def _gen_bead_pupil(X, Y, beadsize):
r2 = X*X + Y*Y
dx = X[1, 0] - X[0, 0]
bead_proj = np.sqrt(np.maximum(beadsize*beadsize - (r2 - dx*dx), 0))
return abs(fftshift(fftn(bead_proj)))
def OnColoc(self, event):
from PYME.Analysis import binAvg
voxelsize = self.image.voxelsize
#assume we have exactly 2 channels #FIXME - add a selector
#grab image data
imA = self.image.data[:,:,:,0].squeeze()
imB = self.image.data[:,:,:,1].squeeze()
X, Y = np.mgrid[0:float(imA.shape[0]), 0:float(imA.shape[1])]
X = X/X.shape[0]
Y = Y/X.shape[1]
X = X - .5
Y = Y - .5
R = np.sqrt(X**2 + Y**2)
H1 = pylab.fftn(imA)
H2 = pylab.fftn(imB)
rB = np.linspace(0,R.max())
bn, bm, bs = binAvg.binAvg(R, pylab.fftshift(abs(H1*H2)), rB)
bn1, bm1, bs1 = binAvg.binAvg(R, pylab.fftshift(abs(H1*H1)), rB)
bn2, bm2, bs2 = binAvg.binAvg(R, pylab.fftshift(abs(H2*H2)), rB)
pylab.figure()
ax = pylab.gca()
ax.plot(rB[:-1], bm/np.sqrt(bm1*bm2))
ax.plot(rB[:-1], 2./np.sqrt(bn/2))
xt = np.array([10., 15, 20, 30, 50, 80, 100, 150])
rt = voxelsize[0]/xt
pylab.xticks(rt[::-1],['%d' % xi for xi in xt[::-1]])
pylab.show()
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 OnColoc(self, event):
from PYME.Analysis import binAvg
voxelsize = self.image.voxelsize
#assume we have exactly 2 channels #FIXME - add a selector
#grab image data
imA = self.image.data[:, :, :, 0].squeeze()
imB = self.image.data[:, :, :, 1].squeeze()
X, Y = np.mgrid[0:float(imA.shape[0]), 0:float(imA.shape[1])]
X = X / X.shape[0]
Y = Y / X.shape[1]
X = X - .5
Y = Y - .5
R = np.sqrt(X**2 + Y**2)
H1 = pylab.fftn(imA)
H2 = pylab.fftn(imB)
rB = np.linspace(0, R.max())
bn, bm, bs = binAvg.binAvg(R, pylab.fftshift(abs(H1 * H2)), rB)
bn1, bm1, bs1 = binAvg.binAvg(R, pylab.fftshift(abs(H1 * H1)), rB)
bn2, bm2, bs2 = binAvg.binAvg(R, pylab.fftshift(abs(H2 * H2)), rB)
pylab.figure()
ax = pylab.gca()
ax.plot(rB[:-1], bm / np.sqrt(bm1 * bm2))
ax.plot(rB[:-1], 2. / np.sqrt(bn / 2))
xt = np.array([10., 15, 20, 30, 50, 80, 100, 150])
rt = voxelsize[0] / xt
pylab.xticks(rt[::-1], ['%d' % xi for xi in xt[::-1]])
pylab.show()
def OnCheckSpacing(self, event):
voxx = 0.07
voxy = 0.07
im = self.scope.frameWrangler.currentFrame
F = (abs(pylab.fftshift(pylab.fftn(im - im.mean()))) + 1e-2).squeeze()
currVoxelSizeID = self.scope.settingsDB.execute(
"SELECT sizeID FROM VoxelSizeHistory ORDER BY time DESC").fetchone(
)
if not currVoxelSizeID is None:
voxx, voxy = self.scope.settingsDB.execute(
"SELECT x,y FROM VoxelSizes WHERE ID=?",
currVoxelSizeID).fetchone()
pylab.figure(2)
pylab.clf()
xd = F.shape[0] / 2.
yd = F.shape[1] / 2.
cd = xd * 2 * voxx / 5
#kill central spike
F[(xd - cd):(xd + cd), (yd - cd):(yd + cd)] = F.mean()
pylab.imshow(F.T, interpolation='nearest', cmap=cm.hot)
xd = F.shape[0] / 2.
yd = F.shape[1] / 2.
pylab.plot(
xd + (xd * 2 * voxx / 1.8) * np.cos(np.arange(0, 2.1 * np.pi, .1)),
yd + (xd * 2 * voxx / 1.8) * np.sin(np.arange(0, 2.1 * np.pi, .1)),
lw=2,
label='$1.8 {\mu}m$')
pylab.plot(
xd + (xd * 2 * voxx / 2.) * np.cos(np.arange(0, 2.1 * np.pi, .1)),
yd + (xd * 2 * voxx / 2.) * np.sin(np.arange(0, 2.1 * np.pi, .1)),
lw=1,
label='$2 {\mu}m$')
pylab.plot(
xd + (xd * 2 * voxx / 1.6) * np.cos(np.arange(0, 2.1 * np.pi, .1)),
yd + (xd * 2 * voxx / 1.6) * np.sin(np.arange(0, 2.1 * np.pi, .1)),
lw=1,
label='$1.6 {\mu}m$')
pylab.xlim(xd - xd * 2 * voxx / 1, xd + xd * 2 * voxx / 1)
pylab.ylim(yd - xd * 2 * voxx / 1, yd + xd * 2 * voxx / 1)
pylab.legend()
self.F = F
def Fraunhofer(i, z) :
print "Propagation:Fraunhofer"
ft = pl.fftshift(pl.fftn(pl.fftshift(i.i)))
dx = i.wl*z/(i.nx*i.dx)
dy = i.wl*z/(i.ny*i.dy)
po = pl.exp(1j*2*pl.pi/i.wl*i.dx*i.dx)/(1j*i.wl*z)
p = pl.arange(0,i.nx)-(i.nx+0.5)/2.0
q = pl.arange(0,i.ny)-(i.ny+0.5)/2.0
[pp,qq] = pl.meshgrid(p,q)
pm = pl.exp(1j*pl.pi/(i.wl*z)*((pp*dx)**2+(qq*dy)**2))
i2 = Intensity.Intensity2D(i.nx,-i.nx*dx/2,i.nx*dy/2,i.ny,-i.ny*dy/2,i.ny*dy/2)
i2.i = po*pm*ft
return i2
print "Propagation:Fraunhofer>",dx,dy,i.nx*dx,i.ny*dy
def Fraunhofer(i, z):
print "Propagation:Fraunhofer"
ft = pl.fftshift(pl.fftn(pl.fftshift(i.i)))
dx = i.wl * z / (i.nx * i.dx)
dy = i.wl * z / (i.ny * i.dy)
po = pl.exp(1j * 2 * pl.pi / i.wl * i.dx * i.dx) / (1j * i.wl * z)
p = pl.arange(0, i.nx) - (i.nx + 0.5) / 2.0
q = pl.arange(0, i.ny) - (i.ny + 0.5) / 2.0
[pp, qq] = pl.meshgrid(p, q)
pm = pl.exp(1j * pl.pi / (i.wl * z) * ((pp * dx)**2 + (qq * dy)**2))
i2 = Intensity.Intensity2D(i.nx, -i.nx * dx / 2, i.nx * dy / 2, i.ny,
-i.ny * dy / 2, i.ny * dy / 2)
i2.i = po * pm * ft
return i2
print "Propagation:Fraunhofer>", dx, dy, i.nx * dx, i.ny * dy
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 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 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