Use h5 file format with ‘antaresRead’

Installation

To use h5 file format, you must install packages zlibbioc and rhdf5 (>= 2.20.0) from bioconductor. If your proxy allows it, you can use :

With R < 3.5.0, use:

source("https://bioconductor.org/biocLite.R')
biocLite("rhdf5')

With R >= 3.5.0 :

install.packages("BiocManager")
BiocManager::install("rhdf5")

An other solution is to install manualy this two packages from zip file. They are available here : https://bioconductor.org/packages/release/bioc/html/zlibbioc.html http://bioconductor.org/packages/release/bioc/html/rhdf5.html

Avantages of h5 transformation

With h5 file, antaresRead will be running faster. Your reading will take between 2 and 4 times less time. An other avantage is the compression, a study can pass from 15Go in txt to 2.5Go in h5. Furthermore, a h5 transformation convert lot of txt file in a single h5 file, it will be easier to move it, a copy/paste of a study with 137 thousand files (15Go) takes 45 minutes in txt and 30 seconds in h5.

Finally, you can use in the same way function of antaresProcessing and antaresViz packages. You can also use addProcessingH5 function to add columns to your h5 file.

Comparaison between Conventional and H5

Write h5 file from antares study

The function writeAntaresH5 is used to write h5 file from antares output. You can add inputs data like in readAntares.

Basic use

setSimulationPath("study_path/output/simulation_name")
writeAntaresH5()

Add intput data

setSimulationPath("study_path/output/simulation_name")
writeAntaresH5(misc = TRUE, thermalAvailabilities = TRUE,
  hydroStorage = TRUE, hydroStorageMaxPower = TRUE, reserve = TRUE,
  linkCapacity = TRUE, mustRun = TRUE, thermalModulation = TRUE,
  writeAllSimulations = TRUE)

#with a shorcut 
writeAntaresH5(allData = TRUE,
  writeAllSimulations = TRUE)

Overwrite

By default writeAntaresH5 returns an error if the h5 file already exists. You can use overwrite = TRUE.

setSimulationPath("study_path/output/simulation_name")
writeAntaresH5(overwrite = TRUE)

Write all your simulations in parallel

setSimulationPath("study_path/output/simulation_name")
writeAntaresH5(nbCores = 5, writeAllSimulations = TRUE)

Read data from your h5 file

You can use setSimulationPath and readAntares in the same way than on normal study.

setSimulationPath("mySim.h5")
readAntares()
readAntares(areas = "all", links = "all")
readAntares(areas = "all", mcYears = "all")
readAntares(timeStep = "weekly")

Add columns to your h5 file (hourly data only)

You can use function addProcessingH5 from antaresProcessing package.

 library(antaresProcessing)
 opts <- setSimulationPath("mySim.h5")
 addProcessingH5(opts = opts,  mcY = "mcInd",
                addDownwardMargin = TRUE,
                evalAreas = list(Tota = "`H. STOR` + `MISC. DTG`",
                                 Tota2 = "`NODU` + `NP COST` + 1")
                )

For read data after adding addDownwardMargin, you can use alias Out_addDownwardMargin, use showAliases() to see them.

readAntares(mcYears = "all", select = c("Tota", "Tota2"))
readAntares(mcYears = "all", select = "Out_addDownwardMargin")

Use h5 opts for vizualisation

It’s possible to use opts from h5 with all antaresViz modules.

library(antaresViz)
opts <- setSimulationPath("mySim.h5")

prodStack(opts)
plot(opts)
exchangesStack(opts)

#Run on more than one opts :
opts2 <- setSimulationPath("mySim2.h5")
plot(list(opts, opts2))