def zoom(self, event):
newxlim = numpy.array(self.sp_iq.get_xlim())
curxlim = numpy.array(self.xlim)
if (newxlim[0] != curxlim[0] or newxlim[1] != curxlim[1]):
self.xlim = newxlim
#xmin = max(0, int(ceil(self.sample_rate*(self.xlim[0] - self.position))))
#xmax = min(int(ceil(self.sample_rate*(self.xlim[1] - self.position))), len(self.iq))
xmin = max(0, int(ceil(self.sample_rate * (self.xlim[0]))))
xmax = min(int(ceil(self.sample_rate * (self.xlim[1]))),
len(self.iq))
iq = self.iq[xmin:xmax]
time = self.time[xmin:xmax]
iq_fft = self.dofft(iq)
freq = self.calc_freq(time, self.sample_rate)
self.plot_fft[0].set_data(freq, iq_fft)
self.sp_fft.axis(
[freq.min(),
freq.max(),
iq_fft.min() - 10,
iq_fft.max() + 10])
draw()
def hacerfft(channel):
tamanho = len(channel)
fdata = fft(channel)
print('> FFT realizada')
nUniquePts = int(ceil((tamanho)/2))
fdata = fdata[0:nUniquePts]
fdata = abs(fdata)
fdata = fdata/float(leng)
fdata = fdata**2
if leng % 2 > 0:
fdata[1:int(ceil(len(fdata)))] = fdata[1:int(ceil(len(fdata)))] * 2
else:
fdata[1:int(ceil(len(fdata)))-1] = fdata[1:int(ceil(len(fdata)))-1] * 2
freqArray = arange(0, nUniquePts, 1.0)*(fs/tamanho)
plot(freqArray/1000, 10*log10(fdata[0:tamanho:1]))
xlabel('Frequency (kHz)')
ylabel('Power (dB)')
plt.show()
print('> FFT graficada')
return fdata
def hacerfft(channel, texto=None):
fdata = fft(channel)
print('\t> FFT realizada')
nUniquePts = int(ceil((leng) / 2))
fdata = fdata[0:nUniquePts]
fdata = abs(fdata)
fdata = fdata / float(leng)
fdata = fdata**2
if leng % 2 > 0:
fdata[1:int(ceil(len(fdata)))] = fdata[1:int(ceil(len(fdata)))] * 2
else:
fdata[1:int(ceil(len(fdata))) -
1] = fdata[1:int(ceil(len(fdata))) - 1] * 2
freqArray = arange(0, nUniquePts, 1.0) * (fs / leng)
plot(freqArray / 1000, 10 * log10(fdata[0:leng:1]))
if texto == None:
xlabel('Frequency (kHz)')
else:
xlabel('Frequency (kHz) | ' + str(texto))
ylabel('Power (dB)')
plt.show()
print('\t> FFT graficada')
return fdata, freqArray
def hacerfft(channel, freq): # en Hz
fdata = fft(channel)
print('> FFT realizada: ' + str(freq))
nUniquePts = int(ceil((N) / 2))
fdata = fdata[0:nUniquePts]
fdata = abs(fdata)
fdata = fdata / float(N)
fdata = fdata**2
if N % 2 > 0:
fdata[1:int(ceil(len(fdata)))] = fdata[1:int(ceil(len(fdata)))] * 2
else:
fdata[1:int(ceil(len(fdata))) -
1] = fdata[1:int(ceil(len(fdata))) - 1] * 2
freqArray = arange(0, nUniquePts, 1.0) * (fs / N)
plot(freqArray, 10 * log10(fdata[0:int(N):1]))
xlabel('Frequency (Hz)')
ylabel('Power (dB)')
plt.show()
print('> FFT graficada ' + str(freq))
return fdata
def printTrack( fid , resized , frame , pos , sz ):
p0 = [pos[0]-pylab.floor(sz[0]/2),pos[1]-pylab.ceil(sz[1]/2)]
p1 = [pos[0]+pylab.floor(sz[0]/2),pos[1]+pylab.ceil(sz[1]/2)]
if resized:
p0 = [x*2 for x in p0]
p1 = [x*2 for x in p1]
fid.write(str(frame)+","+str(p0[1])+","+str(p0[0])+","+str(p1[1])+","+str(p1[0])+"\n")
def generate_cord():
"""
TODO: Pass the parameters as input arguments.
Parameters:
- Fs : sampling frequency
- F0 : frequency of the notes forming chord
- gain : gains of individual notes in the chord
- duration : duration of the chord in second
- alpha : attenuation in KS algorithm
"""
Fs = 48000
# D2, D3, F3, G3, F4, A4, C5, G5
F0 = 440 * pylab.array(
[2**-(31.0/12), 2**-(19.0/12), 2**-(16.0/12), 2**(-14.0/12),
2**-(4.0/12), 1.0, 2**(3.0/12), 2**(10.0/12)])
gain = [1.2, 3.0, 1.0, 2.2, 1.0, 1.0, 1.0, 3.5]
duration = 4.0
alpha = 0.9785
# Number of samples in the chord.
nbsample_chord = Fs * duration
# This is used to correct alpha later, so that all the notes
# decay together (with the same decay rate).
first_duration = pylab.ceil(nbsample_chord / pylab.round_(Fs/F0[0]))
# Initialization.
chord = pylab.zeros(nbsample_chord)
for i, f in enumerate(F0):
print("Working on %g / %g" % (i+1, len(F0)))
# Get M and duration parameter.
current_M = pylab.round_(Fs/f)
current_duration = pylab.ceil(nbsample_chord / current_M)
# Correct current alpha so that all the notes decay together
# (with the same decay rate)
current_alpha = alpha ** (first_duration / current_duration)
# Let Paul's high D on the bass ring a bit longer.
if i == 1:
current_alpha = current_alpha ** 0.8
# Generate input and output of KS algorithm.
x = pylab.rand(current_M)
y = ks(x, current_alpha, int(current_duration))
y = y[:int(nbsample_chord)]
# Construct the chord by adding the generated note (with the
# appropriate gain).
chord = chord + gain[i] * y
return Fs, duration, chord
def get_rejection(data, department):
# print('department {0} data: {1}'.format(department, len(data)))
data.sort()
q1 = median([i[0] for i in data][:int(ceil(len(data) / 2))])
q3 = median([i[0] for i in data][int(ceil(len(data) / 2)):])
# left = q1 - 1.5 * (q3 - q1)
left = 1
right = q3 + 1.5 * (q3 - q1)
rejection = set(i[1] for i in data if right < i[0] or i[0] < left)
# print('bad amount = {0}'.format(len(rejection)))
# print('bad percent = {0}'.format(100 * len(rejection) / len(data)))
return rejection
def circular_conv(x,h):
P = len(h)
n_ = int(ceil(log2(P)))
h_ = np.concatenate((h,np.zeros(int(2**n_)-P)))
P = len(h_)
n1 = int(ceil(len(x)/2**n_))
x_ = np.concatenate((x,np.zeros(n1*(int(2**n_))-len(x))))
y = np.zeros(len(x_)+len(h_)-1)
for i in range(n1):
temp = np.concatenate((x_[i*P:(i+1)*P],np.zeros(P-1)))
y[i*P:(i+1)*P+P-1] += np.fft.ifft(np.fft.fft(temp)*np.fft.fft(np.concatenate((h_,np.zeros(len(temp)-len(h_)))))).real
return y
def inject(self, simulation, time, dtlast):
#outer_wall = int((time-dtlast)/self.time_between_walls)+1
#inner_wall = int(time/self.time_between_walls)
outer_wall = int(ceil((time-dtlast)/self.time_between_walls))
inner_wall = int(ceil(time/self.time_between_walls)-1)
inner_handled_wall = inner_wall+self.handled_walls
s = ''
for i in range(inner_handled_wall, inner_wall, -1):
self.inject_wall(simulation, i, time, self.particles_per_wall*(inner_handled_wall-i), boundary=True)
for i in range(inner_wall, outer_wall-1, -1):
npart = simulation.get_npart()
self.inject_wall(simulation, i, time, npart, boundary=False)
def plot_spike_histogram(spikes, bin=0.1, total_neurons=None):
print 'Plotting activity histogram.'
