if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("rhdf5")


library(rhdf5)

#-----------------------------------------------------------------------------------------------------------------------
# Q1
#-----------------------------------------------------------------------------------------------------------------------
setwd("D:/data_GEDI/export")
files <- list.files(path="D:\data_GEDI\unzip",
                    full.names = T, recursive = T, pattern = ".h5", include.dirs = T) 

beams = c("BEAM0000", "BEAM0001", "BEAM0010", "BEAM0011", "BEAM0101", "BEAM0110", "BEAM1000", "BEAM1011")



#-----------------------------------------------------------------------------------------------------------------------
# file:///F:/__UK_GEDI_DATA_Czechia/_00_GEDI_L2B_DATA_Czechia/gedi_l2b_dictionary_P001_v1.html
#-----------------------------------------------------------------------------------------------------------------------

for (b in beams) {
  
  # The L2B algorithm is run if this flag is set to 1 indicating data have sufficient waveform fidelity for L2B to run
  algorithmrun_flag = vector() 
  
  # Beam identifier
  beam = vector() 
  FLY = vector()
  lat_lowestmode = vector() #Latitude of center of lowest mode
  lon_lowestmode = vector() #Longitude of center of lowest mode
  shot_number  = vector() #Unique shot ID.
  

  for (x in files) {
    
    # b = "BEAM0101"
    #x="F:/__UK_GEDI_DATA/_02_KRNAP_DATA/GEDI_L2A_Downloaded_20210903/2432362146/processed_GEDI02_A_2019112075017_O02026_02_T00059_02_003_01_V002.h5"

    #-----------------------------------------------------------------------
    # OPEN AND READ CONTENTES OF H5 FILE
    #-----------------------------------------------------------------------
    h5f = H5Fopen(x)
    

   
    value <- tryCatch(
      as.vector(h5read(h5f, paste(b, "/geolocation/lat_lowestmode", sep=""))),
      error = function(c) {NA}
    )
    lat_lowestmode <- c(lat_lowestmode, value)
    
    
    value <- tryCatch(
      as.vector(h5read(h5f, paste(b, "/geolocation/lon_lowestmode", sep=""))),
      error = function(c) {NA}
    )
    LENGTH=length(value) #Pocet radku, abych v dalsim kroku tusil kolik jich je treba vytahat
    lon_lowestmode <- c(lon_lowestmode, value)
    print(length(lon_lowestmode))
    
    
    value <- tryCatch(
      as.vector(replicate(n = LENGTH, b)),
      error = function(c) {NA}
    )
    beam <- c(beam, value)
    
    #beam = c(beam, as.vector(replicate(n = length(lon_lowestmode), b))) #Priradi kazdemu radku kterej je to BEAM
    
    
    #value <- tryCatch(
    #  as.vector(h5read(h5f, paste(b, "/shot_number", sep=""), bit64conversion='double')),
    #  error = function(c) {NA}
    #)
    #shot_number <- c(shot_number, value)
    
    
    file_name = strsplit(basename(x), "\\.")[[1]][1]  # odst?ihnu koncovku
    fly_id = strsplit(file_name, "_")[[1]][4]  # vyt?hnu ?as
    
    
     value <- tryCatch(
      as.vector(replicate(n = LENGTH, fly_id)),
     error = function(c) {NA}
    )
     FLY <- c(FLY, value)
    
    
    
     #SHOT_NUMBER = c(SHOT_NUMBER, as.vector(h5read(h5f, paste(b, "/shot_number", sep=""), bit64conversion='double')))
    # BACHA Pouziva 64 bitovej integer a muze dojit ke ztrate dat, vic zde: https://www.bioconductor.org/packages/release/bioc/vignettes/rhdf5/inst/doc/rhdf5.html
  }
  
  #-----------------------------------------------------------------------
  # Export CSV / SHAPEFILE
  #-----------------------------------------------------------------------
  
  #55555
  #print(length(LAT), length(LON), length(CANOPY))
  TEMP <- data.frame( lat_lowestmode, lon_lowestmode, beam, FLY)
  
  target <- paste(basename(b), ".csv", sep = "")
  print(target)
  write.csv(TEMP, target)
  
  H5Fclose(h5f)
}


#z toho jedno velk? csv
#https://stackoverflow.com/questions/30242065/trying-to-merge-multiple-csv-files-in-r

setwd("F:/__UK_GEDI_DATA_Czechia_L2B/_02_Czechia_L2B_CSV/Q4")



library(dplyr)
library(readr)
toutou <- list.files(full.names = TRUE) %>% 
  lapply(read_csv) %>% 
  bind_rows 

#http://sphweb.bumc.bu.edu/otlt/MPH-Modules/BS/R/R-Manual/R-Manual5.html
write.csv(toutou, 'csvelky.csv')