multi-color overlays?

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multi-color overlays?

Kenneth Sloan-3
I'm stumbling through an attempt to use Overlays...

Java plugin (not macro)

I would *really* like to put overlays on a single slice of a stack containing multiple FloatProcessor images.  I suspect
that this doesn't work.  So, while I verify that, I'm working with a single ImagePlus displaying a ColorProcessor.

The desired Overlay has several ROI elements - each with it's own StrokeWidth and Color.  Sample code fragment is shown below.
My problem is that all the ROIs are displayed with the same color - the color assigned to the last ROI added to the Overlay.

Question: is this the expected behavior?  If not, what am I doing wrong?  Should I be using a different technique all together?

In extremis, I suppose that I could re-create the ColorProcessor image on every change to the annotation, and destructively draw the overlay information on the image - but that seems wasteful.  I'd really like to leave the image intact, and simply re-create the Overlay.  

I suppose another option is to create an Image Roi and draw the multi-colored vector graphics on it.  But, the code below seems to be the "right" way to do it.  I would appreciate an explanation of why it doesn't work, and advice on the best technique to use.

Here's the relevant code (everything is drawn in the right place and at the right scale, but it's all RED):

              // create window for centering                                                                                
                ColorProcessor cpMPOD = fpMPOD.convertToColorProcessor();


                // draw overlay showing center                                                                                

                ImagePlus ipMPOD = new ImagePlus("MPOD", cpMPOD);
                Overlay crosshairOverlay = new Overlay();
                Roi horizontalAxis = new Line(0.0, (double) this.foveaY,
                                              (double) width, (double) this.foveaY);
                horizontalAxis.setStrokeWidth(1.0f);
                horizontalAxis.setColor(Color.WHITE);
                crosshairOverlay.add(horizontalAxis);

                Roi verticalAxis = new Line((double) this.foveaX, 0.0,
                                            (double) this.foveaX, (double) height);
                verticalAxis.setStrokeWidth(1.0f);
                verticalAxis.setColor(Color.WHITE);
                crosshairOverlay.add(verticalAxis);

                double oval6Radius = 6.0*(double)width/(double)this.angle;
                double oval6X = this.foveaX - oval6Radius;
                double oval6Y = this.foveaY - oval6Radius;
                double oval6Diameter = oval6Radius * 2.0;
                Roi circle6Degree = new OvalRoi(oval6X,oval6Y,oval6Diameter,oval6Diameter);
                circle6Degree.setStrokeWidth(1.0f);
                circle6Degree.setColor(Color.GREEN);
                crosshairOverlay.add(circle6Degree);

                double oval2Radius = 2.0*(double)width/(double)this.angle;
                double oval2X = this.foveaX - oval2Radius;
                double oval2Y = this.foveaY - oval2Radius;
                double oval2Diameter = oval2Radius * 2.0;
                Roi circle2Degree = new OvalRoi(oval2X,oval2Y,oval2Diameter,oval2Diameter);
                circle2Degree.setStrokeWidth(1.0f);
                circle2Degree.setColor(Color.BLUE);
                crosshairOverlay.add(circle2Degree);


                double oval1Radius = 1.0*(double)width/(double)this.angle;
                double oval1X = this.foveaX - oval1Radius;
                double oval1Y = this.foveaY - oval1Radius;
                double oval1Diameter = oval1Radius * 2.0;
                Roi circle1Degree = new OvalRoi(oval1X,oval1Y,oval1Diameter,oval1Diameter);
                circle1Degree.setStrokeWidth(1.0f);
                circle1Degree.setColor(Color.RED);
                crosshairOverlay.add(circle1Degree);

                ipMPOD.setOverlay(crosshairOverlay);

                ipMPOD.show();




--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.






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Re: multi-color overlays?

