def do_fast_ica(pca_first): mo1_cj_inverse = numpy.array(mo1_cj).T mo2_cj_inverse = numpy.array(mo2_cj).T if pca_first: mo1_cj_array = mdp.pca(mo1_cj_inverse, input_dim=4, output_dim=3) mo2_cj_array = mdp.pca(mo2_cj_inverse, input_dim=4, output_dim=3) else: mo1_cj_array = mo1_cj_inverse mo2_cj_array = mo2_cj_inverse a = mdp.fastica(mo1_cj_array) b = mdp.fastica(mo2_cj_array) return a,b
def do_fast_ica(pca_first):
mo1_cj_inverse = numpy.array(mo1_cj).T
mo2_cj_inverse = numpy.array(mo2_cj).T
if pca_first:
mo1_cj_array = mdp.pca(mo1_cj_inverse, input_dim=4, output_dim=3)
mo2_cj_array = mdp.pca(mo2_cj_inverse, input_dim=4, output_dim=3)
else:
mo1_cj_array = mo1_cj_inverse
mo2_cj_array = mo2_cj_inverse
a = mdp.fastica(mo1_cj_array)
b = mdp.fastica(mo2_cj_array)
return a, b
def perform(self):
self.source_list = numpy.array(self.source_list, 'double')
self.source_list = self.source_list.transpose()
guess_matrix = None
self.source_list = mdp.fastica(self.source_list,
approach='defl',
g='gaus',
guess=guess_matrix,
fine_g='gaus',
mu=0.01,
stabilization=0.001,
sample_size=1,
fine_tanh=1,
max_it=50000000,
max_it_fine=100,
failures=500,
limit=0.001,
verbose=False,
whitened=False,
white_comp=self.nout,
white_parm={'svd': True})
result = []
print self.source_list.shape
for i in range(0, nout):
result.append(self.one_to_two(self.source_list[:, i]))
#sources=self.source_list
self.source_list = []
return result
def GET(self, name):
min,max=[],[]
if not name:
names="&artist=the+beatles"
else:
names=""
for n in name.split(','):
names = names + "&artist=" +n
rawdata = json.loads(urllib.urlopen("http://developer.echonest.com/api/v4/playlist/static?api_key=N6E4NIOVYMTHNDM8J&artist=%s&format=json&results=100&type=artist-radio&bucket=id:7digital&bucket=audio_summary&audio=true&variety=0.999"%(names)).read())['response']["songs"]
keys = [u'key', u'tempo', u'mode', u'time_signature', u'duration', u'loudness']
x=[]
for s in rawdata:
x.append([])
for k in keys:
x[-1].append(s['audio_summary'][k])
y = mdp.fastica(scipy.array(x))
maxc,minc = [],[]
for col in range(len(keys)):
maxc.append(y[:, col].max())
minc.append( y[:, col].min())
for col in range(len(keys)):
rang = maxc[col] - minc[col]
for row in range(100):
y[row,col] = (y[row,col] - minc[col])/rang
return json.dumps({'characteristics_keys':keys, 'characteristics':x, 'ica':y.tolist() , 'echo':rawdata})
def compute( self , waveforms , sampling_rate , output_dim =2) :
#~ waveforms2 = empty( (waveforms.shape[0] , waveforms.shape[1]*waveforms.shape[2] ) )
#~ for i in range(waveforms.shape[0]):
#~ waveforms2[i,:] = waveforms[i].reshape( (waveforms.shape[1]*waveforms.shape[2]) )
waveforms2 = waveforms.reshape(waveforms.shape[0], -1)
ica_mat = mdp.fastica(waveforms2 , whitened = 0,
white_comp = output_dim,
g = 'tanh' ,
approach= 'symm' )
return ica_mat
def Main(self, model):
# self.model = model
data = array(model.GetCurrentData()[:])
k = wx.GetNumberFromUser("ICA Dialog", "Enter number of independent components", "k", 1)
ica_node = mdp.nodes.FastICANode()
ica_node.set_output_dim(k)
ica_data = mdp.fastica(data)
# ica_data = r.fastICA(data, k, alg_typ = "deflation", fun = "logcosh", alpha = 1, method = "R", row_norm = 0, maxit = 200, tol = 0.0001, verbose = 1)
fields = ["Comp%02d" % c for c in range(1, k + 1)]
model.updateHDF("IcaPY", ica_data, fields=fields)
def apply_ica(x, i, g):
'''
Seperate the original rgb sources into 3 different channels
i is between 0 to 2, which is the channel
g is the mode to converge
'''
#x1 = numpy.transpose(x)
x1 = numpy.array(x)
#channels = mdp.fastica(x1, input_dim=3)
#channels = mdp.fastica(x1, input_dim=3, verbose=True, g=g)
channels = mdp.fastica(x1, input_dim=3, g=g)
tmp = channels.transpose()
return tmp[i]
def apply_ica(x, i, g):
'''
Seperate the original rgb sources into 3 different channels
i is between 0 to 2, which is the channel
g is the mode to converge
'''
#x1 = numpy.transpose(x)
x1 = numpy.array(x)
#channels = mdp.fastica(x1, input_dim=3)
#channels = mdp.fastica(x1, input_dim=3, verbose=True, g=g)
channels = mdp.fastica(x1, input_dim=3, g=g)
tmp = channels.transpose()
return tmp[i]
def split_audio(self):
self.fs, self.data = wav.read(os.getcwd() + '\\content\\' +
self.file_name + '.wav')
ww = wave.open(os.getcwd() + "\\content\\" + self.file_name + ".wav",
'wb')
voices = []
#FastICA - to separate channels and waves
source = fastica(self.data.astype(float))
#normalize
source = np.int16(source / np.max(abs(source), axis=0) * 32767)
#plt.plot(np.array(source))
#plt.savefig(os.getcwd() + "\\content\\fastICA_plot.png")
#Creating mono channele files:
wav.write(
os.getcwd() + '\\content\\' + self.file_name + '_ICAleft.wav',
44100, source[:, 0])
wav.write(
os.getcwd() + '\\content\\' + self.file_name + '_ICAright.wav',
44100, source[:, 1])
##########################PLOTTING#######################################
plt.figure(1)
plt.subplot(511)
plt.title("fastICA")
plt.plot(source)
plt.subplot(513)
plt.title("fastICA-left channel")
plt.plot(source[:, 0])
plt.subplot(515)
plt.title("fastICA - right channel")
plt.plot(source[:, 1], color='orange')
plt.savefig(os.getcwd() + "\\content\\fastICA.png")
###########################SEPARATE VOICES##############################################
#chunk = 1024#buffer
#self.treshold = audioop.avg(self.data, 2) #treshold for silence
#rms = 0 ## root-mean-square -> measure of the power in an audio signal.
