imref3d

Reference 3-D image to world coordinates

Description

An imref3d object stores the relationship between the intrinsic coordinates anchored to the columns, rows, and planes of a 3-D image and the spatial location of the same column, row, and plane locations in a world coordinate system.

The image is sampled regularly in the planar world-x, world-y, and world-z coordinates of the coordinate system such that intrinsic-x, -y and -z values align with world-x, -y, and -z values, respectively. The resolution in each dimension can be different.

Creation

You can create an imref3d object in these ways.

• affineOutputView — Store the spatial extent of an image that is warped by a 3-D affine geometric transformation.

• The imref3d function described here

Syntax

R = imref3d

R = imref3d(imageSize)

R = imref3d(imageSize,pixExtentWorldX,pixExtentWorldY,pixExtentWorldZ)

R = imref3d(imageSize,xWorldLim,yWorldLim,zWorldLim)

Description

R = imref3d creates an imref3d object with default property settings.

R = imref3d(imageSize) specifies the image size in each spatial dimension.

R = imref3d(imageSize,pixExtentWorldX,pixExtentWorldY,pixExtentWorldZ) also specifies the spatial extent of a single pixel in the x-, y-, and z-dimensions in the world coordinate system.

R = imref3d(imageSize,xWorldLim,yWorldLim,zWorldLim) also specifies the limits of the image in the x-, y-, and z-dimensions in the world coordinate system.

Input Arguments

imageSize — Number of elements in each spatial dimension

2-element positive row vector

Number of elements in each spatial dimension, specified as a 2-element positive row vector. imageSize is the same form as that returned by the size function.

This argument sets the ImageSize property.

Data Types: double

pixExtentWorldX — Size of single pixel in x-dimension

positive number

Size of a single pixel in the x-dimension measured in the world coordinate system, specified as a positive number.

This argument sets the PixelExtentInWorldX property.

Data Types: double

pixExtentWorldY — Size of single pixel in y-dimension

positive number

Size of a single pixel in the y-dimension measured in the world coordinate system, specified as a positive number.

This argument sets the PixelExtentInWorldY property.

Data Types: double

pixExtentWorldZ — Size of single pixel in z-dimension

positive number

Size of a single pixel in the z-dimension measured in the world coordinate system, specified as a positive number.

This argument sets the PixelExtentInWorldZ property.

Data Types: double

xWorldLim — Limits of image in world x-dimension

2-element numeric row vector

Limits of image in world x-dimension, specified as a 2-element row numeric vector [xMin xMax].

This argument sets the XWorldLimits property.

Data Types: double

yWorldLim — Limits of image in world y-dimension

2-element numeric row vector

Limits of image in world y-dimension, specified as a 2-element numeric row vector [yMin yMax].

This argument sets the YWorldLimits property.

Data Types: double

zWorldLim — Limits of image in world z-dimension

2-element numeric row vector

Limits of image in world z-dimension, specified as a 2-element numeric row vector [zMin zMax].

This argument sets the ZWorldLimits property.

Data Types: double

Output Arguments

R — 3-D spatial referencing

imref3d object

3-D spatial referencing, returned as an imref3d object.

Properties

ImageExtentInWorldX — Span of image in x-dimension in world coordinate system

numeric scalar

Span of image in the x-dimension in the world coordinate system, specified as a numeric scalar. The imref3d object calculates this value as PixelExtentInX * ImageSize(2).

Data Types: double

ImageExtentInWorldY — Span of image in y-dimension in world coordinate system

numeric scalar

Span of image in the y-dimension in the world coordinate system, specified as a numeric scalar. The imref3d object calculates this value as PixelExtentInY * ImageSize(1).

Data Types: double

ImageExtentInWorldZ — Span of image in z-dimension in world coordinate system

numeric scalar

Span of image in the z-dimension in the world coordinate system, specified as a numeric scalar. The imref3d object calculates this value as PixelExtentInZ * ImageSize(3).

Data Types: double

ImageSize — Number of elements in each spatial dimension

3-element positive row vector

Number of elements in each spatial dimension, specified as a 3-element positive row vector. ImageSize is the same form as that returned by the size function.

Data Types: double

PixelExtentInWorldX — Size of single pixel in x-dimension measured in world coordinate system

positive number

Size of a single pixel in the x-dimension measured in the world coordinate system, specified as a positive number.

