|
0
|
1 #Rscript
|
|
|
2
|
|
|
3 ###########################################
|
|
|
4 ## Preprocessing Sentinel 2 data ##
|
|
|
5 ###########################################
|
|
|
6
|
|
|
7 #####Packages : sen2r,
|
|
|
8 # jqr,
|
|
|
9 # protolite,
|
|
|
10 # raster,
|
|
|
11 # sf,
|
|
|
12 # rgeos,
|
|
|
13 # sp,
|
|
|
14 # raster,
|
|
|
15 # stars,
|
|
|
16 # stringr,
|
|
|
17 # progress,
|
|
|
18 # rgdal,
|
|
|
19 # R.utils,
|
|
|
20 # gdalUtils,
|
|
|
21 # fasterize,
|
|
|
22 # XML,
|
|
|
23 # XML2
|
|
|
24
|
|
|
25 #####Load arguments
|
|
|
26
|
|
|
27 args <- commandArgs(trailingOnly = TRUE)
|
|
|
28
|
|
|
29 if (length(args) < 1) {
|
|
|
30 stop("This tool needs at least 1 argument")
|
|
|
31 }else {
|
|
|
32 data <- args[1]
|
|
|
33 source(args[2])
|
|
|
34 data_source <- as.character(args[3])
|
|
|
35 sat_type <- as.character(args[4])
|
|
|
36 }
|
|
|
37
|
|
|
38 ##____________________________________________________________________##
|
|
|
39 ## Define where data is stored and where to write results ##
|
|
|
40 ##--------------------------------------------------------------------##
|
|
|
41
|
|
|
42 #Create a directory where to unzip your folder of data
|
|
|
43 dir.create("data_dir")
|
|
|
44 unzip(data, exdir = "data_dir")
|
|
|
45
|
|
|
46 # Result directory
|
|
|
47 result_path <- "results"
|
|
|
48 dir.create(path = result_path, showWarnings = FALSE, recursive = TRUE)
|
|
|
49
|
|
|
50 #Csv file for output useless but needed for linter
|
|
|
51 write.csv(data_source, "Mission.csv")
|
|
|
52
|
|
|
53 # define raster path
|
|
|
54 if (data_source == "SAFE") {
|
|
|
55 path_s2 <- file.path("data_dir", list.files("data_dir", pattern = ".SAFE"))
|
|
|
56 #To define the level and know if a correction is needed (convert not ready yet)
|
|
|
57 level_info <- get_s2_level(path_s2)
|
|
|
58 if (level_info == "L1C") {
|
|
|
59 stop("! This tool works for data of L2A level and NOT for the L1C level which is currently a work in progress !")
|
|
|
60 }
|
|
|
61 }else {
|
|
|
62 path_s2 <- file.path("data_dir")
|
|
|
63 }
|
|
|
64
|
|
|
65 ##____________________________________________________________________##
|
|
|
66 ## Extract, resample & stack data ##
|
|
|
67 ##--------------------------------------------------------------------##
|
|
|
68 # define resolution
|
|
|
69 resolution <- 10
|
|
|
70 # define source of data
|
|
|
71 s2source <- data_source
|
|
|
72
|
|
|
73 s2obj <- extract_from_s2_l2a(path_dir_s2 = path_s2,
|
|
|
74 path_vector = NULL,
|
|
|
75 s2source = s2source,
|
|
|
76 resolution = resolution)
|
|
|
77
|
|
|
78 ##____________________________________________________________________##
|
|
|
79 ## Write CLOUD MASK ##
|
|
|
80 ##--------------------------------------------------------------------##
|
|
|
81
|
|
|
82 # directory for cloud mask
|
|
|
83 cloud_path <- file.path(result_path, "CloudMask")
|
|
|
84 dir.create(path = cloud_path, showWarnings = FALSE, recursive = TRUE)
|
|
|
85 # Filename for cloud mask
|
|
|
86 cloudmasks <- save_cloud_s2(s2_stars = s2obj$s2_stack,
|
|
|
87 cloud_path = cloud_path,
|
|
|
88 s2source = s2source, saveraw = TRUE)
|
|
|
89
|
|
|
90 zip_cloud <- file.path("Cloud.zip")
|
|
|
91 zip::zip(zip_cloud, cloud_path)
|
|
|
92 ##____________________________________________________________________##
|
|
|
93 ## Write REFLECTANCE ##
|
|
|
94 ##--------------------------------------------------------------------##
|
|
|
95
|
|
|
96 # directory for Reflectance
|
|
|
97 refl_dir <- file.path(result_path, "Reflectance")
|
|
|
98 dir.create(path = refl_dir, showWarnings = FALSE, recursive = TRUE)
|
|
|
99
|
|
|
100 if (data_source == "SAFE") {
|
|
|
101 # filename for Reflectance
|
|
|
102 refl_path <- file.path(refl_dir, paste(basename(s2obj$s2_bands$GRANULE), "_Refl", sep = ""))
|
|
|
103
|
|
|
104 # Save Reflectance file as ENVI image with BIL interleaves
|
|
|
105 tile_s2 <- substring(strsplit(basename(s2obj$s2_bands$GRANULE), "_")[[1]][2], 2)
|
|
|
106 dateacq_s2 <- as.Date(substring(strsplit(basename(s2obj$s2_bands$GRANULE), "_")[[1]][4], 1, 8), format = "%Y%m%d")
|
|
|
107 }else {
|
|
|
108 # filename for Reflectance
|
|
|
109 refl_path <- file.path(refl_dir, paste(basename(s2obj$s2_bands$path_tile_s2), "_Refl", sep = ""))
|
|
|
110
|
|
|
111 # Save Reflectance file as ENVI image with BIL interleaves
|
|
|
112 tile_s2 <- substring(strsplit(basename(s2obj$s2_bands$path_tile_s2), "_")[[1]][2], 2)
|
|
|
113 dateacq_s2 <- as.Date(substring(strsplit(basename(s2obj$s2_bands$path_tile_s2), "_")[[1]][4], 1, 8), format = "%Y%m%d")
|
|
|
114 }
|
|
|
115
|
|
|
116 save_data <- save_reflectance_s2(s2_stars = s2obj$s2_stack, refl_path = refl_path,
|
|
|
117 s2sat = sat_type, tile_s2 = tile_s2, dateacq_s2 = dateacq_s2,
|
|
|
118 format = "ENVI", datatype = "Int16", mtd = s2obj$s2_bands$metadata, mtd_msi = s2obj$s2_bands$metadata_MSI)
|
|
|
119
|
|
|
120 zip_files <- file.path("Refl.zip")
|
|
|
121 zip::zip(zip_files, refl_dir)
|
