Mercurial > repos > ecology > srs_spectral_indices

annotate preprocess_S2.r @ 1:0c6db524ae70 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit 0f331043178bbfbe5cda0e31d887971464b3071c
author ecology
date Fri, 07 Apr 2023 16:00:20 +0000
parents 20604db47df5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
1 #Rscript
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
2
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
3 ###########################################
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
4 ## Preprocessing Sentinel 2 data ##
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
5 ###########################################
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
6
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
7 #####Packages : sen2r,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
8 # jqr,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
9 # protolite,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
10 # raster,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
11 # sf,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
12 # rgeos,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
13 # sp,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
14 # raster,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
15 # stars,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
16 # stringr,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
17 # progress,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
18 # rgdal,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
19 # R.utils,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
20 # gdalUtils,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
21 # fasterize,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
22 # XML,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
23 # XML2
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
24
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
25 #####Load arguments
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
26
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
27 args <- commandArgs(trailingOnly = TRUE)
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
28
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
29 if (length(args) < 1) {
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
30 stop("This tool needs at least 1 argument")
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
31 }else {
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
32 data <- args[1]
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
33 source(args[2])
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
34 data_source <- as.character(args[3])
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
35 sat_type <- as.character(args[4])
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
36 }
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
37
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
38 ##____________________________________________________________________##
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
39 ## Define where data is stored and where to write results ##
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
40 ##--------------------------------------------------------------------##
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
41
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
42 #Create a directory where to unzip your folder of data
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
43 dir.create("data_dir")
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
44 unzip(data, exdir = "data_dir")
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
45
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
46 # Result directory
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
47 result_path <- "results"
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
48 dir.create(path = result_path, showWarnings = FALSE, recursive = TRUE)
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
49
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
50 #Csv file for output useless but needed for linter
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
51 write.csv(data_source, "Mission.csv")
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
52
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
53 # define raster path
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
54 if (data_source == "SAFE") {
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
55 path_s2 <- file.path("data_dir", list.files("data_dir", pattern = ".SAFE"))
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
56 #To define the level and know if a correction is needed (convert not ready yet)
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
57 level_info <- get_s2_level(path_s2)
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
58 if (level_info == "L1C") {
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
59 stop("! This tool works for data of L2A level and NOT for the L1C level which is currently a work in progress !")
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
60 }
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
61 }else {
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
62 path_s2 <- file.path("data_dir")
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
63 }
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
64
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
65 ##____________________________________________________________________##
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
66 ## Extract, resample & stack data ##
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
67 ##--------------------------------------------------------------------##
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
68 # define resolution
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
69 resolution <- 10
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
70 # define source of data
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
71 s2source <- data_source
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
72
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
73 s2obj <- extract_from_s2_l2a(path_dir_s2 = path_s2,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
74 path_vector = NULL,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
75 s2source = s2source,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
76 resolution = resolution)
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
77
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
78 ##____________________________________________________________________##
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
79 ## Write CLOUD MASK ##
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
80 ##--------------------------------------------------------------------##
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
81
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
82 # directory for cloud mask
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
83 cloud_path <- file.path(result_path, "CloudMask")
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
84 dir.create(path = cloud_path, showWarnings = FALSE, recursive = TRUE)
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
85 # Filename for cloud mask
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
86 cloudmasks <- save_cloud_s2(s2_stars = s2obj$s2_stack,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
87 cloud_path = cloud_path,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
88 s2source = s2source, saveraw = TRUE)
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
89
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
90 zip_cloud <- file.path("Cloud.zip")
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
91 zip::zip(zip_cloud, cloud_path)
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
92 ##____________________________________________________________________##
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
93 ## Write REFLECTANCE ##
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
94 ##--------------------------------------------------------------------##
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
95
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
96 # directory for Reflectance
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
97 refl_dir <- file.path(result_path, "Reflectance")
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
98 dir.create(path = refl_dir, showWarnings = FALSE, recursive = TRUE)
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
99
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
100 if (data_source == "SAFE") {
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
101 # filename for Reflectance
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
102 refl_path <- file.path(refl_dir, paste(basename(s2obj$s2_bands$GRANULE), "_Refl", sep = ""))
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
103
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
104 # Save Reflectance file as ENVI image with BIL interleaves
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
105 tile_s2 <- substring(strsplit(basename(s2obj$s2_bands$GRANULE), "_")[[1]][2], 2)
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
106 dateacq_s2 <- as.Date(substring(strsplit(basename(s2obj$s2_bands$GRANULE), "_")[[1]][4], 1, 8), format = "%Y%m%d")
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
107 }else {
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
108 # filename for Reflectance
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
109 refl_path <- file.path(refl_dir, paste(basename(s2obj$s2_bands$path_tile_s2), "_Refl", sep = ""))
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
110
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
111 # Save Reflectance file as ENVI image with BIL interleaves
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
112 tile_s2 <- substring(strsplit(basename(s2obj$s2_bands$path_tile_s2), "_")[[1]][2], 2)
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
113 dateacq_s2 <- as.Date(substring(strsplit(basename(s2obj$s2_bands$path_tile_s2), "_")[[1]][4], 1, 8), format = "%Y%m%d")
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
114 }
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
115
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
116 save_data <- save_reflectance_s2(s2_stars = s2obj$s2_stack, refl_path = refl_path,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
117 s2sat = sat_type, tile_s2 = tile_s2, dateacq_s2 = dateacq_s2,
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
118 format = "ENVI", datatype = "Int16", mtd = s2obj$s2_bands$metadata, mtd_msi = s2obj$s2_bands$metadata_MSI)
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
119
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
120 zip_files <- file.path("Refl.zip")
20604db47df5 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
121 zip::zip(zip_files, refl_dir)