getSubImage

This code is to get an array of pixel values of sub region in large Tiff image that saved by ImageJ/Fiji.

This code is memory-efficient (VirtualStack in ImageJ)) and utilizes cache (MappedByteBuffer in Java).

Usage of Java version in Matlab:

0. (Add ImageJ/Fiji classes to javaclasspath in matlab.)

1. (Add MyFileInfoVirtualStack.class to javaclasspath in matlab.)

2. Create an instance of MyFileInfoVirtualStack in matlab.

> mfivs = MyFileInfoVirtualStack(PATH_TO_IMAGE,BOOLEAN_TO_SHOW);

3. Get an array of pixel values of sub region.

> SUB_REGION = [xstart,ystart,xend,yend];

> pixels = mfivs.getSubImage(FRAME_INDEX,SUB_REGION)

4. typecast and reshape may be needed.

> TYPE = 'uint8'; % type of image

> subimage = reshape(typecast(pixles,TYPE),SUB_REGION(3:4)-SUB_REGION(1:2)+1);