From 0013da4b06d4037e1a2f42c150dfbc18788576e1 Mon Sep 17 00:00:00 2001
From: "louis.heraut" <louis.heraut@inrae.fr>
Date: Wed, 10 Nov 2021 14:49:29 +0100
Subject: [PATCH] New structure
---
README.txt | 14 +--
init.R | 33 -------
plotting/panel.R | 44 ++++-----
processing/.#extract.R | 1 -
processing/extract.R | 209 +++++++++++++++++++++++++----------------
processing/read.R | 0
script_analyse.R | 24 -----
script_new_user.R | 44 ---------
script_plot.R | 37 --------
9 files changed, 145 insertions(+), 261 deletions(-)
delete mode 100644 init.R
delete mode 120000 processing/.#extract.R
delete mode 100644 processing/read.R
delete mode 100644 script_analyse.R
delete mode 100644 script_new_user.R
delete mode 100644 script_plot.R
diff --git a/README.txt b/README.txt
index 304328f..9a49439 100644
--- a/README.txt
+++ b/README.txt
@@ -1,15 +1,7 @@
-install argparser
-"""
-$ git clone https://bitbucket.org/djhshih/argparser.git
-$ cd argparser
-$ R
-R> library(roxygen2)
-R> roxygenize()
-R> quit()
+tools
-$ R CMD INSTALL .
-"""
+install_github("https://github.com/benRenard/BFunk")
-library('here')
+install.packages("ggplot2")
diff --git a/init.R b/init.R
deleted file mode 100644
index ef9d558..0000000
--- a/init.R
+++ /dev/null
@@ -1,33 +0,0 @@
-#' 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('')
diff --git a/plotting/panel.R b/plotting/panel.R
index 0c84294..d614239 100644
--- a/plotting/panel.R
+++ b/plotting/panel.R
@@ -1,37 +1,25 @@
-library(here)
-
-source(file.path(dirname(here()), 'init.R'))
-source(file.path(dirname(here()), 'processing', 'extract.R'))
-
+library(ggplot2)
# Time panel
-panel = function (filedir, filename, pan) {
+panel = function (df_data, df_info, figdir, filedir, span=Inf) {
+
+ # If there is not a dedicated figure directory it creats one
+ outdir = file.path(figdir, filedir, paste('span_', as.character(span), '_years', sep=''))
+ if (!(file.exists(outdir))) {
+ dir.create(outdir)
+ }
- file_path = file.path(computer_data_path, filedir, filename)
+ # Create name for the figure file
+ outfile = paste('Panel_', df_info$code, '.png', sep='')
- for (p in pan) {
- # If there is not a dedicated figure directory it creats one
- out_dir = file.path(res_dir, filedir)
- if (!(file.exists(out_dir))) {
- dir.create(out_dir)
- }
-
- # Get info
- info = extract_info(filedir, filename)
-
- # Create name for the figure file
- out_file = paste('Panel_', info$code, '.png', sep='')
-
- # Extract data
- data = extract_data(filedir, filename)
-
+ plot =
+ ggplot(df_data, aes(x=Date, y=Qls)) +
+ geom_line()
+
+ return (plot)
+}
- }
-
- return (NA)
-}
-# panel('', 'H5920011_HYDRO_QJM.txt')
diff --git a/processing/.#extract.R b/processing/.#extract.R
deleted file mode 120000
index c0b140a..0000000
--- a/processing/.#extract.R
+++ /dev/null
@@ -1 +0,0 @@
-louis@botan.31363:1636457477
\ No newline at end of file
diff --git a/processing/extract.R b/processing/extract.R
index 067a91e..e7c593d 100644
--- a/processing/extract.R
+++ b/processing/extract.R
@@ -1,77 +1,84 @@
-library(here)
library(tools)
-source(file.path(dirname(here()), 'init.R'))
+# 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')
-# 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)
-}
+# Extraction of information
+extract_info = function (data_path, filedir, filename) {
-# data = extract_data('', 'H5920011_HYDRO_QJM.txt')
+ filename = c(filename)
+
+ if (all(filename == 'all') | length(filename) > 1) {
+ if (all(filename == 'all')) {
+ filelist = c()
+ filelist_tmp = list.files(file.path(data_path,
+ filedir))
+ for (f in filelist_tmp) {
+ if (file_ext(f) == 'txt') {
+ filelist = c(filelist, f)
+ }
+ }
+ } else if (length(filename > 1)) {
+ filelist = filename
+ }
+ df_info = data.frame()
+ for (f in filelist) {
+ df_info = rbind(df_info,
+ extract_info(data_path,
+ filedir,
+ f)
+ )
+ }
+ rownames(df_info) = NULL
+ return (df_info)
+ }
+ filename = filename[1]
-# 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))
