Summary and function reference

Summary and function reference

Below, [] in an argument list means an optional argument.

Image loading and saving

using FileIO
img = load("myimage.png")
save("imagecopy.jpg", img)

Standard test images are available in the TestImages package:

using TestImages
img = testimage("mandrill")

Image construction, conversion, and views

Any array can be treated as an Image. In graphical environments, only arrays with Colorant element types (Gray, RGB, ARGB, etc.) are automatically displayed as images.

ImageCore.colorviewFunction.
colorview(C, A)

returns a view of the numeric array A, interpreting successive elements of A as if they were channels of Colorant C. This is almost identical to ColorView{C}(A), except that if A is a ChannelView, it will simply return the parent of A, or use reinterpret when appropriate. Consequently, the output may not be a ColorView array.

Of relevance for types like RGB and BGR, the elements of A are interpreted in constructor-argument order, not memory order (see reinterpret if you want to use memory order).

Example

A = rand(3, 10, 10)
img = colorview(RGB, A)
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colorview(C, gray1, gray2, ...) -> imgC

Combine numeric/grayscale images gray1, gray2, etc., into the separate color channels of an array imgC with element type C<:Colorant.

As a convenience, the constant zeroarray fills in an array of matched size with all zeros.

Example

imgC = colorview(RGB, r, zeroarray, b)

creates an image with r in the red chanel, b in the blue channel, and nothing in the green channel.

See also: StackedView.

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ColorView{C}(A)

creates a "view" of the numeric array A, interpreting the first dimension of A as if were the channels of a Colorant C. The first dimension must have the proper number of elements for the constructor of C. For example, if A is a 3-by-m-by-n N0f8 array, ColorView{RGB}(A) will create an m-by-n array with element type RGB{N0f8}. Color spaces with a single element (i.e., grayscale) do not "consume" the first dimension of A.

Of relevance for types like RGB and BGR, the elements of A are interpreted in constructor-argument order, not memory order (see reinterpret if you want to use memory order).

The opposite transformation is implemented by ChannelView. See also colorview.

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ImageCore.channelviewFunction.
channelview(A)

returns a view of A, splitting out (if necessary) the color channels of A into a new first dimension. This is almost identical to ChannelView(A), except that if A is a ColorView, it will simply return the parent of A, or will use reinterpret when appropriate. Consequently, the output may not be a ChannelView array.

Of relevance for types like RGB and BGR, the channels of the returned array will be in constructor-argument order, not memory order (see reinterpret if you want to use memory order).

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ChannelView(A)

creates a "view" of the Colorant array A, splitting out (if necessary) the separate color channels of eltype(A) into a new first dimension. For example, if A is a m-by-n RGB{N0f8} array, ChannelView(A) will return a 3-by-m-by-n N0f8 array. Color spaces with a single element (i.e., grayscale) do not add a new first dimension of A.

Of relevance for types like RGB and BGR, the channels of the returned array will be in constructor-argument order, not memory order (see reinterpret if you want to use memory order).

The opposite transformation is implemented by ColorView. See also channelview.

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ImageCore.normedviewFunction.
normedview([T], img::AbstractArray{Unsigned})

returns a "view" of img where the values are interpreted in terms of Normed number types. For example, if img is an Array{UInt8}, the view will act like an Array{N0f8}. Supply T if the element type of img is UInt16, to specify whether you want a N6f10, N4f12, N2f14, or N0f16 result.

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ImageCore.rawviewFunction.
rawview(img::AbstractArray{FixedPoint})

returns a "view" of img where the values are interpreted in terms of their raw underlying storage. For example, if img is an Array{N0f8}, the view will act like an Array{UInt8}.

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permuteddimsview(A, perm)

returns a "view" of A with its dimensions permuted as specified by perm. This is like permutedims, except that it produces a view rather than a copy of A; consequently, any manipulations you make to the output will be mirrored in A. Compared to the copy, the view is much faster to create, but generally slower to use.

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StackedView(B, C, ...) -> A

Present arrays B, C, etc, as if they are separate channels along the first dimension of A. In particular,

B == A[1,:,:...]
C == A[2,:,:...]

and so on. Combined with colorview, this allows one to combine two or more grayscale images into a single color image.

See also: colorview.

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Aspad = paddedviews(fillvalue, A1, A2, ....)

Pad the arrays A1, A2, ..., to a common size or set of indices, chosen as the span of indices enclosing all of the input arrays.

Example:

julia> a1 = reshape([1,2], 2, 1)
2×1 Array{Int64,2}:
 1
 2

julia> a2 = [1.0,2.0]'
1×2 Array{Float64,2}:
 1.0  2.0

julia> a1p, a2p = paddedviews(0, a1, a2);

julia> a1p
2×2 PaddedViews.PaddedView{Int64,2,Tuple{Base.OneTo{Int64},Base.OneTo{Int64}},Array{Int64,2}}:
 1  0
 2  0

julia> a2p
2×2 PaddedViews.PaddedView{Float64,2,Tuple{Base.OneTo{Int64},Base.OneTo{Int64}},Array{Float64,2}}:
 1.0  2.0
 0.0  0.0
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Images with defined geometry and axis meaning can be constructed using the AxisArrays package:

using AxisArrays
img = AxisArray(A, (:y, :x, :time), (0.25μm, 0.25μm, 0.125s))  # see Unitful.jl for units

Custom metadata can be added as follows:

img = ImageMeta(A, date=now(), patientID=12345)

Any of these operations may be composed together, e.g., if you have an m×n×3 UInt8 array, you can put it in canonical RGB format and add metadata:

img = ImageMeta(colorview(RGB, normedview(permuteddimsview(A, (3,1,2)))), sample="control")

Traits

These functions are the preferred way to access certain types of "internal" data about an image. They can sometimes be useful in allowing you to write generic code.

pixelspacing(img) -> (sx, sy, ...)

Return a tuple representing the separation between adjacent pixels along each axis of the image. Defaults to (1,1,...). Use ImagesAxes for images with anisotropic spacing or to encode the spacing using physical units.

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spacedirections(img) -> (axis1, axis2, ...)

Return a tuple-of-tuples, each axis[i] representing the displacement vector between adjacent pixels along spatial axis i of the image array, relative to some external coordinate system ("physical coordinates").

By default this is computed from pixelspacing, but you can set this manually using ImagesMeta.

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spacedirections(img)

Using ImageMetadata, you can set this property manually. For example, you could indicate that a photograph was taken with the camera tilted 30-degree relative to vertical using

img["spacedirections"] = ((0.866025,-0.5),(0.5,0.866025))

If not specified, it will be computed from pixelspacing(img), placing the spacing along the "diagonal". If desired, you can set this property in terms of physical units, and each axis can have distinct units.

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ImageCore.sdimsFunction.
sdims(img)

Return the number of spatial dimensions in the image. Defaults to the same as ndims, but with ImagesAxes you can specify that some axes correspond to other quantities (e.g., time) and thus not included by sdims.

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coords_spatial(img)

Return a tuple listing the spatial dimensions of img.

Note that a better strategy may be to use ImagesAxes and take slices along the time axis.

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size_spatial(img)

Return a tuple listing the sizes of the spatial dimensions of the image. Defaults to the same as size, but using ImagesAxes you can mark some axes as being non-spatial.

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indices_spatial(img)

Return a tuple with the indices of the spatial dimensions of the image. Defaults to the same as indices, but using ImagesAxes you can mark some axes as being non-spatial.

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ImageCore.nimagesFunction.
nimages(img)

Return the number of time-points in the image array. Defaults to

  1. Use ImagesAxes if you want to use an explicit time dimension.

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assert_timedim_last(img)

Throw an error if the image has a time dimension that is not the last dimension.

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Element transformation and intensity scaling

ImageCore.clamp01Function.
clamp01(x) -> y

Produce a value y that lies between 0 and 1, and equal to x when x is already in this range. Equivalent to clamp(x, 0, 1) for numeric values. For colors, this function is applied to each color channel separately.

See also: clamp01nan.

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ImageCore.clamp01nanFunction.
clamp01nan(x) -> y

Similar to clamp01, except that any NaN values are changed to 0.

