def easiest_sqi_interval(self):
"""
Easiest sequential-quadratic-interpolation NIP, if there
is any and the estimate is better than xmin - epsilon.
Note that to use NIP index as interval index, you should check
if the qxmin[i] is smaller or larger than points[i+1] - the
NIP covers three points, not just two!
"""
# Do not take guesses that are too near one of the interval
# pair boundaries
if self.axis is None:
qxmin_suitable = np.logical_and(self.qxmin - self.points > self.tolx,
np.roll(self.points, -2) - self.qxmin > self.tolx)
else:
qxmin_suitable = np.logical_and(self.qxmin[:,self.axis] - self.points[:,self.axis] > self.tolx,
np.roll(self.points[:,self.axis], -2) - self.qxmin[:,self.axis] > self.tolx)
iqfmin = filter(lambda (i, qfmin): qxmin_suitable[i], enumerate(self.qfmin))
if len(iqfmin) == 0:
# print('stop split')
return None # We cannot split further
i, qfmin = min(iqfmin, key=itemgetter(1))
if qfmin > self.fmin - self.epsilon and (self.force_Brent == 0 or self.itercnt % self.force_Brent > 0):
# print('%s > %s' % (qfmin, self.fmin - self.epsilon))
return None # Even the best estimate is too high
return i
def generate_RI_text_fast(N, RI_letters, cluster_sz, ordered, text_name, alph=alphabet): text_vector = np.zeros((1, N)) text = utils.load_text(text_name) cluster2 = '' vector = np.ones((1,N)) for char_num in xrange(len(text)): cluster = cluster + text[char_num] if len(cluster) < cluster_sz: continue elif len(cluster) > cluster_sz: prev_letter = cluster[0] prev_letter_idx = alphabet.find(letter) inverse = np.roll(RI_letters[prev_letter_idx,:], cluster_sz-1) vector = np.multiply(vector, inverse) vector = np.roll(vector, 1) letter = text[char_num] letter_idx = alphabet.find(letter) vector = np.multiply(vector, RI_letters[letter_idx,:]) cluster = cluster[1:] else: # (len(cluster) == cluster_size), happens once letters = list(cluster) for letter in letters: vector = np.roll(vector,1) letter_idx = alphabet.find(letter) vector = np.multiply(vector, RI_letters[letter_idx,:]) text_vector += vector return text_vector
def build_loss(self):
r"""Implements the N-dim version of function
$$TV^{\beta}(x) = \sum_{whc} \left ( \left ( x(h, w+1, c) - x(h, w, c) \right )^{2} +
\left ( x(h+1, w, c) - x(h, w, c) \right )^{2} \right )^{\frac{\beta}{2}}$$
to return total variation for all images in the batch.
"""
image_dims = K.ndim(self.img) - 2
# Constructing slice [1:] + [:-1] * (image_dims - 1) and [:-1] * (image_dims)
start_slice = [slice(1, None, None)] + [slice(None, -1, None) for _ in range(image_dims - 1)]
end_slice = [slice(None, -1, None) for _ in range(image_dims)]
samples_channels_slice = [slice(None, None, None), slice(None, None, None)]
# Compute pixel diffs by rolling slices to the right per image dim.
tv = None
for i in range(image_dims):
ss = tuple(samples_channels_slice + start_slice)
es = tuple(samples_channels_slice + end_slice)
diff_square = K.square(self.img[utils.slicer[ss]] - self.img[utils.slicer[es]])
tv = diff_square if tv is None else tv + diff_square
# Roll over to next image dim
start_slice = np.roll(start_slice, 1).tolist()
end_slice = np.roll(end_slice, 1).tolist()
tv = K.sum(K.pow(tv, self.beta / 2.))
return normalize(self.img, tv)
def plot_filter(filter_type, alpha, ts, sc, overlap):
import matplotlib.pyplot as plt
time_taps = gfdm_filter_taps(filter_type, alpha, ts, sc)
freq_taps = gfdm_freq_taps(time_taps)
freq_taps_sparse = gfdm_freq_taps_sparse(freq_taps, ts, overlap)
fig = plt.figure()
tp = fig.add_subplot('211')
t = np.arange(0, ts, 1. / sc)
time_taps = np.fft.ifftshift(time_taps)
plt.plot(t, np.abs(time_taps))
plt.plot(t, np.abs(np.fft.ifftshift(freq_tapered_raised_cosine(t - 1. * ts / 2., alpha))))
plt.plot(t, np.roll(np.abs(time_taps), sc))
plt.xlim((0, ts))
plt.xlabel('timeslot')
plt.grid()
fp = fig.add_subplot('212')
f = np.arange(0, sc, 1. / ts)
plt.plot(f, np.abs(freq_taps))
plt.plot(f, np.abs(np.fft.fft(freq_tapered_raised_cosine(t - 1. * ts / 2., alpha))))
plt.plot(f, np.abs(np.concatenate((freq_taps_sparse[0:len(freq_taps_sparse) / 2],
np.zeros(sc * ts - len(freq_taps_sparse)),
freq_taps_sparse[len(freq_taps_sparse) / 2:]))), linestyle='--')
plt.plot(f, np.roll(np.abs(freq_taps), ts * (sc // 2)))
plt.plot(f, np.roll(np.abs(freq_taps), ts * (sc // 2 + 1)))
plt.xlim((0, sc))
plt.xlabel('subcarrier')
plt.grid()
plt.gcf().suptitle("GFDM filter: type='{}' with M={}, K={}, L={}".format(filter_type.upper(), ts, sc, overlap), fontsize=16)
plt.show()
def _make_segment(self,x,y,threshold=None):
if threshold is None:
threshold = self._segment_threshold
x,y=np.atleast_1d(x),np.atleast_1d(y)
d2 = np.sqrt((np.roll(x,1)-x)**2+(np.roll(y,1)-y)**2)
w=np.where(d2 > threshold)[0]
#w=w[w!=0]
xx=[]
yy=[]
if len(w) == 1:
x=np.roll(x,-w[0])
y=np.roll(y,-w[0])
xx.append(x)
yy.append(y)
elif len(w) >= 2:
xx.append(x[0:w[0]])
yy.append(y[0:w[0]])
for i in xrange(len(w)-1):
xx.append(x[w[i]:w[i+1]])
yy.append(y[w[i]:w[i+1]])
xx.append(x[w[-1]:])
yy.append(y[w[-1]:])
else:
xx.append(x)
yy.append(y)
return xx,yy
def imageCoCenter(self, inst, algo):
x1, y1, tmp = getCenterAndR_ef(self.image)
if algo.debugLevel >= 3:
print('imageCoCenter: (x1,y1)=(%8.2f,%8.2f)\n' % (x1, y1))
stampCenterx1 = inst.sensorSamples / 2. + 0.5
stampCentery1 = inst.sensorSamples / 2. + 0.5
radialShift = 3.5 * algo.upReso * \
(inst.offset / 1e-3) * (10e-6 / inst.pixelSize)
radialShift = radialShift * self.fldr / 1.75
if (self.fldr > 1.75):
radialShift = 0
if self.fldr != 0:
I1c = self.fieldX / self.fldr
I1s = self.fieldY / self.fldr
else:
I1c = 0
I1s = 0
stampCenterx1 = stampCenterx1 + radialShift * I1c
stampCentery1 = stampCentery1 + radialShift * I1s
self.image = np.roll(self.image, int(
np.round(stampCentery1 - y1)), axis=0)
self.image = np.roll(self.image, int(
np.round(stampCenterx1 - x1)), axis=1)
def laplacian(grid, out):
np.copyto(out, grid)
out *= -4
out += np.roll(grid, +1, 0)
out += np.roll(grid, -1, 0)
out += np.roll(grid, +1, 1)
out += np.roll(grid, -1, 1)
def preprocessing(signal, param):
"""
各シグナルの前処理（確認済）
@param singal: fNIRS信号 1次元array型
@param param: パラメータモジュール
@return: 前処理終了後のシグナル値 1次元array型（特徴次元数）
"""
###### データの前処理
# バンドパスフィルタ
if param.FILTER_TYPE == "butter":
preprocessed_signal = prba.butter_bandpass_filter(signal, param.BPF_BAND[0], param.BPF_BAND[1],
param.FS, order = param.BUTTER_WORTH_ORDER)
else: # フィルタ処理無し
preprocessed_signal = signal
# 平滑化
if param.SMOOTHING_TYPE:
preprocessed_signal = prsm.smoothing(preprocessed_signal, param.SMOOTHING_LENGTH)
else: # 平滑化処理無し
pass
# 1次微分
if param.DIFF >= 1:
preprocessed_signal_n = np.roll(preprocessed_signal, -1)
preprocessed_signal = preprocessed_signal_n - preprocessed_signal
# 2次微分
elif param.DIFF == 2:
preprocessed_signal_n = np.roll(preprocessed_signal, -1)
preprocessed_signal_p = np.roll(preprocessed_signal, 1)
preprocessed_signal = (preprocessed_signal_n - preprocessed_signal) - (preprocessed_signal - preprocessed_signal_p)
return preprocessed_signal
def _decorate_contour_segment(data, stride=1, options={}, tomax=True, labelled=False, outline=None, aspect=1):
default_options = {'scale': 0.2,
'scale_units': 'dots',
'headaxislength': 2,
'headlength': 2,
'headwidth': 2,
'minshaft': 1,
'units': 'dots',
#'angles': 'xy',
'edgecolor': outline,
'linewidth': 0 if outline is None else 0.2
}
default_options.update(options)
x = data[::stride,0]
y = data[::stride,1]
sign = 1 if tomax else -1
dx = -sign*np.diff(y)*aspect
dy = sign*np.diff(x)
l = np.sqrt(dx**2+dy**2)
dx /= l
dy /= l
x = 0.5*(x+np.roll(x,-1))
y = 0.5*(y+np.roll(y,-1))
if labelled:
x,y,dx,dy = x[1:-2], y[1:-2], dx[1:-1], dy[1:-1]
else:
x,y = x[:-1], y[:-1]
plt.quiver(x, y, dx, dy, **default_options)
def apply_channel_deconvolution (self, img, psfsize=10, snrVal=8): # Based on deconvolution.py in python samples of opencv
img = img.astype('double')/255.0
img = self.blur_edge(img)
IMG = cv2.dft(img, flags=cv2.DFT_COMPLEX_OUTPUT)
if (psfsize==0): return img
defocus = True
ang = 0
d = psfsize
snr = snrVal
noise = 10**(-0.1*snr)
if defocus:
psf = self.defocus_kernel(d)
else:
psf = self.motion_kernel(ang, d)
psf /= psf.sum()
psf_pad = np.zeros_like(img)
kh, kw = psf.shape
psf_pad[:kh, :kw] = psf
PSF = cv2.dft(psf_pad, flags=cv2.DFT_COMPLEX_OUTPUT, nonzeroRows = kh)
PSF2 = (PSF**2).sum(-1)
iPSF = PSF / (PSF2 + noise)[...,np.newaxis]
RES = cv2.mulSpectrums(IMG, iPSF, 0)
res = cv2.idft(RES, flags=cv2.DFT_SCALE | cv2.DFT_REAL_OUTPUT )
res = np.roll(res, -kh//2, 0)
res = np.roll(res, -kw//2, 1)
return res
def make_step(net, step_size=1.5, end=default_layer, jitter=32, clip=True, objective=objective_L2, sigma=0):
'''Basic gradient ascent step.'''
src = net.blobs['data'] # input image is stored in Net's 'data' blob
dst = net.blobs[end] # the layer targeted by default_layer
ox, oy = np.random.randint(-jitter, jitter+1, 2)
src.data[0] = np.roll(np.roll(src.data[0], ox, -1), oy, -2) # apply jitter shift
net.forward(end=end) # inference of features
objective(dst) # set an objective
net.backward(start=end) # retrain
g = src.diff[0]
# apply normalized ascent step to the input image
src.data[:] += step_size/np.abs(g).mean() * g
src.data[0] = np.roll(np.roll(src.data[0], -ox, -1), -oy, -2) # unshift image
if clip:
bias = net.transformer.mean['data']
src.data[:] = np.clip(src.data, -bias, 255-bias)
if sigma:
src.data[0] = blur(src.data[0], sigma)
def draw_svd(self,comp='V',nmodes=6,center=False,zoom = False,
interp='none'):
#compute svd is not present . . later
fig = plt.figure()
try:
y = self.svd[comp]
except:
y = self.svd['V']
for i in xrange(nmodes):
canvas = fig.add_subplot(2,3,i+1)
# if comp=='V':
# y_i = y[i,:,:]
# else:
# y_i = y[:,i]
y_i = y[i]
nx,ny = y_i.shape
if center:
y_i = np.roll(np.roll(y_i,nx/2,axis=0),ny/2,axis=1)
if zoom and not center:
y_i = y_i[0:nx/8.0,0:ny/8.]
if zoom and center:
y_i = y_i[nx/2-nx/8:nx/2.0+nx/8,
ny/2-ny/16:ny/2.0+ny/16,]
canvas.imshow(np.real(y_i),aspect='auto',interpolation= interp)
plt.close(fig)
return fig
def local_maxima(array2d,user_peak,index=False,count=4,floor=0,bug=False):
from operator import itemgetter, attrgetter
if user_peak == 0:
where = ((array2d >= np.roll(array2d,1,0)) &
(array2d >= np.roll(array2d,-1,0)) &
(array2d >= np.roll(array2d,0,1)) &
(array2d >= np.roll(array2d,0,-1)) &
(array2d >= array2d.max()/5.0) &
(array2d > floor*np.ones(array2d.shape)) &
(array2d >= array2d.mean()))
else: #some simpler filter if user indicated some modes
where = array2d > floor
#ignore the lesser local maxima, throw out anything with a ZERO
if bug==True:
print array2d,array2d[where.nonzero()],where.nonzero()[0]
peaks = zip(where.nonzero()[0],where.nonzero()[1],array2d[where.nonzero()])
peaks = sorted(peaks,key=itemgetter(2),reverse=True)
if len(peaks) > count and user_peak==0:
peaks = peaks[0:count]
keys = ['y_i','z_i','amp']
peaks = [dict(zip(keys,peaks[x])) for x in range(len(peaks))]
return peaks
def GetReconstructionWithBoundary(self,N,orientationmap,filename):
"""
Decorate the orientation map with boundaries.
"""
indexmap = self.GetIndexmap()
newindexmap = numpy.empty(numpy.array(indexmap.shape)*4)
for i in range(4):
for j in range(4):
newindexmap[i::4,j::4] = indexmap
neworientationmap = numpy.empty([4*N,4*N,3])
for k in range(3):
for i in range(4):
for j in range(4):
neworientationmap[i::4,j::4,k] = orientationmap[:,:,k]
boundarymap = 1-(indexmap==numpy.roll(indexmap, 1,0))*(indexmap==numpy.roll(indexmap,-1,0))*\
(indexmap==numpy.roll(indexmap, 1,1))*(indexmap==numpy.roll(indexmap,-1,1))
xs,ys = boundarymap.nonzero()
for (i,j) in zip(xs,ys):
temp = [indexmap[i,j]==indexmap[(i-1+N)%N,j],indexmap[i,j]==indexmap[(i+1)%N,j],\
indexmap[i,j]==indexmap[i,(j-1+N)%N],indexmap[i,j]==indexmap[i,(j+1)%N]]
pos = [[(4*i,4*j),(4*i+1,4*j+4)],[(4*i+3,4*j),(4*i+4,4*j+4)],\
[(4*i,4*j),(4*i+4,4*j+1)],[(4*i,4*j+3),(4*i+4,4*j+4)]]
for n in range(4):
if not temp[n]:
newindexmap[pos[n][0][0]:pos[n][1][0],pos[n][0][1]:pos[n][1][1]] = -1
for k in range(3):
neworientationmap[:,:,k] *= (newindexmap!=-1)
"""
Use PIL to plot for larger sizes, since we want to be able to draw pixel by pixel.