+ file_path = file.path(data_path, filedir, filename)
+ 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]))),
@@ -88,31 +95,67 @@ extract_info = function (filedir, filename) {
QME=iQME[trimws(substr(infotxt[26], 74, 74))],
QHE=iQHE[trimws(substr(infotxt[26], 76, 76))]
)
-
- return (info=info)
+
+ df_info = data.frame(info, file_path=file_path)
+
+ return (df_info)
}
-# info = extract_info('', 'H5920011_HYDRO_QJM.txt')
+# df_info = extract_info(
+# "/home/louis/Documents/bouleau/INRAE/CDD_stationnarite/data",
+# '',
+# c('H5920011_HYDRO_QJM.txt', 'K4470010_HYDRO_QJM.txt'))
-# Extraction and dataframing
-extract_df = function (filedir, filename) {
+# Extraction of data
+extract_data = function (data_path, filedir, filename) {
- if (filename == 'all') {
- filelist = c()
- for (f in list.files()) {
- if (file_ext() == 'txt') {
- filelist = c(filelist, f)
+ filename = c(filename)
+
+ if (all(filename == 'all') | length(filename) > 1) {
+ if (all(filename == 'all')) {
+ filelist = c()
+ filelist_tmp = list.files(file.path(data_path,
+ filedir))
+ for (f in filelist_tmp) {
+ if (file_ext(f) == 'txt') {
+ filelist = c(filelist, f)
+ }
}
-
+ } else if (length(filename > 1)) {
+ filelist = filename
+ }
+ df_data = data.frame()
+ for (f in filelist) {
+ df_data = rbind(df_data,
+ extract_data(data_path,
+ filedir,
+ f)
+ )
}
+ rownames(df_data) = NULL
+ return (df_data)
}
+
+ filename = filename[1]
+
+ file_path = file.path(data_path, filedir, filename)
- data_path = file.path(computer_data_path, filedir, filename)
- info = extract_info(filedir, filename)
- df = data.frame(info, data_path=data_path)
+ df_data = read.table(file_path,
+ header=TRUE,
+ na.strings=c(' -99'),
+ sep=';',
+ skip=41)[,1:2]
- return (df)
+ df_info = extract_info(data_path, filedir, filename)
+ code = df_info$code
+
+ df_data = cbind(df_data, code=code)
+
+ return (df_data)
}
-# df = extract_df('', 'H5920011_HYDRO_QJM.txt')
+# df_data = extract_data(
+ # "/home/louis/Documents/bouleau/INRAE/CDD_stationnarite/data",
+ # '',
+ # c('H5920011_HYDRO_QJM.txt', 'K4470010_HYDRO_QJM.txt'))
diff --git a/processing/read.R b/processing/read.R
deleted file mode 100644
index e69de29..0000000
diff --git a/script_analyse.R b/script_analyse.R
deleted file mode 100644
index c92f20e..0000000
--- a/script_analyse.R
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env Rscript
-
-library(here)
-library(argparser, quietly=TRUE)
-
-source(file.path(dirname(here()), 'init.R'))
-
-# Create a parser
-p = arg_parser("Analyse data.")
-
-# Add command line arguments
-p = add_argument(p, '--filedir',
- type="character",
- help="Directory(ies) in the data directory to search for data.")
-
-p = add_argument(p, '--filename',
- type="character",
- help="Filename(s) in the data directory to search for data. If 'all', the whole directory(ies) will used.")
-
-
-# Parse the command line arguments
-argv = parse_args(p)
-
-# Run approriate function
diff --git a/script_new_user.R b/script_new_user.R
deleted file mode 100644
index 50302d3..0000000
--- a/script_new_user.R
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/usr/bin/env Rscript
-
-library(here)
-library(argparser, quietly=TRUE)
-
-setwd(here())
-
-# Create a parser
-p = arg_parser("Add a new user to the environment with is work and data path.")
-
-# Add command line arguments
-p = add_argument(p, '--data_dir',
- type="character",
- help="Data directory.")
-
-p = add_argument(p, '--work_dir',
- type="character",
- help="Working directory.")
-
-# Parse the command line arguments
-argv = parse_args(p)
-
-# Create path file
-user = Sys.getenv('USER')
-computer_data_path = c(argv$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=';')
diff --git a/script_plot.R b/script_plot.R
deleted file mode 100644
index 46bd851..0000000
--- a/script_plot.R
+++ /dev/null
@@ -1,37 +0,0 @@
-#!/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')
-
- }
-}
--
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