Mercurial > repos > ecology > srs_preprocess_s2

annotate prosail-master/R/Lib_PROSAIL_HybridInversion.R @ 0:33a1e15f7252 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 13:37:05 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
1 # ============================================================================= =
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
2 # prosail
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
3 # Lib_PROSAIL_HybridInversion.R
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
4 # ============================================================================= =
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
5 # PROGRAMMERS:
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
6 # Jean-Baptiste FERET <jb.feret@teledetection.fr>
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
7 # Florian de BOISSIEU <fdeboiss@gmail.com>
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
8 # Copyright 2019 / 11 Jean-Baptiste FERET
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
9 # ============================================================================= =
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
10 # This Library includes functions dedicated to PROSAIL inversion using hybrid
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
11 # approach based on SVM regression
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
12 # ============================================================================= =
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
13
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
14
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
15 #" This function applies SVR model on raster data in order to estimate
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
16 #" vegetation biophysical properties
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
17 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
18 #" @param raster_path character. path for a raster file
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
19 #" @param hybridmodel list. hybrid models produced from train_prosail_inversion
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
20 #" each element of the list corresponds to a set of hybrid models for a vegetation parameter
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
21 #" @param pathout character. path for directory where results are written
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
22 #" @param selectedbands list. list of spectral bands to be selected from raster (identified by name of vegetation parameter)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
23 #" @param bandname character. spectral bands corresponding to the raster
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
24 #" @param maskraster character. path for binary mask defining ON (1) and OFF (0) pixels in the raster
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
25 #" @param multiplyingfactor numeric. multiplying factor used to write reflectance in the raster
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
26 #" --> PROSAIL simulates reflectance between 0 and 1, and raster data expected in the same range
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
27 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
28 #" @return None
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
29 #" @importFrom progress progress_bar
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
30 #" @importFrom stars read_stars
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
31 #" @importFrom raster raster brick blockSize readStart readStop getValues writeStart writeStop writeValues
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
32 #" @import rgdal
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
33 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
34 apply_prosail_inversion <- function(raster_path, hybridmodel, pathout,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
35 selectedbands, bandname,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
36 maskraster = FALSE, multiplyingfactor = 10000) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
37
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
38 # explain which biophysical variables will be computed
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
39 bpvar <- names(hybridmodel)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
40 print("The following biophysical variables will be computed")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
41 print(bpvar)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
42
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
43 # get image dimensions
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
44 if (attr(rgdal::GDALinfo(raster_path, returnStats = FALSE), "driver") == "ENVI") {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
45 hdr <- read_envi_header(get_hdr_name(raster_path))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
46 dimsraster <- list("rows" = hdr$lines, "cols" = hdr$samples, "bands" = hdr$bands)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
47 } else {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
48 dimsraster <- dim(read_stars(raster_path))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
49 dimsraster <- list("rows" = as.numeric(dimsraster[2]), "cols" = as.numeric(dimsraster[1]), "bands" = as.numeric(dimsraster[3]))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
50 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
51
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
52 # Produce a map for each biophysical property
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
53 for (parm in bpvar) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
54 print(paste("Computing", parm, sep = " "))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
55 # read by chunk to avoid memory problem
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
56 blk <- blockSize(brick(raster_path))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
57 # reflectance file
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
58 r_in <- readStart(brick(raster_path))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
59 # mask file
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
60 r_inmask <- FALSE
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
61 if (maskraster == FALSE) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
62 selectpixels <- "ALL"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
63 } else if (!maskraster == FALSE) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
64 if (file.exists(maskraster)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
65 r_inmask <- readStart(raster(maskraster))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
66 } else if (!file.exists(maskraster)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
67 message("WARNING: Mask file does not exist:")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
68 print(maskraster)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
69 message("Processing all image")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
70 selectpixels <- "ALL"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
71 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
72 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
73 # initiate progress bar
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
