SpimDataOpener for BDVHDF5?

[tischi]

@KateMoreva @K-Meech @constantinpape

I am confused, how do we open BDV HDF5 data?

mobie-io/src/main/java/org/embl/mobie/io/n5/openers/SpimDataOpener.java

Line 33 in 8251113

public SpimData openSpimData( String imagePath, ImageDataFormat imageDataFormat ) {

[constantinpape]

@tischi that's a good point. It looks like the code currently doesn't support bdv hdf5 any more. But I agree that we should still support it here. I guess that the problem is that we currently don't have an example project for it, so @KateMoreva wasn't really aware that we should still support it.
I will create an example project with bdv.hdf5 later.

[tischi]

like this?
@SerializedName("bdv.hdf5")

[constantinpape]

like this?
@SerializedName("bdv.hdf5")

I am not sure what you mean by this, but I think there should be a case BdvHDF5. And most likely this can be opened via BdVUtils.openSpimData so it can be just added here.
(The shared queue function of course needs to also be adapted)

[tischi]

That's what's written in the BDV XML in the image loader tag:

public enum ImageDataFormat {
    @SerializedName("bdv.h5") <--- IS THIS CORRECT?
    BdvHDF5,
    @SerializedName("bdv.n5")
    BdvN5,
    @SerializedName("bdv.n5.s3")
    BdvN5S3,
    @SerializedName("openOrganelle.s3")
    OpenOrganelleS3,
    @SerializedName("ome.zarr")
    OmeZarr,
    @SerializedName("ome.zarr.s3")
    OmeZarrS3,
    // OME Zarr with BDV XML
    @SerializedName("bdv.ome.zarr")
    BdvOmeZarr,
    // OME Zarr S3 with BDV XML
    @SerializedName("bdv.ome.zarr.s3")
    BdvOmeZarrS3;

[constantinpape]

That's what's written in the BDV XML in the image loader tag:

Ah, I see. I think that the correct tag is bdv.hdf5. I will double check this.

[constantinpape]

I have added an example project with hdf5 here: /g/kreshuk/pape/Work/mobie/hdf5-example-project.
And I also double checked, the tag should indeed be bdv.hdf5.

[KateMoreva]

/kreshuk/pape/Work/mobie/hdf5-example-project

Thanks, @constantinpape! I made a branch (mobie/mobie-viewer-fiji#565) to test this (opening via BdVUtils.openSpimData)
but faced this

java.util.concurrent.ExecutionException: ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException: Datatype:Can't convert datatypes ["H5Tconv.c line 8180 in H5T__conv_float_short(): can't handle conversion exception"]
	at net.imglib2.cache.ref.SoftRefLoaderCache.get(SoftRefLoaderCache.java:145)
	at net.imglib2.cache.util.LoaderCacheKeyAdapter.get(LoaderCacheKeyAdapter.java:53)
	at net.imglib2.cache.util.LoaderCacheAsCacheAdapter.get(LoaderCacheAsCacheAdapter.java:76)
	at net.imglib2.cache.ref.WeakRefVolatileCache.getBlocking(WeakRefVolatileCache.java:484)
	at net.imglib2.cache.ref.WeakRefVolatileCache.access$000(WeakRefVolatileCache.java:53)
	at net.imglib2.cache.ref.WeakRefVolatileCache$FetchEntry.call(WeakRefVolatileCache.java:531)
	at net.imglib2.cache.ref.WeakRefVolatileCache$FetchEntry.call(WeakRefVolatileCache.java:508)
	at net.imglib2.cache.queue.FetcherThreads$Fetcher.run(FetcherThreads.java:181)
Caused by: ncsa.hdf.hdf5lib.exceptions.HDF5DatatypeInterfaceException: Datatype:Can't convert datatypes ["H5Tconv.c line 8180 in H5T__conv_float_short(): can't handle conversion exception"]
	at ch.systemsx.cisd.hdf5.hdf5lib.H5.H5Dread(Native Method)
	at ch.systemsx.cisd.hdf5.hdf5lib.H5D.H5Dread(H5D.java:381)
	at bdv.img.hdf5.HDF5AccessHack.readShortMDArrayBlockWithOffset(HDF5AccessHack.java:197)
	at bdv.img.hdf5.HDF5AccessHack.readShortMDArrayBlockWithOffset(HDF5AccessHack.java:182)
	at bdv.img.hdf5.Hdf5VolatileShortArrayLoader.loadArray(Hdf5VolatileShortArrayLoader.java:46)
	at bdv.img.hdf5.Hdf5VolatileShortArrayLoader.loadArray(Hdf5VolatileShortArrayLoader.java:34)
	at bdv.img.cache.VolatileGlobalCellCache.lambda$createImg$0(VolatileGlobalCellCache.java:196)
	at net.imglib2.cache.util.LoaderCacheKeyAdapter.lambda$get$0(LoaderCacheKeyAdapter.java:55)
	at net.imglib2.cache.ref.SoftRefLoaderCache.get(SoftRefLoaderCache.java:135)
	... 7 more

and thinking about solving it.

[constantinpape]

Thanks! I made a branch (mobie/mobie-viewer-fiji#565) to test this (opening via BdVUtils.openSpimData)
but faced this
and thinking about solving it.

Oh, that's a known issue with datatypes in hdf5 with java ... Please don't do anything about this for now, I will try to fix the data.

[constantinpape]

@KateMoreva I have removed the h5 volume that causes this issue (I think). Could you please try again and see if it works now?

[KateMoreva]

@KateMoreva I have removed the h5 volume that causes this issue (I think). Could you please try again and see if it works now?

@constantinpape
Unfortunately, the error is still there.

[constantinpape]

Ok, I will give it another update that will hopefully fix it later (and if that doesn't help we need to think about this closer.)
(I am busy for the next 2 hrs will do it after that and ping you)

[constantinpape]

@KateMoreva I updated the project again, could you check if you still get the same error?

[KateMoreva]

@KateMoreva I updated the project again, could you check if you still get the same error?

@constantinpape
No errors this time! 😃
The image with the default brightness:

[constantinpape]

@constantinpape
No errors this time! smiley
The image with the default brightness:

Ok! The image looks a bit weird, but I might know why. I have just replaced the data once more. Could you try to load it again and paste another screenshot?

[KateMoreva]

@constantinpape
No errors this time! smiley
The image with the default brightness:

Ok! The image looks a bit weird, but I might know why. I have just replaced the data once more. Could you try to load it again and paste another screenshot?

@constantinpape

[constantinpape]

@KateMoreva great, that's how it's supposed to look :).

[constantinpape]

I think this is done, can we close the issue @tischi ?