"""
from PIL import Image
pilImage = Image.fromarray(neworientationmap.astype('uint8'), 'RGB')
pilImage.save(filename+'.png')
def _process_data_gated(self):
"""
Processes the raw data from the counting device
@return:
"""
# remember the new count data in circular array
self.countdata[0] = np.average(self.rawdata[0])
# move the array to the left to make space for the new data
self.countdata = np.roll(self.countdata, -1)
# also move the smoothing array
self.countdata_smoothed = np.roll(self.countdata_smoothed, -1)
# calculate the median and save it
self.countdata_smoothed[-int(self._smooth_window_length / 2) - 1:] = np.median(
self.countdata[-self._smooth_window_length:])
# save the data if necessary
if self._saving:
# if oversampling is necessary
if self._counting_samples > 1:
self._sampling_data = np.empty((self._counting_samples, 2))
self._sampling_data[:, 0] = time.time() - self._saving_start_time
self._sampling_data[:, 1] = self.rawdata[0]
self._data_to_save.extend(list(self._sampling_data))
# if we don't want to use oversampling
else:
# append tuple to data stream (timestamp, average counts)
self._data_to_save.append(np.array((time.time() - self._saving_start_time,
self.countdata[-1])))
return
def imageShiftAndCrop( mage, shiftby ):
""" imageShiftAndCrop( mage, shiftby )
This is a relative shift, integer pixel only, pads with zeros to cropped edges
mage = input image
shiftby = [y,x] pixel shifts
"""
# Actually best approach is probably to roll and then zero out the parts we don't want
# The pad function is expensive in comparison
shiftby = np.array( shiftby, dtype='int' )
# Shift X
if(shiftby[1] < 0 ):
mage = np.roll( mage, shiftby[1], axis=1 )
mage[:, shiftby[1]+mage.shape[1]:] = 0.0
elif shiftby[1] == 0:
pass
else: # positive shift
mage = np.roll( mage, shiftby[1], axis=1 )
mage[:, :shiftby[1]] = 0.0
# Shift Y
if( shiftby[0] < 0 ):
mage = np.roll( mage, shiftby[0], axis=0 )
mage[shiftby[0]+mage.shape[0]:,:] = 0.0
elif shiftby[0] == 0:
pass
else: # positive shift
mage = np.roll( mage, shiftby[0], axis=0 )
mage[:shiftby[0],:] = 0.0
return mage
def polyhedra(self, wm):
'''Iterates through the polyhedra that make up the closest volume to a certain vertex'''
for p, facerow in enumerate(self.connected):
faces = facerow.indices
pts, polys = _ptset(), _quadset()
if len(faces) > 0:
poly = np.roll(self.polys[faces[0]], -np.nonzero(self.polys[faces[0]] == p)[0][0])
assert pts[wm[p]] == 0
assert pts[self.pts[p]] == 1
pts[wm[poly[[0, 1]]].mean(0)]
pts[self.pts[poly[[0, 1]]].mean(0)]
for face in faces:
poly = np.roll(self.polys[face], -np.nonzero(self.polys[face] == p)[0][0])
a = pts[wm[poly].mean(0)]
b = pts[self.pts[poly].mean(0)]
c = pts[wm[poly[[0, 2]]].mean(0)]
d = pts[self.pts[poly[[0, 2]]].mean(0)]
e = pts[wm[poly[[0, 1]]].mean(0)]
f = pts[self.pts[poly[[0, 1]]].mean(0)]
polys((0, c, a, e))
polys((1, f, b, d))
polys((1, d, c, 0))
polys((1, 0, e, f))
polys((f, e, a, b))
polys((d, b, a, c))
yield pts.points, np.array(list(polys.triangles))
def add_new( self, new_timestamp, new_data ):
"""
---------------------------------------------------------------------------
Add a new data item to the buffer
"""
if np.rank( new_data )==1:
if np.shape( new_data )[0] != self._dimensions:
return False
else:
# make sure incoming data has correct shape
if np.shape( new_data ) != self._dimensions:
return False
self._lock.acquire()
# roll the arrays forward by one
self._data = np.roll( self._data, 1 , 0 )
self._timestamps = np.roll( self._timestamps, 1 , 0 )
# insert the new data at the head
self._data[0] = copy.deepcopy( new_data )
self._timestamps[0] = copy.deepcopy( new_timestamp )
# increment the rollcounter
self._rollcount += 1
# release the lock
self._lock.release()
return True
def sphericalpolygon_area(lons, lats, R=6371000.): """ USAGE ----- area = sphericalpolygon_area(lons, lats, R=6371000.) Calculates the area of a polygon on the surface of a sphere of radius R using Girard's Theorem, which states that the area of a polygon of great circles is R**2 times the sum of the angles between the polygons minus (N-2)*pi, where N is number of corners. R = 6371000 m (6371 km, default) is a typical value for the mean radius of the Earth. Source: http://stackoverflow.com/questions/4681737/how-to-calculate-the-area-of-a-polygon-on-the-earths-surface-using-python """ lons, lats = map(np.asanyarray, (lons, lats)) N = lons.size angles = np.empty(N) for i in xrange(N): phiB1, phiA, phiB2 = np.roll(lats, i)[:3] LB1, LA, LB2 = np.roll(lons, i)[:3] # calculate angle with north (eastward) beta1 = greatCircleBearing(LA, phiA, LB1, phiB1) beta2 = greatCircleBearing(LA, phiA, LB2, phiB2) # calculate angle between the polygons and add to angle array angles[i] = np.arccos(np.cos(-beta1)*np.cos(-beta2) + np.sin(-beta1)*np.sin(-beta2)) return (np.sum(angles) - (N-2)*np.pi)*R**2
def find_max_cov(fwd_vals, rev_vals):
max_cov = 0.0
max_cov_shift = 0
for i in range(MIN_SHIFT, MAX_SHIFT):
# shift fwd values ahead by i bp
# shift rev values back by i bp
matrix = np.vstack((np.roll(fwd_vals, i),
np.roll(rev_vals, -i)))
# compute covariance between fwd and rev
cov = np.cov(matrix)[0,1]
max_str = ""
if cov > max_cov:
# this is the highest covariance we've seen yet
max_cov = cov
max_cov_shift = i
max_str = " *"
last_max = i - max_cov_shift
if last_max > MAX_SHIFT_MAX_DIST:
# we seem to be well past the peak covariance
break
sys.stderr.write("shift: %d, cov: %g%s\n" % (i, cov, max_str))
sys.stderr.write("shift: %d, cov: %g\n" % (max_cov_shift, max_cov))
return max_cov_shift
def make_step2(net, step_size=1.5, end='inception_4c/output',
jitter=32, clip=True, objective=objective_L2):
'''Basic gradient ascent step.'''
src = net.blobs['data'] # input image is stored in Net's 'data' blob
dst = net.blobs[end]
if jitter==0:
ox=0
oy=0
else:
ox, oy = np.random.randint(-jitter, jitter+1, 2)
src.data[0] = np.roll(np.roll(src.data[0], ox, -1), oy, -2) # apply jitter shift
net.forward(end=end)
objective(dst) # specify the optimization objective
net.backward(start=end)
g = src.diff[0]
# apply normalized ascent step to the input image
if not np.abs(g).mean()==0:
src.data[:] += step_size/np.abs(g).mean() * g
src.data[:] -= 0.005*step_size*src.data[:]
src.data[0] = np.roll(np.roll(src.data[0], -ox, -1), -oy, -2) # unshift image
if clip:
bias = net.transformer.mean['data']
src.data[:] = np.clip(src.data, -bias, 255-bias)
def get_corr_map_photon(coo1, coo2, skypos, skyrange, sec, bound, bandwidth):
imsz = imagetools.deg2pix(skypos, skyrange, 0.0001)
count = np.zeros(imsz)
print(imsz)
co_rel = np.array([[0,0]])
len1 = coo1.shape[0]
len2 = coo2.shape[0]
print(len1,len2)
wcs = imagetools.define_wcs(skypos,skyrange,width=False,height=False,verbose=0,pixsz=0.0001)
if len2<=80 or len1<=80:
return count, np.array([0.0, 0.0])
if len2>len1:
for i in range(len2):
#print(i)
tmp_co = np.roll(coo2, i, axis=0)[0:len1,:]-coo1
tmp_co = tmp_co[np.absolute(tmp_co[:,0])<=bound,:]
tmp_co = tmp_co[np.absolute(tmp_co[:,1])<=bound,:]
co_rel = np.concatenate((co_rel, tmp_co), axis = 0)
else:
for i in range(len1):
#print(i)
tmp_co = coo2-np.roll(coo1, i, axis=0)[0:len2,:]
tmp_co = tmp_co[np.absolute(tmp_co[:,0])<=bound,:]
tmp_co = tmp_co[np.absolute(tmp_co[:,1])<=bound,:]
co_rel = np.concatenate((co_rel, tmp_co), axis = 0)
print co_rel.shape
if co_rel.shape[0]>1000:
centroid = ck.find_centroid(co_rel[1:], bandwidth, 11, bound)
else:
return count, np.array([0.0, 0.0])
return count, centroid
def GetPerimeter(self,sites=None):
"""
Find out the associated perimeter of this cluster.
"""
if sites is None:
indices = self.sites.get_indices()
else:
indices = sites.get_indices()
area = len(indices)
if area <= 3:
return 2.*(area+1.)
else:
cluster = numpy.zeros((self.N,self.N))
cluster[indices[:,0],indices[:,1]] = 1.
mask = (cluster>0)
newcluster = numpy.copy(cluster)
newcluster += 1.*(cluster==numpy.roll(cluster,1,0))*mask
newcluster += 1.*(cluster==numpy.roll(cluster,1,1))*mask
newcluster += 1.*(cluster==numpy.roll(cluster,-1,0))*mask
newcluster += 1.*(cluster==numpy.roll(cluster,-1,1))*mask
"""
Any site with n (1<=n<=4) neighbors will contribute (4-n) to the perimeter;
"""
perimeter = numpy.sum(newcluster==2.)*3.+numpy.sum(newcluster==3.)*2.+numpy.sum(newcluster==4.)
return perimeter
def __init__(self,*arg,**kw):
super(build_model, self).__init__(*arg, **kw)
self['nlayers'] = 5
self['nx'] = 500
fault_throw = 20
self['dz'] = np.array([40, 80, 40, 200, 400, ])
self['vp'] = np.array([800., 2200., 1800., 2400., 4500., ])
self['vs'] = self['vp']/2.
self['rho'] = np.array([1500., 2500., 1400., 2700., 4500., ])
self['depths'] = np.cumsum(self['dz'])
self['model'] = {}
for model in ['vp', 'vs', 'rho']:
layer_list = []
for index in range(self['nlayers']):
layer = np.ones((self['nx'], self['dz'][index]), 'f')
layer *= self[model][index]
layer_list.append(layer)
self['model'][model] = np.hstack(layer_list)
self['model'][model][250:500,120:160] = self[model][1]
self['model'][model][250:500,120+fault_throw:160+fault_throw] = self[model][2]
self['model']['z'] = self['model']['vp'] * self['model']['rho']
self['model']['R'] = (np.roll(self['model']['z'], shift=-1) - self['model']['z'])/(np.roll(self['model']['z'], shift=-1) + self['model']['z'])
self['model']['R'][:,0] *= 0
self['model']['R'][:,-1:] *= 0
self['model']['R'][:,:self['dz'][0]+2] = 0
def normals_numpy(depth, rect=((0,0),(640,480)), win=7, mat=None):
assert depth.dtype == np.float32
from scipy.ndimage.filters import uniform_filter
(l,t),(r,b) = rect
v,u = np.mgrid[t:b,l:r]
depth = depth[v,u]
depth[depth==0] = -1e8 # 2047
depth = calibkinect.recip_depth_openni(depth)
depth = uniform_filter(depth, win)
global duniform
duniform = depth
dx = (np.roll(depth,-1,1) - np.roll(depth,1,1))/2
dy = (np.roll(depth,-1,0) - np.roll(depth,1,0))/2
#dx,dy = np.array(depth),np.array(depth)
#speedup.gradient(depth.ctypes.data, dx.ctypes.data,
# dy.ctypes.data, depth.shape[0], depth.shape[1])
X,Y,Z,W = -dx, -dy, 0*dy+1, -(-dx*u + -dy*v + depth).astype(np.float32)
mat = calibkinect.projection().astype('f').transpose()
mat = np.ascontiguousarray(mat)
x = X*mat[0,0] + Y*mat[0,1] + Z*mat[0,2] + W*mat[0,3]
y = X*mat[1,0] + Y*mat[1,1] + Z*mat[1,2] + W*mat[1,3]
z = X*mat[2,0] + Y*mat[2,1] + Z*mat[2,2] + W*mat[2,3]
w = np.sqrt(x*x + y*y + z*z)
w[z<0] *= -1
weights = z*0+1
weights[depth<-1000] = 0
weights[(z/w)<.1] = 0
#return x/w, y/w, z/w
return np.dstack((x/w,y/w,z/w)), weights
def face_ibug_68_mirrored_to_face_ibug_68(pcloud):
r"""
Apply the IBUG 68-point semantic labels, on a pointcloud that has been
mirrored around the vertical axis (flipped around the Y-axis). Thus, on
the flipped image the jaw etc would be the wrong way around. This
rectifies that and returns a new PointCloud whereby all the points
are oriented correctly.
