imglib/imglib2

A generic next-generation Java library for image processing

Curtis Rueden

@ctrueden

(I didn't add TXT entries for scijava.com or any of the other things we have aliased for those orgs.)

Stephan Saalfeld

@axtimwalde

ok---removed again, will be updated in 1/2h

Kyle I S Harrington

@kephale

thank you!

Philipp Hanslovsky

@hanslovsky

@tpietzsch With the new imglib2-cache, is there a good way to invalidate all of a volatile wrapped img?

final RandomAccessibleInterval<?> vimg = VolatileViews.wrapAsVolatile(img);
final Cache<?, ?> cache = vimg.... // how to access cache?
cache.invalidateAll();

Or is that not necessary if I have the cache for img and call img.getCache().invalidateAll()?

Philipp Hanslovsky

@hanslovsky

Currently, I extract the relevant parts of VolatileViews.createVolatileCachedCellImg but that only works as long as I have control over creating the the volatile wrapped image.

Tobias Pietzsch

@tpietzsch

@hanslovsky hmm, invalidateAll for img is not enough

and there is no way yet to get to the cache of the volatileview

We should add that probably, but I need to think about it

If it is an option, you could as a workaround re-create the volatile wrapper whenever you invalidate the img cache

Philipp Hanslovsky

@hanslovsky

@tpietzsch Yes that is what I am doing at the moment and it works reasonably well for me.

Nicolas Chiaruttini

@NicoKiaru

Hi everybody, I was wondering : in an xml file of a dataset, in there a way to define the color of converter + min max display range / groupings. Is there some code example and/or documentation for that ? Thanks

Tobias Pietzsch

@tpietzsch

@NicoKiaru next to a somename.xml file, there can be a somename.settings.xmlfile that has this info

(if the names match, the settings.xml will be loaded when the xml file is opened)

for code, you could start digging here: https://github.com/bigdataviewer/bigdataviewer-core/blob/0e2b99fbbc7a2bd10baed806201c19c5bb6c47b1/src/main/java/bdv/BigDataViewer.java#L529-L598

For example settings.xml, you can just open a dataset and run Save Settings from the BDV menu

Nicolas Chiaruttini

@NicoKiaru

Perfect, thanks! Is this saveSettings method accessible through the Bdv interface ?

I'll look no worry

Tobias Pietzsch

@tpietzsch

Yes

in the menu

and shortcut F11 I think

https://github.com/bigdataviewer/bigdataviewer-core/blob/master/src/main/java/bdv/BigDataViewerActions.java#L105-L106

by Bdv interface, you mean vistools?

Nicolas Chiaruttini

@NicoKiaru

by Bdv interface, you mean vistools?

More the BdvHandle, because it's what we discussed was appropriate in order to make a bunch of Scijava compatible commands for Bdv (see https://forum.image.sc/t/fiji-commands-for-bigdataviewer/25601 and our current attempt located in the repo : https://github.com/BIOP/bigdataviewer_scijava)

Tobias Pietzsch

@tpietzsch

Hmm, no it's not yet supported through BdvHandle

but should be relatively easy to add if you want to make a PR

Nicolas Chiaruttini

@NicoKiaru

Actually after spending some time trying to understand the functioning of BigDataViewer, I realized that most of the communication between plugins is made through the dataset xml file (registrations, sources, etc). So I'm less convinced that bdv scijava commands will be very useful. Perhaps if a dataset.xml file could be accessed from/linked to a BdvHandle, that would be more useful.

But for now I'm not stuck, so that's good. I'll file a PR when I know if I need such a possibility.

Tobias Pietzsch

@tpietzsch

@NicoKiaru the bdv scijava commands would be a step on the way to better integrate BDV into the IJ2 framework

I think it will be very useful

I'm very thankful that you are exploring this!

Nicolas Chiaruttini

@NicoKiaru

Hi everybody, is there a way to retrieve the xml dataset file from a SpimDataobject ? To me it looks like no, only the basepath can be retrieved, but not the file name. Do you confirm ?

Tobias Pietzsch

@tpietzsch

yes

confirmed...

Nicolas Chiaruttini

@NicoKiaru

oki doki, thanks!

Curtis Rueden

@ctrueden

You could get it via reflection for now, no?

Tobias Pietzsch

@tpietzsch

I don't think so

Nicolas Chiaruttini

@NicoKiaru

not even sure, it's contains in the xmlio object, but I don't think in the spimdata object

Curtis Rueden

@ctrueden

Maybe I am looking at the wrong SpimData code then.

mpicbg.spim.data.SpimData?

Nicolas Chiaruttini

@NicoKiaru

Hum, I have AbstractSpimData

Curtis Rueden

@ctrueden

Oh, I see, basePath is not what you want.

Nicolas Chiaruttini

@NicoKiaru

Because it can be SpimData or SpimData2

Indeed

Curtis Rueden

@ctrueden

And the I/O code throws away the filename. Ouch.

Tobias Pietzsch

@tpietzsch

@NicoKiaru What do you need the xml path for?

We could add it

It would be optional however

Nicolas Chiaruttini

@NicoKiaru

It's again along the line of communicating objects within scijava commands

Tobias Pietzsch

@tpietzsch

There are instances where SpimData is not constructed from XML

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