Stack.setChannel works inconsistently?

[TimFeinstein]

Hi folks,

Here is a large macro that I am working on which is a bit of a stretch for my skills, but it seems to be pretty close.  I am specifically pinging the board about the Stack.SetChannel() command, which only seems to work once.  The first time I use Stack.setChannel() it correctly selects stain#2 ("GPR161Channel") for thresholding.  However the next time when I want it to duplicate stain#1 ("ciliaChannel") for analysis in a smaller window it just copies stain#2 again.  This is line 59 in the macro.  I don't see why Stack.setChannel() should work the first time and not the second.

I am also working out how to correctly call up point ROIs from the ROI manager one at a time for making rectangles (lines 62 and 68) but that looks more like I need to keep learning the syntax of working with arrays.  The select channels problem feels like it might be a bug.

Here is a link to the macro and an example image:

https://www.dropbox.com/sh/gh0zkznpsrkalfi/AAAL_gqTXoKCTbjGegpN2AjNa?dl=0

Thanks!


Tim

Timothy Feinstein, Ph.D.
Research Scientist
University of Pittsburgh Department of Developmental Biology


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[TimFeinstein]

After more troubleshooting I discovered that Stack.selectChannel() works
fine, but selecting a ROI from the ROI manager interferes with it.  In the
following two examples, Stack.setChannel() works in example #1 but does
not work in #2.  

#1:

for (i = 0; i < roiManager("count"); i++){
 roiManager("select", i);
 getSelectionCoordinates(x, y);
 //***
 selectWindow(name);
 Stack.setChannel(ciliaChannel);
 //***
 makeRectangle(x[i]-50, y[i]-50, 100, 100);
 run("Duplicate...", name);
 //etc


}

#2:

for (i = 0; i < roiManager("count"); i++){
 //***

 selectWindow(name);
 Stack.setChannel(ciliaChannel);
 //***
 roiManager("select", i);

 getSelectionCoordinates(x, y);
 makeRectangle(x[i]-50, y[i]-50, 100, 100);
 run("Duplicate...", name)

 //etc

}


After cleaning up some problems with my looping design, the macro works
quite well.  

All the best,


Tim  

Timothy Feinstein, Ph.D.
Research Scientist
University of Pittsburgh Department of Developmental Biology





On 9/8/16, 9:24 AM, "ImageJ Interest Group on behalf of Feinstein, Timothy
N" <[hidden email] on behalf of [hidden email]> wrote:

>Hi folks,
>
>Here is a large macro that I am working on which is a bit of a stretch
>for my skills, but it seems to be pretty close.  I am specifically
>pinging the board about the Stack.SetChannel() command, which only seems
>to work once.  The first time I use Stack.setChannel() it correctly
>selects stain#2 ("GPR161Channel") for thresholding.  However the next
>time when I want it to duplicate stain#1 ("ciliaChannel") for analysis in
>a smaller window it just copies stain#2 again.  This is line 59 in the
>macro.  I don't see why Stack.setChannel() should work the first time and
>not the second.
>
>I am also working out how to correctly call up point ROIs from the ROI
>manager one at a time for making rectangles (lines 62 and 68) but that
>looks more like I need to keep learning the syntax of working with
>arrays.  The select channels problem feels like it might be a bug.
>
>Here is a link to the macro and an example image:
>
>https://na01.safelinks.protection.outlook.com/?url=https%3a%2f%2fwww.dropb
>ox.com%2fsh%2fgh0zkznpsrkalfi%2fAAAL_gqTXoKCTbjGegpN2AjNa%3fdl%3d0&data=01
>%7c01%7ctnf8%40pitt.edu%7c85eb85cf32ec4e37d6b808d3d7ed5bf3%7c9ef9f489e0a04
>eeb87cc3a526112fd0d%7c1&sdata=ymZS7qfHMLy05SMyJVooN9GbE%2bN7fRNojiHPoHV2nL
>g%3d
>
>Thanks!
>
>
>Tim
>
>Timothy Feinstein, Ph.D.
>Research Scientist
>University of Pittsburgh Department of Developmental Biology
>
>
>--
>ImageJ mailing list:
>https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2fimagej.nih
>.gov%2fij%2flist.html&data=01%7c01%7ctnf8%40pitt.edu%7c85eb85cf32ec4e37d6b
>808d3d7ed5bf3%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=nPcOCDYn37bLCCD
>uXw3brhFUi6kU2rqXXYFgs0Y6ak0%3d

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[Jan Eglinger]

Hi Tim,

On 12.09.2016 14:59, Feinstein, Timothy N wrote:
> After more troubleshooting I discovered that Stack.selectChannel() works
> fine, but selecting a ROI from the ROI manager interferes with it.

