def monogenic_filter_one_scale_gray(img, ss=1, minWaveLength=3, mult=2.1, sigmaOnf=0.55):
# float point is very important in order to compute the fft2
if img.dtype not in ['float32', 'float64']:
img = np.float64(img)
imgdtype = 'float64'
else:
imgdtype = img.dtype
# for 3 channel we make one channel computing the mean value
if img.ndim == 3: # hay que cambiar esto
img = img.mean(2)
rows, cols = img.shape
#compute the monnogenic scale in frequency domain
logGabor, logGabor_H1, logGabor_H2 = monogenic_scale(cols,rows, ss, minWaveLength, mult, sigmaOnf)
# FFT2 in the corner
IM = fft2(img) # Discrete Fourier Transform of image
IMF = IM * logGabor # Frequency bandpassed image
f = np.real(ifft2(IMF)) # Spatially bandpassed image
# Bandpassed monogenic filtering, real part of h contains
IMH1=IM*logGabor_H1
IMH2=IM*logGabor_H2
h1= np.real(ifft2(IMH1))
h2= np.real(ifft2(IMH2))
# Amplitude of this scale component
An = np.sqrt(f * f + h1 * h1 + h2 * h2)
#Orientation computation
ori = np.arctan(-h2 / h1)
# Wrap angles between -pi and pi and convert radians to degrees
ori_d = np.fix((ori % np.pi) / np.pi * 180.)
# Feature type (a phase angle between -pi/2 and pi/2)
ft = np.arctan2(f, np.sqrt(h1 * h1 + h2 * h2))
#proyectionin ij plane
fr= np.sqrt(h1 * h1 + h2 * h2)
return An,ori_d,ori,ft,fr,f
def _hilbert(self, data):
pci1 = fft.fft2(fft.fftshift(np.float32(data)))
pci2 = fft.ifftshift(pci1)*self.filter1
fpci0 = fft.ifftshift(fft.ifft2(fft.fftshift(pci2)))
fpci = np.imag(fpci0)
result = fpci
return result
def psf_correction(self, mat, win, pad_width):
(nrow, ncol) = mat.shape
mat_pad = np.pad(mat, pad_width, mode="reflect")
win_pad = np.pad(win, pad_width, mode="constant", constant_values=1.0)
mat_dec = fft.ifft2(fft.fft2(mat_pad) / fft.ifftshift(win_pad))
return np.abs(mat_dec)[pad_width:pad_width + nrow,
pad_width:pad_width + ncol]
def _hilbert(self, data):
pci1 = fft.fft2(fft.fftshift(np.float32(data)))
pci2 = fft.ifftshift(pci1) * self.filter1
fpci0 = fft.ifftshift(fft.ifft2(fft.fftshift(pci2)))
fpci = np.imag(fpci0)
result = fpci
return result
def remove_stripe_based_fft(sinogram, u, n, v, pad=150):
"""
Remove stripes using the method in Ref. [1].
Angular direction is along the axis 0.
Parameters
----------
sinogram : array_like
2D array.
u,n : int
To define the shape of 1D Butterworth low-pass filter.
v : int
Number of rows (* 2) to be applied the filter.
pad : int
Padding for FFT
Returns
-------
ndarray
2D array. Stripe-removed sinogram.
References
----------
.. [1] https://doi.org/10.1063/1.1149043
"""
if pad > 0:
sinogram = np.pad(sinogram, ((pad, pad), (0, 0)), mode='mean')
sinogram = np.pad(sinogram, ((0, 0), (pad, pad)), mode='edge')
(nrow, ncol) = sinogram.shape
window2d = create_2d_window(ncol, nrow, u, v, n)
sinogram = fft.ifft2(
np.fft.ifftshift(np.fft.fftshift(fft.fft2(sinogram)) * window2d))
return np.real(sinogram[pad:nrow - pad, pad:ncol - pad])
def apply_gaussian_filter(mat, sigmax, sigmay, pad):
"""
Filtering an image using a 2D Gaussian window.
Parameters
----------
mat : array_like
2D array.
sigmax : int
Sigma in the x-direction.
sigmay : int
Sigma in the y-direction.
pad : int
Padding for the Fourier transform.