global figure_dir
pylab.figure(get_free_figure_number())
pylab.clf()
pylab.hist([spike[0] for spike in spikes],
bins=pylab.ceil(max([spike[0] for spike in spikes])/bin))
if total_neurons is not None:
pylab.ylim([0, total_neurons])
pylab.xlim([0., pylab.ceil(max([spike[0] for spike in spikes]))])
pylab.xlabel('Time, ms')
pylab.ylabel('Amount of active neurons')
pylab.title('Average network activity')
pylab.savefig(os.path.join(figure_dir, 'activity.png'))
def getAvgGreenTime(intergreen1, intergreen2):
doc = libxml2.parseFile('tls.out')
lNS = doc.xpathEval("count(/tls-states/tlsstate[@phase='0'])")
lWE = doc.xpathEval("count(/tls-states/tlsstate[@phase='2'])")
lIG1 = doc.xpathEval("count(/tls-states/tlsstate[@phase='1'])")
lIG2 = doc.xpathEval("count(/tls-states/tlsstate[@phase='3'])")
doc.freeDoc()
greenNS = lNS / ceil((lIG1 / intergreen1))
greenWE = lWE / ceil((lIG2 / intergreen2))
return greenWE, greenNS
def imshow(self,shape,only=None):
from pylab import subplot,imshow,cm,title,sqrt,ceil
if only is None:
only=list(range(len(self.weights)))
L=len(only)
c=ceil(sqrt(L))
r=ceil(L/c)
for i,idx in enumerate(only):
w=self.weights[idx]
w=w.reshape(shape)
subplot(r,c,i+1)
imshow(w,cmap=cm.gray,interpolation='nearest')
title('PC %d' % (idx))
def old_spike_psth(data, t1_ms=-250., t2_ms=0., bin_ms=10):
"""Uses data format returned by get_spikes"""
spike_time_ms = data['spike times ms']
N_trials = data['trials']
t2_ms = pylab.ceil((t2_ms - t1_ms) / bin_ms) * bin_ms + t1_ms
N_bins = (t2_ms - t1_ms) / bin_ms
if N_trials > 0:
all_spikes_ms = pylab.array([], dtype=float)
for trial in range(len(spike_time_ms)):
if spike_time_ms[trial] is None:
continue
idx = pylab.find((spike_time_ms[trial] >= t1_ms)
& (spike_time_ms[trial] <= t2_ms))
all_spikes_ms = \
pylab.concatenate((all_spikes_ms, spike_time_ms[trial][idx]))
spike_n_bin, bin_edges = \
pylab.histogram(all_spikes_ms, bins = N_bins,
range = (t1_ms, t2_ms), new = True)
spikes_per_trial_in_bin = spike_n_bin / float(N_trials)
spike_rate = 1000 * spikes_per_trial_in_bin / bin_ms
else:
spike_rate = pylab.nan
bin_center_ms = (bin_edges[1:] + bin_edges[:-1]) / 2.0
return spike_rate, bin_center_ms
def spike_psth(spike_time_ms, t1_ms=-50., t2_ms=250., bin_ms=1):
"""."""
N_trials = len(spike_time_ms)
t2_ms = pylab.ceil((t2_ms - t1_ms) / bin_ms) * bin_ms + t1_ms
N_bins = (t2_ms - t1_ms) / bin_ms
spike_count_by_trial = pylab.zeros((N_trials, N_bins), dtype=float)
if N_trials > 0:
all_spikes_ms = pylab.array([], dtype=float)
for trial in range(len(spike_time_ms)):
if spike_time_ms[trial] is None:
continue
idx = pylab.find((spike_time_ms[trial] >= t1_ms)
& (spike_time_ms[trial] <= t2_ms))
spike_count_by_trial[trial,:], bin_edges = \
pylab.histogram(spike_time_ms[trial][idx], bins = N_bins,
range = (t1_ms, t2_ms))
spike_rate = 1000 * spike_count_by_trial.mean(axis=0) / bin_ms
else:
spike_rate = pylab.nan
dummy, bin_edges = \
pylab.histogram(None, bins = N_bins, range = (t1_ms, t2_ms))
bin_center_ms = (bin_edges[1:] + bin_edges[:-1]) / 2.0
return spike_rate, spike_count_by_trial, bin_center_ms
def plot_viz_of_stochs(vars, viz_func, figsize=(8, 6)):
""" Plot autocorrelation for all stochs in a dict or dict of dicts
:Parameters:
- `vars` : dictionary
- `viz_func` : visualazation function such as ``acorr``, ``show_trace``, or ``hist``
- `figsize` : tuple, size of figure
"""
pl.figure(figsize=figsize)
cells, stochs = tally_stochs(vars)
# for each stoch, make an autocorrelation plot for each dimension
rows = pl.floor(pl.sqrt(cells))
cols = pl.ceil(cells / rows)
tile = 1
for s in sorted(stochs, key=lambda s: s.__name__):
trace = s.trace()
if len(trace.shape) == 1:
trace = trace.reshape((len(trace), 1))
for d in range(len(pl.atleast_1d(s.value))):
pl.subplot(rows, cols, tile)
viz_func(pl.atleast_2d(trace)[:, d])
pl.title('\n\n%s[%d]' % (s.__name__, d),
va='top',
ha='center',
fontsize=8)
tile += 1
def panel():
global Ras, Rms, Ie, Ies
global tstart
global pan, t0, t1
#Pulse start time
tstart = 0.1
#Ras = [1.,500.,20.] #Ohm*cm
#Rms = [200.,10000.,200.] #Ohm*cm^2
Ras = [5.0, 500.0, 50.0] #Ohm*cm
Rms = [200.0, 10000.0, 1000.0] #Ohm*cm^2
Ie = 4. #nA
Ies = pl.c_[pl.ones_like(ns.t)]
Ies[:pl.ceil(tstart / ns.dt)] = 0.
