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NEPH_P20_1907.R
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NEPH_P20_1907.R
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###########################################################################################################################
## Project: NEXTDATA ##
## Parameter: NEPH ##
## Script first purpose: create a formatted Level-0 dataset (in EBAS format) from raw data ##
## Script second purpose: create daily acquisition graphs of all instrumentation variables ##
## Run time: the script may run daily (e.g. by using a crontab) or may be used when needed ##
##_______________________________________________________________________________________________________________________##
## Authors: Luca Naitza, Davide Putero ##
## Organization: National Research Council of Italy, Institute for Atmospheric Science and Climate (CNR-ISAC) ##
## Address: Via Gobetti 101, 40129, Bologna, Italy ##
## Project Contact: Paolo Cristofanelli ##
## Email: P.Cristofanelli@isac.cnr.it ##
## Phone number: (+39) 051 639 9597 ##
##_______________________________________________________________________________________________________________________##
## Script filename: NEPH_D20_1810.R ##
## Version Date: July 2019
## Jul. 31st, 2019: "days_ref" substituted with "dependent_col", i.e., the number of dependent data columns (in the header)
###########################################################################################################################
# > > > > > > > > > > > > > > I N S T R U C T I O N S < < < < < < < < < < < < < < < < < < < < < < < < #
#
# This script consists of several parts and sub-parts.
#
# Part 0 is the setting section, in which the User should replace the marked values (e.g. directory paths)
# Part 0.1 defines environmental variables, such as raw data and destination directories. The user should modify these values.
# Part 0.2 specifies some characteristics of raw data tables, such as file extension, fields separators, etc. The user should
# modify these values according to his/her tables format. If the procedure requires more than one parameter
# setting, Part 0.2 is divided in sub-sub-parts (e.g. 0.2.1 , 0.2.2,...)
# Part 0.3 specifies the characteristics of User Station/Laboratory/Instrument/parameter. Most of these variables are used
# as metadata in the EBAS file format header. The User should provide proper information.
#
# Part 1 is another setting section; it should not be modified by the user unless strictly needed.
# Part 1.1 sets and loads the most commonly used R libraries. The user should not modify this sub-part.
# Part 1.2 specifies the time variables used in the processing. The user should not modify this sub-part. If the user needs
# to apply the script to data older than the current year, he/she may modify the lines explicitly marked for this purpose.
#
# Part 2 is the data processing section, it should not be modified by the user.
# Part 2.x contain the code to produce the EBAS format file and to process data. The User should not modify this sub-part(s).
#
# Part 3 is the data reporting section, it should not be modified by the user.
# Part 3.x contain the code to produce graphic reports. The user should not modify this sub-part(s).
#
# > > > > > > > > > > > > > > > > > > > > > > > > > > > < < < < < < < < < < < < < < < < < < < < < < < < < < < < < < < < < #
###########################################################################################################################
## # PART 0.1 #
## ______________________________________________________________________________________________________________________##
## Setting environmental variables
## ______________________________________________________________________________________________________________________##
## USE: set the following paths of origin raw data and of destination processing data, replacing values with yours
# WARNING: Proper setting up of the following paths and values is crucial. Please, replace the strings correctly
#
setwd("~/")
# -------- RAW DATA PATH ----------------------------------------------------------------------# REPLACE THE FOLLOWING PATHS
CALIB_DIR = '../naitza/NEXTDATA/PROD/CIMONE/AEROSOL/NEPH/RAW_DATA_UTC/CALIB'
RAW_DIR = '../naitza/NEXTDATA/PROD/CIMONE/AEROSOL/NEPH/RAW_DATA_UTC'
#
# -------- DATA DESTINATION PATH --------------------------------------------------------------# REPLACE THE FOLLOWING PATHS
L0_DIR = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/AEROSOL/NEPH/LEVEL_0'
L1_DIR = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/AEROSOL/NEPH/LEVEL_1'
L2_DIR = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/AEROSOL/NEPH/LEVEL_2'
L0_ANCIL_DIR = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/AEROSOL/NEPH/LEVEL_0/ANCILLARY'
#
# -------- GRAPH DESTINATION PATH -------------------------------------------------------------# REPLACE THE FOLLOWING PATHS
REP_DIR = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/AEROSOL/NEPH/REPORT'
REP_GRAPH_DIR = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/AEROSOL/NEPH/REPORT/DAILY_GRAPH'
PLOT_DIR_M = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/AEROSOL/NEPH/REPORT/MONTHLY_GRAPH'
PLOT_DIR_S = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/AEROSOL/NEPH/REPORT/SEASONAL_GRAPH'
PLOT_DIR_Y = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/AEROSOL/NEPH/REPORT/ANNUAL_GRAPH'
PLOT_DIR_Y_PDF = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/AEROSOL/NEPH/REPORT/ANNUAL_GRAPH/PDF'
