def generateCorrelations(self,doDetrend=True):
# auto correlation corefficient of u
if doDetrend:
ux=signal.detrend(self.ux());
uy=signal.detrend(self.uy());
uz=signal.detrend(self.uz());
umag=signal.detrend(self.Umag());
else:
ux=self.ux();
uy=self.uy();
uz=self.uz();
umag=self.Umag();
#ux=ux[-samples:-1]
#uy=uy[-samples:-1]
#uz=uz[-samples:-1]
self.data['r11'],self.data['taur11'] = tt.xcorr_fft(ux, maxlags=None, norm='coeff')
self.data['r22'],self.data['taur22'] = tt.xcorr_fft(uy, maxlags=None, norm='coeff')
self.data['r33'],self.data['taur33'] = tt.xcorr_fft(uz, maxlags=None, norm='coeff')
self.data['r12'],self.data['taur12'] = tt.xcorr_fft(ux,y=uy, maxlags=None, norm='coeff')
self.data['r13'],self.data['taur13'] = tt.xcorr_fft(ux,y=uz, maxlags=None, norm='coeff')
self.data['r23'],self.data['taur23'] = tt.xcorr_fft(uy,y=uz, maxlags=None, norm='coeff')
self.data['rmag'],self.data['taurmag'] = tt.xcorr_fft(umag, maxlags=None, norm='coeff')
# auto correlation of u
self.data['R11'],self.data['tauR11'] = tt.xcorr_fft(ux, maxlags=None, norm='biased')
self.data['R22'],self.data['tauR22'] = tt.xcorr_fft(uy, maxlags=None, norm='biased')
self.data['R33'],self.data['tauR33'] = tt.xcorr_fft(uz, maxlags=None, norm='biased')
def remt(st):
'''
rmean and retrend
'''
st.data = detrend(st.data, type='linear')
st.data = detrend(st.data, type='constant')
return st
def __init__(self, path):
# convertir el archivo a objeto python
self.doc2event(path)
# @warning: se requieren convertir las matrices y los atributos que
# tienen puntos a arrays y a atributos de estructuras respectivamenente
#convertimos todos los sismos a campos de desplazamiento
acelerometers_id = [76, 82, 118, 126, 146, 147]
#transformar todo a campo de desplazamiento
for s in self.seismograms:
#guardar los datos crudos para analisis posteriores
s.raw_data = s.data
# si es acelerometro
if s.site_id in acelerometers_id:
s.data = sig.detrend(np.cumsum(sig.detrend(np.cumsum(s.data[
:,2:5], axis=0), axis=0), axis=0), axis=0)
# si es velocimetro
else:
s.data = sig.detrend(np.cumsum(s.data[:, 2:5], axis=0), axis=0)
timevector = s.timevector
s.data = pd.DataFrame(s.data, index = timevector)
s.raw_data = pd.DataFrame(s.raw_data[:,2:5], index = timevector)
pass
def slidingWindow(P,inX=3,outX=32,inY=3,outY=64,maxM=50,norm=True):
""" Enhance the constrast
Cut off extreme values and demean the image
Utilize scipy convolve2d to get the mean at a given pixel
Remove local mean with inner exclusion region
Args:
P: 2-d numpy array image
inX: inner exclusion region in the x-dimension
outX: length of the window in the x-dimension
inY: inner exclusion region in the y-dimension
outY: length of the window in the y-dimension
maxM: size of the output image in the y-dimension
norm: boolean to cut off extreme values
Returns:
Q: 2-d numpy contrast enhanced
"""
Q = P.copy()
m, n = Q.shape
Q = exposure.equalize_hist(Q.astype('Float32'), nbins = 65)
Q = detrend(Q.astype('Float32'), axis = 1)
Q = detrend(Q.astype('Float32'), axis = 0)
Q = wiener(Q.astype('Float32'), 4)
return Q[:maxM,:]
def phases_from_complex(wts, continuous=False, do_detrend=False):
"""Calculates phases from 1d or 2d wavelet/hilbert arrays, dim0 is time"""
if len(wts.shape) == 1:
#1d
phasen = n.arctan2(wts.imag,wts.real)
if not (continuous or do_detrend):
return phasen
else:
phasen = make_phases_continuous(phasen)
if do_detrend:
phasen = detrend(phasen,axis=0)
return phasen
elif len(wts.shape) == 2:
#2d
phasen = n.arctan2(wts.imag,wts.real)
if not (continuous or do_detrend):
return phasen
else:
phasen = make_phases_continuous(phasen)
if do_detrend:
phasen = detrend(phasen,axis=0)
return phasen
else:
raise ValueError("Only 1d and 2d arrays supported")
def preProcess(self,
periodF0 = 0.06,
deltaF_div_F0 = True,
max_threshold = None,
min_threshold = None,
nan_to_zeros = True,
detrend = False,
#~ band_filter = None,
gaussian_filter = None,
f1 = None,
f2 = None,
**kargs):
images = self.images
if deltaF_div_F0:
ind = self.t()<=self.t_start+periodF0
m0 = mean(images[ind,:,:] , axis = 0)
images = (images-m0)/m0*1000.
if max_threshold is not None:
#~ images[images>max_threshold] = max_threshold
images[images>max_threshold] = nan
if min_threshold is not None:
#~ images[images<min_threshold] = min_threshold
images[images<min_threshold] = nan
if nan_to_zeros:
images[isnan(images) ] = 0.
if detrend and not nan_to_zeros:
m = any(isnan(images) , axis = 0)
images[isnan(images) ] = 0.
images = signal.detrend( images , axis = 0)
images[:,m] = nan
elif detrend and nan_to_zeros:
images = signal.detrend( images , axis = 0)
if gaussian_filter is not None:
images = ndimage.gaussian_filter( images , (0 , gaussian_filter , gaussian_filter))
if f1 is not None or f2 is not None:
from ..computing.filter import fft_passband_filter
if f1 is None: f1=0.
if f2 is None: f1=inf
nq = self.sampling_rate/2.
images = fft_passband_filter(images, f_low = f1/nq , f_high = f2/nq , axis = 0)
return images
def preprocess(matr, prepr, Fs, fc_min, fc_max, taper_fract):
"""
:type matr: numpy.ndarray
:param matr: time series of used stations (dim: [number of samples, number of stations])
:type prepr: integer
:param prepr: type of preprocessing. 0=None, 1=bandpass filter, 2=spectral whitening
:type Fs: float
:param Fs: sampling rate of data streams
:type fc_min, fc_max: float
:param fc_min, fc_max: corner frequencies used for preprocessing
:type taper_fract: float
:param taper_fract: percentage of frequency band which is tapered after spectral whitening
:return: preprocessed data (dim: [number of samples, number of stations])
"""
if prepr == 0:
data = signal.detrend(matr, axis=0)
elif prepr == 1:
# generate frequency vector and butterworth filter
b, a = signal.butter(4, np.array([fc_min, fc_max]) / Fs * 2, btype="bandpass")
# filter data and normalize it by maximum energy
data = signal.filtfilt(b, a, signal.detrend(matr, axis=0), axis=0)
fact = np.sqrt(np.dot(np.ones((data.shape[0], 1)), np.sum(data**2, axis=0).reshape((1, data.shape[1]))))
data = np.divide(data, fact)
elif prepr == 2:
nfft = nearest_powof2(matr.shape[0])
Y = np.fft.fft(matr, n=nfft, axis=0)
f = np.fft.fftfreq(nfft, 1./float(Fs))
# whiten: discard all amplitude information within range fc
Y_white = np.zeros(Y.shape)
J = np.where((f > fc_min) & (f < fc_max))
Y_white[J, :] = np.exp(1j * np.angle(Y[J, :]))
# now taper within taper_fract
deltaf = (fc_max - fc_min) * taper_fract
Jdebut = np.where((f > fc_min) & (f < (fc_min + deltaf)))
Jfin = np.where((f > (fc_max - deltaf)) & (f < fc_max))
for ii in range(Y.shape[1]):
if len(Jdebut[0]) > 1:
Y_white[Jdebut, ii] = np.multiply(Y_white[Jdebut, ii],
np.sin(np.pi / 2 * np.arange(0, len(Jdebut[0])) / len(Jdebut[0]))**2)
if len(Jfin[0]) > 1:
Y_white[Jfin, ii] = np.multiply(Y_white[Jfin, ii],
np.cos(np.pi / 2 * np.arange(0, len(Jfin[0])) / len(Jfin[0]))**2)
# perform inverse fft to obtain time signal
# data = 2*np.real(np.fft.ifft(Y_white, n=nfft, axis=0))
data = np.fft.ifft(Y_white, n=nfft, axis=0)
# normalize it by maximum energy
fact = np.sqrt(np.dot(np.ones((data.shape[0], 1)), np.sum(data**2, axis=0).reshape((1, data.shape[1]))))
data = np.divide(data, fact)
return data
def generateStatistics(self,doDetrend=True):
'''
Generates statistics and populates member variable data.
Arguments:
doDetrend: detrend data bevor sigbal processing
Populates the "data" python dict with with the following keys:
rii: [numpy.array of shape=(?)] Auto-correlation coefficent rii. For i=1,2,3
taurii: [numpy.array of shape=(?)] Time lags for rii. For i=1,2,3
Rii: [numpy.array of shape=(?)] Auto-correlation Rii. For i=1,2,3
tauRii: [numpy.array of shape=(?)] Time lags for Rii. For i=1,2,3
uifrq: [numpy.array of shape=(?)] u1 in frequency domain. For i=1,2,3
uiamp: [numpy.array of shape=(?)] amplitude of u1 in frequency domain. For i=1,2,3
Seiifrq:[numpy.array of shape=(?)] Frequencies for energy spectrum Seii. For i=1,2,3
Seii: [numpy.array of shape=(?)] Energy spectrum Seii derived from Rii. For i=1,2,3
'''
# auto correlation corefficient of u
if doDetrend:
ux=signal.detrend(self.ux());
uy=signal.detrend(self.uy());
uz=signal.detrend(self.uz());
umag=signal.detrend(self.Umag());
else:
ux=self.ux();
uy=self.uy();
uz=self.uz();
umag=self.Umag();
#ux=ux[-samples:-1]
#uy=uy[-samples:-1]
#uz=uz[-samples:-1]
self.data['r11'],self.data['taur11'] = tt.xcorr_fft(ux, maxlags=None, norm='coeff')
self.data['r22'],self.data['taur22'] = tt.xcorr_fft(uy, maxlags=None, norm='coeff')
self.data['r33'],self.data['taur33'] = tt.xcorr_fft(uz, maxlags=None, norm='coeff')
self.data['r12'],self.data['taur12'] = tt.xcorr_fft(ux,y=uy, maxlags=None, norm='coeff')
self.data['r13'],self.data['taur13'] = tt.xcorr_fft(ux,y=uz, maxlags=None, norm='coeff')
self.data['r23'],self.data['taur23'] = tt.xcorr_fft(uy,y=uz, maxlags=None, norm='coeff')
self.data['rmag'],self.data['taurmag'] = tt.xcorr_fft(umag, maxlags=None, norm='coeff')
# auto correlation of u
self.data['R11'],self.data['tauR11'] = tt.xcorr_fft(ux, maxlags=None, norm='none')
self.data['R22'],self.data['tauR22'] = tt.xcorr_fft(uy, maxlags=None, norm='none')
self.data['R33'],self.data['tauR33'] = tt.xcorr_fft(uz, maxlags=None, norm='none')
#u in frequency domain
self.data['u1frq'],self.data['u1amp'] = tt.dofft(sig=ux,samplefrq=self.data['frq'])
self.data['u2frq'],self.data['u2amp'] = tt.dofft(sig=uy,samplefrq=self.data['frq'])
self.data['u3frq'],self.data['u3amp'] = tt.dofft(sig=uz,samplefrq=self.data['frq'])
#Time energy sectrum Se11 (mean: Rii in frequency domain...)
self.data['Se11frq'],self.data['Se11'] = tt.dofft(sig=self.data['R11'],samplefrq=self.data['frq'])
self.data['Se22frq'],self.data['Se22'] = tt.dofft(sig=self.data['R22'],samplefrq=self.data['frq'])
self.data['Se33frq'],self.data['Se33'] = tt.dofft(sig=self.data['R33'],samplefrq=self.data['frq'])
def ts_ft(data, name):
data /= np.max(np.abs(data), axis=0)
plt.subplot(311)
plt.plot(ma.mean(ma.mean(data, 2), 1))
plt.axis('tight')
plt.subplot(312)
plt.plot(signal.detrend(ma.mean(ma.mean(data, 2), 1), axis=0))
plt.axis('tight')
plt.subplot(313)
plt.plot(np.log(np.fft.rfft(ma.mean(ma.mean(signal.detrend(data, axis=0), 2), 1)))[0:365])
plt.axis('tight')
plt.savefig(FIGDIR+'time_freq_'+name+'.png')
plt.close('all')
def summarize_timeseries(functional_path, masks_path, summary):
if type(summary) is not dict:
summary = {'method': summary}
masks_img = [nb.load(mask_path) for mask_path in masks_path]
mask = np.sum(np.array([
mask_img.get_data() for mask_img in masks_img
]), axis=0) > 0.0
if mask.sum() == 0:
raise Exception(
"The provided mask does not contains voxels. "
"Please check if mask is being eroded and if the segmentation worked correctly."
)
functional_img = nb.load(functional_path)
masked_functional = functional_img.get_data()[mask]
regressors = np.zeros(masked_functional.shape[-1])
if summary['method'] == 'Mean':
regressors = masked_functional.mean(0)
if summary['method'] == 'NormMean':
masked_functional /= np.linalg.norm(masked_functional, 2)
regressors = np.nan_to_num(masked_functional).mean(0)
if summary['method'] == 'DetrendNormMean':
masked_functional = \
signal.detrend(masked_functional, type='linear').T
masked_functional /= np.linalg.norm(masked_functional, 2)
regressors = np.nan_to_num(masked_functional).mean(0)
if summary['method'] in ['DetrendPC', 'PC']:
if summary['method'] == 'DetrendPC':
Y = signal.detrend(masked_functional, type='linear').T
else:
Y = masked_functional.T
Yc = Y - np.tile(Y.mean(0), (Y.shape[0], 1))
Yc = np.nan_to_num(Yc / np.tile(np.array(Y.std(0)).reshape(1,Y.shape[1]), (Y.shape[0],1)))
U, _, _ = np.linalg.svd(Yc)
regressors = U[:, 0:summary['components']]
output_file_path = os.path.join(os.getcwd(), 'summary_regressors.1D')
np.savetxt(output_file_path, regressors, fmt='%.18f')
return output_file_path
def standardize(X,stdtype='column'): """Standardizes a two dimensional input matrix X, by either row or column. Resulting matrix will have row or column mean 0 and row or column std. dev. equal to 1.0.""" if len(X.shape) > 2: print 'ERROR: standardize() not defines for matrices that are not two-dimenional' return if stdtype == 'column': F = signal.detrend(X,type='constant',axis=0) F = F/std(F,axis=0) else: F = signal.detrend(X.T,type='constant',axis=0) F = F/std(F,axis=0) F = F.T return F
def generateAutoCorrelations(self,doDetrend=True):
# auto correlation corefficient of u
if doDetrend:
ux=signal.detrend(self.ux());
uy=signal.detrend(self.uy());
uz=signal.detrend(self.uz());
else:
ux=self.ux();
uy=self.uy();
uz=self.uz();
self.data['r11'],self.data['taur11'] = tt.xcorr_fft(ux, maxlags=None, norm='coeff')
self.data['r22'],self.data['taur22'] = tt.xcorr_fft(uy, maxlags=None, norm='coeff')
self.data['r33'],self.data['taur33'] = tt.xcorr_fft(uz, maxlags=None, norm='coeff')
def deriv2_of_horiz_bands(img, hband_size):
"""For each horizontal band in image, calculate second
derivatives of pixel densities.
Divide the image into horizontal bands with each
band consisting of hband_size scanlines.
For each band, sum the pixels in the vertical direction.
Return the second difference of the summation in the
corresponding result row, as well as the detrended
sums divided by the standard deviation of the sums
for each band.
"""
#FIXME: a partial band at the bottom of the image is ignored
img_height, img_width = img.shape[:2]
n_bands = img_height / hband_size
d2 = np.empty((n_bands, img_width-2))
detr = np.empty((n_bands, img_width))
for sl_index in range(n_bands):
window_top = sl_index*hband_size
band = img[window_top:window_top+hband_size,...]
sum_ = band.sum(axis=0)
d2[sl_index,...] = np.diff(sum_, n=2)
dd = -signal.detrend(sum_)
detr[sl_index,...] = dd / dd.std()
return np.pad(d2, ((0,0), (1,1)), 'edge'), detr
def enframe(x, win, inc):
"""
Splits the vector up into (overlapping) frames beginning at increments
of inc. Each frame is multiplied by the window win().
The length of the frames is given by the length of the window win().
The centre of frame I is x((I-1)*inc+(length(win)+1)/2) for I=1,2,...
