Plugin - assigning roi measurements to a variable

Posted by dplatten on Jul 11, 2007; 8:52am
URL: http://imagej.273.s1.nabble.com/Plugin-assigning-roi-measurements-to-a-variable-tp3698886.html

I'm sure that this is straightforward, but I am new to Java and writing
ImageJ plugins. I would be extremely grateful for a little help.

I have written a macro that creates a signal-to-noise map of the open image
(see the bottom of this message). I am a medical physicist working in a
hospital - this routine is useful for checking the response of digital x-ray
detectors. However, I'd like to use it with 10x10 pixel samples, but this
takes ages. I have therefore started to translate the macro into a plugin.
This is where I am having trouble. I need to assign the std_dev measured in
an roi to a variable. An example of how to do this would be great. I want to
avoid displaying and updating the results table if possible. Here's a
(non-working) code snippet:

ip.setRoi(x, y, sub_sample_size, sub_sample_size);
Analyzer ana = new Analyzer();
int measurements = Analyzer.getMeasurements();
measurements = (ana.STD_DEV);
IJ.write(Integer.toString(measurements));

This just returns the value 4.

Many thanks for any help,

David Platten
Clinical Scientist
Northampton General Hospital
Billing Road
Northampton NN1 5BD
tel [phone]


//-----------------------------------------------------------
macro "Signal to noise map" {
  // Calculates the signal to noise of sub-samples
  // over an image.
  // Displays the results as a new image.
  // SNR taken as mean pixel value in ROI divided
  // by standard deviation in the region.
  // David Platten, July 2007

  // Ask the user for the size of the sub-samples.
  Dialog.create("Signal to noise image");
  Dialog.addMessage("Click OK to analyze, or cancel to exit (!).");
  Dialog.addNumber("Sub-sample size:", 50);
  Dialog.show();
  sub_sample_size = Dialog.getNumber();

  // Find the dimensions of the image and then
  // determine the number of sub-samples that
  // will go into it.
  width = getWidth;
  height = getHeight;
  i_max = floor(width/sub_sample_size) + 1;
  j_max = floor(height/sub_sample_size) + 1;

  // Create an array to hold the results
  results = newArray(i_max * j_max);

  // Loop through the image, stepping through in
  // increments equal to the sub-sample size.
  i = 0;
  j = 0;
  max_snr = 0; // Used to scale the results image

  for(x=0; x<width; x+=sub_sample_size) {
    j = 0;
    for(y=0; y<height; y+=sub_sample_size) {
      // Specify the width, height and position of the ROI, then
      // measure the standard deviation and mean within it.
      // SNR is calculated as mean / standard deviation and
      // written into the appropriate element of the results array.
      run("Specify...", "width="+sub_sample_size+"
height="+sub_sample_size+" x="+x+" y="+y);
      run("Set Measurements...", "mean standard decimal=5");
      run("Measure");

      mean = getResult("Mean", nResults-1);
      stdev = getResult("StdDev", nResults-1);

      results[i + (j*i_max)] = mean / stdev;
               
      // Check to see if this is a new maximum snr. This is
      // used to scale the results at the end.
      if(results[i + (j*i_max)] > max_snr) max_snr = results[i + (j*i_max)];

      j++;
    }
    i ++;
  }

  // Create new image to display the results.
  // At the moment this is an 8-bit image, 256 shades of grey.
  image_title = "SNR, " + sub_sample_size + " pixel sub-samples";
  newImage(image_title, "8-bit Black", i_max, j_max, 1);

  // Step through the results array, scaling the values using
  // the known maximum figure and then allocating the value to
  // the appropriate pixel.
  for(i=0;i<i_max; i++) {
    for(j=0;j<j_max; j++) {
      temp = round(results[i + (j*i_max)] / max_snr * 256);
      setPixel(i, j, temp);
    }
  }

  // Resize the results image to have the same dimensions
  // as the original and then enhance the contrast (an
  // auto window and level).
  run("Size...", "width="+width+" height="+height+" constrain");
  run("Enhance Contrast", "saturated=0.5");
}
//-----------------------------------------------------------