The mean intensity values are strange

[Avital Steinberg]

Hi,
I'm trying to do some measurements using Javascript. When I run the
following code on the attached image:

importClass(Packages.ij.IJ);
importClass(Packages.ij.plugin.frame.RoiManager);
importClass(Packages.ij.io.OpenDialog);
importClass(Packages.ij.io.DirectoryChooser);
importClass(Packages.java.io.File);
importClass(Packages.ij.gui.GenericDialog);
importClass(Packages.ij.util.Tools);
importClass(Packages.ij.plugin.Duplicator);
importClass(Packages.ij.measure.ResultsTable);
importClass(Packages.ij.ImagePlus);
importClass(Packages.ij.process.ImageProcessor);
importClass(Packages.ij.gui.OvalRoi);

IJ = IJ();
rm = RoiManager.getInstance();
rt = ResultsTable.getResultsTable();
if (rm==null) rm = new RoiManager();
if (rt==null) rt = new ResultsTable();
impProc = IJ.getImage();
impProc.setRoi(new OvalRoi(405,585,54,57));
IJ.run("ROI Manager...", "");
rm.addRoi(impProc.getRoi());
rm.select(impProc, 0);
ipProc = impProc.getProcessor();
stats = ipProc.getStatistics();
mean = stats.mean;
print("The mean is: " + mean);

stats2 = impProc.getStatistics();
mean2 = stats.mean;
print("Mean2 is: " + mean2);

I get the following output:

The mean is: 49.10071474983756
Mean2 is: 49.10071474983756

However, if I use analyze, measure in the graphical user interface, I get a
mean intensity value of 60.8043.


What might the problem be?

Thanks,
Avital

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[Gabriel Landini]

On Monday 24 Aug 2015 21:42:23 Avital Steinberg wrote:
> Hi,
> I'm trying to do some measurements using Javascript. When I run the
> following code on the attached image:

> However, if I use analyze, measure in the graphical user interface, I get a
> mean intensity value of 60.8043.
>
>
> What might the problem be?

With that code, you are computing the mean of the rectangular region bounding
the circular ROI, I think.
Cheers

Gabriel

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[Avital Steinberg]

Hi Gabriel,
I'm using the same ROI in both cases, so I should get the same value
regardless of the shape of the ROI.

So this isn't the answer.

Thanks,
Avital

On Mon, Aug 24, 2015 at 10:33 PM, Gabriel Landini <[hidden email]>
wrote:

> On Monday 24 Aug 2015 21:42:23 Avital Steinberg wrote:
> > Hi,
> > I'm trying to do some measurements using Javascript. When I run the
> > following code on the attached image:
>
> > However, if I use analyze, measure in the graphical user interface, I
> get a
> > mean intensity value of 60.8043.
> >
> >
> > What might the problem be?
>
> With that code, you are computing the mean of the rectangular region
> bounding
> the circular ROI, I think.
> Cheers
>
> Gabriel
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Avital Steinberg]

Actually, Gabriel - you may be right that it's measuring the bounding
rectangle, because when I tried to use the ImageProcessor getHistogram
function in Javascript, it measured more pixeis than it did in the macro. I
think it's a bug, so I submitted a bug report.

Correct me if I'm wrong - I'll be very happy if changing my code would help.

Thanks,
Avital

On Mon, Aug 24, 2015 at 10:33 PM, Gabriel Landini <[hidden email]>
wrote:

> On Monday 24 Aug 2015 21:42:23 Avital Steinberg wrote:
> > Hi,
> > I'm trying to do some measurements using Javascript. When I run the
> > following code on the attached image:
>
> > However, if I use analyze, measure in the graphical user interface, I
> get a
> > mean intensity value of 60.8043.
> >
> >
> > What might the problem be?
>
> With that code, you are computing the mean of the rectangular region
> bounding
> the circular ROI, I think.
> Cheers
>
> Gabriel
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

> On Aug 24, 2015, at 2:42 PM, Avital Steinberg <[hidden email]> wrote:
>
> Hi,
> I'm trying to do some measurements using Javascript. When I run the
> following code on the attached image:

You need to assign the ROI to the ImageProcessor by calling ImageProcessor.setRoi(). This JavaScript

   img = IJ.getImage();
   roi = new OvalRoi(405,585,54,57);
   img.setRoi(roi);
   ip = img.getProcessor();
   ip.setRoi(roi);
   stats = ip.getStatistics();
   print("The mean is: " + stats.mean);
   stats2 = img.getStatistics();
   print("Mean2 is: " + stats2.mean);