74 pgbarlength <- length(hybridmodel[[parm]]) * blk$n
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
75 pb <- progress_bar$new(
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
76 format = "Hybrid inversion on raster [:bar] :percent in :elapsedfull, estimated time remaining :eta",
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
77 total = pgbarlength, clear = FALSE, width = 100)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
78
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
79 # output files
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
80 bpvarpath <- file.path(pathout, paste(basename(raster_path), parm, sep = "_"))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
81 bpvarsdpath <- file.path(pathout, paste(basename(raster_path), parm, "STD", sep = "_"))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
82 r_outmean <- writeStart(raster(raster_path), filename = bpvarpath, format = "ENVI", overwrite = TRUE)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
83 r_outsd <- writeStart(raster(raster_path), filename = bpvarsdpath, format = "ENVI", overwrite = TRUE)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
84 selbands <- match(selectedbands[[parm]], bandname)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
85
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
86 # loop over blocks
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
87 for (i in seq_along(blk$row)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
88 # read values for block
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
89 # format is a matrix with rows the cells values and columns the layers
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
90 blockval <- getValues(r_in, row = blk$row[i], nrows = blk$nrows[i])
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
91 fulllength <- dim(blockval)[1]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
92
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
93 if (typeof(r_inmask) == "logical") {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
94 blockval <- blockval[, selbands]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
95 # automatically filter pixels corresponding to negative values
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
96 selectpixels <- which(blockval[, 1] > 0)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
97 blockval <- blockval[selectpixels, ]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
98 } else if (typeof(r_inmask) == "S4") {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
99 maskval <- getValues(r_inmask, row = blk$row[i], nrows = blk$nrows[i])
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
100 selectpixels <- which(maskval == 1)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
101 blockval <- blockval[selectpixels, selbands]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
102 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
103 mean_estimatefull <- NA * vector(length = fulllength)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
104 std_estimatefull <- NA * vector(length = fulllength)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
105 if (length(selectpixels) > 0) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
106 blockval <- blockval / multiplyingfactor
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
107 modelsvr_estimate <- list()
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
108 for (modind in 1:seq_along(hybridmodel[[parm]])) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
109 pb$tick()
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
110 modelsvr_estimate[[modind]] <- predict(hybridmodel[[parm]][[modind]], blockval)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
111 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
112 modelsvr_estimate <- do.call(cbind, modelsvr_estimate)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
113 # final estimated value = mean parm value for all models
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
114 mean_estimate <- rowMeans(modelsvr_estimate)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
115 # "uncertainty" = STD value for all models
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
116 std_estimate <- rowSds(modelsvr_estimate)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
117 mean_estimatefull[selectpixels] <- mean_estimate
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
118 std_estimatefull[selectpixels] <- std_estimate
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
119 } else {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
120 for (modind in 1:seq_along(hybridmodel[[parm]])) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
121 pb$tick()
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
122 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
123 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
124 r_outmean <- writeValues(r_outmean, mean_estimatefull, blk$row[i], format = "ENVI", overwrite = TRUE)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
125 r_outsd <- writeValues(r_outsd, std_estimatefull, blk$row[i], format = "ENVI", overwrite = TRUE)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
126 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
127 # close files
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
128 r_in <- readStop(r_in)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
129 if (typeof(r_inmask) == "S4") {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
130 r_inmask <- readStop(r_inmask)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
131 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
132 r_outmean <- writeStop(r_outmean)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
133 r_outsd <- writeStop(r_outsd)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
134 # write biophysical variable name in headers
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
135 hdr <- read_envi_header(get_hdr_name(bpvarpath))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
136 hdr$`band names` <- paste("{", parm, "}", sep = "")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
137 write_envi_header(hdr, get_hdr_name(bpvarpath))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
138 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
139 print("processing completed")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
140 return(invisible())
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
141 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
142
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
143 #" get hdr name from image file name, assuming it is BIL format
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
144 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
145 #" @param impath path of the image
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
146 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
147 #" @return corresponding hdr
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
148 #" @importFrom tools file_ext file_path_sans_ext
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
149 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
150 get_hdr_name <- function(impath) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
151 if (tools::file_ext(impath) == "") {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
152 impathhdr <- paste(impath, ".hdr", sep = "")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
