def correltrack(data,
start=0,
avgover=10,
pixelsize=70.0,
centersize=7,
centroidfrac=1.5):
cs = centersize
shp = [d for d in data.shape if d > 1]
nsteps = long((shp[2] - start) / avgover)
shh = (shp[0] / 2, shp[1] / 2)
xctw = np.zeros((2 * centersize + 1, 2 * centersize + 1, nsteps))
shifts = []
i1 = data[:, :, start:start + avgover].squeeze().mean(axis=2)
I1 = fftn(i1)
for i in range(nsteps):
xc = abs(
ifftshift(
ifftn(I1 *
ifftn(data[:, :, start + i * avgover:start +
(i + 1) * avgover].squeeze().mean(axis=2)))))
xct = xc - xc.min()
xct = (xct -
xct.max() / centroidfrac) * (xct > xct.max() / centroidfrac)
xctw[:, :, i] = xct[shh[0] - cs:shh[0] + cs + 1,
shh[1] - cs:shh[1] + cs + 1]
shifts.append(scipy.ndimage.measurements.center_of_mass(xctw[:, :, i]))
sh = np.array(shifts)
t = start + np.arange(nsteps) * avgover
sh = pixelsize * (sh - sh[0])
return t, sh, xctw
def correlateFrames(A, B):
A = A.squeeze()/A.mean() - 1
B = B.squeeze()/B.mean() - 1
X, Y = np.mgrid[0.0:A.shape[0], 0.0:A.shape[1]]
C = ifftshift(np.abs(ifftn(fftn(A)*ifftn(B))))
Cm = C.max()
Cp = np.maximum(C - 0.5*Cm, 0)
Cpsum = Cp.sum()
x0 = (X*Cp).sum()/Cpsum
y0 = (Y*Cp).sum()/Cpsum
return x0 - A.shape[0]/2, y0 - A.shape[1]/2, Cm, Cpsum
def correlateFrames(A, B):
A = A.squeeze() / A.mean() - 1
B = B.squeeze() / B.mean() - 1
X, Y = np.mgrid[0.0:A.shape[0], 0.0:A.shape[1]]
C = ifftshift(np.abs(ifftn(fftn(A) * ifftn(B))))
Cm = C.max()
Cp = np.maximum(C - 0.5 * Cm, 0)
Cpsum = Cp.sum()
x0 = (X * Cp).sum() / Cpsum
y0 = (Y * Cp).sum() / Cpsum
return x0 - A.shape[0] / 2, y0 - A.shape[1] / 2, Cm, Cpsum
def calcCorrShift(im1, im2):
im1 = im1 - im1.mean()
im2 = im2 - im2.mean()
xc = np.abs(ifftshift(ifftn(fftn(im1) * ifftn(im2))))
xct = (xc - xc.max() / 1.1) * (xc > xc.max() / 1.1)
print((xct.shape))
#figure(1)
#imshow(xct)
#dx, dy = ndimage.measurements.center_of_mass(xct)
#print np.where(xct==xct.max())
dx, dy = np.where(xct == xct.max())
return dx[0] - im1.shape[0] / 2, dy[0] - im1.shape[1] / 2
def setIllumPattern(pattern, z0):
global illPattern, illZOffset, illPCache
sx, sy = pattern.shape
psx, psy, sz = interpModel.shape
il = np.zeros([sx,sy,sz], 'f')
il[:,:,sz/2] = pattern
ps = np.zeros_like(il)
if sx > psx:
ps[(sx/2-psx/2):(sx/2+psx/2), (sy/2-psy/2):(sy/2+psy/2), :] = interpModel
else:
ps[:,:,:] = interpModel[(psx/2-sx/2):(psx/2+sx/2), (psy/2-sy/2):(psy/2+sy/2), :]
ps= ps/ps[:,:,sz/2].sum()
illPattern = abs(ifftshift(ifftn(fftn(il)*fftn(ps)))).astype('f')
illPCache = None
def propagate(self, F, z):
""" Propagate a complex pupil, F, a distance z from the nominal focus and return the electric field amplitude
Parameters
==========
F : 2D array
complex pupil
z : float
distance in nm to propagate
"""
pf = self.propFac*float(z)
fs = F*self.pfm*(np.cos(pf) + j*np.sin(pf))
self._F[:] = ifftshift(fs)
self._plan_F_f()
return fftshift(self._f/np.sqrt(self._f.size))
def propagate_r(self, f, z):
"""
Backpropagate an electric field distribution, f, at defocus z to the nominal focus and return the complex pupil
Parameters
----------
f : 2D array
