roi select two rois

[Thomas Boudier]

Hello,

I would like to write a macro that select several rois, but it seems
that the "Shift" key is not taking into account while selecting :

roiManager("Select", 1);
setKeyDown("shift");
roiManager("Select", 2);

this macro will select only roi2, while I would like roi1 and 2 to be
selected.

Any idea ? thanks.

Thomas

--
/*****************************************************/
 Thomas Boudier, MCU Université Pierre et Marie Curie
 UMR 7101 / IFR 83. Bat A 328, Campus Jussieu
 Tél : [phone]  Fax : [phone]
/*****************************************************/


 

[Jan Eglinger-5]

Hello Thomas,

> I would like to write a macro that select several rois, but it seems
> that the "Shift" key is not taking into account while selecting :
>
> roiManager("Select", 1);
> setKeyDown("shift");
> roiManager("Select", 2);
>
> this macro will select only roi2, while I would like roi1 and 2 to be
> selected.
>

This code works fine for me (tried with v1.41c and v1.41i on WinXP),
i.e. it selects the combination of the two ROIs.
I tried only with rectangular ROIs, however.

best,
jan

--
Jan Eglinger
PhD Student, Eckhard Lammert group
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 Dresden
Germany

Tel:  [phone]

[Thomas Boudier]

Jan Eglinger a écrit :

> Hello Thomas,
>
>> I would like to write a macro that select several rois, but it seems
>> that the "Shift" key is not taking into account while selecting :
>>
>> roiManager("Select", 1);
>> setKeyDown("shift");
>> roiManager("Select", 2);
>>
>> this macro will select only roi2, while I would like roi1 and 2 to be
>> selected.
>>
>
> This code works fine for me (tried with v1.41c and v1.41i on WinXP),
> i.e. it selects the combination of the two ROIs.
> I tried only with rectangular ROIs, however.

Hi,

I'm running ImageJ 1.41i on linux with java1.6.0_06, what I would like
is to select specifically two rois (to perform some computation on
them), when I run this code :

roiManager("Select", 0);
setKeyDown("shift");
roiManager("Select", 1);
roiManager("measure");


I only have one measure instead of two. Not sure if the shift key
applies to the list inside roiManager or to Rois in the image where they
are combined.

Thomas

>
> best,
> jan
>


--
/*****************************************************/
 Thomas Boudier, MCU Université Pierre et Marie Curie
 UMR 7101 / IFR 83. Bat A 328, Campus Jussieu
 Tél : [phone]  Fax : [phone]
/*****************************************************/


 

[Jan Eglinger-5]

Hi Thomas,

>
> I'm running ImageJ 1.41i on linux with java1.6.0_06, what I would like
> is to select specifically two rois (to perform some computation on
> them), when I run this code :
>
> roiManager("Select", 0);
> setKeyDown("shift");
> roiManager("Select", 1);
> roiManager("measure");
>
>
> I only have one measure instead of two. Not sure if the shift key
> applies to the list inside roiManager or to Rois in the image where they
> are combined.
>

When running:

roiManager("Select", 0);
setKeyDown("shift");
roiManager("Select", 1);

the picture ends up with a combination of two ROIs, but when you run the

roiManager("measure");

command afterwards, it only measures one selection.


Try one of the following:
- If you want to have one measurement of the combined ROIs, do:

run("Measure");

- If you want to have measurements for all the ROIs in the manager, do:

roiManager("deselect");
roiManager("measure");



Interestingly, the "Deselect" command doesn't seem to be recorded by the
Macro Recorder.


Hth,
Jan

--
Jan Eglinger
PhD Student, Eckhard Lammert group
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 Dresden
Germany

Tel:  [phone]

[John Alexander-7]

I think the confusion is that you are creating ONE roi - and not two.  A
ROI does not have to be contiguous.  So, when using the shift key, you
are still making ONE roi (in two parts).  So, the macro is working just
fine, it is measuring the content in that one roi.

