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getFullLevel

(Not recommended) Get all data in one level of bigimage object

The getFullLevel function of the bigimage object is not recommended. Use the gather function associated with the blockedImage object instead. For more information, see Compatibility Considerations.

Description

I = getFullLevel(bigimg) reads the big image data in bigimg at the coarsest resolution level and returns the single-resolution image I.

example

I = getFullLevel(bigimg,level) reads the big image data in bigimg at the specified resolution level and returns the single-resolution image I.

Examples

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Create a blocked image from the sample image tumor_091R.tif. This sample image is a training image of a lymph node containing tumor tissue from the CAMELYON16 data set. The image has been modified to have three coarse resolution levels, and has been adjusted to enforce a consistent aspect ratio and to register features at each level.

bim = blockedImage('tumor_091R.tif');

Display the entire blocked image at the finest resolution level, including a grid of the block boundaries.

bshow = bigimageshow(bim,'ResolutionLevel','fine', ...
    'GridVisible','on','GridLevel',1);

Create a mask of the coarsest resolution level.

First create a single-resolution image of the coarsest resolution level. By default, the gather function gets data from the coarsest resolution level.

imcoarse = gather(bim);

Convert the coarse image to grayscale.

graycoarse = rgb2gray(imcoarse);

Binarize the grayscale image. In the binarized image, the object of interest is black and the background is white.

bwcoarse = imbinarize(graycoarse);

Take the complement of the binarized image. The resulting mask follows the convention in which the object of interest is white and the background is black.

mask = imcomplement(bwcoarse);

Create a blocked image containing the mask.

Use the same spatial referencing as the original blocked image. Determine the coarsest resolution level and capture the spatial referencing information of the blocked image at the first two dimensions at that level.

coarsestLevel = bim.NumLevels;
originalWorldStartCoarsest = bim.WorldStart(coarsestLevel,1:2);
originalWorldEndCoarsest = bim.WorldEnd(coarsestLevel,1:2);

Create the blocked image for the mask.

bmask = blockedImage(mask,'WorldStart',originalWorldStartCoarsest, ...
   'WorldEnd',originalWorldEndCoarsest);

Display the mask image.

figure
bigimageshow(bmask)

Overlay the mask on the display of the original blocked image using the showmask function. To highlight all blocks that contain at least one nonzero mask pixel, specify an inclusion threshold of 0.

showmask(bshow,bmask,'InclusionThreshold',0)

Input Arguments

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Big image, specified as a bigimage object.

Resolution level, specified as a positive integer that is less than or equal to the number of resolution levels of bigimg. The default level is the coarsest resolution level, bigimg.CoarsestResolutionLevel.

Output Arguments

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Single-resolution image, returned as a numeric array.

Tips

  • Check the LevelSizes property of the input big image bigimg to confirm that the size of image data at the specified level is small enough to fit in memory.

Compatibility Considerations

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Not recommended starting in R2021a

Introduced in R2019b