset.attrs['units'] == 'samples':
data = dataset.value / dataset.attrs['sampling_rate']
else:
data = dataset.value
if (self.settings_panel.raster_check.checkState()==QtCore.Qt.Checked or
self.settings_panel.psth_check.checkState()==QtCore.Qt.Checked or
self.settings_panel.isi_check.checkState()==QtCore.Qt.Checked):
toes.append(data)
continue
''' complex event '''
elif utils.is_complex_event(dataset):
if (self.settings_panel.label_check.checkState()
==QtCore.Qt.Checked):
#creating new extensible dataset if not extensible
if dataset.maxshape != (None,):
data = dataset[:]
name = dataset.name
group= dataset.parent
attributes = dataset.attrs
del group[name]
del dataset
dataset = arf.create_dataset(group, name, data,
maxshape=(None,),**attributes)
pl = labelPlot(dataset, title=dataset.name, name=str(len(self.subplots)))
data_layout.addItem(pl, row=len(self.subplots), col=0)
pl.showLabel('left', show=False)
self.subplots.append(pl)
else:
print('I don\'t know how to plot {} of type {} \
with datatype {}'.format(dataset,
type(dataset),
dataset.attrs['datatype']))
continue
'''adding spectrograms'''
if dataset.attrs['datatype'] in [0, 1]: # show spectrogram
if (self.settings_panel.spectrogram_check.checkState()
==QtCore.Qt.Checked):
#getting spectrogram settings
sr = float(dataset.attrs['sampling_rate'])
win_size_text = self.settings_panel.win_size.text()
t_step_text = self.settings_panel.step.text()
min_text = self.settings_panel.freq_min.text()
max_text = self.settings_panel.freq_max.text()
if win_size_text:
win_size = int(float(win_size_text))
else:
win_size = self.settings_panel.defaults['win_size']
self.settings_panel.win_size.setText(str(win_size))
if t_step_text:
t_step = int(float(t_step_text) * sr/1000.)
else:
t_step = self.settings_panel.defaults['step']
self.settings_panel.win_size.setText(str(int(tstep*1000)))
if min_text:
freq_min = int(min_text)
else:
freq_min = self.settings_panel.defaults['freq_min']
self.settings_panel.freq_min.setText(str(freq_min))
if max_text:
freq_max = int(max_text)
else:
freq_max = self.settings_panel.defaults['freq_max']
self.settings_panel.freq_max.setText(str(freq_max))
window_name = self.settings_panel.window.currentText()
if window_name == "Hann":
window = scipy.signal.hann(win_size)
elif window_name == "Bartlett":
window = scipy.signal.bartlett(win_size)
elif window_name == "Blackman":
window = scipy.signal.blackman(win_size)
elif window_name == "Boxcar":
window = scipy.signal.boxcar(win_size)
elif window_name == "Hamming":
window = scipy.signal.hamming(win_size)
elif window_name == "Parzen":
window = scipy.signal.parzen(win_size)
#computing and interpolating image
Pxx = libtfr.stft(dataset,w=window,step=t_step)
spec = np.log(Pxx.T)
res_factor = 1.0 #factor by which resolution is increased
# spec = interpolate_spectrogram(spec, res_factor=res_factor)
#making color lookup table
pos = np.linspace(0,1,7)
color = np.array([[100,100,255,255],[0,0,255,255],[0,255,255,255],[0,255,0,255],
[255,255,0,255],[255,0,0,255],[100,0,0,255]], dtype=np.ubyte)
color_map = pg.ColorMap(pos,color)
lut = color_map.getLookupTable(0.0,1.0,256)
img = pg.ImageItem(spec,lut=lut)
#img.setLevels((-5, 10))
pl = data_layout.addPlot(name=str(len(self.subplots)), row=len(self.subplots), col=0)
self.subplots.append(pl)
pl.addItem(img)
image_scale = t_step/sr/res_factor
img.setScale(image_scale)
df = sr/float(win_size)
plot_scale = df/res_factor/image_scale
pl.getAxis('left').setScale(plot_scale)
pl.setXRange(0, dataset.size / dataset.attrs['sampling_rate'])
pl.setYRange(freq_min/plot_scale, freq_max/plot_scale)
pl.setMouseEnabled(x=True, y=False)
if toes:
if self.settings_panel.raster_check.checkState()==QtCore.Qt.Checked:
pl= rasterPlot(toes)
data_layout.addItem(pl, row=len(self.subplots), col=0)
pl.showLabel('left', show=False)
self.subplots.append(pl)
if self.settings_panel.psth_check.checkState()==QtCore.Qt.Checked:
all_toes = np.zeros(sum(len(t) for t in toes))
k=0
for t in toes:
all_toes[k:k+len(t)] = t
k += len(t)
if self.settings_panel.psth_bin_size.text():
bin_size = float(self.settings_panel.psth_bin_size.text())/1000.
