|
|
Hi List,
I am trying to use imagej as a library in some image analysis programs I am writing (in Java). Ideally, I would like to avoid ever showing an image and, for the most part, I can achieve this. However, there is one step that I cannot figure out how to write without showing an image.
Here's what I need to do:
1) Threshold a 16-bit grayscale image. (Using setAutoThreshold).
2) Make a mask out of this threshold. (Using IJ.run(img, "Convert to Mask","");)
3) Make a selection out of this mask.
4) Apply this selection to the original image.
To accomplish the transition between steps 3 and 4, I am using the following code:
<code>
RoiManager rm = new RoiManager(false);
IJ.run(bgmask, "Create Selection","");
bgmask.show();
rm.runCommand("Add");
bgmask.close();
Roi[] roi = rm.getRoisAsArray();
bs.setRoi(roi[0]);
ImageStatistics fg_stats = bs.getStatistics(ImageStatistics.MEDIAN);
</code>
The problem is that if I don't run "bgmask.show()" the roi manager complains that "there are no images open" and aborts the run.
Is there a way to circumvent this?
Thanks in advance,
Adam
=====
Science is more of an art than a science.
|
Locked