outputs

   The mean is: 60.80429397192403
   Mean2 is: 60.80429397192403

If you remove "ip.setRoi(roi);” and run it again you get

   The mean is: 49.10071474983756
   Mean2 is: 60.80429397192403

-wayne

> importClass(Packages.ij.IJ);
> importClass(Packages.ij.plugin.frame.RoiManager);
> importClass(Packages.ij.io.OpenDialog);
> importClass(Packages.ij.io.DirectoryChooser);
> importClass(Packages.java.io.File);
> importClass(Packages.ij.gui.GenericDialog);
> importClass(Packages.ij.util.Tools);
> importClass(Packages.ij.plugin.Duplicator);
> importClass(Packages.ij.measure.ResultsTable);
> importClass(Packages.ij.ImagePlus);
> importClass(Packages.ij.process.ImageProcessor);
> importClass(Packages.ij.gui.OvalRoi);
>
> IJ = IJ();
> rm = RoiManager.getInstance();
> rt = ResultsTable.getResultsTable();
> if (rm==null) rm = new RoiManager();
> if (rt==null) rt = new ResultsTable();
> impProc = IJ.getImage();
> impProc.setRoi(new OvalRoi(405,585,54,57));
> IJ.run("ROI Manager...", "");
> rm.addRoi(impProc.getRoi());
> rm.select(impProc, 0);
> ipProc = impProc.getProcessor();
> stats = ipProc.getStatistics();
> mean = stats.mean;
> print("The mean is: " + mean);
>
> stats2 = impProc.getStatistics();
> mean2 = stats.mean;
> print("Mean2 is: " + mean2);
>
> I get the following output:
>
> The mean is: 49.10071474983756
> Mean2 is: 49.10071474983756
>
> However, if I use analyze, measure in the graphical user interface, I get a
> mean intensity value of 60.8043.
>
>
> What might the problem be?
>
> Thanks,
> Avital

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[Avital Steinberg]

Thank you, Wayne! Now I understand how to update the ImageProcessor about
the current selection. For example, if I have ROIs in the ROI manager from
an overlay, and I'd like to use the ImageProcessor, I can use the following
commands:

impProc = IJ.getImage(); // getting the ImagePlus
rm.select(selectIndex); // selecting the ROI from the manager
selectedRoi = rm.getRoi(selectIndex); // getting the selected ROI
//impProc.setRoi(selectedRoi); // Making sure the ImagePlus has the
selection.

ipProc = impProc.getProcessor();
ipProc.setRoi(selectedRoi); // Making sure the ImageProcessor has the
selection.

I appreciate your help!

Avital

On Tue, Aug 25, 2015 at 5:14 PM, Rasband, Wayne (NIH/NIMH) [E] <
[hidden email]> wrote:

>
> > On Aug 24, 2015, at 2:42 PM, Avital Steinberg <[hidden email]>
> wrote:
> >
> > Hi,
> > I'm trying to do some measurements using Javascript. When I run the
> > following code on the attached image:
>
> You need to assign the ROI to the ImageProcessor by calling
> ImageProcessor.setRoi(). This JavaScript
>
>    img = IJ.getImage();
>    roi = new OvalRoi(405,585,54,57);
>    img.setRoi(roi);
>    ip = img.getProcessor();
>    ip.setRoi(roi);
>    stats = ip.getStatistics();
>    print("The mean is: " + stats.mean);
>    stats2 = img.getStatistics();
>    print("Mean2 is: " + stats2.mean);
>
> outputs
>
>    The mean is: 60.80429397192403
>    Mean2 is: 60.80429397192403
>
> If you remove "ip.setRoi(roi);” and run it again you get
>
>    The mean is: 49.10071474983756
>    Mean2 is: 60.80429397192403
>
> -wayne
>
>
> > importClass(Packages.ij.IJ);
> > importClass(Packages.ij.plugin.frame.RoiManager);
> > importClass(Packages.ij.io.OpenDialog);
> > importClass(Packages.ij.io.DirectoryChooser);
> > importClass(Packages.java.io.File);
> > importClass(Packages.ij.gui.GenericDialog);
> > importClass(Packages.ij.util.Tools);
> > importClass(Packages.ij.plugin.Duplicator);
> > importClass(Packages.ij.measure.ResultsTable);
> > importClass(Packages.ij.ImagePlus);
> > importClass(Packages.ij.process.ImageProcessor);
> > importClass(Packages.ij.gui.OvalRoi);
> >
> > IJ = IJ();
> > rm = RoiManager.getInstance();
> > rt = ResultsTable.getResultsTable();
> > if (rm==null) rm = new RoiManager();
> > if (rt==null) rt = new ResultsTable();
> > impProc = IJ.getImage();
> > impProc.setRoi(new OvalRoi(405,585,54,57));
> > IJ.run("ROI Manager...", "");
> > rm.addRoi(impProc.getRoi());
> > rm.select(impProc, 0);
> > ipProc = impProc.getProcessor();
> > stats = ipProc.getStatistics();
> > mean = stats.mean;
> > print("The mean is: " + mean);
> >
> > stats2 = impProc.getStatistics();
> > mean2 = stats.mean;
> > print("Mean2 is: " + mean2);
> >
> > I get the following output:
> >
> > The mean is: 49.10071474983756
> > Mean2 is: 49.10071474983756
> >
> > However, if I use analyze, measure in the graphical user interface, I
> get a
> > mean intensity value of 60.8043.
> >
> >
> > What might the problem be?
> >
> > Thanks,
> > Avital
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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