Need to read several .h5 files using loop with indices

Question

I have been given a crap ton of files I need to read over and graph. Some of the datasets have more files that other. So I need to write a loop that will do this. The code that I have written so far works but I cannot for the life of me figure out how to index the loop to call the files. I have tried a simple

i <-0 
for (i in files){
i <- i + 1
file_[i] <-H5fopen(files[i])
 }

I have tried other versions but I have changed it so much I can't remember. But when I load the files individually at the bottom. They load So I know that everything before the area where the loop is needed works.


library(data.table)
library(zoo)
library(Rtools)
library(tidyr)
library( dplyr)
library(scales)
library(readr)
library(tools)
library(plotly)
library(rootSolve)
library(stringr)
library(rhdf5)

library( ggplot2)
library(tokenizers)
library(readr)
library(tools)

library(stringr)
library(h5)
options(max.print=10000)
options(digits = 5, scipen = -2)



askUser_file_x <-0
while(askUser_file_x != "none"){

  askUser_file_x <- readline(prompt="Please, type on DS you wish to analyze, else type none (format DS##):   ")


  x <- str_extract(askUser_file_x, "(?<=DS)[0-9]+")
  x <-as.numeric(x) 
if (x==23){
  setwd("/H5files/08/14/")

  }else if  (x>=24 & x<=26){
    setwd("C:/H5files/08/15/")

  }else if  (x>=27 & x<=30){  
    setwd("C:s/H5files/08/21/")
  }else if  (x>=31 & x<=36){  
    setwd("C:/H5files/08/20/")

  }else if  (x>=01 & x<=06){
    setwd("C:/H5files/08/21/")
  }else if  (x>=37 & x<=44){
    setwd("C:/H5files/08/21/")
  }else if  (x>=07 & x<=18){
    setwd("C:/H5files/08/26/")
  }else if  (x>=19 & x<=22){
    setwd("C:/H5files/08/27/")
  }else if  (x>=45 & x<=46){
    setwd("C:/H5files/08/28/")
  }else if  (x>=47 & x<=50){
    setwd("C:/H5files/08/29/")

  }else
    print( "Data Set does not exist")



switch(askUser_file_x,
       DS01= (file <-paste0("TIVA_000",c(282:286))),
       DS03= (file <-paste0("TIVA_000",c(266:271))),
       DS04= (file <-paste0("TIVA_000",c(272:276))),
       DS05= (file <-paste0("TIVA_000",c(277:281))),
       DS06= (file <-paste0("TIVA_000",c(290:294))),
       DS07= (file <-paste0("TIVA_000",c(316:320))),
       DS08 =(file <-paste0("TIVA_000",c(321:325))),
       DS09 =(file <-paste0("TIVA_000",c(326:330))),
       DS10 =(file <-paste0("TIVA_000",c(331:335))),
       DS11 =(file <-paste0("TIVA_000",c(295:300))),
       DS12 =(file <-paste0("TIVA_000",c(301:305))),
       DS13 =(file <-paste0("TIVA_000",c(306:310))),
       DS14 =(file <-paste0("TIVA_000",c(311:315))),
       DS15 =(file <-paste0("TIVA_000",c(336:340))),
       DS16 =(file <-paste0("TIVA_000",c(341:345))),
       DS17 =(file <-paste0("TIVA_000",c(346:350))),
       DS18 =(file <-paste0("TIVA_000",c(351:355))),
       DS19 =(file <-paste0("TIVA_000",c(356:360))),
       DS20 =(file <-paste0("TIVA_000",c(361:365))),
       DS21 =(file <-paste0("TIVA_000",c(366:370))),
       DS22 =(file <-paste0("TIVA_000",c(371:375))),
       DS23 =(file <-paste0("TIVA_000",c(100:115))),
       DS24 =(file <-paste0("TIVA_000",c(116:121))),
       DS25a =(file<-paste0("TIVA_000",c(121:125))),
       DS25b =(file<-paste0("TIVA_000",c(126:130))),
       DS26 =(file<-paste0("TIVA_000",c(131:133))),
       DS27 =(file<-paste0("TIVA_000",c(161:163))),
       DS28a =(file<-paste0("TIVA_000",c(146:150))),
       DS28b =(file<-paste0("TIVA_000",c(156:160))),
       DS29 =(file<-paste0("TIVA_000",c(151:155))),
       DS30 =(file<-paste0("TIVA_000",c(156:160))),
       DS31 =(file<-paste0("TIVA_000",c(164:170))),
       DS32 =(file<-paste0("TIVA_000",c(171:175))),
       DS33 =(file<-paste0("TIVA_000",c(175:180))),
       DS34 =(file<-paste0("TIVA_000",c(181:188))),
       DS35 =(file<-paste0("TIVA_000",c(189:193))),
       DS36 =(file<-paste0("TIVA_000",c(194:198))),
       DS37 =(file<-paste0("TIVA_000",c(199:198))),
       DS38 =(file<-paste0("TIVA_000",c(211:220))),
       DS39a =(file<-paste0("TIVA_000",c(221:230))),
       DS39b =(file<-paste0("TIVA_000",c(231:240))),
       DS40 =(file<-paste0("TIVA_000",c(241:243))),
       DS41 =(file<-paste0("TIVA_000",c(244:245))),
       DS42a =(file<-paste0("TIVA_000",c(246:249))),
       DS43a =(file<-paste0("TIVA_000",c(250:252))),
       DS44 =(file<-paste0("TIVA_000",c(253:255)))

       )

    files <-paste0(file, ".h5")



 ## this is the part I need to loop some DS's have 3-5 files one has eleven

       file_1<- H5Fopen(files[1])  

       file_2<- H5Fopen(files[2])  

       file_3<- H5Fopen(files[3])

       file_4<- H5Fopen(files[4])

      file_5<- H5Fopen(files[5])

      h5ls(file_1)

``````
Edited for clarity

If I choose say DS23 then files becomes [1:6] TIVA_000116.h5 , TIVA_000117.h5, ... 
which is what I want, and if I run ``` file_1<- H5Fopen(files[1])``` it opens the files the way I expect it too. Is there a way  loop over files 
and create something like this 
````
file_1 <- H5Fopen(files[1])  # where file_1 take its name from  i = 1 and  
                             #H5Fopen(files[1]) is selected from the 1 element in the files vector
````
I want it to be able to select them because I have 45 Data sets of 5 files each that have to be created and converted. So I am trying to automate as much as possible. 
THanks in advance

Need to read several .h5 files using loop with indices

Answers (1)

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