The semantic labels applied are as follows:
- jaw
- left_eyebrow
- right_eyebrow
- nose
- left_eye
- right_eye
- mouth
References
----------
.. [1] http://www.multipie.org/
.. [2] http://ibug.doc.ic.ac.uk/resources/300-W/
"""
new_pcloud, old_map = face_ibug_68_to_face_ibug_68(pcloud,
return_mapping=True)
lms_map = np.hstack([old_map['jaw'][::-1],
old_map['right_eyebrow'][::-1],
old_map['left_eyebrow'][::-1],
old_map['nose'][:4],
old_map['nose'][4:][::-1],
np.roll(old_map['right_eye'][::-1], 4),
np.roll(old_map['left_eye'][::-1], 4),
np.roll(old_map['mouth'][:12][::-1], 7),
np.roll(old_map['mouth'][12:][::-1], 5)])
return new_pcloud.from_vector(pcloud.points[lms_map]), old_map
def test_shift():
amp = 1
v0 = 0 * u.m / u.s
sigma = 8
spectral_axis = np.arange(-50, 51) * u.m / u.s
true_spectrum = gaussian(spectral_axis.value,
amp, v0.value, sigma)
# Shift is an integer, so rolling is equivalent
rolled_spectrum = np.roll(true_spectrum, 10)
shift_spectrum = fourier_shift(true_spectrum, 10)
np.testing.assert_allclose(shift_spectrum,
rolled_spectrum,
rtol=1e-4)
# With part masked
masked_spectrum = true_spectrum.copy()
mask = np.abs(spectral_axis.value) <= 30
masked_spectrum[~mask] = np.NaN
rolled_mask = np.roll(mask, 10)
rolled_masked_spectrum = rolled_spectrum.copy()
rolled_masked_spectrum[~rolled_mask] = np.NaN
shift_spectrum = fourier_shift(masked_spectrum, 10)
np.testing.assert_allclose(shift_spectrum,
rolled_masked_spectrum,
rtol=1e-4)
def gradient_ascent_step(net, step_size=1.5, end="inception_4c/output", jitter=32, clip=True, objective_fn=None, **objective_params): # if the objective function is None, initialize it as # the standard L2 objective if objective_fn is None: objective_fn = BatCountry.L2_objective # input image is stored in Net's 'data' blob src = net.blobs["data"] dst = net.blobs[end] # apply jitter shift ox, oy = np.random.randint(-jitter, jitter + 1, 2) src.data[0] = np.roll(np.roll(src.data[0], ox, -1), oy, -2) net.forward(end=end) objective_fn(dst, **objective_params) net.backward(start=end) g = src.diff[0] # apply normalized ascent step to the input image src.data[:] += step_size / np.abs(g).mean() * g # unshift image src.data[0] = np.roll(np.roll(src.data[0], -ox, -1), -oy, -2) # unshift image if clip: bias = net.transformer.mean["data"] src.data[:] = np.clip(src.data, -bias, 255 - bias)
def _calculate_series(self, attr):
mi = getattr(self, '{}_min'.format(attr))
amp = getattr(self, '{}_max'.format(attr)) - mi
funcname = getattr(self, '{}_func'.format(attr))
period = getattr(self, '{}_period'.format(attr))
offset = getattr(self, '{}_offset'.format(attr))
speriod = getattr(self, '{}_sample'.format(attr))
duty = getattr(self, '{}_duty'.format(attr))
duration = getattr(self, '{}_duration'.format(attr))
x, y, sx, sy = [], [], [], []
if funcname != NULL_STR:
if self.xy_pattern_enabled and getattr(self, '{}_use_transit_time'.format(attr)):
t = self.calculate_transit_time()
else:
t = duration
t = t or 1
x = linspace(0, t, 500)
speriod = speriod or 1
sx = arange(0, t, speriod)
if sx[-1] < t:
sx = append(sx, t)
if funcname == 'Sine':
def func(xx):
return (mi + amp) + amp * sin(period * xx + offset)
y = func(x)
elif funcname == 'Square':
def func(xx):
return 0.5 * amp * (signal.square(period * xx * 2 * pi + offset, duty=duty / 100.) + 1) + mi
y = func(x)
bx = asarray(diff(y), dtype=bool)
bx = roll(bx, 1)
sx = x[bx]
sx = append(asarray([0]), sx)
sx = append(sx, asarray([t]))
elif funcname == 'Saw':
def func(xx):
return 0.5 * amp * (signal.sawtooth(period * xx * 2 * pi + offset) + 1) + mi
y = func(x)
asign = sign(gradient(y))
signchange = ((roll(asign, 1) - asign) != 0).astype(bool)
signchange[0] = False
nsx = x[signchange]
sx = hstack((sx, nsx))
sy = func(sx)
return x, y, sx, sy
def main():
args = parse_args()
gdb = genome.db.GenomeDB(assembly=args.assembly)
fwd_track = gdb.open_track(args.fwd_track)
rev_track = gdb.open_track(args.rev_track)
combined_track = gdb.create_track(args.combined_track)
shift = find_strand_shift(gdb, fwd_track, rev_track)
sys.stderr.write("shifting fwd/rev by +%d/-%d bp\n" % (shift, shift))
for chrom in gdb.get_chromosomes():
sys.stderr.write("%s\n" % chrom.name)
carray = create_carray(combined_track, chrom, args.dtype)
fwd_vals = fwd_track.get_nparray(chrom)
rev_vals = rev_track.get_nparray(chrom)
# shift fwd / rev values by the offset that gave
# the maximum covariance2
fwd_vals = np.roll(fwd_vals, shift)
rev_vals = np.roll(rev_vals, -shift)
fwd_vals[:shift] = 0
rev_vals[-shift:] = 0
carray[:] = fwd_vals + rev_vals
fwd_track.close()
rev_track.close()
combined_track.close()
def _coil_trans_to_loc(coil_trans):
"""Convert coil_trans to loc."""
coil_trans = coil_trans.astype(np.float64)
return np.roll(coil_trans.T[:, :3], 1, 0).flatten()
def run_noPlt(self, inits, nstepmax = 10):
import numpy as np
import time
from scipy.interpolate import interp1d
#import matplotlib.pyplot as plt
inits_x = inits[0]
inits_y = inits[1]
# max number of iterations
# frequency of plotting
nstepplot = 1e1
# plot string every nstepplot if flag1 = 1
flag1 = 1
# temperature ###?!!!
mu=9
mu = 3
#mu = 4
# parameter used as stopping criterion
tol1 = 1e-7
# number of images during prerelaxation
n2 = 1e1;
# number of images along the string (try from n1 = 3 up to n1 = 1e4)
n1 = 25
n1 = len(inits_x)
# time-step (limited by the ODE step on line 83 & 84 but independent of n1)
h = 1e-4
#h = 3e-5
# end points of the initial string
# notice that they do NOT have to be at minima of V -- the method finds
# those automatically
# initialization
x = np.array(inits_x)
y = np.array(inits_y)
dx = x-np.roll(x, 1)
dy = y-np.roll(y, 1)
dx[0] = 0
dy[0] = 0
xi = x
yi = y
# parameters in Mueller potential
aa = [-0.3] # inverse radius in x
bb = [0] # radius in xy
cc = [-0.3] # inverse radius in y
AA = 300*[-200] # strength
XX = [0] # center_x
YY = [0] # center_y
zxx = np.mgrid[-2.5:2.51:0.01]
zyy = np.mgrid[-2.5:2.51:0.01]
xx, yy = np.meshgrid(zxx, zyy)
V1 = AA[0]*np.exp(aa[0] * np.square(xx-XX[0]) + bb[0] * (xx-XX[0]) * (yy-YY[0]) +cc[0]*np.square(yy-YY[0]))
##### Main loop
trj_x = []
trj_y = []
for nstep in range(int(nstepmax)):
# calculation of the x and y-components of the force, dVx and dVy respectively
ee = AA[0]*np.exp(aa[0]*np.square(x-XX[0])+bb[0]*(x-XX[0])*(y-YY[0])+cc[0]*np.square(y-YY[0]))
dVx = (aa[0]*(x-XX[0])+bb[0]*(y-YY[0]))*ee
dVy = (bb[0]*(x-XX[0])+cc[0]*(y-YY[0]))*ee
x0 = x
y0 = y
x = x - h*dVx + np.sqrt(h*mu)*np.random.randn(1,n1)
y = y - h*dVy + np.sqrt(h*mu)*np.random.randn(1,n1)
trj_x.append(x)
trj_y.append(y)
return trj_x, trj_y
def render_lights(size=MAP_WINDOW_SIZE, show_weather=True): if not SETTINGS['draw lights']: return False reset_lights(size=size) _weather_light = weather.get_lighting() #Not entirely my code. Made some changes to someone's code from libtcod's Python forum. RGB_LIGHT_BUFFER[0] = numpy.add(RGB_LIGHT_BUFFER[0], _weather_light[0]) RGB_LIGHT_BUFFER[1] = numpy.add(RGB_LIGHT_BUFFER[1], _weather_light[1]) RGB_LIGHT_BUFFER[2] = numpy.add(RGB_LIGHT_BUFFER[2], _weather_light[2]) (x, y) = SETTINGS['light mesh grid'] if show_weather: weather.generate_effects(size) _remove_lights = [] for light in WORLD_INFO['lights']: _x_range = light['pos'][0]-CAMERA_POS[0] _y_range = light['pos'][1]-CAMERA_POS[1] if _x_range <= -20 or _x_range>=size[0]+20: continue if _y_range <= -20 or _y_range>=size[1]+20: continue if not 'old_pos' in light: light['old_pos'] = (0, 0, -2) else: light['old_pos'] = light['pos'][:] if 'follow_item' in light: if not light['follow_item'] in ITEMS: _remove_lights.append(light) continue light['pos'] = items.get_pos(light['follow_item'])[:] _render_x = light['pos'][0]-CAMERA_POS[0] _render_y = light['pos'][1]-CAMERA_POS[1] _x = numbers.clip(light['pos'][0]-(size[0]/2),0,MAP_SIZE[0]) _y = numbers.clip(light['pos'][1]-(size[1]/2),0,MAP_SIZE[1]) _top_left = (_x,_y,light['pos'][2]) #TODO: Render only on move if not tuple(light['pos']) == tuple(light['old_pos']): light['los'] = cython_render_los.render_los((light['pos'][0],light['pos'][1]), light['brightness']*2, view_size=size, top_left=_top_left) los = light['los'].copy() _x_scroll = _x-CAMERA_POS[0] _x_scroll_over = 0 _y_scroll = _y-CAMERA_POS[1] _y_scroll_over = 0 if _x_scroll<0: _x_scroll_over = _x_scroll _x_scroll = los.shape[1]+_x_scroll if _y_scroll<0: _y_scroll_over = _y_scroll _y_scroll = los.shape[0]+_y_scroll los = numpy.roll(los, _y_scroll, axis=0) los = numpy.roll(los, _x_scroll, axis=1) los[_y_scroll_over:_y_scroll,] = 1 los[:,_x_scroll_over:_x_scroll] = 1 if SETTINGS['diffuse light']: _y, _x = diffuse_light((y, x)) (x, y) = numpy.meshgrid(_x, _y) sqr_distance = (x - (_render_x))**2.0 + (y - (_render_y))**2.0 brightness = numbers.clip(random.uniform(light['brightness']*light['shake'], light['brightness']), 0.01, 50) / sqr_distance brightness *= los #brightness *= LOS_BUFFER[0] #_mod = (abs((WORLD_INFO['length_of_day']/2)-WORLD_INFO['real_time_of_day'])/float(WORLD_INFO['length_of_day']))*5.0 #_mod = numbers.clip(_mod-1, 0, 1) #(255*_mod, 165*_mod, 0*_mod) #print brightness #light['brightness'] = 25 #light['color'][0] = 255*(light['brightness']/255.0) #light['color'][1] = (light['brightness']/255.0) #light['color'][2] = 255*(light['brightness']/255.0) RGB_LIGHT_BUFFER[0] -= (brightness.clip(0, 2)*(light['color'][0]))#numpy.subtract(RGB_LIGHT_BUFFER[0], light['color'][0]).clip(0, 255) RGB_LIGHT_BUFFER[1] -= (brightness.clip(0, 2)*(light['color'][1]))#numpy.subtract(RGB_LIGHT_BUFFER[1], light['color'][1]).clip(0, 255) RGB_LIGHT_BUFFER[2] -= (brightness.clip(0, 2)*(light['color'][2]))#numpy.subtract(RGB_LIGHT_BUFFER[2], light['color'][2]).clip(0, 255)
def test_axis_diff_and_interp_nonperiodic_2d(all_2d, boundary, axis_name,
varname, this, to):
ds, periodic, expected = all_2d
try:
ax_periodic = axis_name in periodic
except TypeError:
ax_periodic = periodic
boundary_arg = boundary if not ax_periodic else None
axis = Axis(ds, axis_name, periodic=ax_periodic, boundary=boundary_arg)
da = ds[varname]
# everything is left shift
data = ds[varname].data
axis_num = da.get_axis_num(axis.coords[this])
# lookups for numpy.pad
numpy_pad_arg = {"extend": "edge", "fill": "constant"}
# args for numpy.pad
pad_left = (1, 0)
pad_right = (0, 1)
pad_none = (0, 0)
if this == "center":
if ax_periodic:
data_left = np.roll(data, 1, axis=axis_num)
data_right = data
else:
pad_width = [
pad_left if i == axis_num else pad_none
for i in range(data.ndim)
]
the_slice = tuple([
slice(0, -1) if i == axis_num else slice(None)
for i in range(data.ndim)
])
data_left = np.pad(data, pad_width,
numpy_pad_arg[boundary])[the_slice]
data_right = data
elif this == "left":
if ax_periodic:
data_left = data
data_right = np.roll(data, -1, axis=axis_num)
else:
pad_width = [
pad_right if i == axis_num else pad_none
for i in range(data.ndim)
]
the_slice = tuple([
slice(1, None) if i == axis_num else slice(None)
for i in range(data.ndim)
])
data_right = np.pad(data, pad_width,
numpy_pad_arg[boundary])[the_slice]
data_left = data
data_interp = 0.5 * (data_left + data_right)
data_diff = data_right - data_left
# determine new dims
dims = list(da.dims)
dims[axis_num] = axis.coords[to]
coords = {dim: ds[dim] for dim in dims}
da_interp_expected = xr.DataArray(data_interp, dims=dims, coords=coords)
da_diff_expected = xr.DataArray(data_diff, dims=dims, coords=coords)
da_interp = axis.interp(da, to)
da_diff = axis.diff(da, to)
assert da_interp_expected.equals(da_interp)
assert da_diff_expected.equals(da_diff)
if boundary_arg is not None:
if boundary == "extend":
bad_boundary = "fill"
elif boundary == "fill":
bad_boundary = "extend"
da_interp_wrong = axis.interp(da, to, boundary=bad_boundary)
assert not da_interp_expected.equals(da_interp_wrong)
da_diff_wrong = axis.diff(da, to, boundary=bad_boundary)
assert not da_diff_expected.equals(da_diff_wrong)
def shift(audio, shift_sec, fs):
"""Shifts audio.
"""
shift_count = int(shift_sec * fs)
return np.roll(audio, shift_count)
def random_sample(self,
inputs,
n,
topk=None,
topp=None,
states=None,
temperature=1,
min_ends=1):
"""随机采样n个结果
说明：非None的topk表示每一步只从概率最高的topk个中采样；而非None的topp
表示每一步只从概率最高的且概率之和刚好达到topp的若干个token中采样。
返回：n个解码序列组成的list。
"""
inputs = [np.array([i]) for i in inputs]
output_ids = self.first_output_ids
results = []
for step in range(self.maxlen):
probas, states = self.predict(inputs, output_ids, states,
temperature, 'probas') # 计算当前概率
probas /= probas.sum(axis=1, keepdims=True) # 确保归一化
if step == 0: # 第1步预测后将结果重复n次
probas = np.repeat(probas, n, axis=0)
inputs = [np.repeat(i, n, axis=0) for i in inputs]
output_ids = np.repeat(output_ids, n, axis=0)
if topk is not None:
k_indices = probas.argpartition(-topk,
axis=1)[:, -topk:] # 仅保留topk
probas = np.take_along_axis(probas, k_indices,
axis=1) # topk概率
probas /= probas.sum(axis=1, keepdims=True) # 重新归一化
if topp is not None:
p_indices = probas.argsort(axis=1)[:, ::-1] # 从高到低排序
probas = np.take_along_axis(probas, p_indices, axis=1) # 排序概率
cumsum_probas = np.cumsum(probas, axis=1) # 累积概率
flag = np.roll(cumsum_probas >= topp, 1, axis=1) # 标记超过topp的部分
flag[:, 0] = False # 结合上面的np.roll，实现平移一位的效果
probas[flag] = 0 # 后面的全部置零
probas /= probas.sum(axis=1, keepdims=True) # 重新归一化
sample_func = lambda p: np.random.choice(len(p), p=p) # 按概率采样函数
sample_ids = np.apply_along_axis(sample_func, 1, probas) # 执行采样
sample_ids = sample_ids.reshape((-1, 1)) # 对齐形状
if topp is not None:
sample_ids = np.take_along_axis(p_indices, sample_ids,
axis=1) # 对齐原id
if topk is not None:
sample_ids = np.take_along_axis(k_indices, sample_ids,
axis=1) # 对齐原id
output_ids = np.concatenate([output_ids, sample_ids], 1) # 更新输出
end_counts = (output_ids == self.end_id).sum(1) # 统计出现的end标记
if output_ids.shape[1] >= self.minlen: # 最短长度判断
flag = (end_counts == min_ends) # 标记已完成序列
if flag.any(): # 如果有已完成的
for ids in output_ids[flag]: # 存好已完成序列
results.append(ids)
flag = (flag == False) # 标记未完成序列
inputs = [i[flag] for i in inputs] # 只保留未完成部分输入
output_ids = output_ids[flag] # 只保留未完成部分候选集
end_counts = end_counts[flag] # 只保留未完成部分end计数
if len(output_ids) == 0:
break
# 如果还有未完成序列，直接放入结果
for ids in output_ids:
results.append(ids)
# 返回结果
return results
def nearest_value_and_distance(refpixels, domain, nodata):
"""
Returns distance in pixels !
