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"""
*finite_difference.py* is the main package to compute finite differences in
1D, 2D, and 3D on numpy arrays (class FD_np) and pytorch tensors (class FD_torch).
The package supports first and second order derivatives and Neumann and linear extrapolation
boundary conditions (though the latter have not been tested extensively yet).
"""
from __future__ import absolute_import
# from builtins import object
from abc import ABCMeta, abstractmethod
import torch
from torch.autograd import Variable
import numpy as np
from future.utils import with_metaclass
class FD(with_metaclass(ABCMeta, object)):
"""
*FD* is the abstract class for finite differences. It includes most of the actual finite difference code,
but requires the definition (in a derived class) of the methods *get_dimension*, *create_zero_array*, and *get_size_of_array*.
In this way the numpy and pytorch versions can easily be derived. All the method expect BxXxYxZ format (i.e., they process a batch at a time)
"""
def __init__(self, spacing, bcNeumannZero=True):
"""
Constructor
:param spacing: 1D numpy array defining the spatial spacing, e.g., [0.1,0.1,0.1] for a 3D image
:param bcNeumannZero: Defines the boundary condition. If set to *True* (default) zero Neumann boundary conditions
are imposed. If set to *False* linear extrapolation is used (this is still experimental, but may be beneficial
for better boundary behavior)
"""
self.dim = len(spacing) # In my code, data_spacing is a list # spacing.size
"""spatial dimension"""
self.spacing = np.ones(self.dim)
"""spacing"""
self.bcNeumannZero = bcNeumannZero # if false then linear interpolation
"""should Neumann boundary conditions be used? (otherwise linear extrapolation)"""
if len(spacing) == 1: #spacing.size==1:
self.spacing[0] = spacing[0]
elif len(spacing) == 2: # spacing.size==2:
self.spacing[0] = spacing[0]
self.spacing[1] = spacing[1]
elif len(spacing) == 3: # spacing.size==3:
self.spacing[0] = spacing[0]
self.spacing[1] = spacing[1]
self.spacing[2] = spacing[2]
else:
print('Current dimension:', len(spacing))
raise ValueError('Finite differences are only supported in dimensions 1 to 3')
def dXb(self,I):
"""
Backward difference in x direction:
:math:`\\frac{dI(i)}{dx}\\approx\\frac{I_i-I_{i-1}}{h_x}`
:param I: Input image
:return: Returns the first derivative in x direction using backward differences
"""
return (I-self.xm(I))/self.spacing[0]
def dXf(self,I):
"""
Forward difference in x direction:
:math:`\\frac{dI(i)}{dx}\\approx\\frac{I_{i+1}-I_{i}}{h_x}`
:param I: Input image
:return: Returns the first derivative in x direction using forward differences
"""
return (self.xp(I)-I)/self.spacing[0]
def dXc(self,I):
"""
Central difference in x direction:
:math:`\\frac{dI(i)}{dx}\\approx\\frac{I_{i+1}-I_{i-1}}{2h_x}`
:param I: Input image
:return: Returns the first derivative in x direction using central differences
"""
return (self.xp(I)-self.xm(I))/(2*self.spacing[0])
def ddXc(self,I):
"""
Second deriative in x direction
:param I: Input image
:return: Returns the second derivative in x direction
"""
return (self.xp(I)-2*I+self.xm(I))/(self.spacing[0]**2)
def dYb(self,I):
"""
Same as dXb, but for the y direction
:param I: Input image
:return: Returns the first derivative in y direction using backward differences
"""
return (I-self.ym(I))/self.spacing[1]
def dYf(self,I):
"""
Same as dXf, but for the y direction
:param I: Input image
:return: Returns the first derivative in y direction using forward differences
"""
return (self.yp(I)-I)/self.spacing[1]
def dYc(self,I):
"""
Same as dXc, but for the y direction
:param I: Input image
:return: Returns the first derivative in y direction using central differences
"""
return (self.yp(I)-self.ym(I))/(2*self.spacing[1])
def ddYc(self,I):
"""
Same as ddXc, but for the y direction
:param I: Input image
:return: Returns the second derivative in the y direction
"""
return (self.yp(I)-2*I+self.ym(I))/(self.spacing[1]**2)
def dZb(self,I):
"""
Same as dXb, but for the z direction
:param I: Input image
:return: Returns the first derivative in the z direction using backward differences
"""
return (I - self.zm(I))/self.spacing[2]
def dZf(self, I):
"""
Same as dXf, but for the z direction
:param I: Input image
:return: Returns the first derivative in the z direction using forward differences
"""
return (self.zp(I)-I)/self.spacing[2]
def dZc(self, I):
"""
Same as dXc, but for the z direction
:param I: Input image
:return: Returns the first derivative in the z direction using central differences
"""
return (self.zp(I)-self.zm(I))/(2*self.spacing[2])
def ddZc(self,I):
"""
Same as ddXc, but for the z direction
:param I: Input iamge
:return: Returns the second derivative in the z direction
"""
return (self.zp(I)-2*I+self.zm(I))/(self.spacing[2]**2)
def lap(self, I):
"""
Compute the Lapacian of an image
!!!!!!!!!!!