Returns
-------
ndarray
2D array. Filtered image.
"""
mat_pad = np.pad(mat, ((0, 0), (pad, pad)), mode='edge')
mat_pad = np.pad(mat_pad, ((pad, pad), (0, 0)), mode='mean')
(nrow, ncol) = mat_pad.shape
window = make_2d_gaussian_window(nrow, ncol, sigmax, sigmay)
listx = np.arange(0, ncol)
listy = np.arange(0, nrow)
x, y = np.meshgrid(listx, listy)
mat_sign = np.power(-1.0, x + y)
mat_filt = np.real(
fft.ifft2(fft.fft2(mat_pad * mat_sign) * window) * mat_sign)
return mat_filt[pad:nrow - pad, pad:ncol - pad]
def _paganin(self, data):
pci1 = fft.fft2(np.float32(data))
pci2 = fft.fftshift(pci1) / self.filtercomplex
fpci = np.abs(fft.ifft2(pci2))
result = -0.5 * self.parameters['Ratio'] * np.log(
fpci + self.parameters['increment'])
return result
def _paganin(self, data):
pci1 = fft.fft2(np.float32(data))
pci2 = fft.fftshift(pci1) / self.filtercomplex
fpci = np.abs(fft.ifft2(pci2))
result = -0.5 * self.parameters['Ratio'] * np.log(
fpci + self.parameters['increment'])
return result
def get_digital_phase_mask(self, psi):
"""
Calculate the digital phase mask (i.e. reference wave), as in Colomb et
al. 2006, Eqn. 26 [1]_.
Fit for a second order polynomial, numerical parametric lens with least
squares to remove tilt, spherical aberration.
.. [1] http://www.ncbi.nlm.nih.gov/pubmed/16512526
Parameters
----------
psi : `~numpy.ndarray`
The product of the Fourier transform of the hologram and the Fourier
transform of impulse response function
Returns
-------
phase_mask : `~numpy.ndarray`
Digital phase mask, used for correcting phase aberrations.
"""
inverse_psi = fftshift(ifft2(psi, axes=(0, 1)), axes=(0, 1))
unwrapped_phase_image = np.atleast_3d(
unwrap_phase(inverse_psi)) / 2 / self.wavenumber
smooth_phase_image = gaussian_filter(
unwrapped_phase_image, [50, 50, 0]) # do not filter along axis 2
high = np.percentile(unwrapped_phase_image, 99)
low = np.percentile(unwrapped_phase_image, 1)
smooth_phase_image[high < unwrapped_phase_image] = high
smooth_phase_image[low > unwrapped_phase_image] = low
# Fit the smoothed phase image with a 2nd order polynomial surface with
# mixed terms using least-squares.
# This is iterated over all wavelength channels separately
# TODO: can this be done on the smooth_phase_image along axis 2 instead
# of direct iteration?
smooth_phase_image = smooth_phase_image
channels = np.split(smooth_phase_image,
smooth_phase_image.shape[2],
axis=2)
fits = list()
# Need to flip mgrid indices for this least squares solution
y, x = self.mgrid - self.n / 2
x, y = np.squeeze(x), np.squeeze(y)
for channel in channels:
v = np.array([
np.ones(len(x[0, :])), x[0, :], y[:, 0], x[0, :]**2,
x[0, :] * y[:, 0], y[:, 0]**2
])
coefficients = np.linalg.lstsq(v.T, np.squeeze(channel))[0]
fits.append(np.dot(v.T, coefficients))
field_curvature_mask = np.stack(fits, axis=2)
digital_phase_mask = np.exp(-1j * self.wavenumber *
field_curvature_mask)
return digital_phase_mask
def mapFromFFT(self,kFilter=None,kFilterFromList=None,showFilter=False,setMeanToZero=False,returnFFT=False):
"""
@brief Performs inverse fft (map from FFT) with an optional filter.