PLOT_DIR_T = '../naitza/NEXTDATA/DISTRIBUTION_DIR/CIMONE/AEROSOL/NEPH/REPORT/TIMEVARIATION_GRAPH'
#
# -------- DAILY GRAPH PREFIX & SUFFIX -------------------------------------------------------# REPLACE THE FOLLOWING VALUES
DAILY_PREFIX <-"CMN_NEPH" # choose a prefix for your daily graph (e.g. StationCodeName_ParameterCodeName)
DAILY_SUFFIX <-"01M" # choose a suffix for your daily graph (e.g. AcquisitionTiming)
#
# -------- SCRIPTS PATH ----------------------------------------------------------------------# REPLACE THE FOLLOWING PATHS
SCRIPT_DIR = '../naitza/NEXTDATA/R_SCRIPT'
## Loading functions for numflags
## The "NXD_numflag_functions_180301.R" scripts assigns the numflag value to the dataset, according to EBAS Flag List
## (https://ebas-submit.nilu.no/Submit-Data/List-of-Data-flags)
## The "NXD_EBAS_numflag_FullList_210429.txt" text file contains the EBAS Flag List, reporting codes, category and description
## Please do NOT apply any change to the following function settings, unless you need to specify a different table of flags
#
source(paste(SCRIPT_DIR,"NXD_numflag_functions_180301.R", sep="/"))
tab_nf <- read.table(file = paste(SCRIPT_DIR,"NXD_EBAS_numflag_FullList_210429.txt",sep="/"),
sep = ";", header = TRUE, quote = NULL)
## # END PART 0.1 #
###########################################################################################################################
###########################################################################################################################
## # PART 0.2 #
## ______________________________________________________________________________________________________________________##
## Setting NEPH Data
## ______________________________________________________________________________________________________________________##
## USE: set the following values of NEPH dataset
## WARNING: NEPH raw data should be recorded according to the following specifications:
## FILENAME: the filename should contain the acquisition date (YYYYMMDD). E.g.: CMN_METEO_20181215_01M.dat;
#
# -------- NEPH RAW DATASET EXTENSION ----------------------------------------------------------# REPLACE THE FOLLOWING VALUES
#
NEPH_EXT <-".dat" # if different, replace ".dat" with the extesion of your NEPH Raw Data set
#
# -------- NEPH RAW DATA FIELD SEPARATOR -------------------------------------------------------# REPLACE THE FOLLOWING VALUES
#
NEPH_FIELD_SEP <-" " # if different, replace " " with the field separator of your NEPH Raw Data set (e.g. "," or "\t")
#
# -------- NEPH RAW DATA HEADER ----------------------------------------------------------------# REPLACE THE FOLLOWING VALUES
#
NEPH_FIELD_NAM <- T # if different, replace T with F if NEPH Row Data tables do not have the header (field names)
#
# -------- NEPH FIELD POSITION IN THE TABLE -----------------------------------------------------# REPLACE THE FOLLOWING VALUES
#
NEPH_DEC_DATE <- 6 # if different, replace with the field position of start_time (julian date) field in your NEPH Raw Data set
NEPH_Status <- 7 # if different, replace with the field position of status field in your NEPH Raw Data set
NEPH_p_int <- 16 # if different, replace with the field position of pressure inlet field in your NEPH Raw Data set
NEPH_T_int <- 18 # if different, replace with the field position of temperature inlet field in your NEPH Raw Data set
NEPH_T_out <- 17 # if different, replace with the field position of temperature outlet field in your NEPH Raw Data set
NEPH_RH_int <- 19 # if different, replace with the field position of RH inlet field in your NEPH Raw Data set
NEPH_RH_out <- 0 # if different, replace with the field position of RH outlet field in your NEPH Raw Data set
NEPH_flow <- 0 # if different, replace with the field position of flow field in your NEPH Raw Data set
NEPH_lamp_v <- 20 # if different, replace with the field position of lamp_v field in your NEPH Raw Data set
NEPH_lamp_c <- 21 # if different, replace with the field position of lamp_c field in your NEPH Raw Data set
NEPH_flags <- 23 # if different, replace with the field position of flags field in your NEPH Raw Data set
NEPH_sc450 <- 9 # if different, replace with the field position of sc450 field in your NEPH Raw Data set
NEPH_sc550 <- 10 # if different, replace with the field position of sc550 field in your NEPH Raw Data set
NEPH_sc700 <- 11 # if different, replace with the field position of sc700 field in your NEPH Raw Data set
NEPH_bsc450 <- 12 # if different, replace with the field position of bsc450 field in your NEPH Raw Data set
NEPH_bsc550 <- 13 # if different, replace with the field position of bsc550 field in your NEPH Raw Data set
NEPH_bsc700 <- 14 # if different, replace with the field position of bsc700 field in your NEPH Raw Data set
NEPH_sc450z <- 24 # if different, replace with the field position of sc450z field in your NEPH Raw Data set
NEPH_sc550z <- 25 # if different, replace with the field position of sc550z field in your NEPH Raw Data set
NEPH_sc700z <- 26 # if different, replace with the field position of sc700z field in your NEPH Raw Data set
NEPH_bsc450z <- 27 # if different, replace with the field position of bsc450z field in your NEPH Raw Data set
NEPH_bsc550z <- 28 # if different, replace with the field position of bsc550z field in your NEPH Raw Data set
NEPH_bsc700z <- 29 # if different, replace with the field position of bsc700z field in your NEPH Raw Data set
NEPH_sc450r <- 30 # if different, replace with the field position of sc450r field in your NEPH Raw Data set
