Initial commit

README.txt

+
+install argparser
+"""
+$ git clone https://bitbucket.org/djhshih/argparser.git
+$ cd argparser
+$ R
+
+R> library(roxygen2)
+R> roxygenize()
+R> quit()
+
+$ R CMD INSTALL .
+"""
+
+library('here')

init.R

+#' Initialization of global environnemental variable
+#' 
+#' @param x A number.
+#' @param y A number.
+#' @return The sum of \code{x} and \code{y}.
+#' @examples
+#' add(1, 1)
+#' add(10, 1)
+
+
+# Computer informations
+data_path = c(louis="/home/louis/Documents/bouleau/INRAE/CDD_stationnarite/data",
+              other='...')
+work_path = c(louis="/home/louis/Documents/bouleau/INRAE/CDD_stationnarite/ASH",
+              other='.../ASH')
+
+user = Sys.getenv('USER')
+
+# Path to the data
+computer_data_path = data_path[user]
+print(paste('computer_data_path :', computer_data_path))
+
+# Work path
+computer_work_path = work_path[user]
+setwd(computer_work_path)
+print(paste('computer_work_path :', computer_work_path))
+
+# Output directory
+res_dir = file.path(computer_work_path, 'results')
+print(paste('res_dir :', res_dir))
+fig_dir = file.path(computer_work_path, 'figures')
+print(paste('fig_dir :', fig_dir))
+print('')

init.R~

+#' Initialization of global environnemental variable
+#' 
+#' @param x A number.
+#' @param y A number.
+#' @return The sum of \code{x} and \code{y}.
+#' @examples
+#' add(1, 1)
+#' add(10, 1)
+
+
+# Computer informations
+data_path = c(louis="/home/louis/Documents/bouleau/INRAE/CDD_stationnarite/data",
+              other='...')
+work_path = c(louis="/home/louis/Documents/bouleau/INRAE/CDD_stationnarite/ASH",
+              other='.../ASH')
+
+user = Sys.getenv('USER')
+
+# Path to the data
+computer_data_path = data_path[user]
+print(paste('computer_data_path :', computer_data_path, sep=' '))
+
+# Work path
+computer_work_path = work_path[user]
+setwd(computer_work_path)
+print(paste('computer_work_path :', computer_work_path, sep=' '))
+
+# Output directory
+res_dir = 'results/'
+print(paste('res_dir : ', res_dir, sep=''))
+fig_dir = 'figures/'
+print(paste('fig_dir : ', fig_dir, sep=''))
+print('')

plotting/panel.R

+library(here)
+
+source(file.path(dirname(here()), 'init.R'))
+source(file.path(dirname(here()), 'processing', 'extract.R'))
+
+
+# Time panel
+panel = function (filedir, filename, pan) {
+    
+    file_path = file.path(computer_data_path, filedir, filename)
+    
+    for (p in pan) {
+        # If there is not a dedicated figure directory it creats one
+        out_dir = file.path(res_dir, filedir)
+        if (!(file.exists(out_dir))) {
+            dir.create(out_dir)
+        }
+        
+        # Get info
+        info = extract_info(filedir, filename)
+
+        # Create name for the figure file
+        out_file = paste('Panel_', info$code, '.png', sep='')
+
+        # Extract data
+        data = extract_data(filedir, filename)
+        
+
+
+
+
+    }
+ 
+    return (NA)
+}
+
+# panel('', 'H5920011_HYDRO_QJM.txt')

plotting/panel.R~

+library(here)
+
+source(file.path(dirname(here()), 'init.R'))
+source(file.path(dirname(here()), 'processing', 'extract.R'))
+
+
+# Time panel
+panel = function (filedirs, filenames, pan) {
+    
+    file_path = file.path(computer_data_path, filedirs, filenames)
+    
+    for (p in pan) {
+        # If there is not a dedicated figure directory it creats one
+        out_dir = file.path(res_dir, filedirs)
+        if (!(file.exists(out_dir))) {
+            dir.create(out_dir)
+        }
+        
+        # Get info
+        info = extract_info(filedirs, filenames)
+
+        # Create name for the figure file
+        out_file = paste('Panel_', info$code, '.png', sep='')
+
+        # Extract data
+        data = extract_data(filedirs, filenames)
+        
+
+
+
+
+    }
+ 
+    return (NA)
+}
+
+# panel('', 'H5920011_HYDRO_QJM.txt')

