Posted by
lechristophe on
Jun 14, 2017; 1:15pm
URL: http://imagej.273.s1.nabble.com/Get-ROI-statistics-in-Javascript-tp5018887p5018891.html
Hi Avita,
Thank you for the pointer. It works well with a rectangular ROI (I get the
mean intensity inside the ROI). However, using this with a segmented line
ROI returns the mean intensity of the whole image, not the mean intensity
value for the segmented line ROI (given manually by using "Measure" with
the ROI activated). What am I doing wrong here?
- open a sample image.
- draw a segmented line ROi on it, store it in the ROI manager.
- run this script:
importClass(Packages.ij.IJ);
importClass(Packages.ij.plugin.frame.RoiManager);
importClass(Packages.ij.gui.Roi);
var imp = IJ.getImage();
var rm = RoiManager.getInstance();
var roi = rm.getRoi(0);
imp.setRoi(roi, false);
var stat = imp.getStatistics();
var mean = stat.mean;
IJ.log(mean);
the value returned is the mean intensity of the whole image, not of the
segmented line ROI.
Christophe
On Wed, Jun 14, 2017 at 1:41 PM, Avital Steinberg <
[hidden email]
> wrote:
> Hi Christophe,
> You can get the Roi statistics like this:
>
> imp.setRoi(roi, false);
> var stats = imp.getAllStatistics();
> var median = stats.median;
>
> The stats objects is an ImageStatistics object, so you can see which fields
> it has here:
>
>
https://imagej.nih.gov/ij/developer/api/ij/process/ImageStatistics.html>
> Good luck,
> Avital
>
> On Wed, Jun 14, 2017 at 12:24 PM, Christophe Leterrier <
>
[hidden email]> wrote:
>
> > Dear ImageJers,
> >
> > I'm trying to write a javascript snippet that retrieves a ROI from the
> ROI
> > manager, and returns the mean intensity but I can't seem to find out how
> to
> > do it.
> >
> > Here am I so far:
> >
> > - open a sample image
> > - draw a ROi on it, store it in the ROI manager
> > - run this script:
> >
> > importClass(Packages.ij.IJ);
> > importClass(Packages.ij.plugin.frame.RoiManager);
> > importClass(Packages.ij.gui.Roi);
> >
> > var imp = IJ.getImage();
> > var rm = RoiManager.getInstance();
> >
> > var roi = rm.getRoi(0);
> > roi.setImage(imp);
> > var stat = roi.getStatistics();
> > IJ.log(stat.mean);
> >
> > the "mean" property of the ImageStatistic returned by getStatistics()
> has a
> > value of NaN. How come? How to access the roi statistics in a purely
> > programmatic manner (ie without displaying stuff)?
> >
> > Thanks for your help,
> >
> > Christophe
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
>
> --
> ImageJ mailing list:
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