@param kFilter Optional; If applied, resulting map = IFFT(fft*kFilter)
@return (optinally filtered) 2D real array
"""
kMap = self.kMap.copy()
kFilter0 = numpy.real(kMap.copy())*0.+ 1.
if kFilter != None:
kFilter0 *= kFilter
if kFilterFromList != None:
kFilter = kMap.copy()*0.
l = kFilterFromList[0]
Fl = kFilterFromList[1]
FlSpline = splrep(l,Fl,k=3)
ll = numpy.ravel(self.modLMap)
kk = (splev(ll,FlSpline))
kFilter = numpy.reshape(kk,[self.Ny,self.Nx])
kFilter0 *= kFilter
if setMeanToZero:
id = numpy.where(self.modLMap == 0.)
kFilter0[id] = 0.
#showFilter = True
if showFilter:
pylab.semilogy(l,Fl,'r',ll,kk,'b.')
#utils.saveAndShow()
#sys.exit()
pylab.matshow(fftshift(kFilter0),origin="down",extent=[numpy.min(self.lx),\
numpy.max(self.lx),\
numpy.min(self.ly),\
numpy.max(self.ly)])
pylab.show()
kMap[:,:] *= kFilter0[:,:]
if returnFFT:
ftMap = self.copy()
ftMap.kMap = kMap.copy()
return numpy.real(ifft2(kMap)),ftMap
else:
return numpy.real(ifft2(kMap))
def process_frames(self, data):
sino = data[0]
sino2 = np.fliplr(sino[1:])
(Nrow, Ncol) = sino.shape
mask = self._create_mask(
2*Nrow-1, Ncol, 0.5*self.parameters['ratio']*Ncol)
FT1 = fft.fftshift(fft.fft2(np.vstack((sino, sino2))))
sino = fft.ifft2(fft.ifftshift(FT1 - FT1*mask))
return sino[0:Nrow].real
def sampling_op_adjoint(image, mask_as_image):
""" Adjoint of sampling operator
:param image: Assumed to be an array with shape [N,N]
:param mask_as_image:
:param mask_as_image: Mask of shape [N,N] where middle of the image
corresponds to zero frequency. Values should be 0,1 or
True/False.
:return: Array of shape [N, N] with the adjoint data.
"""
N = max(image.shape)
image_domain_data = fftw.ifft2(fftw.ifftshift(image)) * N
return image_domain_data
def process_frames(self, data):
sinogram = data[0]
(height, _) = sinogram.shape
if height%2==0:
height = height - 1
sinofit = np.abs(savgol_filter(
sinogram, height, self.order, axis=0, mode = 'mirror'))
sinofit2 = np.pad(
sinofit,((0, 0), (self.pad, self.pad)), mode = 'edge')
sinofit2 = np.pad(
sinofit2,((self.pad, self.pad), (0, 0)), mode = 'mean')
sinofitsmooth = np.real(fft.ifft2(fft.fft2(
sinofit2*self.matsign)*self.window2d)*self.matsign)
sinofitsmooth = sinofitsmooth[self.pad:self.height1-self.pad,
self.pad:self.width1-self.pad]
num1 = np.mean(sinofit)
num2 = np.mean(sinofitsmooth)
sinofitsmooth = num1*sinofitsmooth/num2
return sinogram/sinofit*sinofitsmooth
def process_frames(self, data):
sinogram = data[0]
(height, _) = sinogram.shape
if height % 2 == 0:
height = height - 1
sinofit = np.abs(
savgol_filter(sinogram, height, self.order, axis=0, mode='mirror'))
sinofit2 = np.pad(sinofit, ((0, 0), (self.pad, self.pad)), mode='edge')
sinofit2 = np.pad(sinofit2, ((self.pad, self.pad), (0, 0)),
mode='mean')
sinofitsmooth = np.real(
fft.ifft2(fft.fft2(sinofit2 * self.matsign) * self.window2d) *
self.matsign)
sinofitsmooth = sinofitsmooth[self.pad:self.height1 - self.pad,
self.pad:self.width1 - self.pad]
num1 = np.mean(sinofit)
num2 = np.mean(sinofitsmooth)
sinofitsmooth = num1 * sinofitsmooth / num2
return sinogram / sinofit * sinofitsmooth
def apply_filter(self, mat, window, pattern, pad_width):
(nrow, ncol) = mat.shape
if pattern == "PROJECTION":
top_drop = 10 # To remove the time stamp at some data
mat_pad = np.pad(mat[top_drop:],
((pad_width + top_drop, pad_width),
(pad_width, pad_width)),
mode="edge")
win_pad = np.pad(window, pad_width, mode="edge")
mat_dec = fft.ifft2(
fft.fft2(-np.log(mat_pad)) / fft.ifftshift(win_pad))
mat_dec = np.abs(mat_dec[pad_width:pad_width + nrow,
pad_width:pad_width + ncol])
else:
mat_pad = np.pad(-np.log(mat), ((0, 0), (pad_width, pad_width)),
mode='edge')
win_pad = np.pad(window, ((0, 0), (pad_width, pad_width)),
mode="edge")
mat_fft = np.fft.fftshift(fft.fft(mat_pad), axes=1) / win_pad
mat_dec = fft.ifft(np.fft.ifftshift(mat_fft, axes=1))
mat_dec = np.abs(mat_dec[:, pad_width:pad_width + ncol])
return np.float32(np.exp(-mat_dec))
def _2d_filter(mat, sigmax, sigmay, pad):
"""
Filtering an image using 2D Gaussian window.