t0 = 0.101
t1 = 0.6
pan = simulationpanel.SimulationPanel()
pan.Move((640, 600))
pan.setdict(globals())
pan.addcommand('sim()')
pan.addcommand('plottao()')
pan.addvar('Ras')
pan.addvar('Rms')
pan.addvar('Ie')
pan.addvar('t0')
pan.addvar('t1')
def performFourierDataReturn(self, wav_name, input_location=None):
if input_location == None:
input_location = ''
if wav_name.endswith('.wav'):
wav_file_name = os.path.join(
os.path.join(__location__, input_location), wav_name)
else:
wav_file_name = os.path.join(
os.path.join(__location__, input_location), wav_name) + '.wav'
sampFreq, snd = wavfile.read(wav_file_name)
# convert 16 bit values to be between -1 to 1
snd /= 2.0**15
# get average of data if more than 1 channels
if self.channels > 1:
s1 = self.getAverageData(snd)
else:
s1 = snd.T[0]
n = len(s1)
p = fft(s1)
nUniquePts = int(ceil((n + 1) / 2.0))
p = p[0:nUniquePts]
p = abs(p)
p /= float(n)
p **= 2
if n % 2 > 0:
p[1:len(p)] = p[1:len(p)] * 2
else:
p[1:len(p) - 1] = p[1:len(p) - 1] * 2
return sampFreq, nUniquePts, n, p
def plot_viz_of_stochs(vars, viz_func, figsize=(8,6)):
""" Plot autocorrelation for all stochs in a dict or dict of dicts
:Parameters:
- `vars` : dictionary
- `viz_func` : visualazation function such as ``acorr``, ``show_trace``, or ``hist``
- `figsize` : tuple, size of figure
"""
pl.figure(figsize=figsize)
cells, stochs = tally_stochs(vars)
# for each stoch, make an autocorrelation plot for each dimension
rows = pl.floor(pl.sqrt(cells))
cols = pl.ceil(cells/rows)
tile = 1
for s in sorted(stochs, key=lambda s: s.__name__):
trace = s.trace()
if len(trace.shape) == 1:
trace = trace.reshape((len(trace), 1))
for d in range(len(pl.atleast_1d(s.value))):
pl.subplot(rows, cols, tile)
viz_func(pl.atleast_2d(trace)[:, d])
pl.title('\n\n%s[%d]'%(s.__name__, d), va='top', ha='center', fontsize=8)
tile += 1
def stack_vectors(data, win=1, hop=1, zero_pad=True):
"""
::
create an overlapping stacked vector sequence from a series of vectors
data - row-wise multidimensional data to stack
win - number of consecutive vectors to stack [1]
hop - number of vectors to advance per stack [1]
zero_pad - zero pad if incomplete stack at end
"""
data = pylab.atleast_2d(data)
nrows, dim = data.shape
hop = min(hop, nrows)
nvecs = nrows / int(hop) if not zero_pad else int(
pylab.ceil(nrows / float(hop)))
features = pylab.zeros((nvecs, win * dim))
i = 0
while i < nrows - win + 1:
features[i / hop, :] = data[i:i + win, :].reshape(1, -1)
i += hop
if i / hop < nvecs:
x = data[i::, :].reshape(1, -1)
features[i / hop, :] = pylab.c_[x,
pylab.zeros(
(1, win * dim - x.shape[1]))]
return features
def decodefft(finf, data, dropheights=False):
#output: decoded data with the number of heights reduced
#two variables are added to the finfo class:
#deco_num_hei, deco_hrange
#data must be arranged:
# (channels,heights,times) (C-style, profs change faster)
#fft along the entire(n=None) acquired heights(axis=1), stores in data
num_chan = data.shape[0]
num_ipps = data.shape[2]
num_codes = finf.subcode.shape[0]
num_bauds = finf.subcode.shape[1]
NSA = finf.num_hei + num_bauds - 1
uppower = py.ceil(py.log2(NSA))
extra = int(2**uppower - finf.num_hei)
NSA = int(2**uppower)
fft_code = py.fft(finf.subcode, n=NSA, axis=1).conj()
data = py.fft(data, n=NSA,
axis=1) #n= None: no cropped data or padded zeros
for ch in range(num_chan):
for ipp in range(num_ipps):
code_i = ipp % num_codes
data[ch, :, ipp] = data[ch, :, ipp] * fft_code[code_i, :]
data = py.ifft(data, n=NSA, axis=1) #fft along the heightsm
if dropheights:
return data[:, :-extra - (num_bauds - 1), :]
else:
return data[:, :-extra, :]
def old_spike_psth(data, t1_ms = -250., t2_ms = 0., bin_ms = 10):
"""Uses data format returned by get_spikes"""
spike_time_ms = data['spike times ms']
N_trials = data['trials']
t2_ms = pylab.ceil((t2_ms - t1_ms) / bin_ms)*bin_ms + t1_ms
N_bins = (t2_ms - t1_ms) / bin_ms
if N_trials > 0:
all_spikes_ms = pylab.array([],dtype=float)
for trial in range(len(spike_time_ms)):
if spike_time_ms[trial] is None:
continue
idx = pylab.find((spike_time_ms[trial] >= t1_ms) &
(spike_time_ms[trial] <= t2_ms))
all_spikes_ms = \
pylab.concatenate((all_spikes_ms, spike_time_ms[trial][idx]))
spike_n_bin, bin_edges = \
pylab.histogram(all_spikes_ms, bins = N_bins,
range = (t1_ms, t2_ms), new = True)
spikes_per_trial_in_bin = spike_n_bin/float(N_trials)
spike_rate = 1000*spikes_per_trial_in_bin/bin_ms
else:
spike_rate = pylab.nan
bin_center_ms = (bin_edges[1:] + bin_edges[:-1])/2.0
return spike_rate, bin_center_ms
def spike_psth(spike_time_ms, t1_ms = -50., t2_ms = 250., bin_ms = 1):
"""."""
N_trials = len(spike_time_ms)
t2_ms = pylab.ceil((t2_ms - t1_ms) / bin_ms)*bin_ms + t1_ms
N_bins = (t2_ms - t1_ms) / bin_ms
spike_count_by_trial = pylab.zeros((N_trials,N_bins),dtype=float)
if N_trials > 0:
all_spikes_ms = pylab.array([],dtype=float)
for trial in range(len(spike_time_ms)):
if spike_time_ms[trial] is None:
continue
idx = pylab.find((spike_time_ms[trial] >= t1_ms) &
(spike_time_ms[trial] <= t2_ms))
spike_count_by_trial[trial,:], bin_edges = \
pylab.histogram(spike_time_ms[trial][idx], bins = N_bins,
range = (t1_ms, t2_ms))
spike_rate = 1000*spike_count_by_trial.mean(axis=0)/bin_ms
else:
spike_rate = pylab.nan
dummy, bin_edges = \
pylab.histogram(None, bins = N_bins, range = (t1_ms, t2_ms))
bin_center_ms = (bin_edges[1:] + bin_edges[:-1])/2.0
return spike_rate, spike_count_by_trial, bin_center_ms
def NI_init_ctr(self, intTime=100):
# intTime in milliseconds
frequency = int(pl.ceil(1.0e7 / float(intTime)))
self.trig = Trigger(0, frequency)
self.trig.StartTask()
self.ctr = InputCounter(self.trig.get_term(), 1)
self.voltT = VoltOut('/Weetabix/ao0', self.trig.get_term())
def decodefft(finf,data, dropheights = False):
#output: decoded data with the number of heights reduced
#two variables are added to the finfo class:
#deco_num_hei, deco_hrange
#data must be arranged:
# (channels,heights,times) (C-style, profs change faster)
#fft along the entire(n=None) acquired heights(axis=1), stores in data
num_chan = data.shape[0]
num_ipps = data.shape[2]
num_codes = finf.subcode.shape[0]
num_bauds = finf.subcode.shape[1]
NSA = finf.num_hei + num_bauds - 1
uppower = py.ceil(py.log2(NSA))
extra = int(2**uppower - finf.num_hei)
NSA = int(2**uppower)
fft_code = py.fft(finf.subcode,n = NSA,axis=1).conj()
data = py.fft(data,n=NSA,axis=1) #n= None: no cropped data or padded zeros
for ch in range(num_chan):
for ipp in range(num_ipps):
code_i = ipp % num_codes
data[ch,:,ipp] = data[ch,:,ipp] * fft_code[code_i,:]
data=py.ifft(data,n=NSA,axis=1) #fft along the heightsm
if dropheights:
return data[:,:-extra-(num_bauds-1),:]
else:
return data[:,:-extra,:]
def displayData(X):
print "Visualizing"
m, n = X.shape
width = round(sqrt(n))
height = width
display_rows = int(floor(sqrt(m)))
display_cols = int(ceil(m/display_rows))
print "Cell width:", width
print "Cell height:", height
print "Display rows:", display_rows
print "Display columns:", display_cols
display = zeros((display_rows*height,display_cols*width))
