Originally posted on 2021-05-07
Last updated 2021-07-02

1 Setup your project

First load the following libraries:

# PLANET API
library(planetR)
library(httr)
library(jsonlite)

# RASTER STUFF
library(raster)
library(stars)
library(sf)

# TIDYNESS
library(stringr)
library(tidyverse)

# PARALLEL
library(future.apply)

2 Project

# Set API
api_key = "" 
site = "MyProjectName"

# Date range of interest
start_year = 2016
end_year   = 2020
start_doy  = as.numeric(format(as.Date('2000-04-15'),"%j"))
end_doy    = as.numeric(format(as.Date('2000-10-15'),"%j"))
date_start = as.Date(paste0(start_year,"-01-01"))+start_doy
date_end   = as.Date(paste0(end_year,"-01-01"))+end_doy

# Metadata filters
cloud_lim    = 0.10 # percent from 0-1
item_name    = "PSScene4Band" #PSOrthoTile, PSScene3Band, Sentinel2L1C 
product      = "analytic_sr" #analytic_b1, analytic_b2 

#(see https://developers.planet.com/docs/data/items-assets/)
#(see https://developers.planet.com/docs/data/items-assets/)
  
# Create Folders
root = "E:/Planet/"
dir.create(root, showWarnings = F)

exportfolder = paste0(root,site,"_",item_name,"_",product,"_",start_year,"_",end_year,"_",start_doy,"_",end_doy,"/")
dir.create(exportfolder, showWarnings = F)
    
aoi_folder <- paste0(exportfolder,"1_aoi/")
dir.create(aoi_folder, showWarnings = F)
    
raw_folder <- paste0(exportfolder,"2_raw/")
dir.create(raw_folder, showWarnings = F)
    
smooth_folder <- paste0(exportfolder,"3_smooth/")
dir.create(smooth_folder, showWarnings = F)
    
png_folder <- paste0(exportfolder,"4_png/")
dir.create(png_folder, showWarnings = F)

gif_folder <- paste0(exportfolder,"5_gif/")
dir.create(gif_folder, showWarnings = F)
    
# Set AOI (many ways to set this!) ultimately just need an extent()
    
my_aoi = mapedit::editMap() # Set in GUI
sf::write_sf(my_aoi, paste0(aoi_folder,site,".gpkg"))
my_aoi <- sf::st_read(paste0(aoi_folder,site,".gpkg"))
# my_aoi %>% mapview::mapview()
bbox  <-  extent(my_aoi)

3 Planet

3.2 Activate

for(i in 1:nrow(response)) {
  planet_activate(i, item_name = item_name)
  print(paste("Activating", i, "of", nrow(response)))}

3.3 Wait

Sys.sleep(10*60)

3.4 Download

plan(multisession)
future_lapply(1:nrow(response), 
              planet_download_withClip, 
              my_aoi = my_aoi, 
              out_dir = raw_folder)

4 Local

4.1 Impute missing data

raw_list <- list.files(raw_folder, pattern = "*.tif$")
bands <- c("blue","green","red","nir")
resolution <- 3

# Make a blank Canvas
my_aoi_r <- my_aoi %>% mutate(val = 1) %>% 
  dplyr::select(val) %>%
  st_transform(crs = st_crs(read_stars(paste0(raw_folder,raw_list[1])))) %>% 
  st_rasterize(st_as_stars(st_bbox(.), 
                           dx = resolution, 
                           dy = resolution, 
                           values = NA_integer_))

# Format dates
dates <- as.character(as.Date(
  str_split(sub(exportfolder,"",raw_list),"_", simplify = T)[,1],
  format = "%Y%m%d"))

# Impute stack function 
imputer <- function(band = 1){
  stack <- do.call(c, lapply(1:length(raw_list), function(i){
    date <- date[i]
    r <- read_stars(paste0(raw_folder,raw_list[i]))[,,,band, drop = T] %>% 
      st_warp(dest = my_aoi_r)
    names(r) <- date
    print(date)
    return(r)})) %>% 
    st_redimension()
  
  write_stars(stack, paste0(smooth_folder,"/",bands[band],"_",resolution,"m.tif"))
      
  my_func_ma <- function(vals){
    vals[vals==0] <- NA
    if(sum(!is.na(vals))>10){
      return(as.numeric(forecast::na.interp(vals)))}else{
        return(vals)}}
  
  stack_imp <- st_apply(stack,
                        MARGIN = c("x", "y"),
                        FUN = my_func_ma)
  
  write_stars(stack_imp, paste0(smooth_folder,"/",bands[band],"_smooth_",
                                resolution,"m.tif"))}
  
plan(multisession)
future_lapply(1:length(bands), imputer)

4.2 Stack to RGB figures

smooth_stacks <- list.files(path = smooth_folder, 
                            pattern = paste0("_smooth_",resolution,"m.tif"))

    
my_rgbER <- function(j){
  myrgb <- raster::stack(
    raster::stack(paste0(smooth_folder,smooth_stacks[4]))[[j]],
    raster::stack(paste0(smooth_folder,smooth_stacks[2]))[[j]],
    raster::stack(paste0(smooth_folder,smooth_stacks[1]))[[j]])
  
  myrgb_stretch <- myrgb %>% st_as_stars() %>% 
    st_rgb(maxColorValue = 65535, probs = c(0.01,0.95), stretch = T)
  
  png(paste0(png_folder,dates[j],"_v2.png"), 
      width = 2000, 
      height = 2000, 
      pointsize = 60)
  myrgb_stretch %>% plot(main = dates[j])
  dev.off()
  return(j)}
    
plan(multisession)
future_lapply(1:length(dates), my_rgbER)

4.3 Animate

png_files <- list.files(png_folder, full.names = T)
      
speed_s <- 0.1
      
gifski::gifski(png_files = png_files, 
               gif_file = paste0(gif_folder,site,"_",speed_s*1000,"ms_full.gif"),
               width = ncol(png::readPNG(png_files[1])),
               height = nrow(png::readPNG(png_files[1])),
               delay = speed_s,
               loop = TRUE,
               progress = TRUE)