---------
Parameters: - mat: 2D array.
- sigmax, sigmay: sigmas of the window.
- pad: padding for FFT
---------
Return: - filtered image.
"""
matpad = np.pad(mat, ((0, 0), (pad, pad)), mode='edge')
matpad = np.pad(matpad, ((pad, pad), (0, 0)), mode='mean')
(nrow, ncol) = matpad.shape
win2d = _2d_window_ellipse(nrow, ncol, sigmax, sigmay)
listx = np.arange(0, ncol)
listy = np.arange(0, nrow)
x, y = np.meshgrid(listx, listy)
matsign = np.power(-1.0, x + y)
# matfilter = np.real(ifft2(fft2(matpad*matsign)*win2d)*matsign)
matfilter = np.real(
fft_vo.ifft2(fft_vo.fft2(matpad * matsign) * win2d) * matsign)
return matfilter[pad:nrow - pad, pad:ncol - pad]
def adjoint_of_samples(samp_batch, k_mask_idx1, k_mask_idx2, N=128):
if len(samp_batch.shape) != 2:
print('Warning: adjoint_of_samples -> samp_batch.shape is wrong')
batch_size = samp_batch.shape[0]
nbr_samples = samp_batch.shape[1]
samp_batch = ((2 * 4096) / 0.0075) * samp_batch
adjoint_batch = np.zeros([batch_size, N, N], dtype=np.complex64)
for i in range(batch_size):
samples_concat = samp_batch[i]
samples_real = samples_concat[:int(nbr_samples / 2)]
samples_imag = samples_concat[int(nbr_samples / 2):]
samples = samples_real - 1j * samples_imag
if len(samples.shape) == 1:
samples = np.expand_dims(samples, axis=1)
fft_im = np.zeros([N, N], dtype=samples.dtype)
fft_im[k_mask_idx1, k_mask_idx2] = samples
adjoint = fftw.ifft2(fft_im) / 4096
adjoint_batch[i, :, :] = adjoint
return adjoint_batch
def _reconstruct(self, propagation_distance, fourier_mask=None):
"""
Reconstruct the wave at a single ``propagation_distance`` for a single ``wavelength``.
Parameters
----------
propagation_distance : float
Propagation distance [m]
spectral_peak : integer pair [x,y]
Centroid of spectral peak for wavelength in power spectrum of hologram FT
fourier_mask : array_like or None, optional
Fourier-domain mask. If None (default), a mask is determined from the position of the
main spectral peak.
Returns
-------
reconstructed_wave : `~numpy.ndarray` ndim 3
The reconstructed wave as an array of dimensions (X, Y, wavelengths)
"""
x_peak, y_peak = self.spectral_peak
# Calculate mask radius. TODO: Update 250 to an automated guess based on input values.
if self.rebin_factor != 1:
mask_radius = 150. / self.rebin_factor
elif self.crop_fraction is not None and self.crop_fraction != 0:
mask_radius = 150. * self.crop_fraction
else:
mask_radius = 150.
