Deleting ROIs during a macro

[ElisabethT]

Hi there,

I am running a macro and would like to pause the macro after ROI selection, to delete any ROIs that are not 'good', then would like to continue to run the macro so that the measurements are made.

After I have set a threshold, and selected the ROIs, I can pause the macro using

while (isOpen("RGB")) {
wait(10);
}

But during that time, when I click on an entry in ROI Manager, the ROI does not light up in the image window (i.e. with a yellow outline). However, if I scroll using my scroll wheel on my mouse, the yellow outlines do appear. The problem is that the scroll only selects every second entry in ROI Manager!

When the macro is finished, and I click on the ROI entries, the yellow outlines appear with no problem.

Any help with this would be much appreciated.

Thanks,
Elisabeth

[Mario Faretta]

you can try to replace the "while" loop with
/
waitForUser("Clearing of unuseful ROIs");/

it will pauses the macro until you press "Ok" in the dialog giving you
the possibility to adjust different parameters. Maybe it corrects the
strange behavior you detect
Mario

ElisabethT wrote:

> Hi there,
>
> I am running a macro and would like to pause the macro after ROI selection,
> to delete any ROIs that are not 'good', then would like to continue to run
> the macro so that the measurements are made.
>
> After I have set a threshold, and selected the ROIs, I can pause the macro
> using
>
> while (isOpen("RGB")) {
> wait(10);
> }
>
> But during that time, when I click on an entry in ROI Manager, the ROI does
> not light up in the image window (i.e. with a yellow outline). However, if I
> scroll using my scroll wheel on my mouse, the yellow outlines do appear. The
> problem is that the scroll only selects every second entry in ROI Manager!
>
> When the macro is finished, and I click on the ROI entries, the yellow
> outlines appear with no problem.
>
> Any help with this would be much appreciated.
>
> Thanks,
> Elisabeth
>  

--
Mario Faretta
Department of Experimental Oncology
European Institute of Oncology
c/o IFOM-IEO Campus for Oncogenomics
via Adamello 16
20139 Milan
Italy
Phone: ++39-02574303054
email: [hidden email]
http://www.ifom-ieo-campus.it

[Michael Schmid]

Hi Elisabeth,

wait(10) waits for 10 milliseconds.
I am not sure that you are that fast ;-)

By the way, maybe the "waitForUser" macro command would be better?

Michael
________________________________________________________________

On 4 Feb 2010, at 12:05, ElisabethT wrote:

> Hi there,
>
> I am running a macro and would like to pause the macro after ROI  
> selection,
> to delete any ROIs that are not 'good', then would like to continue  
> to run
> the macro so that the measurements are made.
>
> After I have set a threshold, and selected the ROIs, I can pause  
> the macro
> using
>
> while (isOpen("RGB")) {
> wait(10);
> }
>
> But during that time, when I click on an entry in ROI Manager, the  
> ROI does
> not light up in the image window (i.e. with a yellow outline).  
> However, if I
> scroll using my scroll wheel on my mouse, the yellow outlines do  
> appear. The
> problem is that the scroll only selects every second entry in ROI  
> Manager!
>
> When the macro is finished, and I click on the ROI entries, the yellow
> outlines appear with no problem.
>
> Any help with this would be much appreciated.
>
> Thanks,
> Elisabeth

[ElisabethT]

Hi Michael,

Thanks for the suggestion, but unfortunately "waitForUser" produces the same results.

Elisabeth



Hi Elisabeth,

wait(10) waits for 10 milliseconds.
I am not sure that you are that fast ;-)

By the way, maybe the "waitForUser" macro command would be better?

Michael
________________________________________________________________

On 4 Feb 2010, at 12:05, ElisabethT wrote:

> Hi there,
>
> I am running a macro and would like to pause the macro after ROI  
> selection,
> to delete any ROIs that are not 'good', then would like to continue  
> to run
> the macro so that the measurements are made.
>
> After I have set a threshold, and selected the ROIs, I can pause  
> the macro
> using
>
> while (isOpen("RGB")) {
> wait(10);
> }
>
> But during that time, when I click on an entry in ROI Manager, the  
> ROI does
> not light up in the image window (i.e. with a yellow outline).  
> However, if I
> scroll using my scroll wheel on my mouse, the yellow outlines do  
> appear. The
> problem is that the scroll only selects every second entry in ROI  
> Manager!
>
> When the macro is finished, and I click on the ROI entries, the yellow
> outlines appear with no problem.
>
> Any help with this would be much appreciated.
>
> Thanks,
> Elisabeth

[ElisabethT]

Hi Mario,

Thanks for the suggestion, but unfortunately it produces the same results.

