apply

Process blocks of blocked image

Since R2021a

Syntax

bimProc = apply(bim,fcn)

[bimProc1,bimProc2,...] = apply(bim,fcn)

[bimArrayProc1,bimArrayProc2,...] = apply(bimArray,fcn)

[___] = apply(___,Name,Value)

Description

bimProc = apply(bim,fcn) processes the entire blocked image bim by applying the function handle fcn to each block. The function returns bimProc, a new blocked image containing the processed data.

[bimProc1,bimProc2,...] = apply(bim,fcn) returns multiple blocked images. The specified function handle, fcn, must point to a user function that returns the same number of output arguments.

[bimArrayProc1,bimArrayProc2,...] = apply(bimArray,fcn) processes the array of blocked images bimArray by applying the function handle fcn to each block of each blocked image. The function returns one or more arrays of blocked images containing the processed data. The specified function handle, fcn, must point to a user function that returns the same number of output arguments.

[___] = apply(___,Name,Value) modifies aspects of the block processing using name-value arguments.

Examples

Enhance Image Details to Better Visualize Region Boundaries

Create blocked image.

bim = blockedImage("tumor_091R.tif");

Create a smoothing filter and apply it to the blocks in the blocked image.

smoothing = 2000;

imguidedfilter operates on a default neighborhood of 5 pixels. Add a border to the input to read additional data. This border pixels automatically get trimmed from the output since its the same size as the input.

benh= apply(bim,...
    @(bs)imguidedfilter(bs.Data,bs.Data,"DegreeOfSmoothing", smoothing),...
    "BorderSize", [5 5]);

Display the original image and the enhanced image.

ha1 = subplot(1,2,1);
bigimageshow(bim,"ResolutionLevel",1);
ha2 = subplot(1,2,2);
bigimageshow(benh);
linkaxes([ha1, ha2]);
xlim([2100, 2600])
ylim([1800 2300])

Improve Efficiency By Using Mask to Limit Processed Region

Create a blocked image.

bim = blockedImage("tumor_091R.tif");

Create a mask at the coarsest level and display it.

bmask = apply(bim, @(bs)im2gray(bs.Data)<80,Level=3);
figure
bigimageshow(bmask)

Use the mask to limit regions processed by the call to the apply object function.

bls = selectBlockLocations(bim,Mask=bmask,InclusionThreshold=0.005);
benh = apply(bim, @(bs)imguidedfilter(bs.Data,bs.Data,DegreeOfSmoothing=2000), ...
    BorderSize=[5 5],BlockLocationSet=bls); 

Display the original image and the enhanced image.

figure
ha1 = subplot(1,2,1);
bigimageshow(bim,ResolutionLevel=1);
ha2 = subplot(1,2,2);
bigimageshow(benh);

linkaxes([ha1, ha2]);      

Process Array of Blocked Images

Create a file set of all the JPEG images in the toolbox sample images folder.

fs = matlab.io.datastore.FileSet( ...
    fullfile(matlabroot,"toolbox","images","imdata"), ...
    "FileExtensions",".jpg");

Create an array of blocked images from the file set.

bims = blockedImage(fs);

Create an adapter that saves a blocked image to disk as a single image file.

outputFolder = tempname;
outputAdapter = images.blocked.GenericImage;
outputAdapter.Extension = "jpg";

Convert the images to binary images on disk.

bos = apply(bims, @(b)imbinarize(im2gray(b.Data)), ...
    "OutputLocation",outputFolder,"Adapter",outputAdapter);

View the contents of the output folder using the Image Browser app by running this command: imageBrowser(outputFolder)

Input Arguments

bim — Blocked image

blockedImage object

Blocked image, specified as a blockedImage object.

bimArray — Blocked images

array of blockedImage objects

Blocked images, specified as an array of blockedImage objects.

fcn — Processing function

function handle

Processing function, specified as a function handle. For more information, see Create Function Handle. The processing function fcn must accept a bstruct as input. To pass additional arguments, specify fcn as an anonymous function. For more information, see Anonymous Functions.