See also: clamp01.

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ImageCore.scaleminmaxFunction.
scaleminmax(min, max) -> f
scaleminmax(T, min, max) -> f

Return a function f which maps values less than or equal to min to 0, values greater than or equal to max to 1, and uses a linear scale in between. min and max should be real values.

Optionally specify the return type T. If T is a colorant (e.g., RGB), then scaling is applied to each color channel.

Examples

Example 1

julia> f = scaleminmax(-10, 10)
(::#9) (generic function with 1 method)

julia> f(10)
1.0

julia> f(-10)
0.0

julia> f(5)
0.75

Example 2

julia> c = RGB(255.0,128.0,0.0)
RGB{Float64}(255.0,128.0,0.0)

julia> f = scaleminmax(RGB, 0, 255)
(::#13) (generic function with 1 method)

julia> f(c)
RGB{Float64}(1.0,0.5019607843137255,0.0)

See also: takemap.

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ImageCore.scalesignedFunction.
scalesigned(maxabs) -> f

Return a function f which scales values in the range [-maxabs, maxabs] (clamping values that lie outside this range) to the range [-1, 1].

See also: colorsigned.

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scalesigned(min, center, max) -> f

Return a function f which scales values in the range [min, center] to [-1,0] and [center,max] to [0,1]. Values smaller than min/max get clamped to min/max, respectively.

See also: colorsigned.

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ImageCore.colorsignedFunction.
colorsigned()
colorsigned(colorneg, colorpos) -> f
colorsigned(colorneg, colorcenter, colorpos) -> f

Define a function that maps negative values (in the range [-1,0]) to the linear colormap between colorneg and colorcenter, and positive values (in the range [0,1]) to the linear colormap between colorcenter and colorpos.

The default colors are:

  • colorcenter: white

  • colorneg: green1

  • colorpos: magenta

See also: scalesigned.

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ImageCore.takemapFunction.
takemap(f, A) -> fnew
takemap(f, T, A) -> fnew

Given a value-mapping function f and an array A, return a "concrete" mapping function fnew. When applied to elements of A, fnew should return valid values for storage or display, for example in the range from 0 to 1 (for grayscale) or valid colorants. fnew may be adapted to the actual values present in A, and may not produce valid values for any inputs not in A.

Optionally one can specify the output type T that fnew should produce.

Example:

julia> A = [0, 1, 1000];

julia> f = takemap(scaleminmax, A)
(::#7) (generic function with 1 method)

julia> f.(A)
3-element Array{Float64,1}:
 0.0
 0.001
 1.0
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Storage-type transformation

ImageCore.float32Function.
float32.(img)

converts the raw storage type of img to Float32, without changing the color space.

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ImageCore.float64Function.
float64.(img)

converts the raw storage type of img to Float64, without changing the color space.

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ImageCore.n0f8Function.
n0f8.(img)

converts the raw storage type of img to N0f8, without changing the color space.

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ImageCore.n6f10Function.
n6f10.(img)

converts the raw storage type of img to N6f10, without changing the color space.

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ImageCore.n4f12Function.
n4f12.(img)

converts the raw storage type of img to N4f12, without changing the color space.

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ImageCore.n2f14Function.
n2f14.(img)

converts the raw storage type of img to N2f14, without changing the color space.

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ImageCore.n0f16Function.
n0f16.(img)

converts the raw storage type of img to N0f16, without changing the color space.

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Color conversion

imgg = Gray.(img)

calculates a grayscale representation of a color image using the Rec 601 luma.

imghsv = HSV.(img)

converts to an HSV representation of color information.

Image algorithms

Linear filtering

imfilter([T], img, kernel, [border="replicate"], [alg]) --> imgfilt
imfilter([r], img, kernel, [border="replicate"], [alg]) --> imgfilt
imfilter(r, T, img, kernel, [border="replicate"], [alg]) --> imgfilt

Filter an array img with kernel kernel by computing their correlation.

kernel[0,0,..] corresponds to the origin (zero displacement) of the kernel; you can use centered to place the origin at the array center, or use the OffsetArrays package to set kernel's indices manually. For example, to filter with a random centered 3x3 kernel, you could use either of the following:

kernel = centered(rand(3,3))
kernel = OffsetArray(rand(3,3), -1:1, -1:1)

kernel can be specified as an array or as a "factored kernel," a tuple (filt1, filt2, ...) of filters to apply along each axis of the image. In cases where you know your kernel is separable, this format can speed processing. Each of these should have the same dimensionality as the image itself, and be shaped in a manner that indicates the filtering axis, e.g., a 3x1 filter for filtering the first dimension and a 1x3 filter for filtering the second dimension. In two dimensions, any kernel passed as a single matrix is checked for separability; if you want to eliminate that check, pass the kernel as a single-element tuple, (kernel,).

Optionally specify the border, as one of Fill(value), "replicate", "circular", "symmetric", "reflect", NA(), or Inner(). The default is "replicate". These choices specify the boundary conditions, and therefore affect the result at the edges of the image. See padarray for more information.

alg allows you to choose the particular algorithm: FIR() (finite impulse response, aka traditional digital filtering) or FFT() (Fourier-based filtering). If no choice is specified, one will be chosen based on the size of the image and kernel in a way that strives to deliver good performance. Alternatively you can use a custom filter type, like KernelFactors.IIRGaussian.

Optionally, you can control the element type of the output image by passing in a type T as the first argument.

You can also dispatch to different implementations by passing in a resource r as defined by the ComputationalResources package. For example,

imfilter(ArrayFire(), img, kernel)

would request that the computation be performed on the GPU using the ArrayFire libraries.

See also: imfilter!, centered, padarray, Pad, Fill, Inner, KernelFactors.IIRGaussian.

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imfilter!(imgfilt, img, kernel, [border="replicate"], [alg])
imfilter!(r, imgfilt, img, kernel, border, [inds])
imfilter!(r, imgfilt, img, kernel, border::NoPad, [inds=indices(imgfilt)])

Filter an array img with kernel kernel by computing their correlation, storing the result in imgfilt.

The indices of imgfilt determine the region over which the filtered image is computed–-you can use this fact to select just a specific region of interest, although be aware that the input img might still get padded. Alteratively, explicitly provide the indices inds of imgfilt that you want to calculate, and use NoPad boundary conditions. In such cases, you are responsible for supplying appropriate padding: img must be indexable for all of the locations needed for calculating the output. This syntax is best-supported for FIR filtering; in particular, that that IIR filtering can lead to results that are inconsistent with respect to filtering the entire array.

See also: imfilter.

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imgradients(img, kernelfun=KernelFactors.ando3, border="replicate") -> gimg1, gimg2, ...

Estimate the gradient of img at all points of the image, using a kernel specified by kernelfun. The gradient is returned as a tuple-of-arrays, one for each dimension of the input; gimg1 corresponds to the derivative with respect to the first dimension, gimg2 to the second, and so on. At the image edges, border is used to specify the boundary conditions.

kernelfun may be one of the filters defined in the KernelFactors module, or more generally any function which satisfies the following interface:

kernelfun(extended::NTuple{N,Bool}, d) -> kern_d

kern_d is the kernel for producing the derivative with respect to the dth dimension of an N-dimensional array. extended[i] is true if the image is of size > 1 along dimension i. kern_d may be provided as a dense or factored kernel, with factored representations recommended when the kernel is separable.

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imgradients(img, points, [kernelfunc], [border]) -> G

Performs edge detection filtering in the N-dimensional array img. Gradients are computed at specified points (or indexes) in the array.

All kernel functions are specified as KernelFactors.func. For 2d images, the choices for func include sobel, prewitt, ando3, ando4, and ando5. For other dimensionalities, the ando4 and ando5 kernels are not available.

Border options:"replicate", "circular", "reflect", "symmetric".

Returns a 2D array G with the gradients as rows. The number of rows is the number of points at which the gradient was computed and the number of columns is the dimensionality of the array.

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Kernel

diff1, diff2 = sobel()

Return kernels for two-dimensional gradient compution using the Sobel operator. diff1 computes the gradient along the first (y) dimension, and diff2 computes the gradient along the second (x) dimension.

