getFullLevel

(To be removed) Get all data in one level of bigimage object

The getFullLevel function of the bigimage object will be removed in a future release. Use the gather function associated with the blockedImage object instead. For more information, see Version History.

Syntax

I = getFullLevel(bigimg)

I = getFullLevel(bigimg,level)

Description

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

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

Examples

Create Single-Resolution Mask from Multiresolution Big Image

Create a big 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 = bigimage("tumor_091R.tif");

Display the entire bigimage at the finest resolution level. Display a grid of the block boundaries.

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

Determine the coarsest resolution level and the spatial referencing of the bigimage at that level.

clevel = bim.CoarsestResolutionLevel;
clevelLims = bim.SpatialReferencing(clevel);

Create a mask of the coarsest resolution level by following these steps:

• Get a single-resolution image of the coarsest resolution level.

• Convert the image to grayscale.

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

• 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.

imcoarse = getFullLevel(bim,clevel);
graycoarse = rgb2gray(imcoarse);
bwcoarse = imbinarize(graycoarse);
mask = imcomplement(bwcoarse);

Create a bigimage containing the mask. Use the same spatial referencing as the original bigimage.

bmask = bigimage(mask,'SpatialReferencing',clevelLims);

Display the mask.

figure
bigimageshow(bmask);

Overlay the mask on the original bigimage. 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

bigimg — Big image

bigimage object

Big image, specified as a bigimage object.

level — Resolution level

positive integer

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

I — Single-resolution image

numeric array

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.

Version History

Introduced in R2019b

R2024b: Warns

The getFullLevel function issues a warning that it will be removed in a future release.

R2023b: To be removed

The bigimage object and this function will be removed in a future release. Use the gather function of the blockedImage object instead.

To update your code, first create a blockedImage object to read your image data. Then, follow these steps:

• Replace instances of the getFullLevel function name with the gather function.

• Replace the first input argument with the blockedImage object.

• If you want to get the block at a different resolution level, then specify that level by using the Level name-value argument.

Discouraged Usage	Recommended Replacement
This example uses the getFullLevel function with a bigimage object to return the image at the coarsest resolution level. filename = "tumor_091R.tif"; bim = bigimage(filename); img = getFullLevel(bim);	Here is equivalent code using a blockedImage object and the gather function. filename = "tumor_091R.tif"; blockedIm = blockedImage(filename); img = gather(blockedIm);
This example repeats the operation at resolution level 2. lvl = 2; img = getFullLevel(bim,lvl);	This example repeats the operation at resolution level 2 by specifying the Level name-value argument. lvl = 2; img = gather(blockedIm,Level=lvl);

R2021a: getFullLevel function is not recommended

The getFullLevel function of the bigimage object is not recommended. Use the gather function of the blockedImage object instead. The blockedImage object offers several advantages including extension to N-D processing, a simpler interface, and custom support for reading and writing nonstandard image formats.