getBlock

(To be removed) Read block of bigimage object

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

Syntax

data = getBlock(bigimg,level,locationWorld)

Description

data = getBlock(bigimg,level,locationWorld) reads the big image data in bigimg at the specified resolution level, and returns pixel data for the entire block that contains coordinate locationWorld.

example

Examples

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Select and Display `bigimage` Block Interactively

Open Script

Create a bigimage using a modified version of image "tumor_091.tif" from the CAMELYON16 data set. The original image is a training image of a lymph node containing tumor tissue. The original image has eight resolution levels, and the finest level has resolution 53760-by-61440. The modified image has only three coarse resolution levels. The spatial referencing of the modified image has been adjusted to enforce a consistent aspect ratio and to register features at each level.

bim = bigimage('tumor_091R.tif');

Display the bigimage by using the bigimageshow function. Overlay a grid that shows the block boundaries at the finest resolution level.

hb = subplot(1,2,1);
bigimageshow(bim,'GridVisible','on','GridLevel',1);

Specify the (x,y) coordinate of a block to display. Get the block containing the coordinate. Add a Point ROI over the displayed bigimage at the specified coordinate.

coord = [2500,2500];
blk = getBlock(bim,1,coord);
hp = drawpoint(hb,'Position',coord);

In the figure, display the block next to the entire bigimage. You can use imshow to display the block because the block fits in memory and has a single resolution level.

ha = subplot(1,2,2);
imshow(blk,'Parent',ha)

Add a listener to the Point ROI. When you drag the ROI with the mouse, the figure is updated to show the block containing the current ROI coordinates.

title(hb,'Drag Point to Select Block');
addlistener(hp, ...
    'ROIMoved',@(~,~) imshow(getBlock(bim,1,hp.Position),'Parent',ha));

Input Arguments

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`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.

`locationWorld` — Coordinate of a point
1-by-2 numeric vector

Coordinate of a point, specified as a 1-by-2 numeric vector of the form [x y]. The location is specified in world coordinates, which are the pixel locations relative to the highest resolution level. The position must be a valid position within bigimg.

Output Arguments

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`data` — Pixel data
numeric array

Pixel data, returned as a numeric array of the same data type as the big image, bigimg.ClassUnderlying.

Version History

Introduced in R2019b

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R2024b: Warns

The getBlock 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 getBlock function of the blockedImage object instead.

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

Convert from (x, y) world coordinates to (row, column) world coordinates by switching the order of the two elements.
Convert the world coordinates to pixel subscripts using the world2sub function. If you want to get the block at a resolution level other than level 1, then specify that level by using the Level name-value argument.
Convert the pixel subscripts to block subscripts using the sub2blocksub function. If you want to get the block at a resolution level other than level 1, then specify that level by using the Level name-value argument.
Note that if the dimensionality of the blocked image is greater than 2, then increase the length of the vector of pixel subscripts by one for each unspecified dimension. You can specify the value 1 for these additional elements. For example, a 2-D color image has a dimensionality of 3 because of the color channel. You must append one element to the vector of pixel subscripts when you call the sub2blocksub function.
Pass the blocked image and the block subscripts to the getBlock function. If you want to get the block at a resolution level other than level 1, then specify that level by using the Level name-value argument.

Discouraged Usage Recommended Replacement

Discouraged Usage	Recommended Replacement
This example uses the `getBlock` function with a `bigimage` object to get the image data in the block surrounding world (x, y) coordinates (1000, 2500) at the highest resolution level. filename = "tumor_091R.tif"; bim = bigimage(filename); coordWorld = [1000 2500]; blk = getBlock(bim,1,coordWorld);	Here is equivalent code using a `blockedImage` object. Because this image is a color image with dimensionality 3, add an element to the pixel subscripts to represent the unspecified dimension. filename = "tumor_091R.tif"; blockedIm = blockedImage(filename); coordWorld = [1000 2500]; coordRC = flip(coordWorld); subPixel = world2sub(blockedIm,coordRC); subBlock = sub2blocksub(blockedIm,[subPixel 1]); blk = getBlock(blockedIm,subBlock);
This example repeats the operation at resolution level 2. lvl = 2; blk = getBlock(bim,lvl,coordWorld);	This example repeats the operations at resolution level 2 by specifying the `Level` name-value argument. lvl = 2; subPixel = world2sub(blockedIm,coordRC,Level=lvl); subBlock = sub2blocksub(blockedIm,[subPixel 1],Level=lvl); blk = getBlock(blockedIm,subBlock,Level=lvl);

This example uses the getBlock function with a bigimage object to get the image data in the block surrounding world (x, y) coordinates (1000, 2500) at the highest resolution level.

filename = "tumor_091R.tif";
bim = bigimage(filename);
coordWorld = [1000 2500];
blk = getBlock(bim,1,coordWorld);

Here is equivalent code using a blockedImage object. Because this image is a color image with dimensionality 3, add an element to the pixel subscripts to represent the unspecified dimension.

filename = "tumor_091R.tif";
blockedIm = blockedImage(filename);
coordWorld = [1000 2500];
coordRC = flip(coordWorld);
subPixel = world2sub(blockedIm,coordRC);
subBlock = sub2blocksub(blockedIm,[subPixel 1]);
blk = getBlock(blockedIm,subBlock);

This example repeats the operation at resolution level 2.

lvl = 2;
blk = getBlock(bim,lvl,coordWorld);

This example repeats the operations at resolution level 2 by specifying the Level name-value argument.

lvl = 2;
subPixel = world2sub(blockedIm,coordRC,Level=lvl);
subBlock = sub2blocksub(blockedIm,[subPixel 1],Level=lvl);
blk = getBlock(blockedIm,subBlock,Level=lvl);

R2021a: `getBlock` function is not recommended

The getBlock function of the bigimage object is not recommended. Use the getBlock 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.

getBlock

Syntax

Description

Examples

Select and Display bigimage Block Interactively

Input Arguments

bigimg — Big image bigimage object

level — Resolution level positive integer

locationWorld — Coordinate of a point 1-by-2 numeric vector

Output Arguments

data — Pixel data numeric array

Version History

R2024b: Warns

R2023b: To be removed

R2021a: getBlock function is not recommended

See Also

Select and Display `bigimage` Block Interactively

`bigimg` — Big image
`bigimage` object

`level` — Resolution level
positive integer

`locationWorld` — Coordinate of a point
1-by-2 numeric vector

`data` — Pixel data
numeric array

R2021a: `getBlock` function is not recommended