#i = 0
eps = 200
#for i in range(len(source)):
pos = []
pos.append(0)
i = 1
value = 0
def fastICA(mix_file, jamming_file):
sig1, fs1, enc1 = wavread(mix_file)
sig2, fs2, enc2 = wavread(jamming_file)
sig1, sig2 = chop_sig(sig1, sig2)
wavwrite(array([sig1, sig2]).T, "mixed.wav", fs1, enc1)
# Load in the stereo file
recording, fs, enc = wavread("mixed.wav")
# Perform FastICA algorithm on the two channels
sources = fastica(recording)
# The output levels of this algorithm are arbitrary, so normalize them to 1.0.
m = []
for k in sources:
m.append(k[0])
# Write back to a file
wavwrite(array(m), "sources.wav", fs, enc)
def pid_pca(args):
# import modular data processing toolkit
import mdp
# load data file
tblfilename = "bf_optimize_mavlink.h5"
h5file = tb.open_file(tblfilename, mode = "a")
# table = h5file.root.v1.evaluations
# get tabke handle
table = h5file.root.v2.evaluations
# sort rows
if not table.cols.mse.is_indexed:
table.cols.mse.createCSIndex()
if not args.sorted:
pids = [ [x["alt_p"], x["alt_i"], x["alt_d"], x["vel_p"], x["vel_i"], x["vel_d"]]
for x in table.iterrows() ]
mses = [ [x["mse"]] for x in table.iterrows() ]
else:
pids = [ [x["alt_p"], x["alt_i"], x["alt_d"], x["vel_p"], x["vel_i"], x["vel_d"]] for x in table.itersorted("mse")]
mses = [ [x["mse"]] for x in table.itersorted("mse")]
print "best two", pids
mses_a = np.log(np.clip(np.array(mses), 0, 200000.))
mses_a /= np.max(mses_a)
# FIXME: try kernel pca on this
from sklearn.decomposition import PCA, KernelPCA, SparsePCA
kpca = KernelPCA(n_components = None,
kernel="rbf", degree=6, fit_inverse_transform=True,
gamma=1/6., alpha=1.)
# kpca = SparsePCA(alpha=2., ridge_alpha=0.1)
X_kpca = kpca.fit_transform(np.asarray(pids).astype(float))
# X_back = kpca.inverse_transform(X_kpca)
Z_kpca = kpca.transform(np.asarray(pids).astype(float))
print Z_kpca.shape, X_kpca.shape
print "|Z_kpca|", np.linalg.norm(Z_kpca, 2, axis=1)
# for i in range(8):
# pl.subplot(8,1,i+1)
# pl.plot(Z_kpca[:,i])
# pl.legend()
# pl.show()
# fast PCA
# pid_p = mdp.pca(np.array(pids).astype(float))
pid_array = np.array(pids).astype(float)
print "pid_array.shape", pid_array.shape
pcanode = mdp.nodes.PCANode(output_dim = 6)
# pcanode.desired_variance = 0.75
pcanode.train(np.array(pids).astype(float))
pcanode.stop_training()
print "out dim", pcanode.output_dim
pid_p = pcanode.execute(np.array(pids).astype(float))
# pid_array_mse = np.hstack((np.array(pids).astype(float), mses_a))
pid_ica = mdp.fastica(np.array(pids).astype(float))
print "ica.shape", pid_ica.shape
# pid_p = np.asarray(pids)[:,[0, 3]]
# pid_p = pids[:,0:2]
# [:,0:2]
sl_start = 0
sl_end = 100
sl = slice(sl_start, sl_end)
print "expl var", pcanode.explained_variance
pl.subplot(111)
colors = np.zeros((100, 3))
# colors = np.hstack((colors, 1-(0.5*mses_a)))
colors = np.hstack((colors, 1-(0.8*mses_a)))
# print colors.shape
# pl.scatter(pid_p[sl,0], pid_p[sl,1], color=colors)
# ica spektrum
pid_ica_sum = np.sum(np.square(pid_ica), axis=0)
# pid_ica_sum_sort = np.sort(pid_ica_sum)
pid_ica_sum_0 = np.argmax(pid_ica_sum)
pid_ica_sum[pid_ica_sum_0] = 0
pid_ica_sum_1 = np.argmax(pid_ica_sum)
# pl.scatter(pid_p[sl,0], pid_p[sl,1], color=colors)
pl.scatter(pid_ica[sl,pid_ica_sum_0], pid_ica[sl,pid_ica_sum_1], color=colors)
# pl.scatter(X_kpca[:,0], X_kpca[:,1], color=colors)
pl.gca().set_aspect(1)
