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scenerygraphics / corvo-core

Scenery-dependent repository for visualisation of scanpy output datasets with a 3D obsm entry in VR.
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Zarr Reading #12

Closed ljjh20 closed 3 years ago

ljjh20 commented 3 years ago

Appears to be no good way of reading the data directly from hdf5. From Zarr using N5Zarr, numerical primitives can be read, but strings can not. Datatype |0 is ambiguous and can not even be read in in byte form.

ljjh20 commented 3 years ago

Solution: Build VR part in Kotlin and bundle as JAR file. Write python script to read h5ad data using python libraries (either scanPy or zarr). Run JAR file from command line, passing path to file storing translated data.

Possibly build small qt gui to drag and drop appropriate h5ad files in to avoid needing to package them together with the python program.

ljjh20 commented 3 years ago

Update: Translate annotations to csv with scanPy, read sparse matrix with jHDF5. It may be possible to read annotations with jHDF5 as well, as new datasets don't seem to compound the var.

ljjh20 commented 3 years ago

Not reading data in through zarr