bstruct is a struct with these fields:

Field	Description
Data	Block of data from bim
Start	Subscripts of the first element in the block. If BorderSize is specified, this subscript can be out-of-bounds for edge blocks.
End	Subscripts of the last element in the block. If BorderSize is specified, this subscript can be out-of-bounds for edge blocks.
Blocksub	Block subscripts of the current block
BorderSize	Value of the BorderSize argument.
BlockSize	Value of the BlockSize argument. Note: size(data) can be less than this value for border blocks when PadPartialValue is false.
BatchSize	Value of the BatchSize parameter
ImageNumber	Index into bim array for the current image.
Level	The resolution level from which the data is being read.

The function fcn typically returns the results for one block. The results can be numeric, a struct, or categorical.

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Before R2021a, use commas to separate each name and value, and enclose Name in quotes.

Example: "Level",3

Adapter — Adapter used for writing blocked image data

adapter object

Adapter used for writing blocked image data, specified as an adapter object. To specify different adapters for different outputs, use a cell array. Scalar values are expanded.

This table lists the adapters included with the toolbox that support writing.

Adapter	Description
BINBlocks	Store each block as a binary file in a folder
GenericImage	Store blocks in a single image
GenericImageBlocks	Store each block as an image file in a folder
H5	Store blocks in a single HDF5 image
H5Blocks	Store each block as an HDF5 file in a folder
InMemory	Store blocks in a variable in main memory
JPEGBlocks	Store each block as a JPEG file in a folder
MATBlocks	Store each block as a MAT file in a folder
PNGBlocks	Store each block as a PNG file in a folder
TIFF	Store blocks in a single TIFF file

You can also specify a custom adapter that performs custom writing operations. For more information, see images.blocked.Adapter.

BatchSize — Batch size

1 (default) | numeric scalar

Batch size, specified as a numeric scalar. BatchSize is the last dimension of input to fcn. All outputs of fcn must have the last dimension be the same as BatchSize.

The batch size is the maximum number of blocks supplied to the processing function fcn in each batch. On the first call to fcn, the apply function sends only one block. On subsequent calls, the apply function sends BatchSize blocks. On the last call to fcn, the apply function sends all remaining blocks, which can be fewer than BatchSize.

Set BatchSize greater than 1 to optimally load GPUs when applying deep learning inference calls. When BatchSize is greater than 1, PadPartialBlocks must be true.

BlockLocationSet — Set of blocks to process

all non-overlapping BlockSize-sized blocks (default) | blockLocationSet object

Set of blocks to process, specified as a blockLocationSet object. The ImageNumber property of the blockLocationSet object indexes into the bimArray array. Specifying the blocks to process can improve efficiency by limiting the number of blocks processed. For example, use selectBlockLocations with a mask to limit applying the processing function to certain regions. Blocks contained must be on a regular grid.

BlockSize — Block size

value of BlockSize property of blocked image (default) | integer-valued vector

Block size of data supplied as the input to the processing function fcn, specified as an integer-valued vector of length equal to the NumDimensions property of bim. If BlockSize contains fewer elements, then the apply function pads the missing dimensions with elements from the Size property.

BorderSize — Border size

0 (default) | integer-valued vector

Border size, specified as an integer-valued vector of length equal to the NumDimensions property of bim. Specifies additional data from neighboring region to be included in a block. For edge blocks, the apply function uses the PadMethod argument. If BorderSize contains fewer elements, the apply function pads the border with 0s.

DisplayWaitbar — Display wait bar

true (default) | false

Display wait bar, specified as a logical scalar. When set to true, the apply function displays a wait bar for long-running operations. If you cancel the wait bar, the apply function returns partial output, if available.