"""
height, width = domain.shape
midpoints = 0.5*(refpixels + np.roll(refpixels, 1, axis=0))
midpoints_valid = (refpixels[:-1, 3] == refpixels[1:, 3])
# midpoints = midpoints[1:, :2][midpoints_valid]
midpoints = midpoints[1:, :2]
midpoints[~midpoints_valid, 0] = -999999.0
midpoints[~midpoints_valid, 1] = -999999.0
midpoints_index = cKDTree(midpoints, balanced_tree=True)
distance = np.zeros_like(domain)
values = np.copy(distance)
nearest_axes = np.zeros_like(domain, dtype='uint32')
# semi-vectorized code, easier to understand
# for i in range(height):
# js = np.arange(width)
# row = np.column_stack([np.full_like(js, i), js])
# valid = domain[row[:, 0], row[:, 1]] != nodata
# query_pixels = row[valid]
# nearest_dist, nearest_idx = midpoints_index.query(query_pixels, k=1, jobs=4)
# nearest_a = np.take(refpixels, nearest_idx, axis=0, mode='wrap')
# nearest_b = np.take(refpixels, nearest_idx+1, axis=0, mode='wrap')
# nearest_m = np.take(midpoints[:, 2], nearest_idx+1, axis=0, mode='wrap')
# # same as
# # nearest_value = 0.5*(nearest_a[:, 2] + nearest_b[:, 2])
# dist, signed_dist, pos = ta.signed_distance(
# np.float32(nearest_a),
# np.float32(nearest_b),
# np.float32(query_pixels))
# faster fully-vectorized code
pixi, pixj = np.meshgrid(np.arange(height), np.arange(width), indexing='ij')
valid = domain != nodata
query_pixels = np.column_stack([pixi[valid], pixj[valid]])
del pixi
del pixj
del valid
_, nearest_idx = midpoints_index.query(query_pixels, k=1)
# nearest_a = np.take(refpixels, nearest_idx, axis=0, mode='wrap')
# nearest_b = np.take(refpixels, nearest_idx+1, axis=0, mode='wrap')
nearest_p = np.take(refpixels, np.column_stack([nearest_idx, nearest_idx+1]), axis=0, mode='wrap')
nearest_a = nearest_p[:, 0, :]
nearest_b = nearest_p[:, 1, :]
dist, signed_dist, pos = ta.signed_distance(
np.float32(nearest_a),
np.float32(nearest_b),
np.float32(query_pixels))
# interpolate between points A and B
nearest_value = nearest_a[:, 2] + pos*(nearest_b[:, 2] - nearest_a[:, 2])
nearest_axis = np.copy(nearest_a[:, 3])
nearest_axis[nearest_axis != nearest_b[:, 3]] = 0
# almost same as
# nearest_m = 0.5*(nearest_a[:, 2] + nearest_b[:, 2])
# same as
# nearest_m = np.take(midpoints[:, 2], nearest_idx+1, axis=0, mode='wrap')
distance[query_pixels[:, 0], query_pixels[:, 1]] = dist * np.sign(signed_dist)
values[query_pixels[:, 0], query_pixels[:, 1]] = nearest_value
nearest_axes[query_pixels[:, 0], query_pixels[:, 1]] = nearest_axis
return nearest_axes, values, distance
if RunMode == 1:
cuda = torch.device("cuda")
CRSM = torch.zeros((BASELINE, 2, CHOUT, 2), dtype=torch.float32, device=cuda)
elif RunMode == 2:
CRSM = cp.zeros((BASELINE, 2, CHOUT), dtype=cp.complex64)
#### Read sub File ####
with open(str(FILEN1),'rb') as fn1:
for t in range(INTNUM):
fn1.seek(HEADSIZE+t*BLOCKSIZE)
RAW1 = np.fromfile(fn1, dtype=np.int8, count = BLOCKSIZE).reshape(
SMPNUM//INTNUM*ANTNUM*2*SAMPLE//FINECH, FINECH, 2)
# Raw to Complex #
if RunMode == 0:
FFT1 = RAW1[:, 0] + 1j*RAW1[:, 1]
# FFT #
FFT1 = np.roll(np.fft.fft(FFT1, n=FINECH, norm = "ortho")[:, OUT_STR: OUT_END].reshape(
SMPNUM//INTNUM, ANTNUM, 2, SAMPLE//FINECH, CHOUT), FINECH//2, axis=4)
# print("FFT %.2f sec"%(time.time() - tstart))
# Cross Correlate #
ss = 0
for i in range(ANTNUM):
for ii in range(i, ANTNUM):
CRSMCPU[ss, 0, t, :] = (FFT1[:, i, 0, :, :] * np.conj(FFT1[:, ii, 0, :, :])).mean(axis = (0, 1))
CRSMCPU[ss, 1, t, :] = (FFT1[:, i, 1, :, :] * np.conj(FFT1[:, ii, 1, :, :])).mean(axis = (0, 1))
ss += 1
elif RunMode == 1:
FFT1 = torch.from_numpy(RAW1).float().cuda()
# FFT #
FFT1 = torch.roll(torch.fft(FFT1, 1, normalized = True)[:, OUT_STR: OUT_END, :].view(
SMPNUM//INTNUM, ANTNUM, 2, SAMPLE//FINECH, CHOUT, 2), FINECH//2, dims=4)
# print("FFT %.2f sec"%(time.time() - tstart))
def poly_area(x, y):
""" Ref: http://stackoverflow.com/questions/24467972/calculate-area-of-polygon-given-x-y-coordinates """
return 0.5 * np.abs(np.dot(x, np.roll(y, 1)) - np.dot(y, np.roll(x, 1)))
def count_datacube(datacube,
counted_shape,
sigmathresh=4,
nsamples=40,
upperlimit=10,
drwidth=100,
sub_pixel=True,
plot_histogram=False,
plot_electrons=False):
data = datacube.data4D
#Get dimensions
y, x, z, t = [datacube.Q_Ny, datacube.Q_Nx, datacube.R_Ny, datacube.R_Nx]
print('Getting dark current reference')
#Remove dark background
dr, mean, stddev = get_dark_reference(data,
ndrsamples=nsamples,
upperlimit=upper_limit,
drwidth=drwidth)
print('Calculating threshhold')
#Get threshhold
thresh = calculate_counting_threshhold(data,
dr,
sigmathresh=sigmathresh,
nsamples=nsamples,
upper_limit=upper_limit,
plot_histogram=plot_histogram)
counted = np.zeros(counted_shape + (z, t), dtype=np.uint16)
#S
total_electrons = 0
e_list = None
for tt in range(t):
printProgressBar(tt,
t - 1,
prefix='Counting:',
suffix='Complete',
length=50)
for zz in range(z):
#Background subtract and remove X-rays\hot pixels
workingarray = data[:, :, zz, tt] - dr[:, np.newaxis]
workingarray[workingarray > mean + upper_limit * stddev] = 0
#Create a map of events (pixels with value greater than
#the threshhold value)
events = np.greater(workingarray, thresh)
#Now find local maxima by circular shift and comparison to neighbours
#if we want diagonal neighbours to be considered seperate electron
#counts then we would add a second for loop to do these extra
#comparisons
for i in range(4):
events = np.logical_and(
np.greater(
workingarray,
np.roll(workingarray, i % 2 * 2 - 1, axis=i // 2)),
events)
events[0, :] = False
events[-1, :] = False
events[:, 0] = False
events[:, -1] = False
electron_posn = np.asarray(np.argwhere(events), dtype=np.float)
num_electrons = np.shape(electron_posn)[0]
if (sub_pixel):
#Now do center of mass in local region 3x3 region to refine position
# estimate
for i in range(num_electrons):
event = electron_posn[i, :]
electron_posn[i, :] += center_of_mass(
workingarray[int(event[0] - 1):int(event[0] + 2),
int(event[1] - 1):int(event[1] + 2)])
electron_posn -= np.asarray([1, 1])[np.newaxis, :]
if (plot_electrons):
if (not os.path.exists(count_plots)): os.mkdir('count_plots')
figsize = max(np.shape(data[:, :, zz, tt])[:2]) // 200
fig = plt.figure(figsize=(figsize, figsize))
ax = fig.add_subplot(111)
ax.imshow(data[:, :, zz, tt], origin='lower', vmax=2 * thresh)
ax.plot(electron_posn[:, 1], electron_posn[:, 0], 'rx')
ax.set_title('Found {0} electrons'.format(num_electrons))
plt.show()
fig.savefig('count_plots/Countplot_{0}_{1}.pdf'.format(tt, zz))
#Update total number of electrons
total_electrons += num_electrons
#Put the electron_posn in fractional coordinates
#where the positions are fractions of the original array
electron_posn /= np.asarray([max(y, x), max(y, x)])[np.newaxis, :]
electron_posn = np.hstack(
(electron_pons, np.asarray([tt, xx],
dtype=np.float32)[np.newaxis, :]))
if (e_list is None): e_list = electron_posn
else: e_list = np.vstack((e_list, electron_posn))
return electron_posn
def ZOGY(R, N, Pr, Pn, sr, sn, fr, fn, Vr, Vn, dx, dy):
"""
Optimal image subtraction in a pythonic layout!
Where the magic happens. Algorithm from
Zackay et al. (2016)
"""
R_hat = fft.fft2(R)
N_hat = fft.fft2(N)
Pn_hat = fft.fft2(Pn)
Pn_hat2_abs = np.abs(Pn_hat**2)
Pr_hat = fft.fft2(Pr)
Pr_hat2_abs = np.abs(Pr_hat**2)
sn2 = sn**2
sr2 = sr**2
fn2 = fn**2
fr2 = fr**2
fD = fr * fn / np.sqrt(sn2 * fr2 + sr2 * fn2)
denom = sn2 * fr2 * Pr_hat2_abs + sr2 * fn2 * Pn_hat2_abs
if np.any(denom == 0):
print('There are zeros!')
D_hat = (fr * Pr_hat * N_hat - fn * Pn_hat * R_hat) / np.sqrt(denom)
D = np.real(fft.ifft2(D_hat)) / fD
P_D_hat = (fr * fn / fD) * (Pr_hat * Pn_hat) / np.sqrt(denom)
S_hat = fD * D_hat * np.conj(P_D_hat)
S = np.real(fft.ifft2(S_hat))
kr_hat = fr * fn2 * np.conj(Pr_hat) * Pn_hat2_abs / denom
kr = np.real(fft.ifft2(kr_hat))
kr2 = kr**2
kr2_hat = fft.fft2(kr2)
kn_hat = fn * fr2 * np.conj(Pn_hat) * Pr_hat2_abs / denom
kn = np.real(fft.ifft2(kn_hat))
kn2 = kn**2
kn2_hat = fft.fft2(kn2)
Vr_hat = fft.fft2(Vr)
Vn_hat = fft.fft2(Vn)
VSr = np.real(fft.ifft2(Vr_hat * kr2_hat))
VSn = np.real(fft.ifft2(Vn_hat * kn2_hat))
dx2 = dx**2
dy2 = dy**2
# and calculate astrometric variance
Sn = np.real(fft.ifft2(kn_hat * N_hat))
dSndy = Sn - np.roll(Sn, 1, axis=0)
dSndx = Sn - np.roll(Sn, 1, axis=1)
VSn_ast = dx2 * dSndx**2 + dy2 * dSndy**2
Sr = np.real(fft.ifft2(kr_hat * R_hat))
dSrdy = Sr - np.roll(Sr, 1, axis=0)
dSrdx = Sr - np.roll(Sr, 1, axis=1)
VSr_ast = dx2 * dSrdx**2 + dy2 * dSrdy**2
# and finally S_corr
V_S = VSr + VSn
V_ast = VSr_ast + VSn_ast
V = V_S + V_ast
# make sure there's no division by zero
S_corr = np.copy(S)
S_corr[V > 0] /= np.sqrt(V[V > 0])
F_S = np.sum((fn2 * Pn_hat2_abs * fr2 * Pr_hat2_abs) / denom)
F_S /= R.size
alpha = S / F_S
alpha_std = np.zeros(alpha.shape)
alpha_std[V_S > 0] = np.sqrt(V_S[V_S > 0]) / F_S
return (D, S, S_corr, alpha, alpha_std)
def is_clockwise(p):
x = p[:, 0]
y = p[:, 1]
return np.dot(x, np.roll(y, 1)) - np.dot(y, np.roll(x, 1)) > 0
def L_BFGS_nls(x0,
d0,
fdf,
qlist,
glist,
fdf0=None,
big_step=100,
tol=1.0e-6,
itmax=100,
init_step=1.0e-3,
m=0,
k=0):
"""L-BFGS minimization without line search
Does one step.
Arguments:
fdf: function and gradient
fdf0: initial function and gradient value
d0: initial direction for line minimization
x0: initial point
qlist: list of previous positions used for reduced inverse Hessian construction
glist: list of previous gradients used for reduced inverse Hessian construction
m: number of corrections to store and use
k: iteration (MD step) number
big_step: limit on step length
tol: convergence tolerance
itmax: maximum number of allowed iterations
init_step: initial step size
"""
# Original function value, gradient, other initializations
zeps = 1.0e-10
if fdf0 is None: fdf0 = fdf(x0)
f0, df0 = fdf0
n = len(x0.flatten())
dg = np.zeros(n)
g = df0
x = np.zeros(n)
linesum = np.dot(x0.flatten(), x0.flatten())
alpha = np.zeros(m)
beta = np.zeros(m)
rho = np.zeros(m)
q = np.zeros(n)
# Initial line direction
xi = d0
dg = df0
# Step size
stepsize = np.sqrt(np.dot(d0.flatten(), d0.flatten()))
# First iteration; use initial step
if k == 0:
scale = 1.0
while np.sqrt(np.dot(g.flatten(), g.flatten())) >= np.sqrt(np.dot(df0.flatten(), df0.flatten()))\
or np.isnan(np.sqrt(np.dot(g.flatten(), g.flatten()))) == True\
or np.isinf(np.sqrt(np.dot(g.flatten(), g.flatten()))) == True:
x = np.add(x0, (scale * init_step * d0 /
np.sqrt(np.dot(d0.flatten(), d0.flatten()))))
scale *= 0.1
fx, g = fdf(x)
else:
# Scale if attempted step is too large
if stepsize > big_step:
d0 = big_step * d0 / np.sqrt(np.dot(d0.flatten(), d0.flatten()))
info(" @MINIMIZE: Scaled step size", verbosity.debug)
x = np.add(x0, d0)
print "step size:", np.sqrt(np.dot(d0.flatten(), d0.flatten()))
fx, g = fdf(x)
info(" @MINIMIZE: Started L-BFGS", verbosity.debug)
info(" @MINIMIZE: Updated gradient", verbosity.debug)
# Update line direction (xi) and current point (x0)
xi = np.subtract(x, x0)
# Build list of previous positions
if k < m:
qlist[k] = xi.flatten()
else:
qlist = np.roll(qlist, -1, axis=0)
qlist[m - 1] = xi.flatten()
# Update current point
x0 = x
# Compute difference of gradients
q = g.flatten()
dg = np.subtract(g, dg)
# Build list of previous gradients
if k < m:
glist[k] = dg.flatten()
else:
glist = np.roll(glist, -1, axis=0)
glist[m - 1] = dg.flatten()
# Determine bounds for L-BFGS 'two loop recursion'
if k < (m - 1):
bound1 = k
bound2 = k + 1
else:
bound1 = m - 1
bound2 = m
# Begin two loop recursion:
# First loop
for j in range(bound1, -1, -1):
rho[j] = 1.0 / np.dot(glist[j], qlist[j])
alpha[j] = rho[j] * np.dot(qlist[j], q)
q = q - alpha[j] * glist[j]
info(" @MINIMIZE: First L-BFGS loop recursion completed", verbosity.debug)
# Two possiblities for scaling: using first or most recent
# members of the gradient and position lists
hk = np.dot(glist[bound1], qlist[bound1]) / np.dot(glist[bound1],
glist[bound1])
#hk = np.dot(glist[0], qlist[0]) / np.dot(glist[0], glist[0])
xi = hk * q
# Second loop
for j in range(0, bound2, 1):
beta[j] = rho[j] * np.dot(glist[j], xi)
xi = xi + qlist[j] * (alpha[j] - beta[j])
# Update direction xi
xi = -xi.reshape(d0.shape)
info(" @MINIMIZE: Second L-BFGS loop recursion completed", verbosity.debug)
info(" @MINIMIZE: Updated search direction", verbosity.debug)
return (x, fx, xi, qlist, glist)
def boundary_info(p,bars):
"""
If Bflag = 1, it returns a 1D array of nodes ('boundary_nodes') and
a 2D array of bars ('boundary').
