# Use h5 file format with ‘antaresRead’

#### Titouan Robert

#### 2020-03-18

This document describes use of the `antaresRead` package with h5 file format.

## 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))