# pl.scatter(pid_p[:,0], pid_p[:,1], alpha=1.)
# pl.show()
# plot raw pid values
pl.subplot(411)
pl.plot(pid_array[sl,[0,3]], "o")
pl.xlim((sl_start - 0.2, sl_end + 0.2))
pl.subplot(412)
pl.plot(pid_array[sl,[1,4]], "o")
pl.xlim((sl_start - 0.2, sl_end + 0.2))
pl.subplot(413)
pl.plot(pid_array[sl,[2,5]], "o")
# plot compressed pid values: pca, ica, ...
# pl.subplot(211)
# pl.plot(pid_p, ".")
# pl.plot(pid_p[sl], "o")
# pl.plot(pid_ica[sl] + np.random.uniform(-0.01, 0.01, size=pid_ica[sl].shape), "o")
pl.xlim((sl_start - 0.2, sl_end + 0.2))
# pl.plot(Z_kpca[:,:], "-o", label="kpca")
# pl.plot(Z_kpca[:,:], ".", label="kpca")
# pl.legend()
# pl.subplot(212)
pl.subplot(414)
pl.plot(mses_a[sl], "ko")
# pl.gca().set_yscale("log")
pl.xlim((sl_start - 0.2, sl_end + 0.2))
pl.show()
# gp fit
x = mses_a[sl]
x_sup = np.atleast_2d(np.arange(0, x.shape[0])).T
x_ones = x != 1.
x_ones[0:20] = False
print x, x_sup, x_ones, x_ones.shape
print "x[x_ones]", x[x_ones].shape
print "x_sup[x_ones]", x_sup[x_ones].shape
from sklearn.gaussian_process import GaussianProcess
# gp = GaussianProcess(regr='constant', corr='absolute_exponential',
# theta0=[1e-4] * 1, thetaL=[1e-12] * 1,
# thetaU=[1e-2] * 1, nugget=1e-2, optimizer='Welch')
gp = GaussianProcess(corr="squared_exponential",
theta0=1e-2, thetaL=1e-4, thetaU=1e-1,
nugget=1e-1/x[x_ones])
gp.fit(x_sup[x_ones,np.newaxis], x[x_ones,np.newaxis])
x_pred, sigma2_pred = gp.predict(x_sup, eval_MSE=True)
print x_pred, sigma2_pred
from sklearn import linear_model
clf = linear_model.Ridge (alpha = .5)
clf.fit(x_sup[x_ones,np.newaxis], x[x_ones,np.newaxis])
x_pred = clf.predict(x_sup[20:100])
pl.subplot(111)
pl.plot(mses_a[sl], "ko")
x_mean = np.mean(x[0:20])
pl.plot(np.arange(0, 20), np.ones((20, )) * x_mean, "k-", alpha=0.5)
pl.plot(np.arange(20, 100), x_pred, "k-", alpha=0.5)
pl.axhspan(0.5, 1.1, 0, 0.19, facecolor="0.5", alpha=0.25)
# pl.plot(x_pred + sigma2_pred, "k-", alpha=0.5)
# pl.plot(x_pred - sigma2_pred, "k-", alpha=0.5)
# pl.gca().set_yscale("log")
pl.xlim((sl_start - 0.2, sl_end + 0.2))
pl.ylim((0.5, 1.1))
pl.text(5, 0.6, "Random\ninitialization")
pl.text(40, 0.6, "Optimizer\nsuggestions")
pl.xlabel("Episode #")
pl.ylabel("MSE")
if args.plotsave:
pl.gcf().set_size_inches((10, 3))
pl.gcf().savefig("%s-mse.pdf" % (sys.argv[0][:-3]), dpi=300,
bbox_inches="tight")
pl.show()
# Mostly from http://www.endolith.com/wordpress/2009/11/22/a-simple-fastica-example/
from mdp import fastica
from scikits.audiolab import wavread, wavwrite
from numpy import abs, max, array
# Load in the microphone audio files
mic1, fs1, enc1 = wavread('channel1.wav')
mic2, fs2, enc2 = wavread('channel2.wav')
mic3, fs3, enc3 = wavread('channel3.wav')
mic4, fs4, enc4 = wavread('channel4.wav')
# transpose() because MDP expects each COLUMN to be an
# observed data stream. Each ROW is one observation of that data across
# all data streams.
sources = fastica(array([mic1, mic2, mic3, mic4]).transpose())
# The output levels of this algorithm are arbitrary, so normalize them to 1.0.
sources /= max(abs(sources), axis = 0)
(frames, inputs) = sources.shape
# Write one output file for each resulting ICA transform.
for i in range(inputs):
sourceColumn = sources[:,[i]] # extract a column from the numpy ndarray
wavwrite(sourceColumn, "resolved-source%d.wav" % i, fs1, enc1)
def ica(data, precision = 'float32'): return(mdp.fastica(data, dtype=precision))
def HRF_ICA(arq_withSS,arq,cromophore,MinIc=2,condition=1):
"""
Computes the ICA algorithm and uses the criteria to define an HRF.