The first element in 'boundary_nodes' identifies the node (by its
number) that has the minimum x-coordinate. If there are several nodes
in the boundary with minimum x, it will choose the node from this set
the node with minimum y-coordinate. This will be the 'reference node'
of the set of nodes on the boundary, easy to find out visually in the
boundary plot. Following this reference node the elements in the
'boundary_nodes' array appear in the same order as they appear on
the boundary plot as one follows the perimeter of the boundary in a
ccw direction, defined as the direction in which we see all the nodes
inside the mesh at our left.
Likewise, the first element in the 2D array 'boundary' defines the
first bar in the boundary (using a pair of nodes). The order of the
bars follows the same order used by the 'boundary_nodes' array.
If Bflag=2, it returns two 1D arrays of nodes ('ext_bound_nodes' and
'int_bound_nodes') and two 2D arrays of bars ('ext_bound' and
'int_bound'). The first set, 'ext_bound_nodes' and 'ext_bound' refers
to the external boundary and the second set, 'int_bound_nodes' and
'int_bound' refers to the internal boundary. In both cases the order
of the nodes and bars is such that as we go along the boundary we
see the internal nodes of the mesh towards our left ('ccw' convention)
"""
bars = bars.tolist()
Bflag = 1 # boundary flag default, indicating only 1 boundary
bound = [bars[0]]
del bars[0]
while bound[0][0] != bound[-1][1]:
for bar in bars:
if bar[0] == bound[-1][1]:
to_remove = bar
b = [bar[0],bar[1]]
bound.append(b)
break
if bar[1] == bound[-1][1]:
to_remove = bar
b = [bar[1],bar[0]]
bound.append(b)
break
bars.remove(to_remove)
if len(bars) > 0:
Bflag = 2 # two boundaries, nodes between boundaries(external flow)
next_bound = [bars[0]]
del bars[0]
while next_bound[0][0] != next_bound[-1][1]:
for bar in bars:
if bar[0] == next_bound[-1][1]:
to_remove = bar
b = [bar[0],bar[1]]
next_bound.append(b)
break
if bar[1] == next_bound[-1][1]:
to_remove = bar
b = [bar[1],bar[0]]
next_bound.append(b)
break
bars.remove(to_remove)
if len(bars) > 0:
print ('Error: there are more than 2 boundaries')
print (' number of bars left out = %4d' % len(bars))
# ---------------------------------------------------------------------
# If there is more than one boundary find out which one is external and
# which one is internal
# ---------------------------------------------------------------------
p = np.asarray(p)
if Bflag == 1:
bound = np.asarray(bound)
if Bflag == 2:
bound = np.asarray(bound)
next_bound = np.asarray(next_bound)
# find the node(s) with minimum x-coordinate in bound
# find the node(s) with minimum x-coordinate in next_bound
# the one with the minimum x-coord is the external boundary
# since the nodes in bound appear twice each (once to the left of a bar,
# the second time to the right of a bar) all the nodes are represented
# either in p[bound[:,0]] or p[bound[:,1]]
px_min_bound,py_min_bound = np.amin(p[bound[:,0]],axis=0)
# px_min_bound = -3.0; py_min_bound = -1.0
if Bflag == 1:
boundary = np.copy(bound)
px_min_boundary = np.copy(px_min_bound)
if Bflag == 2:
px_min_next_bound, py_min_next_bound = \
np.amin(p[next_bound[:,0]],axis=0)
if px_min_bound < px_min_next_bound:
ext_bound = np.copy(bound)
int_bound = np.copy(next_bound)
px_min_ext = px_min_bound
px_min_int = px_min_next_bound
else:
ext_bound = np.copy(next_bound)
int_bound = np.copy(bound)
px_min_ext = np.copy(px_min_next_bound)
px_min_int = np.copy(px_min_bound)
# -------------------------------------------------------------
# put the nodes making the boundary in a separate array(s)
# -------------------------------------------------------------
if Bflag == 1:
bpoints = np.reshape(boundary[0::2],2*len(boundary[0::2]))
if len(boundary) % 2 == 0: # even
boundary_nodes = bpoints
else:
boundary_nodes = bpoints[0:-1]
if Bflag == 2:
bpoints = np.reshape(ext_bound[0::2],2*len(ext_bound[0::2]))
if len(ext_bound) % 2 == 0: # even
ext_bound_nodes = bpoints
else:
ext_bound_nodes = bpoints[0:-1]
bpoints = np.reshape(int_bound[0::2],2*len(int_bound[0::2]))
if len(int_bound) % 2 == 0: # even
int_bound_nodes = bpoints
else:
int_bound_nodes = bpoints[0:-1]
# Note ext_bound_nodes and int_bound_nodes contain the indexes
# of the nodes on the boundary. To find their coordinates, do
# p[ext_bound_nodes] and p[int_bound_nodes]
# -------------------------------------------------------------
# Find the reference node (index) for each array of boundary nodes
# -------------------------------------------------------------
eps = 0.0001
if Bflag == 1:
ind_min_x = np.where(p[boundary_nodes,0] < px_min_boundary + eps)
nn = np.argmin(p[boundary_nodes[ind_min_x],1])
ref_ind = ind_min_x[0][nn]
if Bflag == 2:
ind_min_x = np.where(p[ext_bound_nodes,0] < px_min_ext + eps)
nn = np.argmin(p[ext_bound_nodes[ind_min_x],1])
ext_ref_ind = ind_min_x[0][nn]
ind_min_x = np.where(p[int_bound_nodes,0] < px_min_int + eps)
nn = np.argmin(p[int_bound_nodes[ind_min_x],1])
int_ref_ind = ind_min_x[0][nn]
# --------------------------------------------------------------
# roll the boundaries so the ref point is the first point
#---------------------------------------------------------------
if Bflag == 1:
boundary = np.roll(boundary, len(boundary) - ref_ind, axis=0)
boundary_nodes = np.roll(boundary_nodes, len(boundary_nodes) - ref_ind)
if Bflag == 2:
ext_bound = np.roll(ext_bound, len(ext_bound) - ext_ref_ind, axis=0)
int_bound = np.roll(int_bound, len(int_bound) - int_ref_ind, axis=0)
ext_bound_nodes = np.roll(ext_bound_nodes,len(ext_bound_nodes) - ext_ref_ind)
int_bound_nodes = np.roll(int_bound_nodes,len(int_bound_nodes) - int_ref_ind)
# --------------------------------------------------------------
# Order the boundary(s) such that as we travel along the boundary(s)
# we always see the nodes of the grid to our left ('ccw')
# Test of ccw:
# For the boundary (Bflag=1) or ext_bound Bflag=2), as we traverse the
# periphery of the boundary increasing the index of the node, the total
# area enclosed in a complete turn must be negative
# For the int_bound the total area enclosed in a complete turn along the
# boundary must be positive
# to change from ccw to cw (or viceversa):
# 1) swap the columns of the array
# 2) reverse the order of the elements in the array: 1st becomes last,
# 2nd becomes next to last, and so on
# --------------------------------------------------------------
def kintegrate(y,x):
area = 0.0
for i in range(len(x)-1):
dx = x[i+1] - x[i]
h = 0.5*(y[i+1] + y[i])
area += h*dx
return area
if Bflag == 1:
y = np.concatenate((p[boundary_nodes,1],[p[boundary_nodes[0],1]]))
x = np.concatenate((p[boundary_nodes,0],[p[boundary_nodes[0],0]]))
area = kintegrate(y,x)
if area > 0:
# invert the order
boundary_nodes = boundary_nodes[::-1]
boundary_nodes = np.roll(boundary_nodes,1)
boundary[:,[0,1]] = boundary[:,[1,0]]
boundary = boundary[::-1]
return boundary_nodes, boundary
if Bflag == 2:
y_ext = np.concatenate((p[ext_bound_nodes,1],[p[ext_bound_nodes[0],1]]))
x_ext = np.concatenate((p[ext_bound_nodes,0],[p[ext_bound_nodes[0],0]]))
y_int = np.concatenate((p[int_bound_nodes,1],[p[int_bound_nodes[0],1]]))
x_int = np.concatenate((p[int_bound_nodes,0],[p[int_bound_nodes[0],0]]))
area_ext = kintegrate(y_ext,x_ext)
area_int = kintegrate(y_int,x_int)
if area_ext > 0:
# invert the order
ext_bound_nodes = ext_bound_nodes[::-1]
ext_bound_nodes = np.roll(ext_bound_nodes,1)
ext_bound[:,[0,1]] = ext_bound[:,[1,0]]
ext_bound = ext_bound[::-1]
if area_int < 0:
# invert the order
int_bound_nodes = int_bound_nodes[::-1]
int_bound_nodes = np.roll(int_bound_nodes,1)
int_bound[:,[0,1]] = int_bound[:,[1,0]]
int_bound = int_bound[::-1]
return ext_bound_nodes,ext_bound,int_bound_nodes,int_bound
def _pad_signal(self, data, pad_len, mode='symm', center=False):
'''
inputs:
-------
- data: rank 3 ndarray with shape (n_data, n_channels, data_len)
- pad_len: int type, length after padding
- mode: string type either symm, per, zero.
- center: bool type indicating whether to bring the padded signal to the center
outputs:
--------
- data: ndarray type padded data shaped (n_data, n_channels, pad_len)
'''
n_data = data.shape[0]
n_channels = data.shape[1]
data_len = data.shape[2]
has_imag = np.linalg.norm(np.imag(data)) > 0 # bool type that checks if any of the elements has imaginary component
if mode == 'symm':
idx0 = np.concatenate([np.arange(data_len), np.arange(data_len, 0, -1) - 1], axis=0)
conjugate0 = np.concatenate([np.zeros(data_len), np.ones(data_len)], axis=0)
elif mode == 'per' or mode == 'zero':
idx0 = np.arange(data_len)
conjugate0 = np.zeros(data_len)
else:
raise ValueError('Invalid boundary conditions!')
if mode != 'zero':
idx = np.zeros(pad_len)
conjugate = np.zeros(pad_len)
idx[:data_len] = np.arange(data_len)
conjugate[:data_len] = np.zeros(data_len)
src = np.arange(data_len, data_len + np.floor((pad_len-data_len) / 2), dtype=int) % len(idx0)
dst = np.arange(data_len, data_len + np.floor((pad_len - data_len) / 2), dtype=int)
idx[dst] = idx0[src]
conjugate[dst] = conjugate0[src]
src = (len(idx0) - np.arange(1, np.ceil((pad_len - data_len) / 2) + 1, dtype=int)) % len(idx0)
dst = np.arange(pad_len - 1, data_len + np.floor((pad_len - data_len) / 2 ) - 1, -1, dtype=int)
idx[dst] = idx0[src]
conjugate[dst] = conjugate0[src]
# conjugate is shaped (pad_len,)
else:
idx = np.arange(data_len)
conjugate = np.zeros(data_len)
# conjugate is shaped (data_len,)
idx = idx.astype(int)
# idx, idx0, conjugate, conjugate0, src, dst are all rank 1 ndarrays
data = data[:, :, idx] # data shape: (n_data, n_channels, data_len or pad_len)
conjugate = conjugate[np.newaxis, np.newaxis, :] # conjugate shape: (1, 1, data_len or pad_len)
if has_imag:
data = data - 2j * np.imag(data) * conjugate
# data is shaped (n_data, data_len or pad_len)
if mode == 'zero':
data = np.concatenate([data, np.zeros((n_data, n_channels, pad_len - data_len))], axis=2)
if center: # if center is nonzero (negative values are allowed, too)
margin = int(np.floor((pad_len - data_len) / 2))
data = np.roll(data, margin, axis=2)
return data
def L_BFGS(x0, d0, fdf, qlist, glist, fdf0, big_step, tol, itmax, m, scale, k):
"""L-BFGS minimization. Uses approximate line minimizations.
Does one step.
Arguments:
fdf = function and gradient
fdf0 = initial function and gradient value
d0 = initial direction for line minimization
x0 = initial point
qlist = list of previous positions used for reduced inverse Hessian construction
glist = list of previous gradients used for reduced inverse Hessian construction
m = number of corrections to store and use
k = iteration (MD step) number
big_step = limit on step length
tol = convergence tolerance
itmax = maximum number of allowed iterations
"""
zeps = 1.0e-10
n = len(x0.flatten())
alpha = np.zeros(m)
beta = np.zeros(m)
rho = np.zeros(m)
u0, g0 = fdf0
# Maximum step size
linesum = np.dot(x0.flatten(), x0.flatten())
big_step = big_step * max(np.sqrt(linesum), n)
# Perform approximate line minimization in direction d0
x, u, g = min_approx(fdf, x0, fdf0, d0, big_step, tol, itmax)
# Compute difference of positions (gradients)
# Build list of previous 'd_positions (d_gradients)'
d_x = np.subtract(x, x0)
if k < m:
qlist[k] = d_x.flatten()
else:
qlist_aux = np.roll(qlist, -1, axis=0)
qlist[:] = qlist_aux
qlist[m - 1] = d_x.flatten()
d_g = np.subtract(g, g0)
if k < m:
glist[k] = d_g.flatten()
else:
glist_aux = np.roll(glist, -1, axis=0)
glist[:] = glist_aux
glist[m - 1] = d_g.flatten()