# Iterate through the training sets, reshape each one and populate
# the display matrix with the letter matrixes.
for xrow in range(0, m):
rowindex = divide(xrow, display_cols)
columnindex = remainder(xrow, display_cols)
rowstart = int(rowindex*height)
rowend = int((rowindex+1)*height)
colstart = int(columnindex*width)
colend = int((columnindex+1)*width)
display[rowstart:rowend, colstart:colend] = X[xrow,:].reshape(height,width).transpose()
imshow(display, cmap=get_cmap('binary'), interpolation='none')
# Show plot without blocking
draw()
def gauss1(s, func):
'''Construct a 1-D Gaussian mask'''
# for sufficient result use ceil(6s) by ceil(6s) for a gaussian filter
# read: http://en.wikipedia.org/wiki/Gaussian_blur for more explaination
s = float(s)
r = int(ceil(3 * s))
n = int(ceil(6 * s) + 1)
# n * n zero matrix of floats
gaussFilter = zeros((n), dtype=float)
# fill gaussFilter[] with gaussian values on x
for x in range(n):
gaussFilter[x] = func(s, x - r)
return gaussFilter
def panel():
global Ras,Rms,Ie,Ies
global tstart
global pan,t0,t1
#Pulse start time
tstart = 0.1
#Ras = [1.,500.,20.] #Ohm*cm
#Rms = [200.,10000.,200.] #Ohm*cm^2
Ras = [5.0, 500.0, 50.0] #Ohm*cm
Rms = [200.0, 10000.0, 1000.0] #Ohm*cm^2
Ie = 4. #nA
Ies = pl.c_[pl.ones_like(ns.t)]
Ies[:pl.ceil(tstart/ns.dt)] = 0.
t0 = 0.101
t1 = 0.6
pan = simulationpanel.SimulationPanel()
pan.Move((640,600))
pan.setdict(globals())
pan.addcommand('sim()')
pan.addcommand('plottao()')
pan.addvar('Ras')
pan.addvar('Rms')
pan.addvar('Ie')
pan.addvar('t0')
pan.addvar('t1')
def make_run_files(output_folder,
sequence_globals,
shots,
sequence_id,
shuffle=False):
"""Does what it says. sequence_globals and shots are of the datatypes
returned by get_globals and get_shots, one is a nested dictionary with
string values, and the other a flat dictionary. sequence_id should
be some identifier unique to this sequence, use generate_sequence_id
to follow convention. shuffle will randomise the order that the run
files are generated in with respect to which element of shots they
come from. This function returns a *generator*. The run files are
not actually created until you loop over this generator (which gives
you the filepaths). This is useful for not having to clean up as many
unused files in the event of failed compilation of labscripts. If you
want all the run files to be created at some point, simply convert
the returned generator to a list. The filenames the run files are
given is simply the sequence_id with increasing integers appended."""
basename = os.path.join(output_folder, sequence_id)
nruns = len(shots)
ndigits = int(pylab.ceil(pylab.log10(nruns)))
if shuffle:
random.shuffle(shots)
for i, shot_globals in enumerate(shots):
runfilename = ('%s_%0' + str(ndigits) + 'd.h5') % (basename, i)
make_single_run_file(runfilename, sequence_globals, shot_globals,
sequence_id, i, nruns)
yield runfilename
def latest_result_page(log_file_names, index=-1, output_name=None):
dpi = 50
if output_name is None:
fig = figure(figsize=(38, 24), dpi=dpi)
else:
fig = Figure(figsize=(38, 24), dpi=dpi)
reports = [
extract_diff_failure_reports(log_file)
for log_file in sorted(log_file_names)
]
last_reports = [
report[index] for report in reports
if len(report) > (1 + abs(1 + 2 * index)) / 2
]
columns = int(floor(sqrt(len(last_reports)) * 1.5))
rows = int(ceil(len(last_reports) / float(columns)))
for number, report in enumerate(last_reports):
ax = fig.add_subplot(rows, columns, number + 1)
report.plot(ax)
fig.subplots_adjust(left=0.02,
right=0.98,
top=0.98,
bottom=0.02,
hspace=0.2)
if output_name is not None:
canvas = FigureCanvasAgg(fig)
canvas.print_figure(output_name, dpi=dpi)
def show_blocking(self, plotfile=''):
'''Print out the blocking data and show a graph of the behaviour of the standard error with block size.
If plotfile is given, then the graph is saved to the specifed file rather than being shown on screen.'''
# print blocking output
# header...
print '%-11s' % ('# of blocks'),
fmt = '%-14s %-15s %-18s '
header = ('mean (X_%i)', 'std.err. (X_%i)', 'std.err.err. (X_%i)')
for data in self.data:
data_header = tuple(x % (data.data_col) for x in header)
print fmt % data_header,
for key in self.covariance:
str = 'cov(X_%s,X_%s)' % tuple(key.split(','))
print '%-14s' % (str),
for key in self.combination_stats:
fmt = ['mean (X_%s'+self.combination+'X_%s)', 'std.err. (X_%s'+self.combination+'X_%s)']
strs = tuple([s % tuple(key.split(',')) for s in fmt])
print '%-16s %-18s' % strs,
print
# data
block_fmt = '%-11i'
fmt = '%-#14.12g %-#12.8e %-#18.8e '
for s in range(len(self.data[0].stats)):
print block_fmt % (self.data[0].stats[s].block_size),
for data in self.data:
print fmt % (data.stats[s].mean, data.stats[s].se, data.stats[s].se_error),
for cov in self.covariance.itervalues():
print '%+-#14.5e' % (cov[s]),
for comb in self.combination_stats.itervalues():
print '%-#16.12f %-#18.12e' % (comb[s].mean, comb[s].se),
print
# plot standard error
if PYLAB:
# one sub plot per data set.
nplots = len(self.data)
for (i, data) in enumerate(self.data):
pylab.subplot(nplots, 1, i+1)
blocks = [stat.block_size for stat in data.stats]
se = [stat.se for stat in data.stats]
se_error = [stat.se_error for stat in data.stats]
pylab.semilogx(blocks, se, 'g-', basex=2, label=r'$\sigma(X_{%s})$' % (data.data_col))
pylab.errorbar(blocks, se, yerr=se_error, fmt=None, ecolor='g')
xmax = 2**pylab.ceil(pylab.log2(blocks[0]+1))
pylab.xlim(xmax, 1)
pylab.ylabel('Standard error')
pylab.legend(loc=2)
if i != nplots - 1:
# Don't label x axis points.
ax = pylab.gca()
ax.set_xticklabels([])
pylab.xlabel('# of blocks')
if plotfile:
pylab.savefig(plotfile)
else:
pylab.draw()
pylab.show()
def smooth(x,window_len=11,window='hanning'):
"""smooth the data using a window with requested size.