:param x: signal to split in frames
:param win: window multiplied to each frame, length determines frame length
:param inc: increment to shift frames, in samples
:return f: output matrix, each frame occupies one row
:return length, no_win: length of each frame in samples, number of frames
"""
nx = len(x)
nwin = len(win)
if (nwin == 1):
length = win
else:
# length = next_pow_2(nwin)
length = nwin
nf = int(fix((nx - length + inc) // inc))
# f = np.zeros((nf, length))
indf = inc * np.arange(nf)
inds = np.arange(length) + 1
f = x[(np.transpose(np.vstack([indf] * length)) +
np.vstack([inds] * nf)) - 1]
if (nwin > 1):
w = np.transpose(win)
f = f * np.vstack([w] * nf)
f = signal.detrend(f, type='constant')
no_win, _ = f.shape
return f, length, no_win
def decode_efm():
""" Decode EFM from STDIN, assuming it's a 28Mhz 8bit raw stream """
datao = np.fromstring(sys.stdin.read(SAMPLES), dtype=np.uint8).astype(np.int16)
datao = sps.detrend(datao, type='constant') # Remove DC
datao = auto_gain(datao, 10000, 'pre-filter') # Expand before filtering, since we'll lose much of signal otherwise
low_pass = sps.butter(4, 1.75 / FREQ_MHZ, btype='lowpass') # Low pass at 1.75 Mhz
datao = sps.lfilter(low_pass[0], low_pass[1], datao)
high_pass = sps.butter(4, 0.01333 / FREQ_MHZ, btype='highpass') # High pass at 13.333 khz
datao = sps.lfilter(high_pass[0], high_pass[1], datao)
# This is too slow, need to work out a way to do it in scipy
de_emphasis_filter = biquad_filter(-1.8617006585639506, 0.8706642683920058, 0.947680874725466, -1.8659578411373265, 0.9187262110931641)
datao = np.fromiter(run_filter(de_emphasis_filter, datao), np.int16) # De-emph - 26db below 500khz
# Could tie edge_pll and run_filter together as generators, but we want to see the filter output
bit_gen = edge_pll(datao, EFM_PIXEL_RATE) # This is a ultra-naive PLL that returns a bit-stream of 1 = edge, 0 = no-edge
try:
while 1:
run_until_start_code(bit_gen)
eat_three_bits(bit_gen)
process_efm_frame(bit_gen, 31) # 31 14 bit EFM codes in a frame
except StopIteration:
printerr('Hit the end of the bitstream')
datao = np.clip(datao, 0, 255).astype(np.uint8)
sys.stdout.write(datao.tostring())
def _iter_contrasts(n_subjects, factor_levels, effect_picks):
""" Aux Function: Setup contrasts """
sc, sy, = [], []
# prepare computation of Kronecker products
for n_levels in factor_levels:
# for each factor append
# 1) column vector of length == number of levels,
# 2) square matrix with diagonal == number of levels
# main + interaction effects for contrasts
sc.append([np.ones([n_levels, 1]),
detrend(np.eye(n_levels), type='constant')])
# main + interaction effects for component means
sy.append([np.ones([n_levels, 1]) / n_levels, np.eye(n_levels)])
# XXX component means not returned at the moment
for (c1, c2, c3) in defaults_twoway_rm['iter_contrasts'][effect_picks]:
# c1 selects the first factors' level in the column vector
# c3 selects the actual factor
# c2 selects either its column vector or diag matrix
c_ = np.kron(sc[0][c1], sc[c3][c2])
# for 3 way anova accumulation of c_ across factors required
df1 = matrix_rank(c_)
df2 = df1 * (n_subjects - 1)
yield c_, df1, df2
def test_detrend_external_nd_0(self):
x = np.arange(20, dtype=np.float64) + 0.04
x = x.reshape((2,1,10))
x = np.rollaxis(x, 2, 0)
f, p = csd(x, x, nperseg=10, axis=0,
detrend=lambda seg: signal.detrend(seg, axis=0, type='l'))
assert_allclose(p, np.zeros_like(p), atol=1e-15)
def multitaper_spectrogram(data, spec_params):
data = _change_row_to_column(data)
fs = spec_params.fs
nfft = spec_params.nfft
nstep = spec_params.nstep
shift = spec_params.shift
nblocks = _get_nblocks(len(data), shift, nstep)
nfreqs = spec_params.nfreqs
if spec_params.trial_avg:
Ch = data.shape[1]
S = np.zeros((nblocks, nfreqs, Ch))
else:
S = np.zeros((nblocks, nfreqs))
for idx in xrange(nblocks):
datawin = signal.detrend(
data[idx * nstep:idx * nstep + shift], type == 'constant')
if idx < 2:
N = len(datawin)
taps = _dpsschk(spec_params.tapers, N, fs)
J = _mtfftc(datawin, taps, nfft, fs)[
spec_params.findx, :]
s = np.mean((np.multiply(np.conj(J), J)), axis=1).squeeze()
if spec_params.trial_avg:
s = np.mean(s, axis=1).squeeze()
S[idx, :] = s
spect = S.squeeze()
return spect
def sources_to_nifti(CHECKPOINT, MASKMAT, BASENIFTI, ONAME, savepath, voxels, win):
bnifti = load_image(BASENIFTI)
mask = loadmat(MASKMAT)['mask']
model = np.load(CHECKPOINT) # Numpy array of sources from Infomax ICA
for i in range(len(model)): # Goes component by component
W = model[i,:].reshape([voxels,win])
f = zeros(len(mask))
idx = where(mask==1)
data = zeros((bnifti.shape[0],bnifti.shape[1],bnifti.shape[2],W.shape[1]))
f[idx[0].tolist()] = detrend(W)/std(W)
for j in range(0,W.shape[1]):
data[:,:,:,j] = reshape(f,(bnifti.shape[0],bnifti.shape[1],bnifti.shape[2] ), order='F')
img = Image.from_image(bnifti,data=data)
os.chdir(savepath)
fn = ONAME + "%s.nii" % (str(i)) # Where result should be saved and under what name
save_image(img,fn)
def detrend(A,args,params):
"""
Remove trend from data
Remove the trend from the time series data in `A`. Several methods are \\
possible. The method is specified as the value of the `type` keyword in
the argument dictionary `args`.
Possible `types` of detrending:
-`constant` or `demean`: substract mean of traces
-`linear`: substract a least squares fitted linear trend form the data
:type A: numpy.ndarray
:param A: time series data with time oriented along the first \\
dimension (columns)
:type args: dictionary
:param args: the only used keyword is `type`
:type params: dictionary
:param params: not used here
:rtype: numpy.ndarray
:return: detrended time series data
"""
# for compatibility with obspy
if args['type'] == 'demean':
args['type'] = 'constant'
if args['type'] == 'detrend':
args['type'] = 'linear'
A = signal.detrend(A,axis=0,type=args['type'])
return A
def _run_interface(self,runtime):
""" linear detrending
"""
print("Linear detrending")
print("=================")
# Output from previous preprocessing step
ref_path = self.inputs.in_file
# Load data
dataimg = nib.load( ref_path )
data = dataimg.get_data()
tp = data.shape[3]
# GLM: regress out nuisance covariates
new_data_det = data.copy()
gm = nib.load(self.inputs.gm_file[0]).get_data().astype( np.uint32 )
for index,value in np.ndenumerate( gm ):
if value == 0:
continue
Ydet = signal.detrend(data[index[0],index[1],index[2],:].reshape(tp,1), axis=0)
new_data_det[index[0],index[1],index[2],:] = Ydet[:,0]
img = nib.Nifti1Image(new_data_det, dataimg.get_affine(), dataimg.get_header())
nib.save(img, os.path.abspath('fMRI_detrending.nii.gz'))
print("[ DONE ]")
return runtime
def spec(T, axis=0):
'''Combined detrending, windowing and real-valued FFT over axis.
Usually, the FFT is preceded by a detrending and windowing to reduce
edge effects. This function performs the detrending, windowing and
real-valued FFT.
Parameters
----------
T : ndarray
Tensor containing data to be detrended.
axis : int, optional
Specifies the axis over which the spectrum is calculated.
Returns
-------
out: ndarray
Array similar to `T` where the time dimension is replace with
it's frequency spectrum.
See also:
---------
windows : extract windows from continuous data.
spec_weight : filter in the frequency domain.
'''
T = signal.detrend(T, axis=axis)
win = np.hanning(T.shape[axis])
win.shape = (np.where(np.arange(T.ndim) == axis, -1, 1))
return np.fft.rfft(T * win, axis=axis)
def psd1d(hh = None,dx = 1.,tap = 0.05, detrend = True):
hh = hh-numpy.mean(hh)
nx = numpy.shape(hh)[0]
if detrend:
hh = signal.detrend(hh)
if tap>0:
ntaper = numpy.int(tap * nx + 0.5)
taper = numpy.zeros(nx)+1.
taper[:ntaper] = numpy.cos(numpy.arange(ntaper)/(ntaper-1.)*pi/2+3*pi/2)
taper[-ntaper:] = numpy.cos(-numpy.arange(-ntaper+1,1)/(ntaper-1.)*pi/2+3*pi/2)
hh = hh*taper
ss = fft(hh)
if nx % 2 != 0 : nx-=1
ff = numpy.arange(1,nx/2-1)/(nx*dx)
PSD = 2*dx/(nx)*numpy.abs(ss[1:int(nx/2)-1])**2
return ff, PSD
def process_traces(self, s, h):
""" Performs data processing operations on traces
"""
# remove linear trend
s = _signal.detrend(s)
# mute
if PAR.MUTE:
vel = PAR.MUTESLOPE
off = PAR.MUTECONST
inn = PAR.MUTEINNER
# mute early arrivals
s = smute(s, h, vel, off, inn, constant_spacing=False)
# mute late arrivals
vel = PAR.MUTESLOPE_BTM
s = smutelow(s, h, vel, off, inn, constant_spacing=False)
# filter data
if PAR.FREQLO and PAR.FREQHI:
s = sbandpass(s, h, PAR.FREQLO, PAR.FREQHI)
# scale all traces by a single value (norm)
if PAR.NORMALIZE_ALL:
sum_norm = np.linalg.norm(s, ord=2)
if sum_norm > 0:
s /= sum_norm
return s
def detrend4d(para):
"""docs
Parameters
----------
para :
Contributions
-------------
Date :
Author :
Reviewer :
"""
intnorm_file = para[0][0]
mask_file = para[0][1]
imgseries = load(intnorm_file)
mask = load(mask_file)
voxel_timecourses = imgseries.get_data()
m = np.nonzero(mask.get_data())
for a in range(len(m[1])):
voxel_timecourses[m[0][a],m[1][a],m[2][a]] = detrend(voxel_timecourses[m[0][a],m[1][a],m[2][a]], type='linear')
imgseries.data = voxel_timecourses
outfile = para[0][0] + '_dt.nii.gz'
imgseries.to_filename(outfile)
return outfile
def smooth(X, tr=1.5, ub=0.10, lb=0.001):
"""Smooth columns in X.
Parameters:
-----------
X - a 2d array with features in cols
tr - the repetition time or sampling (in seconds)
ub - upper bound of the band pass (Hz/2*tr)
lb - lower bound of the band pass (Hz/2*tr)
Note:
----
Smoothing is a linear detrend followed by a bandpass filter from
0.0625-0.15 Hz
"""
# Linear detrend
Xf = signal.detrend(X, axis=0, type="linear", bp=0)
# Band pass
ts = nt.TimeSeries(Xf.transpose(), sampling_interval=tr)
Xf = nt.analysis.FilterAnalyzer(ts, ub=ub, lb=lb).fir.data
## ub and lb selected after some experimentation
## with the simiulated accumulator data
## ub=0.10, lb=0.001).fir.data
Xf = Xf.transpose()
## TimeSeries assumes last axis is time, and we need
## the first axis to be time.
return Xf
def test_dft_3d_dask(self, dask):
"""Test the discrete Fourier transform on 3D dask array data"""
N=16
da = xr.DataArray(np.random.rand(N,N,N), dims=['time','x','y'],
coords={'time':range(N),'x':range(N),
'y':range(N)}
)
if dask:
da = da.chunk({'time': 1})
daft = xrft.dft(da, dim=['x','y'], shift=False)
npt.assert_almost_equal(daft.values,
np.fft.fftn(da.chunk({'time': 1}).values,
axes=[1,2])
)
da = da.chunk({'x': 1})
with pytest.raises(ValueError):
xrft.dft(da, dim=['x'])
da = da.chunk({'time':N})
daft = xrft.dft(da, dim=['time'],
shift=False, detrend='linear')
da_prime = sps.detrend(da, axis=0)
npt.assert_almost_equal(daft.values,
np.fft.fftn(da_prime, axes=[0])
)
def calc_compcor_components(data, nComponents, wm_sigs, csf_sigs):
import scipy.signal as signal
wmcsf_sigs = np.vstack((wm_sigs, csf_sigs)).astype("float32")
# filter out any voxels whose variance equals 0
print "Removing zero variance components"
wmcsf_sigs = wmcsf_sigs[wmcsf_sigs.std(1) != 0, :]
if wmcsf_sigs.shape.count(0):
print "No wm or csf signals left after removing those with zero variance"
raise IndexError
print "Detrending and centering data"
Y = signal.detrend(wmcsf_sigs, axis=1, type="linear").T
Yc = Y - np.tile(Y.mean(0), (Y.shape[0], 1))
Yc = Yc / np.tile(np.array(Y.std(0)).reshape(1, Y.shape[1]), (Y.shape[0], 1))
print Yc.dtype
print "Calculating SVD decomposition of Y*Y'"
# U, S, Vh = np.linalg.svd(Yc)
# U, S, Vh = scipy.linalg.svd(Yc)
U, S, Vh = scipy.sparse.linalg.svds(Yc)
return U[:, :nComponents]
def __call__(self, tvec, acc, gyro, mag):
# Get the inclination measurements
horRef = np.cross(self.sagittalDir, self.vertRefDir)
(tauK, yinc) = inclination(acc, self.vertRefDir, horRef,
self.g, self.gThreshold)
# Integrate the projected zero-mean gyro data
w = detrend(np.dot(gyro, self.sagittalDir), type='constant')
wint = cumtrapz(w, tvec)
wint = np.insert(wint, 0, wint[0])
# translate the angle (add constant offset) to best match inclination
# measurements
# phi[tauK] = wint[tauK] + offset = yinc
# 1*offset = yinc - wint[tauK]
# offset = 1' * (yinc - wint[tauK])/len(tauK)
phi = wint + np.mean(yinc - wint[tauK])
self.phi = phi
self.yinc = np.column_stack( (tvec[tauK], yinc))
self.tvec = tvec
self.gyrodta = gyro
self.accdta = acc
# Return a Quaternion array
return [quat.QuaternionFromAxis(self.sagittalDir, phi_) for phi_ in self.phi]
def applyMeth(self, x, fMeth):
"""Apply the methods
x : array signal
fMeth : list of methods
-> 3D array of the transform signal
"""
npts, ntrial = x.shape
nFce = len(fMeth)
xf = n.zeros((nFce, npts, ntrial))
# Detrend the signal :
if self.dtrd:
x = detrend(x, axis=0)
# Apply methods :
for k in range(0, nFce): # For each frequency in the tuple
xf[k, ...] = fMeth[k](x)
# Correction for the wavelet (due to the wavelet width):
if (self.method == 'wavelet') and (self.wltCorr is not None):
w = 3*self.wltWidth
xf[:, 0:w, :] = xf[:, w+1:2*w+1, :]
xf[:, npts-w:npts, :] = xf[:, npts-2*w-1:npts-w-1, :]
return xf
def main(parser):
# print(bcolors.HEADER + "*** Conduction Velocity Analyzer ***" + bcolors.ENDC) # on windows cmd colors don't work
print('\n***************************************')
print('*** Conduction Velocity Analyzer ******')
print('\n***************************************')
# parse arguments
args = parser.parse_args()
txt_path = args.input_filepath[0]
# extract filename and directory path
filename = os.path.basename(txt_path)
folderpath = os.path.dirname(txt_path)
# extract experiment parameters from filename and print info to console
burst, param = extract_info(filename, _print=True)
# create excel file
wb, sheet, out_path, n_col_sheet_block = prepare_excel_wb(
folderpath, filename, burst, param)
# read OM tracks values
values = np.loadtxt(txt_path, dtype=np.float, usecols=(0, 1, 2))
param[pKeys.exp_duration] = values.shape[0] / param[pKeys.frame_rate]
print("- Duration of record : {} ms".format(param[pKeys.exp_duration]))
# split timing, roi1 (apex) and roi2 (base) values
full_ms, full_apex, full_base = values[:, 0], values[:, 1], values[:, 2]
''' ===== [ START ANALISIS ] ===== - for each burst '''
for (i_burst, b) in enumerate(burst):
print('\n\n********* Analyzing Burst at {}Hz *********'.format(
b[bKeys.freq_stim]))
# extract ramp
ms = full_ms[b[bKeys.start_ms]:b[bKeys.stop_ms]]
apex = full_apex[b[bKeys.start_ms]:b[bKeys.stop_ms]]
base = full_base[b[bKeys.start_ms]:b[bKeys.stop_ms]]
# plot_signals(apex, base, title="Ramp at {}Hz".format(b[keys.freq_stim]))
# detrend signals
apex_flat = sign.detrend(apex, type='linear')
base_flat = sign.detrend(base, type='linear')
# plot original and flattened
# plot_signals(apex, base, title="Original Tracks")
# plot_signals(apex_flat, base_flat, title="Detrended Tracks")
# if selected, apply median filter and plot results
if param[pKeys.rank] is not 0:
apex_filt = sign.medfilt(apex_flat, kernel_size=param[pKeys.rank])
base_filt = sign.medfilt(base_flat, kernel_size=param[pKeys.rank])
# plot_signals(apex_filt, base_filt, title="Filtered Tracks (rank = {})".format(param[keys.rank]))
# ENSURE TO USE THE RIGHT SIGNAL (filtered or only flattened)
(apex_sgn,
base_sgn) = (apex_filt,
base_filt) if param[pKeys.rank] is not 0 else (apex_flat,
base_flat)
''' ===== [ FIND PEAKS, PERIODS and SELECT AP TO ANALYZE ] ===== '''
# find peaks - restituisce (x, y) dei picchi
# -> io passo il segnale invertito (perchè usa il 'max')
# impongo che i picchi siano distanti fra loro almeno più di 2/3 del periodo
# e prendo solo la x (tempo): [0]-> prendi solo la x del picco
a_peaks = sign.find_peaks(-apex_sgn,
distance=(2 / 3) * b[bKeys.AP_duration])[0]
b_peaks = sign.find_peaks(-base_sgn,
distance=(2 / 3) * b[bKeys.AP_duration])[0]
# plotto i segnali con picchi e durate dei periodi
plot_signals_with_peaks([apex_sgn, base_sgn], [a_peaks, b_peaks],
['Apex', 'Base'],
"Ramp at {}Hz".format(b[bKeys.freq_stim]),
_enum_peaks=True,
_plot_intervals=True,
frame_rate=param[pKeys.frame_rate])
# stima durata di ogni AP da differenza picchi consecutivi nell'apice
print("- Control of stimulation frequency in the apex signal... ")
AP_periods = np.diff(a_peaks) / param[pKeys.frame_rate]
freq_stim_estimated = 1 / np.mean(AP_periods / 1000)
print("-- Stimulation Frequency obtained: {0:0.1f}Hz".format(
freq_stim_estimated))
# user can select which potentials use to estimmate mean conduction velocity
selection = input(
"\n***AP selection to estimate mean current velocity.\n"
" Insert AP indexex between spaces. Example:\n"
" 0 2 3 5 7 8 9 [<- then press 'Enter'].\n"
" Please, enter your selection here and the press 'Enter': \n")
# extract selected indexes
ap_selected_idx = selection.split(' ')
print('- AP selected for Conduction Velocity Estimation: ')
for l in ap_selected_idx:
print(l, end='°, ')
''' ===== [ ANALYZE EACH ACTION POTENTIALS TO FIND DELAY APEX-BASE ] ===== '''
# USE INTERPOLATION AND CROSS-CORRELATION TO ESTIMATE DELAY
# from selected AP potentials
# Idea: per ogni picco, prendo l'intorno giusto per selezionare il potenziale d'azione,
# interpolo, calcolo delay usando il picco della cross-correlazione e poi medio tutti i delay
cv_list = list() # list of conduction velocity extracted for each AP
# for each AP selected
for (i_spike, spike_num) in enumerate(
np.asarray(ap_selected_idx).astype(np.int)):
# calculate extremes of selected action potential signal
t1, t2 = np.int(b[bKeys.AP_duration] * spike_num), np.int(
b[bKeys.AP_duration] * (spike_num + 1))
ms_sel = ms[t1:t2] # time
base_sel = base_sgn[t1:t2] # base
apex_sel = apex_sgn[t1:t2] # apex
# interpolo i due segnali di fattore 0.2 (come su LabView)
dt = 0.2
# calcolo funzione di interpolazione delle due tracce
f_apex = interpolate.interp1d(ms_sel, apex_sel)
f_base = interpolate.interp1d(ms_sel, base_sel)
# creo nuovo asse temporale
ms_res = np.arange(ms_sel[0], ms_sel[-1], dt)
# resample signals using interpolation functions calculated above
apex_res = f_apex(ms_res)
base_res = f_base(ms_res)
# estimate delay by cross-correlation max values
delay_ms = lag_finder_in_ms(apex_res, base_res, 1000 / dt)
# estimate and save conduction velocity
cv = param[pKeys.ROI_distance_mm] / delay_ms
cv_list.append(cv)
# write spike_num and cv
sheet.write(i_spike + 7, (i_burst * (n_col_sheet_block + 1)) + 1,
"{}".format(int(spike_num)))
sheet.write(i_spike + 7, (i_burst * (n_col_sheet_block + 1)) + 2,
"{0:0.3f}".format(cv))
# estimate mean and std. error
avg = np.mean(np.asarray(cv_list))
sem = stats.sem(np.asarray(cv_list))
# write mean and std. error into excel file
sheet.write(17, (i_burst * (n_col_sheet_block + 1)) + 2,
"{0:0.3f}".format(avg))
sheet.write(18, (i_burst * (n_col_sheet_block + 1)) + 2,
"{0:0.3f}".format(sem))
# print results and average
print("*** RESULTS:")
print("- Conduction velocities in m/s:")
for cv in cv_list:
print("-- {0:0.3f} m/s".format(cv))
print("\n- Average Conduction velocity: ", end='')
print("-- {0:0.3f} +- {1:0.3f} m/s".format(avg, sem))
# save excel file
wb.save(out_path)
print('\nOutput saved in:')
print(out_path)
print(
' --------- Conduction Velocity Analyzer: Process finished. ---------\n'
)
def _nuisanceRegression(subj,
run,
inputdata,
outputdir,
model='24pXaCompCorXVolterra',
spikeReg=False,
zscore=False,
nproc=8):
"""
This function runs nuisance regression on the Glasser Parcels (360) on a single subjects run
Will only regress out noise parameters given the model choice (see below for model options)
Input parameters:
subj : subject number as a string
run : task run
outputdir: Directory for GLM output, as an h5 file (each run will be contained within each h5)
model : model choices for linear regression. Models include:
1. 24pXaCompCorXVolterra [default]
Variant from Ciric et al. 2017.
