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annotate functions.r @ 1:21e21363a8b4 draft default tip

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planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit 0f331043178bbfbe5cda0e31d887971464b3071c
author ecology
date Fri, 07 Apr 2023 14:38:58 +0000
parents 0931c98270c9
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0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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1 #Rscript
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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3 #########################
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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4 ## Functions ##
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5 #########################
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7 #####Packages : raster
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8 # sp
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9 # ggplot2
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0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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11 ####Set paramaters for all tools using BiodivMapR
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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13 # path for the Mask raster corresponding to image to process
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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14 # expected to be in ENVI HDR format, 1 band, integer 8bits
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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15 # expected values in the raster: 0 = masked, 1 = selected
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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16 # set to FALSE if no mask available
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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17 input_mask_file <- FALSE
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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19 # relative or absolute path for the Directory where results will be stored
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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20 # For each image processed, a subdirectory will be created after its name
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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21 output_dir <- "RESULTS"
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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23 # SPATIAL RESOLUTION
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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24 # resolution of spatial units for alpha and beta diversity maps (in pixels), relative to original image
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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25 # if Res.Map = 10 for images with 10 m spatial resolution, then spatial units will be 10 pixels x 10m = 100m x 100m surfaces
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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26 # rule of thumb: spatial units between 0.25 and 4 ha usually match with ground data
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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27 # too small window_size results in low number of pixels per spatial unit, hence limited range of variation of diversity in the image
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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28 window_size <- 10
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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30 # PCA FILTERING: Set to TRUE if you want second filtering based on PCA outliers to be processed. Slower
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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31 filterpca <- TRUE
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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33 ################################################################################
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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34 ## DEFINE PARAMETERS FOR METHOD ##
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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35 ################################################################################
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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36 nbcpu <- 4
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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37 maxram <- 0.5
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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38 nbclusters <- 50
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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40 ################################################################################
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41 ## PROCESS IMAGE ##
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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42 ################################################################################
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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43 # 1- Filter data in order to discard non vegetated / shaded / cloudy pixels
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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44 ndvi_thresh <- 0.5
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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45 blue_thresh <- 500
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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46 nir_thresh <- 1500
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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47 continuum_removal <- TRUE
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0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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51 #### Convert raster to dataframe
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0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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53 # Convert raster to SpatialPointsDataFrame
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54 convert_raster <- function(data_raster) {
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55 r_pts <- raster::rasterToPoints(data_raster, spatial = TRUE)
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57 # reproject sp object
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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58 geo_prj <- "+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0"
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59 r_pts <- sp::spTransform(r_pts, sp::CRS(geo_prj))
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62 # Assign coordinates to @data slot, display first 6 rows of data.frame
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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63 r_pts@data <- data.frame(r_pts@data, longitude = sp::coordinates(r_pts)[, 1],
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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64 latitude = sp::coordinates(r_pts)[, 2])
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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66 return(r_pts@data)
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67 }
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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70 #### Potting indices
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72 plot_indices <- function(data, titre) {
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73 graph_indices <- ggplot2::ggplot(data) +
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74 ggplot2::geom_point(ggplot2::aes_string(x = data[, 2], y = data[, 3], color = data[, titre]), shape = "square", size = 2) + ggplot2::scale_colour_gradient(low = "blue", high = "orange", na.value = "grey50") +
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75 ggplot2::xlab("Longitude") + ggplot2::ylab("Latitude") +
0931c98270c9 planemo upload for repository https://github.com/Marie59/Sentinel_2A/srs_tools commit b32737c1642aa02cc672534e42c5cb4abe0cd3e7
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76 ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1), plot.title = ggplot2::element_text(color = "black", size = 12, face = "bold")) + ggplot2::ggtitle(titre)
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78 ggplot2::ggsave(paste0(titre, ".png"), graph_indices, width = 12, height = 10, units = "cm")
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79 }