R/multiple_sounds.R

In soundecology: Soundscape Ecology

#Multiple sounds
#
# Script to process all .wav files in a directory and save
# the requested index to a .csv file.
#
#

multiple_sounds <- function(directory, resultfile, soundindex = c("ndsi", "acoustic_complexity", "acoustic_diversity", "acoustic_evenness", "bioacoustic_index", "H"), no_cores = 1, flac = FALSE, from = NA, to = NA, units = NA, ...){

	if (any(soundindex %in% c("ndsi", "acoustic_complexity", "acoustic_diversity", "acoustic_evenness", "bioacoustic_index", "H")) == FALSE){
		stop(paste("Unknown function", soundindex))
		}
	
	if (file.access(directory) == -1) {
		stop(paste("The directory specified does not exist or this user is not autorized to read it:\n    ", directory))
		}
	
	if (is.na(from)==FALSE){
	  if (is.na(to) || is.na(units)){
	    stop("All three arguments 'from', 'to', and 'units' must be specified.")
	  }
	}
	if (is.na(to)==FALSE){
	  if (is.na(from) || is.na(units)){
	    stop("All three arguments 'from', 'to', and 'units' must be specified.")
	  }
	}
	if (is.na(units)==FALSE){
	  if (is.na(from) || is.na(to)){
	    stop("All three arguments 'from', 'to', and 'units' must be specified.")
	  }
	}
  
	#How many cores this machine has?
	#require(parallel)
	thismachine_cores <- detectCores()
	
	if (no_cores == 0){
		stop("Number of cores can not be 0.")
	}else if (no_cores < -1){
		stop("Number of cores can not be negative.")
	}else if (no_cores == "max"){
		no_cores = thismachine_cores
	}else if (no_cores == -1){
		no_cores = thismachine_cores - 1
	}else if (no_cores > thismachine_cores){
		#Don't try to use more than the number of cores in the machine
		warning(paste(" The number of cores to use can not be more than the
					  cores in this computer: ", detectCores()), immediate.=TRUE)
		no_cores <- thismachine_cores
		}
	
	#Are the files flac
	if (flac == TRUE){
		wav_files <- dir(path = directory, pattern = "flac$", ignore.case = TRUE)
		if (length(wav_files) == 0) {
			stop(paste("Could not find any .flac files in the specified directory:\n    ", directory))
		}
	}else{
		wav_files <- dir(path = directory, pattern = "wav$", ignore.case = TRUE)
		if (length(wav_files) == 0) {
			stop(paste("Could not find any .wav files in the specified directory:\n    ", directory))
			}
		}
	
	#Open flac files
	get_wav <- function(directory, flacsoundfile){
		#is it windows?
		if (.Platform$OS.type == "windows"){
			from_file = paste(directory, "\\", flacsoundfile, sep = "")
		}else{
			from_file = paste(directory, "/", flacsoundfile, sep = "")
		}
		
		wav_file = paste(strtrim(flacsoundfile, nchar(flacsoundfile) - 5), "wav", sep = ".")

		file.copy(from = from_file, to = flacsoundfile)
		wav2flac(flacsoundfile, reverse = TRUE, overwrite = TRUE)
		file.remove(flacsoundfile)
		if (file.exists(wav_file)){
				return(wav_file)
			}else{
				return(NA)
			}
		}
	
	#Bioacoustic index
	if (soundindex == "bioacoustic_index"){
    
	  fileheader <- c("FILENAME,SAMPLINGRATE,BIT,DURATION,CHANNELS,INDEX,FFT_W,MIN_FREQ,MAX_FREQ,LEFT_CHANNEL,RIGHT_CHANNEL")
    
		getindex <- function(soundfile, inCluster = FALSE, ...){
			#If launched in cluster, require the package for each node created
			if (inCluster == TRUE){
				require(soundecology)
			}
			
			#Get args
			args <- list(...)
	
			if(!is.null(args[['min_freq']])) {
				min_freq = args[['min_freq']]
			}else{
				min_freq = formals(bioacoustic_index)$min_freq
			}
			if(!is.null(args[['max_freq']])) {
				max_freq = args[['max_freq']]
			}else{
				max_freq = formals(bioacoustic_index)$max_freq
			}
			if(!is.null(args[['fft_w']])) {
				fft_w = args[['fft_w']]
			}else{
				fft_w = formals(bioacoustic_index)$fft_w
			}
		