Includes (64 regressors total):
- Movement parameters (6 directions; x, y, z displacement, and 3 rotations) and their derivatives, and their quadratics (24 regressors)
- aCompCor (5 white matter and 5 ventricle components) and their derivatives, and their quadratics (40 regressors)
2. 18p (the legacy default)
Includes (18 regressors total):
- Movement parameters (6 directions) and their derivatives (12 regressors)
- Global signal and its derivative (2 regressors)
- White matter signal and its derivative (2 regressors)
- Ventricles signal and its derivative (2 regressors)
3. 16pNoGSR (the legacy default, without GSR)
Includes (16 regressors total):
- Movement parameters (6 directions) and their derivatives (12 regressors)
- White matter signal and its derivative (2 regressors)
- Ventricles signal and its derivative (2 regressors)
4. 12pXaCompCor (Typical motion regression, but using CompCor (noGSR))
Includes (32 regressors total):
- Movement parameters (6 directions) and their derivatives (12 regressors)
- aCompCor (5 white matter and 5 ventricle components) and their derivatives (no quadratics; 20 regressors)
5. 36p (State-of-the-art, according to Ciric et al. 2017)
Includes (36 regressors total - same as legacy, but with quadratics):
- Movement parameters (6 directions) and their derivatives and quadratics (24 regressors)
- Global signal and its derivative and both quadratics (4 regressors)
- White matter signal and its derivative and both quadratics (4 regressors)
- Ventricles signal and its derivative (4 regressors)
spikeReg : spike regression (Satterthwaite et al. 2013) [True/False]
Note, inclusion of this will add additional set of regressors, which is custom for each subject/run
zscore : Normalize data (across time) prior to fitting regression
nproc = number of processes to use via multiprocessing
"""
data = inputdata
tMask = np.ones((data.shape[1], ))
tMask[:framesToSkip] = 0
# Skip frames
data = data[:, framesToSkip:]
# Demean each run
data = signal.detrend(data, axis=1, type='constant')
# Detrend each run
data = signal.detrend(data, axis=1, type='linear')
tMask = np.asarray(tMask, dtype=bool)
nROIs = data.shape[0]
# Load nuisance regressors for this data
h5f = h5py.File(nuis_reg_dir + subj + '_nuisanceRegressors.h5', 'r')
if model == '24pXaCompCorXVolterra':
# Motion parameters + derivatives
motion_parameters = h5f[run]['motionParams'][:].copy()
motion_parameters_deriv = h5f[run]['motionParams_deriv'][:].copy()
# WM aCompCor + derivatives
aCompCor_WM = h5f[run]['aCompCor_WM'][:].copy()
aCompCor_WM_deriv = h5f[run]['aCompCor_WM_deriv'][:].copy()
# Ventricles aCompCor + derivatives
aCompCor_ventricles = h5f[run]['aCompCor_ventricles'][:].copy()
aCompCor_ventricles_deriv = h5f[run][
'aCompCor_ventricles_deriv'][:].copy()
# Create nuisance regressors design matrix
nuisanceRegressors = np.hstack(
(motion_parameters, motion_parameters_deriv, aCompCor_WM,
aCompCor_WM_deriv, aCompCor_ventricles,
aCompCor_ventricles_deriv))
quadraticRegressors = nuisanceRegressors**2
nuisanceRegressors = np.hstack(
(nuisanceRegressors, quadraticRegressors))
elif model == '18p':
# Motion parameters + derivatives
motion_parameters = h5f[run]['motionParams'][:].copy()
motion_parameters_deriv = h5f[run]['motionParams_deriv'][:].copy()
# Global signal + derivatives
global_signal = h5f[run]['global_signal'][:].copy()
global_signal_deriv = h5f[run]['global_signal_deriv'][:].copy()
# white matter signal + derivatives
wm_signal = h5f[run]['wm_signal'][:].copy()
wm_signal_deriv = h5f[run]['wm_signal_deriv'][:].copy()
# ventricle signal + derivatives
ventricle_signal = h5f[run]['ventricle_signal'][:].copy()
ventricle_signal_deriv = h5f[run]['ventricle_signal_deriv'][:].copy()
# Create nuisance regressors design matrix
tmp = np.vstack(
(global_signal, global_signal_deriv, wm_signal, wm_signal_deriv,
ventricle_signal, ventricle_signal_deriv
)).T # Need to vstack, since these are 1d arrays
nuisanceRegressors = np.hstack(
(motion_parameters, motion_parameters_deriv, tmp))
elif model == '16pNoGSR':
# Motion parameters + derivatives
motion_parameters = h5f[run]['motionParams'][:].copy()
motion_parameters_deriv = h5f[run]['motionParams_deriv'][:].copy()
# white matter signal + derivatives
wm_signal = h5f[run]['wm_signal'][:].copy()
wm_signal_deriv = h5f[run]['wm_signal_deriv'][:].copy()
# ventricle signal + derivatives
ventricle_signal = h5f[run]['ventricle_signal'][:].copy()
ventricle_signal_deriv = h5f[run]['ventricle_signal_deriv'][:].copy()
# Create nuisance regressors design matrix
tmp = np.vstack((wm_signal, wm_signal_deriv, ventricle_signal,
ventricle_signal_deriv
)).T # Need to vstack, since these are 1d arrays
nuisanceRegressors = np.hstack(
(motion_parameters, motion_parameters_deriv, tmp))
elif model == '12pXaCompCor':
# Motion parameters + derivatives
motion_parameters = h5f[run]['motionParams'][:].copy()
motion_parameters_deriv = h5f[run]['motionParams_deriv'][:].copy()
# WM aCompCor + derivatives
aCompCor_WM = h5f[run]['aCompCor_WM'][:].copy()
aCompCor_WM_deriv = h5f[run]['aCompCor_WM_deriv'][:].copy()
# Ventricles aCompCor + derivatives
aCompCor_ventricles = h5f[run]['aCompCor_ventricles'][:].copy()
aCompCor_ventricles_deriv = h5f[run][
'aCompCor_ventricles_deriv'][:].copy()
# Create nuisance regressors design matrix
nuisanceRegressors = np.hstack(
(motion_parameters, motion_parameters_deriv, aCompCor_WM,
aCompCor_WM_deriv, aCompCor_ventricles,
aCompCor_ventricles_deriv))
elif model == '36p':
# Motion parameters + derivatives
motion_parameters = h5f[run]['motionParams'][:].copy()
motion_parameters_deriv = h5f[run]['motionParams_deriv'][:].copy()
# Global signal + derivatives
global_signal = h5f[run]['global_signal'][:].copy()
global_signal_deriv = h5f[run]['global_signal_deriv'][:].copy()
# white matter signal + derivatives
wm_signal = h5f[run]['wm_signal'][:].copy()
wm_signal_deriv = h5f[run]['wm_signal_deriv'][:].copy()
# ventricle signal + derivatives
ventricle_signal = h5f[run]['ventricle_signal'][:].copy()
ventricle_signal_deriv = h5f[run]['ventricle_signal_deriv'][:].copy()
# Create nuisance regressors design matrix
tmp = np.vstack(
(global_signal, global_signal_deriv, wm_signal, wm_signal_deriv,
ventricle_signal, ventricle_signal_deriv
)).T # Need to vstack, since these are 1d arrays
nuisanceRegressors = np.hstack(
(motion_parameters, motion_parameters_deriv, tmp))
quadraticRegressors = nuisanceRegressors**2
nuisanceRegressors = np.hstack(
(nuisanceRegressors, quadraticRegressors))
if spikeReg:
# Obtain motion spikes
try:
motion_spikes = h5f[run]['motionSpikes'][:].copy()
nuisanceRegressors = np.hstack((nuisanceRegressors, motion_spikes))
except:
print 'Spike regression option was chosen... but no motion spikes for subj', subj, '| run', run, '!'
# Update the model name - to keep track of different model types for output naming
model = model + '_spikeReg'
if zscore:
model = model + '_zscore'
h5f.close()
# Skip first 5 frames of nuisanceRegressors, too
nuisanceRegressors = nuisanceRegressors[framesToSkip:, :].copy()
betas, resid = regression.regression(data.T,
nuisanceRegressors,
constant=True)
betas = betas.T # Exclude nuisance regressors
residual_ts = resid.T
if zscore:
residual_ts = stats.zscore(residual_ts, axis=1)
outname1 = run + '/nuisanceReg_resid_' + model
outname2 = run + '/nuisanceReg_betas_' + model
outputfilename = outputdir + subj + '_glmOutput_data.h5'
h5f = h5py.File(outputfilename, 'a')
try:
h5f.create_dataset(outname1, data=residual_ts)
h5f.create_dataset(outname2, data=betas)
except:
del h5f[outname1], h5f[outname2]
h5f.create_dataset(outname1, data=residual_ts)
h5f.create_dataset(outname2, data=betas)
h5f.close()
def linear_detrend(self):
"""Remove linear trend from `values`"""
self.values = detrend(self.values, type="linear")
self._setattr("proc_linear_detrend")
return self
def _calc_norm_affine(affines, use_differences, brain_pts=None):
"""Calculates the maximum overall displacement of the midpoints
of the faces of a cube due to translation and rotation.
Parameters
----------
affines : list of [4 x 4] affine matrices
use_differences : boolean
brain_pts : [4 x n_points] of coordinates
Returns
-------
norm : at each time point
displacement : euclidean distance (mm) of displacement at each coordinate
"""
if brain_pts is None:
respos = np.diag([70, 70, 75])
resneg = np.diag([-70, -110, -45])
all_pts = np.vstack((np.hstack((respos, resneg)), np.ones((1, 6))))
displacement = None
else:
all_pts = brain_pts
n_pts = all_pts.size - all_pts.shape[1]
newpos = np.zeros((len(affines), n_pts))
if brain_pts is not None:
displacement = np.zeros((len(affines), int(n_pts / 3)))
for i, affine in enumerate(affines):
newpos[i, :] = np.dot(affine, all_pts)[0:3, :].ravel()
if brain_pts is not None:
displacement[i, :] = np.sqrt(
np.sum(
np.power(
np.reshape(newpos[i, :], (3, all_pts.shape[1]))
- all_pts[0:3, :],
2,
),
axis=0,
)
)
# np.savez('displacement.npz', newpos=newpos, pts=all_pts)
normdata = np.zeros(len(affines))
if use_differences:
newpos = np.concatenate(
(np.zeros((1, n_pts)), np.diff(newpos, n=1, axis=0)), axis=0
)
for i in range(newpos.shape[0]):
normdata[i] = np.max(
np.sqrt(
np.sum(
np.reshape(
np.power(np.abs(newpos[i, :]), 2), (3, all_pts.shape[1])
),
axis=0,
)
)
)
else:
from scipy.signal import detrend
newpos = np.abs(detrend(newpos, axis=0, type="constant"))
normdata = np.sqrt(np.mean(np.power(newpos, 2), axis=1))
return normdata, displacement
def __demean_filter(self):
# Compute the mean using a sliding window
filtered = sig.detrend(self.__data_buffer)
self.__data_buffer = filtered
return
def update():
global specmax_curr, specmin_curr, specmax_hist, specmin_hist, fft_prev, fft_hist, redfreq, redwidth, bluefreq, bluewidth, counter, history
# get last data
last_index = ft_input.getHeader().nSamples
begsample = (last_index - window)
endsample = (last_index - 1)
data = ft_input.getData([begsample, endsample])
if debug > 0:
print("reading from sample %d to %d" % (begsample, endsample))
# demean and detrend data before filtering to reduce edge artefacts and center timecourse
data = detrend(data, axis=0)
# taper data
taper = np.hanning(len(data))
data = data * taper[:, np.newaxis]
# shift data to next sample
history = np.roll(history, 1, axis=2)
for ichan in range(numchannel):
channr = int(chanarray[ichan])
# estimate FFT at current moment, apply some temporal smoothing
fft_temp = abs(fft(data[:, channr]))
fft_curr[ichan] = fft_temp * lrate + fft_prev[ichan] * (1 - lrate)
fft_prev[ichan] = fft_curr[ichan]
# update FFT history with current estimate
history[ichan, :, numhistory - 1] = fft_temp
fft_hist = np.nanmean(history, axis=2)
# user-selected frequency band
arguments_freqrange = patch.getfloat('arguments',
'freqrange',
multiple=True)
freqrange = np.greater(freqaxis,
arguments_freqrange[0]) & np.less_equal(
freqaxis, arguments_freqrange[1])
# update panels
spect_curr[ichan].setData(freqaxis[freqrange],
fft_curr[ichan][freqrange])
spect_hist[ichan].setData(freqaxis[freqrange],
fft_hist[ichan][freqrange])
# adapt the vertical scale to the running mean of min/max
specmax_curr[ichan] = float(specmax_curr[ichan]) * (
1 - lrate) + lrate * max(fft_curr[ichan][freqrange])
specmin_curr[ichan] = float(specmin_curr[ichan]) * (
1 - lrate) + lrate * min(fft_curr[ichan][freqrange])
specmax_hist[ichan] = float(specmax_hist[ichan]) * (
1 - lrate) + lrate * max(fft_hist[ichan][freqrange])
specmin_hist[ichan] = float(specmin_hist[ichan]) * (
1 - lrate) + lrate * min(fft_hist[ichan][freqrange])
freqplot_curr[ichan].setXRange(arguments_freqrange[0],
arguments_freqrange[1])
freqplot_hist[ichan].setXRange(arguments_freqrange[0],
arguments_freqrange[1])
freqplot_curr[ichan].setYRange(specmin_curr[ichan],
specmax_curr[ichan])
freqplot_hist[ichan].setYRange(specmin_hist[ichan],
specmax_hist[ichan])
# update plotted lines
redfreq = patch.getfloat('input',
'redfreq',
default=10. / arguments_freqrange[1])
redfreq = EEGsynth.rescale(redfreq, slope=scale_red,
offset=offset_red) * arguments_freqrange[1]
redwidth = patch.getfloat('input',
'redwidth',
default=1. / arguments_freqrange[1])
redwidth = EEGsynth.rescale(redwidth,
slope=scale_red,
offset=offset_red) * arguments_freqrange[1]
bluefreq = patch.getfloat('input',
'bluefreq',
default=20. / arguments_freqrange[1])
bluefreq = EEGsynth.rescale(
bluefreq, slope=scale_blue,
offset=offset_blue) * arguments_freqrange[1]
bluewidth = patch.getfloat('input',
'bluewidth',
default=4. / arguments_freqrange[1])
bluewidth = EEGsynth.rescale(
bluewidth, slope=scale_blue,
offset=offset_blue) * arguments_freqrange[1]
if showred:
redleft_curr[ichan].setData(
x=[redfreq - redwidth, redfreq - redwidth],
y=[specmin_curr[ichan], specmax_curr[ichan]])
redright_curr[ichan].setData(
x=[redfreq + redwidth, redfreq + redwidth],
y=[specmin_curr[ichan], specmax_curr[ichan]])
if showblue:
blueleft_curr[ichan].setData(
x=[bluefreq - bluewidth, bluefreq - bluewidth],
y=[specmin_curr[ichan], specmax_curr[ichan]])
blueright_curr[ichan].setData(
x=[bluefreq + bluewidth, bluefreq + bluewidth],
y=[specmin_curr[ichan], specmax_curr[ichan]])
if showred:
redleft_hist[ichan].setData(
x=[redfreq - redwidth, redfreq - redwidth],
y=[specmin_hist[ichan], specmax_hist[ichan]])
redright_hist[ichan].setData(
x=[redfreq + redwidth, redfreq + redwidth],
y=[specmin_hist[ichan], specmax_hist[ichan]])
if showblue:
blueleft_hist[ichan].setData(
x=[bluefreq - bluewidth, bluefreq - bluewidth],
y=[specmin_hist[ichan], specmax_hist[ichan]])
blueright_hist[ichan].setData(
x=[bluefreq + bluewidth, bluefreq + bluewidth],
y=[specmin_hist[ichan], specmax_hist[ichan]])
# update labels at plotted lines
if showred:
text_redleft.setText('%0.1f' % (redfreq - redwidth))
text_redleft.setPos(redfreq - redwidth, specmax_curr[0])
text_redright.setText('%0.1f' % (redfreq + redwidth))
text_redright.setPos(redfreq + redwidth, specmax_curr[0])
else:
text_redleft.setText("")
text_redright.setText("")
if showblue:
text_blueleft.setText('%0.1f' % (bluefreq - bluewidth))
text_blueleft.setPos(bluefreq - bluewidth, specmax_curr[0])
text_blueright.setText('%0.1f' % (bluefreq + bluewidth))
text_blueright.setPos(bluefreq + bluewidth, specmax_curr[0])
else:
text_blueleft.setText("")
text_blueright.setText("")
if showred:
text_redleft_hist.setText('%0.1f' % (redfreq - redwidth))
text_redleft_hist.setPos(redfreq - redwidth, specmax_hist[0])
text_redright_hist.setText('%0.1f' % (redfreq + redwidth))
text_redright_hist.setPos(redfreq + redwidth, specmax_hist[0])
else:
text_redleft_hist.setText("")
text_redright_hist.setText("")
if showblue:
text_blueleft_hist.setText('%0.1f' % (bluefreq - bluewidth))
text_blueleft_hist.setPos(bluefreq - bluewidth, specmax_hist[0])
text_blueright_hist.setText('%0.1f' % (bluefreq + bluewidth))
text_blueright_hist.setPos(bluefreq + bluewidth, specmax_hist[0])
else:
text_blueleft_hist.setText("")
text_blueright_hist.setText("")
key = "%s.%s.%s" % (prefix, 'redband', 'low')
patch.setvalue(key, redfreq - redwidth)
key = "%s.%s.%s" % (prefix, 'redband', 'high')
patch.setvalue(key, redfreq + redwidth)
key = "%s.%s.%s" % (prefix, 'blueband', 'low')
patch.setvalue(key, bluefreq - bluewidth)
key = "%s.%s.%s" % (prefix, 'blueband', 'high')
patch.setvalue(key, bluefreq + bluewidth)
