Skip to content

Commit

Permalink
First set of changes to make these scripts compatible with
Browse files Browse the repository at this point in the history 
the tagged new version of harp (0.2.0). It has been tested under ATOS with
a conda environment for producing rds (point_verif.R) and collection of verification
figures (point_verif_local.R) for the Spain_202205 case.
  • Loading branch information
Samuel Viana-Jimenez committed Jan 8, 2024
1 parent dabf911 commit 03b7042
Show file tree
Hide file tree
Showing 8 changed files with 193 additions and 184 deletions.
51 changes: 24 additions & 27 deletions R/point_verif/point_verif.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -73,18 +73,15 @@ run_verif <- function(prm_info, prm_name) {

# Read the forecast
fcst <- read_point_forecast(
start_date = start_date,
end_date = end_date,
fcst_model = fcst_model,
fcst_type = fcst_type,
parameter = prm_name,
lead_time = lead_time,
lags = lags,
by = by_step,
file_path = fcst_path,
vertical_coordinate = vertical_coordinate
)

dttm=seq_dttm(start_date,end_date,by_step),
fcst_model = fcst_model,
fcst_type = fcst_type,
parameter = prm_name,
lead_time = lead_time,
lags = lags,
file_path = fcst_path,
vertical_coordinate = vertical_coordinate
)
# Find the common cases - for upper air parmeters we need to ensure
# that the level column is included in the check
fcst <- switch(
Expand All @@ -98,38 +95,39 @@ run_verif <- function(prm_info, prm_name) {
# function with a named list containing the arguments.
if (!is.null(prm_info$scale_fcst)) {
fcst <- do.call(
scale_point_forecast,
c(list(.fcst = fcst), prm_info$scale_fcst))
scale_param,list(fcst, prm_info$scale_obs$scaling, prm_info$scale_obs$new_units, prm_info$scale_obs$mult)
)
}

# Read the observations getting the dates and stations from
# the forecast
obs <- read_point_obs(
start_date = first_validdate(fcst),
end_date = last_validdate(fcst),
#dttm=seq_dttm(start_date,end_date,by_step),
dttm=unique_valid_dttm(fcst),
parameter = prm_name,
obs_path = obs_path,
stations = pull_stations(fcst),
stations = unique_stations(fcst),
vertical_coordinate = vertical_coordinate
)

)
# optional rescaling of observations using the scale_obs part of the
# params list. We use do.call to call the scale_point_forecast
# function with a named list containing the arguments.
if (!is.null(prm_info$scale_obs)) {
if (!is.null(prm_info$scale_obs)) {
obs <- do.call(
scale_point_obs,
c(list(.obs = obs, parameter = prm_name), prm_info$scale_obs)
scale_param, list(obs, prm_info$scale_obs$scaling, prm_info$scale_obs$new_units, prm_info$scale_obs$mult, col = {{prm_name}})
)
}

# Join observations to the forecast
fcst <- join_to_fcst(fcst, obs)
fcst <- join_to_fcst(fcst, obs, force=TRUE)
#Note by Samuel: Some stop clause is needed here if any of the models
#intersects 0 with the observations' SIDS

# Check for errors removing obs that are more than a certain number
# of standard deviations from the forecast. You could add a number
# of standard deviations to use in the params list
fcst <- check_obs_against_fcst(fcst, prm_name)

# Make sure that grps is a list so that it adds on the vertical
# coordinate group correctly
if (!is.list(grps)) {
Expand Down Expand Up @@ -168,15 +166,14 @@ print(params)
# Use possibly from the purrr package to allow the script to continue
# if it fails for a parameter - it returns NULL if it fails. See
# ?safely and ?quietly if you want to retain the errors.
possible_run_verif <- possibly(run_verif, otherwise = NULL)
print(possible_run_verif)
possible_run_verif <- safely(run_verif, otherwise = NULL, quiet= FALSE)

# Use imap from the purrr package to map each element of the params list
# to the possible_run_verif function. imap passes the element of the list
# as the first argument and the name of the element as the second.
verif <- imap(params, possible_run_verif)

# This will be addd in the visualization part
# This will be added in the visualization part
# You can open the results in a shiny app using
# shiny_plot_point_verif(verif_path)

58 changes: 30 additions & 28 deletions R/point_verif/point_verif_local.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,8 @@ library(RColorBrewer) # Some colourmaps (some of which are colourblind friendly)
library(gridExtra) # For grid arrange
library(grid) # For grid arrange
library(pracma) # For logseq
library(boomer)
library(mapproj)

