I found that it must be due to the image cache not being updated.  Flushing the image cache followed by regenerating the mipmaps for the respective patches renders them with the PPS applied (or removed, removing it shows the same effect).

Found a candidate:  The method Cache.removeImagePlus(Pyramid) does lots of things but only removed the ImagePlus if ImagePlusUsers was empty.  In the described situation, ImagePlusUsers was null.  Albert, can you please review this commit and check if the desired behavior is still there?  I do not know what those ImagePlusUsers are.  Thanks in advance.

(In reply to comment #2)
> Found a candidate:  The method Cache.removeImagePlus(Pyramid) does lots of
> things but only removed the ImagePlus if ImagePlusUsers was empty.  In the
> described situation, ImagePlusUsers was null.  Albert, can you please review
> this commit and check if the desired behavior is still there?  I do not know
> what those ImagePlusUsers are.  Thanks in advance.

Two or more Patch instances may point to exactly the same image file. Therefore they are users of the same ImagePlus. Generally there is only one user. A situation when there are two is after splitting an image in two parts.

If ImagePlusUsers was null, then there is an error somewhere else in the Cache: adding an ImagePlus is not adding an ImagePlusUser but it should.

I think I got it:

/** Returns null if the ImagePlus was preprocessed or doesn't have an original FileInfo
	 * (which means the image does not come from a file). */
static public final String getPath(final ImagePlus imp) {

... the above indicates that when there is a preprocessor script, the ImagePlus does not have an associated file path and is not stored as having any users, given that the combination of file path and preprocessor script generates a unique ImagePlus.

I've pushed a couple of fixes that ensure that cache space is reclaimed only when the ImagePlus is no longer referenced. Let me know if the bug can be closed.

More fixes pushed for the Cache. There was a long-standing error that caused ImagePlus to never be released when calling removeImagePlus(long id).

See: http://repo.or.cz/w/trakem2.git/commit/bee086761f1d7609b18d6f2c4d28f86608dc52f0

Thanks!