This method is based on the convolution of a scaled window with the signal.
The signal is prepared by introducing reflected copies of the signal
(with the window size) in both ends so that transient parts are minimized
in the begining and end part of the output signal.
Copied and modified from http://scipy-cookbook.readthedocs.io/items/SignalSmooth.html (16/10/2017 - RProux)
input:
x: the input signal
window_len: the dimension of the smoothing window; should be an odd integer
window: the type of window from 'flat', 'hanning', 'hamming', 'bartlett', 'blackman'
flat window will produce a moving average smoothing.
output:
the smoothed signal
example:
t=linspace(-2,2,0.1)
x=sin(t)+randn(len(t))*0.1
y=smooth(x)
see also:
numpy.hanning, numpy.hamming, numpy.bartlett, numpy.blackman, numpy.convolve
scipy.signal.lfilter
TODO: the window parameter could be the window itself if an array instead of a string
NOTE: the window_len parameter should always be odd for reliable output (will shift slightly the data if even)
"""
if x.ndim != 1:
raise ValueError("smooth only accepts 1 dimension arrays.")
if x.size < window_len:
raise ValueError("Input vector needs to be bigger than window size.")
if window_len < 3:
return x
if window not in ['flat', 'hanning', 'hamming', 'bartlett', 'blackman']:
raise ValueError("Window is one of 'flat', 'hanning', 'hamming', 'bartlett', 'blackman'")
s = pl.r_[x[window_len-1:0:-1],x,x[-2:-window_len-1:-1]]
print(s)
print(len(s))
if window == 'flat': #moving average
w = pl.ones(window_len, 'd')
else:
w = eval('pl.{}(window_len)'.format(window))
y = pl.convolve(w / w.sum(), s, mode='valid')
return y[int(pl.floor(window_len/2)) : -int(pl.ceil(window_len/2) - 1)]
def zoom(self, event):
newxlim = numpy.array(self.sp_iq.get_xlim())
curxlim = numpy.array(self.xlim)
if(newxlim[0] != curxlim[0] or newxlim[1] != curxlim[1]):
#xmin = max(0, int(ceil(self.sample_rate*(newxlim[0] - self.position))))
#xmax = min(int(ceil(self.sample_rate*(newxlim[1] - self.position))), len(self.iq))
xmin = max(0, int(ceil(self.sample_rate*(newxlim[0]))))
xmax = min(int(ceil(self.sample_rate*(newxlim[1]))), len(self.iq))
iq = numpy.array(self.iq[xmin : xmax])
time = numpy.array(self.time[xmin : xmax])
iq_psd, freq = self.dopsd(iq)
self.draw_psd(freq, iq_psd)
self.xlim = numpy.array(self.sp_iq.get_xlim())
draw()
def plot(self,only=None):
from pylab import plot,subplot,sqrt,ceil,title
weights=self.weights_xh.T
if only is None:
only=list(range(len(weights)))
L=len(only)
c=ceil(sqrt(L))
r=ceil(L/c)
for i,idx in enumerate(only):
w=weights[idx]
subplot(r,c,i+1)
plot(w,'-o')
title('Filter %d' % (idx))
def calculate_activity_histogram(spikes, total_neurons, bin=0.1):
"""Calculates histogram and bins specifically for neurons.
Bins are provided in seconds instead of milliseconds."""
hist, bin_edges = pylab.histogram(
[spike[0] for spike in spikes],
bins=pylab.ceil(max([spike[0] for spike in spikes])/bin))
bin_edges = pylab.delete(bin_edges, len(bin_edges)-1) / 1000.
return [[float(i)/total_neurons for i in hist], bin_edges]
def create_band(band, res, plt=False, high=0, conv=False):
'''
print, "create_band, band, res, /bw, /plt, high=high, /conv"
print, "This program will create a top hat band convolved with a gaussain of sigma = res with freq data spaced from 0 to 1000 (default) GHz"
print, "band = bandpass region in GHz"
print, "res = freq. spacing in GHz"
print, "/plt plot bandpass"
print, "high=high upper GHz region"
print, "r = create_band([140, 160], 2.0, /bw, high=500.0)"
return, 0
'''
npts = pl.ceil(4000.0)
if high : npts = pl.ceil(high*1.0/.25)
freq = pl.arange(npts)*.25
response = pl.zeros(len(freq))
inb = pl.where((freq < band[1]) & (freq > band[0]))[0]
if band[0] == band[1] : inb = pl.where_closest(freq, band(0))[0]
if inb[0] == -1:
print "Band not between 0-1000 GHZ"
return 0
response[inb] = 1
#let's convolve the band with our resolution.
if conv:
xx = .25*pl.arange(6*res/.25+1)-3*res
con =pl.exp(-xx**2/(2*res**2))/pl.sqrt(2*pl.pi)/res
normalization=1./sum(abs(con))
response = pl.convolve(response, con,'same')*normalization
if plt:
pl.figure()
pl.plot(freq, response,'D')
pl.xlabel('Freq(GHz)')
pl.ylabel('Reponse')
pl.xlim(band[0] - 3*res, band[1] + 3*res)
result = {'Freq': freq, 'resp': response}
return result
def visualize_priors(priors):
from matplotlib import pyplot as plt
N = len(priors)
m = round(sqrt(N * 3 / 4.))
n = ceil(N / m)
fig = plt.figure()
for i, var in enumerate(priors):
ax = fig.add_subplot(n, m, i)
ax = ax.hist(priors[var].rvs(1000), 20)
plt.show()
def visualize_priors(priors):
from matplotlib import pyplot as plt
N = len(priors)
m = round(sqrt(N*3/4.))
n = ceil(N/m)
fig = plt.figure()
for i, var in enumerate(priors):
ax = fig.add_subplot(n,m,i)
ax = ax.hist(priors[var].rvs(1000), 20)
plt.show()
def zoom(self, event):
newxlim = numpy.array(self.sp_iq.get_xlim())
curxlim = numpy.array(self.xlim)
if (newxlim[0] != curxlim[0] or newxlim[1] != curxlim[1]):
#xmin = max(0, int(ceil(self.sample_rate*(newxlim[0] - self.position))))
#xmax = min(int(ceil(self.sample_rate*(newxlim[1] - self.position))), len(self.iq))
xmin = max(0, int(ceil(self.sample_rate * (newxlim[0]))))
xmax = min(int(ceil(self.sample_rate * (newxlim[1]))),
len(self.iq))
iq = numpy.array(self.iq[xmin:xmax])
time = numpy.array(self.time[xmin:xmax])
iq_psd, freq = self.dopsd(iq)
self.draw_psd(freq, iq_psd)
self.xlim = numpy.array(self.sp_iq.get_xlim())
draw()
def zeroPadd(self,fbins):
#zero padd the underlying tdData such that the fbins afterwards are fbins
spac=1/self._tdData.dt/fbins
actlen=self._tdData.getLength()
nozeros=py.ceil(spac-actlen)
self._tdData.zeroPaddData(nozeros)
#leave the old bnds in place
bnds=[min(self.getfreqs()),max(self.getfreqs())]
zpd=self._calculatefdData(self._tdData)
self.setFDData(self.getcroppedData(zpd,bnds[0],bnds[1]))
def dispims_old(M, height, width, border=0, bordercolor=0.0):
""" Display a whole stack (colunmwise) of vectorized matrices. Useful
eg. to display the weights of a neural network layer.