153 } else if (tools::file_ext(impath) == "bil") {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
154 impathhdr <- gsub(".bil", ".hdr", impath)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
155 } else if (tools::file_ext(impath) == "zip") {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
156 impathhdr <- gsub(".zip", ".hdr", impath)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
157 } else {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
158 impathhdr <- paste(tools::file_path_sans_ext(impath), ".hdr", sep = "")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
159 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
160
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
161 if (!file.exists(impathhdr)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
162 message("WARNING : COULD NOT FIND hdr FILE")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
163 print(impathhdr)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
164 message("Process may stop")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
165 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
166 return(impathhdr)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
167 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
168
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
169 #" This function applies the regression models trained with prosail_hybrid_train
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
170 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
171 #" @param regressionmodels list. List of regression models produced by prosail_hybrid_train
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
172 #" @param refl numeric. LUT of bidirectional reflectances factors used for training
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
173 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
174 #" @return hybridres list. Estimated values corresponding to refl. Includes
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
175 #" - meanestimate = mean value for the ensemble regression model
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
176 #" - stdestimate = std value for the ensemble regression model
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
177 #" @importFrom stats predict
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
178 #" @importFrom matrixStats rowSds
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
179 #" @importFrom progress progress_bar
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
180 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
181
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
182 prosail_hybrid_apply <- function(regressionmodels, refl) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
183
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
184 # make sure refl is right dimensions
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
185 refl <- t(refl)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
186 nbfeatures <- regressionmodels[[1]]$dim
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
187 if (!ncol(refl) == nbfeatures && nrow(refl) == nbfeatures) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
188 refl <- t(refl)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
189 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
190 nbensemble <- length(regressionmodels)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
191 estimatedval <- list()
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
192 pb <- progress_bar$new(
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
193 format = "Applying SVR models [:bar] :percent in :elapsed",
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
194 total = nbensemble, clear = FALSE, width = 100)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
195 for (i in 1:nbensemble) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
196 pb$tick()
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
197 estimatedval[[i]] <- predict(regressionmodels[[i]], refl)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
198 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
199 estimatedval <- do.call(cbind, estimatedval)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
200 meanestimate <- rowMeans(estimatedval)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
201 stdestimate <- rowSds(estimatedval)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
202 hybridres <- list("meanestimate" = meanestimate, "stdestimate" = stdestimate)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
203 return(hybridres)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
204 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
205
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
206 #" This function trains a suppot vector regression for a set of variables based on spectral data
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
207 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
208 #" @param brf_lut numeric. LUT of bidirectional reflectances factors used for training
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
209 #" @param inputvar numeric. biophysical parameter corresponding to the reflectance
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
210 #" @param figplot Boolean. Set to TRUE if you want a scatterplot
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
211 #" @param nbensemble numeric. Number of individual subsets should be generated from brf_lut
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
212 #" @param withreplacement Boolean. should subsets be generated with or without replacement?
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
213 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
214 #" @return modelssvr list. regression models trained for the retrieval of inputvar based on brf_lut
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
215 #" @importFrom liquidSVM svmRegression
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
216 #" @importFrom stats predict
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
217 #" @importFrom progress progress_bar
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
218 #" @importFrom graphics par
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
219 #" @importFrom expandFunctions reset.warnings
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
220 #" @importFrom stringr str_split
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
221 #" @importFrom simsalapar tryCatch.W.E
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
222 #" @import dplyr
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
223 #" @import ggplot2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
224 # @" @import caret
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
225 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
226
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
227 prosail_hybrid_train <- function(brf_lut, inputvar, figplot = FALSE, nbensemble = 20, withreplacement = FALSE) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
228
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
229 x <- y <- ymean <- ystdmin <- ystdmax <- NULL
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
230 # split the LUT into nbensemble subsets
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
231 nbsamples <- length(inputvar)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