Herbie
Good day Kenneth,

I understand that you wish to see Java code, but this macro will perhaps
give you an idea of what is a way to go:

Open an image with at least one overlay, then run the macro:

// imagej-macro "_overlayFillColors" (Herbie G., 21. Dec 2017)
run( "To ROI Manager" );
idx = roiManager( "count" );
rois = Array.getSequence( idx );
for ( i=0; i < idx; i++ ) { rois[i] = d2s( 1+rois[i], 0 ); }
Dialog.create("Set Overlay Fill");
Dialog.addChoice( "Index", rois );
Dialog.addSlider( "Opacity", 0, 255, 128 );
Dialog.addSlider( "Red", 0, 255, 0 );
Dialog.addSlider( "Green", 0, 255, 0 );
Dialog.addSlider( "Blue", 0, 255, 0 );
Dialog.show();
idx = parseInt( Dialog.getChoice() ) - 1;
c = padStr( toHex( Dialog.getNumber() ) );
c = c + padStr( toHex( Dialog.getNumber() ) );
c = c + padStr( toHex( Dialog.getNumber() ) );
c = c + padStr( toHex( Dialog.getNumber() ) );
roiManager( "select", idx );
roiManager( "Set Fill Color", c );
run( "From ROI Manager" );
run( "Overlay Options...", "stroke=none width=0 fill=none" ); // removes
lable
close( "ROI Manager" );
exit();
function padStr( hex ) {
    if ( lengthOf( hex ) < 2 ) { return "0" + hex; } else { return hex; }
}
// imagej-macro "_overlayFillColors" (Herbie G., 21. Dec 2017)

This macro only sets fill colors but contour coloring works quite similar.

Regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::
Am 06.10.18 um 12:35 schrieb Kenneth Sloan:

> I'm stumbling through an attempt to use Overlays...
>
> Java plugin (not macro)
>
> I would *really* like to put overlays on a single slice of a stack containing multiple FloatProcessor images.  I suspect
> that this doesn't work.  So, while I verify that, I'm working with a single ImagePlus displaying a ColorProcessor.
>
> The desired Overlay has several ROI elements - each with it's own StrokeWidth and Color.  Sample code fragment is shown below.
> My problem is that all the ROIs are displayed with the same color - the color assigned to the last ROI added to the Overlay.
>
> Question: is this the expected behavior?  If not, what am I doing wrong?  Should I be using a different technique all together?
>
> In extremis, I suppose that I could re-create the ColorProcessor image on every change to the annotation, and destructively draw the overlay information on the image - but that seems wasteful.  I'd really like to leave the image intact, and simply re-create the Overlay.
>
> I suppose another option is to create an Image Roi and draw the multi-colored vector graphics on it.  But, the code below seems to be the "right" way to do it.  I would appreciate an explanation of why it doesn't work, and advice on the best technique to use.
>
> Here's the relevant code (everything is drawn in the right place and at the right scale, but it's all RED):
>
>                // create window for centering
