Parameterize dtype for h5path with SlideData
constructor
#335
+56
−11
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Currently, PathML stores all images with
float16
, forcing all image inputs to be upcast or downcast to this data type, which increases storage size or loses information. There already is adtype
parameter in theSlideData
constructor, but it's only used to assist theBioFormatsBackend
in loading images correctly. This repurposes that parameter to control what dtype h5py uses when writing image data.I also changed masks to stored as ENUM and use the strongest compression setting as boolean masks are highly compressible and easily compressed. The compression made a huge difference in file size, and using (HDFView)[https://www.hdfgroup.org/downloads/hdfview/] showed a compression ratio of 100-200x for masks. The ENUM data type is stored as an 8-bit integer (https://docs.h5py.org/en/stable/special.html#enumerated-types) but at least this is less than using
float16
.