From ea8a4a591baa44cfbac05bb4a898b4ad3ccbbb9a Mon Sep 17 00:00:00 2001
From: "louis.heraut" <louis.heraut@inrae.fr>
Date: Tue, 4 Jan 2022 14:13:33 +0100
Subject: [PATCH] Extract NV rm
---
processing/extractNV.R | 216 -----------------------------------------
1 file changed, 216 deletions(-)
delete mode 100644 processing/extractNV.R
diff --git a/processing/extractNV.R b/processing/extractNV.R
deleted file mode 100644
index 012084e..0000000
--- a/processing/extractNV.R
+++ /dev/null
@@ -1,216 +0,0 @@
-# Usefull library
-library(tools)
-library(dplyr)
-
-
-iRegHydro = c('D'='Affluents du Rhin',
- 'E'="Fleuves côtiers de l'Artois-Picardie",
- 'A'='Rhin',
- 'B'='Meuse',
- 'F'='Seine aval (Marne incluse)',
- 'G'='Fleuves côtiers haut normands',
- 'H'='Seine amont',
- 'I'='Fleuves côtiers bas normands',
- 'J'='Bretagne',
- 'K'='Loire',
- 'L'='Loire',
- 'M'='Loire',
- 'N'='Fleuves côtiers au sud de la Loire',
- 'O'='Garonne',
- 'P'='Dordogne',
- 'Q'='Adour',
- 'R'='Charente',
- 'S'="Fleuves côtiers de l'Adour-Garonne",
- 'U'='Saône',
- 'V'='Rhône',
- 'W'='Isère',
- 'X'='Durance',
- 'Y'='Fleuves côtiers du Rhône-Méditérannée et Corse',
- 'Z'='Îles',
- '1'='Guadeloupe',
- '2'='Martinique',
- '5'='Guyane',
- '6'='Guyane',
- '7'='Guyane',
- '8'='Guyane',
- '9'='Guyane',
- '4'='Réunion')
-
-
-# Extraction of metadata
-extractNVlist_meta = function (computer_data_path, filedir, listdir, listname, verbose=TRUE) {
-
- # Print metadata if asked
- if (verbose) {
- print(paste("extraction of NV meta for file :", listname))
- }
-
- # Get the file path to the list of station
- list_path = file.path(computer_data_path, listdir, listname)
-
- if (file.exists(list_path) & substr(list_path, nchar(list_path), nchar(list_path)) != '/') {
-
- # Extract the data as a data frame
- df_meta = read.table(list_path,
- header=TRUE,
- encoding='UTF-8'
- )
-
- # Create a filelist to store all the filename
- codelist = c()
-
- dir_path = file.path(computer_data_path, filedir)
-
- # Get all the filename in the data directory selected
- filelist_tmp = list.files(dir_path)
-
- # For all the filename in the directory selected
- for (f in filelist_tmp) {
- # If the filename extention is 'txt'
- if (file_ext(f) == 'txt') {
- # Store the filename in the filelist
- codelist = c(codelist, gsub('.txt', '', f))
- }
- }
-
- exist = df_meta$CODE %in% codelist
- missing = codelist[!(codelist %in% df_meta$CODE)]
-
- # Display stations for which it misses metadata
- print(paste('missing station meta for :', missing))
-
- df_meta = df_meta[exist,]
-
- # Create a tibble with all the metadata needed
- df_meta =
- tibble(code=as.character(df_meta$CODE),
- nom=as.character(df_meta$NOM),
- L93X=df_meta$X_L2E,
- L93Y=df_meta$Y_L2E,
- surface_km2=df_meta$S_km2,
- altitude_m=df_meta$Alt,
- file_path=file.path(dir_path,
- paste(df_meta$CODE, '.txt', sep='')),
- source='NV',
- )
-
- df_meta = bind_rows(df_meta,
- data.frame(code=missing,
- file_path=file.path(dir_path,
- paste(missing,
- '.txt',
- sep=''))))
-
- df_meta = df_meta[order(df_meta$code),]
-
- df_meta$region_hydro = iRegHydro[substr(df_meta$code, 1, 1)]
-
- } else {
- print(paste('filename', list_path, 'do not exist'))
- return (NULL)
- }
-
- return (df_meta)
-}
-
-# Example
-# df_meta = extractNVlist_meta(
-# "/home/louis/Documents/bouleau/INRAE/CDD_stationnarite/data",
-# 'France207',
-# '',
-# 'liste_bv_principaux_global.txt')
-
-
-# Extraction of data
-extractNV_data = function (computer_data_path, filedir, filename, verbose=TRUE) {
-
- # Convert the filename in vector
- filename = c(filename)
-
- # If the filename is 'all' or regroup more than one filename
- if (all(filename == 'all') | length(filename) > 1) {
-
- # If the filename is 'all'
- if (all(filename == 'all')) {
- # Create a filelist to store all the filename
- filelist = c()
- # Get all the filename in the data directory selected
- filelist_tmp = list.files(file.path(computer_data_path,
- filedir))
-
- # For all the filename in the directory selected
- for (f in filelist_tmp) {
- # If the filename extention is 'txt'
- if (file_ext(f) == 'txt') {
- # Store the filename in the filelist
- filelist = c(filelist, f)
- }
- }
- # If the filename regroup more than one filename
- } else if (length(filename > 1)) {
- # The filelist correspond to the filename
- filelist = filename
- }
-
- # Create a blank data frame
- df_data = data.frame()
-
- # For all the file in the filelist
- for (f in filelist) {
-
- # Concatenate by raw data frames created by this function when filename correspond to only one filename
- df_data = rbind(df_data,
- extractNV_data(computer_data_path,
- filedir,
- f))
- }
-
- # Set the rownames by default (to avoid strange numbering)
- rownames(df_data) = NULL
- return (df_data)
- }
-
- # Get the filename from the vector
- filename = filename[1]
-
- # Print metadata if asked
- if (verbose) {
- print(paste("extraction of NV data for file :", filename))
- }
-
- # Get the file path to the data
- file_path = file.path(computer_data_path, filedir, filename)
-
- if (file.exists(file_path) & substr(file_path, nchar(file_path), nchar(file_path)) != '/') {
-
- # Extract the data as a data frame
- df_data = read.table(file_path,
- header=FALSE,
- skip=1,
- na.strings=c('-1', '-99.000'))
-
- # Create a tibble with the date as Date class and the code of the station
- date = paste(df_data[,1],
- df_data[,2],
- df_data[,3],
- sep='-')
-
- df_data = tibble(Date=as.Date(as.character(date),
- format="%Y-%m-%d"),
- Qm3s=df_data[,4],
- QCode=df_data[,5],
- code=gsub('.txt', '', filename))
-
- return (df_data)
-
- } else {
- print(paste('filename', file_path, 'do not exist'))
- return (NULL)
- }
-}
-
-# Example
-# df_data = extractNV_data(
- # "/home/louis/Documents/bouleau/INRAE/CDD_stationnarite/data",
- # 'France207',
- # c('O0015310.txt', 'Q0214010.txt', 'P0115020.txt'))
--
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