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Curtis Rueden
@ctrueden
It makes sense as its own project during the learnathons... but then why not follow up by migrating shared useful materials out of learnathon space and into the official tutorials repo?
Kyle I S Harrington
@kephale
whoa, there is an imagej-roi course!
Curtis Rueden
@ctrueden
@kephale It was from the last Learnathon @ CSBD. Evolved over a couple of them, IIRC.
Unfortunately, they have been a hodge-podge of git repositories. Which ends up being fine during the event, and really tough afterward to see what's been presented.
Curtis Rueden
@ctrueden
@imagejan @kephale imglib/imglib2-roi#50
Jan Eglinger
@imagejan
:+1:
Christian Tischer
@tischi

@NicoKiaru I have the following workflow:

  1. I open a XML/H5 (that contains only a single Source) and view it in BDV.
  2. In BDV I change its AffineTransform using the manual transform UI of BDV
  3. Now I would like to save a new *.xml file that looks exactly as the original one that I opened, but I want a new <affine>...</affine> content, reflecting the additional transform that I manually added in BDV.

Do you know how to do this most efficiently? Do I have to construct a new SpimData object from the TransformedSource and then use XmlIoSpimData.save()? If so, would you have code already to construct SpimData from a single Source and the path to the corresponding .h5 file? Or are there other ways to save such an .xml file?

Nicolas Chiaruttini
@NicoKiaru
Hi Christian, you can use this spimData.getViewRegistrations().getViewRegistration(timePoint,iViewSetup).preconcatenateTransform(myAffineTransform); or spimData.getViewRegistrations().getViewRegistration(timePoint,iViewSetup).concatenateTransform(myAffineTransform);, with myAffineTransform being the transform retrieved from the TransformedSource. Then you can resave the dataset. FYI, I also found a trick to update the spimData when it's shown in the bdv (thanks to reflection to access a private method see https://github.com/BIOP/bigdataviewer_scijava/blob/master/src/main/java/ch/epfl/biop/bdv/scijava/command/spimdata/UpdateSpimDataDisplay.java)
Christian Tischer
@tischi
thanks!! ok, does that mean that spimData.getViewRegistrations().getViewRegistration(timePoint,iViewSetup).preconcatenateTransform(myAffineTransform); will not change the spimData displayed in Bdv?! (unless one does your trick)
Nicolas Chiaruttini
@NicoKiaru
For the moment yes, you're correct. If the loadTimepoint method in AbstractSpimSource was made public, then it would be a bit easier. (https://github.com/bigdataviewer/bigdataviewer-core/blob/5be52618026c6734911d9c150a9e2ba1140799e0/src/main/java/bdv/AbstractSpimSource.java#L187)
Stephan Preibisch
@StephanPreibisch
you have to call data.getViewRegistrations().getViewRegistration( 0, 0 ).updateModel();
to update the final model
@tischi
after concatenating or preconcatenating
it just adds it to the list of transformations
we do not automatically re-compute the final model every time you add
Christian Tischer
@tischi
thanks!
Christian Tischer
@tischi

@StephanPreibisch somehow I do not manage. It is not updating the image in BDV. Probably I am doing something wrong:

final Source< ? > source = bdv.getBdvHandle().getViewerPanel().getState().getSources().get( currentSource ).getSpimSource();
final SpimData spimData = sourceToSpimData.get( source );
spimData.getViewRegistrations().getViewRegistration( 0, 0 ).concatenateTransform( new ViewTransformAffine( "My transform", myTransfrom ) );
spimData.getViewRegistrations().getViewRegistration( 0, 0 ).updateModel();
bdv.getBdvHandle().getViewerPanel().requestRepaint();

sourceToSpimData is a Map that I generate while adding new SpimData to BDV in order to keep track of things.

