## ----filter-pipeline, echo = FALSE, fig.cap="The default compression pipeline used by rhdf5"---- knitr::include_graphics("filter_pipeline.png") ## ----plugin-path, eval = TRUE------------------------------------------------- rhdf5filters::hdf5_plugin_path() ## ----warning = FALSE, eval = FALSE-------------------------------------------- # ## blosc compressed file # blosc_file <- system.file("h5examples/h5ex_d_blosc.h5", # package = "rhdf5filters") # ## unset environment variable # Sys.setenv("HDF5_PLUGIN_PATH" = "") ## ----h5dump-1, warning = FALSE, eval = FALSE---------------------------------- # h5dump_out <- system2('h5dump', # args = c('-p', '-d /dset', blosc_file), # stdout = TRUE, stderr = TRUE) # cat(h5dump_out, sep = "\n") ## ----h5dump-1-out, eval = TRUE, echo = FALSE---------------------------------- cat( 'HDF5 "rhdf5filters/h5examples/h5ex_d_blosc.h5" { DATASET "/dset" { DATATYPE H5T_IEEE_F32LE DATASPACE SIMPLE { ( 30, 10, 20 ) / ( 30, 10, 20 ) } STORAGE_LAYOUT { CHUNKED ( 10, 10, 20 ) SIZE 3347 (7.171:1 COMPRESSION) } FILTERS { USER_DEFINED_FILTER { FILTER_ID 32001 COMMENT blosc PARAMS { 2 2 4 8000 4 1 0 } } } FILLVALUE { FILL_TIME H5D_FILL_TIME_IFSET VALUE H5D_FILL_VALUE_DEFAULT } ALLOCATION_TIME { H5D_ALLOC_TIME_INCR } DATA {h5dump error: unable to print data } } }' ) ## ----h5dump-2, eval = FALSE--------------------------------------------------- # ## set environment variable to hdf5filter location # Sys.setenv("HDF5_PLUGIN_PATH" = rhdf5filters::hdf5_plugin_path()) # h5dump_out <- system2('h5dump', # args = c('-p', '-d /dset', '-w 50', blosc_file), # stdout = TRUE, stderr = TRUE) # # ## find the data entry and print the first few lines # DATA_line <- grep(h5dump_out, pattern = "DATA \\{") # cat( h5dump_out[ (DATA_line):(DATA_line+2) ], sep = "\n" ) ## ----h5dump-2-out, eval = TRUE, echo = FALSE---------------------------------- cat( ' DATA { (0,0,0): 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, (0,0,11): 11, 12, 13, 14, 15, 16, 17, 18,' ) ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()