IMPORTANT:
ALL THE FOLLOWING IMPLEMENTED CODE ADD 1 ON DIMENSION, WHICH REPRESENT BATCH DIMENSION.
THIS IS FOR COMPUTATIONAL EFFICIENCY.
:param I: Input image [batch, X,Y,Z]
:return: Returns the Laplacian
"""
ndim = self.getdimension(I)
if ndim == 1+1:
return self.ddXc(I)
elif ndim == 2+1:
return (self.ddXc(I) + self.ddYc(I))
elif ndim == 3+1:
return (self.ddXc(I) + self.ddYc(I) + self.ddZc(I))
else:
raise ValueError('Finite differences are only supported in dimensions 1 to 3')
def grad_norm_sqr_c(self, I):
"""
Computes the gradient norm of an image
!!!!!!!!!!!
IMPORTANT:
ALL THE FOLLOWING IMPLEMENTED CODE ADD 1 ON DIMENSION, WHICH REPRESENT BATCH DIMENSION.
THIS IS FOR COMPUTATIONAL EFFICIENCY.
:param I: Input image [batch, X,Y,Z]
:return: returns ||grad I||^2
"""
ndim = self.getdimension(I)
if ndim == 1 + 1:
return self.dXc(I)**2
elif ndim == 2 + 1:
return (self.dXc(I)**2 + self.dYc(I)**2)
elif ndim == 3 + 1:
return (self.dXc(I)**2 + self.dYc(I)**2 + self.dZc(I)**2)
else:
raise ValueError('Finite differences are only supported in dimensions 1 to 3')
def grad_norm_sqr_f(self, I):
"""
Computes the gradient norm of an image
!!!!!!!!!!!
IMPORTANT:
ALL THE FOLLOWING IMPLEMENTED CODE ADD 1 ON DIMENSION, WHICH REPRESENT BATCH DIMENSION.
THIS IS FOR COMPUTATIONAL EFFICIENCY.
:param I: Input image [batch, X,Y,Z]
:return: returns ||grad I||^2
"""
ndim = self.getdimension(I)
if ndim == 1 + 1:
return self.dXf(I)**2
elif ndim == 2 + 1:
return (self.dXf(I)**2 + self.dYf(I)**2)
elif ndim == 3 + 1:
return (self.dXf(I)**2 + self.dYf(I)**2 + self.dZf(I)**2)
else:
raise ValueError('Finite differences are only supported in dimensions 1 to 3')
def grad_norm_sqr_b(self, I):
"""
Computes the gradient norm of an image
!!!!!!!!!!!
IMPORTANT:
ALL THE FOLLOWING IMPLEMENTED CODE ADD 1 ON DIMENSION, WHICH REPRESENT BATCH DIMENSION.
THIS IS FOR COMPUTATIONAL EFFICIENCY.
:param I: Input image [batch, X,Y,Z]
:return: returns ||grad I||^2
"""
ndim = self.getdimension(I)
if ndim == 1 + 1:
return self.dXb(I)**2
elif ndim == 2 + 1:
return (self.dXb(I)**2 + self.dYb(I)**2)
elif ndim == 3 + 1:
return (self.dXb(I)**2 + self.dYb(I)**2 + self.dZb(I)**2)
else:
raise ValueError('Finite differences are only supported in dimensions 1 to 3')
@abstractmethod
def getdimension(self,I):
"""
Abstract method to return the dimension of an input image I
:param I: Input image
:return: Returns the dimension of the image I
"""
pass
@abstractmethod
def create_zero_array(self, sz):
"""
Abstract method to create a zero array of a given size, sz. E.g., sz=[10,2,5]
:param sz: Size array
:return: Returns a zero array of the specified size
"""
pass
@abstractmethod
def get_size_of_array(self, A):
"""
Abstract method to return the size of an array (as a vector)
:param A: Input array
:return: Returns its size (e.g., [5,10] or [3,4,6]
"""
pass
def xp(self,I):
"""
!!!!!!!!!!!
