These are chat archives for fiji/fiji

3rd
Jun 2016
Jean-Yves Tinevez
@tinevez
Jun 03 2016 12:09
@imagejan Waiting for your go to release. But I would like to do it today, if possible.
Jan Eglinger
@imagejan
Jun 03 2016 12:35
blob

@tinevez sorry for the delay. Here are some comments:

  • the choice of 'R' for invoking the display config is a bit unfortunate: in my trials, it worked about 50% of the time; I had to click into the image and be at least at step 2 of the wizard (Select a detector); otherwise it would simpy call File > Revert which has 'R' as default shortcut
  • as soon as I actually have some tracks, but also some spots that do not belong to any track, I get the following NPE when trying to color by "Number of spots in track" or similar:
    Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
     at fiji.plugin.trackmate.FeatureModel.getTrackFeature(FeatureModel.java:423)
     at fiji.plugin.trackmate.FeatureModel.getTrackFeatureValues(FeatureModel.java:115)
     at fiji.plugin.trackmate.gui.panels.components.ColorByFeatureGUIPanel.getValues(ColorByFeatureGUIPanel.java:492)
     at fiji.plugin.trackmate.gui.panels.components.ColorByFeatureGUIPanel.repaintColorCanvas(ColorByFeatureGUIPanel.java:193)
     at fiji.plugin.trackmate.gui.panels.components.ColorByFeatureGUIPanel.access$600(ColorByFeatureGUIPanel.java:36)
     at fiji.plugin.trackmate.gui.panels.components.ColorByFeatureGUIPanel$2.paint(ColorByFeatureGUIPanel.java:388)
  • the dialog looks a bit weird when trying to resize it (see pasted screenshot)

Otherwise, I really like the addition! :smile:

Jean-Yves Tinevez
@tinevez
Jun 03 2016 12:39
Thanks @imagejan !
What would you suggest as key for this?
Jan Eglinger
@imagejan
Jun 03 2016 12:39
(The weird resizing only seems to happen after inducing a NullPointerException by the above method, otherwise all is well)

What would you suggest as key for this?

Any shortcut that is not yet taken (I know that's difficult ;)?

Actually, it would be great to have a button in the main wizard for invoking the display, and a keylistener active in the wizard (and not necessarily on the Image frame).
Jan Eglinger
@imagejan
Jun 03 2016 12:48
Within the letters 'G' and 'Q' are not taken yet, otherwise you can use a function key. But introducing default shortcut is dangerous IMHO, because they can be different in various (possibly customized) ImageJ installations.
Jean-Yves Tinevez
@tinevez
Jun 03 2016 12:48
Yep ok. Let's see if I can do that today.
But for the key shortcut, I do not know.
For the first panel in the GUI, there is no view yet, and the TrackMate tool is not launched yet. So all keys will map to ImageJ.
Sincerely, I would welcome suggestion. F & G are taken by TrackMate for stepwise time browsing.
Jan Eglinger
@imagejan
Jun 03 2016 12:51
If you can reliably disable ImageJ's default shortcuts when TrackMate is running, that's fine. But I fear that by simply switching between different ImageJ windows, things might get mixed up. I'm not familiar enough with how KeyListeners work in Java and ImageJ.
Maybe @ctrueden or @hinerm can advise?
Jean-Yves Tinevez
@tinevez
Jun 03 2016 13:01

MaMuT updated:

Release v0.21.0.

  • Record movies from MaMuT viewer windows.
    You can now record movies and max. projection movies from the MaMuT
    viewer. The annotations will be recorded as well.

  • Use the BDV bookmarks system in MaMuT.
    With the same kep mapping by default (Shift-B + some key to store a
    bookmark, B + bookmark key to recall it, O + bookmar key to recall just
    its orientation).

  • Use the BDV grouping system in MaMuT.

  • Import bookmarks from existing settings file.
    When launching a new MaMuT annotation, if a settings file is found, we
    import bookmarks from it. They are then saved inside the MaMuT file.

  • Load or determine display defaults for BDV sources:
    If a BigDataViewer settings file is found, we fetch the SetupAssignments
    settings from it. We cannot fetch the grouping and visibility settings
    and the viewer settings, because these settings are proper to a single
    viewer. If a settings file is not present, we compute a default brightness
    for each source.

Jean-Yves Tinevez
@tinevez
Jun 03 2016 13:18
@imagejan I could not reproduce the bug you mention, at least on MacOSX.
I will try again tonight on a PC.
Jean-Yves Tinevez
@tinevez
Jun 03 2016 14:11
@imagejan Could you pull fiji/TrackMate master branch again?
I made the main change you requested, and this is a much better option actually:
There is now a new button in the GUI (an orange wrench) that shows the display config panel when pressed. Every time you press it, all features are recalculated.
Jan Eglinger
@imagejan
Jun 03 2016 14:24

@tinevez this looks great now! Works smoothly.

Last comment: you could maybe disable the TrackScheme and/or Analysis buttons when there are no data available (yet), so they don't produce empty results windows. Try for example going back to start in the wizard, then clicking the wrench and trying those buttons.

Jean-Yves Tinevez
@tinevez
Jun 03 2016 14:25
I thought about it, but empty windows are fine: the GUI does not have to know whether the model is empty or not.
Plus right now I am tweaking these buttons so that with something-like shift-click they generate something useful even if the there are no tracks yet.
Jan Eglinger
@imagejan
Jun 03 2016 14:27
Ok, perfect! Thanks for the great work!
@tinevez another question: is your PIV_Analyzer plugin still the preferred way to measure (and possibly correct for) inhomogenous regional movements in time lapse images? Or do you know of other options?
Jean-Yves Tinevez
@tinevez
Jun 03 2016 14:31
The field as improved a lot since, and at the time I already knew close to nothing.
@axtimwalde at the time developed the optic flow block matching plugin.
The only advantage the PIV analyzer had at the time was that it could do some sub-pixel accuracy.
So: I do not know, and it is very unlikely that it is the preferred way for anything.
Jan Eglinger
@imagejan
Jun 03 2016 14:33
ok, thanks for that info :)
Jean-Yves Tinevez
@tinevez
Jun 03 2016 14:41
Done. If you are happy, can save / reload etc I will release.
Jan Eglinger
@imagejan
Jun 03 2016 14:48
Unfortunately I couldn't find any documentation about the Optic Flow plugins. Will try to update the wiki (also http://imagej.net/PIV_analyser) with some info next week...
Current TrackMate master works fine, also with Shift-click for all spots, and saving the xml file.
Jean-Yves Tinevez
@tinevez
Jun 03 2016 14:55
The literature is VERY dense and abundant. I think there have been a grand challenge on this.
No I was mistaken.
Also, you want to check this plugin: https://sites.google.com/site/qingzongtseng/piv
It supersede PIV_analyzer, but depends on native libraries, and cannot deal with time directly.
Jan Eglinger
@imagejan
Jun 03 2016 15:08
:+1: thanks