You should give the as inputs:
-a file name string (arq)
-which chromophore to compute the ICs (chromohpore= 'HbO' or 'HbR')
-the minimum number of ICs to be computed (MinIc)
-which condition to analyze (condition)
"""
cla()
close()
pretime = 2
posttime = 20
# arq = '6'
# cromophore = 'HbR'
if cromophore == 'HbO':
crmo = 0
if cromophore == 'HbR':
crmo = 1
# MinIc = 3
IcFor = range(MinIc,4)
# Define the file paths and file names
nonlin = 'gaus'
# Set the name of the folder to save the results in
#The figures folder
fol = 'Output/Min{2}/{0}/{1}'.format(os.path.split(arq)[1],cromophore,MinIc)
folder = '{0}/{1}'.format(fol, nonlin)
if not os.path.exists(folder):
os.makedirs(folder)
#The .mat files folder
folder2 = 'Output/MatFiles/Min = {0}'.format(MinIc)
if not os.path.exists(folder2):
os.makedirs(folder2)
#Read the group averages
# avgFiles = glob.glob('Input/*.mat')
#
# group_avg = sio.loadmat(avgFiles[0])
# group_avg_withoutss = sio.loadmat(avgFiles[1])
#
# #Get only the group HRF results
# avgHRF = read_group(group_avg)
# avgHRF_withoutss = read_group(group_avg_withouss)
#Load the Homer2 data into a hmr2 object
filecw6 = sio.loadmat(arq,appendmat = False)
d1 = hmr2(filecw6,condition)
del filecw6
filecw6 = sio.loadmat(arq_withSS,appendmat = False)
d1.HRF_withSS = filecw6['dcAvg'][:,:,:,condition]
del filecw6
# Resample the data to remove the unwated stimulus
if condition == 1:
resample_aux = find(d1.s == 1)
resample_pts = range(resample_aux[0]-15*d1.fs,resample_aux[-1]+30*d1.fs)
elif condition == 0:
resample_aux = find(d1.s == 1)
resample_pts = range(0,resample_aux[-2]+30*d1.fs)
d1 = hmr2.Resample(d1,resample_pts)
d1 = hmr2.CalcOD(d1,100)
d1.dod = d1.dOD
fb,fa = sp.signal.butter(4,array([0.0001,2])*2/d1.fs,btype='bandpass')
d1.dod = sp.signal.filtfilt(fb,fa,d1.dod)
d1.conc = hmr2.MBLL(d1,d1.dod,6)
del d1.dOD
schan = []
for i in range(len(d1.Chan)):
rho = np.linalg.norm(d1.SrcPos[d1.ml[i,0]-1,:]-d1.DetPos[d1.ml[i,1]-1,:])
if rho <= 15:
schan.append(i)
###########################################################################
canais = array([29,32,34])
###########################################################################
## Mean HRF for the large channels
mHRF_large = mean(d1.HRF[:,crmo,canais],1)
mHRF_large_withSS = mean(d1.HRF_withSS[:,crmo,canais],1)
close()
cla()
# mHRF_large /= max(abs(mHRF_large))
plot(d1.tHRF,mHRF_large,'red')
plot(d1.tHRF,mHRF_large_withSS,'black')
## Mean HRF for the short channels
mHRF_short = mean(d1.HRF[:,crmo,schan],1)
# mHRF_short /= max(abs(mHRF_short))
plot(d1.tHRF,mHRF_short,'blue')
savefig('{0}/mHRF.png'.format(fol),format='png')
plt.show()
close()
cla()
contralateral_channels = range(21,42)
HRF_MITC_HbO = np.zeros((len(d1.Chan)))
HRF_MITC_HbR = np.zeros((len(d1.Chan)))
for i in range(len(d1.Chan)):
HRF_MITC_HbO[i] = MITC(d1,d1.conc[:,i,0],pretime,posttime)
HRF_MITC_HbR[i] = MITC(d1,d1.conc[:,i,1],pretime,posttime)
close()
cla()
#
# return d1, HRF_MITC_HbO, HRF_MITC_HbR
magica = 0
for nic in IcFor:
print nic
y = mdp.fastica(d1.conc[:,canais,crmo],g='tanh',white_comp= nic,mu=0.8)
close()
cla()
freq = np.fft.rfftfreq(d1.t.size,d = 1/d1.fs)
amin = find(freq>= 0.005)[0]
amax = find(freq>= 20)[0]
yfft = np.zeros((size(y,0),size(y,1)))
yfft2 = np.zeros((size(y,0)/2+1,size(y,1)))
resp_frac = np.zeros((size(y,1)))
fb,fa = sp.signal.butter(5,array([3])*2/d1.fs,btype='low')
for i in range(size(y,1)):
y[:,i] = sp.signal.filtfilt(fb,fa,y[:,i])
y[:,i] /= max(abs(y[:,i]))
# yfft2[:,i] = abs(np.fft.fft(y[:,i]))**2
yfft2[:,i] = abs(np.fft.rfft(y[:,i]))**2
# yfft2[:,i] /= max(abs(yfft2[:,i]))
# yfft2[:,i] = abs(real(np.fft.fft(y[:,i])))
dummy1 = find(freq>=0.01)
dummy2 = find(freq>=0.1)
dummy3 = find(freq>=2)
fnoise = 1/freq**2
yfft2[:,i] -= fnoise
# #Define the threshold (1/f area)
fthr_aux1 = sp.integrate.simps(y=fnoise[dummy1[0]:dummy2[0]]**2, x=freq[dummy1[0]:dummy2[0]], dx=freq[1]-freq[0])
fthr_aux2 = sp.integrate.simps(y=fnoise[dummy2[0]:dummy3[0]]**2, x=freq[dummy2[0]:dummy3[0]], dx=freq[1]-freq[0])
fthr = fthr_aux2/fthr_aux1
#Area for the activation region
activ_area = sp.integrate.simps(yfft2[dummy1[0]:dummy2[0],i],freq[dummy1[0]:dummy2[0]], dx=freq[1]-freq[0])