def compute_wavelets_tremor(lats, lons, radius_tremor, wavelet, J):
"""
"""
# Read tremor files (A. Wech)
data_2009 = pd.read_csv('../data/tremor/tremor_events-2009-08-06T00 00 00-2009-12-31T23 59 59.csv')
data_2009['time '] = pd.to_datetime(data_2009['time '], format='%Y-%m-%d %H:%M:%S')
data_2010 = pd.read_csv('../data/tremor/tremor_events-2010-01-01T00 00 00-2010-12-31T23 59 59.csv')
data_2010['time '] = pd.to_datetime(data_2010['time '], format='%Y-%m-%d %H:%M:%S')
data_2011 = pd.read_csv('../data/tremor/tremor_events-2011-01-01T00 00 00-2011-12-31T23 59 59.csv')
data_2011['time '] = pd.to_datetime(data_2011['time '], format='%Y-%m-%d %H:%M:%S')
data_2012 = pd.read_csv('../data/tremor/tremor_events-2012-01-01T00 00 00-2012-12-31T23 59 59.csv')
data_2012['time '] = pd.to_datetime(data_2012['time '], format='%Y-%m-%d %H:%M:%S')
data_2013 = pd.read_csv('../data/tremor/tremor_events-2013-01-01T00 00 00-2013-12-31T23 59 59.csv')
data_2013['time '] = pd.to_datetime(data_2013['time '], format='%Y-%m-%d %H:%M:%S')
data_2014 = pd.read_csv('../data/tremor/tremor_events-2014-01-01T00 00 00-2014-12-31T23 59 59.csv')
data_2014['time '] = pd.to_datetime(data_2014['time '], format='%Y-%m-%d %H:%M:%S')
data_2015 = pd.read_csv('../data/tremor/tremor_events-2015-01-01T00 00 00-2015-12-31T23 59 59.csv')
data_2015['time '] = pd.to_datetime(data_2015['time '], format='%Y-%m-%d %H:%M:%S')
data_2016 = pd.read_csv('../data/tremor/tremor_events-2016-01-01T00 00 00-2016-12-31T23 59 59.csv')
data_2016['time '] = pd.to_datetime(data_2016['time '], format='%Y-%m-%d %H:%M:%S')
data_2017 = pd.read_csv('../data/tremor/tremor_events-2017-01-01T00 00 00-2017-12-31T23 59 59.csv')
data_2017['time '] = pd.to_datetime(data_2017['time '], format='%Y-%m-%d %H:%M:%S')
data_2018 = pd.read_csv('../data/tremor/tremor_events-2018-01-01T00 00 00-2018-12-31T23 59 59.csv')
data_2018['time '] = pd.to_datetime(data_2018['time '], format='%Y-%m-%d %H:%M:%S')
data_2019 = pd.read_csv('../data/tremor/tremor_events-2019-01-01T00 00 00-2019-12-31T23 59 59.csv')
data_2019['time '] = pd.to_datetime(data_2019['time '], format='%Y-%m-%d %H:%M:%S')
data_2020 = pd.read_csv('../data/tremor/tremor_events-2020-01-01T00 00 00-2020-12-31T23 59 59.csv')
data_2020['time '] = pd.to_datetime(data_2020['time '], format='%Y-%m-%d %H:%M:%S')
data_2021 = pd.read_csv('../data/tremor/tremor_events-2021-01-01T00 00 00-2021-04-29T23 59 59.csv')
data_2021['time '] = pd.to_datetime(data_2020['time '], format='%Y-%m-%d %H:%M:%S')
data = pd.concat([data_2009, data_2010, data_2011, data_2012, data_2013, \
data_2014, data_2015, data_2016, data_2017, data_2018, data_2019, \
data_2020, data_2021])
data.reset_index(drop=True, inplace=True)
# To convert lat/lon into kilometers
a = 6378.136
e = 0.006694470
# Time vector
time = pickle.load(open('tmp/time.pkl', 'rb'))
# Loop on latitude and longitude
for index, (lat, lon) in enumerate(zip(lats, lons)):
# Keep only tremor in a given radius
dx = (pi / 180.0) * a * cos(lat * pi / 180.0) / sqrt(1.0 - e * e * \
sin(lat * pi / 180.0) * sin(lat * pi / 180.0))
dy = (3.6 * pi / 648.0) * a * (1.0 - e * e) / ((1.0 - e * e * \
sin(lat * pi / 180.0) * sin(lat * pi / 180.0)) ** 1.5)
x = dx * (data['lon'] - lon)
y = dy * (data['lat'] - lat)
distance = np.sqrt(np.power(x, 2.0) + np.power(y, 2.0))
data['distance'] = distance
tremor = data.loc[data['distance'] <= radius_tremor].copy()
tremor.reset_index(drop=True, inplace=True)
# Convert tremor time
nt = len(tremor)
time_tremor = np.zeros(nt)
for i in range(0, nt):
year = tremor['time '].loc[i].year
month = tremor['time '].loc[i].month
day = tremor['time '].loc[i].day
hour = tremor['time '].loc[i].hour
minute = tremor['time '].loc[i].minute
second = tremor['time '].loc[i].second
time_tremor[i] = date.ymdhms2day(year, month, day, hour, minute, second)
# Interpolate
tremor = np.interp(time, np.sort(time_tremor), (1.0 / nt) * np.arange(0, len(time_tremor)))
# Start figure
params = {'xtick.labelsize':24,
'ytick.labelsize':24}
pylab.rcParams.update(params)
fig = plt.figure(1, figsize=(60, 5 * (J + 3)))
# First method: Detrending
tremor_detrend = detrend(tremor)
# MODWT
(W, V) = pyramid(tremor_detrend, wavelet, J)
(D, S) = get_DS(tremor_detrend, W, wavelet, J)
# Save wavelets
# pickle.dump([time, tremor_detrend, W, V, D, S], \
# open('tmp/tremor_' + str(index) + '.pkl', 'wb'))
maxD = max([np.max(Dj) for Dj in D])
minD = min([np.min(Dj) for Dj in D])
# Plot data
plt.subplot2grid((J + 2, 4), (J + 1, 0))
plt.plot(time, tremor_detrend, 'k', label='Data')
plt.legend(loc=3, fontsize=14)
# Plot details
for j in range(0, J):
plt.subplot2grid((J + 2, 4), (J - j, 0))
plt.plot(time, D[j], 'k', label='D' + str(j + 1))
plt.ylim(minD, maxD)
plt.legend(loc=3, fontsize=14)
# Plot smooth
plt.subplot2grid((J + 2, 4), (0, 0))
plt.plot(time, S[J], 'k', label='S' + str(J))
plt.ylim(minD, maxD)
plt.legend(loc=3, fontsize=14)
plt.title('Detrended data', fontsize=24)
# Second method: Moving average (5 days)
ma_filter = np.repeat(1, 5) / 5
tremor_averaged_5 = tremor[:-4] - np.convolve(tremor, ma_filter, 'valid')
# MODWT
(W, V) = pyramid(tremor_averaged_5, wavelet, J)
(D, S) = get_DS(tremor_averaged_5, W, wavelet, J)
maxD = max([np.max(Dj) for Dj in D])
minD = min([np.min(Dj) for Dj in D])
# Plot data
plt.subplot2grid((J + 2, 4), (J + 1, 1))
plt.plot(time[:-4], tremor_averaged_5, 'k', label='Data')
plt.legend(loc=3, fontsize=14)
# Plot details
for j in range(0, J):
plt.subplot2grid((J + 2, 4), (J - j, 1))
plt.plot(time[:-4], D[j], 'k', label='D' + str(j + 1))
plt.ylim(minD, maxD)
plt.legend(loc=3, fontsize=14)
# Plot smooth
plt.subplot2grid((J + 2, 4), (0, 1))
plt.plot(time[:-4], S[J], 'k', label='S' + str(J))
plt.ylim(minD, maxD)
plt.legend(loc=3, fontsize=14)
plt.title('Moving average (5 days)', fontsize=24)
# Second method: Moving average (15 days)
ma_filter = np.repeat(1, 15) / 15
tremor_averaged_15 = tremor[:-14] - np.convolve(tremor, ma_filter, 'valid')
# MODWT
(W, V) = pyramid(tremor_averaged_15, wavelet, J)
(D, S) = get_DS(tremor_averaged_15, W, wavelet, J)
maxD = max([np.max(Dj) for Dj in D])
minD = min([np.min(Dj) for Dj in D])
# Plot data
plt.subplot2grid((J + 2, 4), (J + 1, 2))
plt.plot(time[:-14], tremor_averaged_15, 'k', label='Data')
plt.legend(loc=3, fontsize=14)
# Plot details
for j in range(0, J):
plt.subplot2grid((J + 2, 4), (J - j, 2))
plt.plot(time[:-14], D[j], 'k', label='D' + str(j + 1))
plt.ylim(minD, maxD)
plt.legend(loc=3, fontsize=14)
# Plot smooth
plt.subplot2grid((J + 2, 4), (0, 2))
plt.plot(time[:-14], S[J], 'k', label='S' + str(J))
plt.ylim(minD, maxD)
plt.legend(loc=3, fontsize=14)
plt.title('Moving average (15 days)', fontsize=24)
# Third method: Low-pass filter
param1, param2 = butter(4, 0.1, btype='low')
tremor_filtered = tremor - lfilter(param1, param2, tremor)
# MODWT
(W, V) = pyramid(tremor_filtered, wavelet, J)
(D, S) = get_DS(tremor_filtered, W, wavelet, J)
maxD = max([np.max(Dj) for Dj in D])
minD = min([np.min(Dj) for Dj in D])
# Plot data
plt.subplot2grid((J + 2, 4), (J + 1, 3))
plt.plot(time, tremor_filtered, 'k', label='Data')
plt.legend(loc=3, fontsize=14)
# Plot details
for j in range(0, J):
plt.subplot2grid((J + 2, 4), (J - j, 3))
plt.plot(time, D[j], 'k', label='D' + str(j + 1))
plt.ylim(minD, maxD)
plt.legend(loc=3, fontsize=14)
# Plot smooth
plt.subplot2grid((J + 2, 4), (0, 3))
plt.plot(time, S[J], 'k', label='S' + str(J))
plt.ylim(minD, maxD)
plt.legend(loc=3, fontsize=14)
plt.title('Low-pass filter', fontsize=24)
# Save figure
plt.savefig('tremor_' + str(index) + '.pdf', format='pdf')
plt.close(1)
if __name__ == '__main__':
station_file = '../data/PANGA/stations.txt'
tremor_file = '../data/tremor/mbbp_cat_d_forHeidi'
radius_GPS = 50
radius_tremor = 50
direction = 'lon'
dataset = 'cleaned'
wavelet = 'LA8'
J = 8
slowness = np.arange(-0.1, 0.105, 0.005)
lats = [47.20000, 47.30000, 47.40000, 47.50000, 47.60000, 47.70000, \
47.80000, 47.90000, 48.00000, 48.10000, 48.20000, 48.30000, 48.40000, \
48.50000, 48.60000, 48.70000]
lons = [-122.74294, -122.73912, -122.75036, -122.77612, -122.81591, \
-122.86920, -122.93549, -123.01425, -123.10498, -123.20716, \
-123.32028, -123.44381, -123.57726, -123.72011, -123.87183, \
-124.03193]
tmin_GPS = 2017.28
tmax_GPS = 2018.28
tmin_tremor = 2017.75
tmax_tremor = 2017.81
lonmin = -125.4
lonmax = -121.4
latmin = 46.3
latmax = 49.6
j = 4
compute_wavelets_tremor(lats, lons, radius_tremor, wavelet, J)
DS_tempg = xr.open_dataset("sst_global.nc")
da_tempg = DS_tempg.temperature_anomaly
#local climate
DS_cli = xr.open_dataset("era5_sst_global_2.nc")
DS_cli = DS_cli.sel(time=slice('1981-01-01', '2012-12-31'),
longitude=slice(-150, 0),
latitude=slice(60, -60))
#US-shape
da_cli_us = mask_shape_border(DS_cli, 'gadm36_USA_0.shp').t2m
da_cli_us_mean = (da_cli_us.to_dataframe().groupby(['time'
]).mean()).to_xarray().t2m
da_cli_us_mean = da_cli_us_mean - 273.15
#detrend
mean_temp = da_cli_us_mean.mean()
da_cli_us_det = xr.DataArray(signal.detrend(da_cli_us_mean, axis=0),
dims=da_cli_us_mean.dims,
coords=da_cli_us_mean.coords,
attrs=da_cli_us_mean.attrs) + mean_temp
# Climate for each month
monthDict = {
1: 'Jan',
2: 'Feb',
3: 'Mar',
4: 'Apr',
5: 'May',
6: 'Jun',
7: 'Jul',
8: 'Aug',
9: 'Sep',
10: 'Oct',
from scipy import signal
from matplotlib.dates import DateFormatter, DayLocator, MonthLocator
from scipy import optimize
today = date.today()
start = (today.year - 1, today.month, today.day)
quotes = quotes_historical_yahoo("QQQ", start, today)
quotes = np.array(quotes)
dates = quotes.T[0]
qqq = quotes.T[4]
y = signal.detrend(qqq)
alldays = DayLocator()
months = MonthLocator()
month_formatter = DateFormatter("%b %Y")
fig = plt.figure()
ax = fig.add_subplot(211)
ax.xaxis.set_minor_locator(alldays)
ax.xaxis.set_major_locator(months)
ax.xaxis.set_major_formatter(month_formatter)
amps = np.abs(fftpack.fftshift(fftpack.rfft(y)))
amps[amps < amps.max()] = 0
def update():
global specmax, specmin, specmax_hist, specmin_hist, FFT_old, FFT_hist, redfreq, redwidth, bluefreq, bluewidth, counter, history
# get last data
last_index = ft_input.getHeader().nSamples
begsample = (last_index - window)
endsample = (last_index - 1)
data = ft_input.getData([begsample, endsample])
print "reading from sample %d to %d" % (begsample, endsample)
# demean and detrend data before filtering to reduce edge artefacts and center timecourse
# data = data - np.sum(data, axis=0)/float(len(data))
data = detrend(data, axis=0)
# Notch filter - DOES NOT WORK
# data = notch_filter(data, 10, hdr_input.fSample, 30)
# taper data
taper = np.hanning(len(data))
data = data * taper[:, np.newaxis]
# shift data to next sample
history = np.roll(history, 1, axis=2)
for ichan in range(numchannel):
channr = int(chanarray[ichan])
# current FFT with smoothing
FFT_temp = abs(fft(data[:, int(chanarray[ichan])]))
FFT[ichan] = FFT_temp * lrate + FFT_old[ichan] * (1 - lrate)
FFT_old[ichan] = FFT[ichan]
# update history with current FFT
history[ichan, :, numhistory - 1] = FFT_temp
FFT_hist = np.nanmean(history, axis=2)
# user-selected frequency band
arguments_freqrange = patch.getstring('arguments',
'freqrange').split("-")
arguments_freqrange = [float(s) for s in arguments_freqrange]
freqrange = np.greater(freqaxis,
arguments_freqrange[0]) & np.less_equal(
freqaxis, arguments_freqrange[1])
# update panels
spect[ichan].setData(freqaxis[freqrange], FFT[ichan][freqrange])
spect_hist[ichan].setData(freqaxis[freqrange],
FFT_hist[ichan][freqrange])
# adapt the vertical scale to the running mean of max
specmax[ichan] = float(specmax[ichan]) * (1 - lrate) + lrate * max(
FFT[ichan][freqrange])
specmin[ichan] = float(specmin[ichan]) * (1 - lrate) + lrate * min(
FFT[ichan][freqrange])
specmax_hist[ichan] = float(specmax_hist[ichan]) * (
1 - lrate) + lrate * max(FFT_hist[ichan][freqrange])
specmin_hist[ichan] = float(specmin_hist[ichan]) * (
1 - lrate) + lrate * min(FFT_hist[ichan][freqrange])
freqplot[ichan].setYRange(specmin[ichan], specmax[ichan])
freqplot_hist[ichan].setYRange(specmin_hist[ichan],
specmax_hist[ichan])
# update plotted lines
redfreq = patch.getfloat('input',
'redfreq',
default=10. / arguments_freqrange[1])
redfreq = EEGsynth.rescale(redfreq, slope=scalered,
offset=offsetred) * arguments_freqrange[1]
redwidth = patch.getfloat('input',
'redwidth',
default=1. / arguments_freqrange[1])
redwidth = EEGsynth.rescale(redwidth, slope=scalered,
offset=offsetred) * arguments_freqrange[1]
bluefreq = patch.getfloat('input',
'bluefreq',
default=20. / arguments_freqrange[1])
bluefreq = EEGsynth.rescale(bluefreq,
slope=scaleblue,
offset=offsetblue) * arguments_freqrange[1]
bluewidth = patch.getfloat('input',
'bluewidth',
default=4. / arguments_freqrange[1])
bluewidth = EEGsynth.rescale(
bluewidth, slope=scaleblue,
offset=offsetblue) * arguments_freqrange[1]
redleft[ichan].setData(x=[redfreq - redwidth, redfreq - redwidth],
y=[specmin[ichan], specmax[ichan]])
redright[ichan].setData(x=[redfreq + redwidth, redfreq + redwidth],
y=[specmin[ichan], specmax[ichan]])
blueleft[ichan].setData(x=[bluefreq - bluewidth, bluefreq - bluewidth],
y=[specmin[ichan], specmax[ichan]])
blueright[ichan].setData(
x=[bluefreq + bluewidth, bluefreq + bluewidth],
y=[specmin[ichan], specmax[ichan]])
redleft_hist[ichan].setData(
x=[redfreq - redwidth, redfreq - redwidth],
y=[specmin_hist[ichan], specmax_hist[ichan]])
redright_hist[ichan].setData(
x=[redfreq + redwidth, redfreq + redwidth],
y=[specmin_hist[ichan], specmax_hist[ichan]])
blueleft_hist[ichan].setData(
x=[bluefreq - bluewidth, bluefreq - bluewidth],
y=[specmin_hist[ichan], specmax_hist[ichan]])
blueright_hist[ichan].setData(
x=[bluefreq + bluewidth, bluefreq + bluewidth],
y=[specmin_hist[ichan], specmax_hist[ichan]])
# update labels at plotted lines
text_redleft.setText('%0.1f' % (redfreq - redwidth))
text_redleft.setPos(redfreq - redwidth, specmax[0])
text_redright.setText('%0.1f' % (redfreq + redwidth))
text_redright.setPos(redfreq + redwidth, specmax[0])
text_blueleft.setText('%0.1f' % (bluefreq - bluewidth))
text_blueleft.setPos(bluefreq - bluewidth, specmax[0])
text_blueright.setText('%0.1f' % (bluefreq + bluewidth))
text_blueright.setPos(bluefreq + bluewidth, specmax[0])
text_redleft_hist.setText('%0.1f' % (redfreq - redwidth))
text_redleft_hist.setPos(redfreq - redwidth, specmax_hist[0])
text_redright_hist.setText('%0.1f' % (redfreq + redwidth))
text_redright_hist.setPos(redfreq + redwidth, specmax_hist[0])
text_blueleft_hist.setText('%0.1f' % (bluefreq - bluewidth))
text_blueleft_hist.setPos(bluefreq - bluewidth, specmax_hist[0])
text_blueright_hist.setText('%0.1f' % (bluefreq + bluewidth))
text_blueright_hist.setPos(bluefreq + bluewidth, specmax_hist[0])
key = "%s.%s.%s" % (patch.getstring('output', 'prefix'), 'redband', 'low')
r.set(key, redfreq - redwidth)
key = "%s.%s.%s" % (patch.getstring('output', 'prefix'), 'redband', 'high')
r.set(key, redfreq + redwidth)
key = "%s.%s.%s" % (patch.getstring('output', 'prefix'), 'blueband', 'low')
r.set(key, bluefreq - bluewidth)
key = "%s.%s.%s" % (patch.getstring('output',
'prefix'), 'blueband', 'high')
r.set(key, bluefreq + bluewidth)
def get_results(self):
"""Execute API calls to the timeseries data and tweet data we need for analysis. Perform analysis
as we go because we often need results for next steps."""
