Launching a Histogram from the roi Manager

[Dan McDonald]

Dear List,

 

I am trying to write a macro to get a histogram of a selection via the
roiManager.

 

When I manually click through the steps I get what I expect.  When I try to
execute the same steps through a macro I get different results. I have
included a snip of my code below.

 

I think that when I select a selection through the roiManager in the macro
and then execute run("Histogram") it is not running a histogram on the
selected selection I think I've specified.

 

     selectWindow("rootDiameterImage");

// Transfer roi from roiManager to new file

     run("From ROI Manager");

     totalRootSegments=roiManager("count");

     for(k_rs=0; k_rs <totalRootSegments;k_rs++) {

         roiManager("Select", k_rs);

         run("Histogram");

         getHistogram(Values,Counts,256);

         for(i_Hist=1; i_Hist<Values.length; i_Hist++) {

              thisValue=Values[i_Hist];

              thisCount=Counts[i_Hist];

              thisProduct=thisValue*thisCount;

              sumOfValueTimesCount=sumOfValueTimesCount +thisProduct;

              sumOfCount=sumOfCount+thisCount;

         }

 

Can anyone see what I am doing wrong?

 

When I manually click in the roiManager for a selection and then run a
histogram and examine the values under the histogram "list" I get what I was
expecting.  

 

When I examine the values within the histogram from the macro I get values
not associated with the "selection."

 

Thanks for your assistance,

 

Dan

 

Daniel W. McDonald,

Co-founder and President,

Phenotype Screening Corporation,

4028 Papermill Road, Suite 10,

Knoxville, TN 37909

[phone] cell

[phone] office

[hidden email]

daniel.w.mcdonald1 on Skype

www.phenotypescreening.com

 


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[Herbie]

Good day Dan,

maybe after calling for the histogram you should bring your image again
to the front (e.g. by using selectImage(id)), otherwise you get the next
histogram from the past histogram -- no?

HTH

Herbie

::::::::::::::::::::::::::::::::::::::::::
Am 30.09.16 um 20:44 schrieb Dan McDonald:

> Dear List,
>
>
>
> I am trying to write a macro to get a histogram of a selection via the
> roiManager.
>
>
>
> When I manually click through the steps I get what I expect.  When I try to
> execute the same steps through a macro I get different results. I have
> included a snip of my code below.
>
>
>
> I think that when I select a selection through the roiManager in the macro
> and then execute run("Histogram") it is not running a histogram on the
> selected selection I think I've specified.
>
>
>
>      selectWindow("rootDiameterImage");
>
> // Transfer roi from roiManager to new file
>
>      run("From ROI Manager");
>
>      totalRootSegments=roiManager("count");
>
>      for(k_rs=0; k_rs <totalRootSegments;k_rs++) {
>
>          roiManager("Select", k_rs);
>
>          run("Histogram");
>
>          getHistogram(Values,Counts,256);
>
>          for(i_Hist=1; i_Hist<Values.length; i_Hist++) {
>
>               thisValue=Values[i_Hist];
>
>               thisCount=Counts[i_Hist];
>
>               thisProduct=thisValue*thisCount;
>
>               sumOfValueTimesCount=sumOfValueTimesCount +thisProduct;
>
>               sumOfCount=sumOfCount+thisCount;
>
>          }
>
>
>
> Can anyone see what I am doing wrong?
>
>
>
> When I manually click in the roiManager for a selection and then run a
> histogram and examine the values under the histogram "list" I get what I was
> expecting.
>
>
>
> When I examine the values within the histogram from the macro I get values
> not associated with the "selection."
>
>
>
> Thanks for your assistance,
>
>
>
> Dan
>
>
>
> Daniel W. McDonald,
>
> Co-founder and President,
>
> Phenotype Screening Corporation,
>
> 4028 Papermill Road, Suite 10,
>
> Knoxville, TN 37909
>
> [phone] cell
>
> [phone] office
>
> [hidden email]
>
> daniel.w.mcdonald1 on Skype
>
> www.phenotypescreening.com
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

> On Sep 30, 2016, at 2:44 PM, Dan McDonald <[hidden email]> wrote:
>
> Dear List,
>
> I am trying to write a macro to get a histogram of a selection via the
> roiManager.
>
> When I manually click through the steps I get what I expect.  When I try to
> execute the same steps through a macro I get different results. I have
> included a snip of my code below.
>
> I think that when I select a selection through the roiManager in the macro
> and then execute run("Histogram") it is not running a histogram on the
> selected selection I think I've specified.

Remove the run("Histogram”) line, which is not needed and causes a lot histogram windows to open. You can also avoid using the ROI Manager and activate the selections directly from the overlay, as in this example:

  run("Blobs (25K)");
  setAutoThreshold("Default");
  run("Analyze Particles...", "  show=Overlay");
  resetThreshold;
  for (i=0; i<Overlay.size; i++) {
     Overlay.activateSelection(i);
     getHistogram(values, counts, 256);
     print(i, counts[128]);
  }

-wayne

>     selectWindow("rootDiameterImage");
>
> // Transfer roi from roiManager to new file
>
>     run("From ROI Manager");
>
>     totalRootSegments=roiManager("count");
>
>     for(k_rs=0; k_rs <totalRootSegments;k_rs++) {
>
>         roiManager("Select", k_rs);
>
>         run("Histogram");
>
>         getHistogram(Values,Counts,256);
>
>         for(i_Hist=1; i_Hist<Values.length; i_Hist++) {
>
>              thisValue=Values[i_Hist];
>
>              thisCount=Counts[i_Hist];
>
>              thisProduct=thisValue*thisCount;
>
>              sumOfValueTimesCount=sumOfValueTimesCount +thisProduct;
>
>              sumOfCount=sumOfCount+thisCount;
>
>         }
>
>
> Can anyone see what I am doing wrong?
>
> When I manually click in the roiManager for a selection and then run a
> histogram and examine the values under the histogram "list" I get what I was
> expecting.  
>
> When I examine the values within the histogram from the macro I get values
> not associated with the "selection."
>
> Thanks for your assistance,
>
> Dan

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