def getoverlapz(self,angle,spacingx,spacingz):
''' shift 2nd order data '''
dx = self.dx / 2
dz = self.dz / 2
kx = dx*np.cos(angle)/(spacingx*2)
ky = dx*np.sin(angle)/(spacingx*2)
kz = dz/spacingz
ysh = np.exp(2j*np.pi*(kx*self.xv+ky*self.yv+kz*self.zv))
otf = fftn((self.psf*ysh))
yshf = np.abs(fftn(ysh))
nxh = self.nx
nyh = self.ny
sz, sx, sy = np.unravel_index(yshf.argmax(), yshf.shape)
if (sx<nxh):
sx = sx
else:
sx = sx-2*nxh
if (sy<nyh):
sy = sy
else:
sy = sy-2*nyh
zsp = self.zerosuppression( sz, sx, sy)
otf = otf * zsp
ysh = self.shiftmat(0.,kx,ky).astype(np.complex64)
imgf = self.img_1_0.astype(np.complex64)
imgf = fftn((imgf*ysh))
temp = (np.abs(imgf*otf)**2).sum()
return temp
def shift0(self,plot=False):
nxh = self.nx
nyh = self.ny
nzh = self.nz
self.otf0 = np.zeros((2*nzh,2*nxh,2*nyh),dtype=np.complex64)
zsp = self.zerosuppression( 0., 0., 0.)
self.otf0[:] = fftn(self.psf) * zsp
self.imgf0 = np.zeros((2*nzh,2*nxh,2*nyh),dtype=np.complex64)
self.imgf0 = fftn(self.img_0)
self.imgf0 = self.imgf0
tf.imsave(join('otf_0.tif'),self.otf0)
tf.imsave(join('imgf_0.tif'),self.imgf0)
if plot==True:
tf.imshow(np.abs(fftshift(self.otf0)), photometric='minisblack',title='Angle %d _ 0 order OTF'%self.nangle)
tf.imshow(np.abs(fftshift(self.imgf0)), photometric='minisblack',title='Angle %d _ 0 order frequency spectrum'%self.nangle)
def interp(self,arr):
nz,nx,ny = arr.shape
outarr = np.zeros((2*nz,2*nx,2*ny), dtype=arr.dtype)
arrf = fftn(arr)
arro = self.pad(arrf)
outarr = ifftn(arro)
return outarr
def getoverlap1(self,angle,spacingx,spacingz,plot=False):
''' shift 2nd order data '''
dx = self.dx / 2
dz = self.dz / 2
kx = dx*np.cos(angle)/(spacingx*2)
ky = dx*np.sin(angle)/(spacingx*2)
kz = dz/spacingz
nxh = self.nx
nyh = self.ny
ysh = np.exp(2j*np.pi*(kx*self.xv+ky*self.yv+kz*self.zv))
otf = fftn((self.psf*ysh))
yshf = np.abs(fftn(ysh))
sz, sx, sy = np.unravel_index(yshf.argmax(), yshf.shape)
if (sx<nxh):
sx = sx
else:
sx = sx-2*nxh
if (sy<nyh):
sy = sy
else:
sy = sy-2*nyh
zsp = self.zerosuppression( sz, sx, sy)
otf = otf * zsp
ysh = np.exp(2j*np.pi*(kx*self.xv+ky*self.yv+0.*self.zv))
imgf = self.img_1_0.astype(np.complex64)
imgf = fftn((imgf*ysh))
cutoff = self.cutoff
imgf0 = self.imgf0
otf0 = self.otf0
wimgf0 = otf*imgf0
wimgf1 = otf0*imgf
msk = (np.abs(otf0*otf)>cutoff).astype(np.complex64)
if plot==True:
tf.imshow(np.abs((msk*wimgf1*wimgf0.conj())/(msk*wimgf0*wimgf0.conj())))
tf.imshow(np.angle((msk*wimgf1*wimgf0.conj())/(msk*wimgf0*wimgf0.conj())))
a = np.sum(msk*wimgf1*wimgf0.conj())/np.sum(msk*wimgf0*wimgf0.conj())
mag = np.abs(a)
phase = np.angle(a)
return mag, phase
def shift2(self,angle,spacingx,plot=False):
''' shift 2nd order data '''
dx = self.dx / 2
nxh = self.nx
nyh = self.ny
nzh = self.nz
kx = dx*np.cos(angle)/spacingx
ky = dx*np.sin(angle)/spacingx
kz = 0
ysh = np.zeros((2,2*nzh,2*nxh,2*nyh),dtype=np.complex64)
ysh[0,:,:,:] = self.shiftmat(kz,kx,ky).astype(np.complex64)
ysh[1,:,:,:] = self.shiftmat(kz,-kx,-ky).astype(np.complex64)
otf = np.zeros((2*nzh,2*nxh,2*nyh),dtype=np.complex64)
otf[:,:,:] = fftn(self.psf*ysh[0])
yshf = np.abs(fftn(ysh[0]))
sz, sx, sy = np.unravel_index(yshf.argmax(), yshf.shape)
if (sx<nxh):
sx = sx
else:
sx = sx-2*nxh
if (sy<nyh):
sy = sy
else:
sy = sy-2*nyh
zsp = self.zerosuppression( sz, sx, sy)
otf = otf * zsp
tf.imsave(join('otf_2_0.tif'),otf)
if plot==True:
tf.imshow(np.abs(fftshift(otf)),photometric='minisblack',title='Angle %d _ 2nd order +1 OTF'%self.nangle)
otf = np.zeros((2*nzh,2*nxh,2*nyh),dtype=np.complex64)
otf[:,:,:] = fftn(self.psf*ysh[1])
yshf = np.abs(fftn(ysh[1]))
sz, sx, sy = np.unravel_index(yshf.argmax(), yshf.shape)
if (sx<nxh):
sx = sx
else:
sx = sx-2*nxh
if (sy<nyh):
sy = sy
else:
sy = sy-2*nyh
zsp = self.zerosuppression( sz, sx, sy)
otf = otf * zsp
tf.imsave(join('otf_2_1.tif'),otf)
if plot==True:
tf.imshow(np.abs(fftshift(otf)),photometric='minisblack',title='Angle %d _ 2nd order -1 OTF'%self.nangle)
imgf = np.zeros((2*nzh,2*nxh,2*nyh),dtype=np.complex64)
imgf[:,:,:] = self.img_2_0
imgf[:,:,:] = fftn(imgf*ysh[0])
tf.imsave(join('imgf_2_0.tif'),imgf)
if plot==True:
tf.imshow(np.abs(fftshift(imgf)),photometric='minisblack',title='Angle %d _ 2nd order +1 frequency spectrum'%self.nangle)
imgf = np.zeros((2*nzh,2*nxh,2*nyh),dtype=np.complex64)
imgf[:,:,:] = self.img_2_1
imgf[:,:,:] = fftn(imgf*ysh[1])
tf.imsave(join('imgf_2_1.tif'),imgf)
if plot==True:
tf.imshow(np.abs(fftshift(imgf)),photometric='minisblack',title='Angle %d _ 2nd order -1 frequency spectrum'%self.nangle)