232 if (dim(brf_lut)[2] == nbsamples) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
233 brf_lut <- t(brf_lut)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
234 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
235
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
236 # if subsets are generated from brf_lut with replacement
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
237 if (withreplacement == TRUE) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
238 subsets <- list()
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
239 samples_per_run <- round(nbsamples / nbensemble)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
240 for (run in (1:nbensemble)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
241 subsets[[run]] <- sample(seq(1, nbsamples), samples_per_run, replace = TRUE)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
242 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
243 # if subsets are generated from brf_lut without replacement
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
244 } else if (withreplacement == FALSE) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
245 subsets <- split(sample(seq(1, nbsamples, by = 1)), seq(1, nbensemble, by = 1))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
246 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
247
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
248 # run training for each subset
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
249 modelssvr <- list()
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
250 predictedyall <- list()
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
251 tunedmodelyall <- list()
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
252 pb <- progress_bar$new(
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
253 format = "Training SVR on subsets [:bar] :percent in :elapsed",
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
254 total = nbensemble, clear = FALSE, width = 100)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
255 for (i in 1:nbensemble) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
256 pb$tick()
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
257 Sys.sleep(1 / 100)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
258 trainingset <- list()
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
259 trainingset$X <- brf_lut[subsets[i][[1]], ]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
260 trainingset$Y <- inputvar[subsets[i][[1]]]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
261 # liquidSVM
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
262 r1 <- tryCatch.W.E(tunedmodel <- liquidSVM::svmRegression(trainingset$X, trainingset$Y))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
263 if (!is.null(r1$warning)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
264 msg <- r1$warning$message
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
265 valgamma <- str_split(string = msg, pattern = "gamma=")[[1]][2]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
266 vallambda <- str_split(string = msg, pattern = "lambda=")[[1]][2]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
267 if (!is.na(as.numeric(valgamma))) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
268 message("Adjusting Gamma accordingly")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
269 valgamma <- as.numeric(valgamma)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
270 tunedmodel <- liquidSVM::svmRegression(trainingset$X, trainingset$Y, min_gamma = valgamma)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
271 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
272 if (!is.na(as.numeric(vallambda))) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
273 message("Adjusting Lambda accordingly")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
274 vallambda <- as.numeric(vallambda)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
275 tunedmodel <- liquidSVM::svmRegression(trainingset$X, trainingset$Y, min_lambda = vallambda)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
276 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
277 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
278 modelssvr[[i]] <- tunedmodel
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
279 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
280
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
281 # if scatterplots needed
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
282 if (figplot == TRUE) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
283 # predict for full brf_lut
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
284 for (i in 1:nbensemble) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
285 tunedmodely <- stats::predict(modelssvr[[i]], brf_lut)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
286 tunedmodelyall <- cbind(tunedmodelyall, matrix(tunedmodely, ncol = 1))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
287 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
288 # plot prediction
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
289 df <- data.frame(x = rep(1:nbsamples, nbensemble), y = as.numeric(matrix(tunedmodelyall, ncol = 1)))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
290 df_summary <- df %>%
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
291 dplyr::group_by(x) %>%
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
292 summarize(ymin = min(y), ystdmin = mean(y) - sd(y),
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
293 ymax = max(y), ystdmax = mean(y) + sd(y),
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
294 ymean = mean(y))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
295 par(mar = rep(.1, 4))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
296 p <- ggplot(df_summary, aes(x = inputvar, y = ymean)) +
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
297 geom_point(size = 2) +
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
298 geom_errorbar(aes(ymin = ystdmin, ymax = ystdmax))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
299 meanpredict <- rowMeans(matrix(as.numeric(tunedmodelyall), ncol = nbensemble))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
300 print(p)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
301 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
302 return(modelssvr)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
303 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
304
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
305 #" Reads ENVI hdr file
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
306 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
307 #" @param hdrpath Path of the hdr file
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
308 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
309 #" @return list of the content of the hdr file
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
310 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
311 read_envi_header <- function(hdrpath) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
312 if (!grepl(".hdr$", hdrpath)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
313 stop("File extension should be .hdr")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
314 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
315 hdr <- readLines(hdrpath)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
316 ## check ENVI at beginning of file