IMPORTANT:
ALL THE FOLLOWING IMPLEMENTED CODE ADD 1 ON DIMENSION, WHICH REPRESENT BATCH DIMENSION.
THIS IS FOR COMPUTATIONAL EFFICIENCY.
Returns the values for x-index incremented by one (to the right in 1D)
:param I: Input image [batch, X, Y,Z]
:return: Image with values at an x-index one larger
"""
rxp = self.create_zero_array( self.get_size_of_array( I ) )
ndim = self.getdimension(I)
if ndim == 1+1:
rxp[:,0:-1] = I[:,1:]
if self.bcNeumannZero:
rxp[:,-1] = I[:,-1]
else:
rxp[:,-1] = 2*I[:,-1]-I[:,-2]
elif ndim == 2+1:
rxp[:,0:-1,:] = I[:,1:,:]
if self.bcNeumannZero:
rxp[:,-1,:] = I[:,-1,:]
else:
rxp[:,-1,:] = 2*I[:,-1,:]-I[:,-2,:]
elif ndim == 3+1:
rxp[:,0:-1,:,:] = I[:,1:,:,:]
if self.bcNeumannZero:
rxp[:,-1,:,:] = I[:,-1,:,:]
else:
rxp[:,-1,:,:] = 2*I[:,-1,:,:]-I[:,-2,:,:]
else:
raise ValueError('Finite differences are only supported in dimensions 1 to 3')
return rxp
def xm(self,I):
"""
!!!!!!!!!!!
IMPORTANT:
ALL THE FOLLOWING IMPLEMENTED CODE ADD 1 ON DIMENSION, WHICH REPRESENT BATCH DIMENSION.
THIS IS FOR COMPUTATIONAL EFFICIENCY.
Returns the values for x-index decremented by one (to the left in 1D)
:param I: Input image [batch, X, Y, Z]
:return: Image with values at an x-index one smaller
"""
rxm = self.create_zero_array( self.get_size_of_array( I ) )
ndim = self.getdimension(I)
if ndim == 1+1:
rxm[:,1:] = I[:,0:-1]
if self.bcNeumannZero:
rxm[:,0] = I[:,0]
else:
rxm[:,0] = 2*I[:,0]-I[:,1]
elif ndim == 2+1:
rxm[:,1:,:] = I[:,0:-1,:]
if self.bcNeumannZero:
rxm[:,0,:] = I[:,0,:]
else:
rxm[:,0,:] = 2*I[:,0,:]-I[:,1,:]
elif ndim == 3+1:
rxm[:,1:,:,:] = I[:,0:-1,:,:]
if self.bcNeumannZero:
rxm[:,0,:,:] = I[:,0,:,:]
else:
rxm[:,0,:,:] = 2*I[:,0,:,:]-I[:,1,:,:]
else:
raise ValueError('Finite differences are only supported in dimensions 1 to 3')
return rxm
def yp(self, I):
"""
!!!!!!!!!!!
IMPORTANT:
ALL THE FOLLOWING IMPLEMENTED CODE ADD 1 ON DIMENSION, WHICH REPRESENT BATCH DIMENSION.
THIS IS FOR COMPUTATIONAL EFFICIENCY.
Same as xp, but for the y direction
:param I: Input image
:return: Image with values at y-index one larger
"""
ryp = self.create_zero_array( self.get_size_of_array( I ) )
ndim = self.getdimension(I)
if ndim == 2+1:
ryp[:,:,0:-1] = I[:,:,1:]
if self.bcNeumannZero:
ryp[:,:,-1] = I[:,:,-1]
else:
ryp[:,:,-1] = 2*I[:,:,-1]-I[:,:,-2]
elif ndim == 3+1:
ryp[:,:,0:-1,:] = I[:,:,1:,:]
if self.bcNeumannZero:
ryp[:,:,-1,:] = I[:,:,-1,:]
else:
ryp[:,:,-1,:] = 2*I[:,:,-1,:]-I[:,:,-2,:]
else:
print('Current dimension:', ndim-1)
raise ValueError('Finite differences are only supported in dimensions 1 to 3')
return ryp
def ym(self, I):
"""
Same as xm, but for the y direction
!!!!!!!!!!!
IMPORTANT:
ALL THE FOLLOWING IMPLEMENTED CODE ADD 1 ON DIMENSION, WHICH REPRESENT BATCH DIMENSION.
THIS IS FOR COMPUTATIONAL EFFICIENCY.
