Directional Functions

This is a documentation for CorrelationFunctions.Directional module. The documentation is divided into the following topics:

  • Boundary Conditions page describes boundary conditions when calculations cross the boundary of a system.
  • Directions page describes directions along which the correlation functions are computed.
  • Correlation Functions page contains the exhaustive list of correlation functions supported by this package.
  • Results page contains comparison of correlation functions from this package with some known theoretical results.

Boundary Conditions

Suppose you are calculating correlation functions for a sequence of length $N$. Calculation of a vast majority of the functions in this package can be reduced to a calculation of autocorrelation between two sequences, $a$ and $b$:

\[h_k = \frac{\sum\limits_{l=0}^{\tilde{N}} a_l b_{k+l}}{\tilde{N}}\]

where $\tilde{N}$ is a normalization factor. There are few boundary conditions which define which value $\tilde{N}$ can take. Here they are:

  • Periodic boundary conditions. In this case $\tilde{N} = N$. Indexing to $a$ and $b$ is performed modulo $N$.
  • Non-periodic boundary conditions. In this case $\tilde{N}_k = N - k$.
  • Calculations using a mask. In this case $l$ runs not from $0$ to $\tilde{N}$, but can take only values allowed by a boolean mask, which must be of the same length as the input sequence (or, more generally, of the same shape as the input array).

Boundary conditions are selected by a keyword argument mode. The mode is a value of the type AbstractMode. Constructors for descendants of that type are following:

CorrelationFunctions.Utilities.Mask — Type
Mask(mask)

Calculation mode using a mask. The mask must be a bit array of the same shape as an input array for a correlation function. The result of computations is of the same shape as for non-periodic mode. NaN elements of the result mean that there was not a single trial at that point.

See also: AbstractMode.

Directions

Functions based on two-point statistics from Directional module will require a direction along which the function is calculated (usually as their third argument). You can specify these directions:

The module Map can use these directions to extract directional information from correlation maps.

These rules can help you to memoize the correspondence between symbolic designations and vectors:

  • DirFoo types can contain from one to three characters X, Y and Z. Each character can occur only once (there is a type DirXYZ, but no type DirXXY).
  • When a character does not occur is a designation (e.g, there is no Z in DirXY) that coordinate remains constant in a slice (in the example above $z = \text{const}$).
  • The names of the axes have a "natural order" which is X, Y, Z. In a designation, the first axis which breaks that order get the minus sign in the direction vector (e.g. DirXZY equals to (1, -1, 1) because Y is in the third position, not in the second, DirZX equals to (-1, 0, 1) because X is in the second position, not in the first, etc.)

Functions based on three-point statistics require a set of points in which they are calculated (usually as the third and the fourth arguments). This set can be generated by Utilities.right_triangles function.

Correlation Functions

Two-point statistics

CorrelationFunctions.Directional.s2 — Function
s2(array, phase, direction[; len] [,mode = NonPeriodic()])

Calculate S₂ (two point) correlation function for one-, two- or three-dimensional multiphase system.

S₂(x) equals to probability that corner elements of a line segment with the length x cut from the array belong to the same phase. This implementation calculates S₂(x) for all xes in the range from 1 to len which defaults to half of the minimal dimenstion of the array.

Examples

julia> s2([1,1,1,0,1,1], 1, DirX(); len = 6)
6-element Vector{Float64}:
 0.8333333333333334
 0.6
 0.5
 0.6666666666666666
 1.0
 1.0

See also: Utilities.AbstractDirection, Utilities.AbstractMode.

CorrelationFunctions.Directional.c2 — Function
c2(array, phase, direction[; len,] [mode = NonPeriodic])

Calculate C₂ (cluster) correlation function for one-, two- or three-dimensional multiphase system.

C₂(x) equals to probability that corner elements of a line segment with the length x cut from the array belong to the same cluster of the specific phase. This implementation calculates C2 for all xes in the range from 1 to len which defaults to half of the minimal dimension of the array.

Examples

julia> c2([1,1,1,0,1,1], 1, DirX(); len = 6)
6-element Array{Float64,1}:
 0.8333333333333333
 0.5999999999999999
 0.24999999999999994
 2.4671622769447922e-17
 9.25185853854297e-17
 5.181040781584064e-16

For a list of possible directions, see also: Utilities.AbstractDirection, Utilities.AbstractMode.

CorrelationFunctions.Directional.surf2 — Function
surf2(array, phase, direction[; len] [,mode = NonPeriodic()][, filter])

Calculate surface-surface correlation function for one-, two- or three-dimensional multiphase system. This implementation calculates surface-surface function for all xs in the range from 1 to len which defaults to half of the minimal dimension of the array.

