263 lines
11 KiB
R
263 lines
11 KiB
R
# Functions
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process_spectral_data <- function(file_path, grouping_size = 17, exclude_index = 13, encoding = "UTF-16LE", baum_ids = NULL) {
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spektren <- readLines(file(file_path, encoding = encoding))
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spektren <- gsub("\ufeff", "", spektren)
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spektren <- strsplit(spektren, "\t")
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wavelengths <- as.numeric(sapply(spektren, function(x) strsplit(x[1], ",")[[1]][1]))
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measurements <- do.call(rbind, lapply(spektren, function(row) {
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sapply(row, function(part) as.numeric(strsplit(part, ",")[[1]][2]))
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}))
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if (basename(file_path) == "export_20220721.dat") {
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whites <- c()
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for (j in 1:ncol(measurements)) {
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value <- measurements[1, j]
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if (!is.na(value) && floor(value) == 1) {
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whites <- c(whites,j)
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}
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}
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skipped <- c(88, 138, 139, 180, 293, 311, 312, 313, 317, 395)
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fix <- c(0:11)
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columns_to_remove <- unique(c(whites, skipped, fix))
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measurements <- measurements[, -columns_to_remove]
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spektren.df <- as.data.frame(measurements)
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if (!is.null(baum_ids)) {
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baum_ids_20220721 <- c(
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"ES8 (B 2-10-5-5)", "ES9 (B 2-10-2-4)", "IT8 (B 1-2-2-2)", "DE7 (B3-11-3-3)", "DE8 (B3-11-1-3)",
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"FR1 (A 1-7-2-5)", "FR2 (A 1-7-1-1)", "ES1 (A 2-3-3-3)", "ES2 (A 2-3-3-2)", "IT2 (A 1-9-3-5)",
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"IT3 (A 1-9-4-4)", "FR5 (A 1-1-2-5)", "FR6 (A 1-1-2-3)", "DE1 (B1-10-5-5)", "DE2 (B1-10-5-3)",
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"IT7 (B 1-2-3-3)", "DE4 (B1-10-4-5)", "DE10 (B 3-11-1-1)", "ES10 (B 2-10-3-1)", "IT9 (B 1-2-2-3)",
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"IT5 (A 1-9-5-2)", "ES5 (A 2-3-4-4)", "FR10 (A 1-1-5-4)", "FR4 (A 1-1-1-3)"
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)
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baum_order_20220721 <- match(baum_ids, baum_ids_20220721)
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reordered_columns <- unlist(lapply(baum_order_20220721, function(x) {
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start_col <- (x - 1) * 15 + 1
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end_col <- start_col + 14
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return(start_col:end_col)
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}))
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spektren.df <- spektren.df[, reordered_columns]
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}
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}
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if (basename(file_path) == "export_20220812.dat") {
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measurements_filtered <- list()
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for (i in seq(1, ncol(measurements), by = grouping_size)) {
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tree_index <- (i - 1) / grouping_size + 1
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if (tree_index != exclude_index) {
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measurements_filtered[[length(measurements_filtered) + 1]] <- measurements[, (i + 1):(i + grouping_size - 2)]
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}
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}
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measurements_filtered <- do.call(cbind, measurements_filtered)
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spektren.df <- as.data.frame(measurements_filtered)
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}
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rownames(spektren.df) <- wavelengths
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return(spektren.df)
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}
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calculate_mean_values <- function(spektren.df, baum_id, spalten_pro_baum) {
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start_spalte <- (baum_id - 1) * spalten_pro_baum + 1
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end_spalte <- start_spalte + spalten_pro_baum - 1
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spalten_messungen <- start_spalte:end_spalte
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mean_values <- rowMeans(spektren.df[, spalten_messungen], na.rm = TRUE)
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return(mean_values)
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}
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create_mean_values_df <- function(spektren.df, num_baeume, spalten_pro_baum) {
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mean_values_list <- list()
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for (baum_id in 1:num_baeume) {
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mean_values <- calculate_mean_values(spektren.df, baum_id, spalten_pro_baum)
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mean_values_list[[baum_id]] <- mean_values
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}
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mean_values_df <- as.data.frame(do.call(cbind, mean_values_list))
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colnames(mean_values_df) <- paste0("Tree_", 1:num_baeume)
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rownames(mean_values_df) <- rownames(spektren.df)
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return(mean_values_df)
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}
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integrate_difference <- function(df1, df2, num_baeume, spalten_pro_baum) {
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if (ncol(df1) != ncol(df2) || nrow(df1) != nrow(df2)) {
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stop("The dataframes must have the same dimensions.")