# 			if (file.access(resultfile) == -1) {
# 				cat("FILENAME,INDEX,FFT_W,MIN_FREQ,MAX_FREQ,LEFT_CHANNEL,RIGHT_CHANNEL\n", file=resultfile, append=TRUE)
# 			}
			
			if (flac == TRUE){
				soundfile_path <- get_wav(directory, soundfile)
			}else{
				if (.Platform$OS.type == "windows"){
					soundfile_path = paste(directory, "\\", soundfile, sep="")
				}else{
					soundfile_path = paste(directory, "/", soundfile, sep="")
				}
			}
			
      if (is.na(from)==FALSE){
        this_soundfile <- readWave(soundfile_path, from = from, to = to, units = units)
      }else{
        this_soundfile <- readWave(soundfile_path)
      }
			
			return_list <- bioacoustic_index(this_soundfile, ...)
			
			if (this_soundfile@stereo == TRUE){
				no_channels = 2
			}else{
				no_channels = 1
			}
			
			if (flac == TRUE){
				file.remove(soundfile_path)
			}
			
			return(paste("\n", soundfile, ",", this_soundfile@samp.rate, ",", this_soundfile@bit, ",", round(length(this_soundfile@left)/this_soundfile@samp.rate, 2), ",", no_channels, ",", soundindex, ",", fft_w, ",", min_freq, ",", max_freq, ",", return_list$left_area, ",", return_list$right_area, sep=""))
			}
	}else if (soundindex == "acoustic_diversity"){
    #Acoustic Diversity
		
	  fileheader <- c("FILENAME,SAMPLINGRATE,BIT,DURATION,CHANNELS,INDEX,MAX_FREQ,DB_THRESHOLD,FREQ_STEPS,LEFT_CHANNEL,RIGHT_CHANNEL")
	      
		getindex <- function(soundfile, inCluster = FALSE, ...){
			#If launched in cluster, require the package for each node created
			if (inCluster == TRUE){
				require(soundecology)
			}
							
			#Get args
			args <- list(...)
			
			if(!is.null(args[['db_threshold']])) {
				db_threshold = args[['db_threshold']]
			}else{
				db_threshold = formals(acoustic_diversity)$db_threshold
			}
			if(!is.null(args[['max_freq']])) {
				max_freq = args[['max_freq']]
			}else{
				max_freq = formals(acoustic_diversity)$max_freq
			}
			if(!is.null(args[['freq_step']])) {
				freq_step = args[['freq_step']]
			}else{
				freq_step = formals(acoustic_diversity)$freq_step
			}
		
# 			if (file.access(resultfile) == -1) {
# 				cat("FILENAME,INDEX,MAX_FREQ,DB_THRESHOLD,FREQ_STEPS,LEFT_CHANNEL,RIGHT_CHANNEL\n", file=resultfile, append=TRUE)
# 			}
			
			if (flac == TRUE){
				soundfile_path <- get_wav(directory, soundfile)
			}else{
				if (.Platform$OS.type == "windows"){
					soundfile_path = paste(directory, "\\", soundfile, sep="")
				}else{
					soundfile_path = paste(directory, "/", soundfile, sep="")
				}
			}
			
      if (is.na(from)==FALSE){
        this_soundfile <- readWave(soundfile_path, from = from, to = to, units = units)
      }else{
        this_soundfile <- readWave(soundfile_path)
      }			

			return_list <- acoustic_diversity(this_soundfile, ...)
		
			if (this_soundfile@stereo == TRUE){
				no_channels = 2
			}else{
				no_channels = 1
			}
			
			if (flac == TRUE){
				file.remove(soundfile_path)
			}
			
			return(paste("\n", soundfile, ",", this_soundfile@samp.rate, ",", this_soundfile@bit, ",", round(length(this_soundfile@left)/this_soundfile@samp.rate, 2), ",", no_channels, ",", soundindex, ",", max_freq, ",", db_threshold, ",", freq_step, ",", return_list$adi_left, ",", return_list$adi_right, sep=""))
			}
	}else if (soundindex == "acoustic_complexity"){
    #Acoustic Complexity

	  fileheader <- c("FILENAME,SAMPLINGRATE,BIT,DURATION,CHANNELS,INDEX,FFT_W,MIN_FREQ,MAX_FREQ,J,LEFT_CHANNEL,RIGHT_CHANNEL")
    
		getindex <- function(soundfile, inCluster = FALSE, ...){
			#If launched in cluster, require the package for each node created
			if (inCluster == TRUE){
				require(soundecology)
			}
			