###
source(Sys.getenv('CONFIG_R'))
Expand Down Expand Up @@ -46,6 +48,7 @@ params <- CONFIG$params_details
start_date <- ifelse(is.null(args$start_date),CONFIG$shared$start_date,args$start_date)
end_date <- ifelse(is.null(args$end_date),CONFIG$shared$end_date,args$end_date)
by_step <- CONFIG$verif$by_step #Read from config file
by_obs_step <- CONFIG$verif$by_obs_step #Read from config file
fcst_model <- CONFIG$verif$fcst_model
lead_time_str <- CONFIG$verif$lead_time
lead_time <- eval(parse(text = lead_time_str))
Expand All @@ -57,8 +60,8 @@ verif_path <- CONFIG$verif$verif_path
grps <- CONFIG$verif$grps
plot_output <- CONFIG$post$plot_output # Load in png archive directory

# Verif results by leadtime for each fcst_cycle (should be default choice?)
grps <- list(c("leadtime","fcst_cycle"),"leadtime")
# Verif results by lead_time for each fcst_cycle (should be default choice?)
grps <- list(c("lead_time","fcst_cycle"),"lead_time")

# Useful functions
# This does some renaming of groups (those with NA or "00;12", etc.)
Expand Down Expand Up @@ -114,14 +117,12 @@ run_verif <- function(prm_info, prm_name) {

# Read the forecast
fcst <- read_point_forecast(
start_date = start_date,
end_date = end_date,
dttm=seq_dttm(start_date,end_date,by_step),
fcst_model = fcst_model,
fcst_type = fcst_type,
parameter = prm_name,
lead_time = lead_time,
lags = lags,
by = by_step,
file_path = fcst_path,
get_lat_and_lon = TRUE, # Useful when lat/lon missing from vobs files
vertical_coordinate = vertical_coordinate
Expand All @@ -140,18 +141,17 @@ run_verif <- function(prm_info, prm_name) {
# function with a named list containing the arguments.
if (!is.null(prm_info$scale_fcst)) {
fcst <- do.call(
scale_point_forecast,
c(list(.fcst = fcst), prm_info$scale_fcst))
scale_param,list(fcst, prm_info$scale_obs$scaling, prm_info$scale_obs$new_units, prm_info$scale_obs$mult)
)
}

# Read the observations getting the dates and stations from
# the forecast
obs <- read_point_obs(
start_date = first_validdate(fcst),
end_date = last_validdate(fcst),
dttm=seq_dttm(start_date,end_date,by_obs_step),
parameter = prm_name,
obs_path = obs_path,
stations = pull_stations(fcst),
stations = unique_stations(fcst),
min_allowed = prm_info$obsmin_val, # If obsmin/max not set, reverts to default
max_allowed = prm_info$obsmax_val,
vertical_coordinate = vertical_coordinate
Expand All @@ -162,8 +162,7 @@ run_verif <- function(prm_info, prm_name) {
# function with a named list containing the arguments.
if (!is.null(prm_info$scale_obs)) {
obs <- do.call(
scale_point_obs,
c(list(.obs = obs, parameter = prm_name), prm_info$scale_obs)
scale_param, list(obs, prm_info$scale_obs$scaling, prm_info$scale_obs$new_units, prm_info$scale_obs$mult, col = {{prm_name}})
)
}

Expand All @@ -188,8 +187,9 @@ run_verif <- function(prm_info, prm_name) {
)

# add valid_hour to fcst
#fcst <- mutate_list(fcst,valid_hour=substr(YMDh(validdate),9,10))
fcst <- expand_date(fcst,validdate) # Add in valid_year, valid_month, valid_day, valid_hour
#fcst <- mutate_list(fcst,valid_hour=substr(YMDh(valid_dttm),9,10))
fcst <- expand_date(fcst,valid_dttm) # Add in valid_year, valid_month, valid_day, valid_hour
#fcst <- rig(expand_date)(fcst,valid_dttm) # Add in valid_year, valid_month, valid_day, valid_hour
fcst <- mutate_list(fcst,valid_hour = sprintf("%02d",valid_hour)) # Convert to character and pad
# Remove stations that only occur very infrequently (for surface variables only)
if (is.na(vertical_coordinate)){
Expand Down Expand Up @@ -226,28 +226,29 @@ run_verif <- function(prm_info, prm_name) {
)
verif <- fn_verif_rename(verif)
verif_toplot <- verif # Used for passing to plotting script (as it may be modified below)
verif_toplot[[2]][["leadtime"]] <- as.character(verif_toplot[[2]][["leadtime"]]) # For plotting purposes
verif_toplot[[2]][["lead_time"]] <- as.character(verif_toplot[[2]][["lead_time"]]) # For plotting purposes