resp_area = sp.integrate.simps(yfft2[dummy2[0]:dummy3[0],i],freq[dummy2[0]:dummy3[0]], dx=freq[1]-freq[0])
resp_frac[i] = round((resp_area/activ_area) - fthr,2)
#
# print 'areas:', fthr, resp_frac[i]
## Original Resp_frac
# resp = max(yfft2[dummy1[0]:dummy2[0],i])
# dummy1 = find(freq>=0.01)
# dummy2 = find(freq>=0.05)
# activ = max(yfft2[dummy1[0]:dummy2[0],i])
# resp_frac[i] = round(resp/activ,2)
mitc = np.zeros((size(y,1)))
y_full = np.zeros(y.shape)
for i in range(size(y,1)):
# y_full[:,i] = y[:,i]
# y[:,i] = lob.BandPassFilt(y[:,i],d1.fs,0.01,0.5,3,5)
mitc[i] = MITC(d1,y[:,i],pretime,posttime)
corr_stim = mitc
ts, mICA = lob.HRFAvgICA(d1, y, pretime,posttime)
mHRF_short /= max(abs(mHRF_short))
mHRF_large /= max(abs(mHRF_large))
mHRF_large_withSS /= max(abs(mHRF_large_withSS))
for i in range(nic):
# mICA[:,i] = lob.BandPassFilt(mICA[:,i],d1.fs,0.01,0.5,3,5)
# mICA[:,i] = ndimage.gaussian_filter(mICA[:,i],3)
mICA[:,i] /= max(abs(mICA[:,i]))
##Cross correlation
corr_large = np.zeros((size(y,1)))
for i in range(size(y,1)):
corr_large[i] = round(np.corrcoef(mICA[:,i],mHRF_large)[0,1],2)
corr_short = np.zeros((size(y,1)))
for i in range(size(y,1)):
corr_short[i] = round(np.corrcoef(mICA[:,i],mHRF_short)[0,1],2)
corr_withss = np.zeros((size(y,1)))
for i in range(size(y,1)):
corr_withss[i] = round(np.corrcoef(mICA[:,i],mHRF_large_withSS)[0,1],2)
# corr_hmr = np.zeros((size(y,1)))
# for i in range(size(y,1)):
# corr_hmr[i] = round(np.corrcoef(mICA[:,i],mHRF_hmr)[0,1],2)
close()
cla()
# for i in range(size(y,1)):
# mICA[:,i] = ndimage.gaussian_filter(mICA[:,i],)
fig, axes = plt.subplots(nrows=size(y,1), ncols=3, figsize=(13, 18))
fig.subplots_adjust(wspace=0.24, hspace=0.33, bottom=0.05)
# aux1 = max(max(yfft2[amin:amax,i]) for i in range(size(y,1)))
# aux2 = min(min(yfft2[amin:amax,i]) for i in range(size(y,1)))
# Turn off tick labels everywhere
# for ax in axes.flat:
# for axis in [ax.xaxis, ax.yaxis]:
# axis.set_ticklabels([])
for (i,j), ax in np.ndenumerate(axes):
if j==0:
ax.plot(d1.t,y[:,i])
# ax.plot(d1.t,y[:,i],'red')
ax.plot(d1.t,(d1.s*max(max(y[:,i]),max(y_full[:,i]))),'black',linewidth=3.0)
ax.set_yticklabels([])
ax.set_xlim(left=d1.t[0],right=d1.t[-1])
ax.annotate('{0}'.format(corr_stim[i]), xy=(0.01, 0.5),
xycoords='axes fraction', rotation=90, va='center',
ha='right', size = 15)
if j==1:
dummy1 = find(freq>=0.005)
dummy2 = find(freq>=5)
# fnoise /= max(abs(fnoise))
# ax.semilogx(freq,yfft[:,i])
# f, Pxx_den = sp.signal.periodogram(y_full[:,i],d1.fs)
# ax.semilogx(f,Pxx_den)
ax.loglog(freq,yfft2[:,i])
ax.loglog(freq,fnoise,'black')
ax.set_xlim(left=0.005,right=25)
# ax.set_ylim(0,1)
ax.annotate('{0}'.format(resp_frac[i]), xy=(0.01, 0.5),
xycoords='axes fraction', rotation=90, va='center',
ha='right', size = 15)
# ax.set_ylim(bottom=aux2,top=aux1)
# ax.set_yticks((aux1,aux2))
ax.set_yticklabels([])
# ax.set_xticks(ticks)
# ax.set_xticklabels(tickslabel)
if j==2:
bux1 = max(mICA[:,i])
bux2 = min(mICA[:,i])
ax.plot(ts,mICA[:,i])
ax.set_yticklabels([])
ax.annotate('M {0}'.format(corr_large[i]), xy=(1, 0.5),
xycoords='axes fraction', rotation=90, va='center',
ha='right', size = 15)
ax.annotate('SS {0}'.format(corr_withss[i]), xy=(1.2, 0.5),
xycoords='axes fraction', rotation=90, va='center',
ha='right', size = 15)
ax.annotate('SH {0}'.format(corr_short[i]), xy=(0, 0.5),
xycoords='axes fraction', rotation=90, va='center',
ha='right', size = 15)
ax.axvspan(0, 5, facecolor='0.8', edgecolor ='0.8', alpha=0.5)
# if j==2:
# cor = abs(corr[i,:])
# ax.plot(atraso,cor)
# a = min(cor)
# b = max(cor)
# ax.set_ylim(bottom = a-0.01*a, top = b+0.01*b)
# ax.set_yticks((a,b))
# ax.set_yticklabels(('%.2f'%a,'%.2f'%b))
#
# corr = np.zeros(nic)
# for i in range(nic):
# corr = np.corrcoef(d1.s[:,0],y[:,i])[0,1]
# axes[i,0.5].annotate('{0}'.format("%.2f" %corr), xy=(-0.01, 0.5),
# xycoords='axes fraction', rotation=90, va='center', ha='right')
savefig('{0}/{1}.png'.format(folder,nic),format='png')
close()
cla()
aaa = find(corr_stim>=0.4)
bbb = find(resp_frac<=0)
ics_final = [val for val in aaa if val in bbb]
if (len(ics_final) != 0):
if (len(ics_final) != 1):
print('WARNING: Two or more results are being plotted.')
