Imaris Reader: support for LZ4 compression and performance improvements #4249
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Hello,
this pull request adds support for LZ4 compressed ims files and modifies ImarisHDFReader to avoid multiple reads of the same 3D chunks. See also #4217.
LZ4 support is added using NetCDF-Java's ucar.nc2.filter package, which provides a mechanism for user-supplied filters as described here.
Regarding performance, ImarisHDFReader is modified to have a caching mechanism that reads a stack of planes (as many planes as the chunk z-size) from all channels into a buffer, which only needs to be updated after all data in it has been read. If the size of the buffer would exceed 1GB, the reader falls back to reading the requested plane only. The exact performance improvement will depend on the details of the dataset: in our testing, for 3D datasets the new reader can be over an order of magnitude faster than the existing implementation.