Problem with median filter in version 1.45j

[Xalt]

Hi,

After I changed from ImageJ version 1.45i to 1.45j I experienced problems with the median filters (and minimum, maximum filters as well) in some of my plugins. As an example, see the plugin below with a method to smooth a stack with a median filter. The result is a totally black stack. I have tried many things like updating the ImagePlus, duplicating the ImageProcessor before the filtering but nothing worked. In the end I worked around it by using this command:  IJ.run(imp, "Median...", "radius=2 slice"). So, I am not sure whether this is a bug or we just have to work around it. I suspect it has something to do with a new implementation of filtering as stated in the release notes: " Thanks to Michael Schmid, the Median, Mean, Minimum, Maximum and Variance filters use less memory when processing non-float images."


Thanks for any help!
Leonard Bosgraaf




public class test_smoothStack implements PlugIn {
 public void run(String arg) {
  long time1= System.currentTimeMillis();
  ImagePlus img = WindowManager.getCurrentImage();

  smoothStack( img, 1.1213, "median" );
 
  long time2= System.currentTimeMillis();  
  IJ.log("time to run= "+ (time2- time1) );  
   
  IJ.log("done");
 
 
 } ////-------------------------------------   END RUN --------------------------------------------------------------------

 
//XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
 // Method to perform a smoothing (mean or median of surrounding pixels) on a stack.
 // The strength of the smoothing (radius) must be passed.
 public void smoothStack( ImagePlus img, double smoothRadius, String method) {
  int mode= 0;
  ImageStack stack= img.getStack();  
  ImageProcessor ip;
  RankFilters RF= new RankFilters();
  if ( method== "median") {
   mode= 4;
  } else if (method== "mean") {
   mode= 0;
  } else {
   IJ.log("error in smoothStack method; choosing 'mean' as mode and continuing");
  }
     
  for (int slice= 1; slice<= stack.getSize();  slice++) { // for all slices
   ip = stack.getProcessor(slice);
   RF.rank( ip, smoothRadius, mode); // perform filter with mean or median, with radius smoothRadius
  }
  img.setStack(null, stack);    // update img
 }
 
}

[Rasband, Wayne (NIH/NIMH) [E]]

On Jun 30, 2011, at 6:17 AM, Xalt wrote:

> Hi,
>
> After I changed from ImageJ version 1.45i to 1.45j I experienced problems
> with the median filters (and minimum, maximum filters as well) in some of my
> plugins. As an example, see the plugin below with a method to smooth a stack
> with a median filter. The result is a totally black stack. I have tried many
> things like updating the ImagePlus, duplicating the ImageProcessor before
> the filtering but nothing worked. In the end I worked around it by using
> this command:  IJ.run(imp, "Median...", "radius=2 slice"). So, I am not sure
> whether this is a bug or we just have to work around it. I suspect it has
> something to do with a new implementation of filtering as stated in the
> release notes: " Thanks to Michael Schmid, the Median, Mean, Minimum,
> Maximum and Variance filters use less memory when processing non-float
> images."

This bug is fixed in the ImageJ 1.45k daily build.

-wayne

> public class test_smoothStack implements PlugIn {
> public void run(String arg) {
>  long time1= System.currentTimeMillis();
>  ImagePlus img = WindowManager.getCurrentImage();
>
>  smoothStack( img, 1.1213, "median" );
>
>  long time2= System.currentTimeMillis();  
>  IJ.log("time to run= "+ (time2- time1) );  
>
>  IJ.log("done");
>
>
> } ////-------------------------------------   END RUN
> --------------------------------------------------------------------
>
>
> //XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> // Method to perform a smoothing (mean or median of surrounding pixels) on
> a stack.
> // The strength of the smoothing (radius) must be passed.
> public void smoothStack( ImagePlus img, double smoothRadius, String method)
> {
>  int mode= 0;
>  ImageStack stack= img.getStack();  
>  ImageProcessor ip;
>  RankFilters RF= new RankFilters();
>  if ( method== "median") {
>   mode= 4;
>  } else if (method== "mean") {
>   mode= 0;
>  } else {
>   IJ.log("error in smoothStack method; choosing 'mean' as mode and
> continuing");
>  }
>
>  for (int slice= 1; slice<= stack.getSize();  slice++) { // for all slices
>   ip = stack.getProcessor(slice);
>   RF.rank( ip, smoothRadius, mode); // perform filter with mean or median,
> with radius smoothRadius
>  }
>  img.setStack(null, stack);    // update img
> }
>
> }
>
> --
> View this message in context: http://imagej.588099.n2.nabble.com/Problem-with-median-filter-in-version-1-45j-tp6532622p6532622.html
> Sent from the ImageJ mailing list archive at Nabble.com.