Returns the values for x-index decremented by one (to the left in 1D)
:param I: Input image [batch, X, Y, Z]
:return: Image with values at y-index one smaller
"""
rym = self.create_zero_array( self.get_size_of_array( I ) )
ndim = self.getdimension(I)
if ndim == 2+1:
rym[:,:,1:] = I[:,:,0:-1]
if self.bcNeumannZero:
rym[:,:,0] = I[:,:,0]
else:
rym[:,:,0] = 2*I[:,:,0]-I[:,:,1]
elif ndim == 3+1:
rym[:,:,1:,:] = I[:,:,0:-1,:]
if self.bcNeumannZero:
rym[:,:,0,:] = I[:,:,0,:]
else:
rym[:,:,0,:] = 2*I[:,:,0,:]-I[:,:,1,:]
else:
raise ValueError('Finite differences are only supported in dimensions 1 to 3')
return rym
def zp(self, I):
"""
Same as xp, but for the z direction
!!!!!!!!!!!
IMPORTANT:
ALL THE FOLLOWING IMPLEMENTED CODE ADD 1 ON DIMENSION, WHICH REPRESENT BATCH DIMENSION.
THIS IS FOR COMPUTATIONAL EFFICIENCY.
Returns the values for x-index decremented by one (to the left in 1D)
:param I: Input image [batch, X, Y, Z]
:return: Image with values at z-index one larger
"""
rzp = self.create_zero_array( self.get_size_of_array( I ) )
ndim = self.getdimension(I)
if ndim == 3+1:
rzp[:,:,:,0:-1] = I[:,:,:,1:]
if self.bcNeumannZero:
rzp[:,:,:,-1] = I[:,:,:,-1]
else:
rzp[:,:,:,-1] = 2*I[:,:,:,-1]-I[:,:,:,-2]
else:
raise ValueError('Finite differences are only supported in dimensions 1 to 3')
return rzp
def zm(self, I):
"""
Same as xm, but for the z direction
!!!!!!!!!!!
IMPORTANT:
ALL THE FOLLOWING IMPLEMENTED CODE ADD 1 ON DIMENSION, WHICH REPRESENT BATCH DIMENSION.
THIS IS FOR COMPUTATIONAL EFFICIENCY.
Returns the values for x-index decremented by one (to the left in 1D)
:param I: Input image [batch, X, Y, Z]
:return: Image with values at z-index one smaller
"""
rzm = self.create_zero_array( self.get_size_of_array( I ) )
ndim = self.getdimension(I)
if ndim == 3+1:
rzm[:,:,:,1:] = I[:,:,:,0:-1]
if self.bcNeumannZero:
rzm[:,:,:,0] = I[:,:,:,0]
else:
rzm[:,:,:,0] = 2*I[:,:,:,0]-I[:,:,:,1]
else:
raise ValueError('Finite differences are only supported in dimensions 1 to 3')
return rzm
class FD_np(FD):
"""
Defnitions of the abstract methods for numpy
"""
def __init__(self,spacing,bcNeumannZero=True):
"""
Constructor for numpy finite differences
:param spacing: spatial spacing (array with as many entries as there are spatial dimensions)
:param bcNeumannZero: Specifies if zero Neumann conditions should be used (if not, uses linear extrapolation)
"""
super(FD_np, self).__init__(spacing,bcNeumannZero)
def getdimension(self,I):
"""
Returns the dimension of an image
:param I: input image
:return: dimension of the input image
"""
return I.ndim
def create_zero_array(self, sz):
"""
Creates a zero array
:param sz: size of the zero array, e.g., [3,4,2]
:return: the zero array
"""
return np.zeros( sz )
def get_size_of_array(self, A):
"""
Returns the size (shape in numpy) of an array
:param A: input array
:return: shape/size
"""
return A.shape
class FD_torch(FD):
"""
Defnitions of the abstract methods for torch
"""
def __init__(self,spacing,device,bcNeumannZero=True):
"""
Constructor for torch finite differences
:param spacing: spatial spacing (array with as many entries as there are spatial dimensions)
:param bcNeumannZero: Specifies if zero Neumann conditions should be used (if not, uses linear extrapolation)
"""
super(FD_torch, self).__init__(spacing,bcNeumannZero)
self.device = device
def getdimension(self,I):
"""
Returns the dimension of an image
:param I: input image
:return: dimension of the input image
"""
return I.dim()
def create_zero_array(self, sz):
"""
Creats a zero array
:param sz: size of the array, e.g., [3,4,2]
:return: the zero array
"""
return torch.zeros(sz).float().to(self.device)
def get_size_of_array(self, A):
"""
Returns the size (size()) of an array
:param A: input array
:return: shape/size
"""
return A.size() |