>                  ColorProcessor cpMPOD = fpMPOD.convertToColorProcessor();
>
>
>                  // draw overlay showing center
>
>                  ImagePlus ipMPOD = new ImagePlus("MPOD", cpMPOD);
>                  Overlay crosshairOverlay = new Overlay();
>                  Roi horizontalAxis = new Line(0.0, (double) this.foveaY,
>                                                (double) width, (double) this.foveaY);
>                  horizontalAxis.setStrokeWidth(1.0f);
>                  horizontalAxis.setColor(Color.WHITE);
>                  crosshairOverlay.add(horizontalAxis);
>
>                  Roi verticalAxis = new Line((double) this.foveaX, 0.0,
>                                              (double) this.foveaX, (double) height);
>                  verticalAxis.setStrokeWidth(1.0f);
>                  verticalAxis.setColor(Color.WHITE);
>                  crosshairOverlay.add(verticalAxis);
>
>                  double oval6Radius = 6.0*(double)width/(double)this.angle;
>                  double oval6X = this.foveaX - oval6Radius;
>                  double oval6Y = this.foveaY - oval6Radius;
>                  double oval6Diameter = oval6Radius * 2.0;
>                  Roi circle6Degree = new OvalRoi(oval6X,oval6Y,oval6Diameter,oval6Diameter);
>                  circle6Degree.setStrokeWidth(1.0f);
>                  circle6Degree.setColor(Color.GREEN);
>                  crosshairOverlay.add(circle6Degree);
>
>                  double oval2Radius = 2.0*(double)width/(double)this.angle;
>                  double oval2X = this.foveaX - oval2Radius;
>                  double oval2Y = this.foveaY - oval2Radius;
>                  double oval2Diameter = oval2Radius * 2.0;
>                  Roi circle2Degree = new OvalRoi(oval2X,oval2Y,oval2Diameter,oval2Diameter);
>                  circle2Degree.setStrokeWidth(1.0f);
>                  circle2Degree.setColor(Color.BLUE);
>                  crosshairOverlay.add(circle2Degree);
>
>
>                  double oval1Radius = 1.0*(double)width/(double)this.angle;
>                  double oval1X = this.foveaX - oval1Radius;
> double oval1Y = this.foveaY - oval1Radius;
>        double oval1Diameter = oval1Radius * 2.0;
>                  Roi circle1Degree = new OvalRoi(oval1X,oval1Y,oval1Diameter,oval1Diameter);
>                  circle1Degree.setStrokeWidth(1.0f);
>                  circle1Degree.setColor(Color.RED);
>                  crosshairOverlay.add(circle1Degree);
>
>                  ipMPOD.setOverlay(crosshairOverlay);
>
>                  ipMPOD.show();
>
>
>
>
> --
> Kenneth Sloan
> [hidden email]
> Vision is the art of seeing what is invisible to others.
>
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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Re: multi-color overlays?