processing/#extract.R#

+library(here)
+library(tools)
+source(file.path(dirname(here()), 'init.R'))
+
+
+# Extraction of data
+extract_data = function (filedir, filename) {
+    
+    data_path = file.path(computer_data_path, filedir, filename)
+
+    data = read.table(data_path,
+                      header=TRUE,
+                      na.strings=c('-99.000', '-99'),
+                      sep=';',
+                      skip=41)[,1:2] 
+
+    return (data=data)
+}
+
+# data = extract_data('', 'H5920011_HYDRO_QJM.txt')
+
+
+# Extraction of information
+extract_info = function (filedir, filename) {
+    
+    data_path = file.path(computer_data_path, filedir, filename)
+
+    # General information on station
+    iStatut = c('0'='inconnu', 
+                '1'='station avec signification hydrologique', 
+                '2'='station sans signification hydrologique', 
+                '3'="station d'essai")
+
+    iFinalite = c('0'='inconnue', 
+                  '1'="hydrométrie générale", 
+                  '2'='alerte de crue', 
+                  '3'="hydrométrie générale et alerte de crue",
+                  '4'="gestion d'ouvrage", 
+                  '5'='police des eaux', 
+                  '6'="suivi d'étiage", 
+                  '7'='bassin expérimental', 
+                  '8'='drainage')
+
+    iType = c('0'='inconnu',
+              '1'='une échelle',
+              '2'='deux échelles, station mère',
+              '3'='deux échelles, station fille',
+              '4'='débits mesurés',
+              '5'='virtuelle')
+
+    iInfluence = c('0'='inconnue',
+                   '1'='nulle ou faible',
+                   '2'='en étiage seulement',
+                   '3'='forte en toute saison')
+
+    iDebit = c('0'='reconstitué',
+               '1'="réel (prise en compte de l'eau rajoutée ou retirée du bassin selon aménagements)",
+               '2'='naturel')
+
+    iQBE = c('0'='qualité basses eaux inconnue',
+             '1'='qualité basses eaux bonne',
+             '2'='qualité basses eaux douteuse')
+
+    iQME = c('0'='qualité moyennes eaux inconnue',
+             '1'='qualité moyennes eaux bonne',
+             '2'='qualité moyennes eaux douteuse')
+
+    iQHE = c('0'='qualité hautes eaux inconnue',
+             '1'='qualité hautes eaux bonne',
+             '2'='qualité hautes eaux douteuse')
+
+    data_path = file.path(computer_data_path, filedir, filename)
+
+    infotxt = c(readLines(data_path, n=41))
+    
+    info = list(code=trimws(substr(infotxt[11], 38, nchar(infotxt[11]))),
+                nom=trimws(substr(infotxt[12], 39, nchar(infotxt[12]))),
+                territoire=trimws(substr(infotxt[13], 39, nchar(infotxt[13]))),
+                L93X=as.numeric(substr(infotxt[16], 38, 50)),
+                L93Y=as.numeric(substr(infotxt[16], 52, 63)),
+                surface=as.numeric(substr(infotxt[19], 38, 50)),
+                statut=iStatut[trimws(substr(infotxt[26], 38, 50))],
+                finalite=iFinalite[trimws(substr(infotxt[26], 52, 56))],
+                type=iType[trimws(substr(infotxt[26], 58, 58))],
+                influence=iInfluence[trimws(substr(infotxt[26], 60, 60))],
+                debit=iDebit[trimws(substr(infotxt[26], 62, 62))],
+                QBE=iQBE[trimws(substr(infotxt[26], 72, 72))],
+                QME=iQME[trimws(substr(infotxt[26], 74, 74))],
+                QHE=iQHE[trimws(substr(infotxt[26], 76, 76))]
+                )
+ 
+    return (info=info)
+}
+
+# info = extract_info('', 'H5920011_HYDRO_QJM.txt')
+
+
+# Extraction and dataframing
+extract_df = function (filedir, filename) {
+    
+    if (filename == 'all') {
+        filelist = c()
+        for (f in list.files(file.path(filedir))) {
+            if (file_ext(f) == 'txt') {
+               filelist = c(filelist, f) 
+            }
+            
+        }
+    }
+    
+    data_path = file.path(computer_data_path, filedir, filename)
+    info = extract_info(filedir, filename)
+    df = data.frame(info, data_path=data_path)
+    
+    return (df)
+}
+
+# df = extract_df('', 'H5920011_HYDRO_QJM.txt')