NEPH_sc550r <- 31 # if different, replace with the field position of sc550r field in your NEPH Raw Data set
NEPH_sc700r <- 32 # if different, replace with the field position of sc700r field in your NEPH Raw Data set
#
# -------------------------------------------------------------------------------------------
## # END PART 0.2 #
###########################################################################################################################
###########################################################################################################################
## # PART 0.3 #
## ______________________________________________________________________________________________________________________##
## Setting time and name variables
## Setting EBAS metadata inrofmation
## ______________________________________________________________________________________________________________________##
# Station/Laboratory/Instrument/parameter variables
#
# -------- EBAS HEADER FILE (METADATA) -----------------------------------------------------# REPLACE THE FOLLOWING VALUES
#
s_code <- "IT0009R" # replace the value with your Station code
s_WDCA_ID <- "GAWANO_CMN" # replace the value with your WDCA ID code
s_GAW_Name <- "Monte Cimone" # replace the value with your Station GAW name
s_GAW_ID <- "CMN" # replace the value with your Station GAW ID
s_lat <- "44.16667" # replace the value with your Station latitude
s_lon <- "10.68333" # replace the value with your Station longitude
s_alt <- "2165m" # replace the value with your Station altitude (meters)
s_l_use <- "Remote park" # replace the value with your Station land use
s_setting <- "Mountain" # replace the value with your Station setting
s_GAW_t <- "G" # replace the value with your Station GAW type
s_WMO_reg <- "6" # replace the value with your Station WMO region
lab_code <- "IT06L" # replace the value with your laboratory code
inst_type <- "nephelometer" # replace the value with your instrument type
inst_manu <- "TSI" # replace the value with your instrument manufacter
inst_modl <- "3563" # replace the value with your instrument model
inst_name <- "TSI_3563_3563133901" # replace the value with your your instrument name
inst_s_n <- "3563133901" # replace the value with your instrument serial number
meth_ref <- "IT06L_neph_control_lev0_0_0_1" # replace the value with method reference
dependent_col <- "26" # replace the value with the total number of columns of the file in addition to start_time (i.e., total-1)
component <- "aerosol_light_scattering_coefficient" # replace the value with proper component
matrix <- "aerosol" # replace the value with proper matrix
meas_unit <- "1/Mm" # replace the value with proper measurement unit
meas_lat <- "44.16667" # replace the value with the your Measure latitude
meas_lon <- "10.68333" # replace the value with the your Measure longitude
meas_alt <- "2165m" # replace the value with the your Measure altitude (meters)
Period_code <- "1y" # replace the value with the proper Period code
Resolution_code <- "1mn" # replace the value with the proper Resolution code
Sample_duration <- "1mn" # replace the value with the proper Sample duration
Orig_time_res <- "1mn" # replace the value with the proper Original time resolution
height_AGL <- "10m" # replace the value with Height AGL
inlet_type <- "Hat or hood" # replace the value with Inlet type
inlet_desc <- "Total particle size at ambient humidity inlet, heated head, home made followinfg EUSAAR design, flow 150 l/min" # replace the value with Inlet description
hum_temp_c <- "heating" # replace the value with Humidity/temperature control
hum_temp_c_desc <- "passive, sample heated from atmospheric to lab temperature" # replace the value with Humidity/temperature control description
vol_std_t <- "ambient" # replace the value with Volume std. temperature
vol_std_p <- "ambient" # replace the value with Volume std. pressure
detec_lim <- "0.3 1/Mm" # replace the value with Detection limit
detec_lim_ex <- "Determined by instrument counting statistics, no detection limit flag used" # replace the value with Detection limit expl.
meas_uncr <- "0.5 1/Mm" # replace the value with Measurement uncertainty
meas_uncr_ex <- "average value taken from Anderson et al. 1996 for statistical and calibration uncertainty" # replace the value with Measurement uncertainty expl.
zero_val_code <- "Zero/negative possible" # replace the value with Zero/negative values code
zero_val <- "Zero and neg. values may appear due to statistical variations at very low concentrations" # replace the value with Zero/negative values
std_meth <- "cal-gas=CO2+AIR_truncation-correction=none" # replace the value with Standard method
qa_mes_id <- "not available" # replace the value with QA measure ID
qa_date <- "not available" # replace the value with QA date
qa_doc <- "not available" # replace the value with QA document URL
# The following variabiles concern the originator and the submitter names, surnames, emails and addresses
# NOTE: Please, change these variables with proper names, surnames, emails and addresses
#
# -------- ORIGINATORS (set min 1 originator, max 5) ---------------------------------------------------------------# REPLACE THE FOLLOWING VALUES
Origin_1_n <- "Angela"
Origin_1_s <- "Marinoni"
Origin_1_e <- "a.marinoni@isac.cnr.it"
Origin_1_i <- "Institute of Atmospheric Sciences and Climate, ISAC,, Via P. Gobetti 101,, I-40129, Bologna, Italy"
Origin_2_n <- "Davide"
Origin_2_s <- "Putero"
Origin_2_e <- "d.putero@isac.cnr.it"