# Update direction.
# 1_Determine bounds for L-BFGS 'two loop recursion'
if k < (m - 1):
bound1 = k
bound2 = k + 1
else:
bound1 = m - 1
bound2 = m
# 2
q = g.flatten()
# 3_Loops
fac = np.dot(d_g.flatten(), d_x.flatten())
sumdg = np.dot(d_g.flatten(), d_g.flatten())
sumdx = np.dot(d_x.flatten(), d_x.flatten())
# Skip update if not 'fac' sufficiently positive
if fac > np.sqrt(zeps * sumdg * sumdx):
# Begin two loop recursion:
# First loop
for j in range(bound1, -1, -1):
rho[j] = 1.0 / np.dot(glist[j], qlist[j])
alpha[j] = rho[j] * np.dot(qlist[j], q)
q = q - alpha[j] * glist[j]
info(" @MINIMIZE: First L-BFGS loop recursion completed",
verbosity.debug)
if scale == 0:
hk = 1.0
elif scale == 1:
hk = np.dot(glist[0], qlist[0]) / np.dot(glist[0], glist[0])
elif scale == 2:
hk = np.dot(glist[bound1], qlist[bound1]) / np.dot(
glist[bound1], glist[bound1])
d = hk * q
# Second loop
for j in range(0, bound2, 1):
beta[j] = rho[j] * np.dot(glist[j], d)
d = d + qlist[j] * (alpha[j] - beta[j])
info(" @MINIMIZE: Second L-BFGS loop recursion completed",
verbosity.debug)
d = -1.0 * d.reshape(d0.shape)
else:
info(
" @MINIMIZE: Skipped direction update; direction * gradient insufficient",
verbosity.debug)
#d = d0
d = -1.0 * d_x
d0[:] = d
info(" @MINIMIZE: Updated search direction", verbosity.debug)
def process(self): # 进行数据解析
while self.current > 129: # 如果队列中数据多于2包数据
if self.buf[0] == 170 and self.buf[1] == 85 and self.buf[
2] == 1 and self.buf[3] == 54:
# if self.debug:
# print("检测到帧头，功能字是" + str(self.buf[2]))
quat_w = self.hex2signedint(6) / 10000.0
quat_x = self.hex2signedint(8) / 10000.0
quat_y = self.hex2signedint(10) / 10000.0
quat_z = self.hex2signedint(12) / 10000.0
# quat_x=(self.buf[9]*256+self.buf[8])/10000.0
# quat_y=(self.buf[11]*256+self.buf[10])/10000.0
# quat_z=(self.buf[13]*256+self.buf[12])/10000.0
gyro_x = self.hex2signedint(14) / 50.0
gyro_y = self.hex2signedint(16) / 50.0
gyro_z = self.hex2signedint(18) / 50.0
acc_x = self.hex2signedint(20) / 4000.0
acc_y = self.hex2signedint(22) / 4000.0
acc_z = self.hex2signedint(24) / 4000.0
header = Header(stamp=rospy.Time.now())
header.frame_id = 'pandar'
imu = Imu()
imu.header = header
# quat = Rotation.from_euler('ZYX', [heading, pitch, roll], degrees=True).as_quat()
imu.orientation.w = quat_w
imu.orientation.x = quat_x
imu.orientation.y = quat_y
imu.orientation.z = quat_z
imu.angular_velocity.x = gyro_x
imu.angular_velocity.y = gyro_y
imu.angular_velocity.z = gyro_z
imu.linear_acceleration.x = acc_x
imu.linear_acceleration.y = acc_y
imu.linear_acceleration.z = acc_z
# print 0
# str1=str(rospy.Time.now())+','+str1
pub.publish(imu)
print quat_w, quat_x, quat_y, quat_z, gyro_x, gyro_y, gyro_z, acc_x, acc_y, acc_z
# print quat_w,quat_x,quat_y,quat_z
# datalength = self.buf[3] # 有效数据长度
framelength = self.buf[4] + 2 # 帧长度
# datasum = np.sum(self.buf[0:framelength - 1]) % 256
# if datasum == self.buf[framelength - 1]: # 校验通过
# self.data_signal = self.buf[4:4 + datalength]
# self.data_signal = np.array(
# self.data_signal, dtype='uint8')
# self.data_signal = self.data_signal.reshape(-1, 2)
# self.data_signal = self.data_signal[:, 0] * 256 + \
# self.data_signal[:, 1]
# self.newdata = True
#
# if self.debug:
# print(self.data_signal)
self.buf = np.roll(self.buf, -framelength)
self.current -= framelength
if self.debug:
print("解析到一帧数据")
# else: # 校验失败
# if self.debug:
# print("校验和错误")
#
# if 170 in self.buf[2:self.current]: # 帧头对，但是校验和错误
# temparray = self.buf[2:self.current]
# if not isinstance(temparray, list):
# temparray = temparray.tolist()
# offset = temparray.index(170)
#
# self.buf = np.roll(self.buf, -offset)
# self.current -= offset
# 如果解析不到，舍弃前面的数据，直到data[0] == 170
elif 170 in self.buf[0:self.current]:
if self.debug:
print("接收到无效数据")
# temparray = self.buf[0:self.current]
# if not isinstance(temparray, list):
# temparray = temparray.tolist()
# offset = temparray.index(170)
for i in range(len(self.buf)):
if self.buf[i + 0] == 170 and self.buf[
i + 1] == 85 and self.buf[i + 2] == 1 and self.buf[
i + 3] == 54:
self.buf = np.roll(self.buf, -i)
self.current -= i
break
def _truncate_filter(self, filter, thresh=1e-3):
'''
truncates the given fourier transform of the filter. this filter will have values that are high in
only a small region. in this case, one can make a similar filter which is a hard-thresholded version
of the given filter. this can siginificantly speedup the computation as the convolution in the fourier
domain is a multiplication and so only the nonzero values have to be considered.
first, the smallest region that contains all the values that are above a certain threshold is identified.
this region is extended slightly so that the region length is N/2^m where N is the length of the given
filter and m is some integer. during this process, the adjusted region's start and end point might be
beyond the given filter. In this case, the filter is wrapped around (periodically extend the given filter
and then take the adjusted region.
FIXME: what is the basis of the idea of wrapping around?
in order to use this filter and later reconstruct to the correct original size, keys named
'start' and 'filter_len' are stored in the output dictionary
inputs:
-------
- filter: rank 1 ndarray which is the fourier representation of the filter
- thresh: threshold relative to the maximum value of the given filter's absolute values in fourier domain, between 0 and 1
outputs:
--------
- filter_truncated: dict type object containing the following keys:
coef: the truncated filter
start: starting index of the fourier domain support
filter_len: original length of the filter
'''
# print(filter)
filter_len = len(filter)
filter_truncated = {'filter_len':filter_len}
# FIXME: for consistency the max() function in matlab is implemented below.
# after running tests, consider replacing with idx_max = np.argmax(filter)
maxabs = np.abs(filter).max()
maxangle = np.angle(filter[np.abs(filter) == maxabs]).max()
idx_max = np.where(np.logical_and(np.abs(filter) == maxabs, np.angle(filter) == maxangle))[0][0]
filter = np.roll(filter, int(filter_len / 2) - (idx_max + 1))
# np.where()'s return type is a tuple and so access the 0th index
idx = np.where(np.abs(filter) > (np.abs(filter).max() * thresh))[0]
idx1 = idx[0]
idx2 = idx[-1]
nonzero_len = idx2 - idx1 + 1
nonzero_len = int(np.round(filter_len / 2**(np.floor(np.log2(filter_len / nonzero_len)))))
# before np.round(), add small amount since in np.round(), halfway values are
# rounded to the nearest even value, i.e., np.round(2.5) gives 2.0, NOT 3
# if the amount is too small (1e-17, for example), does not work
idx1 = int(np.round(np.round((idx1 + idx2) / 2 + 1e-6) - nonzero_len / 2 + 1e-6))
idx2 = idx1 + int(nonzero_len) - 1
filter = filter[np.arange(idx1, idx2 + 1) % filter_len]
filter_truncated['coef'] = filter
filter_truncated['start'] = int(idx1 - (filter_len / 2 - idx_max) + 1)
return filter_truncated
def t3_preprocess_data(train, test, structures, contributions, mulliken_charges):
train = pd.merge(train, contributions, how='left',
left_on=['molecule_name', 'atom_index_0', 'atom_index_1', 'type'],
right_on=['molecule_name', 'atom_index_0', 'atom_index_1', 'type'])
# train = pd.merge(train, potential_energy, how='left',
# left_on=['molecule_name'],
# right_on=['molecule_name'])
train = pd.merge(train, mulliken_charges, how='left',
left_on=['molecule_name', 'atom_index_0'],
right_on=['molecule_name', 'atom_index'])
train.drop('atom_index', axis=1, inplace=True)
# train.rename(inplace=True, columns={'mulliken_charge': 'mulliken_charge_0'})
# train = pd.merge(train, mulliken_charges, how='left',
# left_on=['molecule_name', 'atom_index_1'],
# right_on=['molecule_name', 'atom_index'])
# train.drop('atom_index', axis=1, inplace=True)
# train.rename(inplace=True, columns={'mulliken_charge': 'mulliken_charge_1'})
# electronegativity and atomic_radius
# https://www.kaggle.com/vaishvik25/1-r-3-hyperpar-tuning
# from tqdm import tqdm_notebook as tqdm
atomic_radius = {'H': 0.38, 'C': 0.77, 'N': 0.75, 'O': 0.73, 'F': 0.71} # Without fudge factor
fudge_factor = 0.05
atomic_radius = {k: v + fudge_factor for k, v in atomic_radius.items()}
# print(atomic_radius)
electronegativity = {'H': 2.2, 'C': 2.55, 'N': 3.04, 'O': 3.44, 'F': 3.98}
# structures = pd.read_csv(structures, dtype={'atom_index':np.int8})
atoms = structures['atom'].values
atoms_en = [electronegativity[x] for x in atoms]
atoms_rad = [atomic_radius[x] for x in atoms]
structures['EN'] = atoms_en
structures['rad'] = atoms_rad
# print(structures.head())
i_atom = structures['atom_index'].values
p = structures[['x', 'y', 'z']].values
p_compare = p
m = structures['molecule_name'].values
m_compare = m
r = structures['rad'].values
r_compare = r
source_row = np.arange(len(structures))
max_atoms = 28
bonds = np.zeros((len(structures) + 1, max_atoms + 1), dtype=np.int8)
bond_dists = np.zeros((len(structures) + 1, max_atoms + 1), dtype=np.float32)
print('Calculating bonds')
for i in range(max_atoms - 1):
p_compare = np.roll(p_compare, -1, axis=0)
m_compare = np.roll(m_compare, -1, axis=0)
r_compare = np.roll(r_compare, -1, axis=0)
mask = np.where(m == m_compare, 1, 0) # Are we still comparing atoms in the same molecule?
dists = np.linalg.norm(p - p_compare, axis=1) * mask
r_bond = r + r_compare
bond = np.where(np.logical_and(dists > 0.0001, dists < r_bond), 1, 0)
source_row = source_row
target_row = source_row + i + 1 # Note: Will be out of bounds of bonds array for some values of i
target_row = np.where(np.logical_or(target_row > len(structures), mask == 0), len(structures),
target_row) # If invalid target, write to dummy row
source_atom = i_atom
target_atom = i_atom + i + 1 # Note: Will be out of bounds of bonds array for some values of i
target_atom = np.where(np.logical_or(target_atom > max_atoms, mask == 0), max_atoms,
target_atom) # If invalid target, write to dummy col
bonds[(source_row, target_atom)] = bond
bonds[(target_row, source_atom)] = bond
bond_dists[(source_row, target_atom)] = dists
bond_dists[(target_row, source_atom)] = dists
bonds = np.delete(bonds, axis=0, obj=-1) # Delete dummy row
bonds = np.delete(bonds, axis=1, obj=-1) # Delete dummy col
bond_dists = np.delete(bond_dists, axis=0, obj=-1) # Delete dummy row
bond_dists = np.delete(bond_dists, axis=1, obj=-1) # Delete dummy col
print('Counting and condensing bonds')
bonds_numeric = [[i for i, x in enumerate(row) if x] for row in bonds]
bond_lengths = [[dist for i, dist in enumerate(row) if i in bonds_numeric[j]] for j, row in
enumerate(bond_dists)]
bond_lengths_mean = [np.mean(x) for x in bond_lengths]
bond_lengths_median = [np.median(x) for x in bond_lengths]
bond_lengths_std = [np.std(x) for x in bond_lengths]
n_bonds = [len(x) for x in bonds_numeric]
# bond_data = {'bond_' + str(i):col for i, col in enumerate(np.transpose(bonds))}
# bond_data.update({'bonds_numeric':bonds_numeric, 'n_bonds':n_bonds})
bond_data = {'n_bonds': n_bonds, 'bond_lengths_mean': bond_lengths_mean,
'bond_lengths_std': bond_lengths_std, 'bond_lengths_median': bond_lengths_median}
bond_df = pd.DataFrame(bond_data)
structures = structures.join(bond_df)
# print(structures.head(20))
train = map_atom_info(train, 0, structures)
train = map_atom_info(train, 1, structures)
test = map_atom_info(test, 0, structures)
test = map_atom_info(test, 1, structures)
train_p_0 = train[['x_0', 'y_0', 'z_0']].values
train_p_1 = train[['x_1', 'y_1', 'z_1']].values
test_p_0 = test[['x_0', 'y_0', 'z_0']].values
test_p_1 = test[['x_1', 'y_1', 'z_1']].values
train['dist'] = np.linalg.norm(train_p_0 - train_p_1, axis=1)
test['dist'] = np.linalg.norm(test_p_0 - test_p_1, axis=1)
train['dist'] = 1 / (train['dist'] ** 3) # https://www.kaggle.com/vaishvik25/1-r-3-hyperpar-tuning
test['dist'] = 1 / (test['dist'] ** 3)
train['dist_x'] = (train['x_0'] - train['x_1']) ** 2
test['dist_x'] = (test['x_0'] - test['x_1']) ** 2
train['dist_y'] = (train['y_0'] - train['y_1']) ** 2
test['dist_y'] = (test['y_0'] - test['y_1']) ** 2
train['dist_z'] = (train['z_0'] - train['z_1']) ** 2
test['dist_z'] = (test['z_0'] - test['z_1']) ** 2
train['type_0'] = train['type'].apply(lambda x: x[0])
test['type_0'] = test['type'].apply(lambda x: x[0])
return train, test, structures
def _conv_sub_1d(self, data, filter, ds):
'''
performs 1d convolution followed by downsampling in real space, given data and filters in frequency domain.
This corresponds to multiplication followed by
periodization (when downsampling) or zeropadding (when upsampling). the returned signal is in real space.
inputs:
-------
- data: ndarray with shape (n_data, n_channels, data_len). data to be convolved given in the frequency domain
- filter: dict or ndarray type given in the frequency domain.
if filter_format is fourier_multires:
filter is dict type with the following keys: 'coef', 'filter_len'
filter['coef'] is assumed to be a rank 1 list of filters where each filter is rank 1
From the data length and filter['filter_len'], the ndarray with the same size with that of the data is found and convolved.