else:
bin_size = .01
bins = np.arange(all_toes.min(),all_toes.max()+bin_size,bin_size)
y,x = np.histogram(all_toes,bins=bins)
psth = pg.PlotCurveItem(x, y, stepMode=True,
fillLevel=0, brush=(0, 0, 255, 80))
pl = data_layout.addPlot(row=len(self.subplots), col=0)
pl.addItem(psth)
pl.setMouseEnabled(y=False)
self.subplots.append(pl)
if self.settings_panel.isi_check.checkState()==QtCore.Qt.Checked:
isis = np.zeros(sum(len(t)-1 for t in toes))
k=0
for t in toes:
isis[k:k+len(t)-1] = np.diff(t)
k += len(t)-1
if self.settings_panel.psth_bin_size.text():
bin_size = float(self.settings_panel.psth_bin_size.text())/1000.
else:
bin_size = .01
bins = np.arange(isis.min(),isis.max()+bin_size,bin_size)
y,x = np.histogram(isis,bins=bins,normed=True)
isi_hist = pg.PlotCurveItem(x, y, stepMode=True,
fillLevel=0, brush=(0, 0, 255, 80))
pl = data_layout.addPlot(row=len(self.subplots), col=0)
pl.addItem(isi_hist)
pl.setMouseEnabled(y=False)
self.subplots.append(pl)
'''linking x axes'''
masterXLink = None
for pl in self.subplots:
if not masterXLink:
masterXLink = pl
pl.setXLink(masterXLink)
def __init__(self, dataset, settings_panel, *args, **kwargs):
super(spectrogram, self).__init__(*args, **kwargs)
self.dataset = dataset
self.settings_panel = settings_panel
#getting spectrogram settings
sr = float(dataset.attrs['sampling_rate'])
win_size_text = settings_panel.win_size.text()
t_step_text = settings_panel.step.text()
min_text = settings_panel.freq_min.text()
max_text = settings_panel.freq_max.text()
if win_size_text:
win_size = int(float(win_size_text))
else:
win_size = settings_panel.defaults['win_size']
settings_panel.win_size.setText(str(win_size))
if t_step_text:
t_step = int(float(t_step_text) * sr/1000.)
else:
t_step = settings_panel.defaults['step']
settings_panel.win_size.setText(str(int(tstep*1000)))
if min_text:
freq_min = int(min_text)
else:
freq_min = settings_panel.defaults['freq_min']
settings_panel.freq_min.setText(str(freq_min))
if max_text:
freq_max = int(max_text)
else:
freq_max = settings_panel.defaults['freq_max']
settings_panel.freq_max.setText(str(freq_max))
window_name = settings_panel.window.currentText()
if window_name == "Hann":
window = scipy.signal.hann(win_size)
elif window_name == "Bartlett":
window = scipy.signal.bartlett(win_size)
elif window_name == "Blackman":
window = scipy.signal.blackman(win_size)
elif window_name == "Boxcar":
window = scipy.signal.boxcar(win_size)
elif window_name == "Hamming":
window = scipy.signal.hamming(win_size)
elif window_name == "Parzen":
window = scipy.signal.parzen(win_size)
#computing and interpolating image
Pxx = libtfr.stft(dataset,w=window,step=t_step)
spec = np.log(Pxx.T)
res_factor = 1.0 #factor by which resolution is increased
# spec = interpolate_spectrogram(spec, res_factor=res_factor)
#making color lookup table
pos = np.linspace(0,1,7)
color = np.array([[100,100,255,255],[0,0,255,255],[0,255,255,255],[0,255,0,255],
[255,255,0,255],[255,0,0,255],[100,0,0,255]], dtype=np.ubyte)
color_map = pg.ColorMap(pos,color)
lut = color_map.getLookupTable(0.0,1.0,256)
img = pg.ImageItem(spec,lut=lut)
#img.setLevels((-5, 10))
self.addItem(img)
image_scale = t_step/sr/res_factor
img.setScale(image_scale)
df = sr/float(win_size)
plot_scale = df/res_factor/image_scale
self.getAxis('left').setScale(plot_scale)
self.setXRange(0, dataset.size / dataset.attrs['sampling_rate'])
self.setYRange(freq_min/plot_scale, freq_max/plot_scale)
self.setMouseEnabled(x=True, y=False)