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Grid-Generate_plot_polygons.R
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Grid-Generate_plot_polygons.R
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########################################################
# This module generates plot polygons
#
# Edited: 21.2.2022
########################################################
# https://rdrr.io/cran/sf/man/st_bbox.html
generate_plot_polygons <- function(p,
Plot_type,
PlotCorner_X,
PlotCorner_Y,
Plot_ref_point,
Plot_dim1,
Plot_dim2,
map_projection) {
print("POLY 0")
p_df <- st_drop_geometry( p )
print("POLY 1")
my_spatial_polys_df_All <- NA
Plots_n <- ifelse(Plot_type == 'NFMA', 4, length(unique(p_df$Plot_ID)))
zonelist <- unique(p_df$zone)
if (Plot_type=='Z' & length(PlotCorner_X)==1) {
PlotCorner_X <- eval(parse(text=paste("c(", PlotCorner_X, ")", sep="")))
PlotCorner_Y <- eval(parse(text=paste("c(", PlotCorner_Y, ")", sep="")))
}
# geom_plot_x, index: 1: no rotation, 2: -90 degrees, 3: 90 degrees
# order of corner points (geom_plot_x,geom_plot_y): NW,NE,SE,SW
if (Plot_type == 'Z') {
geom_plot_x <- PlotCorner_X
geom_plot_y <- PlotCorner_Y
} else if (Plot_ref_point == 'SW' | Plot_ref_point == 'WS') {
geom_plot_x <- c(0, Plot_dim1, Plot_dim1, 0)
geom_plot_y <- c(Plot_dim2, Plot_dim2, 0, 0)
} else if (Plot_ref_point == 'NW' | Plot_ref_point == 'WN') {
geom_plot_x <- c(0, Plot_dim1, Plot_dim1, 0)
geom_plot_y <- c(0, 0, -Plot_dim2, -Plot_dim2)
} else if (Plot_ref_point == 'C' & Plot_type == 'R') {
geom_plot_x <- c(-Plot_dim1 / 2, Plot_dim1 / 2, Plot_dim1 / 2, -Plot_dim1 / 2)
geom_plot_y <- c(Plot_dim2 / 2, Plot_dim2 / 2, -Plot_dim2 / 2, -Plot_dim2 / 2)
}
#
# direction = 1 # counter-clock
# new_height = Plot_dim1 * direction
# new_width = -Plot_dim2 * direction
# Plot_dim1a = new_width
# Plot_dim2a = new_height
#
# if (Plot_type == 'Z') {
# geom_plot_x[2] <- PlotCorner_X
# geom_plot_y[2] <- PlotCorner_Y
# } else if (Plot_ref_point == 'SW' | Plot_ref_point == 'WS') {
# geom_plot_x[2] <- c(0, Plot_dim1a, Plot_dim1a, 0)
# geom_plot_y[2] <- c(Plot_dim2, Plot_dim2, 0, 0)
# } else if (Plot_ref_point == 'NW' | Plot_ref_point == 'WN') {
# geom_plot_x[2] <- c(0, Plot_dim1a, Plot_dim1a, 0)
# geom_plot_y[2] <- c(0, 0, -Plot_dim2a, -Plot_dim2a)
# } else if (Plot_ref_point == 'C' & Plot_type == 'R') {
# geom_plot_x[2] <- c(-Plot_dim1a / 2, Plot_dim1a / 2, Plot_dim1a / 2, -Plot_dim1a / 2)
# geom_plot_y[2] <- c( Plot_dim2a / 2, Plot_dim2a / 2, -Plot_dim2a / 2, -Plot_dim2a / 2)
# }
#
# direction = -1 # counter-clock
# new_height = Plot_dim1 * direction
# new_width = -Plot_dim2 * direction
# Plot_dim1a = new_width
# Plot_dim2a = new_height
#
# if (Plot_type == 'Z') {
# geom_plot_x[3] <- PlotCorner_X
# geom_plot_y[3] <- PlotCorner_Y
# } else if (Plot_ref_point == 'SW' | Plot_ref_point == 'WS') {
# geom_plot_x[3] <- c(0, Plot_dim1a, Plot_dim1a, 0)
# geom_plot_y[3] <- c(Plot_dim2a, Plot_dim2a, 0, 0)
# } else if (Plot_ref_point == 'NW' | Plot_ref_point == 'WN') {
# geom_plot_x[3] <- c(0, Plot_dim1, Plot_dim1, 0)
# geom_plot_y[3] <- c(0, 0, -Plot_dim2a, -Plot_dim2a)
# } else if (Plot_ref_point == 'C' & Plot_type == 'R') {
# geom_plot_x[3] <- c(-Plot_dim1a / 2, Plot_dim1a / 2, Plot_dim1a / 2, -Plot_dim1a / 2)
# geom_plot_y[3] <- c( Plot_dim2a / 2, Plot_dim2a / 2, -Plot_dim2a / 2, -Plot_dim2a / 2)
# }
print("POLY 2")