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
317 if (!grepl("ENVI", hdr[1])) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
318 stop("Not an ENVI header (ENVI keyword missing)")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
319 } else {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
320 hdr <- hdr [-1]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
321 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
322 ## remove curly braces and put multi-line key-value-pairs into one line
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
323 hdr <- gsub("\\{([^}]*)\\}", "\\1", hdr)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
324 l <- grep("\\{", hdr)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
325 r <- grep("\\}", hdr)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
326
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
327 if (length(l) != length(r)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
328 stop("Error matching curly braces in header (differing numbers).")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
329 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
330
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
331 if (any(r <= l)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
332 stop("Mismatch of curly braces in header.")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
333 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
334
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
335 hdr[l] <- sub("\\{", "", hdr[l])
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
336 hdr[r] <- sub("\\}", "", hdr[r])
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
337
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
338 for (i in rev(seq_along(l))) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
339 hdr <- c(
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
340 hdr [seq_len(l [i] - 1)],
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
341 paste(hdr [l [i]:r [i]], collapse = "\n"),
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
342 hdr [-seq_len(r [i])]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
343 )
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
344 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
345
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
346 ## split key = value constructs into list with keys as names
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
347 hdr <- sapply(hdr, split_line, " = ", USE.NAMES = FALSE)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
348 names(hdr) <- tolower(names(hdr))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
349
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
350 ## process numeric values
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
351 tmp <- names(hdr) %in% c(
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
352 "samples", "lines", "bands", "header offset", "data type",
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
353 "byte order", "default bands", "data ignore value",
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
354 "wavelength", "fwhm", "data gain values"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
355 )
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
356 hdr [tmp] <- lapply(hdr [tmp], function(x) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
357 as.numeric(unlist(strsplit(x, ",")))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
358 })
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
359
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
360 return(hdr)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
361 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
362
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
363 #" ENVI functions
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
364 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
365 #" based on https: / / github.com / cran / hyperSpec / blob / master / R / read.ENVI.R
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
366 #" added wavelength, fwhm, ... to header reading
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
367 #" Title
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
368 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
369 #" @param x character.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
370 #" @param separator character
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
371 #" @param trim_blank boolean.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
372 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
373 #" @return list.
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
374 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
375 split_line <- function(x, separator, trim_blank = TRUE) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
376 tmp <- regexpr(separator, x)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
377 key <- substr(x, 1, tmp - 1)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
378 value <- substr(x, tmp + 1, nchar(x))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
379 if (trim_blank) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
380 blank_pattern <- "^[[:blank:]]*([^[:blank:]] + .*[^[:blank:]] + )[[:blank:]]*$"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
381 key <- sub(blank_pattern, "\\1", key)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
382 value <- sub(blank_pattern, "\\1", value)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
383 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
384 value <- as.list(value)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
385 names(value) <- key
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
386 return(value)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
387 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
388
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
389 #" This function performs full training for hybrid invrsion using SVR with
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
390 #" values for default parameters
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
391 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
392 #" @param minval list. minimum value for input parameters sampled to produce a training LUT
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
393 #" @param maxval list. maximum value for input parameters sampled to produce a training LUT
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
394 #" @param typedistrib list. Type of distribution. Either "Uniform" or "Gaussian"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
395 #" @param gaussiandistrib list. Mean value and STD corresponding to the parameters sampled with gaussian distribution
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
396 #" @param parmset list. list of input parameters set to a specific value
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
397 #" @param nbsamples numeric. number of samples in training LUT
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
398 #" @param nbsamplesperrun numeric. number of training sample per individual regression model
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
399 #" @param nbmodels numeric. number of individual models to be run for ensemble
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
400 #" @param replacement bolean. is there replacement in subsampling?