# Either use a Fourier-domain mask based on coords of spectral peak,
# or a user-specified mask
if fourier_mask is None:
mask = self.real_image_mask(x_peak, y_peak, mask_radius)
else:
mask = np.asarray(fourier_mask, dtype=np.bool)
mask = np.atleast_3d(mask)
# Calculate Fourier transform of impulse response function
G = self.fourier_trans_of_impulse_resp_func(
np.atleast_1d([propagation_distance] *
self.wavelength.size).reshape((1, 1, -1)) -
self.chromatic_shift)
# Now calculate digital phase mask. First center the spectral peak for each channel
x_peak, y_peak = x_peak.reshape(-1), y_peak.reshape(-1)
shifted_ft_hologram = np.empty_like(np.atleast_3d(mask),
dtype=np.complex128)
for channel in range(self.wavelength.size):
shifted_ft_hologram[:, :, channel] = arrshift(
self.ft_hologram * mask[:, :, channel],
[-x_peak[channel], -y_peak[channel]],
axes=(0, 1))
# Apodize the result
psi = self.apodize(shifted_ft_hologram * G)
digital_phase_mask = self.get_digital_phase_mask(psi)
# Reconstruct the image
# fftshift is independent of channel
psi = np.empty_like(np.atleast_3d(shifted_ft_hologram))
for channel in range(psi.shape[2]):
psi[:, :, channel] = arrshift(fftshift(
fft2(self.apodize(self.hologram) *
digital_phase_mask[:, :, channel],
axes=(0, 1))) * mask[:, :, channel],
[-x_peak[channel], -y_peak[channel]],
axes=(0, 1))
psi *= G
return fftshift(ifft2(psi, axes=(0, 1)), axes=(0, 1))
def perfft2(im, compute_P=True, compute_spatial=False):
"""
Moisan's Periodic plus Smooth Image Decomposition. The image is
decomposed into two parts:
im = s + p
where 's' is the 'smooth' component with mean 0, and 'p' is the 'periodic'
component which has no sharp discontinuities when one moves cyclically
across the image boundaries.
useage: S, [P, s, p] = perfft2(im)
where: im is the image
S is the FFT of the smooth component
P is the FFT of the periodic component, returned if
compute_P (default)
s & p are the smooth and periodic components in the spatial
domain, returned if compute_spatial
By default this function returns `P` and `S`, the FFTs of the periodic and
smooth components respectively. If `compute_spatial=True`, the spatial
domain components 'p' and 's' are also computed.
This code is adapted from Lionel Moisan's Scilab function 'perdecomp.sci'
"Periodic plus Smooth Image Decomposition" 07/2012 available at:
<http://www.mi.parisdescartes.fr/~moisan/p+s>
"""
if im.dtype not in ['float32', 'float64']:
im = np.float64(im)
rows, cols = im.shape
# Compute the boundary image which is equal to the image discontinuity
# values across the boundaries at the edges and is 0 elsewhere
s = np.zeros_like(im)
s[0, :] = im[0, :] - im[-1, :]
s[-1, :] = -s[0, :]
s[:, 0] = s[:, 0] + im[:, 0] - im[:, -1]
s[:, -1] = s[:, -1] - im[:, 0] + im[:, -1]
# Generate grid upon which to compute the filter for the boundary image
# in the frequency domain. Note that cos is cyclic hence the grid
# values can range from 0 .. 2*pi rather than 0 .. pi and then pi .. 0
x, y = (2 * np.pi * np.arange(0, v) / float(v) for v in (cols, rows))
cx, cy = np.meshgrid(x, y)
denom = (2. * (2. - np.cos(cx) - np.cos(cy)))
denom[0, 0] = 1. # avoid / 0
S = fft2(s) / denom
S[0, 0] = 0 # enforce zero mean
if compute_P or compute_spatial:
P = fft2(im) - S
if compute_spatial:
s = ifft2(S).real
p = im - s
return S, P, s, p
else:
return S, P
else:
return S
def iFFT2(FT):
[Ny, Nx] = np.shape(FT)
I = fftshift(ifft2(ifftshift(FT))) * np.sqrt(Ny) * np.sqrt(Nx)
return I
def perfft2(im, compute_P=True, compute_spatial=False):
"""
Moisan's Periodic plus Smooth Image Decomposition. The image is
decomposed into two parts:
im = s + p
where 's' is the 'smooth' component with mean 0, and 'p' is the 'periodic'
component which has no sharp discontinuities when one moves cyclically
across the image boundaries.