See also: KernelFactors.sobel, Kernel.prewitt, Kernel.ando3.

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diff1, diff2 = prewitt()

Return kernels for two-dimensional gradient compution using the Prewitt operator. diff1 computes the gradient along the first (y) dimension, and diff2 computes the gradient along the second (x) dimension.

See also: KernelFactors.prewitt, Kernel.sobel, Kernel.ando3.

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diff1, diff2 = ando3()

Return 3x3 kernels for two-dimensional gradient compution using the optimal "Ando" filters. diff1 computes the gradient along the y-axis (first dimension), and diff2 computes the gradient along the x-axis (second dimension).

Citation

Ando Shigeru, IEEE Trans. Pat. Anal. Mach. Int., vol. 22 no 3, March 2000

See also: KernelFactors.ando3, Kernel.ando4, Kernel.ando5.

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diff1, diff2 = ando4()

Return 4x4 kernels for two-dimensional gradient compution using the optimal "Ando" filters. diff1 computes the gradient along the y-axis (first dimension), and diff2 computes the gradient along the x-axis (second dimension).

Citation

Ando Shigeru, IEEE Trans. Pat. Anal. Mach. Int., vol. 22 no 3, March 2000

See also: KernelFactors.ando4, Kernel.ando3, Kernel.ando5.

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diff1, diff2 = ando5()

Return 5x5 kernels for two-dimensional gradient compution using the optimal "Ando" filters. diff1 computes the gradient along the y-axis (first dimension), and diff2 computes the gradient along the x-axis (second dimension).

Citation

Ando Shigeru, IEEE Trans. Pat. Anal. Mach. Int., vol. 22 no 3, March 2000

See also: KernelFactors.ando5, Kernel.ando3, Kernel.ando4.

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gaussian((σ1, σ2, ...), [(l1, l2, ...]) -> g
gaussian(σ)                  -> g

Construct a multidimensional gaussian filter, with standard deviation σd along dimension d. Optionally provide the kernel length l, which must be a tuple of the same length.

If σ is supplied as a single number, a symmetric 2d kernel is constructed.

See also: KernelFactors.gaussian.

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DoG((σp1, σp2, ...), (σm1, σm2, ...), [l1, l2, ...]) -> k
DoG((σ1, σ2, ...))                                   -> k
DoG(σ::Real)                                         -> k

Construct a multidimensional difference-of-gaussian kernel k, equal to gaussian(σp, l)-gaussian(σm, l). When only a single σ is supplied, the default is to choose σp = σ, σm = √2 σ. Optionally provide the kernel length l; the default is to extend by two max(σp,σm) in each direction from the center. l must be odd.

If σ is provided as a single number, a symmetric 2d DoG kernel is returned.

See also: KernelFactors.IIRGaussian.

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LoG((σ1, σ2, ...)) -> k
LoG(σ)             -> k

Construct a Laplacian-of-Gaussian kernel k. σd is the gaussian width along dimension d. If σ is supplied as a single number, a symmetric 2d kernel is returned.

See also: KernelFactors.IIRGaussian and Kernel.Laplacian.

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Laplacian((true,true,false,...))
Laplacian(dims, N)
Lacplacian()

Laplacian kernel in N dimensions, taking derivatives along the directions marked as true in the supplied tuple. Alternatively, one can pass dims, a listing of the dimensions for differentiation. (However, this variant is not inferrable.)

Laplacian() is the 2d laplacian, equivalent to Laplacian((true,true)).

The kernel is represented as an opaque type, but you can use convert(AbstractArray, L) to convert it into array format.

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KernelFactors

kern1, kern2 = sobel()

Factored Sobel filters for dimensions 1 and 2 of a two-dimensional image. Each is a 2-tuple of one-dimensional filters.

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kern = sobel(extended::NTuple{N,Bool}, d)

Return a factored Sobel filter for computing the gradient in N dimensions along axis d. If extended[dim] is false, kern will have size 1 along that dimension.

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kern1, kern2 = prewitt() returns factored Prewitt filters for dimensions 1 and 2 of your image

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kern = prewitt(extended::NTuple{N,Bool}, d)

Return a factored Prewitt filter for computing the gradient in N dimensions along axis d. If extended[dim] is false, kern will have size 1 along that dimension.

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kern1, kern2 = ando3() returns optimal 3x3 gradient filters for dimensions 1 and 2 of your image, as defined in Ando Shigeru, IEEE Trans. Pat. Anal. Mach. Int., vol. 22 no 3, March 2000.

See also: Kernel.ando3, KernelFactors.ando4, KernelFactors.ando5.

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kern = ando3(extended::NTuple{N,Bool}, d)

Return a factored Ando filter (size 3) for computing the gradient in N dimensions along axis d. If extended[dim] is false, kern will have size 1 along that dimension.

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kern1, kern2 = ando4() returns separable approximations of the optimal 4x4 filters for dimensions 1 and 2 of your image, as defined in Ando Shigeru, IEEE Trans. Pat. Anal. Mach. Int., vol. 22 no 3, March 2000.

See also: Kernel.ando4.

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kern = ando4(extended::NTuple{N,Bool}, d)

Return a factored Ando filter (size 4) for computing the gradient in N dimensions along axis d. If extended[dim] is false, kern will have size 1 along that dimension.

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kern1, kern2 = ando5_sep() returns separable approximations of the optimal 5x5 gradient filters for dimensions 1 and 2 of your image, as defined in Ando Shigeru, IEEE Trans. Pat. Anal. Mach. Int., vol. 22 no 3, March 2000.

See also: Kernel.ando5.

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kern = ando5(extended::NTuple{N,Bool}, d)

Return a factored Ando filter (size 5) for computing the gradient in N dimensions along axis d. If extended[dim] is false, kern will have size 1 along that dimension.

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gaussian(σ::Real, [l]) -> g

Construct a 1d gaussian kernel g with standard deviation σ, optionally providing the kernel length l. The default is to extend by two σ in each direction from the center. l must be odd.

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gaussian((σ1, σ2, ...), [l]) -> (g1, g2, ...)

Construct a multidimensional gaussian filter as a product of single-dimension factors, with standard deviation σd along dimension d. Optionally provide the kernel length l, which must be a tuple of the same length.

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IIRGaussian([T], σ; emit_warning::Bool=true)

Construct an infinite impulse response (IIR) approximation to a Gaussian of standard deviation σ. σ may either be a single real number or a tuple of numbers; in the latter case, a tuple of such filters will be created, each for filtering a different dimension of an array.

Optionally specify the type T for the filter coefficients; if not supplied, it will match σ (unless σ is not floating-point, in which case Float64 will be chosen).

Citation

I. T. Young, L. J. van Vliet, and M. van Ginkel, "Recursive Gabor Filtering". IEEE Trans. Sig. Proc., 50: 2798-2805 (2002).

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TriggsSdika(a, b, scale, M)

Defines a kernel for one-dimensional infinite impulse response (IIR) filtering. a is a "forward" filter, b a "backward" filter, M is a matrix for matching boundary conditions at the right edge, and scale is a constant scaling applied to each element at the conclusion of filtering.

Citation

B. Triggs and M. Sdika, "Boundary conditions for Young-van Vliet recursive filtering". IEEE Trans. on Sig. Proc. 54: 2365-2367 (2006).

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TriggsSdika(ab, scale)

Create a symmetric Triggs-Sdika filter (with a = b = ab). M is calculated for you. Only length 3 filters are currently supported.

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Kernel utilities

centered(kernel) -> shiftedkernel

Shift the origin-of-coordinates to the center of kernel. The center-element of kernel will be accessed by shiftedkernel[0, 0, ...].

This function makes it easy to supply kernels using regular Arrays, and provides compatibility with other languages that do not support arbitrary indices.

See also: imfilter.

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kernelfactors(factors::Tuple)

Prepare a factored kernel for filtering. If passed a 2-tuple of vectors of lengths m and n, this will return a 2-tuple of ReshapedVectors that are effectively of sizes m×1 and 1×n. In general, each successive factor will be reshaped to extend along the corresponding dimension.