Elisabeth




you can try to replace the "while" loop with
/
waitForUser("Clearing of unuseful ROIs");/

it will pauses the macro until you press "Ok" in the dialog giving you
the possibility to adjust different parameters. Maybe it corrects the
strange behavior you detect
Mario

ElisabethT wrote:
> Hi there,
>
> I am running a macro and would like to pause the macro after ROI selection,
> to delete any ROIs that are not 'good', then would like to continue to run
> the macro so that the measurements are made.
>
> After I have set a threshold, and selected the ROIs, I can pause the macro
> using
>
> while (isOpen("RGB")) {
> wait(10);
> }
>
> But during that time, when I click on an entry in ROI Manager, the ROI does
> not light up in the image window (i.e. with a yellow outline). However, if I
> scroll using my scroll wheel on my mouse, the yellow outlines do appear. The
> problem is that the scroll only selects every second entry in ROI Manager!
>
> When the macro is finished, and I click on the ROI entries, the yellow
> outlines appear with no problem.
>
> Any help with this would be much appreciated.
>
> Thanks,
> Elisabeth
>  


--
Mario Faretta
Department of Experimental Oncology
European Institute of Oncology
c/o IFOM-IEO Campus for Oncogenomics
via Adamello 16
20139 Milan
Italy
Phone: ++39-02574303054
email: [e-mail]
http://www.ifom-ieo-campus.it

[Michael Schmid]

Hi Elisabeth,

no problem here. While the "Wait for user" panel is visible, I can  
select ROIs in the ROI manager and they are shown in yellow on the  
image.

My configuration: Mac OS X 10.4.11, ImageJ 1.43o, Java 1.5.0_19

Did you try, does it work outside a macro? Did you try to restart  
ImageJ (in case something weird has happened and corrupted something)?

Michael
________________________________________________________________

On 4 Feb 2010, at 13:29, ElisabethT wrote:

> Hi Michael,
>
> Thanks for the suggestion, but unfortunately "waitForUser" produces  
> the same
> results.
>
> Elisabeth
>
>
>
> Hi Elisabeth,
>
> wait(10) waits for 10 milliseconds.
> I am not sure that you are that fast ;-)
>
> By the way, maybe the "waitForUser" macro command would be better?
>
> Michael
> ________________________________________________________________
>
> On 4 Feb 2010, at 12:05, ElisabethT wrote:
>
>> Hi there,
>>
>> I am running a macro and would like to pause the macro after ROI
>> selection,
>> to delete any ROIs that are not 'good', then would like to continue
>> to run
>> the macro so that the measurements are made.
>>
>> After I have set a threshold, and selected the ROIs, I can pause
>> the macro
>> using
>>
>> while (isOpen("RGB")) {
>> wait(10);
>> }
>>
>> But during that time, when I click on an entry in ROI Manager, the
>> ROI does
>> not light up in the image window (i.e. with a yellow outline).
>> However, if I
>> scroll using my scroll wheel on my mouse, the yellow outlines do
>> appear. The
>> problem is that the scroll only selects every second entry in ROI
>> Manager!
>>
>> When the macro is finished, and I click on the ROI entries, the  
>> yellow
>> outlines appear with no problem.
>>
>> Any help with this would be much appreciated.
>>
>> Thanks,
>> Elisabeth
>
>
>
> --
> View this message in context: http://n2.nabble.com/Deleting-ROIs- 
> during-a-macro-tp4512804p4513170.html
> Sent from the ImageJ mailing list archive at Nabble.com.

[ElisabethT]

Hi Michael,

Yes, it works fine outside a macro, and when the macro is finished running, it also works fine. For some reason during the macro, I can only use the scroll wheel. Strange.. maybe just a bug or something?
My configuration is: Mac OS X 10.5.8, ImageJ 1.43o, Java 1.5.0_22
Thank you for trying it out though.

Elisabeth




Hi Elisabeth,

no problem here. While the "Wait for user" panel is visible, I can  
select ROIs in the ROI manager and they are shown in yellow on the  
image.

My configuration: Mac OS X 10.4.11, ImageJ 1.43o, Java 1.5.0_19

Did you try, does it work outside a macro? Did you try to restart  
ImageJ (in case something weird has happened and corrupted something)?

Michael
________________________________________________________________

On 4 Feb 2010, at 13:29, ElisabethT wrote:

> Hi Michael,
>
> Thanks for the suggestion, but unfortunately "waitForUser" produces  
> the same
> results.
>
> Elisabeth
>
>
>
> Hi Elisabeth,
>
> wait(10) waits for 10 milliseconds.
> I am not sure that you are that fast ;-)
>
> By the way, maybe the "waitForUser" macro command would be better?
>
> Michael
> ________________________________________________________________
>
> On 4 Feb 2010, at 12:05, ElisabethT wrote:
>
>> Hi there,
>>
>> I am running a macro and would like to pause the macro after ROI
>> selection,
>> to delete any ROIs that are not 'good', then would like to continue
>> to run
>> the macro so that the measurements are made.
>>
>> After I have set a threshold, and selected the ROIs, I can pause
>> the macro
>> using
>>
>> while (isOpen("RGB")) {
>> wait(10);
>> }
>>
>> But during that time, when I click on an entry in ROI Manager, the
>> ROI does
>> not light up in the image window (i.e. with a yellow outline).
>> However, if I
>> scroll using my scroll wheel on my mouse, the yellow outlines do
>> appear. The
>> problem is that the scroll only selects every second entry in ROI
>> Manager!
>>
>> When the macro is finished, and I click on the ROI entries, the  
>> yellow
>> outlines appear with no problem.
>>
>> Any help with this would be much appreciated.
>>
>> Thanks,
>> Elisabeth
>
>
>
> --
> View this message in context: http://n2.nabble.com/Deleting-ROIs- 
> during-a-macro-tp4512804p4513170.html
> Sent from the ImageJ mailing list archive at Nabble.com.