Re: Get ROI statistics in Javascript?

Posted by Avital Steinberg on Jun 14, 2017; 1:27pm
URL: http://imagej.273.s1.nabble.com/Get-ROI-statistics-in-Javascript-tp5018887p5018892.html

Hi Christophe,
The command you are using is different from what I am using. I am using:

var stats = imp.get*All*Statistics();

And you are using:

var stat = imp.getStatistics();

I hope this helps,
Avital




On Wed, Jun 14, 2017 at 4:15 PM, Christophe Leterrier <
[hidden email]> wrote:

> 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: http://imagej.nih.gov/ij/list.html
>>
>
>

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