Create Mask

Determine the image size at the coarsest level.

coarseLevel = bim.CoarsestResolutionLevel;
coarseLevelSize = bim.LevelSizes(coarseLevel,:)

coarseLevelSize = 1×2

   625   670

Get the image at the coarsest resolution level.

imLowRes = bim.getFullLevel(bim.CoarsestResolutionLevel);

You can generate a mask from the coarse level using the Image Segmenter app. The app expects a grayscale input image, so get the lightness channel from the coarse image.

imLowResL = rgb2lightness(imLowRes);

To run Image Segmenter, enter this command in the command window:

imageSegmenter(imLowResL)

You can export the mask, BW, or code that reproduces the processing pipleline used to create a mask. This section of the example uses code that the app exports. Run this code to create a mask from the coarse input image.

%----------------------------------------------------
% Normalize input data to range in [0,1].
Xmin = min(imLowResL(:));
Xmax = max(imLowResL(:));
if isequal(Xmax,Xmin)
    imLowResL = 0*imLowResL;
else
    imLowResL = (imLowResL - Xmin) ./ (Xmax - Xmin);
end

% Threshold image - global threshold
BW = imbinarize(imLowResL);

% Invert mask
BW = imcomplement(BW);

% Open mask with square
width = 3;
se = strel('square', width);
BW = imopen(BW, se);
%----------------------------------------------------

imshow(BW)

Create a bigimage from the mask with the same spatial referencing as the input mask.

bmask = bigimage(BW, ...
    'SpatialReferencing',bim.SpatialReferencing(coarseLevel));

Display the mask with a green background.

h = bigimageshow(bim);
h.Parent.Color = 'g';
h.Parent.Alphamap = [1 .5];
h.AlphaData = bmask;
h.AlphaDataMapping = 'direct';

Adjust Inclusion Threshold to Cover Region of Interest

The apply function processes big images one block at a time. You can use the 'InclusionThreshold' property with the mask to specify which blocks the apply function uses. The inclusion threshold specifies the percentage of mask pixels that must be true for apply to process the block.

Highlight the blocks that apply will process using the default inclusion threshold, 0.5. Only center blocks, highlighted in green, will be processed.

h = bigimageshow(bim);
showmask(h,bmask,1);
title('Mask with Default Inclusion Threshold')

To process more blocks of the image, decrease the inclusion threshold.

showmask(h,bmask,1,'InclusionThreshold',0.4);
title('InclusionThreshold == 0.4')

In the extreme case, process all blocks that have at least a single true pixel in the mask. To specify this option, set the 'InclusionThreshold' property to 0. Not all blocks of the image are included.

showmask(h,bmask,1,'InclusionThreshold',0);
title('InclusionThreshold == 0')

Using the mask with any value of 'InclusionThreshold' will decrease the total execution time because apply will process fewer blocks than the full image. The benefit of using a mask becomes more significant as the image increases in resolution and as the processing pipelines increases in complexity.

Measure the execution time of filtering the full image.

tic
bout = apply(bim,1, ...
    @(block)imnlmfilt(block,'DegreeOfSmoothing',15));
tFullProcessing = toc;

Measure the execution time of filtering only blocks with the ROI.

tic
boutMasked = apply(bim,1, ...
    @(block)imnlmfilt(block,'DegreeOfSmoothing',15), ...
    'Mask',bmask,'InclusionThreshold',0);
tMaskedProcessing = toc;

bigimageshow(boutMasked)
defaultBlockSize = bim.BlockSize(1,:);
title(['Processed Image Using Mask with Default BlockSize == [' ...
    num2str(defaultBlockSize) ']']);

Compare the execution time of processing the full image compared to processing only blocks in the ROI.

disp(['Speedup using mask: ' ...
    num2str(tFullProcessing/tMaskedProcessing) 'x']);

Speedup using mask: 1.6817x

Adjust Block Size to Follow Contours of Region of Interest

You can decrease the block size to gain a tighter wrap around the ROI. For some block sizes, this will reduce the execution time because apply will process fewer pixels outside the ROI. However, if the block size is too small, then performance will decrease because the overhead of processing a larger number of block will offset the reduction in the number of pixels processed.

Highlight the blocks that apply will process using a smaller block size. To specify the block size, set the 'BlockSize' property.

blockSize = [512 512];
h = bigimageshow(bim);
showmask(h,bmask,1,'BlockSize',blockSize,'InclusionThreshold',0);
title(['BlockSize == [' num2str(blockSize) '], InclusionThreshold == 0'])

Measure the execution time of filtering all blocks within the ROI with a decreased block size.

tic
boutMasked = apply(bim,1, ...
    @(block)imnlmfilt(block,'DegreeOfSmoothing',15), ...
    'Mask',bmask,'BlockSize',blockSize,'InclusionThreshold',0);
tSmallerBlockProcessing = toc;

bigimageshow(boutMasked);
title(['Processed Image Using Mask with BlockSize == [' ...
    num2str(blockSize) ']']);

Compare the execution time of processing the entire ROI with smaller blocks compared to larger blocks.

disp(['Additional speedup using mask with decreased block size: ' ...
    num2str(tMaskedProcessing/tSmallerBlockProcessing) 'x']);

Additional speedup using mask with decreased block size: 1.3684x