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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| #' read_traj reads in the output assosciated with each simulation step | ||
| #' @author James Mineau | ||
| #' | ||
| #' @param file filename argument. Must end with .rds (for serialized R data | ||
| #' output, preferred), .h5 (for Hierarchical Data Format output), | ||
| #' or NULL to return the footprint object for programatic use. | ||
| #' rds files do not require any additional libraries and have | ||
| #' better compression. The \code{rhdf5} package is required for .h5 output. | ||
| #' HDF5 output is slightly less efficient than .rds output, but is more | ||
| #' portable and can be read by other languages. | ||
| #' | ||
| #' @import rhdf5 | ||
| #' @export | ||
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| read_traj <- function(file) { | ||
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| # .rds output (preferred) | ||
| if (!is.null(file) && grepl('\\.rds$', file, ignore.case = T)) { | ||
| return(readRDS(file)) | ||
| } | ||
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| output <- list() # Define output list to rebuild | ||
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| # .h5 output | ||
| if (!is.null(file) && grepl('\\.h5$', file, ignore.case = T)) { | ||
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| # Assign current file path | ||
| output$file <- file | ||
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| # Get receptor attributes | ||
| output$receptor <- rhdf5::h5readAttributes(file, 'receptor') | ||
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| # Get particle data | ||
| output$particle <- rhdf5::h5read(file, 'particle') | ||
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| # Get params attributes | ||
| output$params <- rhdf5::h5readAttributes(file, 'params') | ||
| output$params[output$params == "NA"] <- NA | ||
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| # Get particle error info if it exists | ||
| if ('particle_error' %in% rhdf5::h5ls(file)$name) { | ||
| output$particle_error <- rhdf5::h5read(file, 'particle_error') | ||
| output$particle_error_params <- rhdf5::h5readAttributes(file, 'particle_error_params') | ||
| output$particle_error_params[output$particle_error_params == "NA"] <- NA | ||
| } | ||
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| return(output) | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,90 @@ | ||
| #' write_traj writes out the output assosciated with each simulation step | ||
| #' @author James Mineau | ||
| #' | ||
| #' @param traj output created during simulation_step | ||
| #' @param file filename argument. Must end with .rds (for serialized R data | ||
| #' output, preferred), .h5 (for Hierarchical Data Format output), | ||
| #' or NULL to return the footprint object for programatic use. | ||
| #' rds files do not require any additional libraries and have | ||
| #' better compression. The \code{rhdf5} package is required for .h5 output. | ||
| #' HDF5 output is slightly less efficient than .rds output, but is more | ||
| #' portable and can be read by other languages. | ||
| #' | ||
| #' @import rhdf5 | ||
| #' @export | ||
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| write_traj <- function(traj, file) { | ||
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| # Remove existing trajectory file | ||
| if (!is.null(file) && file.exists(file)) | ||
| system(paste('rm', file)) | ||
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| # .rds output (preferred) | ||
| if (!is.null(file) && grepl('\\.rds$', file, ignore.case = T)) { | ||
| saveRDS(traj, file) | ||
| return(file) | ||
| } | ||
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| # .h5 output | ||
| if (!is.null(file) && grepl('\\.h5$', file, ignore.case = T)) { | ||
| # Check if rhdf5 package is installed | ||
| if (!requireNamespace("rhdf5", quietly = TRUE)) { | ||
| stop("The 'rhdf5' package is required for hdf5 output. Please install it.") | ||
| } | ||
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| # Create HDF5 file | ||
| fid <- rhdf5::H5Fcreate(file) | ||
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| # Write file info | ||
| rhdf5::h5writeAttribute(file, fid, 'file') | ||
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| # Create groups | ||
| rhdf5::h5createGroup(fid, 'receptor') | ||
| rhdf5::h5createGroup(fid, 'params') | ||
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| # Write receptor data | ||
| receptor <- rhdf5::H5Gopen(fid, 'receptor') | ||
| rhdf5::h5writeAttribute(as.numeric(traj$receptor$run_time), | ||
| receptor, 'run_time') | ||
| rhdf5::h5writeAttribute(traj$receptor$lati, receptor, 'lati') | ||
| rhdf5::h5writeAttribute(traj$receptor$long, receptor, 'long') | ||
| rhdf5::h5writeAttribute(traj$receptor$zagl, receptor, 'zagl') | ||
| rhdf5::H5Gclose(receptor) | ||
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| # Write particle dataset | ||
| rhdf5::h5write(traj$particle, fid, 'particle') | ||
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| # Create params group | ||
| params <- rhdf5::H5Gopen(fid, 'params') | ||
| for (p in names(traj$params)) { | ||
| val <- traj$params[[p]] | ||
| if (is.na(val)) val <- 'NA' | ||
| rhdf5::h5writeAttribute(val, params, p) | ||
| } | ||
| rhdf5::H5Gclose(params) | ||
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| # Create particle error group if it exists | ||
| if ('particle_error' %in% names(traj)) { | ||
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| # Write particle_error dataset | ||
| rhdf5::h5write(traj$particle_error, fid, 'particle_error') | ||
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| # Create particle_error_param group | ||
| rhdf5::h5createGroup(fid, 'particle_error_params') | ||
| particle_error_params <- rhdf5::H5Gopen(fid, 'particle_error_params') | ||
| for (p in names(traj$particle_error_params)) { | ||
| val <- traj$particle_error_params[[p]] | ||
| if (is.na(val)) val <- 'NA' | ||
| rhdf5::h5writeAttribute(val, particle_error_params, p) | ||
| } | ||
| rhdf5::H5Gclose(particle_error_params) | ||
| } | ||
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| # Close file | ||
| rhdf5::H5Fclose(fid) | ||
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| return(file) | ||
| } | ||
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| return(traj) | ||
| } |