This dict type object filter is an output of _periodize_filter().
if filter_format is fourier_truncated
filter is dict type with the following keys: 'coef', 'filter_len', 'start'
filter['coef'] is assumed to be a rank 1 ndarray
- ds: downsampling factor exponent when represented in power of 2
outputs:
--------
- y_ds: convolved signal in real space followed by downsampling having shape (n_data, n_channels, data_output_len)
FIXME: understand the idea of wrapping around, and other questions in the comments
'''
n_data = data.shape[0]
n_channels = data.shape[1]
data_len = data.shape[2]
filter_format = self._filter_format
if isinstance(filter, dict):
if filter_format == 'fourier_multires':
# _periodize_filter() generates a set of filters whose lengths are filter_len/2^0, filter_len/2^1, filter_len/2^2, ...
# these filters are grouped into a rank 1 list. therefore, given the original size of the filter filter_len,
# and the length of the data, the length of the filter can be determined which can be found from the list
coef = filter['coef'][int(np.round(np.log2(filter['filter_len'] / data_len)))]
# make coef into rank 3 ndarray sized (1, 1, filter_len) for broadcasting
coef = coef[np.newaxis, np.newaxis, :]
yf = data * coef
elif filter_format == 'fourier_truncated':
# in this case, filter['coef'] is an ndarray
start = filter['start']
coef = filter['coef']
n_coef = len(coef)
if n_coef > data_len:
# if filter is larger than the given data, create a lowpass filter and periodize it
# FIXME: what is the basis of this idea?
start0 = start % filter['filter_len']
if (start0 + n_coef) <= filter['filter_len']:
rng = np.arange(start0, n_coef - 1).astype(int)
else:
rng = np.concatenate([np.arange(start0, filter['filter_len']), np.arange(n_coef + start0 - filter['filter_len'])], axis=0).astype(int)
lowpass = np.zeros(n_coef)
lowpass[rng < int(data_len / 2)] = 1
lowpass[rng == int(data_len / 2)] = 1/2
lowpass[rng == int(filter['filter_len'] - data_len / 2)] = 1/2
lowpass[rng > int(filter['filter_len'] - data_len / 2)] = 1
# filter and periodize
coef = np.reshape(coef * lowpass, [int(n_coef / data_len), data_len]).sum(axis=0)
# coef is rank 1
n_coef = len(coef)
coef = coef[np.newaxis, np.newaxis, :]
j = int(np.round(np.log2(n_coef / data_len)))
start = start % data_len
if start + n_coef <= data_len:
# filter support contained in one period, no wrap-around
yf = data[:, :, start:n_coef+start] * coef
else:
# filter support wraps around, extract both parts
yf = np.concatenate([data[:, :, start:], data[:, :, :n_coef + start - data_len]], axis=2) * coef
else:
# filter is ndarray type. perform fourier transform.
# filter_j is a fraction taken from filter to match length with data_len.
# if data_len is [10,11,12,13,14,15] and filter being range(100),
# filter_j would be [0, 1, 2, (3 + 98)/2, 99, 100].
# REVIEW: figure out why the shifting is done before multiplying.
# Perhaps related to fftshift?
# take only part of filter and shift it
filter_j = np.concatenate([filter[:int(data_len/2)],
[filter[int(data_len / 2)] / 2 + filter[int(-data_len / 2)] / 2],
filter[int(-data_len / 2 + 1):]], axis=0)
filter_j = filter_j[np.newaxis, np.newaxis, :] # shaped (1, 1, data_len)
yf = data * filter_j
# calculate the downsampling factor with respect to yf
dsj = ds + np.round(np.log2(yf.shape[2] / data_len))
assert(float(dsj).is_integer()), "dsj should be an integer"
if dsj > 0:
# downsample (periodize in Fourier)
# REVIEW: don't understand why reshape and sum things. Why is this downsampling in real space? (review 6.003 notes)
# I tested and see that this is correct. try running the following in a notebook:
# a = np.sin(np.linspace(0,100,10000)) + np.sin(np.linspace(0,300,10000)); af = np.fft.fft(a[np.newaxis, :]); af2 = np.reshape(af, [4,2500]).sum(axis=0); a2 = np.fft.ifft(af2)
# fig1,ax1 = plt.subplots(); fig2,ax2 = plt.subplots(); ax1.plot(a); ax2.plot(np.real(a2))
yf_ds = np.reshape(yf, [n_data, n_channels, int(2**dsj), int(np.round(yf.shape[2]/2**dsj))]).sum(axis=2)
elif dsj < 0:
# upsample (zero-pad in Fourier)
# note that this only happens for fourier_truncated filters, since otherwise
# filter sizes are always the same as the signal size
# also, we have to do one-sided padding since otherwise we might break
# continuity of Fourier transform
yf_ds = np.concatenate(yf, np.zeros(n_data, n_channels, (2**(-dsj)-1)*yf.shape[1]), axis=2)
else:
yf_ds = yf
if isinstance(filter, dict):
if filter_format == 'fourier_truncated':
# result has been shifted in frequency so that the zero frequency is actually at -filter.start+1
# always recenter if fourier_truncated
yf_ds = np.roll(yf_ds, filter['start'], axis=2)
y_ds = np.fft.ifft(yf_ds, axis=2) / 2**(ds/2)
# the 2**(ds/2) factor seems like normalization
return y_ds
async def process(self, json: JSONType) -> JSONType:
total_rebuffer = float(json['rebuffer']) / M_IN_K
# compute data
rebuffer_time = total_rebuffer - self.last_rebuffer_time
last_quality = self.last_quality
last_bit_rate = self.last_bit_rate
reward = (get_video_bit_rate(self.video, last_quality) / M_IN_K
- REBUF_PENALTY * rebuffer_time / M_IN_K
- SMOOTH_PENALTY * np.abs(get_video_bit_rate(self.video, last_quality)
- last_bit_rate) / M_IN_K)
# retrieve previous state
if len(self.s_batch) == 0:
state = [np.zeros((S_INFO, S_LEN))]
else:
state = np.array(self.s_batch[-1], copy=True)
# compute bandwidth measurement
bandwidth = max(float(json['bandwidth']), MIN_BW_EST_MBPS * M_IN_K)
chunk_fetch_time = float(json['last_fetch_time'])
# compute number of video chunks left
video_chunk_remain = get_video_chunks(self.video) - self.video_chunk_count
self.video_chunk_count += 1
# dequeue history record
state = np.roll(state, -1, axis=1)
next_video_chunk_sizes = []
for i in range(self.adim):
next_video_chunk_sizes.append(get_chunk_size(
self.video, i, self.video_chunk_count
))
total_buffer = float(json['buffer'])
# this should be S_INFO number of terms
try:
state[0, -1] = (
get_video_bit_rate(self.video, last_quality) /
get_max_video_bit_rate(self.video)
)
state[1, -1] = total_buffer / M_IN_K / BUFFER_NORM_FACTOR # s
state[2, -1] = bandwidth / M_IN_K / 8 # k byte / ms
state[3, -1] = float(chunk_fetch_time) / M_IN_K / BUFFER_NORM_FACTOR # 10 s
state[4, :self.adim] = np.array(next_video_chunk_sizes) / M_IN_K / M_IN_K # m byte
state[5, -1] = np.minimum(video_chunk_remain, CHUNK_TIL_VIDEO_END_CAP) / float(CHUNK_TIL_VIDEO_END_CAP)
print(state[:, -1])
except ZeroDivisionError:
if len(self.s_batch) == 0:
state = [np.zeros((S_INFO, S_LEN))]
else:
state = np.array(self.s_batch[-1], copy=True)
action_prob = self.actor.predict(np.reshape(state, (1, S_INFO, S_LEN)))
action_cumsum = np.cumsum(action_prob)
bit_rate = (action_cumsum > np.random.randint(1, RAND_RANGE) / float(RAND_RANGE)).argmax()
self.s_batch.append(state)
print(f"[Pensieve] > bit rate {bit_rate}")
self.last_rebuffer_time = total_rebuffer
self.last_bit_rate = get_video_bit_rate(self.video, last_quality)
self.last_quality = bit_rate
return {
'decision' : float(bit_rate),
}
def process(self, sweep):
mode = self.sensor_config.mode
if self.sweep == 0:
self.x_mm = utils.get_range_depths(self.sensor_config, self.session_info) * 1000
if mode == Mode.SPARSE:
self.num_sensors, point_repeats, self.data_len = sweep.shape
self.hist_env = np.zeros((self.num_sensors, self.data_len, self.image_buffer))
else:
self.data_len = sweep.size
self.num_sensors = 1
if len(sweep.shape) > 1:
self.num_sensors, self.data_len = sweep.shape
self.hist_env = np.zeros(
(self.num_sensors, self.data_len, self.image_buffer)
)
sweep_data = sweep.copy()
env = None
if mode == Mode.SPARSE:
env = sweep.mean(axis=1)
else:
env = np.abs(sweep_data)
for s in range(self.num_sensors):
self.hist_env[s, :, :] = np.roll(self.hist_env[s, :, :], 1, axis=1)
self.hist_env[s, :, 0] = env[s, :]
plot_data = {
"sweep_data": sweep_data,
"env_ampl": env,
"hist_env": self.hist_env,
"sensor_config": self.sensor_config,
"x_mm": self.x_mm,
"sweep": self.sweep,
"num_sensors": self.num_sensors,
"ml_plotting": True,
"ml_frame_data": None,
"prediction": None,
"prediction_hist": None,
"session_info": self.session_info,
}
plot_data["ml_frame_data"] = self.feature_process.feature_extraction(plot_data)
feature_map = plot_data["ml_frame_data"]["current_frame"]["feature_map"]
complete = plot_data["ml_frame_data"]["current_frame"]["frame_complete"]
if complete and self.evaluate and feature_map is not None:
if plot_data["ml_frame_data"]["frame_info"].get("time_series", 1) > 1:
feature_map = ml_helper.convert_time_series(
plot_data["ml_frame_data"]["current_frame"]["feature_map"],
plot_data["ml_frame_data"]["frame_info"]
)
try:
plot_data["prediction"] = self.evaluate(feature_map)
except Exception as e:
print(e)
plot_data["ml_frame_data"]["current_frame"]["frame_complete"] = False
return plot_data
prediction_label = plot_data["prediction"]["prediction"]
plot_data["ml_frame_data"]["frame_list"][-1]["label"] = prediction_label
if self.prediction_hist is None:
self.prediction_hist = np.zeros((plot_data["prediction"]["number_labels"],
self.hist_len))
predictions = plot_data["prediction"]["label_predictions"]
self.prediction_hist = np.roll(self.prediction_hist, 1, axis=1)
for key in predictions:
pred, idx = predictions[key]
self.prediction_hist[idx, 0] = pred
plot_data["prediction_hist"] = self.prediction_hist
self.sweep += 1
return plot_data
def generate(
c,
fs,
r,
s,
L,
beta=None,
reverberation_time=None,
nsample=None,
mtype=mtype.omnidirectional,
order=-1,
dim=3,
orientation=None,
hp_filter=True,
):
"""Generate room impulse response.
Parameters
----------
c : float
Sound velocity in m/s. Usually between 340 and 350.
fs : float
Sampling frequency in Hz.
r : array_like
1D or 2D array of floats, specifying the :code:`(x, y, z)` coordinates of the receiver(s)
in m. Must be of shape :code:`(3,)` or :code:`(x, 3)` where :code:`x`
is the number of receivers.
s : array_like
1D array of floats specifying the :code:`(x, y, z)` coordinates of the source in m.
L : array_like
1D array of floats specifying the room dimensions :code:`(x, y, z)` in m.
beta : array_like, optional
1D array of floats specifying the reflection coefficients
.. code-block::
[beta_x1, beta_x2, beta_y1, beta_y2, beta_z1, beta_z2]
or
.. code-block::
[(beta_x1, beta_x2), (beta_y1, beta_y2), (beta_z1, beta_z2)]
Must be of shape :code:`(6,)` or :code:`(3, 2)`.
You must define **exactly one** of :attr:`beta` or
:attr:`reverberation_time`.
reverberation_time : float, optional
Reverberation time (T_60) in seconds.
You must define **exactly one** of :attr:`beta` or
:attr:`reverberation_time`.
nsample : int, optional
number of samples to calculate, default is :code:`T_60 * fs`.
mtype : mtype, optional
Microphone type, one of :class:`mtype`.
Defaults to :class:`mtype.omnidirectional`.
order : int, optional
Reflection order, default is :code:`-1`, i.e. maximum order.
dim : int, optional
Room dimension (:code:`2` or :code:`3`), default is :code:`3`.
orientation : array_like, optional
1D array direction in which the microphones are pointed, specified
using azimuth and elevation angles (in radians), default is
:code:`[0, 0]`.
hp_filter : boolean, optional
Enable high-pass filter, the high-pass filter is enabled by default.
Returns
-------
h : array_like
The room impulse response, shaped `(nsample, len(r))`
Example
-------
>>> import rir_generator
>>> h = rir_generator.generate(
... c=340,
... fs=16000,
... r=[
... [2, 1.5, 2],
... [2, 1.5, 3]
... ],
... s=[2, 3.5, 2],
... L=[5, 4, 6],
... reverberation_time=0.4,
... nsample=4096,
... mtype=rir_generator.mtype.omnidirectional,
... )
"""
r = np.atleast_2d(np.asarray(r, dtype=np.double)).T.copy()
assert r.shape[0] == 3
L = np.asarray(L, dtype=np.double)
assert L.shape == (3,)
s = np.asarray(s, dtype=np.double)
assert s.shape == (3,)
if beta is not None:
beta = np.asarray(beta, dtype=np.double)
assert beta.shape == (6,) or beta.shape == (3, 2)
beta = beta.reshape(3, 2)
if (r > L[:, None]).any() or (r < 0).any():
raise ValueError("r is outside the room")
if (s > L).any() or (s < 0).any():
raise ValueError("s is outside the room")
# Make sure orientation is a 2-element array, even if passed a single value
if orientation is None:
orientation = np.zeros(2, dtype=np.double)
orientation = np.atleast_1d(np.asarray(orientation, dtype=np.double))
if orientation.shape == (1,):
orientation = np.pad(orientation, (0, 1), "constant")
assert orientation.shape == (2,)
assert order >= -1
assert dim in (2, 3)
# Volume of room
V = np.prod(L)
# Surface area of walls
A = L[::-1] * np.roll(L[::-1], 1)
if beta is not None:
alpha = np.sum(np.sum(1 - beta ** 2, axis=1) * np.sum(A))
reverberation_time = max(
24 * np.log(10.0) * V / (c * alpha),
0.128,
)
elif reverberation_time is not None:
if reverberation_time != 0:
S = 2 * np.sum(A)
alpha = 24 * np.log(10.0) * V / (c * S * reverberation_time)
if alpha > 1:
raise ValueError(
"Error: The reflection coefficients cannot be "
"calculated using the current room parameters, "
"i.e. room size and reverberation time. Please "
"specify the reflection coefficients or change the "
"room parameters."
)
beta = np.full((3, 2), fill_value=np.sqrt(1 - alpha), dtype=np.double)
else:
beta = np.zeros((3, 2), dtype=np.double)
else:
raise ValueError(
"Error: Specify either RT60 (ex: reverberation_time=0.4) or "
"reflection coefficients (beta=[0.3,0.2,0.5,0.1,0.1,0.1])"
)
if nsample is None:
nsample = int(reverberation_time * fs)
if dim == 2:
beta[-1, :] = 0
numMics = r.shape[1]
imp = np.zeros((nsample, numMics), dtype=np.double)
p_imp = rir.ffi.cast("double*", rir.ffi.from_buffer(imp))
p_r = rir.ffi.cast("double*", rir.ffi.from_buffer(r))
p_s = rir.ffi.cast("double*", rir.ffi.from_buffer(s))
p_L = rir.ffi.cast("double*", rir.ffi.from_buffer(L))
p_beta = rir.ffi.cast("double*", rir.ffi.from_buffer(beta))
p_orientation = rir.ffi.cast("double*", rir.ffi.from_buffer(orientation))
rir.lib.computeRIR(
p_imp,
float(c),
float(fs),
p_r,
numMics,
nsample,
p_s,
p_L,
p_beta,
mtype.value,
order,
p_orientation,
1 if hp_filter else 0,
)
return imp
def find_peaks_noise(win, t, x):
"""
Find peaks in the data via moving polynomial regression
Parameters :
- win : Float. The time window over which to regress.
- t : Float array. The time series.
- x : Float 2D array. The dependent variables.