useage: S, [P, s, p] = perfft2(im)
where: im is the image
S is the FFT of the smooth component
P is the FFT of the periodic component, returned if
compute_P (default)
s & p are the smooth and periodic components in the spatial
domain, returned if compute_spatial
By default this function returns `P` and `S`, the FFTs of the periodic and
smooth components respectively. If `compute_spatial=True`, the spatial
domain components 'p' and 's' are also computed.
This code is adapted from Lionel Moisan's Scilab function 'perdecomp.sci'
"Periodic plus Smooth Image Decomposition" 07/2012 available at:
<http://www.mi.parisdescartes.fr/~moisan/p+s>
"""
if im.dtype not in ['float32', 'float64']:
im = np.float64(im)
rows, cols = im.shape
# Compute the boundary image which is equal to the image discontinuity
# values across the boundaries at the edges and is 0 elsewhere
s = np.zeros_like(im)
s[0, :] = im[0, :] - im[-1, :]
s[-1, :] = -s[0, :]
s[:, 0] = s[:, 0] + im[:, 0] - im[:, -1]
s[:, -1] = s[:, -1] - im[:, 0] + im[:, -1]
# Generate grid upon which to compute the filter for the boundary image
# in the frequency domain. Note that cos is cyclic hence the grid
# values can range from 0 .. 2*pi rather than 0 .. pi and then pi .. 0
x, y = (2 * np.pi * np.arange(0, v) / float(v) for v in (cols, rows))
cx, cy = np.meshgrid(x, y)
denom = (2. * (2. - np.cos(cx) - np.cos(cy)))
denom[0, 0] = 1. # avoid / 0
S = fft2(s) / denom
S[0, 0] = 0 # enforce zero mean
if compute_P or compute_spatial:
P = fft2(im) - S
if compute_spatial:
s = ifft2(S).real
p = im - s
return S, P, s, p
else:
return S, P
else:
return S
def cross_correlation_2d(pixels1, pixels2):
'''Align the second image with the first using max cross-correlation
returns the x,y offsets to add to image1's indexes to align it with
image2
Many of the ideas here are based on the paper, "Fast Normalized
Cross-Correlation" by J.P. Lewis
(http://www.idiom.com/~zilla/Papers/nvisionInterface/nip.html)
which is frequently cited when addressing this problem.
'''
#
# We double the size of the image to get a field of zeros
# for the parts of one image that don't overlap the displaced
# second image.
#
# Since we're going into the frequency domain, if the images are of
# different sizes, we can make the FFT shape large enough to capture
# the period of the largest image - the smaller just will have zero
# amplitude at that frequency.
#
s = np.maximum(pixels1.shape, pixels2.shape)
fshape = s*2
#
# Calculate the # of pixels at a particular point
#
i, j = np.mgrid[-s[0]:s[0],
-s[1]:s[1]]
unit = np.abs(i*j).astype(float)
unit[unit < 1] = 1 # keeps from dividing by zero in some places
#
# Normalize the pixel values around zero which does not affect the
# correlation, keeps some of the sums of multiplications from
# losing precision and precomputes t(x-u,y-v) - t_mean
#
pixels1 = np.nan_to_num(pixels1-nanmean(pixels1))
pixels2 = np.nan_to_num(pixels2-nanmean(pixels2))