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}
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wavelengths <- as.numeric(rownames(df1))
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integral_results <- numeric(num_baeume)
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for (baum_id in 1:num_baeume) {
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mean_values_df1 <- calculate_mean_values(df1, baum_id, spalten_pro_baum)
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mean_values_df2 <- calculate_mean_values(df2, baum_id, spalten_pro_baum)
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difference <- mean_values_df1 - mean_values_df2
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integral_results[baum_id] <- sum(diff(wavelengths) * (head(difference, -1) + tail(difference, -1)) / 2)
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}
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return(integral_results)
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}
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calculate_wbi <- function(mean_values_df) {
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wavelengths <- 325:1075
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wavelength_900 <- which(wavelengths == 900)
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wavelength_970 <- which(wavelengths == 970)
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wbi_values <- apply(mean_values_df, 2, function(column) {
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column[wavelength_900] / column[wavelength_970]
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})
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return(wbi_values)
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}
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calculate_wbi_differences <- function(wbi_values1, wbi_values2) {
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if (length(wbi_values1) != length(wbi_values2)) {
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stop("The two WBI datasets must have the same length.")
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}
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wbi_diff <- wbi_values1 - wbi_values2
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return(wbi_diff)
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}
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plot_spectral_data <- function(mean_values_df, output_file = "all.png", baum_ids, xlim = c(400, 1050), ylim = c(0, 1), date_of_capture) {
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num_baeume <- ncol(mean_values_df)
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png(output_file, width = 1024, height = 720)
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colors <- rainbow(num_baeume)
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plot(as.numeric(rownames(mean_values_df)), rep(NA, nrow(mean_values_df)),
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xlab = "Wavelength (nm)", ylab = "Reflection (%)",
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type = "n", ylim = ylim, xlim = xlim,
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main = paste("Spectral Data -", date_of_capture)
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)
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for (baum_id in 1:num_baeume) {
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lines(as.numeric(rownames(mean_values_df)), mean_values_df[, baum_id], type = "l", col = colors[baum_id], lwd = 6)
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}
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legend("topleft",
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legend = baum_ids,
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text.col = colors,
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pch = rep("-", num_baeume),
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col = colors, lwd = 2
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)
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dev.off()
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}
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plot_side_by_side_spectral_data <- function(mean_values_df1, mean_values_df2, output_file = "side_by_side_plot.png", baum_ids, xlim = c(400, 1050), ylim = c(0, 1), dates) {
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num_baeume <- ncol(mean_values_df1)
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png(output_file, width = 1080, height = 1280)
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par(mfrow = c(2, 1))
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colors <- rainbow(num_baeume)
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plot(as.numeric(rownames(mean_values_df1)), rep(NA, nrow(mean_values_df1)),
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xlab = "Wavelength (nm)", ylab = "Reflection (%)",
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type = "n", ylim = ylim, xlim = xlim,
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main = paste("Spectral Data -", dates[1])
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)
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for (baum_id in 1:num_baeume) {
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lines(as.numeric(rownames(mean_values_df1)), mean_values_df1[, baum_id], type = "l", col = colors[baum_id], lwd = 6)
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}
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legend("topleft",
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legend = baum_ids,
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text.col = colors,
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pch = rep("-", num_baeume),
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col = colors, lwd = 2
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)
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plot(as.numeric(rownames(mean_values_df2)), rep(NA, nrow(mean_values_df2)),
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xlab = "Wavelength (nm)", ylab = "Reflection (%)",
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type = "n", ylim = ylim, xlim = xlim,
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main = paste("Spectral Data -", dates[2])
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)
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for (baum_id in 1:num_baeume) {
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lines(as.numeric(rownames(mean_values_df2)), mean_values_df2[, baum_id], type = "l", col = colors[baum_id], lwd = 6)
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}
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legend("topleft",
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legend = baum_ids,
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text.col = colors,
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pch = rep("-", num_baeume),
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col = colors, lwd = 2
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)
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dev.off()
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}
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plot_wbi_values <- function(wbi_values, baum_ids, output_file = "wbi_values_sorted_scaled.png", date_of_capture) {
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png(output_file, width = 1024, height = 720)
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par(mar = c(10, 5, 4, 2) + 0.1)
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sorted_indices <- order(wbi_values)
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sorted_wbi_values <- wbi_values[sorted_indices]
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sorted_baum_ids <- baum_ids[sorted_indices]