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
401 #" @param sailversion character. Either 4SAIL or 4SAIL2
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
402 #" @param parms2estimate list. list of input parameters to be estimated
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
403 #" @param bands2select list. list of bands used for regression for each input parameter
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
404 #" @param noiselevel list. list of noise value added to reflectance (defined per input parm)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
405 #" @param specprospect list. Includes optical constants required for PROSPECT
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
406 #" @param specsoil list. Includes either dry soil and wet soil, or a unique soil sample if the psoil parameter is not inverted
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
407 #" @param specatm list. Includes direct and diffuse radiation for clear conditions
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
408 #" @param path_results character. path for results
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
409 #" @param figplot boolean. Set TRUE to get scatterplot of estimated biophysical variable during training step
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
410 #" @param force4lowlai boolean. Set TRUE to artificially reduce leaf chemical constituent content for low LAI
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
411 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
412 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
413 #" @return modelssvr list. regression models trained for the retrieval of inputvar based on brf_lut
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
414 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
415
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
416 train_prosail_inversion <- function(minval = NULL, maxval = NULL,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
417 typedistrib = NULL, gaussiandistrib = NULL, parmset = NULL,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
418 nbsamples = 2000, nbsamplesperrun = 100, nbmodels = 20, replacement = TRUE,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
419 sailversion = "4SAIL",
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
420 parms2estimate = "lai", bands2select = NULL, noiselevel = NULL,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
421 specprospect = NULL, specsoil = NULL, specatm = NULL,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
422 path_results = "./", figplot = FALSE, force4lowlai = TRUE) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
423
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
424 ###===================================================================###
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
425 ### 1- PRODUCE A LUT TO TRAIN THE HYBRID INVERSION ###
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
426 ###===================================================================###
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
427 # Define sensor characteristics
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
428 if (is.null(specprospect)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
429 specprospect <- prosail::specprospect
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
430 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
431 if (is.null(specsoil)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
432 specsoil <- prosail::specsoil
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
433 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
434 if (is.null(specprospect)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
435 specatm <- prosail::specatm
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
436 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
437 # define distribution for parameters to be sampled
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
438 if (is.null(typedistrib)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
439 typedistrib <- data.frame("CHL" = "Uniform", "CAR" = "Uniform", "EWT" = "Uniform", "ANT" = "Uniform", "LMA" = "Uniform", "N" = "Uniform", "BROWN" = "Uniform",
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
440 "psoil" = "Uniform", "LIDFa" = "Uniform", "lai" = "Uniform", "q" = "Uniform", "tto" = "Uniform", "tts" = "Uniform", "psi" = "Uniform")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
441 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
442 if (is.null(gaussiandistrib)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
443 gaussiandistrib <- list("Mean" = NULL, "Std" = NULL)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
444 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
445 if (is.null(minval)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
446 minval <- data.frame("CHL" = 10, "CAR" = 0, "EWT" = 0.01, "ANT" = 0, "LMA" = 0.005, "N" = 1.0, "psoil" = 0.0, "BROWN" = 0.0,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
447 "LIDFa" = 20, "lai" = 0.5, "q" = 0.1, "tto" = 0, "tts" = 20, "psi" = 80)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
448 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
449 if (is.null(maxval)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
450 maxval <- data.frame("CHL" = 75, "CAR" = 15, "EWT" = 0.03, "ANT" = 2, "LMA" = 0.03, "N" = 2.0, "psoil" = 1.0, "BROWN" = 0.5,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
451 "LIDFa" = 70, "lai" = 7, "q" = 0.2, "tto" = 5, "tts" = 30, "psi" = 110)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
452 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
453 # define min and max values
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
454 # fixed parameters
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
455 if (is.null(parmset)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
456 parmset <- data.frame("TypeLidf" = 2, "alpha" = 40)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
457 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
458 # produce input parameters distribution
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
459 if (sailversion == "4SAIL") {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
460 inputprosail <- get_distribution_input_prosail(minval, maxval, parmset, nbsamples,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
461 typedistrib = typedistrib,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
462 Mean = gaussiandistrib$Mean, Std = gaussiandistrib$Std,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
463 force4lowlai = force4lowlai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
464 } else if (sailversion == "4SAIL2") {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
465 inputprosail <- get_distribution_input_prosail2(minval, maxval, parmset, nbsamples,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
466 typedistrib = typedistrib,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
467 Mean = gaussiandistrib$Mean, Std = gaussiandistrib$Std,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
468 force4lowlai = force4lowlai)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
469 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
470 if (sailversion == "4SAIL2") {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
471 # Definition of Cv && update LAI
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
472 maxlai <- min(c(maxval$lai), 4)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
473 inputprosail$Cv <- NA * inputprosail$lai
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
474 inputprosail$Cv[which(inputprosail$lai > maxlai)] <- 1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
