fixing some typos/bugs in the RNetCDF conversion for NetCDF writing p…

…rocess
aestears · Jun 14, 2024 · 8462234 · 8462234
1 parent 4891211
commit 8462234
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Showing 2 changed files with 22 additions and 20 deletions.
diff --git a/functions/netcdf_functions_HPC.R b/functions/netcdf_functions_HPC.R
@@ -323,7 +323,7 @@ NULL
 #' unlink(unlist(tmp_nc))
 #'
 #' @export
-create_netCDF <- function(
+create_netCDF_use <- function(
     filename,
     xyspace,
     data = NULL,
@@ -1145,7 +1145,7 @@ var_defs <- var_names
       )
 
 
-      nc_dimvars <- c(nc_dimvars, "vertical_bnds")
+      #nc_dimvars <- c(nc_dimvars, "vertical_bnds")
     }
 
     if (has_T_timeAxis != "none") {
@@ -1160,7 +1160,7 @@ var_defs <- var_names
       )
 
 
-      nc_dimvars <- c(nc_dimvars, varid_timebnds)
+     # nc_dimvars <- c(nc_dimvars, varid_timebnds)
     }
   }
 
@@ -1208,10 +1208,10 @@ var_defs <- var_names
         shuffle = nc_shuffle,
         chunksizes = c(2L, n_yvals)
       )
-    nc_dimvars <- c(bnds_name)
+    #nc_dimvars <- c(bnds_name)
 
   } else {
-    nc_dimvars <- c()
+    #nc_dimvars <- c()
   }
 
   if (has_Z_verticalAxis != "none") {
@@ -1227,7 +1227,7 @@ var_defs <- var_names
       )
 
 
-    nc_dimvars <- c(nc_dimvars, "vertical_bnds")
+    #nc_dimvars <- c(nc_dimvars, "vertical_bnds")
    }
 
   if (has_T_timeAxis != "none") {
@@ -1242,7 +1242,7 @@ var_defs <- var_names
     )
 
 
-    nc_dimvars <- c(nc_dimvars, varid_timebnds)
+    #nc_dimvars <- c(nc_dimvars, varid_timebnds)
   }
 
   #------ Write dimensional variable values ------
@@ -1287,7 +1287,8 @@ var_defs <- var_names
     RNetCDF::var.put.nc(
       nc, 
       variable =  "vertical_bnds",
-      data = t(vertical_bounds), 
+      data = #t(vertical_bounds), 
+        matrix(data = 1, nrow = nrow(t(vertical_bounds)), ncol = ncol(t(vertical_bounds))),
       start = c(1,1), 
       count = c(2L, n_vertical)
     )
@@ -1369,7 +1370,7 @@ var_defs <- var_names
     for (natt in ns_att_vert) {
       RNetCDF::att.put.nc(
         nc, 
-        variable = "variable",
+        variable = "vertical",
         name = natt,
         value = vertical_attributes[[natt]], 
         type = "NC_CHAR"

diff --git a/main/implementation/01.1_create-netcdfs.R b/main/implementation/01.1_create-netcdfs.R
@@ -4,21 +4,21 @@
 
 
 # rm(list = ls(all = TRUE))
- #library(RNetCDF) # this package has parallel capabilities now, so replace pdbNCDF4??
+ library(RNetCDF) # this package has parallel capabilities now, so replace pdbNCDF4??
  library(ncdf4)
  #library(pbdNCDF4)
  #source('functions/netcdf_functions2.R')
  #source('functions/netcdf_functions_HPC.R')
 # source functions
  # Begin ------------------------------------------------------------------------
  #file_list <- list.files(path = "./functions/", full.names = TRUE)
- 
-  # Iterate over the file list and source each file. TO DO: package all these functions
- # for (file in file_list) {
- #   print(file)
- #   source(file)
- # }
- 
+
+ #Iterate over the file list and source each file. TO DO: package all these functions
+ for (file in file_list) {
+   print(file)
+   source(file)
+ }
+
 #devtools::install_github("r4ecology/rcdo", dependencies = TRUE, force = TRUE)
 #library(rcdo)
 # source('projects/03-Make-Climatologies-netCDF/nc_clip_edit.R')
@@ -296,7 +296,7 @@ for(nc in 1:106){
     names(data_dims_nc) <- c("ns", "nx", "ny", "nz", "nt", "nv")
     # create netCDF 
     # create netCDF 
-    assign(names[nc], create_netCDF(
+    assign(names[nc], create_netCDF_use(
       filename = file.path(Output_folder,
                            paste0(attributes$Name[nc], '_', format(currDate, "%m%Y"), '.nc')),
       overwrite = TRUE,
@@ -318,14 +318,15 @@ for(nc in 1:106){
       nc_shuffle = FALSE,
       nc_deflate = 5,
       global_attributes = nc_att_global, 
-      isParallel = isParallel # set in main runner file
+      isParallel = isParallel, # set in main runner file
+      data_type = "float"
     ))
   } else {
     ## data_dims ---------------------------------
     data_dims_nc <- c(0, 739, 585, 0, nrow(time_bounds), 0)
     names(data_dims_nc) <- c("ns", "nx", "ny", "nz", "nt", "nv")
     # create netCDF 
-    assign(names[nc], create_netCDF(
+    assign(names[nc], create_netCDF_use(
       filename = file.path(Output_folder,
                            paste0(attributes$Name[nc], '_', format(currDate, "%m%Y"), '.nc')),
       overwrite = TRUE,