Nicolas Chiaruttini
@NicoKiaru
@tischi I'm pretty sure you need to do the trick I showed you for the Bdv update when using BdvFunctions (at least for the versions I'm using in the POM file). I don't know how the update is done in BigStitcher. But that would be interesting to know! I guess calling the updateModelfunction is useful for updating properly the SpimData object before saving it, but I'm nor sure..
Stephan Preibisch
@StephanPreibisch
BDV caches the transforms additonally if I remember this correctly @tischi
if you would close and open BDV it should update
check this code out
Stephan Preibisch
@StephanPreibisch
here we update registrations interactively
Nicolas Chiaruttini
@NicoKiaru
Thanks @StephanPreibisch ! And you're also using reflection: you call the non public SpimSource.loadTimepoints method through reflection
Christian Tischer
@tischi

Thanks @NicoKiaru & @StephanPreibisch !
It looks like that both of your codes you are calling a method of the Source that is wrapped by the TransformedSource, which is the object BDV is using to display the source. What I did initially was simply:

final TransformedSource transformedSource = ( TransformedSource ) source;
transformedSource.setFixedTransform( myTransform );
bdv.getBdvHandle().getViewerPanel().requestRepaint();

This updates the display of the TransformedSource in the BDV and is much simpler code. I think the difference is that the TransformedSource is something that only exists in BDV and is not talking back to the SpimData object that was initially put into BDV for display. My feeling is that if one just wants to add additional transforms to Sources and display those in BDV, using the TransformedSource.setFixedTransform() approach might be cleaner?! In fact, the only reason I now also want to modify the SpimData object is because I want to save a new xml with myTransform appearing as additional <affine>...<\affine> tags. What do you think?

Christian Tischer
@tischi
...what I need for our users is a solution that works consistently for both adding a ManualTransformation (by pressing T in BDV) and/or adding any kind of other transformation, e.g. as obtained by a phase-correlation algorithm. And they should play well together. E.g. a user might do a rough manual pre-alignment (using T) and then press, e.g., P to compute a fine phase-correlation alignment on top of the manual pre-alignment. I am a bit worried right now that the current ManualTransformation in bdv-core relies on the TransformedSource, while our solutions seem to rather work through SpimData, and thus things might become messy, but I might be wrong as I am still not fully grasping everything...
Nicolas Chiaruttini
@NicoKiaru
That's also what I understood @tischi. If you want to resave, I think it's better to go for the SpimData option. Extra advantage of using SpimData is that the volatile view is taken care of also. It may not be the case fot the TransformedSource ? An alternative : every time you want to save the SpimData, check the transform of the TransformedSource: if it's not identity, then push it to SpimData.
But you may end up with a long chain of transform if the user is doing many attempts.
Christian Tischer
@tischi
image.png
Christian Tischer
@tischi
I am confused :-) I applied the ViewRegistration in the SpimData and also applied your reflection trick, in above example applying a simple translation along the x-axis. The result in BDV is that the yellow box is shifted along the x-axis relative to the grey square (see screenshot). However the coordinates of the upper left corner of the image are still at x=0 and y=0 if you hover there with the mouse. If I would change the transformation via the TransformedSource.setFixTransform() this would be different: the coordinates of the image would actually be shifted. Can someone explain me the meaning of the gray square and why the coordinates do not change using the SpimData approach? (...for me, I think the coordinates really would need to change because I need to move around the relative location of multiple Sources in a physical coordinate system).
Curtis Rueden
@ctrueden
Is there a one-liner in ImgLib2 for copying an image's contents into another image, without using a lambda? I know about imglib/imglib2/pull/237 but that isn't merged. I know about LoopBuilder but that requires a lambda. I want to do this from Python and I'm concerned that writing the lambda will not be elegant and/or performant. My current approach is to use Ops (ij.op().run("copy.rai", result, rai)) but @haesleinhuepf says in imagej/pyimagej#46 that it is too slow and must be fixed immediately.
Christian Tischer
@tischi
@NicoKiaru and @StephanPreibisch ...the solution is that I have to call the loadTimepoint method for both the Source< ? > and the Source< ? extends <Volatile< ? >>. An alternative to twice calling the private loadTimepoint() method via reflection seems to be to simply use transformedSource.setFixedTransform( transform ). This also properly updates the BDV. I don't understand yet what the pros and cons are...
Nicolas Chiaruttini
@NicoKiaru
Ah indeed @tischi! Sorry I forgot about it, and that gave me some headache as well. ... but yeah it was in the first link I sent you.
Always if you want to work with SourceAndConverter, you need to null check the volatile source and apply identical operations on both the volatile and non volatile source...
Christian Tischer
@tischi
@NicoKiaru @bogovicj @tpietzsch I need to implement a BDV UI that enables to save a selected 3D region to a conventional voxel space image, e.g. to an ImagePlus. My plan was to combine the bounding box dialog (https://github.com/bigdataviewer/bigdataviewer-core/tree/master/src/main/java/bdv/tools/boundingbox) with the exporter code from BigWarp (https://github.com/saalfeldlab/bigwarp/blob/master/src/main/java/bigwarp/BigWarpRealExporter.java). I just wanted to double check that this is not already a functionality that exists somewhere. And also, since I feel this is generally useful, I wanted to ask where to put it (in case of doubt I was gonna put it here for now: https://github.com/tischi/bdv-utils/)
Stephan Preibisch
@StephanPreibisch
Hi, I do a very similar thing in the multiview-reconstruction/BigStitcher
Christian Tischer
@tischi
@StephanPreibisch thanks a lot for pointing this out!
John Bogovic
@bogovicj
@tischi , nice! Where you put it probably depends on the dependencies - I'm sure you'll need read/write stuff which probably means we won't want to add to bdv-core, so your bdv-utils seems like a good place (to me)
Christian Tischer
@tischi

