manual transformation triggered with [T] no longer saved in views

[martinschorb]

Hi, --- current release version --- when I apply a manual transformation and then right-click-> save view it no longer is applied in that view.

The generated view only contains an empty: "sourceTransforms": [],

This used to work when I last tried it end of April.

To reproduce:

• open any two images
• press t in the viewer to transform
• move one source
• press t again to fix transform
• right click and save view
• open new view. Transformed source is no longer transformed.

[tischi]

Yes, this is in fact currently not supposed to work anymore.

You have to Right click => Choose Registration - Manual Transform.

I can look into whether one could make it work again but I am not sure...

[tischi]

The point is that the old behaviour tended to created a mess because it was very difficult to save a transformed version of an individual image. Now it forces you save another version (view) of the transformed image(s) (you can select multiple by grouping them in BDV).

But I agree, it would be nice to make it work with the [ T ]...probably I should hijack the [ T ] in MoBiE.

[tischi]

To clarify, I think:

Old logic: If you clicked [T] and then transformed one or more image(s), and the saved the current view, a view with all visible images, including the transformed ones would be saved. Like this it would be impossible to re-use the transformed image in another view.

New logic: The images that you transform are saved as individual transformed image views, such that they can be used to recompose more complex views, including those newly transformed images.

I guess both have pros and cons....

And I guess we would probably need to meet in person on a white-board to really figure this out :-)

[tischi]

ImgLib2 news and tutorials - User-configurable Keymaps

[tischi]

issue branch: issue-1165

[tischi]

@schorb this is how the manual transform command should look like:

TODO

• [x] disable the [ T ] keyboard shortcut of BDV.

[martinschorb]

that would be great!

[martinschorb]

However, I think as it is currently implemented the list would only contain visible sources. Usually you want to register multiple channels while only using one of them for the registration. Would it be possible to list all active/loaded sources independent of being shown or not?

[tischi]

Would it be possible to list all active/loaded sources independent of being shown or not?

Yes, I will change that.

[martinschorb]

btw: https://mobie.github.io/tutorials/volume_registration.html

[martinschorb]

When you open another view but leave the manual registration window open, it crashes, even though the sources it lists are shown. (I guess the BDV IDs change). Would it make sense to auto-close the registration window when accepting a registration?

[ERROR] org.scijava.module.MethodCallException: Error executing method: org.embl.mobie.command.context.ManualTransformationCommand#setMovingImages
    at org.scijava.module.MethodRef.execute(MethodRef.java:71)
    at org.scijava.module.AbstractModuleItem.callback(AbstractModuleItem.java:227)
    at org.scijava.widget.DefaultWidgetModel.callback(DefaultWidgetModel.java:179)
    at org.scijava.widget.DefaultWidgetModel.lambda$setValue$0(DefaultWidgetModel.java:169)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$1(DefaultThreadService.java:233)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
    at java.awt.EventQueue.access$500(EventQueue.java:97)
    at java.awt.EventQueue$3.run(EventQueue.java:709)
    at java.awt.EventQueue$3.run(EventQueue.java:703)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at org.scijava.module.MethodRef.execute(MethodRef.java:67)
    ... 18 more
Caused by: java.lang.NullPointerException
    at org.embl.mobie.command.context.AbstractTransformationCommand.lambda$setMovingImages$5(AbstractTransformationCommand.java:201)
    at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    at java.util.Collections$2.tryAdvance(Collections.java:4719)
    at java.util.Collections$2.forEachRemaining(Collections.java:4727)
    at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
    at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
    at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
    at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:566)
    at org.embl.mobie.command.context.AbstractTransformationCommand.setMovingImages(AbstractTransformationCommand.java:202)
    ... 23 more

[tischi]

Tutorial

great! let's continue discussion here: https://github.com/mobie/mobie.github.io/issues/111

Auto closing the registration window

Yes that would be good, but I have not yet figured out how to do this... let's continue here: https://github.com/mobie/mobie-viewer-fiji/issues/1166

[martinschorb]

Also, could the GUI in the view selection window be changed such that both the Save To and the selection group text box are hidden if the dropdown selectors do not point to "External JSON file" or "new selectiongroup"

[tischi]

This would be great, but unfortunately I don't know how to achieve this (using the IJ Dialog that we currently use, we would need a proper Swing Implementation). But this would be great, could you please open a separate issue for this?