Origin_2_i <- "Institute of Atmospheric Sciences and Climate, ISAC,, Via P. Gobetti 101,, I-40129, Bologna, Italy"
Origin_3_n <- "Luca"
Origin_3_s <- "Naitza"
Origin_3_e <- "l.naitza@isac.cnr.it"
Origin_3_i <- "Institute of Atmospheric Sciences and Climate, ISAC,, Via P. Gobetti 101,, I-40129, Bologna, Italy"
Origin_4_n <- ""
Origin_4_s <- ""
Origin_4_e <- ""
Origin_4_i <- ""
Origin_5_n <- ""
Origin_5_s <- ""
Origin_5_e <- ""
Origin_5_i <- ""
# -------- SUBMITTER (set the submitter) --------------------------------------------------------------------------# REPLACE THE FOLLOWING VALUES
#
Submit_1_n <- "Angela"
Submit_1_s <- "Marinoni"
Submit_1_e <- "a.marinoni@isac.cnr.it"
Submit_1_i <- "Institute of Atmospheric Sciences and Climate, ISAC,, Via P. Gobetti 101,, I-40129, Bologna, Italy"
mycomment <- "calibration, but no truncation correction applied"
#
# Setting the lines of the header
#
if (nchar(Origin_2_n) == 0 && nchar(Origin_3_n) == 0 && nchar(Origin_4_n) == 0 && nchar(Origin_5_n) == 0) { L0_n_lines <- 101 + 0 }
if (nchar(Origin_2_n) > 0 && nchar(Origin_3_n) == 0 && nchar(Origin_4_n) == 0 && nchar(Origin_5_n) == 0) { L0_n_lines <- 101 + 1 }
if (nchar(Origin_2_n) > 0 && nchar(Origin_3_n) > 0 && nchar(Origin_4_n) == 0 && nchar(Origin_5_n) == 0) { L0_n_lines <- 101 + 2 }
if (nchar(Origin_2_n) > 0 && nchar(Origin_3_n) > 0 && nchar(Origin_4_n) > 0 && nchar(Origin_5_n) == 0) { L0_n_lines <- 101 + 3 }
if (nchar(Origin_2_n) > 0 && nchar(Origin_3_n) > 0 && nchar(Origin_4_n) > 0 && nchar(Origin_5_n) > 0) { L0_n_lines <- 101 + 4 }
#
# -------------------------------------------------------------------------------------------
## # END PART 0.3 #
###########################################################################################################################
###########################################################################################################################
## # PART 1.0 #
## ______________________________________________________________________________________________________________________##
## Loading libraries
## ______________________________________________________________________________________________________________________##
## NOTE: some of the following libraries may not be actually used by this script
# Please, do NOT apply any change, unless it is necessary to load specific libraries
#
library(data.table)
library(openair)
library(lattice)
library(RColorBrewer)
library(latticeExtra)
library(proto)
library(gsubfn)
library(RSQLite)
library(padr)
library(caTools)
library(zoo)
library(plyr)
library(forecast)
library("sqldf")
library(TTR)
library(ggplot2)
library(reshape2)
library(stringr)
library(png)
## # END PART 1.0 #
###########################################################################################################################
###########################################################################################################################
## # PART 1.1 #
## ______________________________________________________________________________________________________________________##
## Setting time and name variables
## Cleaning destination directory
## ______________________________________________________________________________________________________________________##
# Station/Laboratory/Instrument/parameter variables
# NOTE: Please, change these variables with proper station and parameter information
#
# The following variabiles reguard the parameter and the level
# NOTE: Please, do NOT change these variables
#
param_code <- "aerosol_light_scattering_coefficient.aerosol.1y.1mn"
level_code <- "lev0.nas"
# -------------------------------------------------------------------------------------------
# Time variables
# NOTE: the following variables should not be modified, except those with explicit comments
#
questo_anno <-format(Sys.Date(), "%Y")
# -------- PREVIOUS YEAR(S) DATA PROCESSING ---------------------------------------# IF NEEDED, UN-COMMENT THE FOLLOWING LINE
#questo_anno <-as.numeric(questo_anno) -1 # the value "-1" means "last year". Change to "-2" or "-3" etc. for previous
questo_mese <-format(Sys.Date(), "%m")
questo_mese_nome <-format(Sys.Date(), "%B")
questo_giorno <-format(Sys.Date(), "%d")
if (questo_mese == "01" & questo_giorno == "01") { questo_anno <- as.numeric(questo_anno)-1 }
questo_capodanno <-paste(questo_anno,"01","01",sep="-")
questo_annomesegiorno <-paste(questo_anno,questo_mese,questo_giorno,sep="")
questa_ora <-format(Sys.time(), "%H")
questo_minuto <-format(Sys.time(), "%M")
questo_inizioanno <-paste(questo_anno,"0101000000",sep = "")
questi_dati <-paste(s_code,questo_inizioanno,sep = ".")
questa_start_time <-as.Date(paste(paste(questo_anno,"01","01",sep = "-"), " 00:00:00",sep = ""))
myweekday <-as.POSIXlt(Sys.Date())$wday
questo_startdate <-paste(questo_anno,"0101",sep="")
new_date <-gsub("-","",
gsub(" ","",
gsub(":","",
as.character(strptime(Sys.time(),
format = "%Y - %m - %d %H : %M")))))
new_date_name <-paste(".",new_date,sep="")
rev_datime <-gsub("-","",
gsub(" ","",
gsub(":","",
as.character(strptime(new_date,
format = "%Y%m%d%H%M%S")-3600))))
DATA_OSS <-paste(questo_anno,"01 01")
DATA_REV <-gsub("-"," ",Sys.Date())
DATA_INSERT <-paste(DATA_OSS,DATA_REV,sep=" ")
# -------------------------------------------------------------------------------------------
# File name variables
# NOTE: the following variables should not be modified
#
EBAS_L0_FILENAME <-paste(s_code,questo_inizioanno,rev_datime,param_code,level_code,sep=".")