Since I am not sure what you want to do ...

if you want a measure for each roi ...

roiManager("Select", 0);
roiManager("measure");
roiManager("Select", 1);
roiManager("measure");



Thomas Boudier wrote:

> Jan Eglinger a écrit :
>> Hello Thomas,
>>
>>> I would like to write a macro that select several rois, but it seems
>>> that the "Shift" key is not taking into account while selecting :
>>>
>>> roiManager("Select", 1);
>>> setKeyDown("shift");
>>> roiManager("Select", 2);
>>>
>>> this macro will select only roi2, while I would like roi1 and 2 to be
>>> selected.
>>>
>>
>> This code works fine for me (tried with v1.41c and v1.41i on WinXP),
>> i.e. it selects the combination of the two ROIs.
>> I tried only with rectangular ROIs, however.
>
> Hi,
>
> I'm running ImageJ 1.41i on linux with java1.6.0_06, what I would like
> is to select specifically two rois (to perform some computation on
> them), when I run this code :
>
> roiManager("Select", 0);
> setKeyDown("shift");
> roiManager("Select", 1);
> roiManager("measure");
>
>
> I only have one measure instead of two. Not sure if the shift key
> applies to the list inside roiManager or to Rois in the image where they
> are combined.
>
> Thomas
>
>>
>> best,
>> jan
>>
>
>

--
John K. Alexander, Ph.D.
Post-Doctoral Fellow
William Green Laboratory
University of Chicago
Dept. Neurobiology, Pharmacology, and Physiology
947 East 58th Street
Abott Hall 402
Chicago, IL 60637
(off) 773-702-9386
(fax) 773-702-3774
[hidden email]

[lechristophe]

There is indeed a problem with selecting multiple ROIs in a macro. This is
more easily seen when trying to use the "Combine" command on two selected
ROIs in a macro. Below is a question I sent a few days ago and the response
of Wayne Rasband :


 I would like to select two ROIs in the manager and combine them in a

> macro. What is wrong in the following code ?
>
> newImage("test", "8-bit Black", 128, 128, 1);
> makeRectangle(54, 35,10,10);
> roiManager("Add");
> makeRectangle(70, 70,10,10);
> roiManager("Add");
> roiManager("select",0);
> setKeyDown("alt");
> roiManager("select",1);
> roiManager("Combine");
>
> The composite macro is displayed, but I get the error : "More than one
> item must be selected, or none". Using shift as a modifier leads to
> the same error. Any ideas ?
>

Dear Christophe,

As far as I know, there is no way in a macro to select a subset of the ROIs
in the ROI Manager. There does appear to be a way to programatically select
multiple items in an java.awt.List.

-wayne

So basically it cannot be done... Too bad this java.awt.List seems a bit
limited (another gripe is that you cannot expand the ROI manager window to
see more ROIs or to see longer names, at least on OSX).

Christophe




On Tue, Jul 29, 2008 at 16:41, John Alexander <[hidden email]> wrote:

> I think the confusion is that you are creating ONE roi - and not two.  A
> ROI does not have to be contiguous.  So, when using the shift key, you
> are still making ONE roi (in two parts).  So, the macro is working just
> fine, it is measuring the content in that one roi.
>
> Since I am not sure what you want to do ...
>
> if you want a measure for each roi ...
>
> roiManager("Select", 0);
> roiManager("measure");
> roiManager("Select", 1);
> roiManager("measure");
>
>
>
> Thomas Boudier wrote:
> > Jan Eglinger a écrit :
> >> Hello Thomas,
> >>
> >>> I would like to write a macro that select several rois, but it seems
> >>> that the "Shift" key is not taking into account while selecting :
> >>>
> >>> roiManager("Select", 1);
> >>> setKeyDown("shift");
> >>> roiManager("Select", 2);
> >>>
> >>> this macro will select only roi2, while I would like roi1 and 2 to be
> >>> selected.
> >>>
> >>
> >> This code works fine for me (tried with v1.41c and v1.41i on WinXP),
> >> i.e. it selects the combination of the two ROIs.
> >> I tried only with rectangular ROIs, however.
> >
> > Hi,
> >
> > I'm running ImageJ 1.41i on linux with java1.6.0_06, what I would like
> > is to select specifically two rois (to perform some computation on
> > them), when I run this code :
> >
> > roiManager("Select", 0);
> > setKeyDown("shift");
> > roiManager("Select", 1);
> > roiManager("measure");
> >
> >
> > I only have one measure instead of two. Not sure if the shift key
> > applies to the list inside roiManager or to Rois in the image where they
> > are combined.
> >
> > Thomas
> >
> >>
> >> best,
> >> jan
> >>
> >
> >
>
> --
> John K. Alexander, Ph.D.
> Post-Doctoral Fellow
> William Green Laboratory
> University of Chicago
> Dept. Neurobiology, Pharmacology, and Physiology
> 947 East 58th Street
> Abott Hall 402
> Chicago, IL 60637
> (off) 773-702-9386
> (fax) 773-702-3774
> [hidden email]
>