#
# Lewis uses an image, f and a template t. He derives a normalized
# cross correlation, ncc(u,v) =
# sum((f(x,y)-f_mean(u,v))*(t(x-u,y-v)-t_mean),x,y) /
# sqrt(sum((f(x,y)-f_mean(u,v))**2,x,y) * (sum((t(x-u,y-v)-t_mean)**2,x,y)
#
# From here, he finds that the numerator term, f_mean(u,v)*(t...) is zero
# leaving f(x,y)*(t(x-u,y-v)-t_mean) which is a convolution of f
# by t-t_mean.
#
fp1 = fft2(pixels1.astype('float32'), fshape)
fp2 = fft2(pixels2.astype('float32'), fshape)
corr12 = ifft2(fp1 * fp2.conj()).real
#
# Use the trick of Lewis here - compute the cumulative sums
# in a fashion that accounts for the parts that are off the
# edge of the template.
#
# We do this in quadrants:
# q0 q1
# q2 q3
# For the first,
# q0 is the sum over pixels1[i:,j:] - sum i,j backwards
# q1 is the sum over pixels1[i:,:j] - sum i backwards, j forwards
# q2 is the sum over pixels1[:i,j:] - sum i forwards, j backwards
# q3 is the sum over pixels1[:i,:j] - sum i,j forwards
#
# The second is done as above but reflected lr and ud
#
p1_si = pixels1.shape[0]
p1_sj = pixels1.shape[1]
p1_sum = np.zeros(fshape)
p1_sum[:p1_si, :p1_sj] = cumsum_quadrant(pixels1, False, False)
p1_sum[:p1_si, -p1_sj:] = cumsum_quadrant(pixels1, False, True)
p1_sum[-p1_si:, :p1_sj] = cumsum_quadrant(pixels1, True, False)
p1_sum[-p1_si:, -p1_sj:] = cumsum_quadrant(pixels1, True, True)
#
# Divide the sum over the # of elements summed-over
#
p1_mean = old_div(p1_sum, unit)
p2_si = pixels2.shape[0]
p2_sj = pixels2.shape[1]
p2_sum = np.zeros(fshape)
p2_sum[:p2_si, :p2_sj] = cumsum_quadrant(pixels2, False, False)
p2_sum[:p2_si, -p2_sj:] = cumsum_quadrant(pixels2, False, True)
p2_sum[-p2_si:, :p2_sj] = cumsum_quadrant(pixels2, True, False)
p2_sum[-p2_si:, -p2_sj:] = cumsum_quadrant(pixels2, True, True)
p2_sum = np.fliplr(np.flipud(p2_sum))
p2_mean = old_div(p2_sum, unit)
#
# Once we have the means for u,v, we can caluclate the
# variance-like parts of the equation. We have to multiply
# the mean^2 by the # of elements being summed-over
# to account for the mean being summed that many times.
#
p1sd = np.sum(pixels1**2) - p1_mean**2 * np.product(s)
p2sd = np.sum(pixels2**2) - p2_mean**2 * np.product(s)
#
# There's always chance of roundoff error for a zero value
# resulting in a negative sd, so limit the sds here
#
sd = np.sqrt(np.maximum(p1sd * p2sd, 0))
with warnings.catch_warnings():
warnings.simplefilter("ignore")
corrnorm = old_div(corr12, sd)
#
# There's not much information for points where the standard
# deviation is less than 1/100 of the maximum. We exclude these
# from consideration.
#
corrnorm[(unit < old_div(np.product(s), 2)) &
(sd < old_div(np.mean(sd), 100))] = 0
# Also exclude possibilites with few observed pixels.
corrnorm[unit < old_div(np.product(s), 4)] = 0
return corrnorm
def cross_correlation_2d(pixels1, pixels2):
'''Align the second image with the first using max cross-correlation
returns the x,y offsets to add to image1's indexes to align it with
image2
Many of the ideas here are based on the paper, "Fast Normalized
Cross-Correlation" by J.P. Lewis
(http://www.idiom.com/~zilla/Papers/nvisionInterface/nip.html)
which is frequently cited when addressing this problem.