Data Types: double

PixelExtentInWorldY — Size of a single pixel in y-dimension measured in world coordinate system

positive number

Size of a single pixel in the y-dimension measured in the world coordinate system, specified as a positive number.

Data Types: double

PixelExtentInWorldZ — Size of a single pixel in z-dimension measured in world coordinate system

positive number

Size of a single pixel in the z-dimension measured in the world coordinate system, specified as a positive number.

Data Types: double

XWorldLimits — Limits of image in world x-dimension

2-element numeric row vector

Limits of image in world x, specified as a 2-element row vector, [xMin xMax].

Data Types: double

YWorldLimits — Limits of image in world y-dimension

2-element numeric row vector

Limits of image in world y, specified as a 2-element row vector, [yMin yMax].

Data Types: double

ZWorldLimits — Limits of image in world z-dimension

2-element numeric row vector

Limits of image in world z, specified as a 2-element row vector, [zMin zMax].

Data Types: double

XIntrinsicLimits — Limits of image in intrinsic units in x-dimension

2-element row vector

Limits of image in intrinsic units in the x-dimension, specified as a 2-element row vector [xMin xMax]. For an m-by-n-by-p image, it equals [0.5, n+0.5].

Data Types: double

YIntrinsicLimits — Limits of image in intrinsic units in y-dimension

2-element row vector

Limits of image in intrinsic units in the y-dimension, specified as a 2-element row vector [yMin yMax]. For an m-by-n-by-p image, it equals [0.5, m+0.5].

Data Types: double

ZIntrinsicLimits — Limits of image in intrinsic units in z-dimension

2-element row vector

Limits of image in intrinsic units in the z-dimension, specified as a 2-element row vector [zMin zMax]. For an m-by-n-by-p image, it equals [0.5, p+0.5].

Data Types: double

Object Functions

contains	Determine if image contains points in world coordinate system
intrinsicToWorld	Convert from intrinsic to world coordinates
sizesMatch	Determine if object and image are size-compatible
worldToIntrinsic	Convert from world to intrinsic coordinates
worldToSubscript	Convert world coordinates to row and column subscripts

Examples

Create imref3d Object Knowing Image Size and Resolution in Each Dimension

Read image.

m = analyze75info("brainMRI.hdr");
A = analyze75read(m);

Create an imref3d object associated with the image, specifying the size of the pixels. The PixelDimensions field of the metadata of the file specifies the resolution in each dimension in millimeters/pixel.

RA = imref3d(size(A),m.PixelDimensions(2),m.PixelDimensions(1),m.PixelDimensions(3));

RA = 

  imref3d with properties:

           XWorldLimits: [0.5000 128.5000]
           YWorldLimits: [0.5000 128.5000]
           ZWorldLimits: [0.5000 27.5000]
              ImageSize: [128 128 27]
    PixelExtentInWorldX: 1
    PixelExtentInWorldY: 1
    PixelExtentInWorldZ: 1
    ImageExtentInWorldX: 128
    ImageExtentInWorldY: 128
    ImageExtentInWorldZ: 27
       XIntrinsicLimits: [0.5000 128.5000]
       YIntrinsicLimits: [0.5000 128.5000]
       ZIntrinsicLimits: [0.5000 27.5000]

Examine the extent of the image in each dimension in millimeters.

RA.ImageExtentInWorldX
RA.ImageExtentInWorldY
RA.ImageExtentInWorldZ

ans =

   128

ans =

   128

ans =

    27

More About

Intrinsic Coordinate System

The intrinsic coordinate values (x,y,z) of the center point of any pixel are identical to the values of the column, row, and plane subscripts for that pixel. For example, the center point of the pixel in row 5, column 3, plane 4 has intrinsic coordinates x = 3.0, y = 5.0, z = 4.0.

The order of the coordinate specification (3.0,5.0,4.0) is reversed in intrinsic coordinates relative to pixel subscripts (5,3,4). Intrinsic coordinates are defined on a continuous plane, while the subscript locations are discrete locations with integer values.

Extended Capabilities

C/C++ Code Generation

Generate C and C++ code using MATLAB® Coder™.

Usage notes and limitations:

• imref3d supports the generation of C and C++ code (requires MATLAB^® Coder™). For more information, see Code Generation for Image Processing.

• When generating code, you can only specify singular objects—arrays of objects are not supported.

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 R2013a