I guess there is: PositionableIterableRegion; but is there a utility function similar to
Regions.iterable(RAI<B>) to retrieve those?
@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.
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.
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).
Let's see...
Right now, you do:
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:
myMaskhas to be aRealMaskRealInterval, not aRealMask. This is unfortunate. We could add aRegions.sample(RealMask, RandomAccessibleInterval)that creates aRealMaskRealIntervalmatching the bounds of the given RAI. I think?- This
myMaskedImagecannot be used withLoopBuilderbecauseLoopBuilderonly supports RAI images, not II images. So we have to use this clunkier cursor code, rather than a nice lambda.¯\_(ツ)_/¯
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.
Hm, so far I've only seen examples of this in discrete space, i.e. going via
RandomAccessible and IntervalView, see imagej-roi-course
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?
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.
@NicoKiaru I have the following workflow:
- I open a XML/H5 (that contains only a single
Source) and view it in BDV. - In BDV I change its
AffineTransformusing the manual transform UI of BDV - Now I would like to save a new
*.xmlfile 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?
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)
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)
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
@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.
@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..
if you would close and open BDV it should update
check this code out