Get Calibration from DICOM stack

[Michael Doube]

Hi everyone

I've just made the leap from macros to plugins, having got to a point
where my macros were getting a bit unmanageable.  The learning curve is
has been steep for the last couple of days!  Could someone please show
me how to get the calibration (voxel dimensions and greyscale->HU) from
my DICOM stacks to use in this simple plugin?

Many thanks

Mike

----------------------------------------------------
/** Work out the centroid of a whole stack
and each of its slices, restricted to thresholded
pixels within an ROI */
import java.awt.Rectangle;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.process.ImageProcessor;
import ij.plugin.filter.PlugInFilter;
import ij.measure.Calibration;

public class Stack_Centroids implements PlugInFilter {
    protected ImageStack stack;
   
    public int setup(String arg, ImagePlus imp) {
        stack = imp.getStack();
        return DOES_16 + STACK_REQUIRED + SUPPORTS_MASKING;
    }
   
    public void run(ImageProcessor ip) {
        int minT = (int)ip.getMinThreshold();
        int maxT = (int)ip.getMaxThreshold();
        //2D centroids
        double xc = 0; double yc = 0;
        //3D centroids
        double xcent = 0; double ycent = 0; double zcent = 0;
        //pixel counters
        double cstack = 0;
        Rectangle r = ip.getRoi();
        int offset, i;
        short[] pixels;  
        int w = stack.getWidth();
        for (int s=1;s<=stack.getSize();s++) {
            double sumx = 0;
            double sumy = 0;
            double cslice = 0;
            pixels = (short[])stack.getPixels(s);
            for (int y=r.y; y<(r.y+r.height); y++) {
                offset = y*w;
                for (int x=r.x; x<(r.x+r.width); x++) {
                    i = offset + x;
                    if (pixels[i] >= minT && pixels[i] <= maxT){
                        cslice++;
                        sumx += x;
                        sumy += y;
                    }
                }
            }
            if (cslice > 0){
                xc = sumx/cslice;
                yc = sumy/cslice;
                xcent += xc*cslice;
                ycent += yc*cslice;
                zcent += cslice*s;
                cstack += cslice;
                IJ.write("Slice "+s+" centroid is at ("+xc+","+yc+"),
"+cslice+" pixels contributed.");  
            } else {
                IJ.write("Slice "+s+": No pixels available to make a
calculation");
            }
        }
        if (cstack > 0){
            IJ.write("3D centroid is at
("+xcent/cstack+","+ycent/cstack+","+zcent/cstack+")");
        } else {
            IJ.write("No voxels available to make a calculation");
        }
    }
}

[Andreas Jahnen]

> I've just made the leap from macros to plugins, having got to a point
> where my macros were getting a bit unmanageable.  The learning curve is
> has been steep for the last couple of days!  Could someone please show
> me how to get the calibration (voxel dimensions and greyscale->HU) from
> my DICOM stacks to use in this simple plugin?

Dear Mike,

I think you use the ij.measure.Calibration class to do that. There are
methods like:

// to find out if a image is calibrated:
myImagePlus.getCalibration().calibrated()

// get the Calibration Coefficient:
myImagePlus.getCalibration().getCoefficients()

and so on....

Best Regards,
Andreas

-----------------------------------------------------------------
ImageJ User and Developer Conference 2008
6-7. November 2008
http://imagejconf.tudor.lu
-----------------------------------------------------------------
Andreas Jahnen  -  Ingenieur de Recherche
[hidden email]
-----------------------------------------------------------------
CRP Henri Tudor  -  http://santec.tudor.lu
2A, rue Kalchesbrück
L-1852 Luxembourg
-----------------------------------------------------------------

>
> Many thanks
>
> Mike
>
> ----------------------------------------------------
> /** Work out the centroid of a whole stack
> and each of its slices, restricted to thresholded
> pixels within an ROI */
> import java.awt.Rectangle;
> import ij.IJ;
> import ij.ImagePlus;
> import ij.ImageStack;
> import ij.process.ImageProcessor;
> import ij.plugin.filter.PlugInFilter;
> import ij.measure.Calibration;
>
> public class Stack_Centroids implements PlugInFilter {
>     protected ImageStack stack;
>
>     public int setup(String arg, ImagePlus imp) {
>         stack = imp.getStack();
>         return DOES_16 + STACK_REQUIRED + SUPPORTS_MASKING;
>     }
>
>     public void run(ImageProcessor ip) {
>         int minT = (int)ip.getMinThreshold();
>         int maxT = (int)ip.getMaxThreshold();
>         //2D centroids
>         double xc = 0; double yc = 0;
>         //3D centroids
>         double xcent = 0; double ycent = 0; double zcent = 0;
>         //pixel counters
>         double cstack = 0;
>         Rectangle r = ip.getRoi();
>         int offset, i;
>         short[] pixels;
>         int w = stack.getWidth();
>         for (int s=1;s<=stack.getSize();s++) {
>             double sumx = 0;
>             double sumy = 0;
>             double cslice = 0;
>             pixels = (short[])stack.getPixels(s);
>             for (int y=r.y; y<(r.y+r.height); y++) {
>                 offset = y*w;
>                 for (int x=r.x; x<(r.x+r.width); x++) {
>                     i = offset + x;
>                     if (pixels[i] >= minT && pixels[i] <= maxT){
>                         cslice++;
>                         sumx += x;
>                         sumy += y;
>                     }
>                 }
>             }
>             if (cslice > 0){
>                 xc = sumx/cslice;
>                 yc = sumy/cslice;
>                 xcent += xc*cslice;
>                 ycent += yc*cslice;
>                 zcent += cslice*s;
>                 cstack += cslice;
>                 IJ.write("Slice "+s+" centroid is at ("+xc+","+yc+"),
> "+cslice+" pixels contributed.");
>             } else {
>                 IJ.write("Slice "+s+": No pixels available to make a
> calculation");
>             }
>         }
>         if (cstack > 0){
>             IJ.write("3D centroid is at
> ("+xcent/cstack+","+ycent/cstack+","+zcent/cstack+")");
>         } else {
>             IJ.write("No voxels available to make a calculation");
>         }
>     }
> }