You can chose how an edge between phases is selected by passing filter argument of type Utilities.AbstractKernel.

If phase is a function it is applied to array to select the phase of interest, otherwise the phase of interest is selected by testing elements of array for equality with phase.

See also: Utilities.AbstractDirection, Utilities.AbstractMode, Utilities.AbstractKernel.

CorrelationFunctions.Directional.surfvoid — Function
surfvoid(array, phase, direction[; len] [, mode = NonPeriodic()][, filter])

Calculate surface-void correlation function for one-, two- or three-dimensional multiphase system. This implementation calculates surface-void function for all xs in the range from 1 to len which defaults to half of the minimal dimension of the array.

You can chose how an edge between phases is selected by passing filter argument of type Utilities.AbstractKernel.

If phase is a function it is applied to array to select the phase of interest, otherwise the phase of interest is selected by testing elements of array for equality with phase.

Void phase is assumed to be 0.

See also: Utilities.AbstractDirection, Utilities.AbstractMode, Utilities.AbstractKernel.

Three-point statistics

CorrelationFunctions.Directional.s3 — Function
s3(array, ps1, ps2[, mode = NonPeriodic()])

Calculate the three-point correlation function in an array of points.

Two arguments ps1 and ps2 must be arrays of N-tuples of integers (where N is a dimensionality of the input array) broadcastable to the same size. Periodic or zero-padding boundary conditions are selected with the choose of mode argument.

The following invariants hold:

julia> data = rand(Bool, (100, 100, 100));
julia> shiftsx = [(i, 0, 0) for i in 0:49];
julia> shiftsy = [(0, i, 0) for i in 0:49];
julia> shiftsz = [(0, 0, i) for i in 0:49];
julia> s2x = D.s2(data, 1, U.DirX());
julia> s2y = D.s2(data, 1, U.DirY());
julia> s2z = D.s2(data, 1, U.DirZ());
julia> s2x_ = D.s3(data, [(0,0,0)], shiftsx);
julia> s2y_ = D.s3(data, [(0,0,0)], shiftsy);
julia> s2z_ = D.s3(data, [(0,0,0)], shiftsz);

julia> s2x == s2x_
true

julia> s2y == s2y_
true

julia> s2z == s2z_
true

See also: right_triangles, s2.

s3(array, phase, ps1, ps2[; mode = NonPeriodic()])

The same as s3(array .== phase; ...). Kept for consistency with other parts of the API.

CorrelationFunctions.Directional.c3 — Function
c3(array, phase[; planes :: Vector{AbstractPlane}, len, mode = NonPeriodic()])

Calculate three-point cluster correlation function.

This function is is internally calculated using s3 and hence uses the same sampling pattern and returns a result in the same format.

See also: s3, AbstractPlane.

CorrelationFunctions.Directional.surf3 — Function
surf3(array, ps1, ps2[; mode = NonPeriodic()][, filter :: AbstractKernel])

Calculate surface-surface-surface ($F_{sss}$) correlation function.

This function is is internally calculated using s3 and hence uses the same sampling pattern and returns a result in the same format.

You can chose how an edge between phases is selected by passing filter argument of type Utilities.AbstractKernel.

See also: s3, right_triangles, AbstractKernel.

surf3(array, phase[; mode = NonPeriodic()][, filter = ConvKernel(7)])

The same as surf3(array .== phase; ...). Kept for consistency with other parts of the API.

CorrelationFunctions.Directional.surf2void — Function
surf2void(array, phase, ps1, ps2[, void_phase = 0][; mode = NonPeriodic()][, filter :: AbstractKernel])

Calculate surface-surface-void ($F_{ssv}$) correlation function.

This function is is internally calculated using s3 and hence uses the same sampling pattern and returns a result in the same format.

You can chose how an edge between phases is selected by passing filter argument of type Utilities.AbstractKernel.

See also: s3, right_triangles, AbstractKernel.

CorrelationFunctions.Directional.surfvoid2 — Function
surfvoid2(array, phase, ps1, ps2[, void_phase = 0][; mode = NonPeriodic()][, filter :: AbstractKernel])

Calculate surface-void-void ($F_{svv}$) correlation function.

This function is is internally calculated using s3 and hence uses the same sampling pattern and returns a result in the same format.

You can chose how an edge between phases is selected by passing filter argument of type Utilities.AbstractKernel.

See also: s3, AbstractPlane, AbstractKernel.

Other correlation functions

CorrelationFunctions.Directional.pore_size — Function
pore_size(array, phase = 0; mode = NonPeriodic())

Calculate pore size correlation function for one-, two- or three-dimensional multiphase systems.