EBAS_L0_FULLFILENAME <-paste(L0_DIR,EBAS_L0_FILENAME,sep = "/")
EBAS_temp_FILENAME <-paste(L0_DIR,paste("temp_",EBAS_L0_FILENAME,sep=""),sep = "/")
#
# -------------------------------------------------------------------------------------------
# Check point: printing variables
#
questo_anno
questo_mese
questo_mese_nome
questo_giorno
questo_capodanno
questo_annomesegiorno
questa_ora
questo_minuto
questo_inizioanno
questa_start_time
myweekday
questo_startdate
new_date
new_date_name
rev_datime
EBAS_L0_FILENAME
EBAS_L0_FULLFILENAME
# # END PART 1.1 #
###########################################################################################################################
###########################################################################################################################
## # PART 2.0 #
## ______________________________________________________________________________________________________________________##
## Creation of Level-0 data file
## Cleaning Destination directory
## Formatting Level-0 header
## ______________________________________________________________________________________________________________________##
# Deleting temporary files in the destination directory (if present)
#
FILE_TMP <-list.files(path = L0_DIR, pattern = glob2rx("temp_*"),
all.files = FALSE,
full.names = F,
recursive = FALSE,
ignore.case = FALSE,
include.dirs = F,
no.. = FALSE)
LISTA_FILE_TMP <-as.character(FILE_TMP)
LISTA_FILE_TMP
for(f in LISTA_FILE_TMP) { file.remove(paste(L0_DIR,f,sep = "/")) }
#
# -------------------------------------------------------------------------------------------
# Cleaning Destination directory
# NOTE: the following process deletes old EBAS Level-0 files within the destination directory
#
MYOLD_FILE <-paste(s_code,".",questo_anno,sep = "")
FILE_OLD <-list.files(path = L0_DIR, pattern = glob2rx(paste(MYOLD_FILE,"*",sep = "")),
all.files = FALSE,
full.names = F,
recursive = FALSE,
ignore.case = FALSE,
include.dirs = F,
no.. = FALSE)
FILE_OLD
LISTA_FILE_OLD <-as.character(FILE_OLD)
for(f in LISTA_FILE_OLD) { file.remove(paste(L0_DIR,f,sep = "/")) }
#
# -------------------------------------------------------------------------------------------
# Creating the new EBAS LEVEL-0 data file
# NOTE: the following process deletes old EBAS Level-0 files within the destination directory
#
write.table(" ", file=EBAS_L0_FULLFILENAME,row.names=F,col.names = F, append = F,sep=" ")
#
# -------------------------------------------------------------------------------------------
# Formatting EBAS LEVEL-0 header and adding information to the data file
# NOTE: information contained in the following lines should be modified with proper station and instrumentation information
#
cat(
paste(L0_n_lines,"1001",sep=" "),
gsub("; $","",gsub("; ;","",paste(paste(Origin_1_n,Origin_1_s,sep=", "),
ifelse(nchar(Origin_2_n)>0,
(paste(Origin_2_n,Origin_2_s,sep=", ")), ""),
ifelse(nchar(Origin_3_n)>0,
(paste(Origin_3_n,Origin_3_s,sep=", ")), ""),
ifelse(nchar(Origin_4_n)>0,
(paste(Origin_4_n,Origin_4_s,sep=", ")), ""),
ifelse(nchar(Origin_5_n)>0,
(paste(Origin_5_n,Origin_5_s,sep=", ")), ""),
sep="; "))),
paste(lab_code, Origin_1_i,sep=", "),
paste(Submit_1_n, Submit_1_s, sep=", "),
"GAW-WDCA, ACTRIS
1 1",
DATA_INSERT,
"0
Days from the file reference point (start_time)",
dependent_col,
"1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
9999.99999999 9999.99 9999.99 9999.99 9999.99 9999.99 9999.99 999.99 999.99 0x9999 999999.999999 999999.999999 999999.999999 999999.999999 999999.999999 999999.999999 999999.999999 999999.999999 999999.999999 999999.999999 999999.999999 999999.999999 999999.999999 999999.999999 999999.999999 9.999999999
end_time of measurement, days from the file reference point
pressure, hPa, Location=instrument internal, Matrix=instrument
temperature, K, Location=instrument inlet, Matrix=instrument
temperature, K, Location=instrument outlet, Matrix=instrument
relative_humidity, %, Location=instrument inlet, Matrix=instrument
relative_humidity, %, Location=instrument outlet, Matrix=instrument
flow_rate, l/min, Location=instrument internal, Matrix=instrument, Volume std. temperature=273.15 K, Volume std. pressure=1013.25 hPa
electric_tension, V, Location=lamp supply, Matrix=instrument
electric_current, A, Location=lamp supply, Matrix=instrument
status, no unit, Status type=overall instrument status, Matrix=instrument
aerosol_light_scattering_coefficient, 1/Mm, Wavelength=450 nm
