forked from GEO-BON/bon-in-a-box-pipelines
-
Notifications
You must be signed in to change notification settings - Fork 2
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Revert "Add resampling and aggregation options to loadFromStac (GEO-B…
- Loading branch information
Showing
5 changed files
with
110 additions
and
196 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,87 @@ | ||
| ## Script to download heatmaps from STAC | ||
| # and uses the 'predictors' argument | ||
|
|
||
| ## Install required packages | ||
| packages <- c("terra", "rjson", "raster", | ||
| "stars", "gdalcubes", "rstac", "downloader") | ||
| new.packages <- packages[!(packages %in% installed.packages()[,"Package"])] | ||
| if(length(new.packages)) install.packages(new.packages) | ||
|
|
||
| library("terra") | ||
| library("rjson") | ||
| library("raster") | ||
| library("stars") | ||
| library("rstac") | ||
| library("gdalcubes") | ||
| library("downloader") | ||
|
|
||
|
|
||
| setwd(outputFolder) | ||
|
|
||
| input <- fromJSON(file=file.path(outputFolder, "input.json")) | ||
| print("Inputs: ") | ||
| print(input) | ||
|
|
||
|
|
||
| stacURL <- "https://stac.geobon.org/" | ||
| taxa <- input$taxa | ||
|
|
||
| # Check if blank of NULL | ||
| # Sometimes it has more than one raster provided, so check ind 1 | ||
| if(is.null(input$predictors[1]) || input$predictors[1]==""){ | ||
| predictors <- NULL | ||
| }else{ | ||
| predictors <- terra::rast(input$predictors) | ||
| } | ||
|
|
||
| fout <- file.path(outputFolder, paste0("heatmapGBIF-",taxa,".tif")) | ||
|
|
||
| if(!is.null(predictors)){ | ||
| s <- stac(stacURL) | ||
|
|
||
| it_obj <- s |> | ||
| stac_search(collections=c('gbif_heatmaps'),limit=5000) |> get_request() | ||
|
|
||
| # Force each dataset to have the data role. Fix 08/2023 | ||
| for (i in 1:length(it_obj$features)){ | ||
| it_obj$features[[i]]$assets[[1]]$roles<-'data' | ||
| } | ||
|
|
||
| st <- gdalcubes::stac_image_collection(it_obj$features,asset_names=c("data"), | ||
| property_filter=function(f){f$taxa==taxa}) | ||
|
|
||
| # Get extent | ||
| ee = as.list(ext(predictors)) | ||
| names(ee) = c("left", "right", "bottom", "top") | ||
| # Add time | ||
| ee[["t0"]] = "2006-01-01" | ||
| ee[["t1"]] = "2006-01-01" | ||
|
|
||
| v = cube_view(srs = crs(predictors, proj = T), | ||
| extent = ee, | ||
| dx = xres(predictors), dy = yres(predictors), dt = "P1D", | ||
| aggregation= "mean", resampling = "bilinear") | ||
|
|
||
| gdalcubes_options(parallel=TRUE) | ||
|
|
||
| raster_cube(st, v) |> | ||
| write_tif(COG = TRUE, creation_options = list("COMPRESS" = "DEFLATE")) |> | ||
| terra::rast() -> raster.out | ||
|
|
||
| writeRaster(raster.out, fout, overwrite = T) | ||
|
|
||
| }else{ | ||
| # Just download the file (some issues using rstac/gdalcubes) | ||
| dlink <- paste0( | ||
| "https://object-arbutus.cloud.computecanada.ca/bq-io/io/gbif_heatmaps/gbif_", | ||
| taxa, | ||
| "_density_06-2022.tif" | ||
| ) | ||
|
|
||
| download(dlink, destfile = fout) | ||
| } | ||
|
|
||
|
|
||
| output <- list("raster" = fout) | ||
| jsonData <- toJSON(output, indent=2) | ||
| write(jsonData, file.path(outputFolder,"output.json")) |
Binary file not shown.
Oops, something went wrong.