If passed a tuple of general arrays, it is assumed that each is shaped appropriately along its "leading" dimensions; the dimensionality of each is "extended" to N = length(factors), appending 1s to the size as needed.

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reflect(kernel) --> reflectedkernel

Compute the pointwise reflection around 0, 0, ... of the kernel kernel. Using imfilter with a reflectedkernel performs convolution, rather than correlation, with respect to the original kernel.

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Boundaries and padding

padarray([T], img, border) --> imgpadded

Generate a padded image from an array img and a specification border of the boundary conditions and amount of padding to add. border can be a Pad, Fill, or Inner object.

Optionally provide the element type T of imgpadded.

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Pad is a type that stores choices about padding. Instances must set style, a Symbol specifying the boundary conditions of the image, one of:

  • :replicate (repeat edge values to infinity)

  • :circular (image edges "wrap around")

  • :symmetric (the image reflects relative to a position between pixels)

  • :reflect (the image reflects relative to the edge itself)

The default value is :replicate.

It's worth emphasizing that padding is most straightforwardly specified as a string,

imfilter(img, kernel, "replicate")

rather than

imfilter(img, kernel, Pad(:replicate))
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Fill(val)
Fill(val, lo, hi)

Pad the edges of the image with a constant value, val.

Optionally supply the extent of the padding, see Pad.

Example:

imfilter(img, kernel, Fill(zero(eltype(img))))
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Inner()
Inner(lo, hi)

Indicate that edges are to be discarded in filtering, only the interior of the result it to be returned.

Example:

imfilter(img, kernel, Inner())
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NA()
NA(lo, hi)

Choose filtering using "NA" (Not Available) boundary conditions. This is most appropriate for filters that have only positive weights, such as blurring filters. Effectively, the output pixel value is normalized in the following way:

          filtered img with Fill(0) boundary conditions
output =  ---------------------------------------------
          filtered 1   with Fill(0) boundary conditions

As a consequence, filtering has the same behavior as nanmean. Indeed, invalid pixels in img can be marked as NaN and then they are effectively omitted from the filtered result.

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NoPad()
NoPad(border)

Indicates that no padding should be applied to the input array, or that you have already pre-padded the input image. Passing a border object allows you to preserve "memory" of a border choice; it can be retrieved by indexing with [].

Example

np = NoPad(Pad(:replicate))
imfilter!(out, img, kernel, np)

runs filtering directly, skipping any padding steps. Every entry of out must be computable using in-bounds operations on img and kernel.

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Algorithms

Filter using a direct algorithm

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Filter using the Fast Fourier Transform

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Filter with an Infinite Impulse Response filter

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Filter with a cascade of mixed types (IIR, FIR)

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Internal machinery

ReshapedOneD{N,Npre}(data)

Return an object of dimensionality N, where data must have dimensionality 1. The indices are 0:0 for the first Npre dimensions, have the indices of data for dimension Npre+1, and are 0:0 for the remaining dimensions.

data must support eltype and ndims, but does not have to be an AbstractArray.

ReshapedOneDs allow one to specify a "filtering dimension" for a 1-dimensional filter.

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Nonlinear filtering and transformation

mapwindow(f, img, window, [border="replicate"]) -> imgf

Apply f to sliding windows of img, with window size or indices specified by window. For example, mapwindow(median!, img, window) returns an Array of values similar to img (median-filtered, of course), whereas mapwindow(extrema, img, window) returns an Array of (min,max) tuples over a window of size window centered on each point of img.

The function f receives a buffer buf for the window of data surrounding the current point. If window is specified as a Dims-tuple (tuple-of-integers), then all the integers must be odd and the window is centered around the current image point. For example, if window=(3,3), then f will receive an Array buf corresponding to offsets (-1:1, -1:1) from the imgf[i,j] for which this is currently being computed. Alternatively, window can be a tuple of AbstractUnitRanges, in which case the specified ranges are used for buf; this allows you to use asymmetric windows if needed.

border specifies how the edges of img should be handled; see imfilter for details.

For functions that can only take AbstractVector inputs, you might have to first specialize default_shape:

f = v->quantile(v, 0.75)
ImageFiltering.MapWindow.default_shape(::typeof(f)) = vec

and then mapwindow(f, img, (m,n)) should filter at the 75th quantile.

See also: imfilter.

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Images.imROFFunction.
imgr = imROF(img, lambda, iterations)

Perform Rudin-Osher-Fatemi (ROF) filtering, more commonly known as Total Variation (TV) denoising or TV regularization. lambda is the regularization coefficient for the derivative, and iterations is the number of relaxation iterations taken. 2d only.

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Edge detection

Images.magnitudeFunction.
m = magnitude(grad_x, grad_y)

Calculates the magnitude of the gradient images given by grad_x and grad_y. Equivalent to $sqrt(grad_x.^2 + grad_y.^2)$.

Returns a magnitude image the same size as grad_x and grad_y.

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Images.phaseFunction.
phase(grad_x, grad_y) -> p

Calculate the rotation angle of the gradient given by grad_x and grad_y. Equivalent to atan2(-grad_y, grad_x), except that when both grad_x and grad_y are effectively zero, the corresponding angle is set to zero.

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Images.orientationFunction.
orientation(grad_x, grad_y) -> orient

Calculate the orientation angle of the strongest edge from gradient images given by grad_x and grad_y. Equivalent to atan2(grad_x, grad_y). When both grad_x and grad_y are effectively zero, the corresponding angle is set to zero.

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magnitude_phase(grad_x, grad_y) -> m, p

Convenience function for calculating the magnitude and phase of the gradient images given in grad_x and grad_y. Returns a tuple containing the magnitude and phase images. See magnitude and phase for details.

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Images.imedgeFunction.
grad_y, grad_x, mag, orient = imedge(img, kernelfun=KernelFactors.ando3, border="replicate")

Edge-detection filtering. kernelfun is a valid kernel function for imgradients, defaulting to KernelFactors.ando3. border is any of the boundary conditions specified in padarray.

Returns a tuple (grad_x, grad_y, mag, orient), which are the horizontal gradient, vertical gradient, and the magnitude and orientation of the strongest edge, respectively.

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Images.thin_edgesFunction.
thinned = thin_edges(img, gradientangle, [border])
thinned, subpix = thin_edges_subpix(img, gradientangle, [border])
thinned, subpix = thin_edges_nonmaxsup(img, gradientangle, [border]; [radius::Float64=1.35], [theta=pi/180])
thinned, subpix = thin_edges_nonmaxsup_subpix(img, gradientangle, [border]; [radius::Float64=1.35], [theta=pi/180])

Edge thinning for 2D edge images. Currently the only algorithm available is non-maximal suppression, which takes an edge image and its gradient angle, and checks each edge point for local maximality in the direction of the gradient. The returned image is non-zero only at maximal edge locations.

border is any of the boundary conditions specified in padarray.

In addition to the maximal edge image, the _subpix versions of these functions also return an estimate of the subpixel location of each local maxima, as a 2D array or image of Graphics.Point objects. Additionally, each local maxima is adjusted to the estimated value at the subpixel location.

Currently, the _nonmaxsup functions are identical to the first two function calls, except that they also accept additional keyword arguments. radius indicates the step size to use when searching in the direction of the gradient; values between 1.2 and 1.5 are suggested (default 1.35). theta indicates the step size to use when discretizing angles in the gradientangle image, in radians (default: 1 degree in radians = pi/180).

Example:

g = rgb2gray(rgb_image)
gx, gy = imgradients(g)
mag, grad_angle = magnitude_phase(gx,gy)
mag[mag .< 0.5] = 0.0  # Threshold magnitude image
thinned, subpix =  thin_edges_subpix(mag, grad_angle)
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Images.cannyFunction.
canny_edges = canny(img, sigma = 1.4, upperThreshold = 0.80, lowerThreshold = 0.20)

Performs Canny Edge Detection on the input image.

