Understanding SpimData

[tischi]

@joshmoore

1. For a SpimData object all contained sources must have the same number of time points

final AbstractSequenceDescription< ?, ?, ? > seq = spimData.getSequenceDescription();
final int numTimepoints = seq.getTimePoints().size();

2. Each ViewSetup contains one Source
3. Adding SpimData to BDV returns a List< BdvStackSource > bss, where bss has a method getSources() which is a another list, however this list always only contains one item.

final List< SourceAndConverter< T > > sources = Collections.singletonList( source );
final BdvStackSource< T > bdvSource = new BdvStackSource<>( handle, numTimepoints, type, setups, sources );

@NicoKiaru
you think that's correct?
and do you get why a BdvStackSource contains a list of sources if there only is one in the list?

[NicoKiaru]

you can define missingviews in the sequence description. If you feel like it you can check the uberdataset repo which contains a way to merge spimdata object into a single one.

When the number of timepoints didn't match, I had to set a number of missing views:

https://github.com/BIOP/bigdataviewer-uberdataset/blob/272ffb69459379c7fedcc609cee8110cc31ec72a/src/main/java/ch/epfl/biop/bdv/uberdataset/MergeXmlDatasets.java#L243-L273

[tischi]

Thanks!

1. Would you say that maybe the whole point of the current design is that Setups are allowed to have missing timepoints?
2. If you open a .lif file the contained images can have all kind of time points; what is seq.getTimePoints().size() returning in that case? The number of time points of the longest movie in the .lif file?

[NicoKiaru]

1. Not sure
2. Yes:

https://github.com/BIOP/bigdataviewer-bioformats/blob/320ee3ff490d43c7aef1905e5943a334dbcae9d5/src/main/java/ch/epfl/biop/bdv/bioformats/export/spimdata/BioFormatsConvertFilesToSpimData.java#L257-L273

I'm getting the maximum number of timepoints and adding missingviews for series which do not reach this maximum

[tischi]

@NicoKiaru
Do you have any idea about the other question that I had?

Adding SpimData to BDV returns a List< BdvStackSource > bss, where each bss has a method bss.getSources() which is an another list, however bss.getSources() in my hands always only contains one item. Is that the same for you?

[NicoKiaru]

Adding SpimData to BDV returns a List< BdvStackSource > bss, where each bss has a method bss.getSources() which is an another list, however bss.getSources() in my hands always only contains one item. Is that the same for you?

Yes. I don't know why.

Which other question : the one about the Setups ? I think it allows to have multiple 'setups' which can be variations on angle / illumination / channel / whatever + you have ViewId which are specific to a certain viewsetup at a certain timepoint. There can be metadata per ViewId also I think, and they can be missing. What are you looking for specifically ?

[tischi]

Which other question :

Sorry for the confusion, I meant the one that you answered with "Yes. I don't know why" :-)
Thanks!