aerosol_light_scattering_coefficient, 1/Mm, Wavelength=550 nm
aerosol_light_scattering_coefficient, 1/Mm, Wavelength=700 nm
aerosol_light_backscattering_coefficient, 1/Mm, Wavelength=450 nm
aerosol_light_backscattering_coefficient, 1/Mm, Wavelength=550 nm
aerosol_light_backscattering_coefficient, 1/Mm, Wavelength=700 nm
aerosol_light_scattering_coefficient_zero_measurement, 1/Mm, Wavelength=450 nm
aerosol_light_scattering_coefficient_zero_measurement, 1/Mm, Wavelength=550 nm
aerosol_light_scattering_coefficient_zero_measurement, 1/Mm, Wavelength=700 nm
aerosol_light_backscattering_coefficient_zero_measurement, 1/Mm, Wavelength=450 nm
aerosol_light_backscattering_coefficient_zero_measurement, 1/Mm, Wavelength=550 nm
aerosol_light_backscattering_coefficient_zero_measurement, 1/Mm, Wavelength=700 nm
aerosol_light_rayleighscattering_coefficient_zero_measurement, 1/Mm, Wavelength=450 nm
aerosol_light_rayleighscattering_coefficient_zero_measurement, 1/Mm, Wavelength=550 nm
aerosol_light_rayleighscattering_coefficient_zero_measurement, 1/Mm, Wavelength=700 nm
numflag
0",
(L0_n_lines - 23),
"Data definition: EBAS_1.1
Data level: 0
Version: 1
Version description: initial revision
Set type code: TI",
paste("Station code: ",s_code,sep=""),
paste("Platform code: ",gsub("R","S",s_code)),
"Timezone: UTC",
paste("Startdate: ",questo_inizioanno[1],sep=""),
paste("Revision date: ",as.numeric(new_date)-7200,sep=""),
paste("Component: ",component,sep=""),
paste("Matrix: ",matrix,sep=""),
paste("Unit: ",meas_unit,sep=""),
paste("Period code: ",Period_code,sep=""),
paste("Resolution code: ",Resolution_code,sep=""),
paste("Sample duration: ",Sample_duration,sep=""),
paste("Orig. time res.: ",Orig_time_res,sep=""),
paste("Laboratory code: ",lab_code,sep=""),
paste("Instrument type: ",inst_type,sep=""),
paste("Instrument manufacturer: ",inst_manu,sep=""),
paste("Instrument model: ",inst_modl,sep=""),
paste("Instrument name: ",inst_name,sep=""),
paste("Instrument serial number: ",inst_s_n,sep=""),
paste("Method ref: ",meth_ref,sep=""),
paste("File name: ",EBAS_L0_FILENAME,sep=""),
paste("File creation: ",rev_datime[1],sep=""),
paste("Station WDCA-ID: ",s_WDCA_ID,sep=""),
paste("Station GAW-Name: ",s_GAW_Name,sep=""),
paste("Station GAW-ID: ",s_GAW_ID,sep=""),
paste("Station latitude: ",s_lat,sep=""),
paste("Station longitude: ",s_lon,sep=""),
paste("Station altitude: ",s_alt,sep=""),
paste("Station land use: ",s_l_use,sep=""),
paste("Station setting: ",s_setting,sep=""),
paste("Station GAW type: ",s_GAW_t,sep=""),
paste("Station WMO region: ",s_WMO_reg,sep=""),
paste("Measurement latitude: ",meas_lat,sep=""),
paste("Measurement longitude: ",meas_lon,sep=""),
paste("Measurement altitude: ",meas_alt,sep=""),
paste("Height AGL: ",height_AGL,sep=""),
paste("Inlet type: ",inlet_type,sep=""),
paste("Inlet description: ",inlet_desc,sep=""),
paste("Humidity/temperature control: ",hum_temp_c,sep=""),
paste("Humidity/temperature control description: ",hum_temp_c_desc,sep=""),
paste("Volume std. temperature: ",vol_std_t,sep=""),
paste("Volume std. pressure: ",vol_std_p,sep=""),
paste("Detection limit: ",detec_lim,sep=""),
paste("Detection limit expl.: ",detec_lim_ex,sep=""),
paste("Measurement uncertainty: ",meas_uncr,sep=""),
paste("Measurement uncertainty expl.: ",meas_uncr_ex,sep=""),
paste("Zero/negative values code: ",zero_val_code,sep=""),
paste("Zero/negative values: ",zero_val,sep=""),
paste("Standard method: ",std_meth,sep=""),
paste("QA measure ID ",qa_mes_id,sep=""),
paste("QA date: ",qa_date,sep=""),
paste("QA document URL: ",qa_doc,sep=""),
paste("Originator: ",paste(Origin_1_n,Origin_1_s,Origin_1_e,Origin_1_i,sep=", "),sep=""),
paste("Originator: ",paste(Origin_2_n,Origin_2_s,Origin_2_e,Origin_2_i,sep=", "),sep=""),
paste("Originator: ",paste(Origin_3_n,Origin_3_s,Origin_3_e,Origin_3_i,sep=", "),sep=""),
if(nchar(Origin_4_n)>0) {paste("Originator: ",paste(Origin_4_n,Origin_4_s,Origin_4_e,Origin_4_i,sep=", "),sep="")},
if(nchar(Origin_5_n)>0) {paste("Originator: ",paste(Origin_5_n,Origin_5_s,Origin_5_e,Origin_5_i,sep=", "),sep="")},
paste("Submitter: ",paste(Submit_1_n,Submit_1_s,Submit_1_e,Submit_1_i,sep=", "),sep=""),
paste("Comment: ",mycomment,sep=""),
"Acknowledgement: Request acknowledgment details from data originator",
paste("start_time","end_time","p_int","T_int","T_out","RH_int","RH_out","flow","lamp_v",
"lamp_c","flags","sc450","sc550","sc700","bsc450","bsc550","bsc700","sc450z","sc550z",