processing/.#extract.R

+louis@botan.31363:1636457477
\ No newline at end of file

processing/.Rhistory

+data

processing/extract.R

+library(here)
+library(tools)
+source(file.path(dirname(here()), 'init.R'))
+
+
+# Extraction of data
+extract_data = function (filedir, filename) {
+    
+    data_path = file.path(computer_data_path, filedir, filename)
+
+    data = read.table(data_path,
+                      header=TRUE,
+                      na.strings=c('-99.000', '-99'),
+                      sep=';',
+                      skip=41)[,1:2] 
+
+    return (data=data)
+}
+
+# data = extract_data('', 'H5920011_HYDRO_QJM.txt')
+
+
+# Extraction of information
+extract_info = function (filedir, filename) {
+    
+    data_path = file.path(computer_data_path, filedir, filename)
+
+    # General information on station
+    iStatut = c('0'='inconnu', 
+                '1'='station avec signification hydrologique', 
+                '2'='station sans signification hydrologique', 
+                '3'="station d'essai")
+
+    iFinalite = c('0'='inconnue', 
+                  '1'="hydrométrie générale", 
+                  '2'='alerte de crue', 
+                  '3'="hydrométrie générale et alerte de crue",
+                  '4'="gestion d'ouvrage", 
+                  '5'='police des eaux', 
+                  '6'="suivi d'étiage", 
+                  '7'='bassin expérimental', 
+                  '8'='drainage')
+
+    iType = c('0'='inconnu',
+              '1'='une échelle',
+              '2'='deux échelles, station mère',
+              '3'='deux échelles, station fille',
+              '4'='débits mesurés',
+              '5'='virtuelle')
+
+    iInfluence = c('0'='inconnue',
+                   '1'='nulle ou faible',
+                   '2'='en étiage seulement',
+                   '3'='forte en toute saison')
+
+    iDebit = c('0'='reconstitué',
+               '1'="réel (prise en compte de l'eau rajoutée ou retirée du bassin selon aménagements)",
+               '2'='naturel')
+
+    iQBE = c('0'='qualité basses eaux inconnue',
+             '1'='qualité basses eaux bonne',
+             '2'='qualité basses eaux douteuse')
+
+    iQME = c('0'='qualité moyennes eaux inconnue',
+             '1'='qualité moyennes eaux bonne',
+             '2'='qualité moyennes eaux douteuse')
+
+    iQHE = c('0'='qualité hautes eaux inconnue',
+             '1'='qualité hautes eaux bonne',
+             '2'='qualité hautes eaux douteuse')
+
+    data_path = file.path(computer_data_path, filedir, filename)
+
+    infotxt = c(readLines(data_path, n=41))
+    
+    info = list(code=trimws(substr(infotxt[11], 38, nchar(infotxt[11]))),
+                nom=trimws(substr(infotxt[12], 39, nchar(infotxt[12]))),
+                territoire=trimws(substr(infotxt[13], 39, nchar(infotxt[13]))),
+                L93X=as.numeric(substr(infotxt[16], 38, 50)),
+                L93Y=as.numeric(substr(infotxt[16], 52, 63)),
+                surface=as.numeric(substr(infotxt[19], 38, 50)),
+                statut=iStatut[trimws(substr(infotxt[26], 38, 50))],
+                finalite=iFinalite[trimws(substr(infotxt[26], 52, 56))],
+                type=iType[trimws(substr(infotxt[26], 58, 58))],
+                influence=iInfluence[trimws(substr(infotxt[26], 60, 60))],
+                debit=iDebit[trimws(substr(infotxt[26], 62, 62))],
+                QBE=iQBE[trimws(substr(infotxt[26], 72, 72))],
+                QME=iQME[trimws(substr(infotxt[26], 74, 74))],
+                QHE=iQHE[trimws(substr(infotxt[26], 76, 76))]
+                )
+ 
+    return (info=info)
+}
+
+# info = extract_info('', 'H5920011_HYDRO_QJM.txt')
+
+
+# Extraction and dataframing
+extract_df = function (filedir, filename) {
+    
+    if (filename == 'all') {
+        filelist = c()
+        for (f in list.files()) {
+            if (file_ext() == 'txt') {
+               filelist = c(filelist, f) 
+            }
+            
+        }
+    }
+    
+    data_path = file.path(computer_data_path, filedir, filename)
+    info = extract_info(filedir, filename)
+    df = data.frame(info, data_path=data_path)
+    
+    return (df)
+}
+
+# df = extract_df('', 'H5920011_HYDRO_QJM.txt')