######################
# (1) Get the timeline
######################
logging.info("retrieving timeline counts")
results_timeseries = Results(self.user,
self.password,
self.stream_url,
self.options.paged,
self.options.output_file_path,
pt_filter=self.options.filter,
max_results=int(self.options.max),
start=self.options.start,
end=self.options.end,
count_bucket=self.options.count_bucket,
show_query=self.options.query)
# sort by date
res_timeseries = sorted(results_timeseries.get_time_series(),
key=itemgetter(0))
# if we only have one activity, probably don't do all of this
if len(res_timeseries) <= 1:
raise ValueError(
"You've only pulled {} Tweets. time series analysis isn't what you want."
.format(len(res_timeseries)))
# calculate total time interval span
time_min_date = min(res_timeseries, key=itemgetter(2))[2]
time_max_date = max(res_timeseries, key=itemgetter(2))[2]
time_min = float(calendar.timegm(time_min_date.timetuple()))
time_max = float(calendar.timegm(time_max_date.timetuple()))
time_span = time_max - time_min
logging.debug("time_min = {}, time_max = {}, time_span = {}".format(
time_min, time_max, time_span))
# create a simple object to hold our data
ts = TimeSeries()
ts.dates = []
ts.x = []
ts.counts = []
# load and format data
for i in res_timeseries:
ts.dates.append(i[2])
ts.counts.append(float(i[1]))
# create a independent variable in interval [0.0,1.0]
ts.x.append((calendar.timegm(
datetime.datetime.strptime(i[0], DATE_FMT).timetuple()) -
time_min) / time_span)
logging.info("read {} time items from search API".format(len(
ts.dates)))
if len(ts.dates) < 35:
logging.warn(
"peak detection with with fewer than ~35 points is unreliable!"
)
logging.debug('dates: ' + ','.join(map(str, ts.dates[:10])) + "...")
logging.debug('counts: ' + ','.join(map(str, ts.counts[:10])) + "...")
logging.debug('indep var: ' + ','.join(map(str, ts.x[:10])) + "...")
######################
# (1.1) Get a second timeline?
######################
if self.options.second_filter is not None:
logging.info("retrieving second timeline counts")
results_timeseries = Results(
self.user,
self.password,
self.stream_url,
self.options.paged,
self.options.output_file_path,
pt_filter=self.options.second_filter,
max_results=int(self.options.max),
start=self.options.start,
end=self.options.end,
count_bucket=self.options.count_bucket,
show_query=self.options.query)
# sort by date
second_res_timeseries = sorted(
results_timeseries.get_time_series(), key=itemgetter(0))
if len(second_res_timeseries) != len(res_timeseries):
logging.error("time series of different sizes not allowed")
else:
ts.second_counts = []
# load and format data
for i in second_res_timeseries:
ts.second_counts.append(float(i[1]))
logging.info("read {} time items from search API".format(
len(ts.second_counts)))
logging.debug('second counts: ' +
','.join(map(str, ts.second_counts[:10])) +
"...")
######################
# (2) Detrend and remove prominent period
######################
logging.info("detrending timeline counts")
no_trend = signal.detrend(np.array(ts.counts))
# determine period of data
df = (ts.dates[1] - ts.dates[0]).total_seconds()
if df == 86400:
# day counts, average over week
n_buckets = 7
n_avgs = {i: [] for i in range(n_buckets)}
for t, c in zip(ts.dates, no_trend):
n_avgs[t.weekday()].append(c)
elif df == 3600:
# hour counts, average over day
n_buckets = 24
n_avgs = {i: [] for i in range(n_buckets)}
for t, c in zip(ts.dates, no_trend):
n_avgs[t.hour].append(c)
elif df == 60:
# minute counts; average over day
n_buckets = 24 * 60
n_avgs = {i: [] for i in range(n_buckets)}
for t, c in zip(ts.dates, no_trend):
n_avgs[t.minute].append(c)
else:
sys.stderr.write("Weird interval problem! Exiting.\n")
logging.error("Weird interval problem! Exiting.\n")
sys.exit()
logging.info("averaging over periods of {} buckets".format(n_buckets))
# remove upper outliers from averages
df_avg_all = {i: np.average(n_avgs[i]) for i in range(n_buckets)}
logging.debug("bucket averages: {}".format(','.join(
map(str, [df_avg_all[i] for i in df_avg_all]))))
n_avgs_remove_outliers = {
i: [
j for j in n_avgs[i]
if abs(j - df_avg_all[i]) / df_avg_all[i] < (1. + OUTLIER_FRAC)
]
for i in range(n_buckets)
}
df_avg = {
i: np.average(n_avgs_remove_outliers[i])
for i in range(n_buckets)
}
logging.debug("bucket averages w/o outliers: {}".format(','.join(
map(str, [df_avg[i] for i in df_avg]))))
# flatten cycle
ts.counts_no_cycle_trend = np.array([
no_trend[i] - df_avg[ts.dates[i].hour]
for i in range(len(ts.counts))
])
logging.debug('no trend: ' +
','.join(map(str, ts.counts_no_cycle_trend[:10])) +
"...")
######################
# (3) Moving average
######################
ts.moving = np.convolve(ts.counts,
np.ones((N_MOVING, )) / N_MOVING,
mode='valid')
logging.debug('moving ({}): '.format(N_MOVING) +
','.join(map(str, ts.moving[:10])) + "...")
######################
# (4) Peak detection
######################
peakind = signal.find_peaks_cwt(ts.counts_no_cycle_trend,
np.arange(MIN_PEAK_WIDTH,
MAX_PEAK_WIDTH),
min_snr=MIN_SNR)
n_peaks = min(MAX_N_PEAKS, len(peakind))
logging.debug('peaks ({}): '.format(n_peaks) +
','.join(map(str, peakind)))
logging.debug('peaks ({}): '.format(n_peaks) +
','.join(map(str, [ts.dates[i] for i in peakind])))
# top peaks determined by peak volume, better way?
# peak detector algorithm:
# * middle of peak (of unknown width)
# * finds peaks up to MAX_PEAK_WIDTH wide
#
# algorithm for geting peak start, peak and end parameters:
# find max, find fwhm,
# find start, step past peak, keep track of volume and peak height,
# stop at end of period or when timeseries turns upward
peaks = []
for i in peakind:
# find the first max in the possible window
i_start = max(0, i - SEARCH_PEAK_WIDTH)
i_finish = min(len(ts.counts) - 1, i + SEARCH_PEAK_WIDTH)
p_max = max(ts.counts[i_start:i_finish])
h_max = p_max / 2.
# i_max not center
i_max = i_start + ts.counts[i_start:i_finish].index(p_max)
i_start, i_finish = i_max, i_max
# start at peak, and go back and forward to find start and end
while i_start >= 1:
if (ts.counts[i_start - 1] <= h_max
or ts.counts[i_start - 1] >= ts.counts[i_start]
or i_start - 1 <= 0):
break
i_start -= 1
while i_finish < len(ts.counts) - 1:
if (ts.counts[i_finish + 1] <= h_max
or ts.counts[i_finish + 1] >= ts.counts[i_finish]
or i_finish + 1 >= len(ts.counts)):
break
i_finish += 1
# i is center of peak so balance window
delta_i = max(1, i - i_start)
if i_finish - i > delta_i:
delta_i = i_finish - i
# final est of start and finish
i_finish = min(len(ts.counts) - 1, i + delta_i)
i_start = max(0, i - delta_i)
p_volume = sum(ts.counts[i_start:i_finish])
peaks.append([
i, p_volume,
(i, i_start, i_max, i_finish, h_max, p_max, p_volume,
ts.dates[i_start], ts.dates[i_max], ts.dates[i_finish])
])
# top n_peaks by volume
top_peaks = sorted(peaks, key=itemgetter(1))[-n_peaks:]
# re-sort peaks by date
ts.top_peaks = sorted(top_peaks, key=itemgetter(0))
logging.debug('top peaks ({}): '.format(len(ts.top_peaks)) +
','.join(map(str, ts.top_peaks[:4])) + "...")
######################
# (5) high/low frequency
######################
ts.cycle, ts.trend = sm.tsa.filters.hpfilter(np.array(ts.counts))
logging.debug('cycle: ' + ','.join(map(str, ts.cycle[:10])) + "...")
logging.debug('trend: ' + ','.join(map(str, ts.trend[:10])) + "...")
######################
# (6) n-grams for top peaks
######################
ts.topics = []
if self.options.get_topics:
logging.info("retrieving tweets for peak topics")
for a in ts.top_peaks:
# start at peak
ds = datetime.datetime.strftime(a[2][8], DATE_FMT2)
# estimate how long to get TWEET_SAMPLE tweets
# a[1][5] is max tweets per period
if a[2][5] > 0:
est_periods = float(TWEET_SAMPLE) / a[2][5]
else:
logging.warn(
"peak with zero max tweets ({}), setting est_periods to 1"
.format(a))
est_periods = 1
# df comes from above, in seconds
# time resolution is hours
est_time = max(int(est_periods * df), 60)
logging.debug("est_periods={}, est_time={}".format(
est_periods, est_time))
#
if a[2][8] + datetime.timedelta(seconds=est_time) < a[2][9]:
de = datetime.datetime.strftime(
a[2][8] + datetime.timedelta(seconds=est_time),
DATE_FMT2)
elif a[2][8] < a[2][9]:
de = datetime.datetime.strftime(a[2][9], DATE_FMT2)
else:
de = datetime.datetime.strftime(
a[2][8] + datetime.timedelta(seconds=60), DATE_FMT2)
logging.info(
"retreive data for peak index={} in date range [{},{}]".
format(a[0], ds, de))
res = Results(self.user,
self.password,
self.stream_url,
self.options.paged,
self.options.output_file_path,
pt_filter=self.options.filter,
max_results=int(self.options.max),
start=ds,
end=de,
count_bucket=None,
show_query=self.options.query,
hard_max=TWEET_SAMPLE)
logging.info("retrieved {} records".format(len(res)))
n_grams_counts = list(
res.get_top_grams(n=self.token_list_size))
ts.topics.append(n_grams_counts)
logging.debug('n_grams for peak index={}: '.format(a[0]) +
','.join(
map(str, [
i[4].encode("utf-8", "ignore")
for i in n_grams_counts
][:10])) + "...")
return ts
def absolute_sdm(obs_cube, mod_cube, sce_cubes, *args, **kwargs):
"""
apply absolute scaled distribution mapping to all scenario cubes
assuming a normal distributed parameter
Args:
* obs_cube (:class:`iris.cube.Cube`):
the observational data
* mod_cube (:class:`iris.cube.Cube`):
the model data at the reference period
* sce_cubes (:class:`iris.cube.CubeList`):
the scenario data that shall be corrected
Kwargs:
* cdf_threshold (float):
limit of the cdf-values (default: .99999)
"""
from scipy.stats import norm
from scipy.signal import detrend
cdf_threshold = kwargs.get('cdf_threshold', .99999)
obs_cube_mask = np.ma.getmask(obs_cube.data)
cell_iterator = np.nditer(obs_cube.data[0], flags=['multi_index'])
while not cell_iterator.finished:
index_list = list(cell_iterator.multi_index)
cell_iterator.iternext()
index_list.insert(0, 0)
index = tuple(index_list)
if obs_cube_mask.any() and obs_cube_mask[index]:
continue
index_list[0] = slice(0, None, 1)
index = tuple(index_list)
# consider only cells with valid observational data
obs_data = obs_cube.data[index]
mod_data = mod_cube.data[index]
obs_len = len(obs_data)
mod_len = len(mod_data)
obs_mean = obs_data.mean()
mod_mean = mod_data.mean()
# detrend the data
obs_detrended = detrend(obs_data)
mod_detrended = detrend(mod_data)
obs_norm = norm.fit(obs_detrended)
mod_norm = norm.fit(mod_detrended)
obs_cdf = norm.cdf(np.sort(obs_detrended), *obs_norm)
mod_cdf = norm.cdf(np.sort(mod_detrended), *mod_norm)
obs_cdf = np.maximum(np.minimum(obs_cdf, cdf_threshold),
1 - cdf_threshold)
mod_cdf = np.maximum(np.minimum(mod_cdf, cdf_threshold),
1 - cdf_threshold)
for sce_cube in sce_cubes:
sce_data = sce_cube[index].data
sce_len = len(sce_data)
sce_mean = sce_data.mean()
sce_detrended = detrend(sce_data)
sce_diff = sce_data - sce_detrended
sce_argsort = np.argsort(sce_detrended)
sce_norm = norm.fit(sce_detrended)
sce_cdf = norm.cdf(np.sort(sce_detrended), *sce_norm)
sce_cdf = np.maximum(np.minimum(sce_cdf, cdf_threshold),
1 - cdf_threshold)
# interpolate cdf-values for obs and mod to the length of the
# scenario
obs_cdf_intpol = np.interp(np.linspace(1, obs_len, sce_len),
np.linspace(1, obs_len, obs_len),
obs_cdf)
mod_cdf_intpol = np.interp(np.linspace(1, mod_len, sce_len),
np.linspace(1, mod_len, mod_len),
mod_cdf)
# adapt the observation cdfs
# split the tails of the cdfs around the center
obs_cdf_shift = obs_cdf_intpol - .5
mod_cdf_shift = mod_cdf_intpol - .5
sce_cdf_shift = sce_cdf - .5
obs_inverse = 1. / (.5 - np.abs(obs_cdf_shift))
mod_inverse = 1. / (.5 - np.abs(mod_cdf_shift))
sce_inverse = 1. / (.5 - np.abs(sce_cdf_shift))
adapted_cdf = np.sign(obs_cdf_shift) * (
1. - 1. / (obs_inverse * sce_inverse / mod_inverse))
adapted_cdf[adapted_cdf < 0] += 1.