[Toby Cornish]

This doesn't really answer the original poster's question, but this may address yours, Christophe.  Here is a macro function for combining an arbitrary number of selections.  There may be a better way, but this seems to work (code below).

toby

newImage("test", "8-bit Black", 128, 128, 1);
makeRectangle(54, 35,10,10);
roiManager("Add");
makeRectangle(70, 70,10,10);
roiManager("Add");

rois = newArray(0, 1);
index = combineSelections(rois,true);
print ("new index = "+index);
exit();

// FUNCTIONS BELOW ================================

function combineSelections(rois,deleteOriginals) {
 
  // get the mimimum width and height for a scratch image
  scratchWidth=0;
  scratchHeight=0;
  for (i =0; i < rois.length; i++) {
    roiManager("select",rois[i]);
    getSelectionBounds(x, y, width, height);
    if (x+width>scratchWidth) scratchWidth = x+width;
    if (y+height>scratchHeight) scratchHeight = y+height;
  }

  //create scratch image
  newImage("scratch", "8-bit Black", scratchWidth, scratchHeight, 1);
  selectWindow("scratch");

  // fill and combine the selections
  for (i =0; i < rois.length; i++) {
    roiManager("select",rois[i]);
    run("Add...", "value=255");
  }
  run("Select All");
  run("Invert LUT");
  run("Create Selection");
  roiManager("Add");
 
  //cleanup
  if (deleteOriginals) {
    sort(rois);
    for (i =0; i < rois.length; i++) {
      roiManager("select",rois[i]-i);
      roiManager("Delete");
    }    
  }
  selectWindow("scratch");
  close();
 
  // return the new selection index
  newIndex = roiManager("Count")-1;
  roiManager("select",newIndex);
  return newIndex;
}

// wayne's qsort

  function sort(a) {quickSort(a, 0, lengthOf(a)-1);}

  function quickSort(a, from, to) {
      i = from; j = to;
      center = a[(from+to)/2];
      do {
          while (i<to && center>a[i]) i++;
          while (j>from && center<a[j]) j--;
          if (i<j) {temp=a[i]; a[i]=a[j]; a[j]=temp;}
          if (i<=j) {i++; j--;}
      } while(i<=j);
      if (from<j) quickSort(a, from, j);
      if (i<to) quickSort(a, i, to);
  }

>Date:    Tue, 29 Jul 2008 17:12:24 +0200
>From:    Christophe Leterrier <[hidden email]>
>Subject: Re: roi select two rois
>
>There is indeed a problem with selecting multiple ROIs in a macro. This is
>more easily seen when trying to use the "Combine" command on two selected
>ROIs in a macro. Below is a question I sent a few days ago and the response
>of Wayne Rasband :
>
>
> I would like to select two ROIs in the manager and combine them in a
>> macro. What is wrong in the following code ?
>>
>> newImage("test", "8-bit Black", 128, 128, 1);
>> makeRectangle(54, 35,10,10);
>> roiManager("Add");
>> makeRectangle(70, 70,10,10);
>> roiManager("Add");
>> roiManager("select",0);
>> setKeyDown("alt");
>> roiManager("select",1);
>> roiManager("Combine");
>>
>> The composite macro is displayed, but I get the error : "More than one
>> item must be selected, or none". Using shift as a modifier leads to
>> the same error. Any ideas ?
>>
>
>Dear Christophe,
>
>As far as I know, there is no way in a macro to select a subset of the ROIs
>in the ROI Manager. There does appear to be a way to programatically select
>multiple items in an java.awt.List.
>
>-wayne
>
>So basically it cannot be done... Too bad this java.awt.List seems a bit
>limited (another gripe is that you cannot expand the ROI manager window to
>see more ROIs or to see longer names, at least on OSX).
>
>Christophe

Toby C. Cornish, M.D., Ph.D.
Pathology Resident
Johns Hopkins Medical Institutions
[hidden email]