# with file('{0}/results.txt'.format(fol), 'a') as outfile:
# for jj in ics_final:
# outfile.write('Results for the IC on the line n {0}\n'.format(jj+1))
# outfile.write('Corellation with large channels = {0}\n'.format(corr_large[jj]))
# outfile.write('Correlation with short channels= {0}\n'.format(corr_short[jj]))
# outfile.write('Correlation with stimulus = {0}\n'.format(corr_stim[jj]))
# outfile.write('R frac = {0}\n'.format(resp_frac[jj]))
# outfile.write('Number of ICs needed {0}\n\n\n'.format(nic))
#
fig, axes = plt.subplots(ncols=len(ics_final), nrows=1,figsize=(len(ics_final)*9,5))#,figsize=(9,7))
fig.subplots_adjust(wspace=0, hspace=0.7, bottom=0.2)
if len(ics_final) != 1:
MinShort = find(abs(corr_short) == min(abs(corr_short[ics_final])))
for kk in range(len(ics_final)):
## Correction for negative correlation
# corr_large[ics_final[kk]] = -corr_large[ics_final[kk]]
# corr_short[ics_final[kk]] = -corr_short[ics_final[kk]]
# corr_large[ics_final[kk]] = -corr_large[ics_final[kk]]
if len(ics_final) == 2:
hh = max(abs(corr_short[ics_final[kk]]),abs(corr_large[ics_final[kk]]))
if hh == abs(corr_short[ics_final[kk]]) and corr_short[ics_final[kk]]<0 or hh == abs(corr_large[ics_final[kk]]) and corr_large[ics_final[kk]]<0:
mICA[:,ics_final[kk]]=-mICA[:,ics_final[kk]]
corr_short[ics_final[kk]] = -corr_short[ics_final[kk]]
corr_large[ics_final[kk]] = -corr_large[ics_final[kk]]
# corr_hmr[ics_final[kk]] = -corr_hmr[ics_final[kk]]
if ics_final[kk] == MinShort.all() and corr_large[ics_final[kk]]<0:
mICA[:,ics_final[kk]]=-mICA[:,ics_final[kk]]
corr_short[ics_final[kk]] = -corr_short[ics_final[kk]]
corr_large[ics_final[kk]] = -corr_large[ics_final[kk]]
# corr_hmr[ics_final[kk]] = -corr_hmr[ics_final[kk]]
if ics_final[kk] != MinShort.all() and corr_short[ics_final[kk]] <0:
mICA[:,ics_final[kk]]=-mICA[:,ics_final[kk]]
corr_short[ics_final[kk]] = -corr_short[ics_final[kk]]
corr_large[ics_final[kk]] = -corr_large[ics_final[kk]]
# corr_hmr[ics_final[kk]] = -corr_hmr[ics_final[kk]]
# if abs(corr_short[ics_final[kk]]) == min(abs(corr_short[ics_final])) and corr_large[ics_final[kk]]>0 and inverteu ==1:
# mICA[:,ics_final[kk]]=-mICA[:,ics_final[kk]]
# if abs(corr_short[ics_final[kk]]) == min(abs(corr_short[ics_final])) and corr_large[ics_final[kk]]<0 and inverteu ==0:
# mICA[:,ics_final[kk]]=-mICA[:,ics_final[kk]]
## Normalization
# mICA[:,ics_final[kk]] -= min(mICA[:,ics_final[kk]])
# mICA[:,ics_final[kk]] /= max(mICA[:,ics_final[kk]])
# mHRF_large -= min(mHRF_large)
# mHRF_large /= max(mHRF_large)
# mHRF_short -= min(mHRF_short)
# mHRF_short /= max(mHRF_short)
mHRF_short /= max(abs(mHRF_short))
mHRF_large /= max(abs(mHRF_large))
mHRF_large_withSS /= max(abs(mHRF_large_withSS))
mICA[:,ics_final[kk]] /= max(abs(mICA[:,ics_final[kk]]))
axes[kk].plot(ts,mICA[:,ics_final[kk]],'black',label='HRF with ICA')
axes[kk].plot(ts,mHRF_large,'red', label = 'Block-Average HRF from long channels',lw = 3)
axes[kk].plot(ts,mHRF_short,'blue', label = 'Block-Average HRF from short Channels',lw = 3)
axes[kk].plot(ts,mHRF_large_withSS,'green', label = 'HRF with SS', lw=3)
axes[kk].set_ylim(-1.05,1.05)
axes[kk].set_xlim(-pretime,posttime)
box = axes[kk].get_position()
axes[kk].set_position([box.x0, box.y0, box.width * 0.8, box.height])
# axes[kk,0].legend()
axes[kk].set_xlabel('Time(s)', size='xx-large')
axes[kk].set_ylabel('Normalized Concentration', size='xx-large')
axes[kk].set_title('IC {0}'.format(kk+1), size='xx-large')
axes[kk].axvspan(0, 5, facecolor='0.8', edgecolor ='0.8', alpha=0.5)
for tick in axes[kk].xaxis.get_major_ticks():
tick.label.set_fontsize('x-large')
for tick in axes[kk].yaxis.get_major_ticks():
tick.label.set_fontsize('x-large')