adapted_cdf = np.maximum(np.minimum(adapted_cdf, cdf_threshold),
1 - cdf_threshold)
xvals = norm.ppf(np.sort(adapted_cdf), *obs_norm) \
+ obs_norm[-1] / mod_norm[-1] \
* (norm.ppf(sce_cdf, *sce_norm) - norm.ppf(sce_cdf, *mod_norm))
xvals -= xvals.mean()
xvals += obs_mean + (sce_mean - mod_mean)
correction = np.zeros(sce_len)
correction[sce_argsort] = xvals
correction += sce_diff - sce_mean
sce_cube.data[index] = correction
#Load the silizon data
fname = 'D:/Data/default_fname_%3d.fits' % si_num
si_data = np.squeeze(fits.getdata(fname))
fname = 'D:/Data/default_fname_%3d.fits' % atm_num
atm_data = np.squeeze(fits.getdata(fname))
c = 2.99792458e11 #[mm/s]
F_max = c / (4 * dx * np.cos(12.2 * np.pi / 180) *
np.cos(5.78 / 2. * np.pi / 180) * 1e12) #[THz]
Fs = F_max / 2 * np.linspace(0, 1, 1598 / 2)
trans = []
for i in range(40):
si = detrend(si_data[:, i])
si_ind = np.argmax(np.abs(si))
si_nsteps = np.min((si_ind, len(si) - si_ind))
si = np.roll(si[si_ind - si_nsteps:si_ind + si_nsteps], si_nsteps)
si_pos = np.roll(pos[si_ind - si_nsteps:si_ind + si_nsteps], si_nsteps)
si_fft = np.fft.fft(si)
si_phi = np.angle(si_fft)
si_amplitude = np.abs(si_fft)**2
si_fft_corr = si_fft.real * np.cos(si_phi) + si_fft.imag * np.sin(si_phi)
si_psd = np.abs(si_fft_corr[:len(si_fft) / 2])**2
#Load the atmosphere data
atm = detrend(np.average(fits.getdata(fname), axis=(0, 2))) * scale_atm
def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None):
"""
Core routine for detecting outliers
"""
from scipy import signal
if not cwd:
cwd = os.getcwd()
# read in functional image
if isinstance(imgfile, (str, bytes)):
nim = load(imgfile, mmap=NUMPY_MMAP)
elif isinstance(imgfile, list):
if len(imgfile) == 1:
nim = load(imgfile[0], mmap=NUMPY_MMAP)
else:
images = [load(f, mmap=NUMPY_MMAP) for f in imgfile]
nim = funcs.concat_images(images)
# compute global intensity signal
(x, y, z, timepoints) = nim.shape
data = nim.get_data()
affine = nim.affine
g = np.zeros((timepoints, 1))
masktype = self.inputs.mask_type
if masktype == "spm_global": # spm_global like calculation
iflogger.debug("art: using spm global")
intersect_mask = self.inputs.intersect_mask
if intersect_mask:
mask = np.ones((x, y, z), dtype=bool)
for t0 in range(timepoints):
vol = data[:, :, :, t0]
# Use an SPM like approach
mask_tmp = vol > (np.nanmean(vol) / self.inputs.global_threshold)
mask = mask * mask_tmp
for t0 in range(timepoints):
vol = data[:, :, :, t0]
g[t0] = np.nanmean(vol[mask])
if len(find_indices(mask)) < (np.prod((x, y, z)) / 10):
intersect_mask = False
g = np.zeros((timepoints, 1))
if not intersect_mask:
iflogger.info("not intersect_mask is True")
mask = np.zeros((x, y, z, timepoints))
for t0 in range(timepoints):
vol = data[:, :, :, t0]
mask_tmp = vol > (np.nanmean(vol) / self.inputs.global_threshold)
mask[:, :, :, t0] = mask_tmp
g[t0] = np.nansum(vol * mask_tmp) / np.nansum(mask_tmp)
elif masktype == "file": # uses a mask image to determine intensity
maskimg = load(self.inputs.mask_file, mmap=NUMPY_MMAP)
mask = maskimg.get_data()
affine = maskimg.affine
mask = mask > 0.5
for t0 in range(timepoints):
vol = data[:, :, :, t0]
g[t0] = np.nanmean(vol[mask])
elif masktype == "thresh": # uses a fixed signal threshold
for t0 in range(timepoints):
vol = data[:, :, :, t0]
mask = vol > self.inputs.mask_threshold
g[t0] = np.nanmean(vol[mask])
else:
mask = np.ones((x, y, z))
g = np.nanmean(data[mask > 0, :], 1)
# compute normalized intensity values
gz = signal.detrend(g, axis=0) # detrend the signal
if self.inputs.use_differences[1]:
gz = np.concatenate((np.zeros((1, 1)), np.diff(gz, n=1, axis=0)), axis=0)
gz = (gz - np.mean(gz)) / np.std(gz) # normalize the detrended signal
iidx = find_indices(abs(gz) > self.inputs.zintensity_threshold)
# read in motion parameters
mc_in = np.loadtxt(motionfile)
mc = deepcopy(mc_in)
(
artifactfile,
intensityfile,
statsfile,
normfile,
plotfile,
displacementfile,
maskfile,
) = self._get_output_filenames(imgfile, cwd)
mask_img = Nifti1Image(mask.astype(np.uint8), affine)
mask_img.to_filename(maskfile)
if self.inputs.use_norm:
brain_pts = None
if self.inputs.bound_by_brainmask:
voxel_coords = np.nonzero(mask)
coords = np.vstack(
(voxel_coords[0], np.vstack((voxel_coords[1], voxel_coords[2])))
).T
brain_pts = np.dot(
affine, np.hstack((coords, np.ones((coords.shape[0], 1)))).T
)
# calculate the norm of the motion parameters
normval, displacement = _calc_norm(
mc,
self.inputs.use_differences[0],
self.inputs.parameter_source,
brain_pts=brain_pts,
)
tidx = find_indices(normval > self.inputs.norm_threshold)
ridx = find_indices(normval < 0)
if displacement is not None:
dmap = np.zeros((x, y, z, timepoints), dtype=np.float)
for i in range(timepoints):
dmap[
voxel_coords[0], voxel_coords[1], voxel_coords[2], i
] = displacement[i, :]
dimg = Nifti1Image(dmap, affine)
dimg.to_filename(displacementfile)
else:
if self.inputs.use_differences[0]:
mc = np.concatenate(
(np.zeros((1, 6)), np.diff(mc_in, n=1, axis=0)), axis=0
)
traval = mc[:, 0:3] # translation parameters (mm)
rotval = mc[:, 3:6] # rotation parameters (rad)
tidx = find_indices(
np.sum(abs(traval) > self.inputs.translation_threshold, 1) > 0
)
ridx = find_indices(
np.sum(abs(rotval) > self.inputs.rotation_threshold, 1) > 0
)
outliers = np.unique(np.union1d(iidx, np.union1d(tidx, ridx)))
# write output to outputfile
np.savetxt(artifactfile, outliers, fmt=b"%d", delimiter=" ")
np.savetxt(intensityfile, g, fmt=b"%.2f", delimiter=" ")
if self.inputs.use_norm:
np.savetxt(normfile, normval, fmt=b"%.4f", delimiter=" ")
if isdefined(self.inputs.save_plot) and self.inputs.save_plot:
import matplotlib
matplotlib.use(config.get("execution", "matplotlib_backend"))
import matplotlib.pyplot as plt
fig = plt.figure()
if isdefined(self.inputs.use_norm) and self.inputs.use_norm:
plt.subplot(211)
else:
plt.subplot(311)
self._plot_outliers_with_wave(gz, iidx, "Intensity")
if isdefined(self.inputs.use_norm) and self.inputs.use_norm:
plt.subplot(212)
self._plot_outliers_with_wave(
normval, np.union1d(tidx, ridx), "Norm (mm)"
)
else:
diff = ""
if self.inputs.use_differences[0]:
diff = "diff"
plt.subplot(312)
self._plot_outliers_with_wave(traval, tidx, "Translation (mm)" + diff)
plt.subplot(313)
self._plot_outliers_with_wave(rotval, ridx, "Rotation (rad)" + diff)
plt.savefig(plotfile)
plt.close(fig)
motion_outliers = np.union1d(tidx, ridx)
stats = [
{"motion_file": motionfile, "functional_file": imgfile},
{
"common_outliers": len(np.intersect1d(iidx, motion_outliers)),
"intensity_outliers": len(np.setdiff1d(iidx, motion_outliers)),
"motion_outliers": len(np.setdiff1d(motion_outliers, iidx)),
},
{
"motion": [
{"using differences": self.inputs.use_differences[0]},
{
"mean": np.mean(mc_in, axis=0).tolist(),
"min": np.min(mc_in, axis=0).tolist(),
"max": np.max(mc_in, axis=0).tolist(),
"std": np.std(mc_in, axis=0).tolist(),
},
]
},
{
"intensity": [
{"using differences": self.inputs.use_differences[1]},
{
"mean": np.mean(gz, axis=0).tolist(),
"min": np.min(gz, axis=0).tolist(),
"max": np.max(gz, axis=0).tolist(),
"std": np.std(gz, axis=0).tolist(),
},
]
},
]
if self.inputs.use_norm:
stats.insert(
3,
{
"motion_norm": {
"mean": np.mean(normval, axis=0).tolist(),
"min": np.min(normval, axis=0).tolist(),
"max": np.max(normval, axis=0).tolist(),
"std": np.std(normval, axis=0).tolist(),
}
},
)
save_json(statsfile, stats)
def calculate_complex_cross_coherence(time_series, epoch_length,
segment_length, segment_shift,
window_function, average_segments,
subtract_epoch_average, zeropad,
detrend_ts, max_freq, npat):
"""
# type: (TimeSeries, float, float, float, str, bool, bool, int, bool, float, float) -> ComplexCoherenceSpectrum
Calculate the FFT, Cross Coherence and Complex Coherence of time_series
broken into (possibly) epochs and segments of length `epoch_length` and
`segment_length` respectively, filtered by `window_function`.
Parameters
__________
time_series : TimeSeries
The timeseries for which the CrossCoherence and ComplexCoherence is to be computed.
epoch_length : float
In general for lengthy EEG recordings (~30 min), the timeseries are divided into equally
sized segments (~ 20-40s). These contain the event that is to be characterized by means of the
cross coherence. Additionally each epoch block will be further divided into segments to which
the FFT will be applied.
segment_length : float
The segment length determines the frequency resolution of the resulting power spectra --
longer windows produce finer frequency resolution.
segment_shift : float
Time length by which neighboring segments are shifted. e.g.
`segment shift` = `segment_length` / 2 means 50% overlapping segments.
window_function : str
Windowing functions can be applied before the FFT is performed.
average_segments : bool
Flag. If `True`, compute the mean Cross Spectrum across segments.
subtract_epoch_average: bool
Flag. If `True` and if the number of epochs is > 1, you can optionally subtract the
mean across epochs before computing the complex coherence.
zeropad : int
Adds `n` zeros at the end of each segment and at the end of window_function. It is not yet functional.
detrend_ts : bool
Flag. If `True` removes linear trend along the time dimension before applying FFT.
max_freq : float
Maximum frequency points (e.g. 32., 64., 128.) represented in the output. Default is segment_length / 2 + 1.
npat : float
This attribute appears to be related to an input projection matrix... Which is not yet implemented.
"""
# self.time_series.trait["data"].log_debug(owner=cls_attr_name)
tpts = time_series.data.shape[0]
time_series_length = tpts * time_series.sample_period
if len(time_series.data.shape) > 2:
time_series_data = numpy.squeeze(
(time_series.data.mean(axis=-1)).mean(axis=1))
# Divide time-series into epochs, no overlapping
if epoch_length > 0.0:
nepochs = int(numpy.floor(time_series_length / epoch_length))
epoch_tpts = int(epoch_length / time_series.sample_period)
time_series_length = epoch_length
tpts = epoch_tpts
else:
epoch_length = time_series_length
nepochs = int(numpy.ceil(time_series_length / epoch_length))
# Segment time-series, overlapping if necessary
nseg = int(numpy.floor(time_series_length / segment_length))
if nseg > 1:
seg_tpts = int(segment_length / time_series.sample_period)
seg_shift_tpts = int(segment_shift / time_series.sample_period)
nseg = int(numpy.floor((tpts - seg_tpts) / seg_shift_tpts) + 1)
else:
segment_length = time_series_length
seg_tpts = time_series_data.shape[0]
# Frequency
nfreq = int(
numpy.min([max_freq,
numpy.floor((seg_tpts + zeropad) / 2.0) + 1]))
resulted_shape, av_result_shape = complex_coherence_result_shape(
time_series.data.shape, max_freq, epoch_length, segment_length,
segment_shift, time_series.sample_period, zeropad, average_segments)
cs = numpy.zeros(resulted_shape, dtype=numpy.complex128)
av = numpy.matrix(numpy.zeros(av_result_shape, dtype=numpy.complex128))
coh = numpy.zeros(resulted_shape, dtype=numpy.complex128)
# Apply windowing function
if window_function is not None:
if window_function not in SUPPORTED_WINDOWING_FUNCTIONS:
log.error("Windowing function is: %s" % window_function)
log.error("Must be in: %s" % str(SUPPORTED_WINDOWING_FUNCTIONS))
window_func = eval("".join(("numpy.", window_function)))
win = window_func(seg_tpts)
window_mask = (numpy.kron(numpy.ones((time_series_data.shape[1], 1)),
win)).T
nave = 0
for j in numpy.arange(nepochs):
data = time_series_data[j * epoch_tpts:(j + 1) * epoch_tpts, :]
for i in numpy.arange(nseg): # average over all segments;
ts = data[i * seg_shift_tpts:i * seg_shift_tpts + seg_tpts, :]
if detrend_ts:
ts = sp_signal.detrend(ts, axis=0)
datalocfft = numpy.fft.fft(ts * window_mask, axis=0)
datalocfft = numpy.matrix(datalocfft)
for f in numpy.arange(nfreq): # for all frequencies
if npat == 1:
if not average_segments:
cs[:, :, f, i] += numpy.conjugate(
datalocfft[f, :].conj().T * datalocfft[f, :])
av[:, f,
i] += numpy.conjugate(datalocfft[f, :].conj().T)
else:
cs[:, :, f] += numpy.conjugate(
datalocfft[f, :].conj().T * datalocfft[f, :])
av[:, f] += numpy.conjugate(datalocfft[f, :].conj().T)
else:
if not average_segments:
cs[:, :, f, j, i] = numpy.conjugate(
datalocfft[f, :].conj().T * datalocfft[f, :])
av[:, f, j,
i] = numpy.conjugate(datalocfft[f, :].conj().T)
else:
cs[:, :, f, j] += numpy.conjugate(
datalocfft[f, :].conj().T * datalocfft[f, :])
av[:, f,
j] += numpy.conjugate(datalocfft[f, :].conj().T)
del datalocfft
nave += 1.0
# End of FORs
if not average_segments:
cs = cs / nave
av = av / nave
else:
nave = nave * nseg
cs = cs / nave
av = av / nave
# Subtract average
for f in numpy.arange(nfreq):
if subtract_epoch_average:
if npat == 1:
if not average_segments:
for i in numpy.arange(nseg):
cs[:, :, f,
i] = cs[:, :, f,
i] - av[:, f, i] * av[:, f, i].conj().T
else:
cs[:, :, f] = cs[:, :, f] - av[:, f] * av[:, f].conj().T
else:
if not average_segments:
for i in numpy.arange(nseg):
for j in numpy.arange(nepochs):
cs[:, :, f, j,
i] = cs[:, :, f, j,
i] - av[:, f, j, i] * av[:, f, j,
i].conj().T
else:
for j in numpy.arange(nepochs):
cs[:, :, f,
j] = cs[:, :, f,
j] - av[:, f, j] * av[:, f, j].conj().T
# Compute Complex Coherence
ndim = len(cs.shape)
if ndim == 3:
for i in numpy.arange(cs.shape[2]):
temp = numpy.matrix(cs[:, :, i])
coh[:, :, i] = cs[:, :, i] / numpy.sqrt(
temp.diagonal().conj().T * temp.diagonal())
elif ndim == 4:
for i in numpy.arange(cs.shape[2]):
for j in numpy.arange(cs.shape[3]):
temp = numpy.matrix(numpy.squeeze(cs[:, :, i, j]))
coh[:, :, i, j] = temp / numpy.sqrt(
temp.diagonal().conj().T * temp.diagonal().T)
log.debug("result")
log.debug(narray_describe(cs))
spectra = spectral.ComplexCoherenceSpectrum(
source=time_series,
array_data=coh,
cross_spectrum=cs,
epoch_length=epoch_length,
segment_length=segment_length,
windowing_function=window_function)
return spectra
lnm_cntrl = np.array(lnm)[::-1]
lnm_per = np.array(x_lnm)[::-1]
hr = np.int(time_diff / 3600.)
mn = np.int((time_diff - hr * 3600) / 60.)
sec = time_diff - hr * 3600 - mn * 60
print "Loaded ", hr, " hr ", mn, " min ", sec, " sec of waveform data."
print "It will analyze ", total_win - 1, " windows of ", time_win, " sec length"
ax = plt.gca()
for i in xrange(total_win - 1):
sys.stdout.write("Processing %d window\r" % (i))
sys.stdout.flush()
amp = []
data_slice = 0
data_slice = station[0].slice(t_start + i * time_shift, t_start +
(i * time_shift + time_win)).copy()
data_slice = sg.detrend(data_slice.data)
num = np.size(data_slice)
n_total = np.power(2, np.int(np.log2(num)) + 1)
if num > 0:
taper = np.hanning(np.size(data_slice))
data_slice = (data_slice - np.mean(data_slice)) * taper
amp = np.fft.rfft(data_slice - np.mean(data_slice) * taper, n_total)
num = n_total
amp = amp[0:int(num / 2) + 1] * np.conjugate(amp[0:int(num / 2) + 1])
norm = 2.0 * station[0].stats.delta / float(n_total)
amp = np.abs(amp[0:int(num / 2) + 1]) * norm
frq = np.fft.rfftfreq(n_total, station[0].stats.delta)
frq = frq[0:int(num / 2) + 1]
frq[1:] = 1. / frq[1:]
frq[0] = time_win
def run(self, tf, dt, c1, c2):
np.random.seed(62)
""" Run a simulation """
n, m, k = self.n, self.m, self.k
# Total simulation time
simTime = int(tf / dt)
# Returns the three synaptic connections kernels
W12, W21, W22, delays = self.build_kernels()
# Compute delays by dividing distances by axonal velocity
delays12 = np.floor(delays[0] / c2)
delays21 = np.floor(delays[1] / c1)
delays22 = np.floor(delays[2] / c2)
maxDelay = int(
max(delays12[0].max(), delays21[0].max(), delays22[0].max()))
# Set the initial conditions and the history
self.initial_conditions(simTime)
# Initialize the cortical and striatal inputs
Cx = 0.5
Str = 0.4
# Presynaptic activities
pre12, pre21, pre22 = np.empty((m, )), np.empty((m, )), np.empty((m, ))
# Simulation
for i in range(maxDelay, simTime):
# Take into account the history of rate for each neuron according
# to its axonal delay
for idxi, ii in enumerate(range(m)):
mysum = 0.0
for jj in range(k, n):
mysum += (W12[ii, jj] *
self.X2[i - delays12[ii, jj], jj]) * self.dx
pre12[idxi] = mysum
for idxi, ii in enumerate(range(k, n)):
mysum = 0.0
for jj in range(0, m):
mysum += (W21[ii, jj] *
self.X1[i - delays21[ii, jj], jj]) * self.dx
pre21[idxi] = mysum
for idxi, ii in enumerate(range(k, n)):
mysum = 0.0
for jj in range(k, n):
mysum += (W22[ii, jj] *
self.X2[i - delays22[ii, jj], jj]) * self.dx
pre22[idxi] = mysum
# Forward Euler step
self.X1[i, :m] = (
self.X1[i - 1, :m] +
(-self.X1[i - 1, :m] + self.S1(-pre12 + Cx)) * dt / self.tau1)
self.X2[i, k:] = (
self.X2[i - 1, k:] +
(-self.X2[i - 1, k:] + self.S2(pre21 - pre22 - Str)) * dt /
self.tau2)
dx = 1.0 / float(m)
fr = self.X1.sum(axis=1) * dx / 1.0
signal = detrend(fr)
windowed = signal * blackmanharris(len(signal))
f = rfft(windowed)
i = np.argmax(np.abs(f))
# true_i = parabolic(np.log(np.abs(f)), i)[0]
return i
utils.draw_face_roi(face_box,frame)
t = np.arange(timestamps[0],timestamps[-1],1/fs)
mean_colors_resampled = np.zeros((3,t.shape[0]))
for color in [B,G,R]:
resampled = np.interp(t,timestamps,np.array(mean_colors)[:,color])
mean_colors_resampled[color] = resampled
# Perform chrominance method
if mean_colors_resampled.shape[1] > window:
col_c = np.zeros((3,window))
for col in [B,G,R]:
col_stride = mean_colors_resampled[col,-window:]# select last samples
y_ACDC = signal.detrend(col_stride/np.mean(col_stride))
col_c[col] = y_ACDC * skin_vec[col]
X_chrom = col_c[R]-col_c[G]
Y_chrom = col_c[R] + col_c[G] - 2* col_c[B]
Xf = utils.bandpass_filter(X_chrom)
Yf = utils.bandpass_filter(Y_chrom)
Nx = np.std(Xf)
Ny = np.std(Yf)
alpha_CHROM = Nx/Ny
x_stride = Xf - alpha_CHROM*Yf
amplitude = np.abs( np.fft.fft(x_stride,window)[:int(window/2+1)])
normalized_amplitude = amplitude/amplitude.max() # Normalized Amplitude
frequencies = np.linspace(0,fs/2,int(window/2) + 1) * 60
# Define the bed geometry
h = bed_pick[line][1]
bed_raw = elev - h
bed = medfilt(bed_raw, 401)
# RMS bed roughness
ED1 = np.empty((len(bed), ))
ED1[:] = np.nan
for n in range(N, len(bed) - N + 1):
z = bed[n - N:n + N]
z = z[np.where(~np.isnan(z))]
if len(z) <= 1:
ED1[n] = np.nan
else:
z_ = detrend(z)
total = 0.
for i in range(len(z)):
total += (z_[i])**2.