Parameters :

(upper, lower) : Bounds for hysteresis thresholding sigma : Specifies the standard deviation of the gaussian filter

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Corner Detection

Images.imcornerFunction.
corners = imcorner(img; [method])
corners = imcorner(img, threshold, percentile; [method])

Performs corner detection using one of the following methods -

1. harris
2. shi_tomasi
3. kitchen_rosenfeld

The parameters of the individual methods are described in their documentation. The maxima values of the resultant responses are taken as corners. If a threshold is specified, the values of the responses are thresholded to give the corner pixels. The threshold is assumed to be a percentile value unless percentile is set to false.

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Images.harrisFunction.
harris_response = harris(img; [k], [border], [weights])

Performs Harris corner detection. The covariances can be taken using either a mean weighted filter or a gamma kernel.

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Images.shi_tomasiFunction.
shi_tomasi_response = shi_tomasi(img; [border], [weights])

Performs Shi Tomasi corner detection. The covariances can be taken using either a mean weighted filter or a gamma kernel.

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kitchen_rosenfeld_response = kitchen_rosenfeld(img; [border])

Performs Kitchen Rosenfeld corner detection. The covariances can be taken using either a mean weighted filter or a gamma kernel.

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Images.fastcornersFunction.
fastcorners(img, n, threshold) -> corners

Performs FAST Corner Detection. n is the number of contiguous pixels which need to be greater (lesser) than intensity + threshold (intensity - threshold) for a pixel to be marked as a corner. The default value for n is 12.

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Feature Extraction

See the ImageFeatures package for a much more comprehensive set of tools.

Images.blob_LoGFunction.
blob_LoG(img, σscales, [edges], [σshape]) -> Vector{BlobLoG}

Find "blobs" in an N-D image using the negative Lapacian of Gaussians with the specifed vector or tuple of σ values. The algorithm searches for places where the filtered image (for a particular σ) is at a peak compared to all spatially- and σ-adjacent voxels, where σ is σscales[i] * σshape for some i. By default, σshape is an ntuple of 1s.

The optional edges argument controls whether peaks on the edges are included. edges can be true or false, or a N+1-tuple in which the first entry controls whether edge-σ values are eligible to serve as peaks, and the remaining N entries control each of the N dimensions of img.

Citation:

Lindeberg T (1998), "Feature Detection with Automatic Scale Selection", International Journal of Computer Vision, 30(2), 79–116.

See also: BlobLoG.

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Images.BlobLoGType.

BlobLoG stores information about the location of peaks as discovered by blob_LoG. It has fields:

  • location: the location of a peak in the filtered image (a CartesianIndex)

  • σ: the value of σ which lead to the largest -LoG-filtered amplitude at this location

  • amplitude: the value of the -LoG(σ)-filtered image at the peak

Note that the radius is equal to σ√2.

See also: blob_LoG.

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findlocalmaxima(img, [region, edges]) -> Vector{Tuple}

Returns the coordinates of elements whose value is larger than all of their immediate neighbors. region is a list of dimensions to consider. edges is a boolean specifying whether to include the first and last elements of each dimension, or a tuple-of-Bool specifying edge behavior for each dimension separately.

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Like findlocalmaxima, but returns the coordinates of the smallest elements.

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Exposure

Images.imhistFunction.
edges, count = imhist(img, nbins)
edges, count = imhist(img, nbins, minval, maxval)

Generates a histogram for the image over nbins spread between (minval, maxval]. If minval and maxval are not given, then the minimum and maximum values present in the image are taken.

edges is a vector that specifies how the range is divided; count[i+1] is the number of values x that satisfy edges[i] <= x < edges[i+1]. count[1] is the number satisfying x < edges[1], and count[end] is the number satisfying x >= edges[end]. Consequently, length(count) == length(edges)+1.

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Images.cliphistFunction.
clipped_hist = cliphist(hist, clip)

Clips the histogram above a certain value clip. The excess left in the bins exceeding clip is redistributed among the remaining bins.

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Images.histeqFunction.
hist_equalised_img = histeq(img, nbins)
hist_equalised_img = histeq(img, nbins, minval, maxval)

Returns a histogram equalised image with a granularity of approximately nbins number of bins.

The histeq function can handle a variety of input types. The returned image depends on the input type. If the input is an Image then the resulting image is of the same type and has the same properties.

For coloured images, the input is converted to YIQ type and the Y channel is equalised. This is the combined with the I and Q channels and the resulting image converted to the same type as the input.

If minval and maxval are specified then intensities are equalized to the range (minval, maxval). The default values are 0 and 1.

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Images.adjust_gammaFunction.
gamma_corrected_img = adjust_gamma(img, gamma)

Returns a gamma corrected image.

The adjust_gamma function can handle a variety of input types. The returned image depends on the input type. If the input is an Image then the resulting image is of the same type and has the same properties.

For coloured images, the input is converted to YIQ type and the Y channel is gamma corrected. This is the combined with the I and Q channels and the resulting image converted to the same type as the input.

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Images.imstretchFunction.

imgs = imstretch(img, m, slope) enhances or reduces (for slope > 1 or < 1, respectively) the contrast near saturation (0 and 1). This is essentially a symmetric gamma-correction. For a pixel of brightness p, the new intensity is 1/(1+(m/(p+eps))^slope).

This assumes the input img has intensities between 0 and 1.

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imadjustintensity(img [, (minval,maxval)]) -> Image

Map intensities over the interval (minval,maxval) to the interval [0,1]. This is equivalent to map(ScaleMinMax(eltype(img), minval, maxval), img). (minval,maxval) defaults to extrema(img).

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Images.complementFunction.
y = complement(x)

Take the complement 1-x of x. If x is a color with an alpha channel, the alpha channel is left untouched.

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Images.histmatchFunction.
hist_matched_img = histmatch(img, oimg, nbins)

Returns a grayscale histogram matched image with a granularity of nbins number of bins. img is the image to be matched and oimg is the image having the desired histogram to be matched to.

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Images.claheFunction.
hist_equalised_img = clahe(img, nbins, xblocks = 8, yblocks = 8, clip = 3)

Performs Contrast Limited Adaptive Histogram Equalisation (CLAHE) on the input image. It differs from ordinary histogram equalization in the respect that the adaptive method computes several histograms, each corresponding to a distinct section of the image, and uses them to redistribute the lightness values of the image. It is therefore suitable for improving the local contrast and enhancing the definitions of edges in each region of an image.

In the straightforward form, CLAHE is done by calculation a histogram of a window around each pixel and using the transformation function of the equalised histogram to rescale the pixel. Since this is computationally expensive, we use interpolation which gives a significant rise in efficiency without compromising the result. The image is divided into a grid and equalised histograms are calculated for each block. Then, each pixel is interpolated using the closest histograms.

The xblocks and yblocks specify the number of blocks to divide the input image into in each direction. nbins specifies the granularity of histogram calculation of each local region. clip specifies the value at which the histogram is clipped. The excess in the histogram bins with value exceeding clip is redistributed among the other bins.

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Spatial transformations and resizing

imresize(img, sz) -> imgr
imresize(img, inds) -> imgr

Change img to be of size sz (or to have indices inds). This interpolates the values at sub-pixel locations. If you are shrinking the image, you risk aliasing unless you low-pass filter img first. For example:

σ = map((o,n)->0.75*o/n, size(img), sz)
kern = KernelFactors.gaussian(σ)   # from ImageFiltering
imgr = imresize(imfilter(img, kern, NA()), sz)

See also restrict.

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restrict(img[, region]) -> imgr

Reduce the size of img by two-fold along the dimensions listed in region, or all spatial coordinates if region is not specified. It anti-aliases the image as it goes, so is better than a naive summation over 2x2 blocks.

See also imresize.

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warp(img, tform, [indices], [degree = Linear()], [fill = NaN]) -> imgw

Transform the coordinates of img, returning a new imgw satisfying imgw[I] = img[tform(I)]. This approach is known as backward mode warping. The transformation tform must accept a SVector as input. A useful package to create a wide variety of such transformations is CoordinateTransformations.jl.

Reconstruction scheme

During warping, values for img must be reconstructed at arbitrary locations tform(I) which do not lie on to the lattice of pixels. How this reconstruction is done depends on the type of img and the optional parameter degree.

