|
|
Hi group - I am still working out the details, but, I believe I've found
a bug with ROI management and cropping a stack.
If I have an ROI on a stack and I crop the image - I get the smallest
rectangular stack that contains the ROI (as expected).
But, I noticed that the ROI I had initially used is now replaced by some
random ROI I had used previously (that is no longer in the ROI manager).
So - the first time you run the plugin - it looks correct. But, change
ROIs and run it again, and you'll see the problem.
Oh, excuse the sloppy code, I was debugging it.
roiManager("reset");
wait(10);
roiManager("Add");
wait(10);
// duplicate image5D
run("Duplicate");
id1=getImageID();
wait(10);
waitForUser("go 1");
//get image5D settings
getDimensions(nw,nh,nch,nsl,nfr);
//convert to hyperstack
run("Image5D to Stack");
id2=getImageID();
waitForUser("go 2");
//crop
selectImage(id2);
roiManager("select",0);
wait(10);
waitForUser("go 3");
run("Crop");
// The resulting CROP now has some strange ROI on it - NOT the one used
to generate it!
selectImage(id2);
waitForUser("go 4");
wait(10);
run("Clear Outside", "stack");
wait(10);
waitForUser("go 5");
//convert back to image5D
run("Stack to Image5D", "3rd=ch 4th=z 3rd_dimension_size="+nch+"
4th_dimension_size="+nsl);
wait(10);
roiManager("Reset");
waitForUser("go 6");
|
Locked
