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Robust find met files (#109)
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* change n_hours_per_met_file parameter to met_file_tres

* roxygen import
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@jmineau
jmineau authored Mar 3, 2025
1 parent bc45316 commit b7d9b6d
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Showing 7 changed files with 33 additions and 31 deletions.
2 changes: 1 addition & 1 deletion docs/configuration.md
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Expand Up @@ -64,7 +64,7 @@ str(receptors)
| -------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| `met_path` | Absolute path to ARL compatible meteorological data files |
| `met_file_format` | String detailing file naming convention for meteorological data files using a mixture of datetime and regex syntax. The formatting string accepts `grep` compatible regular expressions (`.\*.arl`), `strftime` compatible datetime strings (`%Y%m%d%H`) or any combination of the two. Datetime syntax is expanded to all unique combinations required for the receptor and simulation duration and the intersection between the requested files and files available in `met_path` is determined with `grep`, allowing partial matching and compatible regular expressions to be used to identify the relevant data. Matching does not require the full format to be specified - e.g. `\*.arl`, `%Y`, `%Y%m%d`, `%Y%m%d_d0.*.arl` would all match with a file named `20180130_d01.arl`. |
| `n_hours_per_met_file` | Number of hours per meteorological data file. To determine the number of hours in an ARL compatible meteorological data file, refer to the README, including the file naming convention, provided by the data source. For example, the [NOAA HRRR README](https://www.ready.noaa.gov/data/archives/hrrr/README.TXT) specifies a "6 hour data file beginning with 00z - 05z in the first file of the day". Defaults to 6 |
| `met_file_tres` | Time resolution of meteorological data files. To determine the time resolution in an ARL compatible meteorological data file, refer to the README, including the file naming convention, provided by the data source. For example, the [NOAA HRRR README](https://www.ready.noaa.gov/data/archives/hrrr/README.TXT) specifies a "6 hour data file beginning with 00z - 05z in the first file of the day". Defaults to '6 hours' |
| `met_subgrid_buffer` | Percent to extend footprint area for meteorological subdomain when using `met_subgrid_enable`. Defaults to 0.1 (10%) |
| `met_subgrid_enable` | Enables extraction of spatial subdomains from files in `met_path` using HYSPLIT's `xtrct_grid` binary prior to executing simulations. If enabled, will create files in `<output_wd>/met/`. This can substantially accelerate simulation speed at the cost of increased disk usage. Defaults to disabled |
| `met_subgrid_levels` | If set, extracts the defined number of vertical levels from the meteorological data files to further accelerate simulations. Defaults to `NA`, which includes all vertical levels available |
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1 change: 1 addition & 0 deletions r/dependencies.r
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Expand Up @@ -12,6 +12,7 @@ invisible(lapply(rsc, source))
# Load external libraries
if (!'lib.loc' %in% ls()) lib.loc <- NULL
libs <- load_libs('dplyr',
'lubridate',
'ncdf4',
'parallel',
'raster',
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4 changes: 2 additions & 2 deletions r/run_stilt.r
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Expand Up @@ -52,7 +52,7 @@ yres <- xres
# Meteorological data input
met_path <- '<path_to_arl_meteorological_data>'
met_file_format <- '%Y%m%d.%Hz.hrrra'
n_hours_per_met_file <- 6
met_file_tres <- '6 hours'
met_subgrid_buffer <- 0.2
met_subgrid_enable <- F
met_subgrid_levels <- NA
Expand Down Expand Up @@ -236,13 +236,13 @@ stilt_apply(FUN = simulation_step,
maxdim = maxdim,
maxpar = maxpar,
met_file_format = met_file_format,
met_file_tres = met_file_tres,
met_path = met_path,
met_subgrid_buffer = met_subgrid_buffer,
met_subgrid_enable = met_subgrid_enable,
met_subgrid_levels = met_subgrid_levels,
mgmin = mgmin,
n_hours = n_hours,
n_hours_per_met_file = n_hours_per_met_file,
n_met_min = n_met_min,
ncycl = ncycl,
ndump = ndump,
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42 changes: 21 additions & 21 deletions r/src/find_met_files.r
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Expand Up @@ -7,41 +7,41 @@
#' @param t_start time of simulation start
#' @param n_hours number of hours to run each simulation; negative indicates
#' backward in time
#' @param n_hours_per_met_file number of hours of meteorological data in each
#' met file
#' @param met_path directory to find meteorological data
#' @param met_file_format grep compatible file naming convention to identify
#' meteorological data files necessary for the timing of the simulation
#' indicated by \code{t_start} and \code{n_hours}
#' @param met_path directory to find meteorological data
#' @param met_file_tres time resolution of meteorological data files
#'
#' @import dplyr
#' @import lubridate
#' @export

find_met_files <- function(t_start, n_hours, n_hours_per_met_file,
met_file_format, met_path) {
find_met_files <- function(t_start, n_hours, met_path,
met_file_format, met_file_tres) {
require(dplyr)
require(lubridate)

ts <- as.POSIXct(t_start, tz = 'UTC')
is_backward <- n_hours < 0
met_bracket <- n_hours_per_met_file - 1 # ts can be in the middle of a met file
# Simulation timing
sim_start <- as.POSIXct(t_start, tz = 'UTC')
sim_end <- sim_start + as.difftime(n_hours, units = 'hours')

