Adjust output of image->results

[Jacob Keller]

Dear List,

is there a way to have the "image to results" output be a single
column of numbers, rather than a 2-d array? I have been using a text
editor to reformat, but it is getting pretty cumbersome. Better still
would be to get a whole stack to output, with each row a given pixel
ID, and each column being an image/slice.

JPK

--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [hidden email]
*******************************************

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

On Jun 5, 2012, at 11:28 AM, Jacob Keller wrote:

> Dear List,
>
> is there a way to have the "image to results" output be a single
> column of numbers, rather than a 2-d array? I have been using a text
> editor to reformat, but it is getting pretty cumbersome. Better still
> would be to get a whole stack to output, with each row a given pixel
> ID, and each column being an image/slice.

Here is JavaScript code that displays the contents of an image or stack in the Results window, with one image per column. To create a "Stack to Results" command, save it in the plugins folder, or subfolder, as "Stack_to_Results.js" and use the Help>Refresh Menus command.

-wayne

   var imp = IJ.getImage();
   var stack = imp.getStack();
   var nImages = stack.getSize();
   var nPixels = stack.getWidth()*stack.getHeight();  
   var rt = new ResultsTable();
   for (var z=0; z<nImages; z++) {
      IJ.showProgress(z, nImages-1);
      IJ.showStatus((z+1)+"/"+nImages);
      var ip = stack.getProcessor(z+1);
      for (var i=0; i<nPixels; i++) {
         if (z==0) rt.incrementCounter();
         rt.setValue("i"+(z+1), i, ip.getf(i));
      }
   }
   rt.show("Results");

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[Jacob Keller]

Again, right on the money!

Thanks very much,

Jacob

ps now I want to go back the other way: is there a way to make a "heat
map" image of these pixels after re-ordering them, i.e., re-input the
stack as an array of numbers (pixel ID x image number) and make an
image from those data points, to be LUT-ed appropriately? I am trying
to show what each (binned) pixel in a stack does over time (image#),
but first sorted by a given criteria. I have done this before in
gnuplot, but imageJ seems really nice, and I like the LUTs in ImageJ
better.


On Tue, Jun 5, 2012 at 1:16 PM, Rasband, Wayne (NIH/NIMH) [E]
<[hidden email]> wrote:

> On Jun 5, 2012, at 11:28 AM, Jacob Keller wrote:
>
>> Dear List,
>>
>> is there a way to have the "image to results" output be a single
>> column of numbers, rather than a 2-d array? I have been using a text
>> editor to reformat, but it is getting pretty cumbersome. Better still
>> would be to get a whole stack to output, with each row a given pixel
>> ID, and each column being an image/slice.
>
> Here is JavaScript code that displays the contents of an image or stack in the Results window, with one image per column. To create a "Stack to Results" command, save it in the plugins folder, or subfolder, as "Stack_to_Results.js" and use the Help>Refresh Menus command.
>
> -wayne
>
>   var imp = IJ.getImage();
>   var stack = imp.getStack();
>   var nImages = stack.getSize();
>   var nPixels = stack.getWidth()*stack.getHeight();
>   var rt = new ResultsTable();
>   for (var z=0; z<nImages; z++) {
>      IJ.showProgress(z, nImages-1);
>      IJ.showStatus((z+1)+"/"+nImages);
>      var ip = stack.getProcessor(z+1);
>      for (var i=0; i<nPixels; i++) {
>         if (z==0) rt.incrementCounter();
>         rt.setValue("i"+(z+1), i, ip.getf(i));
>      }
>   }
>   rt.show("Results");
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [hidden email]
*******************************************

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html