Consistent Spatial and Frequency Domain Image Filtering with Python
In image reconstruction tasks, it's often convenient to perform filtering operations in either the spatial or frequency domain. Both have their advantages and disadvantages. For the spatial domain, small filters such as finite differences can be evaluated extremely quickly and include local coefficients but objective functions often result in large systems of equations. In contrast, many objective functions diagonalize to yield pixel-wise solutions in the frequency domain but spatial variation cannot be incorporated directly.
As a result, it's common to express reconstruction tasks with individual terms in each domain. The domains are then coupled through penalties or constraints that can be expressed naturally either domain and lead to efficient solvers.
By way of example: in the total-variation regularized inpainting example below, the data term expresses a least-squares penalty on a (fixed) random selection of pixels in the reconstruction \({\bf I}\) and measurements \({\bf Y}\) via the selection mask \({\bf S}\) (\(\odot\) is pixelwise multiplication). This term cannot be expressed efficiently in the Fourier domain. However the regularizers (e.g. \(\lambda \| \frac{\partial}{\partial x} {\bf I} \|_1\)) can and should be since otherwise they couple every pixel in the image together. This is bad because it results in very costly solves.
Solving this efficiently requires splitting the problem into separate solve that couple through constraints and Lagrange multipliers (or more simply through penalties). How to do that is an entire topic in itself but the key thing is that filtering is performed in both domains and must be consistent to produce sensible results. If this is not the case, all sorts of weird things happen: images shifting each iteration, convergence stalling, etc.
This sounds (and is) easy but requires a bit of attention to detail.
Brass Tacks
The starting point here is a definition of a sparse kernel. By sparse, I mean a kernel with very few non-zero weights, generally less than 10-20 or so. This includes common filters like Laplacians, edge filters and finite difference stencils.
In the following code, a kernel is defined by three equal length lists containing the row-offsets, column-offsets and filter values for the kernel. In the code, the user specifies the correlation kernel; this produces results that match typical finite-difference kernels when the correlate_spatial or correlate_fourier methods are called. Here is the code for the kernel class:
import numpy
class SparseKernel2D:
"""Represents a kernel for a 2D convolution operation
Example:
# make a first-order finite difference along the column axis
K = SparseKernel2D( [0,0], [-1,0], [-1.0, 1.0] )
"""
def __init__( self, offy, offx, vals ):
"""Represents a kernel for a 2D convolution operation
Args:
offy (integer array/list) vertical offsets of non-zero kernel values
offx (integer array/list) horizontal offsets of non-zero kernel values
vals (float array/list) non-zero kernel values
Raises:
ValueError whenever offx, offx, vals do not have the same length
"""
if len(offy) != len(offx) or len(vals) != len(offx):
raise ValueError('offx, offy and vals must be 1D array-like with the same size')
self.offx = offx
self.offy = offy
self.vals = vals
def image( self, dim ):
"""Returns an image represenation of the kernel at the specified dimensions with the kernel centered.
Args:
dim (integer tuple) output image dimensions [height,width]
Raises:
ValueError when dim is not 2-element
Returns:
height x width image of float32 elements
"""
if len(dim) != 2:
raise ValueError('Expected a 2-element integer tuple/list for image dimensions')
cen = ( int(dim[0]/2), int(dim[1]/2) )
out = numpy.zeros( dim, dtype=numpy.float32 )
for dx,dy,val in zip( self.offx, self.offy, self.vals):
out[cen[0]+dy,cen[1]+dx] = val
return out
def spectrum( self, dim ):
"""Returns a spectrum representation of the kernel at the specified dimensions. The returned
kernel is *not* centered, i.e. has it's DC component at the corner.
