id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
811	Optimize cmap hdf5 format read speed for light microscopy data	Tom Goddard	Tom Goddard	"The Chimera map format (*.cmap) HDF5 seems to be slow reading subsampled copies of images.  For example, using 2048 x 1889 x 1999 8-bit ratbrain.cmap and reading the step 2 subsampled copy (921 Mbytes), takes about 22 seconds, while reading the step 2 version in MRC format takes about 9 seconds.  This may be because the cmap 3d arrays are fragmented across the disk because the code that writes them writes a slab of planes at a time for all resolutions.  So the highest resolution slab chunks in the HDF5 chunked array are probably interleaved on disk with the step 2 resolution chunks.

Important to get the fastest possible read speed for light microscopy data sets that are many Gbytes.  Try writing each resolution completely without interleaving.  Try larger chunk size (currently using tiny 64 Kbytes).

"	enhancement	assigned	major		Volume Data								all	ChimeraX