#
# axes[1].plot(ts,mICA[:,a],label='mICA')
# # axes[1].plot(ts,mHRF2,'red', label = 'mHRF',lw = 3)
# # axes[1].set_ylim(min(min(mICA[:,a]),min(mHRF2))-0.05,1.05)
# axes[1].legend()
# with file('Output/test.txt', 'a') as outfile:
# axes[1].set_ylabel('Normalized Intensity', size='x-large')
# axes[1].set_title('(B)', size='xx-large')
# axes[1].axvspan(0, 30, facecolor='0.8', edgecolor ='0.8', alpha=0.5)
#
# axes[kk,1].loglog(freq,yfft2[:,ics_final[kk]],label='FFT of the IC')
# axes[kk,1].set_ylim(1,1.15*max(yfft2[:,ics_final[kk]]))
# axes[kk,1].set_xlim(0,2)
# axes[kk,1].set_xlabel('Frequency(Hz)', size='x-large')
# axes[kk,1].set_ylabel('Intensity', size='x-large')
# axes[kk,1].set_title('(B,{0})'.format(ics_final[kk]), size='xx-large')
# # axes[kk,1].legend()
# axes[2].plot(ts,mHRF)
# axes[2].set_xlabel('Time(s)', size='x-large')
# axes[2].set_ylabel('Intensity', size='x-large')
# axes[2].set_title('(C)', s ize='xx-large')
lgd = axes[1].legend(loc='center left', bbox_to_anchor=(1.05,0.5))
plt.savefig('{0}/RESULT, NIC = {1}.pdf'.format(fol,nic),format='pdf',bbox_extra_artists=(lgd,), bbox_inches='tight')
plt.savefig('{0}/RESULT, NIC = {1}.png'.format(fol,nic),format='png',bbox_extra_artists=(lgd,), bbox_inches='tight')
close()
cla()
else:
# Correction for negative correlation
hh = max(abs(corr_short[ics_final]),abs(corr_large[ics_final]))
if hh == abs(corr_short[ics_final]) and corr_short[ics_final]<0 or hh == abs(corr_large[ics_final]) and corr_large[ics_final]<0:
mICA[:,ics_final]=-mICA[:,ics_final]
corr_short[ics_final] = -corr_short[ics_final]
corr_large[ics_final] = -corr_large[ics_final]
# corr_hmr[ics_final] = -corr_hmr[ics_final]
## Normalization
# mICA[:,ics_final] -= min(mICA[:,ics_final])
# mICA[:,ics_final] /= max(mICA[:,ics_final])
# mHRF_large -= min(mHRF_large)
# mHRF_large /= max(mHRF_large)
# mHRF_short -= min(mHRF_short)
# mHRF_short /= max(mHRF_short)
mHRF_short /= max(abs(mHRF_short))
mHRF_large /= max(abs(mHRF_large))
# mHRF_hmr /= max(abs(mHRF_hmr))
mICA[:,ics_final] /= max(abs(mICA[:,ics_final]))
axes.plot(ts,mICA[:,ics_final],'black',label='Mean ICA')
axes.plot(ts,mHRF_large,'red', label = 'Block-Average HRF from long channels',lw = 3)
axes.plot(ts,mHRF_short,'blue', label = 'Block-Average HRF from short channels',lw = 3)
axes.plot(ts,mHRF_large_withSS,'green', label = 'HRF with SS', lw=3)
axes.set_ylim(-1.05,1.05)
axes.set_xlim(-pretime,posttime)
box = axes.get_position()
axes.set_position([box.x0, box.y0, box.width * 0.8, box.height])
lgd = axes.legend(loc='center left', bbox_to_anchor=(1, 0.5))
# axes[kk,0].legend()
axes.set_xlabel('Time(s)', size='x-large')
axes.set_ylabel('Normalized Concentration', size='x-large')
axes.axvspan(0, 5, facecolor='0.8', edgecolor ='0.8', alpha=0.5)
#
# axes[1].plot(ts,mICA[:,a],label='mICA')
# # axes[1].plot(ts,mHRF2,'red', label = 'mHRF',lw = 3)
# # axes[1].set_ylim(min(min(mICA[:,a]),min(mHRF2))-0.05,1.05)
# axes[1].legend()
# with file('Output/test.txt', 'a') as outfile:
# axes[1].set_ylabel('Normalized Intensity', size='x-large')
# axes[1].set_title('(B)', size='xx-large')
# axes[1].axvspan(0, 30, facecolor='0.8', edgecolor ='0.8', alpha=0.5)
# #
# axes[1].loglog(freq,yfft2[:,ics_final],label='FFT of the IC')
# axes[1].set_ylim(1,1.15*max(yfft2[:,ics_final]))
# axes[1].set_xlim(0,2)
# axes[1].set_xlabel('Frequency(Hz)', size='x-large')
# axes[1].set_ylabel('Intensity', size='x-large')
# axes[1].set_title('(B)', size='xx-large')
# axes[kk,1].legend()
# axes[2].plot(ts,mHRF)
# axes[2].set_xlabel('Time(s)', size='x-large')
# axes[2].set_ylabel('Intensity', size='x-large')
# axes[2].set_title('(C)', size='xx-large')
plt.savefig('{0}/RESULT, NIC = {1}.pdf'.format(fol,nic),format='pdf', bbox_extra_artists=(lgd,), bbox_inches='tight')
plt.savefig('{0}/RESULT, NIC = {1}.png'.format(fol,nic),format='png', bbox_extra_artists=(lgd,), bbox_inches='tight')
close()
cla()
magica += 1
if magica == 1:
# scipy.io.savemat('OutputArtigo/MatFiles/Min = {2}/Min{2}_{1}-{0}({3}).mat'.format(arq,cromophore,MinIc,len(ics_final)),
# mdict={'ts':ts, 'large_HRF': mHRF_large, 'short_HRF': mHRF_short,
# 'change': change, 'mICA': mICA, 'corr_large': corr_large,
# 'corr_short': corr_short, 'corr_stim': corr_stim,
# 'resp_frac':resp_frac, 'ics_final': ics_final, 'mHRF_large': mHRF_large,
# 'mHRF_short': mHRF_short, 'mHRF_hmr': mHRF_hmr, 'corr_hmr': corr_hmr})
return
sys.exit()
def decompose_ica(spectrum_array): print '\nDecomposing spectra using ICA...' ics=n.transpose(mdp.fastica(spectrum_array,whitened=True)) return ics
from mdp import fastica
from scikits.audiolab import wavread, wavwrite
from numpy import abs, max
# Load in the stereo file
recording, fs, enc = wavread('./train/input/mixed_1.wav')
# Perform FastICA algorithm on the two channels
sources = fastica(recording)
# The output levels of this algorithm are arbitrary, so normalize them to 1.0.
sources /= max(abs(sources), axis=0)
# Write back to a file
wavwrite(sources, 'sources.wav', fs, enc)
# Mostly from http://www.endolith.com/wordpress/2009/11/22/a-simple-fastica-example/
from mdp import fastica
from scikits.audiolab import wavread, wavwrite
from numpy import abs, max, array
# Load in the microphone audio files
mic1, fs1, enc1 = wavread('channel1.wav')
mic2, fs2, enc2 = wavread('channel2.wav')
mic3, fs3, enc3 = wavread('channel3.wav')
mic4, fs4, enc4 = wavread('channel4.wav')
# transpose() because MDP expects each COLUMN to be an
# observed data stream. Each ROW is one observation of that data across
# all data streams.
sources = fastica(array([mic1, mic2, mic3, mic4]).transpose())
# The output levels of this algorithm are arbitrary, so normalize them to 1.0.
sources /= max(abs(sources), axis=0)
(frames, inputs) = sources.shape
# Write one output file for each resulting ICA transform.
for i in range(inputs):
sourceColumn = sources[:, [i]] # extract a column from the numpy ndarray
wavwrite(sourceColumn, "resolved-source%d.wav" % i, fs1, enc1)
from mdp import fastica
from scikits.audiolab import wavread, wavwrite
from numpy import abs, max
# Load in the stereo file
recording, fs, enc = wavread('test.wav')
# Perform FastICA algorithm on the two channels
sources = fastica(recording)
# The output levels of this algorithm are arbitrary, so normalize them to 1.0.
sources /= (5 * max(abs(sources), axis = 0))
# Write back to a file
wavwrite(sources, 'testout.wav', fs, enc)
def ica(data, precision='float32'):
return (mdp.fastica(data, dtype=precision))
gaussian_pca.learn(xG) xg = gaussian_pca.transform(xG, k=2) ######################################################################## """-------Implement kernel PCA with polynomial kernel------- """ xP= mlpy.kernel_polynomial(z,z, gamma=1.0, b=1.0, d=2.0) # polynomial kernel matrix polynomial_pca = mlpy.KPCA() polynomial_pca.learn(xP) xp = polynomial_pca.transform(xP, k=3) print 'Implementing Kernel PCA' ######################################################################## """-------Implement FastICA------- """ ica = mdp.fastica(z, dtype='float32') """ Implement PCA """ pcan1 = mdp.nodes.CuBICANode() pcar1 = pcan1.execute(z) pcan2 = mdp.nodes.PCANode(output_dim=3) pcar2 = pcan2.execute(z) """-------Select pcar1 as the principal component------- """ x_pc=pcar1 ######################################################################## """-------Implement KMeans------- """ (res1,idx1,plot_id1)=calc_kmeans.getplotid(z,2) (res2,idx2,plot_id2)=calc_kmeans.getplotid(z,3)
import mdp
import numpy as np
A = np.array(
[[1, 2, 3, 4, 5, 6, 7, 8],
[3, 4, 4, 5, 5, 6, 7, 9],
[1, 8, 2, 7, 3, 6, 4, 5],
[9, 8, 7, 6, 5, 4, 3, 2],
[9, 4, 8, 3, 7, 2, 6, 1],
[2, 3, 2, 4, 2, 5, 2, 6],
[3, 4, 3, 4, 4, 3, 4, 3],
[3, 2, 4, 3, 2, 4, 3, 2],
[5, 5, 4, 4, 6, 6, 2, 2],
[2, 3, 6, 5, 4, 6, 7, 2],
[1, 6, 5, 3, 8, 2, 3, 9]])
# perform ICA on some data x using single precision
y = mdp.fastica(A, dtype='float32')
print y