"""
numimages = M.shape[1]
n0 = numpy.int(pylab.ceil(numpy.sqrt(numimages)))
n1 = numpy.int(pylab.ceil(numpy.sqrt(numimages)))
im = bordercolor*\
numpy.ones(((height+border)*n1+border,(width+border)*n0+border),dtype='<f8')
for i in range(n0):
for j in range(n1):
if i * n1 + j < M.shape[1]:
im[j*(height+border)+border:(j+1)*(height+border)+border,\
i*(width+border)+border:(i+1)*(width+border)+border] = \
numpy.vstack((\
numpy.hstack((numpy.reshape(M[:,i*n1+j],(height, width)),\
bordercolor*numpy.ones((height,border),dtype=float))),\
bordercolor*numpy.ones((border,width+border),dtype=float)\
))
pylab.imshow(im, cmap=pylab.cm.gray)
def save_2D_movie(frame_list, filename, frame_duration):
"""
Saves a list of 2D numpy arrays of gray shades between 0 and 1 to a zipped tree of PNG files.
Inputs:
frame_list - a list of 2D numpy arrays of floats between 0 and 1
filename - string specifying the filename where to save the data, has to end on '.zip'
frame_duration - specifier for the duration per frame, will be stored as additional meta-data
Example:
>> import numpy
>> framelist = []
>> for i in range(100): framelist.append(numpy.random.random([100,100])) # creates a list of 2D numpy arrays with random values between 0. and 1.
>> save_2D_movie(framelist, 'randommovie100x100x100.zip', 0.1)
"""
try:
import zipfile
except ImportError:
raise ImportError(
"ERROR: Python module zipfile not found! Needed by NeuroTools.plotting.save_2D_movie(...)!"
)
try:
import StringIO
except ImportError:
raise ImportError(
"ERROR: Python module StringIO not found! Needed by NeuroTools.plotting.save_2D_movie(...)!"
)
assert PILIMAGEUSE, "ERROR: Since PIL has not been detected, the function NeuroTools.plotting.save_2D_movie(...) is not supported!"
filenameConditionStr = "ERROR: Second argument of function NeuroTools.plotting.save_2D_movie(...) must be a string ending on \".zip\"!"
assert (type(filename) == str) and (len(filename) > 4) and (
filename[-4:].lower() == '.zip'), filenameConditionStr
zf = zipfile.ZipFile(filename, 'w', zipfile.ZIP_DEFLATED)
container = filename[:-4] # remove .zip
frame_name_format = "frame%s.%dd.png" % (
"%", pylab.ceil(pylab.log10(len(frame_list))))
for frame_num, frame in enumerate(frame_list):
frame_data = [(p, p, p) for p in frame.flat]
im = Image.new('RGB', frame.shape, 'white')
im.putdata(frame_data)
io = StringIO.StringIO()
im.save(io, format='png')
pngname = frame_name_format % frame_num
arcname = "%s/%s" % (container, pngname)
io.seek(0)
zf.writestr(arcname, io.read())
progress_bar(float(frame_num) / len(frame_list))
# add 'parameters' and 'frames' files to the zip archive
zf.writestr("%s/parameters" % container,
'frame_duration = %s' % frame_duration)
zf.writestr(
"%s/frames" % container,
'\n'.join(["frame%.3d.png" % i for i in range(len(frame_list))]))
zf.close()
def zoom(self, event):
newxlim = numpy.array(self.sp_iq.get_xlim())
curxlim = numpy.array(self.xlim)
if(newxlim[0] != curxlim[0] or newxlim[1] != curxlim[1]):
self.xlim = newxlim
#xmin = max(0, int(ceil(self.sample_rate*(self.xlim[0] - self.position))))
#xmax = min(int(ceil(self.sample_rate*(self.xlim[1] - self.position))), len(self.iq))
xmin = max(0, int(ceil(self.sample_rate*(self.xlim[0]))))
xmax = min(int(ceil(self.sample_rate*(self.xlim[1]))), len(self.iq))
iq = self.iq[xmin : xmax]
time = self.time[xmin : xmax]
iq_fft = self.dofft(iq)
freq = self.calc_freq(time, self.sample_rate)
self.plot_fft[0].set_data(freq, iq_fft)
self.sp_fft.axis([freq.min(), freq.max(),
iq_fft.min()-10, iq_fft.max()+10])
draw()
def show_images(images,which_images=None,max_images=None):
from pylab import imshow,subplot,sqrt,ceil,title,cm,gca
from random import shuffle
if which_images is None:
which_images=list(range(len(images.data)))
if isinstance(which_images[0],str): # target names
which_names=which_images
which_images=[]
for idx in range(len(images.data)):
name=images.target_names[images.targets[idx]]
if name in which_names:
which_images.append(idx)
if not max_images is None:
shuffle(which_images)
which_images=which_images[:max_images]
if not which_images:
raise ValueError("No images selected")
L=len(which_images)
c=ceil(sqrt(L))
r=ceil(L/c)
for i,idx in enumerate(which_images):
im=images.data[idx]
name=images.target_names[images.targets[idx]]
subplot(r,c,i+1)
imshow(im,interpolation='nearest',cmap=cm.gray)
title(name)
if i<(L-c):
gca().set_xticklabels([])
if i%c!=0:
gca().set_yticklabels([])
def plot_spike_rastr(spikes):
print 'Plotting raster plot.'
global figure_dir
pylab.figure(get_free_figure_number())
pylab.clf()
pylab.plot([spike[0] for spike in spikes],
[spike[1] for spike in spikes], 'k.')
