def findPeakPyVersion(dataSample):
peakPoints = []
for i in narange(1., dataSample.size()):
if ((dataSample[0, int(i - 1)] < dataSample[0, int(i)])
and (dataSample[0, int(i)] < dataSample[0, int(i + 1)])):
peakPoints.append(dataSample[int(i)])
return np.array([peakPoints])
def _convert_to_onehot(labels):
# use the original numpy functions
from numpy import zeros as nzeros
from numpy import arange as narange
# to one-hot
new_labels = nzeros((labels.size, labels.max() + 1))
new_labels[narange(labels.size), labels] = 1.
return new_labels
def calculateTripleFrequency(remainder, strobe):
a = np.array([1., 2., 3.])
remainder1 = remainder.copy()
remainder2 = remainder1.copy() - 0.6
strobeLen = strobe.shape[1]
aLen = a.shape[1]
fre_1 = nzeros([strobeLen, aLen], dtype=float)
for i in narange(1., (strobeLen) + 1):
for j in narange(1., (aLen) + 1):
fre_1[int(i) - 1, int(j) - 1] = ndot(strobe[int(i) - 1],
a[int(j) - 1])
t = np.shape(fre_1)
iter = 1.
remainder2Len = remainder2.shape[1]
freq_plus = nzeros([t[0, 0] * t[0, 1], remainder2Len])
freq_minus = nzeros([t[0, 0] * t[0, 1], remainder2Len])
freq_plus_shift_negative1 = nzeros([t[0, 0] * t[0, 1], remainder2Len])
freq_plus_shift_negative2 = nzeros([t[0, 0] * t[0, 1], remainder2Len])
for i in narange(1., (t[0, 0]) + 1):
for j in narange(1., (t[0, 1]) + 1):
fre_11 = fre_1[int(i) - 1, int(j) - 1].copy()
remainder_1 = remainder2[int(i) - 1, :].copy()
for k in narange(1., remainder2Len + 1):
if remainder_1[0, int(k) - 1] > 0.:
freq_plus[int(iter) - 1, int(k) -
1] = fre_11 + remainder_1[0, int(k) - 1]
freq_minus[int(iter) - 1, int(k) -
1] = fre_11 - remainder_1[0, int(k) - 1]
freq_plus_shift_negative1[
int(iter) - 1, int(k) -
1] = fre_11 + 30. - remainder_1[0, int(k) - 1]
freq_plus_shift_negative2[
int(iter) - 1, int(k) -
1] = fre_11 - 30. - remainder_1[0, int(k) - 1]
iter = iter + 1.
est_fre = np.vstack((freq_plus, freq_minus, freq_plus_shift_negative1,
freq_plus_shift_negative2))
frequency1 = nround(est_fre)
frequency2 = nfloor(est_fre)
return [frequency1, frequency2]
def checkValidity_MultiFrquency(X1, Y1, f1, NFFT1):
d1_list = []
d2_list = []
g2_list = []
peak1 = np.sort(findPeakPyVersion((2. * X1[0:int(NFFT1 / 2. + 1.)])),
'descend')
peak1Len = peak1.shape[1]
chk_val1 = nzeros([peak1Len, 1])
index1 = nzeros([peak1Len, 1])
for i in narange(1., (peak1Len + 1)):
chk_val1[int(i) -
1, :] = peak1[int(i) - 1] / (nmean(peak1[int(i):peak1Len]))
if chk_val1[int(i) - 1, :] > 2.:
index1[int(i) - 1, :] = np.nonzero(
X1[0:NFFT1 / 2. + 1.] == peak1[:, int(i) - 1] / 2.)
d1_list.append(f1[index1[int(i) - 1, :]])
mean1 = nmean(peak1[0:peak1Len])
k = 1.