			#Get args
			args <- list(...)
			
			if(!is.null(args[['max_freq']])) {
			  max_freq = args[['max_freq']]
			}else{
			  max_freq = formals(acoustic_complexity)$max_freq
			}
			if(!is.null(args[['min_freq']])) {
			  min_freq = args[['min_freq']]
			}else{
			  min_freq = 1
			}
			if(!is.null(args[['j']])) {
				j = args[['j']]
			}else{
				j = formals(acoustic_complexity)$j
			}
			if(!is.null(args[['fft_w']])) {
				fft_w = args[['fft_w']]
			}else{
				fft_w = formals(acoustic_complexity)$fft_w
			}

# 			if (file.access(resultfile) == -1) {
# 				cat("FILENAME,INDEX,FFT_W,MAX_FREQ,J,LEFT_CHANNEL,RIGHT_CHANNEL\n", file=resultfile, append=TRUE)
# 			}
			
			if (flac == TRUE){
				soundfile_path <- get_wav(directory, soundfile)
			}else{
				if (.Platform$OS.type == "windows"){
					soundfile_path = paste(directory, "\\", soundfile, sep="")
				}else{
					soundfile_path = paste(directory, "/", soundfile, sep="")
				}
			}
			
      if (is.na(from)==FALSE){
        this_soundfile <- readWave(soundfile_path, from = from, to = to, units = units)
      }else{
        this_soundfile <- readWave(soundfile_path)
      }

			return_list <- acoustic_complexity(this_soundfile, ...)
			
			if (this_soundfile@stereo == TRUE){
				no_channels = 2
			}else{
				no_channels = 1
			}
			
			if (flac == TRUE){
				file.remove(soundfile_path)
			}
			
			return(paste("\n", soundfile, ",", this_soundfile@samp.rate, ",", this_soundfile@bit, ",", round(length(this_soundfile@left)/this_soundfile@samp.rate, 2), ",", no_channels, ",", soundindex, ",", fft_w, ",", min_freq, ",", max_freq, ",", j, ",", return_list$AciTotAll_left, ",", return_list$AciTotAll_right, sep=""))
			}
	}else if (soundindex == "ndsi"){
    #NDSI

	  fileheader <- c("FILENAME,SAMPLINGRATE,BIT,DURATION,CHANNELS,INDEX,FFT_W,ANTHRO_MIN,ANTHRO_MAX,BIO_MIN,BIO_MAX,LEFT_CHANNEL,RIGHT_CHANNEL")
    
		getindex <- function(soundfile, inCluster = FALSE, ...){
			#If launched in cluster, require the package for each node created
			if (inCluster == TRUE){
				require(soundecology)
			}
			
			#Get args
			args <- list(...)
			
			if(!is.null(args[['fft_w']])) {
				fft_w = args[['fft_w']]
			}else{
				fft_w = formals(ndsi)$fft_w
			}
			if(!is.null(args[['anthro_min']])) {
				anthro_min = args[['anthro_min']]
			}else{
				anthro_min = formals(ndsi)$anthro_min
			}
			if(!is.null(args[['anthro_max']])) {
				anthro_max = args[['anthro_max']]
			}else{
				anthro_max = formals(ndsi)$anthro_max
			}
			if(!is.null(args[['bio_min']])) {
				bio_min = args[['bio_min']]
			}else{
				bio_min = formals(ndsi)$bio_min
			}
			if(!is.null(args[['bio_max']])) {
				bio_max = args[['bio_max']]
			}else{
				bio_max = formals(ndsi)$bio_max
			}
						
