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  • May 25 16:25
    tinevez synchronize #162
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    tinevez on branch-graph-v2

    Display messages in the BDV for… (compare)

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    tinevez on fix-min-radius

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    tinevez on branch-graph-v2

    Make Link displacement and velo… Make synchronized the value() m… Spot radius feature makes one n… and 2 more (compare)

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    tinevez synchronize #162
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    Return sensible defaults when w… (compare)

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    tinevez synchronize #162
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    Proper menu item label for the … (compare)

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    tinevez synchronize #162
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
oh
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
If you want to make a PR, you can add it to AbstractSpimData
Nicolas Chiaruttini
@NicoKiaru
Let's say you have a command which adds interest points - using sift for instance. You want to get the spimdata object, add interest points, and then potentially resave the xml file
Tobias Pietzsch
@tpietzsch
Would be set when reading a SpimData through XmlIoAbstractSpimData
Otherwise it would be null
Maybe it would be also set, if you save the SpimData to a (different) XML file
but that already gets interesting
Nicolas Chiaruttini
@NicoKiaru
oki doc. Maybe another option is to add an abstract save or resave method to spimdata ? Would that make sense ? The default behaviour would be what you describe. But I'm not familiar with use cases other than the simple ones. I do not want to add a dirty patch which turns out to be annoying.
Tobias Pietzsch
@tpietzsch
I'm not sure how that would play with extensibility
AbstractSpimData and XmlIoAbstractSpimData play together somehow
and then SpimDataMinimal, XmlIoSpimDataMinimal, etc