peak2 = np.sort(findPeakPyVersion((2. * Y1[0:NFFT1 / 2. + 1.])), 'descend')
peak2Len = peak2.shape[1]
chk_val = nzeros([peak2Len, 1])
index2 = nzeros([peak2Len, 1])
for i in narange(1., peak2Len):
chk_val[int(i) -
1, :] = peak2[0, int(i) - 1] / nmean(peak2[int(i):peak2Len])
if chk_val[int(i) - 1, :] > 3.:
g2_list.append(chk_val[int(i) - 1, :])
index2[int(i) - 1, :] = np.nonzero(
(Y1[0:NFFT1 / 2. + 1.] == peak2[:, int(i) - 1] / 2.))
d2_list.append(f1[index2[int(i) - 1, :]])
d2 = np.array([d2_list])
d1 = np.array([d1_list])
g2 = np.array([g2_list])
if g2 >= 0.:
g1 = nmean(g2)
else:
g1 = nmean(g2)
return [g1, d1, d2]
def velocityPendCenter(pend_centers):
time = 1. / 30.
[r, c] = np.shape(pend_centers)
VelocityMarker = nzeros([r, c], dtype=float)
for i in narange(2., (r) + 1):
VelocityMarker[int(i) - 1, int((c - 1.)) - 1] = (
pend_centers[int(i) - 1, int((c - 1.)) - 1] - pend_centers[int(
(i - 1.)) - 1, int((c - 1.)) - 1]) / time
VelocityMarker[int(i) - 1, int(c) -
1] = (pend_centers[int(i) - 1, int(c) - 1] -
pend_centers[int(
(i - 1.)) - 1, int(c) - 1]) / time
return VelocityMarker
def FFT_MultiFrequency_update(s1, s2):
Fs = np.array([[31.]])
#% Sampling frequency
T = 1. / Fs
#% Sample time
L = 512.
#% Length of signal
t = ndot(narange(0., L), T)
NFFT1 = float(pow(2, pyNextPow2(L)))
#% Next power of 2 from length of y
s1[0, :] = s1[0, :] - nmean(s1[0, :])
s2[0, :] = s2[0, :] - nmean(s2[0, :])
X1 = nabs(np.fft(s1, NFFT1) / L)
Y1 = nabs(np.fft(s2, NFFT1) / L)
f1 = ndot(Fs / 2., np.linspace(0., 1., (NFFT1 / 2. + 1.)))
[g1, d1, d2] = checkValidity_MultiFrquency(X1, Y1, f1, NFFT1)
return [d1, X1, Y1, f1, NFFT1, d2, g1]
def mfreq_simulate2(frequency):
nfreq = 4.
nsampl = 33.
sampling_option = 0.
cam_fps = 15.
prime1 = np.array([
61., 67., 71., 73., 79., 83., 89., 97., 101., 103., 107., 109., 113.,
127., 131., 137., 139., 149., 151., 157., 163., 167., 173., 179., 181.,
191., 193., 197., 199., 211., 223., 227., 229.
])
sFile = open('strobe_file.txt', 'w+')
freq = np.random.rand(1., nfreq)
frequencies = np.array([70., 100., 170., 230.])
if sampling_option == 1.:
sampling = nzeros([nsampl])
for i in narange(1., (nsampl) + 1):
stri = "give" + str(i) + "th frequency of strobe"
print stri
sampling[int(i) - 1] = float(raw_input())
else:
sampling = prime1.copy()
print sampling
remainder = nzeros([int(nfreq), int(nsampl)])
remainder2 = remainder.copy()
for j in narange(1., (nsampl) + 1):
for i in narange(1., (nfreq) + 1):
if nmod(
nfloor((np.minimum(
nmod(frequencies[int(i) - 1], sampling[int(j) - 1]),
(sampling[int(j) - 1] - nmod(frequencies[int(i) - 1],
sampling[int(j) - 1]))) /
cam_fps)), 2.) == 0.:
remainder[int(i) - 1, int(j) - 1] = nmod(
np.minimum(
nmod(frequencies[int(i) - 1], sampling[int(j) - 1]),
(sampling[int(j) - 1] - np.mod(frequencies[int(i) - 1],
sampling[int(j) - 1]))),
cam_fps)
else:
remainder[int(i) - 1, int(j) - 1] = 15. - nmod(
np.minimum(
nmod(frequencies[int(i) - 1], sampling[int(j) - 1]),
(sampling[int(j) - 1] - np.mod(frequencies[int(i) - 1],