When img is a plain array, then on-grid b-spline interpolation will be used. It is possible to configure what degree of b-spline to use with the parameter degree. For example one can use degree = Linear() for linear interpolation, degree = Constant() for nearest neighbor interpolation, or degree = Quadratic(Flat()) for quadratic interpolation.

In the case tform(I) maps to indices outside the original img, those locations are set to a value fill (which defaults to NaN if the element type supports it, and 0 otherwise). The parameter fill also accepts extrapolation schemes, such as Flat(), Periodic() or Reflect().

For more control over the reconstruction scheme –- and how beyond-the-edge points are handled –- pass img as an AbstractInterpolation or AbstractExtrapolation from Interpolations.jl.

The meaning of the coordinates

The output array imgw has indices that would result from applying inv(tform) to the indices of img. This can be very handy for keeping track of how pixels in imgw line up with pixels in img.

If you just want a plain array, you can "strip" the custom indices with parent(imgw).

Examples: a 2d rotation (see JuliaImages documentation for pictures)

julia> using Images, CoordinateTransformations, TestImages, OffsetArrays

julia> img = testimage("lighthouse");

julia> indices(img)
(Base.OneTo(512),Base.OneTo(768))

# Rotate around the center of `img`
julia> tfm = recenter(RotMatrix(-pi/4), center(img))
AffineMap([0.707107 0.707107; -0.707107 0.707107], [-196.755,293.99])

julia> imgw = warp(img, tfm);

julia> indices(imgw)
(-196:709,-68:837)

# Alternatively, specify the origin in the image itself
julia> img0 = OffsetArray(img, -30:481, -384:383);  # origin near top of image

julia> rot = LinearMap(RotMatrix(-pi/4))
LinearMap([0.707107 -0.707107; 0.707107 0.707107])

julia> imgw = warp(img0, rot);

julia> indices(imgw)
(-293:612,-293:611)

julia> imgr = parent(imgw);

julia> indices(imgr)
(Base.OneTo(906),Base.OneTo(905))
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Image statistics

Images.minfiniteFunction.

m = minfinite(A) calculates the minimum value in A, ignoring any values that are not finite (Inf or NaN).

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Images.maxfiniteFunction.

m = maxfinite(A) calculates the maximum value in A, ignoring any values that are not finite (Inf or NaN).

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Images.maxabsfiniteFunction.

m = maxabsfinite(A) calculates the maximum absolute value in A, ignoring any values that are not finite (Inf or NaN).

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Images.meanfiniteFunction.

M = meanfinite(img, region) calculates the mean value along the dimensions listed in region, ignoring any non-finite values.

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Images.ssdFunction.

s = ssd(A, B) computes the sum-of-squared differences over arrays/images A and B

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Images.ssdnFunction.

s = ssdn(A, B) computes the sum-of-squared differences over arrays/images A and B, normalized by array size

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Images.sadFunction.

s = sad(A, B) computes the sum-of-absolute differences over arrays/images A and B

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Images.sadnFunction.

s = sadn(A, B) computes the sum-of-absolute differences over arrays/images A and B, normalized by array size

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Morphological operations

imgd = dilate(img, [region])

perform a max-filter over nearest-neighbors. The default is 8-connectivity in 2d, 27-connectivity in 3d, etc. You can specify the list of dimensions that you want to include in the connectivity, e.g., region = [1,2] would exclude the third dimension from filtering.

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ImageMorphology.erodeFunction.
imge = erode(img, [region])

perform a min-filter over nearest-neighbors. The default is 8-connectivity in 2d, 27-connectivity in 3d, etc. You can specify the list of dimensions that you want to include in the connectivity, e.g., region = [1,2] would exclude the third dimension from filtering.

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imgo = opening(img, [region]) performs the opening morphology operation, equivalent to dilate(erode(img)). region allows you to control the dimensions over which this operation is performed.

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imgc = closing(img, [region]) performs the closing morphology operation, equivalent to erode(dilate(img)). region allows you to control the dimensions over which this operation is performed.

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imgth = tophat(img, [region]) performs top hat of an image, which is defined as the image minus its morphological opening. region allows you to control the dimensions over which this operation is performed.

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imgbh = bothat(img, [region]) performs bottom hat of an image, which is defined as its morphological closing minus the original image. region allows you to control the dimensions over which this operation is performed.

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imgmg = morphogradient(img, [region]) returns morphological gradient of the image, which is the difference between the dilation and the erosion of a given image. region allows you to control the dimensions over which this operation is performed.

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imgml = morpholaplace(img, [region]) performs Morphological Laplacian of an image, which is defined as the arithmetic difference between the internal and the external gradient. region allows you to control the dimensions over which this operation is performed.

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label = label_components(tf, [connectivity])
label = label_components(tf, [region])

Find the connected components in a binary array tf. There are two forms that connectivity can take:

  • It can be a boolean array of the same dimensionality as tf, of size 1 or 3

along each dimension. Each entry in the array determines whether a given neighbor is used for connectivity analyses. For example, connectivity = trues(3,3) would use 8-connectivity and test all pixels that touch the current one, even the corners.

  • You can provide a list indicating which dimensions are used to

determine connectivity. For example, region = [1,3] would not test neighbors along dimension 2 for connectivity. This corresponds to just the nearest neighbors, i.e., 4-connectivity in 2d and 6-connectivity in 3d.

The default is region = 1:ndims(A).

The output label is an integer array, where 0 is used for background pixels, and each connected region gets a different integer index.

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component_boxes(labeled_array) -> an array of bounding boxes for each label, including the background label 0

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component_lengths(labeled_array) -> an array of areas (2D), volumes (3D), etc. for each label, including the background label 0

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component_indices(labeled_array) -> an array of pixels for each label, including the background label 0

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component_subscripts(labeled_array) -> an array of pixels for each label, including the background label 0

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component_centroids(labeled_array) -> an array of centroids for each label, including the background label 0

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feature_transform(I::AbstractArray{Bool, N}, [w=nothing]) -> F

Compute the feature transform of a binary image I, finding the closest "feature" (positions where I is true) for each location in I. Specifically, F[i] is a CartesianIndex encoding the position closest to i for which I[F[i]] is true. In cases where two or more features in I have the same distance from i, an arbitrary feature is chosen. If I has no true values, then all locations are mapped to an index where each coordinate is typemin(Int).

Optionally specify the weight w assigned to each coordinate. For example, if I corresponds to an image where voxels are anisotropic, w could be the voxel spacing along each coordinate axis. The default value of nothing is equivalent to w=(1,1,...).

See also: distance_transform.

Citation

'A Linear Time Algorithm for Computing Exact Euclidean Distance Transforms of Binary Images in Arbitrary Dimensions' Maurer et al., 2003

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distance_transform(F::AbstractArray{CartesianIndex}, [w=nothing]) -> D

Compute the distance transform of F, where each element F[i] represents a "target" or "feature" location assigned to i. Specifically, D[i] is the distance between i and F[i]. Optionally specify the weight w assigned to each coordinate; the default value of nothing is equivalent to w=(1,1,...).

See also: feature_transform.

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Interpolation

P = bilinear_interpolation(img, r, c)

Bilinear Interpolation is used to interpolate functions of two variables on a rectilinear 2D grid.

The interpolation is done in one direction first and then the values obtained are used to do the interpolation in the second direction.

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Integral Images

Images.integral_imageFunction.
integral_img = integral_image(img)

Returns the integral image of an image. The integral image is calculated by assigning to each pixel the sum of all pixels above it and to its left, i.e. the rectangle from (1, 1) to the pixel. An integral image is a data structure which helps in efficient calculation of sum of pixels in a rectangular subset of an image. See boxdiff for more information.