complex electric field amplitude
z : float
nominal distance of plane from focus in nm
Returns
-------
"""
self._f[:] = fftshift(f)
self._plan_f_F()
pf = -self.propFac*float(z)
return (ifftshift(self._F)*(np.cos(pf)+j*np.sin(pf)))/np.sqrt(self._f.size)
def correltrack2(data,
start=0,
avgover=10,
pixelsize=70.0,
centersize=15,
centroidfac=0.6,
roi=[0, None, 0, None]):
cs = centersize
shp = [d for d in data.shape if d > 1]
nsteps = long((shp[2] - start) / avgover)
xctw = np.zeros((2 * centersize + 1, 2 * centersize + 1, nsteps))
shifts = []
if avgover > 1:
ref = data[:, :, start:start + avgover].squeeze().mean(axis=2)
else:
ref = data[:, :, start].squeeze()
ref = ref[roi[0]:roi[3], roi[1]:roi[3]]
refn = ref / ref.mean() - 1
Frefn = fftn(refn)
shh = (ref.shape[0] / 2, ref.shape[1] / 2)
for i in range(nsteps):
comp = data[:, :,
start + i * avgover:start + (i + 1) * avgover].squeeze()
if len(comp.shape) > 2:
comp = comp.mean(axis=2)
comp = comp[roi[0]:roi[3], roi[1]:roi[3]]
compn = comp / comp.mean() - 1
xc = ifftshift(np.abs(ifftn(Frefn * ifftn(compn))))
xcm = xc.max()
xcp = np.maximum(xc - centroidfac * xcm, 0)
xctw[:, :, i] = xcp[shh[0] - cs:shh[0] + cs + 1,
shh[1] - cs:shh[1] + cs + 1]
shifts.append(scipy.ndimage.measurements.center_of_mass(xctw[:, :, i]))
sh = np.array(shifts)
t = start + np.arange(nsteps) * avgover
sh = pixelsize * (sh - sh[0])
return t, sh, xctw
def compare(self):
d = 1.0 * self.scope.pa.dsa.squeeze()
dm = d / d.mean() - 1
#find x-y drift
C = ifftshift(np.abs(ifftn(fftn(dm) * self.FA)))
Cm = C.max()
Cp = np.maximum(C - 0.5 * Cm, 0)
Cpsum = Cp.sum()
dx = (self.X * Cp).sum() / Cpsum
dy = (self.Y * Cp).sum() / Cpsum
ds = ndimage.shift(dm, [-dx, -dy]) * self.mask
#print A.shape, As.shape
ds_A = (ds - self.refA)
return dx, dy, self.deltaZ * np.dot(ds_A.ravel(), self.dz) * self.dzn
def compare(self):
d = 1.0*self.scope.pa.dsa.squeeze()
dm = d/d.mean() - 1
#find x-y drift
C = ifftshift(np.abs(ifftn(fftn(dm)*self.FA)))
Cm = C.max()
Cp = np.maximum(C - 0.5*Cm, 0)
Cpsum = Cp.sum()
dx = (self.X*Cp).sum()/Cpsum
dy = (self.Y*Cp).sum()/Cpsum
ds = ndimage.shift(dm, [-dx, -dy])*self.mask
#print A.shape, As.shape
ds_A = (ds - self.refA)
return dx, dy, self.deltaZ*np.dot(ds_A.ravel(), self.dz)*self.dzn
def correlateAndCompareFrames(A, B):
A = A.squeeze() / A.mean() - 1
B = B.squeeze() / B.mean() - 1
X, Y = np.mgrid[0.0:A.shape[0], 0.0:A.shape[1]]
C = ifftshift(np.abs(ifftn(fftn(A) * ifftn(B))))
Cm = C.max()
Cp = np.maximum(C - 0.5 * Cm, 0)
Cpsum = Cp.sum()
x0 = (X * Cp).sum() / Cpsum
y0 = (Y * Cp).sum() / Cpsum
dx, dy = x0 - A.shape[0] / 2, y0 - A.shape[1] / 2
As = ndimage.shift(A, [-dx, -dy])
#print A.shape, As.shape
return (As - B).mean(), dx, dy
def correlateAndCompareFrames(A, B):
A = A.squeeze()/A.mean() - 1
B = B.squeeze()/B.mean() - 1
X, Y = np.mgrid[0.0:A.shape[0], 0.0:A.shape[1]]
C = ifftshift(np.abs(ifftn(fftn(A)*ifftn(B))))
Cm = C.max()
Cp = np.maximum(C - 0.5*Cm, 0)
Cpsum = Cp.sum()
x0 = (X*Cp).sum()/Cpsum
y0 = (Y*Cp).sum()/Cpsum
dx, dy = x0 - A.shape[0]/2, y0 - A.shape[1]/2