This implementation returns an array of pore sizes where each size is equal to the distance from a particular point in the pore to the closest point not belonging to the phase phase.

Example

julia> data = [1 1 1 1 1; 1 1 0 1 1; 1 0 0 0 1; 1 1 0 1 1; 1 1 1 1 1]
5×5 Matrix{Int64}:
 1  1  1  1  1
 1  1  0  1  1
 1  0  0  0  1
 1  1  0  1  1
 1  1  1  1  1

julia> D.pore_size(data, 0)
5-element Vector{Float64}:
 1.0
 1.0
 1.4142135623730951
 1.0
 1.0
CorrelationFunctions.Directional.chord_length — Function
chord_length(array, phase, direction)

Calculate the chord length correlation function for one-, two- or three-dimensional multiphase systems.

A chord is a line segment which touches the boundary of a same-phase cluster with its ends.

This implementation returns an array of chord lengths where each length is equal to a number of voxels in the phase phase belonging to a chord.

Examples

julia> chord_length([1, 0, 0, 0, 0, 1, 0, 1], 0, DirX())
2-element Vector{Int64}:
 4
 1

For a list of possible dimensions, see also: Utilities.AbstractDirection.

CorrelationFunctions.Directional.l2 — Function
l2(array, phase, direction[; len][, mode = NonPeriodic()])

Calculate L₂ (lineal path) correlation function for one-, two- or three-dimensional multiphase system.

L₂(x) equals to probability that all elements of a line segment with length x cut from the array belong to the same phase. This implementation calculates L₂(x) for all xes in the range from 1 to len which defaults to half of the minimal dimension of the array.

Examples

julia> l2([1,1,1,0,1,1], 1, DirX(); len = 6)
6-element Array{Float64,1}:
 0.8333333333333334
 0.6
 0.25
 0.0
 0.0
 0.0

For a list of possible dimensions, see also: Utilities.AbstractDirection, [Utilities.AbstractMode])(@ref).

The pore_size function is also reexported from CorrelationFunctions directly, not being actually a "directional" function.

Results

CorrelationFunctions.jl is tested on overlapping disks and balls of constant radius $R$ with centers generated by Poisson process with parameter $\lambda$ (see section 5.1 of Random Heterogeneous Materials). An example of a two-dimensional two-phase system generated in this way is on the picture ($R = 25$ and $\lambda = 5 \cdot 10^{-4}$):

disks

Plots of all correlation functions calculated by CorrelationFunctions.jl for overlapping disks along with their theoretical values are given below. There are also plots of relative errors calculated as

\[\text{err}(x) = \mid \frac{\text{calculation}(x) - \text{theory}(x)}{\text{theory}(x)} \mid\]

Two-dimensional systems

Methodology

All functions in this section with exception of pore size and chord length functions are calculated on 15 random datasets generated with parameters $R = 25$ and $\lambda = 5 \cdot 10^{-4}$. Each dataset is an image with dimensions 4000x4000 pixels. The final result is an average of results on those 15 datasets. When function fastly decreases to zero a plot of a natural logarithm of that function is provided.

Pore size and chord length functions are calculated on one 4000x4000 dataset with the same parameters as above. A theoretical value is computed by averaging a theoretical function across each bin of a histogram returned by pore_size or chord_length function. Because both pore size and cord length functions decrease to zero with increase of their arguments, the relative errors are calculated for the corresponding cummulative distribution functions.

All functions are called with default optional arguments unless explicitly stated otherwise.

Two point $S_2(x)$ function

S2Error
s2s2 error

Lineal path $L_2(x)$ function

L2Error
l2l2 error

Surface-surface $F_{ss}(x)$ function

Surface-surfaceError
ssss error

Surface-void $F_{sv}(x)$ function

Surface-voidError
ssss error

Pore size $P(x)$ function

Pore sizeError
ssss error

Chord length $p(x)$ function

Chord length function chord_length was called with parameter nbins = 30.

Chord lengthError
ssss error

Three-dimensional systems

Methodology

The idea is the same as in two-dimensional case, but chosen parameters are slightly different. The functions are averaged over 5 500x500x500 datasets with ball radius $R = 20$ and Poisson process parameter $\lambda = 3 \cdot 10^{-5}$.

Two point $S_2(x)$ function

S2Error
s2s2 error

Lineal path $L_2(x)$ function

L2Error
l2l2 error

Surface-surface $F_{ss}(x)$ function

Surface-surfaceError
ssss error

Surface-void $F_{sv}(x)$ function

Surface-voidError
ssss error

Pore size $P(x)$ function

Pore sizeError
ssss error

Chord length $p(x)$ function

Chord length function chord_length was called with parameter nbins = 30.

Chord lengthError
ssss error