Yes, this behavior is expected, since the ROI Manager saves the stack
position of the ROI when it's added. So selecting an ROI in the list
will set the active slice to the position that was saved with the ROI.

Cheers,
Jan

> following two examples, Stack.setChannel() works in example #1 but does
> not work in #2.
>
> #1:
>
> for (i = 0; i < roiManager("count"); i++){
>  roiManager("select", i);
>  getSelectionCoordinates(x, y);
>  //***
>  selectWindow(name);
>  Stack.setChannel(ciliaChannel);
>  //***
>  makeRectangle(x[i]-50, y[i]-50, 100, 100);
>  run("Duplicate...", name);
>  //etc
>
>
> }
>
> #2:
>
> for (i = 0; i < roiManager("count"); i++){
>  //***
>
>  selectWindow(name);
>  Stack.setChannel(ciliaChannel);
>  //***
>  roiManager("select", i);
>
>  getSelectionCoordinates(x, y);
>  makeRectangle(x[i]-50, y[i]-50, 100, 100);
>  run("Duplicate...", name)
>
>  //etc
>
> }
>
>
> After cleaning up some problems with my looping design, the macro works
> quite well.
>
> All the best,
>
>
> Tim
>
> Timothy Feinstein, Ph.D.
> Research Scientist
> University of Pittsburgh Department of Developmental Biology
>
>
>
>
>
> On 9/8/16, 9:24 AM, "ImageJ Interest Group on behalf of Feinstein, Timothy
> N" <[hidden email] on behalf of [hidden email]> wrote:
>
>> Hi folks,
>>
>> Here is a large macro that I am working on which is a bit of a stretch
>> for my skills, but it seems to be pretty close.  I am specifically
>> pinging the board about the Stack.SetChannel() command, which only seems
>> to work once.  The first time I use Stack.setChannel() it correctly
>> selects stain#2 ("GPR161Channel") for thresholding.  However the next
>> time when I want it to duplicate stain#1 ("ciliaChannel") for analysis in
>> a smaller window it just copies stain#2 again.  This is line 59 in the
>> macro.  I don't see why Stack.setChannel() should work the first time and
>> not the second.
>>
>> I am also working out how to correctly call up point ROIs from the ROI
>> manager one at a time for making rectangles (lines 62 and 68) but that
>> looks more like I need to keep learning the syntax of working with
>> arrays.  The select channels problem feels like it might be a bug.
>>
>> Here is a link to the macro and an example image:
>>
>> https://na01.safelinks.protection.outlook.com/?url=https%3a%2f%2fwww.dropb
>> ox.com%2fsh%2fgh0zkznpsrkalfi%2fAAAL_gqTXoKCTbjGegpN2AjNa%3fdl%3d0&data=01
>> %7c01%7ctnf8%40pitt.edu%7c85eb85cf32ec4e37d6b808d3d7ed5bf3%7c9ef9f489e0a04
>> eeb87cc3a526112fd0d%7c1&sdata=ymZS7qfHMLy05SMyJVooN9GbE%2bN7fRNojiHPoHV2nL
>> g%3d
>>
>> Thanks!
>>
>>
>> Tim
>>
>> Timothy Feinstein, Ph.D.
>> Research Scientist
>> University of Pittsburgh Department of Developmental Biology
>>
>>
>> --
>> ImageJ mailing list:
>> https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2fimagej.nih
>> .gov%2fij%2flist.html&data=01%7c01%7ctnf8%40pitt.edu%7c85eb85cf32ec4e37d6b
>> 808d3d7ed5bf3%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=nPcOCDYn37bLCCD
>> uXw3brhFUi6kU2rqXXYFgs0Y6ak0%3d
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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