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Merge branch 'implement_reservoir' into 'master'
implement support for LPJmL reservoir input files in read_io See merge request lpjml/lpjmlkit!95
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| Package: lpjmlkit | ||
| Type: Package | ||
| Title: Toolkit for Basic LPJmL Handling | ||
| Version: 1.4.2 | ||
| Version: 1.5.0 | ||
| Authors@R: c( | ||
| person("Jannes", "Breier", , "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9055-6904")), | ||
| person("Sebastian","Ostberg", , "[email protected]", role = "aut", comment = c(ORCID = "0000-0002-2368-7015")), | ||
|
|
@@ -54,4 +54,4 @@ Suggests: | |
| sf | ||
| Config/testthat/edition: 3 | ||
| VignetteBuilder: knitr | ||
| Date: 2024-04-09 | ||
| Date: 2024-05-16 | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,150 @@ | ||
| # Internal function to read reservoir input file. Called by read_io(). | ||
| read_io_reservoir <- function(filename, meta_data, subset, silent) { | ||
| if (is.null(meta_data$nbands) || meta_data$nbands != length(band_names_reservoir)) { | ||
| stop( | ||
| "Invalid number of bands ", default(meta_data$nbands, 1), | ||
| " in reservoir file ", filename, ". Expected ", | ||
| length(band_names_reservoir), "." | ||
| ) | ||
| } | ||
| if (!is.null(meta_data$nyear) && meta_data$nyear != 1) { | ||
| stop( | ||
| "Invalid number of years ", meta_data$nyear, | ||
| " in reservoir file ", filename, ". Expected 1." | ||
| ) | ||
| } | ||
| if (!is.null(meta_data$nstep) && meta_data$nstep != 1) { | ||
| stop( | ||
| "Invalid number of time steps per year ", meta_data$nstep, | ||
| " in reservoir file ", filename, ". Expected 1." | ||
| ) | ||
| } | ||
| if (!silent) { | ||
| message( | ||
| "Note: Reservoir file detected, which uses a special file structure. ", | ||
| "Time axis in returned LPJmLData object is not meaningful." | ||
| ) | ||
| } | ||
| if (!silent && !is.null(meta_data$band_names) && | ||
| !all(tolower(meta_data$band_names) == tolower(band_names_reservoir)) | ||
| ) { | ||
| warning( | ||
| "Supplied band_names attribute c(", | ||
| toString(dQuote(meta_data$band_names, q = FALSE)), | ||
| ") does not seem to match implemented reservoir file structure. ", | ||
| "Implemented band order: c(", | ||
| toString(dQuote(band_names_reservoir, q = FALSE)), ").", | ||
| immediate. = TRUE, call. = FALSE | ||
| ) | ||
| } | ||
| # Determine all years in the file | ||
| years <- seq( | ||
| from = default(meta_data$firstyear, 1901), | ||
| by = default(meta_data$timestep, 1), | ||
| length.out = default(meta_data$nyear, 1) | ||
| ) | ||
| # Subsetting by year does not work for restart files | ||
| if ("year" %in% names(subset)) { | ||
| warning( | ||
| "Subsetting by year not possible for reservoir files", | ||
| immediate. = TRUE, call. = FALSE | ||
| ) | ||
| } | ||
|
|
||
| # Open binary file connection | ||
| file_connection <- file(filename, "rb") | ||
| # Ensure that file connection is closed even if function is terminated with an | ||
| # error | ||
| on.exit(if (exists("file_connection")) close(file_connection)) # nolint:undesirable_function_linter. | ||
|
|
||
| # Dimension order during reading. Note: Must be 3 dimensions in total, with | ||
| # "time" being last dimension for code below to work. | ||
| read_band_order <- c("cell", "band", "time") | ||
|
|
||
| # Seek to start position of data | ||
| seek(file_connection, default(meta_data$offset, 0)) | ||
|
|
||
| year_data <- array( | ||
| dim = switch( | ||
| default(meta_data$order, "cellyear"), | ||
| cellyear = c( | ||
| band = unname(default(meta_data$nbands, 1)), | ||
| time = unname(default(meta_data$nstep, 1)), | ||
| cell = unname(meta_data$ncell) | ||
| ), | ||
| yearcell = stop("Order yearcell not supported"), | ||
| cellindex = stop("Order cellindex not supported"), | ||
| cellseq = stop("Order cellindex not supported") | ||
| ) | ||
| ) | ||
|
|
||
| # Assign dimension names to array. | ||
| band_names <- default( | ||
| meta_data$band_names, | ||
| band_names_reservoir | ||
| ) | ||
| cell_dimnames <- seq( | ||
| default(meta_data$firstcell, 0), | ||
| length.out = meta_data$ncell | ||
| ) | ||
| dimnames(year_data) <- switch( | ||
| default(meta_data$order, "cellyear"), | ||
| cellyear = list( # order 1 | ||
| band = band_names, | ||
| time = NULL, # Assign dates later | ||
| cell = cell_dimnames | ||
| ), | ||
| yearcell = stop("Order yearcell not supported"), # order 2 | ||
| cellindex = stop("Order cellindex not supported"), # order 3 | ||
| cellseq = stop("Order cellindex not supported") # order 4 | ||
| ) | ||
| # Read data | ||
| for (cell in seq_len(meta_data$ncell)) { | ||
| year_data[1, 1, cell] <- readBin( | ||
| file_connection, | ||
| n = 1, | ||
| what = integer(), | ||
| size = 4, | ||
| endian = ifelse(meta_data$bigendian, "big", "little") | ||
| ) | ||
| year_data[c(2, 3), 1, cell] <- readBin( | ||
| file_connection, | ||
| n = 2, | ||
| what = double(), | ||
| size = 4, | ||
| endian = ifelse(meta_data$bigendian, "big", "little") | ||
| ) | ||
| year_data[seq(4, 10), 1, cell] <- readBin( | ||
| file_connection, | ||
| n = 7, | ||
| what = integer(), | ||
| size = 4, | ||
| endian = ifelse(meta_data$bigendian, "big", "little") | ||
| ) | ||
| } | ||
| # Close binary file connection | ||
| close(file_connection) | ||
| # Delete file_connection to prevent triggering on.exit expression | ||
| rm(file_connection) | ||
|
|
||
| # Convert to read_band_order and apply subsetting along bands or cells | ||
| year_data <- aperm(year_data, perm = read_band_order) | ||
|
|
||
| # Apply any subsetting along bands or cells | ||
| index <- which(!names(subset) %in% c("day", "month", "year", "time")) | ||
| year_data <- subset_array( | ||
| year_data, | ||
| subset[index], | ||
| drop = FALSE, | ||
| silent = silent | ||
| ) | ||
|
|
||
| # Create and assign time dimension names | ||
| time_dimnames <- create_time_names( | ||
| nstep = default(meta_data$nstep, 1), | ||
| years = years | ||
| ) | ||
| dimnames(year_data)$time <- time_dimnames | ||
|
|
||
| year_data | ||
| } |
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