ED1[n] = np.sqrt((1 / (len(z) - 1.)) * total)
# Find the power reduction by Kirchoff theory
g = 4 * np.pi * ED1 / lam
b = (i0((g**2.) / 2.))**2.
pn = np.exp(-(g**2.)) * b
if line == 's5_pole_7_051':
hold = 1. - pn[2723:3233]
pn[2723:3233] = 1. - .1 * hold
power = bed_pick[line][2]
tt1 = np.where(year_data == 1983)[0][0]
tt2 = np.where(year_data == 2012)[0][-1]
nYears = 2012 - 1983 + 1
# Generate predictor matrix for climate modes
if sw_nomodes:
#
# ENSO (MEI index)
#
MEI = np.genfromtxt('../../data/modes/mei.combined.1871_2016')
t_MEI, tmp, tmp, year_MEI, month_MEI, day_MEI, tmp = ecj.timevector(
[1871, 1, 1], [2016, 12, 31])
year_MEI = year_MEI[day_MEI == 15]
MEI = MEI[year_MEI >= yearStart]
MEI = MEI - MEI.mean()
MEI = signal.detrend(MEI)
# Predictor matrix with lags
Nl = 12 # Number of lead-lags
which = []
X = np.zeros((len(MEI), 3 + 2 * Nl + 2))
X[:, 0] += 1 # Mean
X[:, 1] = np.arange(len(MEI)) - np.arange(len(MEI)).mean() # Linear trend
which.append('Mean')
which.append('Trend')
# Mode leads SST
cnt = 1
for k in range(1, Nl + 1):
cnt += 1
X[:-k, cnt] = MEI[k:]
which.append('MEI')
# 0-lag
def my_form_post():
shop_Id = request.form['shop_id']
week_No = request.form['week_no']
ShopID = int(shop_Id)
WeekNo=int(week_No)
# %matplotlib inline
#plt.rcParams['figure.figsize'] = (20, 10)
plt.style.use('ggplot')
data_f = pd.read_csv('weekly sales and labour cost for all shops 2013 to 20177.csv')
data = pd.read_csv('weekly sales and labour cost for all shops 2013 to 20177.csv',index_col='start_date', parse_dates=True)
# shopID = input("Enter your shop id")
shopID1 = ShopID
# if shopID1<min(data.shop_id) or shopID1>max(data.shop_id):
# print("Enter correct shop id number")
# return select_model()
WeekNo1=WeekNo
data2 = data[['sales_id', 'shop_id', 'week_no', 'sales_amount', 'item_sold', 'transactions', 'total_tax', 'sales_status']]
df1 = data2[data2.shop_id == shopID1] # input №1
df2 = df1[df1.sales_status != 0]
df2.week_no.isnull().values.any()
nulldetect = df1.week_no.isnull()
nulldetect[nulldetect == True].index
df2.week_no.loc[nulldetect == True] = 54
df2['week_no'] = df2.week_no - 2
if len(df2.week_no) > 51:
dff = df2[['sales_amount']]
data3 = dff.reset_index()
data4 = data3
data5 = data4.rename(columns={'start_date': 'ds', 'sales_amount': 'y'})
data5.set_index('ds')
data5 = data5.replace([np.inf, -np.inf], np.nan).fillna(0)
# y.plot()
data5['y'] = np.log(data5['y'])
data5.set_index('ds')
model = Prophet()
model.fit(data5)
future = model.make_future_dataframe(periods=52, freq='w')
forecast = model.predict(future)
data5.set_index('ds', inplace=True)
forecast.set_index('ds', inplace=True)
viz_df = dff.join(forecast[['yhat', 'yhat_lower', 'yhat_upper']], how='outer')
viz_df['yhat_rescaled'] = np.exp(viz_df['yhat'])
dff.index = pd.to_datetime(dff.index) # make sure our index as a datetime object
connect_date = dff.index[-2] # select the 2nd to last date
mask = (forecast.index > connect_date)
predict_df = forecast.loc[mask]
viz_df = dff.join(predict_df[['yhat', 'yhat_lower', 'yhat_upper']], how='outer')
viz_df['yhat_scaled'] = np.exp(viz_df['yhat'])
ii = len(dff.sales_amount) - 1
viz_df.yhat_scaled[ii:]
predicted_future_sales = pd.DataFrame(viz_df.yhat_scaled[ii:])
predicted_future_sales1 = predicted_future_sales.rename(columns={'yhat_scaled': 'future_sales'})
predicted_future_sales2 = predicted_future_sales1.reset_index()
week_no = predicted_future_sales2['index'].dt.week
future_sales = predicted_future_sales2['future_sales']
future_sales1 = round(future_sales, 2)
start_date = predicted_future_sales2['index']
predict_data = {'future_sales': future_sales1, 'week_no': week_no, 'start_date': start_date}
predict_data1 = pd.DataFrame(predict_data)
predict_data2 = predict_data1.set_index('start_date')
frames = [df2.sales_amount, predict_data2.future_sales]
join = pd.concat(frames)
detrend_sdata = signal.detrend(join)
trend = join - detrend_sdata
p2 = predict_data1.set_index('start_date')
r = []
for jj in pd.DataFrame(df2.index.year.values).drop_duplicates().index.values:
sale_year = df2.sales_amount[str(int(pd.DataFrame(df2.index.year).drop_duplicates().loc[jj]))].mean()
r.append(sale_year)
years = pd.DataFrame(df2.index.year).drop_duplicates().start_date.values
holday = []
for t in years[0:len(years) - 1]:
h = df2.sales_amount[df2.week_no >= 50][str(t)].mean() + df2.sales_amount[df2.week_no <= 3][str(int(t) + 1)].mean()
holday.append(h / 2)
year_last = p2.future_sales[p2.week_no >= 50][str(years[-1])].mean() + p2.future_sales[p2.week_no <= 3].mean() # 2018
holday.append(year_last / 2)
N = len(r)
Holiday_Means = holday
All_Year_Means = r
ind = np.arange(N)
avg_sale=round(df2.sales_amount.mean(),2)
maxSale=round(max(df2.sales_amount), 2)
minSale=round(min(df2.sales_amount), 2)
itemTrans=round((df2.item_sold / df2.transactions).mean(), 2)
priceofitem=round((df2.sales_amount/df2.item_sold).mean(),2)
avgitems=round(df2.item_sold.mean(), 2)
best = pd.DataFrame(df2[['week_no', 'sales_amount']][(df2.sales_amount <= max(df2.sales_amount))
& (df2.sales_amount >= max(df2.sales_amount) - 2000)])
worst = pd.DataFrame(df2[['week_no', 'sales_amount']][(df2.sales_amount >= min(df2.sales_amount))
& (df2.sales_amount <= min(df2.sales_amount) + 1500)])
best1 = best.rename(columns={'week_no': 'Best Weeks', 'sales_amount': 'Sales'})
worst1 = worst.rename(columns={'week_no': 'Worst Weeks', 'sales_amount': 'Sales'})
result = pd.concat([best1, worst1], axis=1)
# result.fillna(' ')
# result['Date']=result.index.values
result.insert(0, 'Date', result.index.values)
result = result.fillna('-')
fig, ax1 = plt.subplots(figsize=(7, 4))
ax1.plot(viz_df.sales_amount)
ax1.plot(viz_df.yhat_scaled,color='green')
ax1.plot(join.index, trend, color='blue', alpha=0.5, label='Trend')
#ax1.plot(join.index, trend, color='blue', alpha=0.5, label='Trend')
#ax1.fill_between(viz_df.index, np.exp(viz_df['yhat_upper']), np.exp(viz_df['yhat_lower']), alpha=0.5,
#color='darkgray')
ax1.set_title('Sales (Orange) vs Sales Forecast (Green) for shop ' + str(shopID1))
ax1.set_ylabel('Sales amount')
ax1.set_xlabel('Dates')
L = ax1.legend() # get the legend
L.get_texts()[0].set_text('Actual Sales') # change the legend text for 1st plot
L.get_texts()[1].set_text('Forecasted Sales') # change the legend text for 2nd plot
graph = mpld3.fig_to_html(fig)
fig, ax2 = plt.subplots(figsize=(7, 4))
bar_width = 0.4
opacity = 0.8
bar1 = ax2.bar(ind, Holiday_Means, bar_width, opacity, label='Holidays')
bar2 = ax2.bar(ind + bar_width, All_Year_Means, bar_width, opacity, label='Avg sales per year')
ticks = pd.DataFrame(df2.index.year).drop_duplicates().start_date.values
ax2.set_ylabel('Sales_amount')
ax2.set_title('Holiday weekly sales (Xmas & NY) vs Average weekly sales per year (shop #%s)' % shopID1)
plt.xticks(ind+0.25,ticks)
ax2.legend()
graph1 = mpld3.fig_to_html(fig)
fig.clf()
f_sale=str(float(predict_data1.future_sales[predict_data1.week_no == WeekNo1].values[0]))
f_date=str(predict_data1.start_date[predict_data1.week_no == WeekNo1].values[0])[0:10]
n_week = WeekNo1
id_shop = shopID1
sale_mean=avg_sale
max_sale=maxSale
min_sale=minSale
item_trans=itemTrans
price_item=priceofitem
avg_wk_itemsold=avgitems
tab_week=result.to_html(index = False)
else:
a = df2[['sales_amount', 'shop_id', 'week_no', 'transactions', 'item_sold']]
y = a.iloc[:, 0]
x = a.iloc[:, 3:5]
# print (df2)
from sklearn import linear_model
regr2 = linear_model.LinearRegression()
X1 = x
y1 = y
regr2.fit(X1, y1)
y_predictions = regr2.predict(X1)
y_predictions1 = pd.DataFrame(y_predictions)
d = {'actual sales': y, 'predicted sales': y_predictions1}
d1 = np.array(d)
dates = pd.date_range(y.index[-1], periods=52, freq='W-MON', format='%Y-%m-%d')
dates1 = pd.DataFrame(dates)
mean_week_item = []
for i in dates.week:
mean_item_sold = a.item_sold[a.week_no == i].mean()
mean_week_item.append(mean_item_sold)
mean_week_item1 = pd.DataFrame(mean_week_item)
trans_week_item = []
for i1 in dates.week:
mean_trans_sold = a.transactions[a.week_no == i1].mean()
trans_week_item.append(mean_trans_sold)
sales_week = []
for ii1 in dates.week:
mean_sales_sold = a.sales_amount[a.week_no == ii1].mean()
sales_week.append(mean_sales_sold)
dd = {'date': dates, 'weeks_no': dates.week, 'sales': sales_week, 'mean_item': mean_week_item,
'mean_trans': trans_week_item}
dd1 = pd.DataFrame(dd)
dff1 = data_f[data_f.sales_status != 0]
nulldetect = dff1.week_no.isnull()
dff1.week_no.loc[nulldetect == True] = 54
dff1['week_no'] = dff1.week_no - 2
X_Cluster = dff1[['shop_id', 'sales_amount']]
from sklearn.cluster import KMeans
kmeans_model = KMeans(n_clusters=3, random_state=8).fit(X_Cluster)
y_hat = kmeans_model.labels_ # clusters
cen = kmeans_model.cluster_centers_
y_hat1 = pd.DataFrame(y_hat)
group_low_sales = X_Cluster[y_hat == 0]
group_middle_sales = X_Cluster[y_hat == 2]
group_high_sales = X_Cluster[y_hat == 1]
fff = []
for j in X_Cluster.shop_id:
dfdf = X_Cluster.sales_amount[X_Cluster.shop_id == j].mean()
fff.append(dfdf)
f3 = pd.DataFrame(X_Cluster.shop_id.drop_duplicates())
f4 = pd.DataFrame(fff)
f5 = f4.drop_duplicates()
f3['salle'] = f5.values
# from sklearn.cluster import KMeans
Xx2 = f3[['shop_id', 'salle']]
kmeans_model2 = KMeans(n_clusters=3, random_state=8).fit(Xx2)
y_hat2 = kmeans_model2.labels_ # clusters
cen2 = kmeans_model2.cluster_centers_
group_middle_sales2 = Xx2[y_hat2 == 0]
group_high_sales2 = Xx2[y_hat2 == 2]
group_low_sales2 = Xx2[y_hat2 == 1]
nullweeks = dd1.weeks_no[dd1.mean_trans.isnull() == True]
if (group_low_sales2.shop_id.values == shopID1).any() == True:
cx = int(group_low_sales.sales_amount[group_low_sales.shop_id == shopID1].values.mean())
trt = group_low_sales[group_low_sales.sales_amount > cx - 3000]
trt2 = trt[trt.sales_amount < cx + 3000]
valid_cls = dff1[['sales_amount', 'item_sold', 'transactions', 'week_no']].loc[trt2.index.values]
#print("Cluster of shop %s is low sales" % shopID1)
elif (group_middle_sales2.shop_id.values == shopID1).any() == True:
# valid_cls=dff1[['sales_amount','item_sold','transactions','week_no']].loc[group_middle_sales.shop_id.index.values]
cx = int(group_middle_sales.sales_amount[group_middle_sales.shop_id == shopID1].values.mean())
trt = group_middle_sales[group_middle_sales.sales_amount > cx - 3000]
trt2 = trt[trt.sales_amount < cx + 3000]
valid_cls = dff1[['sales_amount', 'item_sold', 'transactions', 'week_no']].loc[trt2.index.values]
#print("Cluster of shop %s is average sales" % shopID1)
elif (group_high_sales2.shop_id.values == shopID1).any() == True:
# valid_cls=dff1[['sales_amount','item_sold','transactions','week_no']].loc[group_high_sales.shop_id.index.values]
cx = int(group_high_sales.sales_amount[group_high_sales.shop_id == shopID1].values.mean())
trt = group_high_sales[group_high_sales.sales_amount > cx - 4000]
trt2 = trt[trt.sales_amount < cx + 4000]
valid_cls = dff1[['sales_amount', 'item_sold', 'transactions', 'week_no']].loc[trt2.index.values]
#print("Cluster of shop %s is high sales" % shopID1)
drr = valid_cls
#print('Avg sales per week for whole period ',
avg_sale=round(df2.sales_amount.mean(), 2) # avg sales per week for whole period
# avg_items_week=round(df2.item_sold[df2.week_no==17].mean(),2)# avg items for input week
#print('Avg items sold per week for whole period ',
#round(df2.item_sold.mean(), 2) # avg items per week for whole period
# avg_trans_week=round(df2.transactions[df2.week_no==17].mean(),2)# avg trans for input week
#print('Avg trans per week for whole period ',
#round(df2.transactions.mean(), 2) # avg trans per week for whole period
# avg_item_per_trans=round((df2.item_sold[df2.week_no==17]/df2.transactions[df2.week_no==17]).mean(),2)#items per transactions w
itemTrans=round((df2.item_sold / df2.transactions).mean(), 2)
# max_w=round(max(df2.sales_amount[df2.week_no==17]),2)
# min_w=round(min(df2.sales_amount[df2.week_no==17]),2)
maxSale=round(max(df2.sales_amount), 2)
minSale=round(min(df2.sales_amount), 2)
priceofitem = round((df2.sales_amount / df2.item_sold).mean(), 2)
avgitems=round(df2.item_sold.mean(), 2)
best = pd.DataFrame(df2[['week_no', 'sales_amount']][(df2.sales_amount <= max(df2.sales_amount))
& (df2.sales_amount >= max(df2.sales_amount) - 2000)])
worst = pd.DataFrame(df2[['week_no', 'sales_amount']][(df2.sales_amount >= min(df2.sales_amount))
& (df2.sales_amount <= min(df2.sales_amount) + 1500)])
best1 = best.rename(columns={'week_no': 'Best Weeks', 'sales_amount': 'Sales'})
worst1 = worst.rename(columns={'week_no': 'Worst Weeks', 'sales_amount': 'Sales'})
result = pd.concat([best1, worst1], axis=1)
# result.fillna(' ')
# result['Date']=result.index.values
result.insert(0, 'Date', result.index.values)
result = result.fillna('-')
# worst=df2.week_no[df2.sales_amount>min(df2.sales_amount)]
#df2[['week_no', 'sales_amount']][(df2.sales_amount >= min(df2.sales_amount)) & (df2.sales_amount <= min(df2.sales_amount) + 1500)])
#df2[['week_no', 'sales_amount']][(df2.sales_amount <= max(df2.sales_amount)) & (df2.sales_amount >= max(df2.sales_amount) - 3000)])
#print('Price of trans ', round((df2.sales_amount / df2.transactions).mean(), 2))
#print('Price of item ', round((df2.sales_amount / df2.item_sold).mean(), 2))
itt = []
trr = []
sale = []
for i3 in nullweeks:
item = drr.item_sold[drr.week_no == i3].mean()
trans = drr.transactions[drr.week_no == i3].mean()
salee = drr.sales_amount[drr.week_no == i3].mean()
itt.append(item)
trr.append(trans)
sale.append(salee)
df_insert = {'sales_amountt': sale, 'ittem': itt, 'trans': trr, 'weeks_no': nullweeks}
df_insert1 = pd.DataFrame(df_insert)
forecastdf = dd1.fillna({'mean_item': df_insert1.ittem, 'mean_trans': df_insert1.trans, 'sales': df_insert1.sales_amountt})
regr3 = linear_model.LinearRegression()
X = forecastdf[['mean_item', 'mean_trans']]
Y = forecastdf.sales
regr3.fit(X, Y)
y_predictionss = regr3.predict(X)
y_predictionss1 = pd.DataFrame(y_predictionss)
forecastdf['future_sales1'] = y_predictionss1.values
f1 = forecastdf.set_index('date')
frames1 = [df2.sales_amount, f1.future_sales1]
join1 = pd.concat(frames1)
detrend_sdata1 = signal.detrend(join1)
trend1 = join1 - detrend_sdata1
r1 = []
for jj1 in pd.DataFrame(df2.index.year.values).drop_duplicates().index.values:
sale_year1 = df2.sales_amount[str(int(pd.DataFrame(df2.index.year).drop_duplicates().loc[jj1]))].mean()
r1.append(sale_year1)
years1 = pd.DataFrame(df2.index.year).drop_duplicates().start_date.values
holday1 = []
for t1 in years1[0:len(years1) - 1]:
h1 = df2.sales_amount[df2.week_no >= 50][str(t1)].mean() + df2.sales_amount[df2.week_no <= 3][str(int(t1) + 1)].mean()
holday1.append(h1 / 2)
year_last1 = f1.future_sales1[f1.weeks_no >= 50][str(years1[-1])].mean() + f1.future_sales1[f1.weeks_no <= 3].mean() # 2018
holday1.append(year_last1 / 2)
N1 = len(r1)
Holiday_Means1 = holday1
All_Year_Means1 = r1
ind1 = np.arange(N1)
f_sale = int(forecastdf.future_sales1[forecastdf.weeks_no == WeekNo1].values)
f_date =str(forecastdf.date[forecastdf.weeks_no==WeekNo1].values[0])[0:10]
n_week = WeekNo1
id_shop = shopID1
sale_mean = avg_sale
max_sale = maxSale
min_sale = minSale
item_trans = itemTrans
price_item=priceofitem
avg_wk_itemsold = avgitems
tab_week=result.to_html(index = False)
# print(y.index)
fig3, ax3 = plt.subplots(figsize=(7,4))
# dates = pd.date_range(y.index[0], periods=104, freq='W-MON',format='%Y-%m-%d')
# plt.plot(y.index,y,color='blue',label="actual sales")
ax3.plot(y.index, a.sales_amount, color='red', label="actual sales")
ax3.plot(dates, y_predictionss1, color='green', label="forecasted sales")
ax3.plot(join1.index, trend1, color='blue', alpha=0.5, label='Trend')
ax3.set_title('Comparison actual and predicted sales for whole period of shop ' + str(shopID1) + '\n')
ax3.set_xlabel('Weeks')
ax3.set_ylabel('Sales amount')
ax3.legend()
graph = mpld3.fig_to_html(fig3)
fig3.clf()
fig4, ax4 = plt.subplots(figsize=(7,4))
bar_width1 = 0.4
opacity1 = 0.8
ax4.bar(ind1, Holiday_Means1, bar_width1, opacity1, label='Holidays')
ax4.bar(ind1 + bar_width1, All_Year_Means1, bar_width1, opacity1, label='Avg sales per year')
ax4.set_ylabel('Sales_amount')
ax4.set_title('Holiday weekly sales (Xmas & NY) vs Average weekly sales per year (shop #%s)' % shopID1)
plt.xticks(ind1 + 0.25, (pd.DataFrame(df2.index.year).drop_duplicates().start_date.values))
ax4.legend()
graph1 = mpld3.fig_to_html(fig4)
return render_template('index.html',graph1=graph1,graph=graph,data=tab_week,value9=f_date,value8=avg_wk_itemsold,value7=price_item,value6=itemTrans,
value5=min_sale,value4=max_sale,value3=sale_mean,
value2=id_shop,value1=n_week,value=f_sale)
def cmplxIQ_fit(paramsVec, freqs, data=None, eps=None, **kwargs):
"""Return complex S21 resonance model or, if data is specified, a residual.