As = ndimage.shift(A, [-dx, -dy])
#print A.shape, As.shape
return (As -B).mean(), dx, dy
def propagate(self, F, z):
"""
Propagate a complex pupil, F, a distance z from the nominal focus and return the electric field amplitude
Parameters
==========
F : 2D array
complex pupil
z : float
distance in nm to propagate
"""
pf = self.propFac*float(z)
r = max(self.appR*(1 -self.apertureZGrad*z), 0)
M = (self.x*self.x + self.y*self.y) < (r*r)
fs = F*M*self.pfm*(np.cos(pf) + j*np.sin(pf))
self._F[:] = fftshift(fs)
self._plan_F_f()
return ifftshift(self._f/np.sqrt(self._f.size))
def propagate(self, F, z):
return ifftshift(ifftn(F*np.exp(self.propFac*z)))
def correction_light(I, method, show_light, mask=None):
"""Corrige la derive eclairement
:I: array_like ou iplimage
:method: 'polynomial' or 'frequency'
:show_light: option affiche correction (true|false)
:mask: array de zone non interet
:returns: iplimage 32bit
"""
from progress import *
import Tkinter
if type(I) == cv.iplimage:
if I.nChannels == 3:
if method == 'None':
I = RGB2L(I)
I = cv2array(I)[:, :, 0]
I = pymorph.hmin(I, 15, pymorph.sedisk(3))
I = array2cv(I)
cv.EqualizeHist(I, I)
return I
I = RGB2L(I)
I_32bit = cv.CreateImage(cv.GetSize(I), cv.IPL_DEPTH_32F, 1)
cv.ConvertScale(I, I_32bit, 3000.0, 0.0)
I = cv.CloneImage(I_32bit)
I = cv2array(I)[:, :, 0]
elif len(I.shape) == 3:
I = (I[:, :, 0] + I[:, :, 0] + I[:, :, 0])\
/ 3.0 # A modifier: non utiliser dans notre cas
elif method == 'None':
I = array2cv(I)
cv.EqualizeHist(I, I)
return I
I = np.log(I + 10 ** (-6))
(H, W) = np.shape(I)
I_out = I * 0 + 10 ** (-6)
if method == 'polynomial':
## I = M.A avec A coeff. du polynome
I_flat = I.flatten()
degree = 3
print("modification degree 3")
#degree du polynome
nb_coeff = (degree + 1) * (degree + 2) / 2 # nombre coefficient
[yy, xx] = np.meshgrid(np.arange(W, dtype=np.float64),
np.arange(H, dtype=np.float64))
if mask is not None:
xx[mask] = 0
yy[mask] = 0
# Creation de M
try:
M = np.zeros((H * W, nb_coeff), dtype=np.float64)
except MemoryError:
print MemoryError
return MemoryError
i, j = 0, 0 # i,j degree de x,y
#Bar progression
bar = Tkinter.Tk(className='Correcting Light...')
m = Meter(bar, relief='ridge', bd=3)
m.pack(fill='x')
m.set(0.0, 'Starting correction...')
for col in np.arange(nb_coeff):
M[:, col] = (xx.flatten() ** i) * (yy.flatten() ** j)
i += 1
m.set(0.5 * float(col) / (nb_coeff - 1))
if i + j == degree + 1:
i = 0
j += 1
# Resolution au sens des moindres carree: pseudo-inverse
try:
M = pl.pinv(M)
A = np.dot(M, I_flat)
except ValueError:
return ValueError
# Calcul de la surface
i, j = 0, 0
surface = np.zeros((H, W), dtype=np.float64)
for cmpt in np.arange(nb_coeff):
surface += A[cmpt] * (xx ** i) * (yy ** j) # forme quadratique
i += 1
m.set(0.5 + 0.5 * float(cmpt) / (nb_coeff - 1))
if i + j == degree + 1:
i = 0
j += 1
bar.destroy()
I_out = np.exp(I / surface)
light = surface
elif method == 'frequency':
Rx, Ry = 2, 2
# zero padding
N = [H, W]
filtre = np.zeros((N[1], N[0]))
centre_x = round(N[0] / 2)
centre_y = round(N[1] / 2)
print("FFT2D...")