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min_wbi <- min(sorted_wbi_values) - 0.002
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max_wbi <- max(sorted_wbi_values) + 0.002
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barplot(
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sorted_wbi_values,
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names.arg = sorted_baum_ids,
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col = "steelblue",
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main = paste("Water Band Index (WBI) -", date_of_capture),
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xlab = "",
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ylab = "WBI Value",
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las = 2,
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ylim = c(min_wbi, max_wbi)
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)
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dev.off()
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}
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plot_combined_wbi_values <- function(wbi_values_1, wbi_values_2, baum_ids, output_file = "combined_wbi_plot.png", dates = c("2022/07/21", "2022/08/12")) {
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combined_wbi <- cbind(wbi_values_1, wbi_values_2)
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colnames(combined_wbi) <- dates
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sorted_indices <- order(wbi_values_1)
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sorted_combined_wbi <- combined_wbi[sorted_indices,]
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sorted_baum_ids <- baum_ids[sorted_indices]
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png(output_file, width = 1024, height = 720)
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par(mar = c(10, 5, 4, 2) + 0.1)
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barplot(
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t(sorted_combined_wbi),
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beside = TRUE,
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names.arg = sorted_baum_ids,
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col = c("steelblue", "darkorange"),
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main = "Water Band Index (WBI) - 2022/07/22 & 2022/08/12",
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xlab = "",
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ylab = "WBI Value",
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las = 2,
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ylim = range(sorted_combined_wbi) * c(0.95, 1.05)
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)
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legend("topleft", legend = dates, fill = c("steelblue", "darkorange"))
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dev.off()
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}
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plot_wbi_differences <- function(wbi_diff, baum_ids, output_file = "wbi_differences_sorted.png") {
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wbi_diff <- -wbi_diff
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sorted_indices <- order(wbi_diff)
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sorted_wbi_diff <- wbi_diff[sorted_indices]
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sorted_baum_ids <- baum_ids[sorted_indices]
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png(output_file, width = 1024, height = 720)
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par(mar = c(10, 5, 4, 2) + 0.1)
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barplot(
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sorted_wbi_diff,
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names.arg = sorted_baum_ids,
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col = "steelblue",
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main = "Differenzen im Water Band Index (WBI)",
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xlab = "",
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ylab = "WBI Differenz",
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las = 2
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)
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dev.off()
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}
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# Variables
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baum_ids_20220812 <- c(
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"DE1 (B1-10-5-5)", "DE2 (B1-10-5-3)", "DE4 (B1-10-4-5)", "DE7 (B3-11-3-3)", "DE8 (B3-11-1-3)",
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"DE10 (B 3-11-1-1)", "IT2 (A 1-9-3-5)", "IT3 (A 1-9-4-4)", "IT5 (A 1-9-5-2)", "IT7 (B 1-2-3-3)",
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"IT8 (B 1-2-2-2)", "IT9 (B 1-2-2-3)", "ES2 (A 2-3-3-2)", "ES5 (A 2-3-4-4)",
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"ES8 (B 2-10-5-5)", "ES9 (B 2-10-2-4)", "ES10 (B 2-10-3-1)", "FR1 (A 1-7-2-5)", "FR2 (A 1-7-1-1)",
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"FR4 (A 1-1-1-3)", "FR5 (A 1-1-2-5)", "FR6 (A 1-1-2-3)", "FR10 (A 1-1-5-4)"
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)
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# Calculation
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spektren20220721.df <- process_spectral_data(file_path = "~/Developer/courses/2021\ Projektbezogenes\ Arbeiten/Abschlussarbeit/data/export_20220721.dat", grouping_size = 17, exclude_index = 8, encoding = "UTF-16LE", baum_ids = baum_ids_20220812)
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spektren20220812.df <- process_spectral_data(file_path = "~/Developer/courses/2021\ Projektbezogenes\ Arbeiten/Abschlussarbeit/data/export_20220812.dat", grouping_size = 17, exclude_index = 13, encoding = "UTF-16LE")
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mean_values_20220721.df <- create_mean_values_df(spektren20220721.df, num_baeume = 23, spalten_pro_baum = 15)
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mean_values_20220812.df <- create_mean_values_df(spektren20220812.df, num_baeume = 23, spalten_pro_baum = 15)
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wbi_20220721 <- calculate_wbi(mean_values_20220721.df)
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wbi_20220812 <- calculate_wbi(mean_values_20220812.df)
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wbi_diff <- calculate_wbi_differences(wbi_20220721,wbi_20220812)
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# Plotting
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plot_spectral_data(mean_values_df = mean_values_20220721.df, output_file = "plots/spectrum_20220721.png", baum_ids = baum_ids_20220812, xlim = c(400, 1050), ylim = c(0, 1), date_of_capture = "2022/07/21")
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plot_spectral_data(mean_values_df = mean_values_20220812.df, output_file = "plots/spectrum_20220812.png", baum_ids = baum_ids_20220812, xlim = c(400, 1050), ylim = c(0, 1), date_of_capture = "2022/08/12")
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plot_wbi_values(wbi_20220721, baum_ids = baum_ids_20220812, output_file = "plots/wbi_20220721.png", date_of_capture = "2022/07/21")
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plot_wbi_values(wbi_20220812, baum_ids = baum_ids_20220812, output_file = "plots/wbi_20220812.png", date_of_capture = "2022/08/12")
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plot_combined_wbi_values(wbi_values_1 = wbi_20220721, wbi_values_2 = wbi_20220812, baum_ids = baum_ids_20220812, output_file = "plots/wbi_combined.png", dates = c("2022/07/21", "2022/08/12"))
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plot_wbi_differences(wbi_diff, baum_ids = baum_ids_20220812, output_file = "plots/wbi_differences.png") |