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## ----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()
## ---- check-h5dump, echo = FALSE, include = FALSE-----------------------------
## error code 127 indicate the command could not be run
h5dump_found <- (system2('h5dump') != 127)
## ---- warning = FALSE, eval = h5dump_found------------------------------------
# ## 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 = h5dump_found--------------------------
# h5dump_out <- system2('h5dump',
# args = c('-p', '-d /dset', blosc_file),
# stdout = TRUE, stderr = TRUE)
# cat(h5dump_out, sep = "\n")
## ---- h5dump-1-out, eval = !h5dump_found, 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 = h5dump_found--------------------------------------------
# ## 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 = !h5dump_found, 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()
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