# Generate the hours to search for
if (is_backward) {
met_hours <- seq(
ts - as.difftime(abs(n_hours) + met_bracket, units = 'hours'),
ts,
by = 3600
)
} else {
met_hours <- seq(
ts - as.difftime(met_bracket, units = 'hours'),
ts + as.difftime(n_hours, units = 'hours'),
by = 3600
)
met_start <- floor_date(min(sim_start, sim_end), unit = met_file_tres)
met_end <- max(sim_start, sim_end)
met_end_ceil <- ceiling_date(met_end, unit = met_file_tres)
if (n_hours < 0
&& hour(met_end) == hour(met_end_ceil) - 1
&& minute(met_end) > 0) {
# If the end time is at the end of a met file,
# add an hour to the end time to include the next file.
# This is necessary to interpolate the last hour of data.
met_end <- met_end_ceil
}
met_times <- seq(met_start, met_end, by = met_file_tres)

# Format the request and remove duplicates
request <- met_hours %>%
request <- met_times %>%
strftime(tz = 'UTC', format = met_file_format) %>%
unique()

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1 change: 1 addition & 0 deletions r/src/link_files.r
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Expand Up @@ -4,6 +4,7 @@
#' @param from location of files
#' @param to location to create links
#'
#' @import R.utils
#' @export

link_files <- function(from, to) {
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12 changes: 6 additions & 6 deletions r/src/simulation_step.r
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Expand Up @@ -53,15 +53,15 @@ simulation_step <- function(before_footprint = list(function() {output}),
lib.loc = NULL,
maxdim = 1,
maxpar = numpar,
met_file_format,
met_file_format,
met_file_tres = '6 hours',
met_path,
met_subgrid_buffer = 0.1,
met_subgrid_enable = F,
met_subgrid_levels = NA,
mgmin = 10,
mhrs = 9999,
n_hours = -24,
n_hours_per_met_file = 6,
n_met_min = 1,
ncycl = 0,
ndump = 0,
Expand Down Expand Up @@ -258,8 +258,8 @@ simulation_step <- function(before_footprint = list(function() {output}),
link_files(exe, rundir)

# Find necessary met files
met_files <- find_met_files(r_run_time, n_hours, n_hours_per_met_file,
met_file_format, met_path)
met_files <- find_met_files(r_run_time, n_hours, met_path,
met_file_format, met_file_tres)
if (length(met_files) < n_met_min) {
msg <- paste('Insufficient number of meteorological files found. Check',
'specifications in run_stilt.r')
Expand All @@ -276,8 +276,8 @@ simulation_step <- function(before_footprint = list(function() {output}),
met_subgrid_buffer = met_subgrid_buffer)

# Find necessary met files for subgrids
met_files <- find_met_files(r_run_time, n_hours, n_hours_per_met_file,
met_file_format, met_path)
met_files <- find_met_files(r_run_time, n_hours, met_path,
met_file_format, met_file_tres)
if (length(met_files) < n_met_min) {
msg <- paste('Insufficient number of meteorological files found. Check',
'specifications in run_stilt.r')
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2 changes: 1 addition & 1 deletion r/stilt_cli.r
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Expand Up @@ -119,13 +119,13 @@ stilt_args <- list(
maxdim = as.numeric(args$maxdim),
maxpar = as.numeric(args$maxpar),
met_file_format = as.character(args$met_file_format),
met_file_tres = as.character(args$met_file_tres),
met_path = as.character(args$met_path),
met_subgrid_buffer = as.numeric(args$met_subgrid_buffer),
met_subgrid_enable = as.logical(args$met_subgrid_enable),
met_subgrid_levels = as.numeric(args$met_subgrid_levels),
mgmin = as.numeric(args$mgmin),
n_hours = as.numeric(args$n_hours),
n_hours_per_met_file = as.numeric(args$n_hours_per_met_file),
n_met_min = as.numeric(args$n_met_min),
ncycl = as.numeric(args$ncycl),
ndump = as.numeric(args$ndump),
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