# 			if (file.access(resultfile) == -1) {
# 				cat("FILENAME,INDEX,FFT_W,ANTHRO_MIN,ANTHRO_MAX,BIO_MIN,BIO_MAX,HZ_INTERVAL,LEFT_CHANNEL,RIGHT_CHANNEL\n", file=resultfile, append=TRUE)
# 			}
			
			if (flac == TRUE){
				soundfile_path <- get_wav(directory, soundfile)
			}else{
				if (.Platform$OS.type == "windows"){
					soundfile_path = paste(directory, "\\", soundfile, sep="")
				}else{
					soundfile_path = paste(directory, "/", soundfile, sep="")
				}
			}
			
      if (is.na(from)==FALSE){
        this_soundfile <- readWave(soundfile_path, from = from, to = to, units = units)
      }else{
        this_soundfile <- readWave(soundfile_path)
      }

			return_list <- ndsi(this_soundfile, ...)
			
			if (this_soundfile@stereo == TRUE){
				no_channels = 2
			}else{
				no_channels = 1
			}
			
			if (flac == TRUE){
				file.remove(soundfile_path)
			}
			
			return(paste("\n", soundfile, ",", this_soundfile@samp.rate, ",", this_soundfile@bit, ",", round(length(this_soundfile@left)/this_soundfile@samp.rate, 2), ",", no_channels, ",", soundindex, ",", fft_w, ",", anthro_min, ",", anthro_max, ",", bio_min, ",", bio_max, ",", return_list$ndsi_left, ",", return_list$ndsi_right, sep=""))
			}
	}else if (soundindex == "H"){
    #H

	  fileheader <- c("FILENAME,SAMPLINGRATE,BIT,DURATION,CHANNELS,INDEX,WL,ENVT,MSMOOTH,KSMOOTH,LEFT_CHANNEL,RIGHT_CHANNEL")
    
		getindex <- function(soundfile, inCluster = FALSE, ...){
			#If launched in cluster, require the package for each node created
			if (inCluster == TRUE){
				require(soundecology)
			}
			
			#Get args
			args <- list(...)
			
			if(!is.null(args[['wl']])) {
				wl = args[['wl']]
			}else{
				wl = formals(H)$wl
			}
			if(!is.null(args[['envt']])) {
				envt = args[['envt']]
			}else{
				envt = formals(H)$envt
			}
			if(!is.null(args[['msmooth']])) {
				msmooth = args[['msmooth']]
			}else{
				msmooth = formals(H)$msmooth
				
				if(is.null(msmooth)) {
					msmooth = "NULL"
				}	
			}
			if(!is.null(args[['ksmooth']])) {
				ksmooth = args[['ksmooth']]
			}else{
				ksmooth = formals(H)$ksmooth
				
				if(is.null(ksmooth)) {
					ksmooth = "NULL"
				}
			}
			
			#library(soundecology)
# 			if (file.access(resultfile) == -1) {
# 				cat("FILENAME,INDEX,WL,ENVT,MSMOOTH,KSMOOTH,LEFT_CHANNEL,RIGHT_CHANNEL\n", file=resultfile, append=TRUE)
# 			}
			
			if (flac == TRUE){
				soundfile_path <- get_wav(directory, soundfile)
			}else{
				if (.Platform$OS.type == "windows"){
					soundfile_path = paste(directory, "\\", soundfile, sep="")
				}else{
					soundfile_path = paste(directory, "/", soundfile, sep="")
				}
			}
			

      if (is.na(from)==FALSE){
        this_soundfile <- readWave(soundfile_path, from = from, to = to, units = units)
      }else{
        this_soundfile <- readWave(soundfile_path)
      }

			if (this_soundfile@stereo == TRUE) {
				left<-channel(this_soundfile, which = c("left"))
				right<-channel(this_soundfile, which = c("right"))
				left_res <- H(left, ...)
				right_res <- H(right, ...)
			}else{
				left<-channel(this_soundfile, which = c("left"))
				left_res <- H(left, ...)
				right_res <- NA
			}
			
			if (this_soundfile@stereo == TRUE){
				no_channels = 2
			}else{
				no_channels = 1
			}
			
			if (flac == TRUE){
				file.remove(soundfile_path)
			}
			
			return(paste("\n", soundfile, ",", this_soundfile@samp.rate, ",", this_soundfile@bit, ",", round(length(this_soundfile@left)/this_soundfile@samp.rate, 2), ",", no_channels, ",", soundindex, ",", wl, ",", envt, ",", msmooth, ",", ksmooth, ",", left_res, ",", right_res, sep=""))
			}
	}else if (soundindex == "acoustic_evenness"){
		#Acoustic evenness

