Threading problem? Montage with Overlay?

[Nathaniel Ryckman]

Here are the goals that I have:

1) I have many stained cells that I would like to cut out and then montage. I have the cells' Rois.
2) After I have a montage, I would like to create an overlay using the Rois from step 1.

Any ideas would be appreciated.

---------------------------------------

I used the following to obtain square images of the cells to montage:

IJ.makeRectangle();
IJ.run("Duplicate...", "title");
IJ.run("Canvas Size...", "width= height= position=");

// Select window
iw = WindowManager.getImage("title").getWindow();
WindowManager.setCurrentWindow(iw);


The problem that I am having is that there seems to be some threading going on that I am not fully aware of or am not handling correctly when I call the IJ commands.....

I suspect that there is a threading problem because, when I run the program normally, I end up with cells that have been duplicated several times (total squares duplicated stays the same though), but, when I run the program in debug mode, I do not get this error.

Thanks again!

[Nathaniel Ryckman]

I probably should investigate the cause further, but, instead, I'll just say that IJ.makeRectangle() was causing the error. When I replaced IJ.makeRectangle() with custom code that should do the same thing, the program worked liked normal:

// Select window
imp = WindowManager.getImage("DAPI");
imp.setActivated();
iw = imp.getWindow();
WindowManager.setCurrentWindow(iw);
               
// Run IJ command
//IJ.makeRectangle(xC - maxDim/2, yC - maxDim/2, maxDim, maxDim);
               
// Create rectangle selection
Rectangle tempRect = new Rectangle(xC - maxDim/2, yC - maxDim/2, maxDim, maxDim);
iw.getImagePlus().setRoi(tempRect);
                                       
// Select window
imp = WindowManager.getImage("DAPI");
imp.setActivated();
iw = imp.getWindow();
WindowManager.setCurrentWindow(iw);
               
// Run IJ command
IJ.run("Duplicate...", "title=DAPI_" + yfpIndex);

Nathaniel Ryckman wrote

Here are the goals that I have:

1) I have many stained cells that I would like to cut out and then montage. I have the cells' Rois.
2) After I have a montage, I would like to create an overlay using the Rois from step 1.

Any ideas would be appreciated.

---------------------------------------

I used the following to obtain square images of the cells to montage:

IJ.makeRectangle();
IJ.run("Duplicate...", "title");
IJ.run("Canvas Size...", "width= height= position=");

// Select window
iw = WindowManager.getImage("title").getWindow();
WindowManager.setCurrentWindow(iw);


The problem that I am having is that there seems to be some threading going on that I am not fully aware of or am not handling correctly when I call the IJ commands.....

I suspect that there is a threading problem because, when I run the program normally, I end up with cells that have been duplicated several times (total squares duplicated stays the same though), but, when I run the program in debug mode, I do not get this error.

Thanks again!

[Nathaniel Ryckman]

I spoke too soon....replacing the IJ.makeRectangle command did not completely fix the problem. The only way that I have the program consistently working is by using this modified select command along with replacing the IJ.makeRectangle command.

// Select
while(WindowManager.getCurrentWindow() != iwDAPI || WindowManager.getCurrentImage() != iwDAPI.getImagePlus())
WindowManager.setCurrentWindow(iwDAPI);

If anyone has any idea about what is the underlying issue, I would really appreciate any advice offered.

By the way, the reason I made the modified select command is because, I have some suspicions that this line of code isn't working quite like the designer had planned (or I'm not using the code the way the designer had planned).

/** Makes the image contained in the specified window the active image. */
        public static void setCurrentWindow(ImageWindow win) {
       
if (win==null || win.isClosed() || win.getImagePlus()==null) // deadlock-"wait to lock"
                        return;
       

Nathaniel Ryckman wrote

I probably should investigate the cause further, but, instead, I'll just say that IJ.makeRectangle() was causing the error. When I replaced IJ.makeRectangle() with custom code that should do the same thing, the program worked liked normal:

// Select window
imp = WindowManager.getImage("DAPI");
imp.setActivated();
iw = imp.getWindow();
WindowManager.setCurrentWindow(iw);
               
// Run IJ command
//IJ.makeRectangle(xC - maxDim/2, yC - maxDim/2, maxDim, maxDim);
               
// Create rectangle selection
Rectangle tempRect = new Rectangle(xC - maxDim/2, yC - maxDim/2, maxDim, maxDim);
iw.getImagePlus().setRoi(tempRect);
                                       
// Select window
imp = WindowManager.getImage("DAPI");
imp.setActivated();
iw = imp.getWindow();
WindowManager.setCurrentWindow(iw);
               
// Run IJ command
IJ.run("Duplicate...", "title=DAPI_" + yfpIndex);

Nathaniel Ryckman wrote

Here are the goals that I have:

1) I have many stained cells that I would like to cut out and then montage. I have the cells' Rois.
2) After I have a montage, I would like to create an overlay using the Rois from step 1.

Any ideas would be appreciated.

---------------------------------------

I used the following to obtain square images of the cells to montage:

IJ.makeRectangle();
IJ.run("Duplicate...", "title");
IJ.run("Canvas Size...", "width= height= position=");

// Select window
iw = WindowManager.getImage("title").getWindow();
WindowManager.setCurrentWindow(iw);


The problem that I am having is that there seems to be some threading going on that I am not fully aware of or am not handling correctly when I call the IJ commands.....

I suspect that there is a threading problem because, when I run the program normally, I end up with cells that have been duplicated several times (total squares duplicated stays the same though), but, when I run the program in debug mode, I do not get this error.

Thanks again!