Wayne Rasband-2
In reply to this post by Kenneth Sloan-3
> On Oct 6, 2018, at 6:35 AM, Kenneth Sloan <[hidden email]> wrote:
>
> I'm stumbling through an attempt to use Overlays...
>
> Java plugin (not macro)
>
> I would *really* like to put overlays on a single slice of a stack containing multiple FloatProcessor images.  I suspect
> that this doesn't work.

It does work. Here is an example that adds a two color overlay to the fifth slice to a 10 slice float stack:

  img = IJ.createImage("Untitled", "32-bit black", 512, 512, 10);
  overlay = new Overlay();
  line1 = new Line(150,100,150,400);
  line1.setStrokeWidth(5);
  line1.setStrokeColor(Color.red);
  line1.setPosition(5);
  overlay.add(line1);
  line2 = new Line(300,100,300,400);
  line2.setStrokeWidth(15);
  line2.setStrokeColor(Color.blue);
  line2.setPosition(5);
  overlay.add(line2);
  img.setOverlay(overlay);
  img.show();
  img.setSlice(5);

-wayne



> So, while I verify that, I'm working with a single ImagePlus displaying a ColorProcessor.
>
> The desired Overlay has several ROI elements - each with it's own StrokeWidth and Color.  Sample code fragment is shown below.
> My problem is that all the ROIs are displayed with the same color - the color assigned to the last ROI added to the Overlay.
>
> Question: is this the expected behavior?  If not, what am I doing wrong?  Should I be using a different technique all together?
>
> In extremis, I suppose that I could re-create the ColorProcessor image on every change to the annotation, and destructively draw the overlay information on the image - but that seems wasteful.  I'd really like to leave the image intact, and simply re-create the Overlay.  
>
> I suppose another option is to create an Image Roi and draw the multi-colored vector graphics on it.  But, the code below seems to be the "right" way to do it.  I would appreciate an explanation of why it doesn't work, and advice on the best technique to use.
>
> Here's the relevant code (everything is drawn in the right place and at the right scale, but it's all RED):
>
>              // create window for centering                                                                                
>                ColorProcessor cpMPOD = fpMPOD.convertToColorProcessor();
>
>
>                // draw overlay showing center                                                                                
>
>                ImagePlus ipMPOD = new ImagePlus("MPOD", cpMPOD);
>                Overlay crosshairOverlay = new Overlay();
>                Roi horizontalAxis = new Line(0.0, (double) this.foveaY,
>                                              (double) width, (double) this.foveaY);
>                horizontalAxis.setStrokeWidth(1.0f);
>                horizontalAxis.setColor(Color.WHITE);
>                crosshairOverlay.add(horizontalAxis);
>
>                Roi verticalAxis = new Line((double) this.foveaX, 0.0,
>                                            (double) this.foveaX, (double) height);
>                verticalAxis.setStrokeWidth(1.0f);
>                verticalAxis.setColor(Color.WHITE);
>                crosshairOverlay.add(verticalAxis);
>
>                double oval6Radius = 6.0*(double)width/(double)this.angle;
>                double oval6X = this.foveaX - oval6Radius;
>                double oval6Y = this.foveaY - oval6Radius;
>                double oval6Diameter = oval6Radius * 2.0;
>                Roi circle6Degree = new OvalRoi(oval6X,oval6Y,oval6Diameter,oval6Diameter);
>                circle6Degree.setStrokeWidth(1.0f);
>                circle6Degree.setColor(Color.GREEN);
>                crosshairOverlay.add(circle6Degree);
>
>                double oval2Radius = 2.0*(double)width/(double)this.angle;
>                double oval2X = this.foveaX - oval2Radius;
>                double oval2Y = this.foveaY - oval2Radius;
>                double oval2Diameter = oval2Radius * 2.0;
>                Roi circle2Degree = new OvalRoi(oval2X,oval2Y,oval2Diameter,oval2Diameter);
>                circle2Degree.setStrokeWidth(1.0f);
>                circle2Degree.setColor(Color.BLUE);
>                crosshairOverlay.add(circle2Degree);
>
>
>                double oval1Radius = 1.0*(double)width/(double)this.angle;
>                double oval1X = this.foveaX - oval1Radius;
> double oval1Y = this.foveaY - oval1Radius;
>        double oval1Diameter = oval1Radius * 2.0;
>                Roi circle1Degree = new OvalRoi(oval1X,oval1Y,oval1Diameter,oval1Diameter);
>                circle1Degree.setStrokeWidth(1.0f);
>                circle1Degree.setColor(Color.RED);
>                crosshairOverlay.add(circle1Degree);
>
>                ipMPOD.setOverlay(crosshairOverlay);
>
>                ipMPOD.show();
>

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Re: multi-color overlays?

Kenneth Sloan-3
Ah...I may have spotted it.  The difference between my code and yours is that I used "SetColor" and you used "SetStrokeColor".

Off to try to get multi-color.

If that works, I'll think about trying to do it on the stack (but, now that I've split off this one image, there
are other reasons to keep it that way.

Thanks for the rapid responses.  I'm going to (naively?) assume that this change will do the trick.

--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.





