ImageDisplay can't retrieve the current position of an Axis

Steps to reproduce :

1. Open Mitosis sample
2. Change the position of the different dimensions
3. Launch this script

# @ImageDisplay img

from net.imagej.axis import Axes

print(img.getLongPosition(Axes.Z))
print(img.getLongPosition(Axes.X))
print(img.getLongPosition(Axes.Y))
print(img.getLongPosition(Axes.TIME))
print(img.getLongPosition(Axes.CHANNEL))

It should print 0 for all the dimensions.

I guess it’s an issue with IJ1 <-> IJ2 synchronization. Should we except such methods to work or it is a limitation of running IJ2 under the IJ1 interface ?

[ctrueden]

One year later…

I also found that sync is not enable by default

So, the goal is to make that option completely obsolete. We have lazy syncing now which is always enabled. We never want to perform expensive up-front syncing. And really, we want to always wrap/unwrap data structures back and forth, rather than ever copying pixels. This can be done in the majority of cases thanks to the ImageJ1 VirtualStack class.

I guess the legacy code is not yet stable and fully working

Definitely not, no. It is—to use the common parlance in my part of the world—extremely half-assed. That’s not to say a lot of work didn’t go into it already—it did—but it has gone through some hurried iterations since the initial implementation, by multiple different programmers, and no one has taken the time to thoroughly update and test it since we fully switched to ImageJ Legacy as the active-by-default UI of ImageJ2. I apologize for that, and unfortunately I will probably not be able to work on it much in 2017, either. But we’ll get there some day.

[hadim]

After some tests I found that PositionHarmonizer.updateLegacyImage() is only called once when an image is open in IJ1. But then it’s never called so I guess this is why the positions are not synced between ImageDisplay and ImagePlus.

I wasn’t able to find how the whole sync process works. So it’s pretty hard for me to debug it. Here is some stuff that I noticed :

• LegacyService.syncActiveImage() does not do any harmonization.
• LegacyCommand seems to be the only class that do harmonization but the code is called only when an IJ1 command is run.

Should not harmonization be run each time something happen on an ImageDisplay or/and ImagePlus ? I guess this way of doing it is very CPU consuming so you may disabled this behaviour.