475 inputprosail$Cv[which(inputprosail$lai <= maxlai)] <- (1 / maxlai) + inputprosail$lai[which(inputprosail$lai <= maxlai)] / (maxlai + 1)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
476 inputprosail$Cv <- inputprosail$Cv * matrix(rnorm(length(inputprosail$Cv), mean = 1, sd = 0.1))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
477 inputprosail$Cv[which(inputprosail$Cv < 0)] <- 0
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
478 inputprosail$Cv[which(inputprosail$Cv > 1)] <- 1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
479 inputprosail$Cv[which(inputprosail$lai > maxlai)] <- 1
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
480 inputprosail$fraction_brown <- 0 + 0 * inputprosail$lai
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
481 inputprosail$diss <- 0 + 0 * inputprosail$lai
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
482 inputprosail$Zeta <- 0.2 + 0 * inputprosail$lai
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
483 inputprosail$lai <- inputprosail$lai * inputprosail$Cv
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
484 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
485
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
486 # generate LUT of BRF corresponding to inputprosail, for a sensor
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
487 brf_lut <- Generate_LUT_BRF(sailversion = sailversion, inputprosail = inputprosail,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
488 specprospect = specprospect, specsoil = specsoil, specatm = specatm)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
489
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
490 # write parameters LUT
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
491 output <- matrix(unlist(inputprosail), ncol = length(inputprosail), byrow = FALSE)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
492 filename <- file.path(path_results, "PROSAIL_LUT_InputParms.txt")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
493 write.table(x = format(output, digits = 3), file = filename, append = FALSE, quote = FALSE,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
494 col.names = names(inputprosail), row.names = FALSE, sep = "\t")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
495 # Write BRF LUT corresponding to parameters LUT
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
496 filename <- file.path(path_results, "PROSAIL_LUT_reflectance.txt")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
497 write.table(x = format(t(brf_lut), digits = 5), file = filename, append = FALSE, quote = FALSE,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
498 col.names = specprospect$lambda, row.names = FALSE, sep = "\t")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
499
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
500 # Which bands will be used for inversion?
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
501 if (is.null(bands2select)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
502 bands2select <- list()
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
503 for (parm in parms2estimate) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
504 bands2select[[parm]] <- seq(1, length(specprospect$lambda))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
505 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
506 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
507 # Add gaussian noise to reflectance LUT: one specific LUT per parameter
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
508 if (is.null(noiselevel)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
509 noiselevel <- list()
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
510 for (parm in parms2estimate) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
511 noiselevel[[parm]] <- 0.01
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
512 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
513 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
514
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
515 # produce LIT with noise
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
516 brf_lut_noise <- list()
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
517 for (parm in parms2estimate) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
518 brf_lut_noise[[parm]] <- brf_lut[bands2select[[parm]], ] + brf_lut[bands2select[[parm]], ] * matrix(rnorm(nrow(brf_lut[bands2select[[parm]], ]) * ncol(brf_lut[bands2select[[parm]], ]),
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
519 0, noiselevel[[parm]]), nrow = nrow(brf_lut[bands2select[[parm]], ]))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
520 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
521
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
522 ###===================================================================###
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
523 ### PERFORM HYBRID INVERSION ###
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
524 ###===================================================================###
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
525 # train SVR for each variable and each run
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
526 modelsvr <- list()
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
527 for (parm in parms2estimate) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
528 colparm <- which(parm == names(inputprosail))
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
529 inputvar <- inputprosail[[colparm]]
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
530 modelsvr[[parm]] <- prosail_hybrid_train(brf_lut = brf_lut_noise[[parm]], inputvar = inputvar,
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
531 figplot = figplot, nbensemble = nbmodels, withreplacement = replacement)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
532 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
533 return(modelsvr)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
534 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
535
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
536 #" writes ENVI hdr file
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
537 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
538 #" @param hdr content to be written
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
539 #" @param hdrpath Path of the hdr file
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
540 #"
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
541 #" @return None
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
542 #" @importFrom stringr str_count
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
543 #" @export
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
544 write_envi_header <- function(hdr, hdrpath) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
545 h <- lapply(hdr, function(x) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
546 if (length(x) > 1 || (is.character(x) && stringr::str_count(x, "\\w + ") > 1)) {
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
547 x <- paste0("{", paste(x, collapse = ","), "}")
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
548 }
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
549 # convert last numerics
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
550 x <- as.character(x)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
551 })
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
552 writeLines(c("ENVI", paste(names(hdr), h, sep = "=")), con = hdrpath)
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
553 return(invisible())
33a1e15f7252 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
ecology
parents:
diff changeset
554 }