for (z in 1:length(zonelist) ) {
pz <- subset(p_df, zone == zonelist[z])
if ( map_projection == 4326 ) {
zone_str <- zonelist[z]
zone <- as.integer(substr(zone_str, 0, nchar(zone_str)-1))
hemispere <- substr(zone_str, nchar(zone_str), nchar(zone_str))
EPSG_utm <- ifelse(hemispere=='S', 32700+zone, 32600+zone)
pz_sf <- st_as_sf(x = pz,
coords = c("X", "Y"),
crs = "EPSG:4326")
pz_sf <- st_transform(x = pz_sf, EPSG_utm)
coord_list <- st_coordinates(pz_sf)
rm(pz_sf)
pz$X_map <- coord_list[,1]
pz$Y_map <- coord_list[,2]
}
rm(coord_list)
# print(str(pz))
if (Plot_type !='C') {
if (Plot_type !='NFMA') { # square or rectangular or custom
x1 <- array(NA, c(length(geom_plot_x) + 1 , nrow(pz)))
y1 <- array(NA, c(length(geom_plot_y) + 1 , nrow(pz)))
for (i in 1:length(geom_plot_x)) { # loop by plots
x1[i,] <- rep(geom_plot_x[i], nrow(pz)) + pz$X_map
y1[i,] <- rep(geom_plot_y[i], nrow(pz)) + pz$Y_map
}
} else { #NFMA
x1 <- array(NA, c(Plots_n + 1, nrow(pz)))
y1 <- array(NA, c(Plots_n + 1, nrow(pz)))
coord_p_x <- matrix(0, ncol = 4, nrow = 4)
coord_p_y <- coord_p_x
# plot 1
coord_p_x[1,] <- c(-Plot_dim2 / 2, Plot_dim2 / 2, Plot_dim2 / 2, -Plot_dim2 / 2)
coord_p_y[1,] <- c(0, 0, Plot_dim1, Plot_dim1)
# plot 2
coord_p_x[2,] <- c(0, Plot_dim1, Plot_dim1, 0)
coord_p_y[2,] <- c(-Plot_dim2 / 2, -Plot_dim2 / 2, Plot_dim2 / 2, Plot_dim2 / 2)
# plot 3
coord_p_x[3,] <- c(-Plot_dim2 / 2,-Plot_dim2 / 2, Plot_dim2 / 2, Plot_dim2 / 2)
coord_p_y[3,] <- c(0, -Plot_dim1, -Plot_dim1, 0)
# plot 4
coord_p_x[4,] <- c(0, -Plot_dim1, -Plot_dim1, 0)
coord_p_y[4,] <- c(Plot_dim2 / 2, Plot_dim2 / 2, -Plot_dim2 / 2, -Plot_dim2 / 2)
nclus <- length(unique(pz$Cluster_ID))
# https://stackoverflow.com/questions/20117458/replicate-rows-of-a-matrix-in-r
coord_p_x <- apply(coord_p_x, 2, function(c) rep(c, nclus))
coord_p_y <- apply(coord_p_y, 2, function(c) rep(c, nclus))
x1[1,] <- coord_p_x[,1] + pz$X_map
y1[1,] <- coord_p_y[,1] + pz$Y_map
x1[2,] <- coord_p_x[,2] + pz$X_map
y1[2,] <- coord_p_y[,2] + pz$Y_map
x1[3,] <- coord_p_x[,3] + pz$X_map
y1[3,] <- coord_p_y[,3] + pz$Y_map
x1[4,] <- coord_p_x[,4] + pz$X_map
y1[4,] <- coord_p_y[,4] + pz$Y_map
i = 4
}
# last point same as first
x1[i+1,] <- x1[1,]
y1[i+1,] <- y1[1,]
# print("POLY 2+")
# polygon corner points into matrix
# matrix, there plot corner coordinates are by rows
outer_x = matrix(x1, ncol = length( x1[,1] ), byrow = TRUE)
outer_y = matrix(y1, ncol = length( x1[,1] ), byrow = TRUE)
# Set indices for the new matrix (https://stackoverflow.com/questions/18861235/combining-matrices-by-alternating-columns)
outer_x.idx <- seq(1, ncol(outer_x) * 2, by = 2)