processing/extract.R~

+library(here)
+source(file.path(dirname(here()), 'init.R'))
+
+
+# Extraction of data
+extract_data = function (filedirs, filenames) {
+    file_path = file.path(computer_data_path, filedirs, filenames)
+
+    data = read.table(file_path,
+                      header=TRUE,
+                      na.strings=c('-99.000', '-99'),
+                      sep=';',
+                      skip=41)[,1:2] 
+
+    return (data=data)
+}
+
+# data = extract_data('', 'H5920011_HYDRO_QJM.txt')
+
+
+# Extraction of information
+extract_info = function (filedirs, filenames) {                                    
+    # General information on station
+    iStatut = c('0'='inconnu', 
+                '1'='station avec signification hydrologique', 
+                '2'='station sans signification hydrologique', 
+                '3'="station d'essai")
+
+    iFinalite = c('0'='inconnue', 
+                  '1'="hydrométrie générale", 
+                  '2'='alerte de crue', 
+                  '3'="hydrométrie générale et alerte de crue",
+                  '4'="gestion d'ouvrage", 
+                  '5'='police des eaux', 
+                  '6'="suivi d'étiage", 
+                  '7'='bassin expérimental', 
+                  '8'='drainage')
+
+    iType = c('0'='inconnu',
+              '1'='une échelle',
+              '2'='deux échelles, station mère',
+              '3'='deux échelles, station fille',
+              '4'='débits mesurés',
+              '5'='virtuelle')
+
+    iInfluence = c('0'='inconnue',
+                   '1'='nulle ou faible',
+                   '2'='en étiage seulement',
+                   '3'='forte en toute saison')
+
+    iDebit = c('0'='reconstitué',
+               '1'="réel (prise en compte de l'eau rajoutée ou retirée du bassin selon aménagements)",
+               '2'='naturel')
+
+    iQBE = c('0'='qualité basses eaux inconnue',
+             '1'='qualité basses eaux bonne',
+             '2'='qualité basses eaux douteuse')
+
+    iQME = c('0'='qualité moyennes eaux inconnue',
+             '1'='qualité moyennes eaux bonne',
+             '2'='qualité moyennes eaux douteuse')
+
+    iQHE = c('0'='qualité hautes eaux inconnue',
+             '1'='qualité hautes eaux bonne',
+             '2'='qualité hautes eaux douteuse')
+
+    file_path = file.path(computer_data_path, filedirs, filenames)
+
+    infotxt = c(readLines(file_path, n=41))
+    
+    info = list(code=trimws(substr(infotxt[11], 38, nchar(infotxt[11]))),
+                nom=trimws(substr(infotxt[12], 39, nchar(infotxt[12]))),
+                territoire=trimws(substr(infotxt[13], 39, nchar(infotxt[13]))),
+                L93X=as.numeric(substr(infotxt[16], 38, 50)),
+                L93Y=as.numeric(substr(infotxt[16], 52, 63)),
+                surface=as.numeric(substr(infotxt[19], 38, 50)),
+                statut=iStatut[trimws(substr(infotxt[26], 38, 50))],
+                finalite=iFinalite[trimws(substr(infotxt[26], 52, 56))],
+                type=iType[trimws(substr(infotxt[26], 58, 58))],
+                influence=iInfluence[trimws(substr(infotxt[26], 60, 60))],
+                debit=iDebit[trimws(substr(infotxt[26], 62, 62))],
+                QBE=iQBE[trimws(substr(infotxt[26], 72, 72))],
+                QME=iQME[trimws(substr(infotxt[26], 74, 74))],
+                QHE=iQHE[trimws(substr(infotxt[26], 76, 76))]
+                )
+ 
+    return (info=info)
+}
+
+# info = extract_info('', 'H5920011_HYDRO_QJM.txt')

script_analyse.R

+#!/usr/bin/env Rscript
+
+library(here)
+library(argparser, quietly=TRUE)
+
+source(file.path(dirname(here()), 'init.R'))
+
+# Create a parser
+p = arg_parser("Analyse data.")
+
+# Add command line arguments
+p = add_argument(p, '--filedir',
+                 type="character",
+                 help="Directory(ies) in the data directory to search for data.")
+
+p = add_argument(p, '--filename',
+                 type="character",
+                 help="Filename(s) in the data directory to search for data. If 'all', the whole directory(ies) will used.")
+
+
+# Parse the command line arguments
+argv = parse_args(p)
+
+# Run approriate function

script_analyse.R~

+#!/usr/bin/env Rscript
+
+library(here)
+library(argparser, quietly=TRUE)
+
+source(file.path(dirname(here()), 'init.R'))
+
+# Create a parser
+p = arg_parser("Analyse data.")
+
+# Add command line arguments
+p = add_argument(p, '--filedirs',
+                 type="character",
+                 help="Directory(ies) in the data directory to search for data.")
+
+p = add_argument(p, '--filenames',
+                 type="character",
+                 help="Filename(s) in the data directory to search for data. If 'all', the whole directory(ies) will used.")
+
+
+# Parse the command line arguments
+argv = parse_args(p)
+
+# Run approriate function