Parameters
----------
params : list-like
A an ``lmfit.Parameters`` object containing (df, f0, qc, qi, gain0, gain1, gain2, pgain0, pgain1, pgain2)
freqs : list-like
A list of frequency points at which the model is calculated
data : list-like (optional)
A list of complex data in the form I + Q where I and Q are both lists of data and
``len(I) == len(Q) == len(freqs)``. If data is not passed, then the return value is the model
calculated at each frequency point.
eps : list-like (optional)
A list of errors, one for each point in data.
kwargs : dict (optional)
Currently no keyword arguments are accepted.
Returns
-------
model or (model-data) : ``numpy.array``
If data is specified, the return is the residuals. If not, the return is the model
values calculated at the frequency points. The returned array is in the form
``I + Q`` or ``residualI + residualQ``.
"""
#Check if the paramsVec looks like a lmfit params object. If so, unpack to list
if hasattr(paramsVec, 'valuesdict'):
paramsDict = paramsVec.valuesdict()
paramsVec = [value for value in paramsDict.values()]
#intrinsic resonator parameters
df = paramsVec[0] #frequency shift due to mismatched impedances
f0 = paramsVec[1] #resonant frequency
qc = paramsVec[2] #coupling Q
qi = paramsVec[3] #internal Q
#0th, 1st, and 2nd terms in a taylor series to handle magnitude gain different than 1
gain0 = paramsVec[4]
gain1 = paramsVec[5]
gain2 = paramsVec[6]
#0th and 1st terms in a taylor series to handle phase gain different than 1
pgain0 = paramsVec[7]
pgain1 = paramsVec[8]
#Need to add an if statement here to keep compatibility with older version
#Will be deprecated in the future
if len(paramsVec) == 12:
pgain2 = paramsVec[9]
#Voltage offset at mixer output. Not needed for VNA
Ioffset = paramsVec[10]
Qoffset = paramsVec[11]
else:
print(
"Warning: new model also fits for quadratic phase. Setting pgain2 = 0."
)
print(
"If using Resonator.do_lmfit() pass kwarg: pgain2_vary = False for legacy behavior."
)
pgain2 = 0
#Voltage offset at mixer output. Not needed for VNA
Ioffset = paramsVec[9]
Qoffset = paramsVec[10]
#Make everything referenced to the shifted, unitless, reduced frequency
fs = f0 + df
ff = (freqs - fs) / fs
#Except for the gain, which should reference the file midpoint
#This is important because the baseline coefs shouldn't drift
#around with changes in f0 due to power or temperature
#Of course, this philosophy goes out the window if different sweeps have
#different ranges.
fm = freqs[int(np.round((len(freqs) - 1) / 2.0))]
ffm = (freqs - fm) / fm
#Calculate the total Q_0
q0 = 1. / (1. / qi + 1. / qc)
#Calculate magnitude and phase gain
gain = gain0 + gain1 * ffm + 0.5 * gain2 * ffm**2
pgain = np.exp(1j * (pgain0 + pgain1 * ffm + 0.5 * pgain2 * ffm**2))
#Allow for voltage offset of I and Q
offset = Ioffset + 1j * Qoffset
#Calculate model from params at each point in freqs
modelCmplx = -gain * pgain * (1. / qi + 1j * 2.0 *
(ff + df / fs)) / (1. / q0 +
1j * 2.0 * ff) + offset
#Package complex data in 1D vector form
modelI = np.real(modelCmplx)
modelQ = np.imag(modelCmplx)
model = np.concatenate((modelI, modelQ), axis=0)
#Calculate eps from stdev of first 10 pts of data if not supplied
if eps is None and data is not None:
dataI, dataQ = np.split(data, 2)
epsI = np.std(sps.detrend(dataI[0:10]))
epsQ = np.std(sps.detrend(dataQ[0:10]))
eps = np.concatenate((np.full_like(dataI,
epsI), np.full_like(dataQ, epsQ)))
#Return model or residual
if data is None:
return model
else:
return (model - data) / eps
human = int(os.path.basename(file)
[:7]) ## get a person's number from file name
for i in range(
int(N_Origin / N)
): # 256 frames are divided by four, and the process is done every 64 frames
for loop in range(
HANDDATA_Num): ## four times (L1,L2,R1,R2)
div_data = data[loop][
i * N:(i + 1) *
N, :].T ## div_data = [L1's first 64 frames, L2's first 64 frames, R1's first 64 frames, … R2's last 64 frames]
for sensor_num in range(PARAMETER_Num):
# if sensor_num < From or sensor_num > To: ## if you want to use only partial feature, you can exclude here freely.
# continue
# if loop == 0 and i == 0: print(sensor_num) #display sensor number
data_window = signal.detrend(
div_data[sensor_num], type="constant"
) * window ## remove trend(constant) & apply window function
F_window = np.abs(
fft(data_window) / (N / 2)
) * 1 / (
sum(window) / N
) ## do FFT & get the absolute value (adjust the amplitude value)
x.append(
F_window[:int(N / 2)]
) ## MinMax Normalization & get the low frequency part
x = np.array(x).flatten()
X.append(
x
) ## add x(frequency data) to list. the data consists of 32 frequency components * four (L1,L2,R1,R2) * four (divide number) * X features = 512*X dimensions
y.append(int(type % 2)) ## add answer to list
human_all.append(int(human)) ## make human list
try:
dt_E = np.mean(np.diff(this_seis[0].times()))
dt_N = np.mean(np.diff(this_seis[1].times()))
dt_Z = np.mean(np.diff(this_seis[2].times()))
except:
continue
if not (dt_E == dt_N == dt_Z and len(this_seis[0].data) == len(
this_seis[1].data) == len(this_seis[2].data)):
continue
dt = dt_E
# -------- Detrend -----------------#
if change_E:
this_seis[0].data = this_seis[0].data * -1
if change_N:
this_seis[1].data = this_seis[1].data * -1
this_seis[0].data = detrend(this_seis[0].data, type='linear')
this_seis[0].data = detrend(this_seis[0].data, type='constant')
this_seis[1].data = detrend(this_seis[1].data, type='linear')
this_seis[1].data = detrend(this_seis[1].data, type='constant')
this_seis[2].data = detrend(this_seis[2].data, type='linear')
this_seis[2].data = detrend(this_seis[2].data, type='constant')
# ------- Rotate ENZ to RTZ ---------#
if comp == 1 or comp == 2 or comp == 3:
E = this_seis[2].data
N = this_seis[1].data
Z = this_seis[0].data
else:
E = this_seis[0].data
N = this_seis[1].data
Z = this_seis[2].data
(this_seis[0].data, this_seis[1].data,
def dCleaner(pm_data, trend):
'''Cleaning data for phasemeter glitching. Also optional detrend of data. '''
for i in range(len(pm_data)):
if pm_data[i] > 5e8: pm_data[i] = 10003.798e5 - pm_data[i]
if trend == True: pm_data = signal.detrend(pm_data, type='linear')
return pm_data
#Q_ek_f_mean = Q_ek_f.mean(dim='time')
#
#Q_ek = Q_ek.where(np.abs(lats) > 0)
# Compute monthly anomaly
if anom_flag:
Q_net_surf, Q_net_surf_clim = st.anom(Q_net_surf)
thf, thf_clim = st.anom(thf)
sst, sst_clim = st.anom(sst)
Q_ek, Q_ek_clim = st.anom(Q_ek)
#Q_ek_f,Q_ek_f_clim = st.anom(Q_ek_f)
# Remove linear trend
if detr:
sst = sst.fillna(0.)
sst = xr.DataArray(signal.detrend(sst, axis=0),
dims=sst.dims,
coords=sst.coords)
# h = h.fillna(0.)
# h = xr.DataArray(signal.detrend(h, axis=0), dims=h.dims, coords=h.coords)
thf = thf.fillna(0.)
thf = xr.DataArray(signal.detrend(thf, axis=0),
dims=thf.dims,
coords=thf.coords)
Q_net_surf = Q_net_surf.fillna(0.)
Q_net_surf = xr.DataArray(signal.detrend(Q_net_surf, axis=0),
dims=Q_net_surf.dims,
coords=Q_net_surf.coords)
### Area 1.9x2.5 grid cell [58466.1 = (278.30) * (210.083)]
valyr[ti, i, j] = 58466.1 * np.cos(np.radians(lat2[i, j]))
ext[ti] = np.nansum(valyr[ti, :, :]) / 1e6
### Reshape array for [year,month]
ext = np.reshape(ext, (ext.shape[0] // 12, 12))
return ext
### Calculate functions
lat, lon, sic = readSIEData()
lon2, lat2 = np.meshgrid(lon, lat)
ext = calcExtent(sic, lat2)
### Detrend data
extdt = sss.detrend(ext, axis=0, type='linear')
### Calculate zscores
extdtzz = sts.zscore(extdt, axis=0)
extzz = sts.zscore(ext, axis=0)
### Calculate standard deviation
extstd = np.std(ext, axis=0)
### Calculate OND sea ice index
extond = np.nanmean(ext[:, -3:], axis=1)
extondzz = sts.zscore(extond, axis=0)
iceslice05_ond = np.where(extondzz <= -0.5)[0]
yearslice05_ond = years[iceslice05_ond]
iceslice1_ond = np.where(extondzz <= -1.)[0]
yearslice1_ond = years[iceslice1_ond]
def _createPhysiologicalNuisanceRegressors(inputname,
subj,
run,
globalmask,
wmmask,
ventriclesmask,
aCompCor=5):
"""
inputname - 4D input time series to obtain nuisance regressors
run - fMRI run
globalmask - whole brain mask to extract global time series
wmmask - white matter mask (functional) to extract white matter time series
ventriclesmask- ventricles mask (functional) to extract ventricle time series
aCompCor - Create PC component time series of white matter and ventricle time series, using first n PCs
"""
# Load raw fMRI data (in volume space)
print 'Loading raw fMRI data'
fMRI4d = nib.load(inputname).get_data()
##########################################################
## Nuisance time series (Global signal, WM, and Ventricles)
print 'Obtaining standard global, wm, and ventricle signals and their derivatives'
# Global signal
globalMask = nib.load(globalmask).get_data()
globalMask = np.asarray(globalMask, dtype=bool)
globaldata = fMRI4d[globalMask].copy()
globaldata = signal.detrend(globaldata, axis=1, type='constant')
globaldata = signal.detrend(globaldata, axis=1, type='linear')
global_signal1d = np.mean(globaldata, axis=0)
# White matter signal
wmMask = nib.load(wmmask).get_data()
wmMask = np.asarray(wmMask, dtype=bool)
wmdata = fMRI4d[wmMask].copy()
wmdata = signal.detrend(wmdata, axis=1, type='constant')
wmdata = signal.detrend(wmdata, axis=1, type='linear')
wm_signal1d = np.mean(wmdata, axis=0)
# Ventricle signal
ventricleMask = nib.load(ventriclesmask).get_data()
ventricleMask = np.asarray(ventricleMask, dtype=bool)
ventricledata = fMRI4d[ventricleMask].copy()
ventricledata = signal.detrend(ventricledata, axis=1, type='constant')
ventricledata = signal.detrend(ventricledata, axis=1, type='linear')
ventricle_signal1d = np.mean(ventricledata, axis=0)
del fMRI4d
## Create derivative time series (with backward differentiation, consistent with 1d_tool.py -derivative option)
# Global signal derivative
global_signal1d_deriv = np.zeros(global_signal1d.shape)
global_signal1d_deriv[1:] = global_signal1d[1:] - global_signal1d[:-1]
# White matter signal derivative
wm_signal1d_deriv = np.zeros(wm_signal1d.shape)
wm_signal1d_deriv[1:] = wm_signal1d[1:] - wm_signal1d[:-1]
# Ventricle signal derivative
ventricle_signal1d_deriv = np.zeros(ventricle_signal1d.shape)
ventricle_signal1d_deriv[
1:] = ventricle_signal1d[1:] - ventricle_signal1d[:-1]
## Write to h5py
# Create h5py output
h5f = h5py.File(nuis_reg_dir + subj + '_nuisanceRegressors.h5', 'a')
try:
h5f.create_dataset(run + '/global_signal', data=global_signal1d)
h5f.create_dataset(run + '/global_signal_deriv',
data=global_signal1d_deriv)
h5f.create_dataset(run + '/wm_signal', data=wm_signal1d)
h5f.create_dataset(run + '/wm_signal_deriv', data=wm_signal1d_deriv)
h5f.create_dataset(run + '/ventricle_signal', data=ventricle_signal1d)
h5f.create_dataset(run + '/ventricle_signal_deriv',
data=ventricle_signal1d_deriv)
except:
del h5f[run +
'/global_signal'], h5f[run + '/global_signal_deriv'], h5f[
run + '/wm_signal'], h5f[run + '/wm_signal_deriv'], h5f[
run +
'/ventricle_signal'], h5f[run +
'/ventricle_signal_deriv']
h5f.create_dataset(run + '/global_signal', data=global_signal1d)
h5f.create_dataset(run + '/global_signal_deriv',
data=global_signal1d_deriv)
h5f.create_dataset(run + '/wm_signal', data=wm_signal1d)
h5f.create_dataset(run + '/wm_signal_deriv', data=wm_signal1d_deriv)
h5f.create_dataset(run + '/ventricle_signal', data=ventricle_signal1d)
h5f.create_dataset(run + '/ventricle_signal_deriv',
data=ventricle_signal1d_deriv)
##########################################################
## Obtain aCompCor regressors using first 5 components of WM and Ventricles (No GSR!)
ncomponents = 5
nTRs = len(global_signal1d)
print 'Obtaining aCompCor regressors and their derivatives'
# WM time series
wmstart = time.time()
# Obtain covariance matrix, and obtain first 5 PCs of WM time series
tmpcov = np.corrcoef(wmdata.T)
eigenvalues, topPCs = scipy.sparse.linalg.eigs(tmpcov,
k=ncomponents,
which='LM')
# Now using the top n PCs
aCompCor_WM = topPCs
# wmend = time.time() - wmstart
# print 'WM aCompCor took', wmend, 'seconds'
# Ventricle time series
ventstart = time.time()
# Obtain covariance matrix, and obtain first 5 PCs of ventricle time series
tmpcov = np.corrcoef(ventricledata.T)
eigenvalues, topPCs = scipy.sparse.linalg.eigs(tmpcov,
k=ncomponents,
which='LM')
# Now using the top n PCs
aCompCor_ventricles = topPCs
# ventricletime = time.time() - ventstart
# print 'Ventricle aCompCor took', ventricletime, 'seconds'
# White matter signal derivative using backwards differentiation
aCompCor_WM_deriv = np.zeros(aCompCor_WM.shape)
aCompCor_WM_deriv[1:, :] = np.real(aCompCor_WM[1:, :]) - np.real(
aCompCor_WM[:-1, :])
# Ventricle signal derivative
aCompCor_ventricles_deriv = np.zeros(aCompCor_ventricles.shape)
aCompCor_ventricles_deriv[1:, :] = np.real(
aCompCor_ventricles[1:, :]) - np.real(aCompCor_ventricles[:-1, :])
## Write to h5py
try:
h5f.create_dataset(run + '/aCompCor_WM', data=aCompCor_WM)
h5f.create_dataset(run + '/aCompCor_WM_deriv', data=aCompCor_WM_deriv)
h5f.create_dataset(run + '/aCompCor_ventricles',
data=aCompCor_ventricles)
h5f.create_dataset(run + '/aCompCor_ventricles_deriv',
data=aCompCor_ventricles_deriv)
except:
del h5f[run + '/aCompCor_WM'], h5f[run + '/aCompCor_WM_deriv'], h5f[
run + '/aCompCor_ventricles'], h5f[run +
'/aCompCor_ventricles_deriv']
h5f.create_dataset(run + '/aCompCor_WM', data=aCompCor_WM)
h5f.create_dataset(run + '/aCompCor_WM_deriv', data=aCompCor_WM_deriv)
h5f.create_dataset(run + '/aCompCor_ventricles',
data=aCompCor_ventricles)
h5f.create_dataset(run + '/aCompCor_ventricles_deriv',
data=aCompCor_ventricles_deriv)
##########################################################
## Load motion parameters, and calculate motion spike regressors
h5f.close()
lon_s4, lat_s4 = np.meshgrid(hgt_s4.longitude.values, hgt_s4.latitude.values) lon_erai, lat_erai = np.meshgrid(hgt_erai.longitude.values, hgt_erai.latitude.values) #seasonal means season = ['ASO', 'SON', 'OND', 'NDJ', 'DJF'] lmonth = ['Aug', 'Sep', 'Oct', 'Nov', 'Dec'] mm = [7, 8, 9, 10, 11, 0, 1] #loop over seasons, selec data and performs all composites for i in np.arange(0, 5): #hgt_erai_seas_mean = hgt_erai['z'].resample(time='QS-' + lmonth[i]).mean(dim='time',skipna=True) mes = datetime.datetime.strptime(lmonth[i], '%b').month #hgt_erai_smean = hgt_erai_seas_mean.sel(time= np.logical_and(hgt_erai_seas_mean['time.month'] == mes, hgt_erai_seas_mean['time.year']!=2002)) hgt_erai_seas_mean = hgt_erai.sel(time= np.logical_and(hgt_erai['time.month'] == mes, hgt_erai['time.year']!=2002)) hgt_erai_smean = hgt_erai_seas_mean.z.values hgt_erai_smean= np.nan_to_num(hgt_erai_smean, np.nanmean(hgt_erai_smean)) hgt_erai_smean = signal.detrend(hgt_erai_smean, axis=0, type='linear') hgt_erai_EN = np.nanmean(hgt_erai_smean[index_ninio_erai_upper.values, :, :], axis=0) SS_erai_EN = np.nanvar(hgt_erai_smean[index_ninio_erai_upper.values, :, :], axis=0) / np.sum(index_ninio_erai_upper.values) hgt_erai_LN = np.nanmean(hgt_erai_smean[index_ninio_erai_lower.values, :, :], axis=0) SS_erai_LN = np.nanvar(hgt_erai_smean[index_ninio_erai_lower.values, :, :], axis=0) / np.sum(index_ninio_erai_lower.values) hgt_erai_N = np.nanmean(hgt_erai_smean[index_ninio_erai_normal.values, :, :], axis=0) hgt_erai_WSPV = np.nanmean(hgt_erai_smean[index_PV_erai_upper.values, :, :], axis=0) SS_erai_WSPV = np.nanvar(hgt_erai_smean[index_PV_erai_upper.values, :, :], axis=0) / np.sum(index_PV_erai_upper.values) hgt_erai_SSPV = np.nanmean(hgt_erai_smean[index_PV_erai_lower.values, :, :], axis=0) SS_erai_SSPV = np.nanvar(hgt_erai_smean[index_PV_erai_lower.values, :, :], axis=0) / np.sum(index_PV_erai_lower.values) hgt_erai_NSPV = np.nanmean(hgt_erai_smean[index_PV_erai_normal.values, :, :], axis=0) #hgt_s4_smean = np.nanmean(hgt_s4.z.values[i:i + 3, :, :, :], axis=0)
def test_detrend(self, random, axis):
x = random.normal(2, 1, (40, 20))
x_out = signals.detrend(x, axis=axis)
x_out_scipy = scipy_signal.detrend(x, axis=axis)
assert np.array_equal(x_out, x_out_scipy)