> On 6 Oct 2018, at 16:23 , Wayne Rasband <[hidden email]> wrote:
>
>> On Oct 6, 2018, at 6:35 AM, Kenneth Sloan <[hidden email] <mailto:[hidden email]>> wrote:
>>
>> I'm stumbling through an attempt to use Overlays...
>>
>> Java plugin (not macro)
>>
>> I would *really* like to put overlays on a single slice of a stack containing multiple FloatProcessor images.  I suspect
>> that this doesn't work.
>
> It does work. Here is an example that adds a two color overlay to the fifth slice to a 10 slice float stack:
>
>  img = IJ.createImage("Untitled", "32-bit black", 512, 512, 10);
>  overlay = new Overlay();
>  line1 = new Line(150,100,150,400);
>  line1.setStrokeWidth(5);
>  line1.setStrokeColor(Color.red);
>  line1.setPosition(5);
>  overlay.add(line1);
>  line2 = new Line(300,100,300,400);
>  line2.setStrokeWidth(15);
>  line2.setStrokeColor(Color.blue);
>  line2.setPosition(5);
>  overlay.add(line2);
>  img.setOverlay(overlay);
>  img.show();
>  img.setSlice(5);
>
> -wayne
>
>
>
>> So, while I verify that, I'm working with a single ImagePlus displaying a ColorProcessor.
>>
>> The desired Overlay has several ROI elements - each with it's own StrokeWidth and Color.  Sample code fragment is shown below.
>> My problem is that all the ROIs are displayed with the same color - the color assigned to the last ROI added to the Overlay.
>>
>> Question: is this the expected behavior?  If not, what am I doing wrong? Should I be using a different technique all together?
>>
>> In extremis, I suppose that I could re-create the ColorProcessor image on every change to the annotation, and destructively draw the overlay information on the image - but that seems wasteful.  I'd really like to leave the image intact, and simply re-create the Overlay.  
>>
>> I suppose another option is to create an Image Roi and draw the multi-colored vector graphics on it.  But, the code below seems to be the "right" way to do it.  I would appreciate an explanation of why it doesn't work, and advice on the best technique to use.
>>
>> Here's the relevant code (everything is drawn in the right place and at the right scale, but it's all RED):
>>
>>             // create window for centering                                
>>               ColorProcessor cpMPOD = fpMPOD.convertToColorProcessor();
>>
>>
>>               // draw overlay showing center                              
>>
>>               ImagePlus ipMPOD = new ImagePlus("MPOD", cpMPOD);
>>               Overlay crosshairOverlay = new Overlay();
>>               Roi horizontalAxis = new Line(0.0, (double) this.foveaY,
>>                                             (double) width, (double) this.foveaY);
>>               horizontalAxis.setStrokeWidth(1.0f);
>>               horizontalAxis.setColor(Color.WHITE);
>>               crosshairOverlay.add(horizontalAxis);
>>
>>               Roi verticalAxis = new Line((double) this.foveaX, 0.0,
>>                                           (double) this.foveaX, (double) height);
>>               verticalAxis.setStrokeWidth(1.0f);
>>               verticalAxis.setColor(Color.WHITE);
>>               crosshairOverlay.add(verticalAxis);
>>
>>               double oval6Radius = 6.0*(double)width/(double)this.angle;
>>               double oval6X = this.foveaX - oval6Radius;
>>               double oval6Y = this.foveaY - oval6Radius;
>>               double oval6Diameter = oval6Radius * 2.0;
>>               Roi circle6Degree = new OvalRoi(oval6X,oval6Y,oval6Diameter,oval6Diameter);
>>               circle6Degree.setStrokeWidth(1.0f);
>>               circle6Degree.setColor(Color.GREEN);
>>               crosshairOverlay.add(circle6Degree);
>>
>>               double oval2Radius = 2.0*(double)width/(double)this.angle;
>>               double oval2X = this.foveaX - oval2Radius;
>>               double oval2Y = this.foveaY - oval2Radius;
>>               double oval2Diameter = oval2Radius * 2.0;
>>               Roi circle2Degree = new OvalRoi(oval2X,oval2Y,oval2Diameter,oval2Diameter);
>>               circle2Degree.setStrokeWidth(1.0f);
>>               circle2Degree.setColor(Color.BLUE);
>>               crosshairOverlay.add(circle2Degree);
>>
>>
>>               double oval1Radius = 1.0*(double)width/(double)this.angle;
>>               double oval1X = this.foveaX - oval1Radius;
>> double oval1Y = this.foveaY - oval1Radius;
>>        double oval1Diameter = oval1Radius * 2.0;
>>               Roi circle1Degree = new OvalRoi(oval1X,oval1Y,oval1Diameter,oval1Diameter);
>>               circle1Degree.setStrokeWidth(1.0f);
>>               circle1Degree.setColor(Color.RED);
>>               crosshairOverlay.add(circle1Degree);
>>
>>               ipMPOD.setOverlay(crosshairOverlay);
>>
>>               ipMPOD.show();
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>

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Re: multi-color overlays?

Kenneth Sloan-3
In reply to this post by Wayne Rasband-2
Success!  "setColor" -> "setStrokeColor" did the trick.

--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.





