add to swap axis if only one time point and several Z

[gletort]

Propose to swap Z and T axis in plugin "Load TrackMate file" if there is one time point and several Z. Same function as in the main TrackMate plugin

[tinevez]

May I suggest going further?

With this approach, the message that the image has only one time-point is shown all the time, regardless of whether the user meant to analyse a 3D image or not. But since we are opening a TrackMate file, we can guess whether the image analyzed was truly 3D or 2D+T, by inspecting the metadata stored in the XML file. For instance:

This would be a true 3D, one time point file:

<Settings>
    <ImageData filename="Celegans-5pc-17timepoints-smoothed.tif" folder="samples/" 
width="240" height="295" nslices="41" nframes="1" pixelwidth="0.1984666072986889"
pixelheight="0.1984666072986889" voxeldepth="1.0" timeinterval="2.0" />

And this would be a 2D+T image file:

  <Settings>
    <ImageData filename="FakeTracks.tif" folder="/Users/tinevez/Development/TrackMateWS/TrackMate/samples/"
width="128" height="128" nslices="1" nframes="50" pixelwidth="1.0" 
pixelheight="1.0" voxeldepth="1.0" timeinterval="1.0" />

Maybe we can read these metadata, check whether they match the dimensionality of the image that was opened, and if not, prompt the user?

[gletort]

Ok, sure. Should I make it then do the swapping automatically in that case (following the settings in the .xml file), or still ask the user ? The .xml settings should be always correct, no ?

[tinevez]

Yes the .xml should have the right metadata: it is taken from the image when the user saved to XML from TrackMate.
So with this PR we could recuperate if they changed the image after loading it, but before running TrackMate.

I would say: prompt the user, if they say yes, flip the image, and then prompts them to fix the dimensionality themselves and resave the image.