Reading a binary file

Posted by Kb Pru on Jun 02, 2009; 1:26pm
URL: http://imagej.273.s1.nabble.com/Reading-a-binary-file-tp3692318.html

Hello All,
  I am new to writing plugins and am trying to read a raw file in through a
plugin. I have several questions:

1. Each file I am reading is 105906380 bytes long. It takes a while to read
the file. How can I speed it up? I am currently reading the file slice by
slice via these commands:

for (int s=0;s<slices;s++){
   img.setSlice(s+1);
   IJ.showProgress( (double) s / slices);
   pixels = (short[]) img.getProcessor().getPixels();
   for(int row=0;row<height;row++){
        offset = (row*width);
        for (int col=0;col<width;col++){
           pixels[offset+col]=swapshort(input.readShort());
        }
   }
}

2. I would like to scale the pixel value linearly. However when I change one
line line from the above snipped to :
pixels[offset+col]=swapshort(input.readShort()-16383);
I get an error message "Incompatible type for method. Explicit cast needed
to convert int to short.". How do I operate on pixel element values.

Many thanks.

KB