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Images.boxdiffFunction.
sum = boxdiff(integral_image, ytop:ybot, xtop:xbot)
sum = boxdiff(integral_image, CartesianIndex(tl_y, tl_x), CartesianIndex(br_y, br_x))
sum = boxdiff(integral_image, tl_y, tl_x, br_y, br_x)

An integral image is a data structure which helps in efficient calculation of sum of pixels in a rectangular subset of an image. It stores at each pixel the sum of all pixels above it and to its left. The sum of a window in an image can be directly calculated using four array references of the integral image, irrespective of the size of the window, given the yrange and xrange of the window. Given an integral image -

    A - - - - - - B -
    - * * * * * * * -
    - * * * * * * * -
    - * * * * * * * -
    - * * * * * * * -
    - * * * * * * * -
    C * * * * * * D -
    - - - - - - - - -

The sum of pixels in the area denoted by * is given by S = D + A - B - C.

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Pyramids

pyramid = gaussian_pyramid(img, n_scales, downsample, sigma)

Returns a gaussian pyramid of scales n_scales, each downsampled by a factor downsample and sigma for the gaussian kernel.

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Phantoms

Images.shepp_loganFunction.
phantom = shepp_logan(N,[M]; highContrast=true)

output the NxM Shepp-Logan phantom, which is a standard test image usually used for comparing image reconstruction algorithms in the field of computed tomography (CT) and magnetic resonance imaging (MRI). If the argument M is omitted, the phantom is of size NxN. When setting the keyword argument highConstrast to false, the CT version of the phantom is created. Otherwise, the high contrast MRI version is calculated.

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Image metadata utilities

ImageMeta is an AbstractArray that can have metadata, stored in a dictionary.

Construct an image with ImageMeta(A, props) (for a properties dictionary props), or with Image(A, prop1=val1, prop2=val2, ...).

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ImageCore.dataFunction.
data(img::ImageMeta) -> array

Extract the data from img, omitting the properties dictionary. array shares storage with img, so changes to one affect the other.

See also: properties.

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properties(imgmeta) -> props

Extract the properties dictionary props for imgmeta. props shares storage with img, so changes to one affect the other.

See also: data.

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copyproperties(img::ImageMeta, data) -> imgnew

Create a new "image," copying the properties dictionary of img but using the data of the AbstractArray data. Note that changing the properties of imgnew does not affect the properties of img.

See also: shareproperties.

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shareproperties(img::ImageMeta, data) -> imgnew

Create a new "image," reusing the properties dictionary of img but using the data of the AbstractArray data. The two images have synchronized properties; modifying one also affects the other.

See also: copyproperties.

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spatialproperties(img)

Return a vector of strings, containing the names of properties that have been declared "spatial" and hence should be permuted when calling permutedims. Declare such properties like this:

img["spatialproperties"] = ["spacedirections"]
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Image segmentation

SegmentedImage type contains the index-label mapping, assigned labels, segment mean intensity and pixel count of each segment.

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edge = ImageEdge(index1, index2, weight)

Construct an edge in a Region Adjacency Graph. index1 and index2 are the integers corresponding to individual pixels/voxels (in the sense of linear indexing via sub2ind), and weight is the edge weight (measures the dissimilarity between pixels/voxels).

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img_labeled = labels_map(seg)

Return an array containing the label assigned to each pixel.

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labels = segment_labels(seg)

Returns the list of assigned labels

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c = segment_pixel_count(seg, l)

Returns the count of pixels that are assigned label l. If no label is supplied, it returns a Dict(label=>pixel_count) of all the labels.

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m = segment_mean(seg, l)

Returns the mean intensity of label l. If no label is supplied, it returns a Dict(label=>mean) of all the labels.

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seg_img = seeded_region_growing(img, seeds, [kernel_dim], [diff_fn])
seg_img = seeded_region_growing(img, seeds, [neighbourhood], [diff_fn])

Segments the N-D image img using the seeded region growing algorithm and returns a SegmentedImage containing information about the segments.

Arguments:

  • img : N-D image to be segmented (arbitrary indices are allowed)

  • seeds : Vector containing seeds. Each seed is a Tuple of a CartesianIndex{N} and a label. See below note for more information on labels.

  • kernel_dim : (Optional) Vector{Int} having length N or a NTuple{N,Int} whose ith element is an odd positive integer representing the length of the ith edge of the N-orthotopic neighbourhood

  • neighbourhood : (Optional) Function taking CartesianIndex{N} as input and returning the neighbourhood of that point.

  • diff_fn : (Optional) Function that returns a difference measure(δ) between the mean color of a region and color of a point

Note

The labels attached to points must be positive integers, although multiple points can be assigned the same label. The output includes a labelled array that has same indexing as that of input image. Every index is assigned to either one of labels or a special label '0' indicating that the algorithm was unable to assign that index to a unique label.

Examples

julia> img = zeros(Gray{N0f8},4,4);
julia> img[2:4,2:4] = 1;
julia> seeds = [(CartesianIndex(3,1),1),(CartesianIndex(2,2),2)];
julia> seg = seeded_region_growing(img, seeds);
julia> labels_map(seg)
4×4 Array{Int64,2}:
 1  1  1  1
 1  2  2  2
 1  2  2  2
 1  2  2  2

Citation:

Albert Mehnert, Paul Jackaway (1997), "An improved seeded region growing algorithm", Pattern Recognition Letters 18 (1997), 1065-1071

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seg_img = unseeded_region_growing(img, threshold, [kernel_dim], [diff_fn])
seg_img = unseeded_region_growing(img, threshold, [neighbourhood], [diff_fn])

Segments the N-D image using automatic (unseeded) region growing algorithm and returns a SegmentedImage containing information about the segments.

Arguments:

  • img : N-D image to be segmented (arbitrary indices are allowed)

  • threshold : Upper bound of the difference measure (δ) for considering pixel into same segment

  • kernel_dim : (Optional) Vector{Int} having length N or a NTuple{N,Int} whose ith element is an odd positive integer representing the length of the ith edge of the N-orthotopic neighbourhood

  • neighbourhood : (Optional) Function taking CartesianIndex{N} as input and returning the neighbourhood of that point.

  • diff_fn : (Optional) Function that returns a difference measure (δ) between the mean color of a region and color of a point

Examples

julia> img = zeros(Gray{N0f8},4,4);
julia> img[2:4,2:4] = 1;
julia> seg = unseeded_region_growing(img, 0.2);
julia> labels_map(seg)
4×4 Array{Int64,2}:
 1  1  1  1
 1  2  2  2
 1  2  2  2
 1  2  2  2
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segments                = felzenszwalb(img, k, [min_size])
index_map, num_segments = felzenszwalb(edges, num_vertices, k, [min_size])

Segments an image using Felzenszwalb's graph-based algorithm. The function can be used in either of two ways -

  1. segments = felzenszwalb(img, k, [min_size])

Segments an image using Felzenszwalb's segmentation algorithm and returns the result as SegmentedImage. The algorithm uses euclidean distance in color space as edge weights for the region adjacency graph.

Parameters:

  • img = input image

  • k = Threshold for region merging step. Larger threshold will result in bigger segments.

  • min_size = Minimum segment size

  1. index_map, num_segments = felzenszwalb(edges, num_vertices, k, [min_size])

Segments an image represented as Region Adjacency Graph(RAG) using Felzenszwalb's segmentation algorithm. Each pixel/region corresponds to a node in the graph and weights on each edge measure the dissimilarity between pixels. The function returns the number of segments and index mapping from nodes of the RAG to segments.

Parameters:

  • edges = Array of edges in RAG. Each edge is represented as ImageEdge.

  • num_vertices = Number of vertices in RAG

  • k = Threshold for region merging step. Larger threshold will result in bigger segments.

  • min_size = Minimum segment size

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seg_img = fast_scanning(img, threshold, [diff_fn])

Segments the N-D image using a fast scanning algorithm and returns a SegmentedImage containing information about the segments.