outer_y.idx <- seq(2, ncol(outer_y) * 2 + 1, by = 2)
# print("POLY 2++")
colnames(outer_x) <- seq(1, ncol(outer_x))
colnames(outer_y) <- seq(1, ncol(outer_y))
DF_outer_x <- as.data.frame(outer_x)
DF_outer_y <- as.data.frame(outer_y)
DF_outer_x$CL <- c(1:nrow(DF_outer_x))
DF_outer_y$CL <- c(1:nrow(DF_outer_y))
# print("POLY 3")
# tidyr
# http://library.open.oregonstate.edu/computationalbiology/chapter/reshaping-and-joining-data-frames/
DF_outer_x <- gather(DF_outer_x, Point, X, as.character(seq(1, ncol(DF_outer_x) - 1, 1)))
DF_outer_y <- gather(DF_outer_y, Point, Y, as.character(seq(1, ncol(DF_outer_y) - 1, 1)))
DF_outer <- cbind(DF_outer_x, DF_outer_y[3])
DF_outer$Point <- as.integer(DF_outer$Point)
# order by cluster, plot numbers
DF_outer <- DF_outer[with(DF_outer, order(CL, Point)),]
# drop out node number
DF_outer$Point <- NULL
# OLD:: https://gis.stackexchange.com/questions/171124/data-frame-to-spatialpolygonsdataframe-with-multiple-polygons
# make a list by clusters, this is a list of dataframes
clusterlist <- unique(pz$Cluster_ID)
DF_outer$Cluster_ID <- c(rep(clusterlist, each = Plots_n))
DF_outer$Plot_ID <- c(rep(seq(1:Plots_n), times = length(clusterlist)))
outer_list <- split(DF_outer, DF_outer$CL)
# CL is polygon id
# outer_list <- lapply(outer_list, function(x) { x["CL"] <- NULL; x })
# print("POLY 4")
for (i in (1:length(outer_list))) {
sps <- sfheaders::sf_polygon(obj = outer_list[[i]], x = "X", y = "Y")
if (i==1) {
sps_sf <- sps
} else
sps_sf <-rbind(sps_sf, sps)
}
# print(str(sps_sf))
# print("POLY 4+")
# create the SpatialPolygonsDataFrame, one unique ID per polygon
# my_spatial_polys_df <- SpatialPolygonsDataFrame(sps,
# data.frame(id = unique(DF_outer$CL),
# row.names = unique(DF_outer$CL)))
if (map_projection != 4326) {
sps_sf <- sps_sf %>% st_set_crs(map_projection)
} else {
sps_sf <- sps_sf %>% st_set_crs(EPSG_utm)
}
my_spatial_polys_df <- sps_sf
}
if (Plot_type == "C") { # circular plot
zone_str <- as.character(zonelist[z])
zone <- as.integer(substr(zone_str, 0, nchar(zone_str)-1))
hemispere <- substr(zone, nchar(zone_str), nchar(zone_str))
projcrs <- ifelse(hemispere=='S', 32700+zone,32600+zone)
sps_sf <- st_as_sf(x = pz,
coords = c("X", "Y"),
crs = 4326,
remove = FALSE)
sps_sf <- st_transform(sps_sf, projcrs)
# buffering
my_spatial_polys_df <- st_buffer(sps_sf, Plot_dim1 )
}
my_spatial_polys_df_latlong <- st_transform( my_spatial_polys_df, 4326)
## my_spatial_polys_df_latlong <- spChFIDs(my_spatial_polys_df_latlong, as.character(paste(my_spatial_polys_df_latlong$Cluster_ID, my_spatial_polys_df_latlong$Plot_ID, sep="_" )))
if ( is.na(my_spatial_polys_df_All )) {
my_spatial_polys_df_All <- my_spatial_polys_df_latlong
} else {
my_spatial_polys_df_All <- rbind( my_spatial_polys_df_All, my_spatial_polys_df_latlong )
}
rm( my_spatial_polys_df_latlong )
rm(sps_sf); rm(pz)
}
return(my_spatial_polys_df_All)
}