pylab.xlabel('Time, ms')
pylab.ylabel('# of neuron')
pylab.title('Network raster activity')
pylab.axis([0., pylab.ceil(max([spike[0] for spike in spikes])),
-1, max([spike[1] for spike in spikes]) + 1])
pylab.savefig(os.path.join(figure_dir, 'spikes.png'))
def val_change(self):
self.v_i = int(pl.floor(self.start_v.value() * 1000)) # in mV
self.v_f = int(pl.ceil(self.end_v.value() * 1000)) # in mV
self.dt = int(self.time.value() * 1000) # in ms
if self.no_of_steps == self.steps.value(): # step_size was modified
self.step_size = self.step_size_field.value() # in mV
self.no_of_steps = int(float(self.v_f - self.v_i) // self.step_size) + 1
self.steps.setValue(self.no_of_steps)
else:
self.no_of_steps = self.steps.value()
self.step_size = int(float(self.v_f - self.v_i) / (self.no_of_steps - 1))
self.step_size_field.setValue(self.step_size)
self.repeats = self.reps.value()
self.counterDev = self.cb.currentIndex()
def visualize ():
sample_rate, snd = load_sample(".\\hh-closed\\dh9.WAV")
print snd.dtype
data = normalize(snd)
print data.shape
n = data.shape[0]
length = float(n)
print length / sample_rate, "s"
timeArray = arange(0, length, 1)
timeArray = timeArray / sample_rate
timeArray = timeArray * 1000 #scale to milliseconds
ion()
if False:
plot(timeArray, data, color='k')
ylabel('Amplitude')
xlabel('Time (ms)')
raw_input("press enter")
exit()
p = fft(data) # take the fourier transform
nUniquePts = ceil((n+1)/2.0)
print nUniquePts
p = p[0:nUniquePts]
p = abs(p)
p = p / float(n) # scale by the number of points so that
# the magnitude does not depend on the length
# of the signal or on its sampling frequency
p = p**2 # square it to get the power
# multiply by two (see technical document for details)
# odd nfft excludes Nyquist point
if n % 2 > 0: # we've got odd number of points fft
p[1:len(p)] = p[1:len(p)] * 2
else:
p[1:len(p) -1] = p[1:len(p) - 1] * 2 # we've got even number of points fft
print p
freqArray = arange(0, nUniquePts, 1.0) * (sample_rate / n);
plot(freqArray/1000, 10*log10(p), color='k')
xlabel('Frequency (kHz)')
ylabel('Power (dB)')
raw_input("press enter")
m = average(freqArray, weights = p)
v = average((freqArray - m)**2, weights= p)
r = sqrt(mean(data**2))
s = var(data**2)
print "mean freq", m #TODO: IMPORTANT: this is currently the mean *power*, not the mean freq. What we want is mean freq weighted by power
print "var freq", v
print "rms", r
print "squared variance", s
def get_uniform_data(*args):
# internally define variables
dist_old = args[0]
elev_old = args[1]
func_class_old = args[2]
wav_lst_old = args[3]
nom_dist_window = args[4]
window_cnt = mp.ceil(max(dist_old) / nom_dist_window)
act_dist_window = max(dist_old) / window_cnt
dist_new = mp.linspace(0.0, dist_old[-1], window_cnt + 1)
elev_new = np.asarray([-1.0] * len(dist_new))
func_class_new = np.zeros(len(dist_new)) - 1.0
wav_lst_new = np.zeros(len(dist_new)) - 1.0
for i in range(len(dist_new)):
logical1 = dist_old >= (dist_new[i] - act_dist_window / 2.0)
logical2 = dist_old <= (dist_new[i] + act_dist_window / 2.0)
ind = mp.find(np.bitwise_and(logical1, logical2))
if len(ind) != 0:
y0 = elev_old[ind]
elev_new[i] = mp.median(y0)
func_class_mode, func_class_mode_cnt = stats.mode(
func_class_old[ind])
func_class_new[i] = np.copy(func_class_mode)
wav_mode, wav_mode_cnt = stats.mode(wav_lst_old[ind])
wav_lst_new[i] = np.copy(wav_mode)
elev_new[0] = 1.0 * elev_old[0]
elev_new[-1] = 1.0 * elev_old[-1]
ind = mp.find(elev_new != -1.0)
if len(ind) > 1:
elev_new_func = interp1d(dist_new[ind], elev_new[ind], kind=1)
elev_new = elev_new_func(dist_new)
ind = mp.find(func_class_new != -1.0)
if len(ind) > 1:
fc_new_func = interp1d(dist_new[ind], func_class_new[ind], kind=0)
func_class_new = fc_new_func(dist_new)
ind = mp.find(wav_lst_new != -1.0)
if len(ind) > 1:
wav_new_func = interp1d(dist_new[ind], wav_lst_new[ind], kind=0)
wav_lst_new = wav_new_func(dist_new)
return dist_new, elev_new, func_class_new, wav_lst_new
def map_eq(t, fs=250., eps=1e-8):
"""
returns the longest array of time which has support points every 1 / fs ms
that is not smaller than min[t] and does not exceed max[t]
==========
Parameter:
==========
t : *array*
vector that contains a smallest and largest element.
fs : *float*
sampling time of new time vector
eps : *float* (internally used!)
========
Returns:
========
teq : *array*
an equally sampled array with a sampling rate of fs
"""
t_min = ceil(min(t) * fs - eps)
t_max = ceil(max(t) * fs + eps)
return 1. / fs * arange(t_min, t_max + 1)
def map_eq(t, fs=250., eps=1e-8):
"""
returns the longest array of time which has support points every 1 / fs ms
that is not smaller than min[t] and does not exceed max[t]
==========
Parameter:
==========
t : *array*
vector that contains a smallest and largest element.
fs : *float*
sampling time of new time vector
eps : *float* (internally used!)
========
Returns:
========
teq : *array*
an equally sampled array with a sampling rate of fs
"""
t_min = ceil(min(t) * fs - eps)
t_max = ceil(max(t) * fs + eps)
return 1. / fs * arange(t_min, t_max + 1)
def analyse_bursts2_CUT(spikes, total_neurons, time_max):
spikes_per_neuron = [[] for _ in xrange(total_neurons)]
for spike in spikes:
spikes_per_neuron[spike[1]].append(spike[0])
# total_neurons = 1000
analysing_neurons = sorted(random.sample(range(total_neurons), 1))
print analysing_neurons
# activity_hist_per_neuron = []
# bins_per_neuron = []
fft_per_neuron = []
fft_sum = pylab.zeros(pylab.ceil(time_max*10.)/2+1)
for i in analysing_neurons:
a, b = calculate_activity_histogram_one_neu(
spikes_per_neuron[i], pylab.ceil(time_max*10.))
