RoiManager multiple selection

[Eirinn Mackay]

Hi all,
Is it possible to select multiple ROIs programmatically? I'd like to  
select all that match a certain characteristic, draw them to the image  
with one foreground color, then select other ROIs and draw them with a  
different foreground color.
I am writing a python script so I'm using the API, but I can always  
call a macro command if necessary.

The API describes a function - select(int index, boolean shiftKeyDown,  
boolean altKeyDown) - but those boolean arguments don't appear to  
work. If either of them are true, nothing can be selected.
I've tried selecting each ROI in turn and drawing it, but this is  
prohibitively slow.

Any ideas?
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _
Eirinn Mackay
Research Assistant
Bartlett Group L6
Queensland Brain Institute
Brisbane, Australia
07 334 66381

[Wayne Rasband]

On Jun 10, 2009, at 7:49 PM, Eirinn Mackay wrote:

> Hi all,
> Is it possible to select multiple ROIs programmatically? I'd like  
> to select all that match a certain characteristic, draw them to the  
> image with one foreground color, then select other ROIs and draw  
> them with a different foreground color.
> I am writing a python script so I'm using the API, but I can always  
> call a macro command if necessary.
>
> The API describes a function - select(int index, boolean  
> shiftKeyDown, boolean altKeyDown) - but those boolean arguments  
> don't appear to work. If either of them are true, nothing can be  
> selected.
> I've tried selecting each ROI in turn and drawing it, but this is  
> prohibitively slow.
>
> Any ideas?

Use the getRoisAsArray() method to get all the ROIs and then use the  
drawPixels() method to draw selected ROIs in the array. Here is a  
JavaScript example that draws half the ROIs in the ROI Manager in red  
and the other half in blue.

    manager = RoiManager.getInstance();
    if (manager==null)
       IJ.error("ROI Manager is not open");
    rois = manager.getRoisAsArray();
    img = IJ.getImage();
    ip = img.getProcessor();
    for (i=0; i<rois.length; i++) {
       if (i<rois.length/2)
           ip.setColor(Color.red);
       else
           ip.setColor(Color.blue);
       rois[i].drawPixels(ip);
    }
    img.updateAndDraw();

-wayne

[Eirinn Mackay]

Thanks for the quick response Wayne. Will this code work with stacks  
or will I need extra code to ensure each ROI is drawn on its  
designated slice?
Cheers,
Eirinn
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _
Eirinn Mackay
Research Assistant
Bartlett Group L6
Queensland Brain Institute
Brisbane, Australia
07 334 66381




On 11/06/2009, at 12:19 PM, Rasband Wayne wrote:

> On Jun 10, 2009, at 7:49 PM, Eirinn Mackay wrote:
>
>> Hi all,
>> Is it possible to select multiple ROIs programmatically? I'd like  
>> to select all that match a certain characteristic, draw them to the  
>> image with one foreground color, then select other ROIs and draw  
>> them with a different foreground color.
>> I am writing a python script so I'm using the API, but I can always  
>> call a macro command if necessary.
>>
>> The API describes a function - select(int index, boolean  
>> shiftKeyDown, boolean altKeyDown) - but those boolean arguments  
>> don't appear to work. If either of them are true, nothing can be  
>> selected.
>> I've tried selecting each ROI in turn and drawing it, but this is  
>> prohibitively slow.
>>
>> Any ideas?
>
> Use the getRoisAsArray() method to get all the ROIs and then use the  
> drawPixels() method to draw selected ROIs in the array. Here is a  
> JavaScript example that draws half the ROIs in the ROI Manager in  
> red and the other half in blue.
>
>   manager = RoiManager.getInstance();
>   if (manager==null)
>      IJ.error("ROI Manager is not open");
>   rois = manager.getRoisAsArray();
>   img = IJ.getImage();
>   ip = img.getProcessor();
>   for (i=0; i<rois.length; i++) {
>      if (i<rois.length/2)
>          ip.setColor(Color.red);
>      else
>          ip.setColor(Color.blue);
>      rois[i].drawPixels(ip);
>   }
>   img.updateAndDraw();
>
> -wayne

[Eirinn Mackay]

Thanks Wayne, that code runs at least 100 times faster than using  
RoiManager.select on each ROI in turn.
Cheers,
Eirinn
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _
Eirinn Mackay
Research Assistant
Bartlett Group L6
Queensland Brain Institute
Brisbane, Australia
07 334 66381




On 11/06/2009, at 12:19 PM, Rasband Wayne wrote:

> On Jun 10, 2009, at 7:49 PM, Eirinn Mackay wrote:
>
>> Hi all,
>> Is it possible to select multiple ROIs programmatically? I'd like  
>> to select all that match a certain characteristic, draw them to the  
>> image with one foreground color, then select other ROIs and draw  
>> them with a different foreground color.
>> I am writing a python script so I'm using the API, but I can always  
>> call a macro command if necessary.
>>
>> The API describes a function - select(int index, boolean  
>> shiftKeyDown, boolean altKeyDown) - but those boolean arguments  
>> don't appear to work. If either of them are true, nothing can be  
>> selected.
>> I've tried selecting each ROI in turn and drawing it, but this is  
>> prohibitively slow.
>>
>> Any ideas?
>
> Use the getRoisAsArray() method to get all the ROIs and then use the  
> drawPixels() method to draw selected ROIs in the array. Here is a  
> JavaScript example that draws half the ROIs in the ROI Manager in  
> red and the other half in blue.
>
>   manager = RoiManager.getInstance();
>   if (manager==null)
>      IJ.error("ROI Manager is not open");
>   rois = manager.getRoisAsArray();
>   img = IJ.getImage();
>   ip = img.getProcessor();
>   for (i=0; i<rois.length; i++) {
>      if (i<rois.length/2)
>          ip.setColor(Color.red);
>      else
>          ip.setColor(Color.blue);
>      rois[i].drawPixels(ip);
>   }
>   img.updateAndDraw();
>
> -wayne