sampling[int(j) - 1]))),
cam_fps)
remainder2[:, int(j) - 1] = np.sort(remainder[:, int(j) - 1])
sFile.write("%f\n" % nfreq)
sFile.write("%f\n" % nsampl)
for j in narange(1., (nsampl) + 1):
sFile.write("%f " % sampling[int(j) - 1])
sFile.write("\n")
for i in narange(1., (nfreq) + 1):
for j in np.arange(1., (nsampl) + 1):
sFile.write('%8.2f ' % remainder2[int(i) - 1, int(j) - 1])
sFile.write('\n')
sFile.close()
return [frequencies, sampling]
def do_plot_dendrogram(data,
nclass=None,
datalinkg=None,
indnames=None,
method='ward',
metric='euclidean',
truncate_mode=None,
title="dendrogram",
titlefnsize=14,
ytitle=0.98,
xlabel=None,
xlabelpad=10,
xlabelrotation=0,
ylabel=None,
ylabelpad=10,
ylabelrotation=90,
labelfnsize=10,
labelrotation=0,
labelsize=10,
labelha='center',
labelva='top',
dendro_linewidth=2,
tickpad=2,
axeshiftfactor=150,
figsize=(14, 6),
wspace=0.0,
hspace=0.2,
top=0.92,
bottom=0.12,
left=0.05,
right=0.99):
"""
plot SOM dendrogram
"""
if datalinkg is None:
# Performs hierarchical/agglomerative clustering on the condensed distance matrix data
datalinkg = linkage(data, method=method, metric=metric)
#
Ncell = data.shape[0]
minref = np.min(data)
maxref = np.max(data)
#
fig = plt.figure(figsize=figsize, facecolor='w')
fignum = fig.number # numero de figure en cours ...
plt.subplots_adjust(wspace=wspace,
hspace=hspace,
top=top,
bottom=bottom,
left=left,
right=right)
#
if nclass is None:
# dendrogramme sans controle de color_threshold (on laisse par defaut ...)
R_ = dendrogram(datalinkg,
p=Ncell,
truncate_mode=truncate_mode,
orientation='top',
leaf_font_size=6,
labels=indnames,
leaf_rotation=labelrotation)
else:
# calcule la limite de decoupage selon le nombre de classes ou clusters
max_d = np.sum(datalinkg[[-nclass + 1, -nclass], 2]) / 2
color_threshold = max_d
with plt.rc_context({'lines.linewidth': dendro_linewidth
}): # Temporarily override the default line width
R_ = dendrogram(datalinkg,
p=Ncell,
truncate_mode=truncate_mode,
color_threshold=color_threshold,
orientation='top',
leaf_font_size=6,
labels=indnames,
leaf_rotation=labelrotation)
plt.axhline(y=max_d, c='k')
plt.tick_params(axis='x', reset=True)
plt.tick_params(
axis='x',
which='major',
direction='inout',
length=7,
width=dendro_linewidth,
pad=tickpad,
top=False,
bottom=True, # rotation_mode='anchor',
labelrotation=labelrotation,
labelsize=labelsize)
if indnames is None:
L = np.narange(Ncell)
else:
L_ = np.array(indnames)
plt.xticks((np.arange(Ncell) * 10) + 5,
L_[R_['leaves']],
horizontalalignment=labelha,
verticalalignment=labelva)
#
plt.grid(axis='y')
if xlabel is not None:
plt.xlabel(xlabel,
labelpad=xlabelpad,
rotation=xlabelrotation,
fontsize=labelfnsize)
if ylabel is not None:
plt.ylabel(ylabel,
labelpad=ylabelpad,
rotation=ylabelrotation,
fontsize=labelfnsize)
if axeshiftfactor is not None:
lax = plt.axis()
daxy = (lax[3] - lax[2]) / axeshiftfactor
plt.axis([lax[0], lax[1], lax[2] - daxy, lax[3]])
plt.title(title, fontsize=titlefnsize, y=ytitle)
return R_