# activity_hist_per_neuron.append(a)
# bins_per_neuron.append(b)
# fft_per_neuron.append(abs(numpy.fft.rfft(a)))
fft_sum += abs(numpy.fft.rfft(a))
print 'Finished %f \r' % (float(i)/total_neurons),
freqs_per_neuron = numpy.fft.rfftfreq(len(a), b[1] - b[0])
print
fft_sum /= len(analysing_neurons)
# pylab.figure(10)
# for i in analysing_neurons:
# pylab.plot(bins_per_neuron[i], activity_hist_per_neuron[i])
pylab.figure(11)
# fft_sum = [sum([fft_per_neuron[neu][i]
# for neu in xrange(len(fft_per_neuron))])
# for i in xrange(len(fft_per_neuron[0]))]
# fft_sum[0] = fft_sum[1]
fft_sum = smooth_data(fft_sum, 100)
pylab.plot(freqs_per_neuron, fft_sum)
def _fastFourier(series, sampRate):
""" Perform a Fast Fourier Transform """
n = len(series)
p = sf.fft(series) # Fast fourier transform
uUniquePts = int(pl.ceil((n + 1) / 2.0))
p = p[0:uUniquePts]
p = abs(p)
p = p / float(n)
p = p**2
if n % 2 > 0:
p[1:len(p)] = p[1:len(p)] * 2
else:
p[1:len(p) - 1] = p[1:len(p) - 1] * 2
freqArray = np.arange(0, uUniquePts, 1.0) * (sampRate / n)
return (p, freqArray)
def getFFT(s1, n):
p = fft(s1) # take the fourier transform
nUniquePts = ceil((n + 1) / 2.0)
p = p[0:nUniquePts]
p = abs(p)
p = p / n # scale by the number of points so that
# the magnitude does not depend on the length
# of the signal or on its sampling frequency
p = p ** 2 # square it to get the power
# multiply by two (see technical document for details)
# odd nfft excludes Nyquist point
if n % 2 > 0: # we've got odd number of points fft
p[1:len(p)] = p[1:len(p)] * 2
else:
p[1:len(p) - 1] = p[1:len(p) - 1] * 2 # we've got even number of points fft
return nUniquePts, p
def print_aligned2(w, r1, r2, n1=None, n2=None):
if n1==None or n2==None:
n1 = int(ceil(sqrt(w.shape[1])))
n2 = n1
assert(r1*r2==w.shape[0])
Z = zeros(((r1+1)*n1, (r2+1)*n2), 'd')
i1, i2 = 0, 0
for i1 in range(n1):
for i2 in range(n2):
i = i1*n2+i2
if i>=w.shape[1]: break
Z[(r1+1)*i1:(r1+1)*(i1+1)-1, (r2+1)*i2:(r2+1)*(i2+1)-1] = w[:,i].reshape(r1,r2)
return Z
def genIm(self, dlg, imb, mdh):
pixelSize = dlg.getPixelSize()
if not pylab.mod(pylab.log2(pixelSize/self.visFr.QTGoalPixelSize), 1) == 0:#recalculate QuadTree to get right pixel size
self.visFr.QTGoalPixelSize = pixelSize
self.visFr.Quads = None
self.visFr.GenQuads()
qtWidth = self.visFr.Quads.x1 - self.visFr.Quads.x0
qtWidthPixels = pylab.ceil(qtWidth/pixelSize)
im = pylab.zeros((qtWidthPixels, qtWidthPixels))
QTrend.rendQTa(im, self.visFr.Quads)
return im[(imb.x0/pixelSize):(imb.x1/pixelSize),(imb.y0/pixelSize):(imb.y1/pixelSize)]
def logBinInt(base,s,ps):
# Bin the data in bins with edges base**1, base**2 ...
# all s such that base**i < x <= base**(i+1) goes in the bin i+1.
# It is assumed that all s are strictly posetive integers and
# that s is sorted.
# Check for sorted input
for ind in range(1,len(s)):
if s[ind] <= s[ind-1]:
print "Unsorted input or repeated integers input. Returning."
return [],[]
# Construct a list of all edges of the bins
maxPow = pylab.ceil(pylab.log(max(s))/pylab.log(base)).astype(int)
maxEdge = pylab.floor(base**maxPow)
# Generate edges of the bins
binEdge = []
lastEdge = pylab.floor(base)
exp = 1.0
while lastEdge < maxEdge:
if pylab.floor(base**exp) > lastEdge:
binEdge.append(lastEdge)
lastEdge = pylab.floor(base**exp)
exp = exp+1
binEdge.append(maxEdge)
binEdge = numpy.array(binEdge)
# Calculate bin sizes and centers
binSize = numpy.zeros(len(binEdge))
binCenter = numpy.zeros(len(binEdge))
binSize[0] = binEdge[0]
binCenter[0] = (1.0 + binEdge[0])*0.5
for j in range(1,len(binEdge)):
binSize[j] = binEdge[j] - binEdge[j-1]
binCenter[j] = (binEdge[j] + binEdge[j-1] + 1)*0.5
# Calculate bin probability
binProb = numpy.zeros(len(binEdge))
binNum = 0
for data, prob in zip(s,ps):
while data > binEdge[binNum]:
binNum = binNum+1
binProb[binNum] = binProb[binNum] + prob
binProb = binProb/binSize
return binCenter, binProb
def save_2D_movie(frame_list, filename, frame_duration):
"""
Saves a list of 2D numpy arrays of gray shades between 0 and 1 to a zipped tree of PNG files.
Inputs:
frame_list - a list of 2D numpy arrays of floats between 0 and 1
filename - string specifying the filename where to save the data, has to end on '.zip'
frame_duration - specifier for the duration per frame, will be stored as additional meta-data
Example:
>> import numpy
>> framelist = []
>> for i in range(100): framelist.append(numpy.random.random([100,100])) # creates a list of 2D numpy arrays with random values between 0. and 1.
>> save_2D_movie(framelist, 'randommovie100x100x100.zip', 0.1)
"""
try:
import zipfile
except ImportError:
raise ImportError("ERROR: Python module zipfile not found! Needed by neurotools.plotting.save_2D_movie(...)!")
try:
import StringIO
except ImportError:
raise ImportError("ERROR: Python module StringIO not found! Needed by neurotools.plotting.save_2D_movie(...)!")
assert PILIMAGEUSE, "ERROR: Since PIL has not been detected, the function neurotools.plotting.save_2D_movie(...) is not supported!"
filenameConditionStr = "ERROR: Second argument of function neurotools.plotting.save_2D_movie(...) must be a string ending on \".zip\"!"
assert (type(filename) == str) and (len(filename) > 4) and (filename[-4:].lower() == '.zip'), filenameConditionStr
zf = zipfile.ZipFile(filename, 'w', zipfile.ZIP_DEFLATED)
container = filename[:-4] # remove .zip
frame_name_format = "frame%s.%dd.png" % ("%", pylab.ceil(pylab.log10(len(frame_list))))
for frame_num, frame in enumerate(frame_list):
frame_data = [(p,p,p) for p in frame.flat]
im = Image.new('RGB', frame.shape, 'white')
im.putdata(frame_data)
io = StringIO.StringIO()
im.save(io, format='png')
pngname = frame_name_format % frame_num
arcname = "%s/%s" % (container, pngname)
io.seek(0)
zf.writestr(arcname, io.read())
progress_bar(float(frame_num)/len(frame_list))
# add 'parameters' and 'frames' files to the zip archive
zf.writestr("%s/parameters" % container,
'frame_duration = %s' % frame_duration)
zf.writestr("%s/frames" % container,
'\n'.join(["frame%.3d.png" % i for i in range(len(frame_list))]))
zf.close()
def _win_mtx(self, x, w, h, nsamples=None, win=None):
num_frames = int( pylab.ceil( x.size / float( h ) ) )
X = pylab.zeros((w, num_frames))
if win is None:
win = pylab.hamming(w)
if nsamples is None:
frames = range(num_frames)
else:
frames = sort(permutation(num_frames)[0: nsamples])
for k in frames:
start_pos = k*h
end_pos = start_pos + w
if x.size < end_pos:
X[:,k] = win * pylab.concatenate((x[start_pos:-1], pylab.zeros(w - (x.size - start_pos - 1))), axis=1)
else:
X[:,k] = win * x[start_pos:end_pos]
return X.T