		fileheader <- c("FILENAME,SAMPLINGRATE,BIT,DURATION,CHANNELS,INDEX,MAX_FREQ,DB_THRESHOLD,FREQ_STEPS,LEFT_CHANNEL,RIGHT_CHANNEL")
		
		getindex <- function(soundfile, inCluster = FALSE, ...){
			#If launched in cluster, require the package for each node created
			if (inCluster == TRUE){
				require(soundecology)
			}
			
			#Get args
			args <- list(...)
			
			if(!is.null(args[['db_threshold']])) {
				db_threshold = args[['db_threshold']]
			}else{
				db_threshold = formals(acoustic_evenness)$db_threshold
			}
			if(!is.null(args[['max_freq']])) {
				max_freq = args[['max_freq']]
			}else{
				max_freq = formals(acoustic_evenness)$max_freq
			}
			if(!is.null(args[['freq_step']])) {
				freq_step = args[['freq_step']]
			}else{
				freq_step = formals(acoustic_evenness)$freq_step
			}
			
			# 			if (file.access(resultfile) == -1) {
			# 				cat("FILENAME,INDEX,MAX_FREQ,DB_THRESHOLD,FREQ_STEPS,LEFT_CHANNEL,RIGHT_CHANNEL\n", file=resultfile, append=TRUE)
			# 			}
			
			if (flac == TRUE){
				soundfile_path <- get_wav(directory, soundfile)
			}else{
				if (.Platform$OS.type == "windows"){
					soundfile_path = paste(directory, "\\", soundfile, sep="")
				}else{
					soundfile_path = paste(directory, "/", soundfile, sep="")
				}
			}
			
			
			if (is.na(from)==FALSE){
			  this_soundfile <- readWave(soundfile_path, from = from, to = to, units = units)
			}else{
			  this_soundfile <- readWave(soundfile_path)
			}
      
			return_list <- acoustic_evenness(this_soundfile, ...)
			
			if (this_soundfile@stereo == TRUE){
				no_channels = 2
			}else{
				no_channels = 1
			}
			
			if (flac == TRUE){
				file.remove(soundfile_path)
			}
			
			return(paste("\n", soundfile, ",", this_soundfile@samp.rate, ",", this_soundfile@bit, ",", round(length(this_soundfile@left)/this_soundfile@samp.rate, 2), ",", no_channels, ",", soundindex, ",", max_freq, ",", db_threshold, ",", freq_step, ",", return_list$aei_left, ",", return_list$aei_right, sep=""))
		}
	}
	
	
	
#Start timer
time0 <- proc.time()

  
#open results file
#sink(resultfile)
cat(fileheader, file = resultfile, append = FALSE)
#Done writing results  
#sink()
  
#Use parallel?
if (no_cores>1){
	#require(parallel)
	no_files <- length(wav_files)
	
	if (no_cores > no_files){
		no_cores <- no_files
		cat("\n The number of cores to use has been reduced because there are less files than cores available\n")
	}
	
	cat(paste("\n Running the function ", soundindex, "() on ", no_files, " files using ", no_cores, " cores", "\n\n", sep=""))
	
  	cl <- makeCluster(no_cores, type = "PSOCK")
	
	res <- parLapply(cl, wav_files, getindex, inCluster = TRUE, ...)

	write.table(res, file = resultfile, append = TRUE, quote = FALSE, col.names = FALSE, row.names = FALSE)
	#return(fileheader)
	#pause to allow all to end
	Sys.sleep(1)
	
	stopCluster(cl)
}else{

	cat(paste(" Running on ", length(wav_files), " files using 1 core", "\n\n", sep=""))
	
	for (soundfile in wav_files){
		this_res <- getindex(soundfile, ...)
		cat(this_res, file = resultfile, append = TRUE)
		}
	}

	#Stop timer
	time1 <- proc.time() - time0
	cat(paste(" The analysis of ", length(wav_files), " files took ", round(time1["elapsed"], 2), " seconds\n\n", sep = ""))
}