"sc700z","bsc450z","bsc550z","bsc700z","sc450r","sc550r","sc700r","numflag"),
file=EBAS_L0_FULLFILENAME, append=F, sep = "\n")
## # END PART 2.0 #
###########################################################################################################################
###########################################################################################################################
## # PART 2.1 #
## ______________________________________________________________________________________________________________________##
## Importing raw data
## Processing, manipulation, transformation of raw data
## Level-0 data flagging
## Writing data in Level-0 data file (EBAS format)
## ______________________________________________________________________________________________________________________##
# Listing the NEPH Raw data
#
lsfiles <-file.info(dir(RAW_DIR, pattern = glob2rx(paste0("*",NEPH_EXT)), full.names = F, ignore.case = TRUE))
lista <-data.frame(lsfiles[order(lsfiles$mtime),])
setDT(lista, keep.rownames = T)[]
names(lista)[1] <-"fileName"
df_lista <-data.frame(lista[fileName %like% questo_anno])
names(df_lista)[1] <-"fileName"
df_lista$mydata <-df_lista
ndata <- NROW(df_lista)
#
# -------------------------------------------------------------------------------------------
# Creating temporary NEPH dataset for current year
#
for(j in df_lista$fileName) {
ULTIMO_DATO <-paste(RAW_DIR,j, sep="/")
ULTIMO_DATO_NAME <-basename(ULTIMO_DATO)
TABELLA <-read.table(file=ULTIMO_DATO,fill = T, header = NEPH_FIELD_NAM, row.names=NULL,
colClasses = c(rep("numeric",6),rep("character",25)))
names(TABELLA)[NEPH_DEC_DATE] <-"start_time"
names(TABELLA)[NEPH_Status] <-"status"
names(TABELLA)[NEPH_p_int] <-"p_int"
names(TABELLA)[NEPH_T_int] <-"T_int"
names(TABELLA)[NEPH_T_out] <-"T_out"
names(TABELLA)[NEPH_RH_int] <-"RH_int"
names(TABELLA)[NEPH_lamp_v] <-"lamp_v"
names(TABELLA)[NEPH_lamp_c] <-"lamp_c"
names(TABELLA)[NEPH_flags] <-"flags"
names(TABELLA)[NEPH_sc450] <-"sc450"
names(TABELLA)[NEPH_sc550] <-"sc550"
names(TABELLA)[NEPH_sc700] <-"sc700"
names(TABELLA)[NEPH_bsc450] <-"bsc450"
names(TABELLA)[NEPH_bsc550] <-"bsc550"
names(TABELLA)[NEPH_bsc700] <-"bsc700"
names(TABELLA)[NEPH_sc450z] <-"sc450z"
names(TABELLA)[NEPH_sc550z] <-"sc550z"
names(TABELLA)[NEPH_sc700z] <-"sc700z"
names(TABELLA)[NEPH_bsc450z] <-"bsc450z"
names(TABELLA)[NEPH_bsc550z] <-"bsc550z"
names(TABELLA)[NEPH_bsc700z] <-"bsc700z"
names(TABELLA)[NEPH_sc450r] <-"sc450r"
names(TABELLA)[NEPH_sc550r] <-"sc550r"
names(TABELLA)[NEPH_sc700r] <-"sc700r"
#
# -------------------------------------------------------------------------------------------
# Adding new fields or setting existing
#
if(NEPH_flow == 0) { TABELLA$flow <- 9999.99 }
else { names(TABELLA)[NEPH_flow] <-"flow" }
if(NEPH_RH_out == 0) { TABELLA$RH_out <- 9999.999 }
else { names(TABELLA)[NEPH_RH_out] <-"RH_out" }
#
# -------------------------------------------------------------------------------------------
# Adding new fields
#
TABELLA$end_time <-as.numeric(TABELLA$start_time) + 0.00069444
TABELLA$numflag <- 0
TABELLA <-subset(TABELLA, select=c("start_time","end_time","status","p_int","T_int","T_out",
"RH_int","RH_out","flow","lamp_v","lamp_c","flags","sc450",
"sc550","sc700","bsc450","bsc550","bsc700","sc450z","sc550z",
"sc700z","bsc450z","bsc550z","bsc700z","sc450r","sc550r","sc700r",
"numflag"))
write.table(TABELLA, file=EBAS_temp_FILENAME,row.names=F,col.names = F, append = T, quote = F,sep=" ")
}
#
# -------------------------------------------------------------------------------------------
# Processing collected data
#
TABELLA <-read.table(EBAS_temp_FILENAME,row.names=NULL, stringsAsFactors = FALSE)
colnames(TABELLA) <-c("start_time","end_time","status","p_int","T_int","T_out","RH_int","RH_out","flow","lamp_v",
"lamp_c","flags","sc450","sc550","sc700","bsc450","bsc550","bsc700","sc450z","sc550z",
"sc700z","bsc450z","bsc550z","bsc700z","sc450r","sc550r","sc700r","numflag")
TABELLA$status <- as.character(TABELLA$status)
TABELLA$flags <- paste0("0x",str_pad(TABELLA$flags, 4, pad = "0"))
#
# -------------------------------------------------------------------------------------------
#
# Flagging NEPH values:
# See PART 0.1 for the setting of numflag script and table
#
# Flagging instrument internal relative humidity above 40%
TABELLA$numflag[TABELLA$RH_int > 40] <- sapply(TABELLA$numflag[TABELLA$RH_int > 40],
nf_aggreg, nf_new = 0.640)
