Re: Problem with Maximum intensity projection

Posted by Michael Schmid on Mar 23, 2018; 6:22pm
URL: http://imagej.273.s1.nabble.com/Problem-with-Maximum-intensity-projection-tp5020309p5020325.html

Hi Fred,

for getting the values along the z direction, e.g. for fitting, you can
do the following:

         int nSlices = stack.getSize();
         ImageProcessor[] inIps = new ImageProcessor[nSlices];
         for (int i=0; i<nSlices; i++)
             inIps[i] = stack.getProcessor(i+1);
         Calibration cal = imp.getCalibration();
         double[] zData = new double[nSlices];
         for (int i=0; i<nSlices; i++)
             zData[i] = cal.getZ(i);

         double[] fitData = new double[nSlices];
         for (int y=0; y<height; y++) {
             IJ.showProgress((double)y/height);
             for (int x=0; x<width; x++) {
                 double[] params = null;
                 for (int i=0; i<nSlices; i++)
                     fitData[i] = inIps[i].getPixelValue(x, y);
                     // do the fit for fitData over zData
                 }
             }
         }

Somewhere I have a Stack_Fitter plugin, I'll upload it to
http://imagejdocu.tudor.lu

Michael
________________________________________________________________
On 23/03/2018 18:32, Fred Damen wrote:

> Greetings,
>
> I would like to second Kenneth's frustration with my version of fetching the
> requisite values:
>
>    for(int iz=0; iz<nz; iz++) {
>        IJ.showStatus("NonLinearFit: z="+iz);
>        IJ.showProgress(((float)iz)/nz);
>
>        for(int ix=0; ix<nx; ix++)
>           for(int iy=0; iy<ny; iy++) {
>              for(int if=0; if<nf; if++)
>                 y[if] =
> ((FloatProcessor)is.getProcessor(imp.getStackIndex(1,iz+1,if+1))).getf(ix,iy);
>                 process(x,y);
>              }
>        }
>
> Ages ago, I tried using the various getVoxel(s) methods to no avail.  If
> memory serves, they would always return the same value. So once I got the
> aforementioned code working I just copy and paste every time I need it; which
> is always.
>
> I would assume that this inner loop can be done extremely more efficiently
> under the hood than through the interface, i.e., repeated calls to
> is.getProcessor and imp.getStackIndex are not free; notice the need for
> showStatus and showProgress. Can the  getVoxels and setVoxels methods that
> include the frame dimension be included.
>
> Thanks for listening,
>
> Fred
>
>
> On Fri, March 23, 2018 11:30 am, Kenneth Sloan wrote:
> ...
>> Obligatory question: I tried to use getVoxels - but failed miserably.  After a
>> few attempts, I just
>> rolled my own.
>>
>> This is slower than dirt - but I hope it's clear.
>>
>> And, as always - I welcome corrections to my chronic mis-understanding of the
>> API.
>>   --
>> Kenneth Sloan
>> [hidden email]
>> Vision is the art of seeing what is invisible to others.
> ...
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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