script_new_user.R

+#!/usr/bin/env Rscript
+
+library(here)
+library(argparser, quietly=TRUE) 
+
+setwd(here())
+
+# Create a parser
+p = arg_parser("Add a new user to the environment with is work and data path.")
+
+# Add command line arguments
+p = add_argument(p, '--data_dir',
+                 type="character",
+                 help="Data directory.")
+
+p = add_argument(p, '--work_dir',
+                 type="character",
+                 help="Working directory.")
+
+# Parse the command line arguments
+argv = parse_args(p)
+
+# Create path file
+user = Sys.getenv('USER')
+computer_data_path = c(argv$data_dir)
+computer_work_path = c(argv$work_dir)
+
+if (file.exists('path.txt')) {
+     computer_path = read.table('path.txt', sep=';')
+     if (!any(computer_path$user == user)) {
+         computer_path = rbind(computer_path, c(user, 
+                                                computer_data_path,
+                                                computer_work_path))
+         } else {
+             stop("User already register")            
+         }
+} else {
+    computer_path = data.frame(user=user,
+                               computer_data_path=computer_data_path,
+                               computer_work_path=computer_work_path)
+    print(paste('New user:', user, sep=' '))
+}
+
+write.table(computer_path, file='path.txt', sep=';')

script_new_user.R~

+#!/usr/bin/env Rscript
+
+library(here)
+library(argparser, quietly=TRUE) 
+library(stringr)
+
+setwd(here())
+
+# Create a parser
+p = arg_parser("Add a new user to the environment with is work and data path.")
+
+# Add command line arguments
+p = add_argument(p, '--data_dir',
+                 type="character",
+                 help="Data directory.")
+
+p = add_argument(p, '--work_dir',
+                 type="character",
+                 help="Working directory.")
+
+# Parse the command line arguments
+argv = parse_args(p)
+
+# Create path file
+user = Sys.getenv('USER')
+computer_data_path = c(argv$data_dir)
+computer_work_path = c(argv$work_dir)
+
+if (file.exists('path.txt')) {
+     computer_path = read.table('path.txt', sep=';')
+     if (!any(computer_path$user == user)) {
+         computer_path = rbind(computer_path, c(user, 
+                                                computer_data_path,
+                                                computer_work_path))
+         } else {
+             stop("User already register")            
+         }
+} else {
+    computer_path = data.frame(user=user,
+                               computer_data_path=computer_data_path,
+                               computer_work_path=computer_work_path)
+    print(paste('New user:', user, sep=' '))
+}
+
+write.table(computer_path, file='path.txt', sep=';')

script_plot.R

+#!/usr/bin/env Rscript
+
+library(here)
+library(argparser, quietly=TRUE)
+
+source(file.path(here(), 'init.R'))
+
+# Create a parser
+p = arg_parser("Plot data.")
+
+# Add command line arguments
+p = add_argument(p, '--filedir',
+                 type="character",
+                 help="Directory(ies) in the data directory to search for data.")
+
+p = add_argument(p, '--filename',
+                 type="character",
+                 help="Filename(s) in the data directory to search for data. If 'all', the whole directory(ies) will used.")
+
+p = add_argument(p, '--panel',
+                 type="numeric",
+                 nargs=Inf,
+                 help="Time span in day of simple time panel.")
+
+# Parse the command line arguments
+argv = parse_args(p)
+
+# Run approriate function
+
+print(argv$panel)
+
+if (any(!is.na(argv$panel))) {
+    for (pan in argv$panel) {
+        print('aaa')
+
+    }
+}

script_plot.R~

+#!/usr/bin/env Rscript
+
+library(here)
+library(argparser, quietly=TRUE)
+
+source(file.path(here(), 'init.R'))
+
+# Create a parser
+p = arg_parser("Plot data.")
+
+# Add command line arguments
+p = add_argument(p, '--filedirs',
+                 type="character",
+                 help="Directory(ies) in the data directory to search for data.")
+
+p = add_argument(p, '--filenames',
+                 type="character",
+                 help="Filename(s) in the data directory to search for data. If 'all', the whole directory(ies) will used.")
+
+p = add_argument(p, '--panel',
+                 type="numeric",
+                 nargs=Inf,
+                 help="Time span in day of simple time panel.")
+
+# Parse the command line arguments
+argv = parse_args(p)
+
+# Run approriate function
+
+print(argv$panel)
+
+if (any(!is.na(argv$panel))) {
+    for (pan in argv$panel) {
+        print('aaa')
+
+    }
+}