neuronlistz - fast access to neuronlists stored as zip files#456
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neuronlistz - fast access to neuronlists stored as zip files#456
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* 3 cores can reduce time ~ 40% in my tests
* I will remove some of this but useful for testing purposes
* this is about 10x faster than gzip for raw compression speed in my tests * including the overhead of writing files etc * this is so fast that it doesn't seem to pay to parallelise writing, so I am tempted to revert support for that
* I think this is probably preferable since there is a CRAN package supporting this rather than it being a roll your own solution * also does actually give time space savings of 5-15% and does not require memory allocation within R
* currently writes in rds format * should probably consider csv e.g. if writing neurons in SWC rather than rds format
* we will not end up using most of these ...
* just unzipping to tmp works best for small to medium files
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@alexanderbates first pass at storing neuronlists as efficient zip files for random access |
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You can also embed the metadata in the zip so that one file should contain everything.
For 3GB files, I get 20ms per record random access. Faster performance (order 5ms) could be obtained with https://github.com/jefferis/razip. Reading sequential groups of files is much faster.