# Do some additional verif depending on UA parameter
if (!is.na(vertical_coordinate)){
# Group by valid_hour for profiles (threshold scores not required)
grps_vh <- lapply(grps_c,function(x) gsub("leadtime","valid_hour",x))
grps_vh <- lapply(grps_c,function(x) gsub("lead_time","valid_hour",x))
verif_vh <- get(verif_fn)(
fcst, prm_name, thresholds = NULL, groupings = grps_vh
)
verif_vh <- fn_verif_rename(verif_vh)

} else {
# Compute scores as a function of validdate (should take the same format as default leadtime groups)
# Compute scores as a function of valid_dttm (should take the same format as default lead_time groups)
# Assuming threshold scores are not required
grps_vd <- lapply(grps_c,function(x) gsub("leadtime","validdate",x))
grps_vd <- lapply(grps_c,function(x) gsub("lead_time","valid_dttm",x))
verif_vd <- get(verif_fn)(
fcst, prm_name, thresholds = NULL, groupings = grps_vd
)
verif_vd <- fn_verif_rename(verif_vd)

# Compute scores for each station for map purposes
grps_sid <- lapply(grps_c,function(x) gsub("leadtime","SID",x))
grps_sid <- lapply(grps_c,function(x) gsub("lead_time","SID",x))
# Replace fcst_cycle by valid_hour
if ("fcst_cycle" %in% grps_sid[[1]]){
grps_sid <- lapply(grps_sid,function(x) gsub("fcst_cycle","valid_hour",x))
Expand All @@ -263,12 +264,12 @@ run_verif <- function(prm_info, prm_name) {
verif_sid <- fn_verif_rename(verif_sid)
# Need to add lat/lon to the SIDs
verif_sid <- fn_sid_latlon(verif_sid,fcst)

# Flag to compute the standard threshold scores over all leadtimes and add
# Flag to compute the standard threshold scores over all lead_times and add
alllt_thresholds <- TRUE
if (alllt_thresholds){
# Compute threshold scores over all leadtimes (as done in Monitor) (retain default group structure)
grps_nolt <- lapply(grps_c,function(x) x[x != "leadtime"])
# Compute threshold scores over all lead_times (as done in Monitor) (retain default group structure)
grps_nolt <- lapply(grps_c,function(x) x[x != "lead_time"])
grps_nolt <- grps_nolt[lapply(grps_nolt,length)>0]
# Note: This will remove character(0) entries but will miss the "All" option for fcst_cycle etc.
# Hence we add a NULL below (NB: this may not be required with updated version of harp)
Expand All @@ -277,10 +278,10 @@ run_verif <- function(prm_info, prm_name) {
fcst, prm_name, thresholds = prm_info$thresholds, groupings = grps_nolt
)
verif_alllt <- fn_verif_rename(verif_alllt)
# Add in indication that we use all leadtimes (important for plotting script and for binding below)
verif_alllt <- mutate_list(verif_alllt,leadtime = "All")
# Add in indication that we use all lead_times (important for plotting script and for binding below)
verif_alllt <- mutate_list(verif_alllt,lead_time = "All")

print("Adding threshold scores over all leadtimes")
print("Adding threshold scores over all lead_times")
# Bind rows will match the column names
verif_toplot[[2]] <- bind_rows(verif_toplot[[2]],verif_alllt[[2]])
}
Expand All @@ -306,7 +307,8 @@ run_verif <- function(prm_info, prm_name) {
# Use possibly from the purrr package to allow the script to continue
# if it fails for a parameter - it returns NULL if it fails. See
# ?safely and ?quietly if you want to retain the errors.
possible_run_verif <- possibly(run_verif, otherwise = NULL)
#possibly(run_verif, otherwise = NULL)
possible_run_verif <- safely(run_verif, otherwise = NULL, quiet= FALSE)
#possible_run_verif <- run_verif
#print(possible_run_verif)

Expand Down
Loading

0 comments on commit 03b7042

Please sign in to comment.