Could someone please help me? I have a BDV with only one source shown, and, correctly, below function returns me a list with one index:

bdv.getBdvHandle().getViewerPanel().getState().getVisibleSourceIndices();

However, when I let the user select a bounding box using (from bdv-core)

new TransformedRealBoxSelectionDialog( ... ).getResult()

above command (bdv.getBdvHandle().getViewerPanel().getState().getVisibleSourceIndices();) returns me a list with two indices. My first guess is that the TransformedRealBoxSelectionDialog maybe does not properly "clean up" the temporary overlay that it generates? Or am I doing something wrong?

Christian Tischer
@tischi
...I think I figured it out. When I put an IJ.wait( 100 ); in-between it does show the correct number of sources. I think reason must be that the TransformedRealBoxSelectionDialog returns its results already before it cleans up. I'll try to fix it and submit a pull-request later.
Christian Tischer
@tischi
@tpietzsch ...I had a look, but it is a bit too involved for me to decide how to best handle this. I created an issue: bigdataviewer/bigdataviewer-core#63
Christian Tischer
@tischi
@bogovicj, @StephanPreibisch, @NicoKiaru just FYI (in case you find it useful), I am implementing code such that in BDV, with multiple sources open, you can press Ctrl+B upon which you can select two sources, then it will open BigWarp for you with those two sources, you can register them and then upon some other keyboard shortcut transfer the transformation back to BDV and close BigWarp. So, in a sense, this is kind of an advanced way of doing a manual transformation.
John Bogovic
@bogovicj
Cool!
Stephan Preibisch
@StephanPreibisch
Nice, would be great if you could send around a little example once it works, would love to see it :)
Christian Tischer
@tischi

@bogovicj , @StephanPreibisch Ok, it seems to work :-) In principle it is as easy as adding this dependency:

<groupId>de.embl.cba</groupId>
<artifactId>bdv-utils</artifactId>
<version>0.3.2</version>

and then adding below line of code to your code, given you have a bdvHandle object which has some sources opened.

BdvBehaviours.addAlignSourcesWithBigWarpBehaviour( bdvHandle, behaviours, "ctrl B" );

However, before this could work, @bogovicj would have to merge my latest PR :-)
I will also during the next days record a video and upload it somewhere.

Christian Tischer
@tischi
John Bogovic
@bogovicj
👍