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  • Nov 27 19:07
    tinevez closed #202
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    tinevez on master

    An action to export to a Motili… Update license blurbs. Bump to next development cycle … (compare)

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    tinevez on TrackMate-7.4.0

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    ctrueden on main

    Update dependency version in RE… Bump to next development cycle … (compare)

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    Say "leading sign", not "minus"… Add parsing of hexidecimal floa… Remove unnecessary null check … (compare)

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Tobias Pietzsch
@tpietzsch
confirmed...
NicoKiaru
@NicoKiaru
oki doki, thanks!
Curtis Rueden
@ctrueden
You could get it via reflection for now, no?
Tobias Pietzsch
@tpietzsch
I don't think so
NicoKiaru
@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?
NicoKiaru
@NicoKiaru
Hum, I have AbstractSpimData
Curtis Rueden
@ctrueden
Oh, I see, basePath is not what you want.
NicoKiaru
@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
NicoKiaru
@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
NicoKiaru
@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
NicoKiaru
@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
I wouldn't do it
But potentially you could make a wrapper around a SpimData and a XmlIo that has these methods and keeps the filename
(then we need to make sure, that the default spimdatas in Fiji always are loaded in a way that they have the wrapper)
something like that?
NicoKiaru
@NicoKiaru
yep. Ok. For now I will not touch anything, and keep things the way they are. I'll let the user define the dataset name, and with the Parameter being persistent, it's not complicated : if he wants to resave and erase the previous dataset, he lets the same name, and if he wants to avoid erasing the dataset, he changes the name - another dataset is created.
Not ideal, because this dataset name is not transfered from one Command to another. I'll investigate more your advice when required. Thanks a lot !
Tobias Pietzsch
@tpietzsch
Maybe you can just make a static Map< SpimData, String (with weak keys)
or attach that association to the Context somehow?
Curtis Rueden
@ctrueden
There is a CacheService backed by a weak hash map, into which you can put that stuff.
Tobias Pietzsch
@tpietzsch
👍
NicoKiaru
@NicoKiaru
I realized I have another related issue. Suppose I call BdvFunctions.show(mySpimData);. If I update a viewRegistration in the mySpimData object, can I update what is displayed in the bdv window ? Should I close it and reopen it ? thanks!
Tobias Pietzsch
@tpietzsch
In practice, it is enough to move to a different timepoint and back to make the transforms reload from the mySpimData
But that is more an implementation detail of the current sources
(but pretty reliable)
otherwise: BdvFunctions.show(mySpimData); returns a List<BdvStackSource<?>>
you can use the BdvSource.removeFromBdv() for each of the BdvStackSource and then use BdvFunctions.show(mySpimData, Bdv.options().addTo(...)); to add them again
NicoKiaru
@NicoKiaru
Ok, since I'm working with 2d slice scanners file, there's no (or a single) timepoint. I'll try the other option.
Tobias Pietzsch
@tpietzsch
Depending on whether its a window or just a panel:
the window will probably close when all sources are removed
so maybe BdvFunctions.show(mySpimData, Bdv.options().addTo(...));
before you remove the old sources
NicoKiaru
@NicoKiaru

There is a CacheService backed by a weak hash map, into which you can put that stuff.

I wasn't aware of the CacheService, and I didn't know what a WeakHashMap was. That looks incredibly useful!

Kyle I S Harrington
@kephale
@maarzt labkit is looking fantastic these days. has anything been developed for applying the classifiers trained with labkit in a headless way (e.g., train on my laptop, segment on a cluster)?