readRelative

(Not recommended) Read neighboring block from bigimageDatastore using relative position

Since R2019b

The readRelative function of the bigimageDatastore object is not recommended. Use the blockedImageDatastore object and its object functions instead. For more information, see Compatibility Considerations.

Syntax

data = readRelative(bigds,sourceInfo,blockOffset)

[data,info] = readRelative(bigds,sourceInfo,blockOffset)

Description

data = readRelative(bigds,sourceInfo,blockOffset) returns the block from big image datastore bigds that neighbors the source block sourceInfo with offset blockOffset.

[data,info] = readRelative(bigds,sourceInfo,blockOffset) also returns information about the extracted data, including metadata, in info.

Examples

Read Neighboring Big Image Blocks

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');

Create a bigimageDatastore that manages blocks of the big image at the finest resolution level.

bimds = bigimageDatastore(bim,1);

Read the first block from the datastore.

[b,binfo] = read(bimds);
b = b{1};

Read the neighboring blocks to the left and right of the block. The left neighboring block is empty because the block is out of the bounds of bim.

bLeft = readRelative(bimds,binfo,[0 -1]);
bRight = readRelative(bimds,binfo,[0 1]);

Display the blocks as a montage. The left neighboring block appears black because it is empty.

montage({bLeft,b,bRight},'Size',[1 3],'BorderSize',5,'BackgroundColor','b')

Input Arguments

bigds — Big image datastore

bigimageDatastore object

Big image datastore, specified as a bigimageDatastore object.

sourceInfo — Information about source block

struct

Information about source block, specified as a struct containing at least these fields. The value of info returned by read is a valid input for sourceInfo.

Field Name	Description
Level	Resolution level of the data, specified as a positive integers.
ImageNumber	Index of the big image providing the data, specified as a positive integer.
BlockStartWorld	(x,y) world coordinates of the top-left corner of the data, specified as a 1-by-2 numeric vector. The coordinates correspond to a position on the boundary of the block, not the center of the top-left pixel.

blockOffset — Block offset

1-by-2 vector of integers

Block offset, specified as a 1-by-2 vector of integers in units of blocks. The two elements specify the vertical and horizontal offset from the source block. respectively.

Output Arguments

data — Output data

numeric array

Output data, returned as a numeric array. If the requested block is outside the bounds of the source image, then readRelative returns an empty block, []

info — Information about output data

struct

Information about output data, returned as a struct containing these fields.

Field Name	Description
Level	Resolution level of the data, specified as a 1-by-ReadSize vector of positive integers.
ImageNumber	Index of the big image providing the data, specified as a 1-by-ReadSize vector of positive integers.
BlockStartWorld	(x,y) coordinates of the center of the top-left pixel of the data, excluding padding, specified as a ReadSize-by-2 numeric vector. Values are in world-coordinates.
BlockEndWorld	(x,y) coordinates of the center of the bottom-right pixel of the data, excluding padding, specified as a ReadSize-by-2 numeric vector. Values are in world-coordinates.
DataStartWorld	(x,y) coordinates of the center of the top-left pixel of the data, including padding, specified as a ReadSize-by-2 numeric vector. Values are in world-coordinates.
DataEndWorld	(x,y) coordinates of the center of the bottom-right pixel of the data, including padding, specified as a ReadSize-by-2 numeric vector. Values are in world-coordinates.

Tips

• readRelative ignores masks.

• readRelative respects the PadMethod and BorderSize properties of the big image datastore.

• If the requested block is incomplete and bigds.IncompleteBlocks has a value of 'exclude', then readRelative returns an empty block

Version History

Introduced in R2019b

R2021a: readRelative function is not recommended

Starting in R2021a, the bigimageDatastore object and its object functions, which operate on data from bigimage objects, are no longer recommended. Instead, use the blockedImageDatastore object and its object functions, which operate on data from blockedImage objects. 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.

Although there are no plans to remove the bigimageDatastore object and its readRelative function at this time, switch to the blockedImageDatastore object to take advantage of the additional capabilities and flexibility.