I_fourier = pl.fftshift(pl.fft2(I, N))
# Gaussian filter
[xx, yy] = np.meshgrid(np.arange(N[0], dtype=np.float),
np.arange(N[1], dtype=np.float))
filtre = np.exp(-2 * ((xx - centre_x) ** 2 + (yy - centre_y) ** 2) /
(Rx ** 2 + Ry ** 2))
filtre = pl.transpose(filtre)
I_fourier = I_fourier * filtre
print("IFFT2D...")
I_out = (np.abs(pl.ifft2(pl.ifftshift(I_fourier), N)))[0:H, 0:W]
light = I_out
I_out = np.exp(I / I_out)
else:
light = I * 0
I_out = I
# Display Light
if show_light:
light = ((light - light.min()) * 3000.0 /
light.max()).astype('float32')
light = array2cv(light)
fig = pl.figure()
pl.imshow(light)
fig.show()
I_out = (I_out - I_out.min()) * 3000.0 / I_out.max()
I_out = I_out.astype('uint8')
#chapeau haut de forme
I_out = pymorph.hmin(I_out, 25, pymorph.sedisk(3))
#Conversion en iplimage et ajustement contraste
gr = array2cv(I_out)
cv.EqualizeHist(gr, gr)
return gr
def compare(self):
d = 1.0 * self.scope.frameWrangler.currentFrame.squeeze()
dm = d / d.mean() - 1
#where is the piezo suppposed to be
#nomPos = self.piezo.GetPos(0)
nomPos = self.piezo.GetTargetPos(0)
#find closest calibration position
posInd = np.argmin(np.abs(nomPos - self.calPositions))
#dz = float('inf')
#count = 0
#while np.abs(dz) > 0.5*self.deltaZ and count < 1:
# count += 1
#retrieve calibration information at this location
calPos = self.calPositions[posInd]
FA = self.calFTs[:, :, posInd]
refA = self.calImages[:, :, posInd]
ddz = self.dz[:, posInd]
dzn = self.dzn[posInd]
#what is the offset between our target position and the calibration position
posDelta = nomPos - calPos
print('%s' % [nomPos, posInd, calPos, posDelta])
#find x-y drift
C = ifftshift(np.abs(ifftn(fftn(dm) * FA)))
Cm = C.max()
Cp = np.maximum(C - 0.5 * Cm, 0)
Cpsum = Cp.sum()
dx = (self.X * Cp).sum() / Cpsum
dy = (self.Y * Cp).sum() / Cpsum
ds = ndimage.shift(dm, [-dx, -dy]) * self.mask
#print A.shape, As.shape
self.ds_A = (ds - refA)
#calculate z offset between actual position and calibration position
dz = self.deltaZ * np.dot(self.ds_A.ravel(), ddz) * dzn
#posInd += np.round(dz / self.deltaZ)
#posInd = int(np.clip(posInd, 0, self.NCalibStates))
# print count, dz
#add the offset back to determine how far we are from the target position
dz = dz - posDelta
# if 1000*np.abs((dz + posDelta))>200 and self.WantRecord:
#dz = np.median(self.buffer)
# tif.imsave('C:\\Users\\Lab-test\\Desktop\\peakimage.tif', d)
# np.savetxt('C:\\Users\\Lab-test\\Desktop\\parameter.txt', self.buffer[-1])
#np.savetxt('C:\\Users\\Lab-test\\Desktop\\posDelta.txt', posDelta)
# self.WantRecord = False
#return dx, dy, dz + posDelta, Cm, dz, nomPos, posInd, calPos, posDelta
return dx, dy, dz, Cm, dz, nomPos, posInd, calPos, posDelta
def _shift_space( self, R ):
R_out = pl.zeros(R.shape)
for itime, _ in enumerate(self.t):
R_out[:,:,itime].real = pl.ifftshift(R[:,:,itime].real)
return R_out