Returns :
- t_peaks : the times of peaks
- x_peaks : the values of peaks
- lr : the likelihood ratios
"""
# Fit a 2nd degree polynomial on a window of like 1 month
# Actually we want to do all this only on the I data right ?
# So we're only passing the I data in x
n = np.shape(t)[0]
#k = np.shape(x)[1]
k = 1
x.shape = (n, k)
t_peaks = list()
x_peaks = list()
ends = np.zeros([n, k])
lra = np.zeros([n, k])
sel = np.zeros([n, k])
l01a = np.zeros([n, 2, k])
tl = list()
x0l = list()
x1l = list()
for i, ti in enumerate(t):
start = i
try:
end = np.where(
t > ti + win)[0][0] # first index that passes the window
except IndexError:
# we've reached the last window
break
ends[i] = end
twin, xwin = t[start:end], x[start:end]
p0, res0, _, _, _ = np.polyfit(twin, xwin, 1, full=True)
p1, res1, _, _, _ = np.polyfit(twin, xwin, 2, full=True)
sig0 = np.sqrt(res0 / (end - start))
sig1 = np.sqrt(res1 / (end - start))
# need to repeat t so that dimensiosn are ok
twin_r = np.repeat(twin[:, np.newaxis], k, axis=1)
l0a = 1 / (np.sqrt(2 * np.pi) * sig0) \
* np.exp(- (xwin - p0[0] * twin_r - p0[1]) ** 2 / (2 * sig0 ** 2))
l1a = 1 / (np.sqrt(2 * np.pi) * sig1) \
* np.exp(- (xwin - p1[0] * twin_r ** 2 - p1[1] * twin_r - p1[2]) ** 2 / (2 * sig1 ** 2)) # likelihood ratio array
# compute the statistic
l0 = np.prod(l0a, axis=0)
l1 = np.prod(l1a, axis=0)
lr = -2 * np.sum(np.log(l0a) - np.log(l1a), axis=0)
# with a type 1 error of 1 % : compare to 6.64
#maxi = np.argmax(xwin, axis=0)
#tmax = twin_r[maxi]
#xmax = xwin[maxi]
# the square poly fits much better and is concave
#sel_polyfit = np.logical_and(lr > 6.64, p1[0] < 0)
sel_polyfit = np.logical_and(lr > 100, p1[0] < 0)
lra[i] = lr
sel[i] = sel_polyfit
l01a[i, 0] = l0
l01a[i, 1] = l1
tl.append(twin)
x0l.append(p0[0] * twin + p0[1])
x1l.append(p1[0] * twin**2 + p1[1] * twin + p1[2])
lows = np.where(
np.logical_and(np.logical_not(sel[:-1]),
np.roll(sel, shift=-1, axis=0)[:-1]))
highs = np.where(
np.logical_and(sel[:-1],
np.logical_not(np.roll(sel, shift=-1, axis=0)[:-1])))
highs = (ends[highs].astype(int), highs[1])
# problem : has to work if k > 1
if t[highs[0][0]] < t[lows[0][0]] + win:
highs = (highs[0][1:], highs[1][1:])
if t[lows[0][-1]] > t[highs[0][-1]]:
lows = (lows[0][:-1], lows[1][:-1])
maxi = np.array([
l0 + np.argmax(x[l0:h0, l1], axis=0)
for (l0, h0, l1, h1) in zip(lows[0], highs[0], lows[1], highs[1])
if (l1 == h1) #and (t[h0] - t[l0] > win)
])
t_peaks = t[maxi]
x_peaks = x[maxi]
#t_peaks = [ np.append(l, tmax[j]) if selection[j] else l for j, l in enumerate(t_peaks) ]
#x_peaks = [ np.append(l, xmax[j]) if selection[j] else l for j, l in enumerate(x_peaks) ]
# pas mal mais il vaut mieux se baser sur des points successifs ayant le fit
# et prendre que un point là-dessus ?
return t_peaks, x_peaks, lra, lows, highs, maxi, sel #, l01a, tl, x0l, x1l
def generator(self, signal):
"""Generator that yields correlation results each hyperplane of the
signal, for each basis function.
signal: An iterable of hyperplanes of the signal (arrays of shape `shape[1:]`
(or `shape[1:]+(n_fields,)`)), or an iterator over such an iterable.
---
Yield: An hyperplane of the correlation results perpendicular to the slowest
varrying dimension (e.g. YX plane of a ZYX image) + a last dimension of size B
that contains one coefficient per basis function, in the same order as the basis.
"""
N = len(self.shape)
if np.iterable(signal):
it_signal = iter(signal)
else:
it_signal = signal
# if self.n_fields is None:
# assert signal.shape == self.shape
# else:
# assert signal.shape == self.shape + (self.n_fields,)
thickness = len(self.applicability[0])
halfth = thickness // 2
#ensures the storage is zero everywhere
for value in self._res.values():
value[:] = 0
#t_hyperplane = 0
#t_out = 0
for z in range(self.shape[0] + thickness):
# Internally, a new hyperplane overwrites the hyperplane that was
# input thickness-of-the-band planes ago.
rollingZ = z % thickness
#t_hp = time.time()
if z < self.shape[0]:
# Store the hyperplane in the band
self._res[(0, ) * N][rollingZ] = next(it_signal)
# Perform correlation on all the dimensions of the hyperplane,
# fastest varrying dimension first
for operation in self.planeops:
self._perform_an_hyperplane_correlation(
rollingZ, **operation)
else:
# if close to the edge, just erase the current hyperplane everywhere
for value in self._res.values():
value[rollingZ] = 0
#t_hyperplane += time.time() - t_hp
if z >= halfth and z - halfth < self.shape[0]:
#t_o = time.time()
# Prepare output
if self.n_fields is None:
out = np.empty(self.shape[1:] + self.basis.shape[1:],
dtype=self.dtype)
else:
out = np.empty(self.shape[1:] + (self.n_fields, ) +
self.basis.shape[1:],
dtype=self.dtype)
#roll monomial and applicability to be in phase with the current plane
rollshift = z + 1
X = np.ascontiguousarray(np.roll(self.X[0].ravel(), rollshift))
app = np.ascontiguousarray(
np.roll(self.applicability[0].ravel(), rollshift))
# Perform correlation in the slowest varrying dimension (along the
# thinckness of the band), in the order of the basis
for b, index in enumerate(self.basis.T):
prior = np.copy(index)
prior[0] = 0
prior = tuple(prior.tolist())
kernel = (app * X**index[0]).reshape(
self.X[0].shape).astype(self.dtype)
#kernel = (app * X**index[0]).astype(self.dtype)
out[..., b] = (self._res[prior] * kernel).sum(axis=0)
#out[...,b] = np.dot(np.moveaxis(self._res[prior], 0, -1), kernel)
#t_out += time.time() - t_o
yield out
def neighbors(arr, x, y, n):
arr = np.roll(np.roll(arr, shift=-x + n // 2, axis=0),
shift=-y + n // 2,
axis=1)
return arr[:n, :n]
def test_play():
f2 = open(path2, 'a')
total_reward = 0
for j in range(3):
obs4steps = np.zeros((4, 84, 84), dtype=np.float32)
obs = env.reset()
obs = cv2.cvtColor(obs, cv2.COLOR_RGB2BGR)
obs = obs[0:170, 0:160]
obs = cv2.resize(obs, (obs.shape[1] * 2, obs.shape[0] * 2))
#顕著性検出,最も顕著性が高い座標を返す
max_loc = saliency(obs)
y1 = 0 if max_loc[1] - h < 0 else max_loc[1] - h
y2 = max_loc[1] + h if max_loc[1] + h < obs.shape[
0] else obs.shape[0] - 1
x1 = 0 if max_loc[0] - w < 0 else max_loc[0] - w
x2 = max_loc[0] + w if max_loc[0] + w < obs.shape[
1] else obs.shape[1] - 1
#print y1,y2,x1,x2
#切り出し
center = obs[y1:y2, x1:x2]
#グラデーションぼかし
obs = blur(x1, y1, x2, y2, 50, 0, obs)
#print obs.shape
#print center.shape
#貼り付け
obs[y1:y2, x1:x2] = center
obs = obs[:, :, 0]
obs = (misc.imresize(obs, (110, 84)))[110 - 84 - 8:110 - 8, :]
obs4steps[0] = obs
r = 0
done = False
R = 0
t = 0
while not done:
env.render()
action = agent.act(obs4steps)
obs, r, done, _ = env.step(action)
obs = cv2.cvtColor(obs, cv2.COLOR_RGB2BGR)
obs = obs[0:170, 0:160]
obs = cv2.resize(obs, (obs.shape[1] * 2, obs.shape[0] * 2))
#顕著性検出,最も顕著性が高い座標を返す
max_loc = saliency(obs)
y1 = 0 if max_loc[1] - h < 0 else max_loc[1] - h
y2 = max_loc[1] + h if max_loc[1] + h < obs.shape[
0] else obs.shape[0] - 1
x1 = 0 if max_loc[0] - w < 0 else max_loc[0] - w
x2 = max_loc[0] + w if max_loc[0] + w < obs.shape[
1] else obs.shape[1] - 1
#切り出し
center = obs[y1:y2, x1:x2]
#グラデーションぼかし
obs = blur(x1, y1, x2, y2, 50, 0, obs)
#貼り付け
obs[y1:y2, x1:x2] = center
obs = obs[:, :, 0]
obs = (misc.imresize(obs, (110, 84)))[110 - 84 - 8:110 - 8, :]
obs4steps = np.roll(obs4steps, 1, axis=0)
obs4steps[0] = obs
R += r
t += 1
print('test play:', j, 'R:', R)
total_reward += R
f2.write(str(total_reward / 3) + "\n")
f2.close()
def prepare_displacement_matrices_homogeneous(A1,
b1,
A2,
b2,
displacement=None):
"""Compute matrices used for displacement estimation as defined by equations
(7.32) and (7.33) in Gunnar Farnebäck's thesis "Polynomial Expansion for
Orientation and Motion Estimation". Here we suppose an homogenous translation.
A1,b1: Local polynomial expension coefficients at time 1. A1 is a N+2
dimensional array, where the first N indices indicates the position in the
signal and the last two contains the matrix for each point. In the same way, b1
is a N+1 dimensional array. Such arrays can be obtained via QuadraticToAbc.
A2,b2: Local polynomial expension coefficients at time 2.
displacement: The global translation vector from time 1 to time 2.
----
Returns
A: Advected average of A1 and A2 matrices (Eq. 7.32)
Delta_b: advected difference of b2 and b1 (Eq. 7.33)
"""
assert A1.shape == A2.shape
assert A1.shape[:-1] == b1.shape
assert A1.shape[-1] == b1.shape[-1]
assert b1.shape == b2.shape
shape = A1.shape[:-2]
# N is the dimensionality of the signal we consider here (it might be
# an hyperplane of the original signal), not the rank of the matrices and
# vectors.
N = len(shape)
if displacement is None:
displacement = np.zeros(N, dtype=A1.dtype)
assert displacement.shape == (N, )
# Integral part of the backward displacement vector
displ = -np.rint(displacement).astype(np.int64)
# Advect back A2 and b2 by rolling
A = np.roll(A2, displ, axis=tuple(range(N)))
Delta_b = -0.5 * np.roll(b2, displ, axis=tuple(range(N)))
#take care of the margins by repeating the last available element of A2 or b2
for dim, d in enumerate(displ):
if d >= 0:
# Use only A1 where A2 is not available
A[(slice(None, None), ) * dim +
(slice(0, d), )] = A1[(slice(None, None), ) * dim +
(slice(0, d), )]
# Use only b1 where b2 is not available (aims for a displacement equal to the homogeneous input)
Delta_b[(slice(None, None), ) * dim +
(slice(0, d), )] = -0.5 * b1[(slice(None, None), ) * dim +
(slice(0, d), )]
# Use the last available element of b2
#Delta_b[(slice(None,None),)*dim + (slice(0,d),)] = -b2[(slice(None,None),)*dim + (slice(0,1),)]
else:
# Use only A1 where A2 is not available
A[(slice(None, None), ) * dim +
(slice(d, None), )] = A1[(slice(None, None), ) * dim +
(slice(d, None), )]
# Use only b1 where b2 is not available (aims for a displacement equal to the homogeneous input)
Delta_b[(slice(None, None), ) * dim +
(slice(d, None), )] = -0.5 * b1[
(slice(None, None), ) * dim + (slice(d, None), )]
# Use the last available element of b2
#Delta_b[(slice(None,None),)*dim + (slice(-d,None),)] = -0.5*b2[(slice(None,None),)*dim + (slice(-1,None),)]
#Advected average for A1 and A2
A += A1
A *= 0.5
# Advected difference for b1 and b2, to which we add back the forward
# rounded a priori displacement. Here we have to expand the displacement
# vector to the same rank as the original signal dimension.
df = np.zeros(A1.shape[-1], A1.dtype)
df[-N:] = -displ #displacement
Delta_b += 0.5 * b1 + A @ df
return A, Delta_b
y1 = 0 if max_loc[1] - h < 0 else max_loc[1] - h
y2 = max_loc[1] + h if max_loc[1] + h < obs.shape[
0] else obs.shape[0] - 1
x1 = 0 if max_loc[0] - w < 0 else max_loc[0] - w
x2 = max_loc[0] + w if max_loc[0] + w < obs.shape[
1] else obs.shape[1] - 1
#切り出し
center = obs[y1:y2, x1:x2]
#グラデーションぼかし
obs = blur(x1, y1, x2, y2, 30, 0, obs)
#貼り付け
obs[y1:y2, x1:x2] = center
cv2.imwrite(path4 + str(j) + ".png", obs)
obs = obs[:, :, 0]
obs = (misc.imresize(obs, (110, 84)))[110 - 84 - 8:110 - 8, :]
obs4steps = np.roll(obs4steps, 1, axis=0)
obs4steps[0] = obs
R += reward
t += 1
frame += 1
print('episode:', i, 'R:', R)
print('time:', time.time() - start)
print('frame:', frame)
agent.stop_episode_and_train(obs4steps, reward, done)
f.write(str(R) + "\n")
f.close()
#if(i % 50 == 0):
# agent.save('saliency-MsPacman-4')
print('Finished')
#agent.save('saliency-MsPacman-4')
def update():
global lines_prog, data, t, frame_num, colors, color_perc_list, \
show_imgs_for_colors, p, pfft, data_fft, axis_fft, RATE, phist_colors
# read frame
img, frame2 = read_frame(0.5)
# calatulate color percentage
color_prec_frame = [] # list of color percentages for current frame
imgs = img # save orginal image
index = 0
for color, threshold in colors:
color_pers_i, img = percent_color_singel(img, color=color, threshold=threshold, disp= str(color))
color_prec_frame.append(color_pers_i)
imgs = np.hstack((imgs,img))
index += 1
if show_imgs_for_colors == 1:
#images_per_row = 2
#cv2.imshow( "ALL_1", np.hstack(imgs))
cv2.imshow( "ALL_1", imgs)
# for x in enumerate(pq_images):
# #pimg.image(x)
# x.setImage(imgs[i])
#x.setData(imgs[i])
# add color from frame the last frames perc list
color_perc_list = np.roll(color_perc_list, -1, axis=1)
color_perc_list[:,-1] = color_prec_frame
# update data for line Progration
for i, x in enumerate(lines_prog):
#print(color_perc_list[i,:])
x.setData(color_perc_list[i,:])
# map(lambda x,y: x.setData(y), lines_prog, color_perc_list.tolist())
# update RGB color space histogram and set plot data
for i, x in enumerate(phist):
histr = cv2.calcHist([frame2], [i], None, [256], [0, 256])
histr = cv2.normalize(histr,histr)
#print(np.shape(histr))
x.setData(np.reshape(histr, np.shape(histr)[0]))
# update fft and set data for plot
for i, x in enumerate(pfft):
# calc fft
data_fft = color_perc_list[i,:]
fft_data=FFT_AMP(data_fft)
axis_pfft=np.fft.fftfreq(len(data_fft), d=1.0/RATE)
#plot data
x.setData(x=np.abs(axis_fft), y=fft_data)
# update lab colorspace histogram and set data for plot
frame2Lab = cv2.cvtColor(frame2, cv2.COLOR_BGR2LAB)
for i, x in enumerate(phist_lab):
histr = cv2.calcHist([frame2Lab], [i], None, [256], [0, 256])
histr = cv2.normalize(histr,histr)
#print(np.shape(histr))
x.setData(np.reshape(histr, np.shape(histr)[0]))
# calc frame rate
if frame_num%10 == 0:
elapsed = time.time() - t
print("fps: " + str(10/elapsed))
t = time.time()
app.processEvents() ## force complete redraw for every plot