Args:
dim (integer tuple) output spectrum dimensions [height,width]
Raises:
ValueError when dim is not 2-element
Returns:
height x width complex image
"""
return numpy.fft.fft2( numpy.roll( self.image(dim), [int(dim[0]/2+0.5),int(dim[1]/2+0.5)], axis=[0,1] ) )
def convolve_spatial( self, I ):
"""Convolves the input image by the kernel in the spatial domain
Args:
I (2d float32 array) input image to convolve with kernel
Raises:
ValueError when input is not a 2D ndarray or I.dtype is not numpy.floating subclass
Returns:
Convolution results as 2D ndarray of I.dtype elements
"""
if not isinstance(I,numpy.ndarray) or I.ndim != 2 or not numpy.issubdtype(I.dtype,numpy.floating):
raise ValueError('Expected a 2D ndarray or float32 values')
result = numpy.zeros( I.shape, dtype=I.dtype )
for dx,dy,val in zip(self.offx, self.offy, self.vals):
result += val*numpy.roll( I, [dy,dx], axis=[0,1] )
return result
def correlate_spatial( self, I ):
"""Correlates the input image with the kernel in the spatial domain
"""
if not isinstance(I,numpy.ndarray) or I.ndim != 2 or not numpy.issubdtype(I.dtype,numpy.floating):
raise ValueError('Expected a 2D ndarray or float32 values')
result = numpy.zeros( I.shape, dtype=I.dtype )
for dx,dy,val in zip(self.offx, self.offy, self.vals):
result += val*numpy.roll( I, [-dy,-dx], axis=[0,1] )
return result
def convolve_fourier( self, I ):
"""Convolves the input image by the kernel in the Fourier domain
Args:
I (2d float32 array) input image to convolve with kernel
Raises:
ValueError when input is not a 2D ndarray or I.dtype is not numpy.floating subclass
Returns:
Convolution results as 2D ndarray of I.dtype elements
"""
if not isinstance(I,numpy.ndarray) or I.ndim != 2 or not numpy.issubdtype(I.dtype,numpy.floating):
raise ValueError('Expected a 2D ndarray or float32 values')
fK = self.spectrum( I.shape )
fI = numpy.fft.fft2( I )
return numpy.real( numpy.fft.ifft2( fK*fI ) )
def correlate_fourier( self, I ):
"""Correlates the input image by the kernel in the Fourier domain
Args:
I (2d float32 array) input image to convolve with kernel
Raises:
ValueError when input is not a 2D ndarray or I.dtype is not numpy.floating subclass
Returns:
Convolution results as 2D ndarray of I.dtype elements
"""
if not isinstance(I,numpy.ndarray) or I.ndim != 2 or not numpy.issubdtype(I.dtype,numpy.floating):
raise ValueError('Expected a 2D ndarray or float32 values')
fK = self.spectrum( I.shape )
fI = numpy.fft.fft2( I )
return numpy.real( numpy.fft.ifft2( numpy.conj(fK)*fI ) )
Testing & Validation
To ensure that indexing is done correctly, it's important to check that the kernel can represent an identity operation correctly for odd and even image sizes in both Fourier and spatial domains. After that, it's important that the convolution and correlation functions return the correct results.
This last point depends on whether the convolution or correlation filter is being defined. The difference between the two is mirroring horizontally and vertically. Personally, I find it most natural to define the correlation filter which coincides with the typical finite difference stencils. Generating some analytic data as well as some known finite difference kernels allows correct operation to be confirmed:
def TestSparseKernel2D():
"""Runs a series of test functions on the SparseKernel2D class"""
# local helper function that will raise an error if the
# results are insufficiently accurate
def MSE( x, ref ):
val = numpy.mean( numpy.power( x-ref, 2 ) )
if val > 1e-6:
raise ValueError('Values do not match!')