> On 6 Oct 2018, at 16:23 , Wayne Rasband <[hidden email]> wrote:
>
>> On Oct 6, 2018, at 6:35 AM, Kenneth Sloan <[hidden email] <mailto:[hidden email]>> wrote:
>>
>> I'm stumbling through an attempt to use Overlays...
>>
>> Java plugin (not macro)
>>
>> I would *really* like to put overlays on a single slice of a stack containing multiple FloatProcessor images.  I suspect
>> that this doesn't work.
>
> It does work. Here is an example that adds a two color overlay to the fifth slice to a 10 slice float stack:
>
>  img = IJ.createImage("Untitled", "32-bit black", 512, 512, 10);
>  overlay = new Overlay();
>  line1 = new Line(150,100,150,400);
>  line1.setStrokeWidth(5);
>  line1.setStrokeColor(Color.red);
>  line1.setPosition(5);
>  overlay.add(line1);
>  line2 = new Line(300,100,300,400);
>  line2.setStrokeWidth(15);
>  line2.setStrokeColor(Color.blue);
>  line2.setPosition(5);
>  overlay.add(line2);
>  img.setOverlay(overlay);
>  img.show();
>  img.setSlice(5);
>
> -wayne
>
>
>
>> So, while I verify that, I'm working with a single ImagePlus displaying a ColorProcessor.
>>
>> The desired Overlay has several ROI elements - each with it's own StrokeWidth and Color.  Sample code fragment is shown below.
>> My problem is that all the ROIs are displayed with the same color - the color assigned to the last ROI added to the Overlay.
>>
>> Question: is this the expected behavior?  If not, what am I doing wrong? Should I be using a different technique all together?
>>
>> In extremis, I suppose that I could re-create the ColorProcessor image on every change to the annotation, and destructively draw the overlay information on the image - but that seems wasteful.  I'd really like to leave the image intact, and simply re-create the Overlay.  
>>
>> I suppose another option is to create an Image Roi and draw the multi-colored vector graphics on it.  But, the code below seems to be the "right" way to do it.  I would appreciate an explanation of why it doesn't work, and advice on the best technique to use.
>>
>> Here's the relevant code (everything is drawn in the right place and at the right scale, but it's all RED):
>>
>>             // create window for centering                                
>>               ColorProcessor cpMPOD = fpMPOD.convertToColorProcessor();
>>
>>
>>               // draw overlay showing center                              
>>
>>               ImagePlus ipMPOD = new ImagePlus("MPOD", cpMPOD);
>>               Overlay crosshairOverlay = new Overlay();
>>               Roi horizontalAxis = new Line(0.0, (double) this.foveaY,
>>                                             (double) width, (double) this.foveaY);
>>               horizontalAxis.setStrokeWidth(1.0f);
>>               horizontalAxis.setColor(Color.WHITE);
>>               crosshairOverlay.add(horizontalAxis);
>>
>>               Roi verticalAxis = new Line((double) this.foveaX, 0.0,
>>                                           (double) this.foveaX, (double) height);
>>               verticalAxis.setStrokeWidth(1.0f);
>>               verticalAxis.setColor(Color.WHITE);
>>               crosshairOverlay.add(verticalAxis);
>>
>>               double oval6Radius = 6.0*(double)width/(double)this.angle;
>>               double oval6X = this.foveaX - oval6Radius;
>>               double oval6Y = this.foveaY - oval6Radius;
>>               double oval6Diameter = oval6Radius * 2.0;
>>               Roi circle6Degree = new OvalRoi(oval6X,oval6Y,oval6Diameter,oval6Diameter);
>>               circle6Degree.setStrokeWidth(1.0f);
>>               circle6Degree.setColor(Color.GREEN);
>>               crosshairOverlay.add(circle6Degree);
>>
>>               double oval2Radius = 2.0*(double)width/(double)this.angle;
>>               double oval2X = this.foveaX - oval2Radius;
>>               double oval2Y = this.foveaY - oval2Radius;
>>               double oval2Diameter = oval2Radius * 2.0;
>>               Roi circle2Degree = new OvalRoi(oval2X,oval2Y,oval2Diameter,oval2Diameter);
>>               circle2Degree.setStrokeWidth(1.0f);
>>               circle2Degree.setColor(Color.BLUE);
>>               crosshairOverlay.add(circle2Degree);
>>
>>
>>               double oval1Radius = 1.0*(double)width/(double)this.angle;
>>               double oval1X = this.foveaX - oval1Radius;
>> double oval1Y = this.foveaY - oval1Radius;
>>        double oval1Diameter = oval1Radius * 2.0;
>>               Roi circle1Degree = new OvalRoi(oval1X,oval1Y,oval1Diameter,oval1Diameter);
>>               circle1Degree.setStrokeWidth(1.0f);
>>               circle1Degree.setColor(Color.RED);
>>               crosshairOverlay.add(circle1Degree);
>>
>>               ipMPOD.setOverlay(crosshairOverlay);
>>
>>               ipMPOD.show();
>>
>
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