medfilt3

3-D median filtering

Syntax

B = medfilt3(A)

B = medfilt3(A,[m n p])

B = medfilt3(___,padopt)

Description

B = medfilt3(A) filters the 3-D image A with a 3-by-3-by-3 filter. By default, medfilt3 pads the image by replicating the values in a mirrored way at the borders.

B = medfilt3(A,[m n p]) performs median filtering of the 3-D image A in three dimensions. Each output voxel in B contains the median value in the m-by-n-by-p neighborhood around the corresponding voxel in A.

B = medfilt3(___,padopt) controls how medfilt3 pads the array boundaries.

Examples

Use Median Filtering to Remove Outliers in 3-D Data

Create a noisy 3-D surface.

[x,y,z,V] = flow(50);
noisyV = V + 0.1*double(rand(size(V))>0.95) - 0.1*double(rand(size(V))<0.05);

Apply median filtering.

filteredV = medfilt3(noisyV);

Display the noisy and filtered surfaces together.

subplot(1,2,1)
hpatch1 = patch(isosurface(x,y,z,noisyV,0));
isonormals(x,y,z,noisyV,hpatch1)
set(hpatch1,FaceColor="red",EdgeColor="none")
daspect([1,4,4])
view([-65,20]) 
axis tight off
camlight left
lighting gouraud

subplot(1,2,2)
hpatch2 = patch(isosurface(x,y,z,filteredV,0));
isonormals(x,y,z,filteredV,hpatch2)
set(hpatch2,FaceColor="red",EdgeColor="none")
daspect([1,4,4])
view([-65,20])
axis tight off
camlight left 
lighting gouraud

Input Arguments

A — Input image

3-D numeric array | 3-D logical array

Input image, specified as a 3-D numeric or logical array.

Data Types: single | double | int8 | int16 | int32 | int64 | uint8 | uint16 | uint32 | uint64 | logical

[m n p] — Neighborhood size

[3 3 3] (default) | 3-element vector

Neighborhood size, specified as a 3-element vector of positive odd integers.

Data Types: single | double | int8 | int16 | int32 | uint8 | uint16 | uint32

padopt — Padding option

"symmetric" (default) | "zeros" | "replicate"

Padding option, specified as one of the following values:

Value	Description	Example
"symmetric"	Pad array with mirror reflections of itself	$$\left[\begin{array}{ccc}3& 1& 4\\ 1& 5& 9\\ 2& 6& 5\end{array}\right]\to \left[\begin{array}{ccccccc}5& 1& 1& 5& 9& 9& 5\\ 1& 3& 3& 1& 4& 4& 1\\ 1& 3& 3& 1& 4& 4& 1\\ 5& 1& 1& 5& 9& 9& 5\\ 6& 2& 2& 6& 5& 5& 6\\ 6& 2& 2& 6& 5& 5& 6\\ 5& 1& 1& 5& 9& 9& 5\end{array}\right]$$
"replicate"	Pad array by repeating border elements	$$\left[\begin{array}{ccc}3& 1& 4\\ 1& 5& 9\\ 2& 6& 5\end{array}\right]\to \left[\begin{array}{ccccccc}3& 3& 3& 1& 4& 4& 4\\ 3& 3& 3& 1& 4& 4& 4\\ 3& 3& 3& 1& 4& 4& 4\\ 1& 1& 1& 5& 9& 9& 9\\ 2& 2& 2& 6& 5& 5& 5\\ 2& 2& 2& 6& 5& 5& 5\\ 2& 2& 2& 6& 5& 5& 5\end{array}\right]$$
"zeros"	Pad array with the value 0	$$\left[\begin{array}{ccc}3& 1& 4\\ 1& 5& 9\\ 2& 6& 5\end{array}\right]\to \left[\begin{array}{ccccccc}0& 0& 0& 0& 0& 0& 0\\ 0& 0& 0& 0& 0& 0& 0\\ 0& 0& 3& 1& 4& 0& 0\\ 0& 0& 1& 5& 9& 0& 0\\ 0& 0& 2& 6& 5& 0& 0\\ 0& 0& 0& 0& 0& 0& 0\\ 0& 0& 0& 0& 0& 0& 0\end{array}\right]$$

Data Types: char | string

Output Arguments

B — Output image

3-D numeric array

Output image, returned as a 3-D numeric array of the same size and data type as the input image A.

Extended Capabilities

Thread-Based Environment

Run code in the background using MATLAB® backgroundPool or accelerate code with Parallel Computing Toolbox™ ThreadPool.

This function fully supports thread-based environments. For more information, see Run MATLAB Functions in Thread-Based Environment.

Version History

Introduced in R2016b

R2022b: Support for thread-based environments

medfilt3 now supports thread-based environments.

R2021b: Improved performance for small neighborhood sizes

The medfilt3 function shows improved performance for neighborhood sizes from [3, 3, 3] up to [31, 31, 31].

For example, this code is about 3x faster than in the previous release.

function timingTestMedfilt3
      load mristack;
      noisyV = imnoise(mristack,'salt & pepper',0.2);
      tic
      filteredV = medfilt3(noisyV);
      toc
end

The approximate execution times are:

R2021a: 0.24 s

R2021b: 0.08 s

The code was timed on a Windows^® 10, Intel^® Xeon^® Gold 5220 CPU @ 2.2 GHz test system by calling the function timingTestMedfilt3.