Arguments:

  • img : N-D image to be segmented (arbitrary indices are allowed)

  • threshold : Upper bound of the difference measure (δ) for considering pixel into same segment; an AbstractArray can be passed having same number of dimensions as that of img for adaptive thresholding

  • diff_fn : (Optional) Function that returns a difference measure (δ) between the mean color of a region and color of a point

Examples:

julia> img = zeros(Float64, (3,3));
julia> img[2,:] = 0.5;
julia> img[:,2] = 0.6;
julia> seg = fast_scanning(img, 0.2);
julia> labels_map(seg)
3×3 Array{Int64,2}:
 1  4  5
 4  4  4
 3  4  6

Citation:

Jian-Jiun Ding, Cheng-Jin Kuo, Wen-Chih Hong, "An efficient image segmentation technique by fast scanning and adaptive merging"

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segments                = watershed(img, markers)

Segments the image using watershed transform. Each basin formed by watershed transform corresponds to a segment. If you are using image local minimas as markers, consider using hmin_transform to avoid oversegmentation.

Parameters:

  • img = input grayscale image

  • markers = An array (same size as img) with each region's marker assigned a index starting from 1. Zero means not a marker. If two markers have the same index, their regions will be merged into a single region. If you have markers as a boolean array, use label_components.

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out = hmin_transform(img, h)

Suppresses all minima in grayscale image whose depth is less than h.

H-minima transform is defined as the reconstruction by erosion of (img + h) by img. See Morphological image analysis by Soille pg 170-172.

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G, vert_map = region_adjacency_graph(seg, weight_fn)

Constructs a region adjacency graph (RAG) from the SegmentedImage. It returns the RAG along with a Dict(label=>vertex) map. weight_fn is used to assign weights to the edges.

weight_fn(label1, label2)

Returns a real number corresponding to the weight of the edge between label1 and label2.

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new_seg = rem_segment(seg, label, diff_fn)

Removes the segment having label label and returns the new SegmentedImage. For more info, see remove_segment!

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rem_segment!(seg, label, diff_fn)

In place removal of the segment having label label, replacing it with the neighboring segment having least diff_fn value.

d = diff_fn(rem_label, neigh_label)

A difference measure between label to be removed and its neighbors. isless must be defined for objects of the type of d.

Examples

    # This removes the label `l` and replaces it with the label of
    # neighbor having maximum pixel count.
    julia> rem_segment!(seg, l, (i,j)->(-seg.segment_pixel_count[j]))

    # This removes the label `l` and replaces it with the label of
    # neighbor having the least value of euclidian metric.
    julia> rem_segment!(seg, l, (i,j)->sum(abs2, seg.segment_means[i]-seg.segment_means[j]))
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new_seg = prune_segments(seg, rem_labels, diff_fn)

Removes all segments that have labels in rem_labels replacing them with their neighbouring segment having least diff_fn. rem_labels is a Vector of labels.

new_seg = prune_segments(seg, is_rem, diff_fn)

Removes all segments for which is_rem returns true replacing them with their neighbouring segment having least diff_fn.

is_rem(label) -> Bool

Returns true if label label is to be removed otherwise false.

d = diff_fn(rem_label, neigh_label)

A difference measure between label to be removed and its neighbors. isless must be defined for objects of the type of d.

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t = region_tree(img, homogeneous)

Creates a region tree from img by splitting it recursively until all the regions are homogeneous.

b = homogeneous(img)

Returns true if img is homogeneous.

Examples

# img is an array with elements of type `Float64`
julia> function homogeneous(img)
           min, max = extrema(img)
           max - min < 0.2
       end
       
julia> t = region_tree(img, homogeneous);
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seg = region_splitting(img, homogeneous)

Segments img by recursively splitting it until all the segments are homogeneous.

b = homogeneous(img)

Returns true if img is homogeneous.

Examples

# img is an array with elements of type `Float64`
julia> function homogeneous(img)
           min, max = extrema(img)
           max - min < 0.2
       end

julia> seg = region_splitting(img, homogeneous);
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ImageFeatures

Types

feature = Feature(keypoint, orientation = 0.0, scale = 0.0)

The Feature type has the keypoint, its orientation and its scale.

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features = Features(boolean_img)
features = Features(keypoints)

Returns a Vector{Feature} of features generated from the true values in a boolean image or from a list of keypoints.

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keypoint = Keypoint(y, x)
keypoint = Keypoint(feature)

A Keypoint may be created by passing the coordinates of the point or from a feature.

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keypoints = Keypoints(boolean_img)
keypoints = Keypoints(features)

Creates a Vector{Keypoint} of the true values in a boolean image or from a list of features.

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brief_params = BRIEF([size = 128], [window = 9], [sigma = 2 ^ 0.5], [sampling_type = gaussian], [seed = 123])
ArgumentTypeDescription
sizeIntSize of the descriptor
windowIntSize of sampling window
sigmaFloat64Value of sigma used for inital gaussian smoothing of image
sampling_typeFunctionType of sampling used for building the descriptor (See BRIEF Sampling Patterns)
seedIntRandom seed used for generating the sampling pairs. For matching two descriptors, the seed used to build both should be same.
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orb_params = ORB([num_keypoints = 500], [n_fast = 12], [threshold = 0.25], [harris_factor = 0.04], [downsample = 1.3], [levels = 8], [sigma = 1.2])
ArgumentTypeDescription
num_keypointsIntNumber of keypoints to extract and size of the descriptor calculated
n_fastIntNumber of consecutive pixels used for finding corners with FAST. See [fastcorners]
thresholdFloat64Threshold used to find corners in FAST. See [fastcorners]
harris_factorFloat64Harris factor k used to rank keypoints by harris responses and extract the best ones
downsampleFloat64Downsampling parameter used while building the gaussian pyramid. See [gaussian_pyramid] in Images.jl
levelsIntNumber of levels in the gaussian pyramid. See [gaussian_pyramid] in Images.jl
sigmaFloat64Used for gaussian smoothing in each level of the gaussian pyramid. See [gaussian_pyramid] in Images.jl
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freak_params = FREAK([pattern_scale = 22.0])
ArgumentTypeDescription
pattern_scaleFloat64Scaling factor for the sampling window
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brisk_params = BRISK([pattern_scale = 1.0])
ArgumentTypeDescription
pattern_scaleFloat64Scaling factor for the sampling window
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Corners

orientations = corner_orientations(img)
orientations = corner_orientations(img, corners)
orientations = corner_orientations(img, corners, kernel)

Returns the orientations of corner patches in an image. The orientation of a corner patch is denoted by the orientation of the vector between intensity centroid and the corner. The intensity centroid can be calculated as C = (m01/m00, m10/m00) where mpq is defined as -

`mpq = (x^p)(y^q)I(y, x) for each p, q in the corner patch`

The kernel used for the patch can be given through the kernel argument. The default kernel used is a gaussian kernel of size 5x5.

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BRIEF Sampling Patterns

sample_one, sample_two = random_uniform(size, window, seed)

Builds sampling pairs using random uniform sampling.

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sample_one, sample_two = random_coarse(size, window, seed)

Builds sampling pairs using random sampling over a coarse grid.

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sample_one, sample_two = gaussian(size, window, seed)

Builds sampling pairs using gaussian sampling.

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sample_one, sample_two = gaussian_local(size, window, seed)

Pairs (Xi, Yi) are randomly sampled using a Gaussian distribution where first X is sampled with a standard deviation of 0.04*S^2 and then the Yi’s are sampled using a Gaussian distribution – Each Yi is sampled with mean Xi and standard deviation of 0.01 * S^2

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sample_one, sample_two = center_sample(size, window, seed)

Builds sampling pairs (Xi, Yi) where Xi is (0, 0) and Yi is sampled uniformly from the window.

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Feature Description

create_descriptor

Feature Matching

distance = hamming_distance(desc_1, desc_2)

Calculates the hamming distance between two descriptors.

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matches = match_keypoints(keypoints_1, keypoints_2, desc_1, desc_2, threshold = 0.1)

Finds matched keypoints using the hamming_distance function having distance value less than threshold.

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Texture Matching

Gray Level Co-occurence Matrix

glcm
glcm_symmetric
glcm_norm
glcm_prop
max_prob
contrast
ASM
IDM
glcm_entropy
energy
dissimilarity
correlation
glcm_mean_ref
glcm_mean_neighbour
glcm_var_ref
glcm_var_neighbour

Local Binary Patterns

lbp
modified_lbp
direction_coded_lbp
lbp_original
lbp_uniform
lbp_rotation_invariant
multi_block_lbp