Mercurial > repos > ecology > srs_diversity_maps

annotate pca_raster.r @ 0:36ff7a0b96dc 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 b32737c1642aa02cc672534e42c5cb4abe0cd3e7
author ecology
date Mon, 09 Jan 2023 13:55:01 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
1 #Rscript
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
2
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
3 ###########################################
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
4 ## Getting PCA raster ##
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
5 ###########################################
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
6
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
7 #####Packages : stars
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
8 # utils
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
9 # biodivmapr
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
10 # raster
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
11 # sf
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
12 # mapview
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
13 # leafpop
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
14 # RColorBrewer
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
15 # labdsv
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
16 # rgdal
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
17 # ggplot2
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
18 # gridExtra
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
19 ## remotes::install_github("jbferet/biodivMapR")
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
20 #####Load arguments
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
21
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
22 args <- commandArgs(trailingOnly = TRUE)
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
23
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
24 #####Import the S2 data
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
25
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
26 if (length(args) < 1) {
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
27 stop("This tool needs at least 1 argument")
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
28 }else {
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
29 data_raster <- args[1]
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
30 rasterheader <- args[2]
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
31 data <- args[3]
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
32 typepca <- as.character(args[4])
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
33 source(args[5])
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
34 }
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
35
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
36 ################################################################################
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
37 ## DEFINE PARAMETERS FOR DATASET TO BE PROCESSED ##
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
38 ################################################################################
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
39 # expected to be in ENVI HDR
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
40
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
41 if (data_raster == "") {
36ff7a0b96dc 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
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
43 dir.create("data_dir")
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
44 unzip(data, exdir = "data_dir")
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
45 # Path to raster
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
46 data_raster <- list.files("data_dir/results/Reflectance", pattern = "_Refl")
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
47 input_image_file <- file.path("data_dir/results/Reflectance", data_raster[1])
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
48 input_header_file <- file.path("data_dir/results/Reflectance", data_raster[2])
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
49
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
50 } else {
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
51 input_image_file <- file.path(getwd(), data_raster, fsep = "/")
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
52 input_header_file <- file.path(getwd(), rasterheader, fsep = "/")
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
53 }
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
54
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
55 ################################################################################
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
56 ## PROCESS IMAGE ##
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
57 ################################################################################
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
58 # 1- Filter data in order to discard non vegetated / shaded / cloudy pixels
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
59 print("PERFORM PCA ON RASTER")
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
60 pca_output <- biodivMapR::perform_PCA(Input_Image_File = input_image_file, Input_Mask_File = input_mask_file,
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
61 Output_Dir = output_dir, TypePCA = typepca, FilterPCA = filterpca, nbCPU = nbcpu, MaxRAM = maxram)
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
62
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
63
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
64 pca_path <- file.path(output_dir, basename(data_raster), typepca, "PCA", "OutputPCA_8_PCs")
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
65 pca_raster <- raster::raster(pca_path)
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
66 get_pca <- convert_raster(pca_raster)
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
67
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
68 colnames(get_pca) <- c("PCA", "longitude", "latitude")
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
69 plot_indices(get_pca, titre = "PCA")
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
70
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
71 write.table(get_pca, file = "PCA.tabular", sep = "\t", dec = ".", na = " ", row.names = FALSE, col.names = TRUE, quote = FALSE)
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
72 #### Get the raster layer files
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
73 pca_files <- file.path("RESULTS", basename(data_raster), typepca, "PCA")
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
74 to_dir_short <- output_dir
36ff7a0b96dc planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
75 file.copy(pca_files, to_dir_short) #copy files from long to short paths