#
# -------------------------------------------------------------------------------------------
# Flagging invalid due to calibration or zero/span check. Used for Level 0.
#
TABELLA$numflag[TABELLA$status == "ZBXX" |
TABELLA$status == "BBXX"] <- sapply(TABELLA$numflag[TABELLA$status == "ZBXX" |
TABELLA$status == "BBXX"],
nf_aggreg, nf_new = 0.682)
#
# -------------------------------------------------------------------------------------------
# Flagging invalid due to mechanical problem, unspecified reason
#
# -------------------------------------------------------------------------------------------
TABELLA$numflag[TABELLA$status != "NBXX" & TABELLA$status != "ZBXX" &
TABELLA$status != "BBXX" & TABELLA$status != "NTXX" &
TABELLA$status != "BTXX" & TABELLA$status != "ZTXX"] <- sapply(TABELLA$numflag[TABELLA$status != "NBXX" &
TABELLA$status != "ZBXX" &
TABELLA$status != "BBXX" &
TABELLA$status != "NTXX" &
TABELLA$status != "BTXX" &
TABELLA$status != "ZTXX"],
nf_aggreg, nf_new = 0.699)
#
TABELLA$numflag[TABELLA$flags != "0x0000"] <- sapply(TABELLA$numflag[TABELLA$flags != "0x0000"],nf_aggreg, nf_new = 0.699)
#
# -------------------------------------------------------------------------------------------
# Appending Data set to EBAS Level-0 Header
#
myEBAS <-TABELLA[,c("start_time","end_time","p_int","T_int","T_out","RH_int","RH_out",
"flow","lamp_v","lamp_c","flags","sc450","sc550","sc700","bsc450","bsc550","bsc700",
"sc450z","sc550z","sc700z","bsc450z","bsc550z","bsc700z","sc450r","sc550r","sc700r",
"numflag")]
#
myEBAS[c(1:10,12:27)] <- sapply(myEBAS[c(1:10,12:27)],as.numeric)
#
myEBAS <- myEBAS[!duplicated(myEBAS[1]),]
#
# -------------------------------------------------------------------------------------------
# Converting NEPH values to Mm-1 units
#
myEBAS[, 12:26] <- myEBAS[, 12:26]*1000000
#
# -------------------------------------------------------------------------------------------
# Writing the final Data set
# Formatting the output matrix as required by EBAS format Level-0
#
# Set the proper output format
#
sprintf_formats <- c(rep("%.8f", 2), rep("%.2f", 8), "%s", rep("%.6f", 15), "%.9f")
myEBAS[] <- mapply(sprintf, sprintf_formats, myEBAS)
#
# Appending Data set to EBAS Level-0 Header
#
write.table(myEBAS, file=EBAS_L0_FULLFILENAME,row.names=F,col.names = F, append = T, quote = F,sep=" ")
#
# -------------------------------------------------------------------------------------------
# Deleting temporary files in the destination directory (if present)
#
FILE_TMP <-list.files(path = L0_DIR, pattern = glob2rx("temp_*"), all.files = FALSE,
full.names = F, recursive = FALSE,
ignore.case = FALSE, include.dirs = F, no.. = FALSE)
LISTA_FILE_TMP <-as.character(FILE_TMP)
LISTA_FILE_TMP
for(f in LISTA_FILE_TMP) { file.remove(paste(L0_DIR,f,sep = "/")) }
#
# -------------------------------------------------------------------------------------------
## # END PART 2.1 #
###########################################################################################################################
##>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DAILY GRAPH REPORTING <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<##
###########################################################################################################################
## # PART 3.0 #
## ______________________________________________________________________________________________________________________##
## Loading data and setting variables
## Timeplot
## ______________________________________________________________________________________________________________________##
# Extracting the calendar day from strat_time
#
REPORTAB <-myEBAS[, c("start_time",
"sc550",
"p_int",
"T_int",
"RH_int",
"lamp_v",
"lamp_c")]
REPORTAB[] <-lapply(REPORTAB, function(x) as.numeric(as.character(x)))
REPORTAB$day <-REPORTAB$start_time-(REPORTAB$start_time-floor(REPORTAB$start_time)-1)
REPORTAB$date <-as.POSIXct(as.Date(REPORTAB$start_time, origin = questo_capodanno))
reportday <-c(REPORTAB[!duplicated(REPORTAB[,c('day')]),]$day)
print(reportday) # check point: print the days in the table
# -------------------------------------------------------------------------------------------
# Creating Visual Inspection Graphs for each calendar day
#
for (d in reportday)
{
THISREPORTTAB <-subset(REPORTAB, day==d)
reportdate <-strptime(paste(questo_anno, d), format="%Y %j")
mydatename <-paste(DAILY_PREFIX,gsub("-","",substring(reportdate,1,10)),DAILY_SUFFIX,sep = "_")
ULTIMO_DATO_PNG <-paste(paste(REP_GRAPH_DIR,mydatename,sep="/"),
"png", sep=".")
if (file.exists(ULTIMO_DATO_PNG)){} else
{png(file = ULTIMO_DATO_PNG,width=10000,height=15000,res=1000)
timePlot(THISREPORTTAB,pollutant=c("sc550",
"p_int",
"T_int",
"RH_int",
"lamp_v",
"lamp_c"
),cex=25,date.breaks=15, y.relation="free", key = FALSE, fontsize = 14)
dev.off()
}
}
## # END PART 3.0 #
###########################################################################################################################
# #
## End of NEPH_D20_1810.R #
# #
###################################################################################### Authors: L u C A, Davide ###########