Mercurial > repos > ecology > srs_preprocess_s2

annotate preprocess_S2.r @ 0:33a1e15f7252 draft default tip

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planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
author ecology
date Mon, 09 Jan 2023 13:37:05 +0000
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33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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1 #Rscript
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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3 ###########################################
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4 ## Preprocessing Sentinel 2 data ##
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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5 ###########################################
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6
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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7 #####Packages : sen2r,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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8 # jqr,
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9 # protolite,
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10 # raster,
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11 # sf,
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12 # rgeos,
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13 # sp,
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14 # raster,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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15 # stars,
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16 # stringr,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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17 # progress,
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18 # rgdal,
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19 # R.utils,
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20 # gdalUtils,
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21 # fasterize,
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22 # XML,
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23 # XML2
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24
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25 #####Load arguments
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27 args <- commandArgs(trailingOnly = TRUE)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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29 if (length(args) < 1) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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30 stop("This tool needs at least 1 argument")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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31 }else {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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32 data <- args[1]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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33 source(args[2])
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34 data_source <- as.character(args[3])
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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35 sat_type <- as.character(args[4])
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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36 }
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37
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38 ##____________________________________________________________________##
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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39 ## Define where data is stored and where to write results ##
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40 ##--------------------------------------------------------------------##
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41
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42 #Create a directory where to unzip your folder of data
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43 dir.create("data_dir")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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44 unzip(data, exdir = "data_dir")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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45
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46 # Result directory
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47 result_path <- "results"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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48 dir.create(path = result_path, showWarnings = FALSE, recursive = TRUE)
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49
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50 #Csv file for output useless but needed for linter
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51 write.csv(data_source, "Mission.csv")
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52
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53 # define raster path
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54 if (data_source == "SAFE") {
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55 path_s2 <- file.path("data_dir", list.files("data_dir", pattern = ".SAFE"))
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56 #To define the level and know if a correction is needed (convert not ready yet)
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57 level_info <- get_s2_level(path_s2)
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58 if (level_info == "L1C") {
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59 stop("! This tool works for data of L2A level and NOT for the L1C level which is currently a work in progress !")
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60 }
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61 }else {
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62 path_s2 <- file.path("data_dir")
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63 }
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64
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65 ##____________________________________________________________________##
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66 ## Extract, resample & stack data ##
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67 ##--------------------------------------------------------------------##
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68 # define resolution
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69 resolution <- 10
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70 # define source of data
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71 s2source <- data_source
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72
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73 s2obj <- extract_from_s2_l2a(path_dir_s2 = path_s2,
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74 path_vector = NULL,
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75 s2source = s2source,
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76 resolution = resolution)
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77
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78 ##____________________________________________________________________##
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79 ## Write CLOUD MASK ##
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80 ##--------------------------------------------------------------------##
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81
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82 # directory for cloud mask
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83 cloud_path <- file.path(result_path, "CloudMask")
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84 dir.create(path = cloud_path, showWarnings = FALSE, recursive = TRUE)
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85 # Filename for cloud mask
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86 cloudmasks <- save_cloud_s2(s2_stars = s2obj$s2_stack,
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87 cloud_path = cloud_path,
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88 s2source = s2source, saveraw = TRUE)
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89
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90 zip_cloud <- file.path("Cloud.zip")
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91 zip::zip(zip_cloud, cloud_path)
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92 ##____________________________________________________________________##
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93 ## Write REFLECTANCE ##
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94 ##--------------------------------------------------------------------##
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95
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96 # directory for Reflectance
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97 refl_dir <- file.path(result_path, "Reflectance")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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98 dir.create(path = refl_dir, showWarnings = FALSE, recursive = TRUE)
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99
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100 if (data_source == "SAFE") {
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101 # filename for Reflectance
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102 refl_path <- file.path(refl_dir, paste(basename(s2obj$s2_bands$GRANULE), "_Refl", sep = ""))
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103
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104 # Save Reflectance file as ENVI image with BIL interleaves
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105 tile_s2 <- substring(strsplit(basename(s2obj$s2_bands$GRANULE), "_")[[1]][2], 2)
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106 dateacq_s2 <- as.Date(substring(strsplit(basename(s2obj$s2_bands$GRANULE), "_")[[1]][4], 1, 8), format = "%Y%m%d")
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107 }else {
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108 # filename for Reflectance
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109 refl_path <- file.path(refl_dir, paste(basename(s2obj$s2_bands$path_tile_s2), "_Refl", sep = ""))
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110
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111 # Save Reflectance file as ENVI image with BIL interleaves
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112 tile_s2 <- substring(strsplit(basename(s2obj$s2_bands$path_tile_s2), "_")[[1]][2], 2)
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113 dateacq_s2 <- as.Date(substring(strsplit(basename(s2obj$s2_bands$path_tile_s2), "_")[[1]][4], 1, 8), format = "%Y%m%d")
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114 }
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115
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116 save_data <- save_reflectance_s2(s2_stars = s2obj$s2_stack, refl_path = refl_path,
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117 s2sat = sat_type, tile_s2 = tile_s2, dateacq_s2 = dateacq_s2,
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118 format = "ENVI", datatype = "Int16", mtd = s2obj$s2_bands$metadata, mtd_msi = s2obj$s2_bands$metadata_MSI)
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119
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120 zip_files <- file.path("Refl.zip")
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121 zip::zip(zip_files, refl_dir)