'''
#
# We double the size of the image to get a field of zeros
# for the parts of one image that don't overlap the displaced
# second image.
#
# Since we're going into the frequency domain, if the images are of
# different sizes, we can make the FFT shape large enough to capture
# the period of the largest image - the smaller just will have zero
# amplitude at that frequency.
#
s = np.maximum(pixels1.shape, pixels2.shape)
fshape = s*2
#
# Calculate the # of pixels at a particular point
#
i,j = np.mgrid[-s[0]:s[0],
-s[1]:s[1]]
unit = np.abs(i*j).astype(float)
unit[unit<1]=1 # keeps from dividing by zero in some places
#
# Normalize the pixel values around zero which does not affect the
# correlation, keeps some of the sums of multiplications from
# losing precision and precomputes t(x-u,y-v) - t_mean
#
pixels1 = np.nan_to_num(pixels1-np.nanmean(pixels1))
pixels2 = np.nan_to_num(pixels2-np.nanmean(pixels2))
#
# Lewis uses an image, f and a template t. He derives a normalized
# cross correlation, ncc(u,v) =
# sum((f(x,y)-f_mean(u,v))*(t(x-u,y-v)-t_mean),x,y) /
# sqrt(sum((f(x,y)-f_mean(u,v))**2,x,y) * (sum((t(x-u,y-v)-t_mean)**2,x,y)
#
# From here, he finds that the numerator term, f_mean(u,v)*(t...) is zero
# leaving f(x,y)*(t(x-u,y-v)-t_mean) which is a convolution of f
# by t-t_mean.
#
fp1 = fft2(pixels1.astype('float32'),fshape)
fp2 = fft2(pixels2.astype('float32'),fshape)
corr12 = ifft2(fp1 * fp2.conj()).real
#
# Use the trick of Lewis here - compute the cumulative sums
# in a fashion that accounts for the parts that are off the
# edge of the template.
#
# We do this in quadrants:
# q0 q1
# q2 q3
# For the first,
# q0 is the sum over pixels1[i:,j:] - sum i,j backwards
# q1 is the sum over pixels1[i:,:j] - sum i backwards, j forwards
# q2 is the sum over pixels1[:i,j:] - sum i forwards, j backwards
# q3 is the sum over pixels1[:i,:j] - sum i,j forwards
#
# The second is done as above but reflected lr and ud
#
p1_si = pixels1.shape[0]
p1_sj = pixels1.shape[1]
p1_sum = np.zeros(fshape)
p1_sum[:p1_si,:p1_sj] = cumsum_quadrant(pixels1, False, False)
p1_sum[:p1_si,-p1_sj:] = cumsum_quadrant(pixels1, False, True)
p1_sum[-p1_si:,:p1_sj] = cumsum_quadrant(pixels1, True, False)
p1_sum[-p1_si:,-p1_sj:] = cumsum_quadrant(pixels1, True, True)
#
# Divide the sum over the # of elements summed-over
#
p1_mean = p1_sum / unit
p2_si = pixels2.shape[0]
p2_sj = pixels2.shape[1]
p2_sum = np.zeros(fshape)
p2_sum[:p2_si,:p2_sj] = cumsum_quadrant(pixels2, False, False)
p2_sum[:p2_si,-p2_sj:] = cumsum_quadrant(pixels2, False, True)
p2_sum[-p2_si:,:p2_sj] = cumsum_quadrant(pixels2, True, False)
p2_sum[-p2_si:,-p2_sj:] = cumsum_quadrant(pixels2, True, True)
p2_sum = np.fliplr(np.flipud(p2_sum))
p2_mean = p2_sum / unit
#
# Once we have the means for u,v, we can caluclate the
# variance-like parts of the equation. We have to multiply
# the mean^2 by the # of elements being summed-over
# to account for the mean being summed that many times.
#
p1sd = np.sum(pixels1**2) - p1_mean**2 * np.product(s)
p2sd = np.sum(pixels2**2) - p2_mean**2 * np.product(s)
#
# There's always chance of roundoff error for a zero value
# resulting in a negative sd, so limit the sds here
#
sd = np.sqrt(np.maximum(p1sd * p2sd, 0))
with warnings.catch_warnings():
warnings.simplefilter("ignore")
corrnorm = corr12 / sd
#
# There's not much information for points where the standard
# deviation is less than 1/100 of the maximum. We exclude these
# from consideration.
#
corrnorm[(unit < np.product(s) / 2) &
(sd < np.mean(sd) / 100)] = 0
# Also exclude possibilites with few observed pixels.
corrnorm[unit < np.product(s) / 4] = 0
return corrnorm