Data Types: logical

ExtraImages — Additional inputs to fcn

array of blockedImage objects

Additional inputs to fcn, specified as an array of blockedImage objects. Blocks from this array are provided to fcn as additional inputs after bstruct: __ = fcn(bstruct,extrablock1,...). The apply function extracts these blocks from the same world region as the main block from bim, represented in bstruct.

ExtraLevels — Resolution level

vector of integers

Resolution level, specified as a vector of integers of the same length as ExtraImages. Each value specifies the resolution level to use from the corresponding blockedImage object in ExtraImages.

Level — Resolution level to use

1 (default) | integer scalar

Resolution level to use, specified as an integer scalar. For a multiresolution blockedImage object, this value determines the resolution level to use to obtain blocks for processing.

OutputLocation — Location of output folder

string scalar | character vector

Location of output folder, specified as a string scalar or character vector. If there is a single output, the apply function writes it directly to this location. For multiple outputs, the apply function creates subfolders of the format output<N>/ for the Nth output. If the input is an array, the apply function derives the output name from the Source property of the corresponding element. If the input is in-memory, the apply function uses a numeric index. When the UseParallel property is true, OutputLocation should be a valid path on the client session. Use the AlternateFileSystemRoots property of the input to specify the required mapping for worker sessions. All outputs inherit this value.

PadMethod — Method used for padding incomplete blocks

"replicate" (default) | "symmetric" | numeric scalar | logical scalar | categorical scalar

Method used for padding incomplete blocks, specified as one of the values in the table. The pad method specifies how to obtain padding pixels to honor the BorderSize or the PadPartialBlocks arguments.

Value	Meaning
numeric, logical, or categorical scalar	Pad array with elements of the specified value. The data type of PadMethod must match the ClassUnderlying property of the blocked image.
"replicate"	Pad by repeating border elements of the block.
"symmetric"	Pad with mirror reflections of pixels from within the same block.

PadPartialBlocks — Pad partial blocks

false (default) | true

Pad partial blocks, specified as logical scalar. Specifies if partial blocks that may exist on the edges need to be padded out to the specified block size. The apply object function uses the method specified in PadMethod to perform the padding operation.

• When false, the processing function fcn operates on partial blocks without padding and can return blocks smaller than BlockSize.

• When true, the apply function pads partial blocks using the specified PadMethod. The processing function fcn operates on and returns full-sized blocks.

When BatchSize is greater than 1, set PadPartialBlocks to true

Data Types: logical

Resume — Continue processing from where previous run stopped

false (default) | true

Continue processing from where the previous run stopped, specified as a logical scalar. If true, and the specified OutputLocation has content from a previous run, the current run will continue processing from where the previous run stopped. This support depends on the output adapter used. If false, the apply function deletes the previous content.

UseParallel — Use parallel processing

false (default) | true

Use parallel processing, specified as a logical scalar. Determines if a new or existing parallel pool should be used. If no parallel pool is active, a new pool is opened based on the default parallel settings. All adapters specified by the Adapter property must support parallel processing. You must specify a valid OutputLocation. This argument requires Parallel Computing Toolbox™.

Data Types: logical

Output Arguments

bimProc — Processed blocked image

blockedImage object

New blocked image, returned as a blockedImage object.

bimArrayProc — Processed blocked images

array of blockedImage objects

Processed blocked images, returned as an array of blockedImage objects.

Tips

• The apply function determines the output size by processing the first block. If processing the first block yields an output block of the same size as the input, then the final output size is set to match the input. Otherwise, the last block is processed to determine the final output size. The first block must not be a partial block.

• The apply function sets the InitialValue property of the output based on the type of the output:

  • Numeric or logical outputs – InitialValue is set to 0.

  • Categorical outputs – InitialValue is set to the <undefined> value of the corresponding type.

  • struct outputs – InitialValue is derived from the first block's output. All fields are set to empty.

Version History

Introduced in R2021a

R2023a: Support for symmetric padding

You can now specify the PadMethod argument as "symmetric". Symmetric padding consists of mirror reflections of pixels from within the same block.