return val
# define a mean-squared error function
#MSE = lambda I, Ref: numpy.mean( numpy.power( I-Ref, 2 ) )
# generate an identity kernel
ident = SparseKernel2D( [0],[0],[1.0] )
# generate some test images
x,y = numpy.meshgrid( numpy.arange(0.,200.), numpy.arange(0.,100.) )
z = x+y
# check that convolving with the identity kernel
# reproduces the input for even mesh sizes
conv_z_s = ident.convolve_spatial( z )
conv_z_f = ident.convolve_fourier( z )
print('Identity test, even sizes: ',z.shape)
print('\tMSE spatial: %f'%MSE(conv_z_s,z) )
print('\tMSE fourier: %f'%MSE(conv_z_f,z) )
# check that convolving with the identity kernel
# reproduces the input for odd/even mesh sizes
tz = z[1:,:]
conv_z_s = ident.convolve_spatial( tz )
conv_z_f = ident.convolve_fourier( tz )
print('Identity test, odd/even sizes: ',tz.shape)
print('\tMSE spatial: %f'%MSE(conv_z_s,tz) )
print('\tMSE fourier: %f'%MSE(conv_z_f,tz) )
# check that convolving with the identity kernel
# reproduces the input for odd/even mesh sizes
tz = z[:,1:]
conv_z_s = ident.convolve_spatial( tz )
conv_z_f = ident.convolve_fourier( tz )
print('Identity test, even/odd sizes: ',tz.shape)
print('\tMSE spatial: %f'%MSE(conv_z_s,tz) )
print('\tMSE fourier: %f'%MSE(conv_z_f,tz) )
# check that convolving with the identity kernel
# reproduces the input for odd/odd mesh sizes
tz = z[:-1,1:]
conv_z_s = ident.convolve_spatial( tz )
conv_z_f = ident.convolve_fourier( tz )
print('Identity test, odd/odd sizes: ',tz.shape)
print('\tMSE spatial: %f'%MSE(conv_z_s,tz) )
print('\tMSE fourier: %f'%MSE(conv_z_f,tz) )
# generate first order finite difference formula
# try convolving in both the spatial and frequency
# domains
ddx = SparseKernel2D( [0,0],[-1,0],[-1.0,1.0] )
ddx_z_s = ddx.correlate_spatial( z )[1:-2,1:-2]
ddx_z_f = ddx.correlate_fourier( z )[1:-2,1:-2]
ones = numpy.ones( ddx_z_s.shape, dtype=numpy.float32 )
print('First order finite-difference d(x+y)/dx')
print('\tMSE spatial: %f' % MSE(ddx_z_s,ones) )
print('\tMSE fourier: %f' % MSE(ddx_z_f,ones) )
# generate first order finite difference formula
# try convolving in both the spatial and frequency
# domains
ddy = SparseKernel2D( [-1,0],[0,0],[-1.0,1.0] )
ddy_z_s = ddy.correlate_spatial( z )[1:-2,1:-2]
ddy_z_f = ddy.correlate_fourier( z )[1:-2,1:-2]
ones = numpy.ones( ddy_z_s.shape, dtype=numpy.float32 )
print('First order finite-difference d(x+y)/dy')
print('\tMSE spatial: %f' % MSE(ddy_z_s,ones) )
print('\tMSE fourier: %f' % MSE(ddy_z_f,ones) )
# now try the convolution functions, this simply
# flips the kernel about the central pixel
# horizontally and vertically. for the filters
# defined above, this negates the results
ddx_z_s = ddx.convolve_spatial( z )[1:-2,1:-2]
ddx_z_f = ddx.convolve_fourier( z )[1:-2,1:-2]
ones = numpy.ones( ddx_z_s.shape, dtype=numpy.float32 )
print('Convolved first order finite-difference d(x+y)/dx')
print('\tMSE spatial: %f' % MSE(ddx_z_s,-ones) )
print('\tMSE fourier: %f' % MSE(ddx_z_f,-ones) )
# generate first order finite difference formula
# try convolving in both the spatial and frequency
# domains
ddy_z_s = ddy.convolve_spatial( z )[1:-2,1:-2]
ddy_z_f = ddy.convolve_fourier( z )[1:-2,1:-2]
ones = numpy.ones( ddy_z_s.shape, dtype=numpy.float32 )
print('Convolved first order finite-difference d(x+y)/dy')
print('\tMSE spatial: %f' % MSE(ddy_z_s,-ones) )
print('\tMSE fourier: %f' % MSE(ddy_z_f,-ones) )
This prints:
Identity test, even sizes: (100, 200)
MSE spatial: 0.000000
MSE fourier: 0.000000
Identity test, odd/even sizes: (99, 200)
MSE spatial: 0.000000
MSE fourier: 0.000000
Identity test, even/odd sizes: (100, 199)
MSE spatial: 0.000000
MSE fourier: 0.000000
Identity test, odd/odd sizes: (99, 199)
MSE spatial: 0.000000
MSE fourier: 0.000000
First order finite-difference d(x+y)/dx
MSE spatial: 0.000000
MSE fourier: 0.000000
First order finite-difference d(x+y)/dy
MSE spatial: 0.000000
MSE fourier: 0.000000
Convolved first order finite-difference d(x+y)/dx
MSE spatial: 0.000000
MSE fourier: 0.000000
Convolved first order finite-difference d(x+y)/dy
MSE spatial: 0.000000
MSE fourier: 0.000000