SpectralEvolutionFileReader

This repository provides functions to read spectral data from Spectral Evolution spectrometers. The functions include handling .sed files, extracting metadata, and cleaning the headings of the data, while examples enable the plotting of spectral data.

License

This project is licensed under the MIT License. See the LICENSE file for details.

Installation

No installation is needed. The functions in this repository use R-packages: "readr", "stringr", "ggplot2", and "dplyr", which will be installed if not already available on your computer. Simply, clone the repository or download and extract it, and source the SEDReader_function.R script as follows:

source("./Scripts/SEDReader_function.R")

Function 1

read_sed(file_path)

Reads a single .sed file, extracts metadata, and returns a list containing both the metadata and spectral data.

Arguments:

file_path: Character string specifying the path to the data file.

Returns:

A list with two elements:

metadata: A named list containing the metadata extracted from the .sed file. data: A data frame containing the spectral data.

Example usage 1 (see usage examples script)

sed_data <- read_sed("path/to/your/file.sed")
print(sed_data$metadata)
head(sed_data$data)

Function 2

read_sed_dir(folder_path)

Reads all .sed files in a specified folder, extracts metadata, and returns a list containing both the metadata and spectral data for each file.

Arguments:

folder_path: Character string specifying the path to the folder containing .sed files.

Returns:

A list of lists, where each inner list contains:

metadata: A named list containing the metadata extracted from the file. data: A data frame containing the spectral data.

Example Usage 2 (see usage examples script)

folder_path <- "./Example_data/SpectralEvolution_files/"
example_sed_files <- read_sed_dir(folder_path)

# Access metadata and data for each file
for (file_name in names(example_sed_files)) {
  cat("File:", file_name, "\n")
  if (!is.null(example_sed_files[[file_name]])) {
    print(example_sed_files[[file_name]]$metadata)
    print(example_sed_files[[file_name]]$data)
  } else {
    cat("Failed to read file:", file_name, "\n")
  }
}

Plotting summary statistics

After reading and having a glimpse of the data, you can plot the minimum, mean, and maximum reflectance values from all files:

# Combine all data into one dataframe for plotting
all_data <- bind_rows(lapply(example_sed_files, function(x) x$data), .id = "file_name")

# Calculate min, mean, and max
summary_data <- all_data %>%
  group_by(Wvl) %>%
  summarize(
    min_Reflect = min(Reflect, na.rm = TRUE),
    mean_Reflect = mean(Reflect, na.rm = TRUE),
    max_Reflect = max(Reflect, na.rm = TRUE)
  )

# Plot the min, mean, and max
ggplot(summary_data, aes(x = Wvl)) +
  geom_line(aes(y = min_Reflect, color = "Min.")) +
  geom_line(aes(y = mean_Reflect, color = "Mean")) +
  geom_line(aes(y = max_Reflect, color = "Max.")) +
  labs(title = "Spectral Data Summary", x = "Wavelength (Wvl)", y = "Reflectance") +
  scale_color_manual(values = c("Min." = "blue", "Mean" = "green", "Max." = "red")) +
  theme_minimal()

Contributing to the scripts

You can contribute to this repository by opening issues or submitting pull requests. Indicate what kind of changes you like to make when submitting a pull request.

Contact

For any questions or suggestions, please contact Mahlatse Kganyago at mahlatse@uj.ac.za.