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  • Jun 27 20:02

    ctrueden on roitree-to-mask-converters

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  • Jun 27 20:02

    ctrueden on master

    First cut: ROITree to SuperElli… Fill out ROITree <-> single mas… Add RealMask support and 9 more (compare)

  • Jun 27 20:02
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  • Jun 27 19:03

    ctrueden on roitree-to-mask-converters

    First cut: ROITree to SuperElli… Fill out ROITree <-> single mas… Add RealMask support and 8 more (compare)

  • Jun 27 18:36
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  • Jun 26 20:40

    ctrueden on master

    POM: add main-class for quick t… (compare)

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    Add Vlado as a contributor Merge pull request #178 from xu… (compare)

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    ctrueden on opSearchResult-improvements

    Use stream(), not parallelStrea… OpListingInfo: ensure OpService… OpList: improve equals implemen… (compare)

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Curtis Rueden
@ctrueden
@imagejan The javadoc for that class says "We put interfaces RandomAccessibleInterval<BooleanType>, IterableRegion<BooleanType>, PositionableIterableRegion<BooleanType> into this sequence such that the Regions methods that "add capabilities" (being iterable, positionable) can have appropriate result types."
This suggests to me that @tpietzsch intended for there to be more Regions methods exposing it. But I don't see them.
In this case though, we just want a LocalizableIterableRegion. Not Positionable. Right? I think the latter is more complex.
Jan Eglinger
@imagejan
Oh, right, we'd want a LocalizableIterableRegion, sure.
Curtis Rueden
@ctrueden
Hmm. I think we're conflating iterables vs iterator/accessors here.
IterableRegion does have a localizingCursor method.
That is: the IterableRegion (similar to RAI and II) does not have a position. But it can give you accessors that do.
Jan Eglinger
@imagejan
Oh, I see. I guess I wasn't getting the concept. Thanks a lot!
Curtis Rueden
@ctrueden
Note that IterableRegion<T extends BooleanType<T>> extends IterableInterval<Void>. So... the cursor() method returns Cursor<Void>. So that you can iterate the positions, but you can't access sample values because there is nothing to access (the backing region is just true at those spots, always).
Jan Eglinger
@imagejan
Yeah, I'd need a Sampler otherwise, right?
Curtis Rueden
@ctrueden
As in: you want to bind a mask to an image and iterate the samples that are not masked out. Right? While knowing their positions?
Let's see...
Right now, you do:
Jan Eglinger
@imagejan
Actually, in my case, having the positions would be enough, no need to sample the values. So I'm fine with localizingCursor I guess.
Curtis Rueden
@ctrueden
RealMaskRealInterval myMask = ...;
RandomAccessible<T> myImage = ...;
IterableInterval<T> myMaskedImage = Regions.sample(myMask, myImage);
Cursor<T> c = myMaskedImage.localizingCursor();
long[] pos = new long[c.numDimensions()];
while (c.hasNext()) {
  T value = c.next();
  c.localize(pos);
  // and now we do something with the position and sample value
}
However, there are some limitations:
  1. myMask has to be a RealMaskRealInterval, not a RealMask. This is unfortunate. We could add a Regions.sample(RealMask, RandomAccessibleInterval) that creates a RealMaskRealInterval matching the bounds of the given RAI. I think?
  2. This myMaskedImage cannot be used with LoopBuilder because LoopBuilder only supports RAI images, not II images. So we have to use this clunkier cursor code, rather than a nice lambda. ¯\_(ツ)_/¯
Jan Eglinger
@imagejan
Thanks for the explanations!
Curtis Rueden
@ctrueden
It's partly explanations, and partly me figuring things out and thinking about to make it better.
Do you agree with (1) that we could have a better utility method here?
Because I think the most common thing is that you have a RealMask (not necessarily a RealMaskRealInterval) and a RAI and you want to combine them.
Jan Eglinger
@imagejan
Yes, agreed.
Curtis Rueden
@ctrueden
I feel dumb, but I'm not finding the mechanism to convert an unbounded mask (RealMask) into a bounded one (RealMaskRealInterval).
Jan Eglinger
@imagejan
Hm, so far I've only seen examples of this in discrete space, i.e. going via RandomAccessible and IntervalView, see imagej-roi-course
Curtis Rueden
@ctrueden
I wish someone besides me (looks at @maarzt in this case) would make more tutorial notebooks in imagej/tutorials. The imagej-roi-course belongs as a notebook there. And likely also a Maven project.
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