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Francomano_et_al_2023_PAM_for_Penguins/IDLE_File_Segmentation_Script.R
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| ###################################################################### | |
| # Code from Francomano et al. (IBIS 2023) # | |
| ###################################################################### | |
| # IDLE File Segmentation Script # | |
| ###################################################################### | |
| # Created by: Dante Francomano (dfrancomano@alumni.purdue.edu) | |
| # Date: 20191116 | |
| ###################################################################### | |
| ###################################################################### | |
| # Load packages | |
| .libPaths("E:/Dante/R_3_5_3_Library") | |
| library(tuneR) | |
| library(parallel) | |
| library(mailR) | |
| # Create function to read and write waves, converting hourly recordings to 1 minute every 5 minutes | |
| waveSegmentation<-function(fileName,writeDirectory) | |
| { | |
| for(i in seq(0,55,5)) | |
| { | |
| tempWave<-readWave(fileName,from=i,to=i+1,units="minutes") | |
| if(i<10) writeWave(tempWave,paste(writeDirectory,substr(fileName,1,21),i,"00.wav",sep="")) | |
| if(i>5) writeWave(tempWave,paste(writeDirectory,substr(fileName,1,20),i,"00.wav",sep="")) | |
| } | |
| } | |
| # Run segmentation | |
| # PM 01 | |
| setwd("J:/Dante/Pinguinos/Datos_Acusticos/Isla_de_los_Estados/Raw_Data/PM_01/S4A00449_20181113_144528") | |
| writeDirectory<-"J:/Dante/Pinguinos/Datos_Acusticos/Isla_de_los_Estados/Trimmed_Data/PM_01/" | |
| firstGood<-"S4A00449_20181208_190000.wav" | |
| lastGood<-"S4A00449_20181218_120000.wav" | |
| goodFiles<-paste(substr(firstGood,1,9),strftime(seq.POSIXt(strptime(substr(firstGood,10,24),"%Y%m%d_%H%M%S"),strptime(substr(lastGood,10,24),"%Y%m%d_%H%M%S"),"hour"),"%Y%m%d_%H%M%S"),".wav",sep="") | |
| cl<-makeCluster(8,type="SOCK") | |
| clusterExport(cl,list("goodFiles","writeDirectory","waveSegmentation","readWave","writeWave")) | |
| parSapply(cl=cl,goodFiles,waveSegmentation,writeDirectory=writeDirectory) | |
| gc() | |
| stopCluster(cl) | |
| send.mail("dfrancomano@gmail.com","dfrancomano@gmail.com","PM 01 complete","Let's see if it actually worked...",smtp=list(host.name="smtp.gmail.com",port=465,user.name="dfrancomano",passwd="*****",ssl=TRUE),authenticate=TRUE,send=TRUE) | |
| # PM 02 | |
| setwd("J:/Dante/Pinguinos/Datos_Acusticos/Isla_de_los_Estados/Raw_Data/PM_02/S4A00440_20181113_144630") | |
| writeDirectory<-"J:/Dante/Pinguinos/Datos_Acusticos/Isla_de_los_Estados/Trimmed_Data/PM_02/" | |
| firstGood<-"S4A00440_20181208_180000.wav" | |
| lastGood<-"S4A00440_20181218_120000.wav" | |
| goodFiles<-paste(substr(firstGood,1,9),strftime(seq.POSIXt(strptime(substr(firstGood,10,24),"%Y%m%d_%H%M%S"),strptime(substr(lastGood,10,24),"%Y%m%d_%H%M%S"),"hour"),"%Y%m%d_%H%M%S"),".wav",sep="") | |
| cl<-makeCluster(8,type="SOCK") | |
| clusterExport(cl,list("goodFiles","writeDirectory","waveSegmentation","readWave","writeWave")) | |
| parSapply(cl=cl,goodFiles,waveSegmentation,writeDirectory=writeDirectory) | |
| gc() | |
| stopCluster(cl) | |
| send.mail("dfrancomano@gmail.com","dfrancomano@gmail.com","PM 02 complete","Let's see if it actually worked...",smtp=list(host.name="smtp.gmail.com",port=465,user.name="dfrancomano",passwd="*****",ssl=TRUE),authenticate=TRUE,send=TRUE) | |
| # PPA 02 | |
| setwd("J:/Dante/Pinguinos/Datos_Acusticos/Isla_de_los_Estados/Raw_Data/PPA_02/S4A03851_20181203_185612") | |
| writeDirectory<-"J:/Dante/Pinguinos/Datos_Acusticos/Isla_de_los_Estados/Trimmed_Data/PPA_02/" | |
| firstGood<-"S4A03851_20181208_210000.wav" | |
| lastGood<-"S4A03851_20181218_100000.wav" | |
| goodFiles<-paste(substr(firstGood,1,9),strftime(seq.POSIXt(strptime(substr(firstGood,10,24),"%Y%m%d_%H%M%S"),strptime(substr(lastGood,10,24),"%Y%m%d_%H%M%S"),"hour"),"%Y%m%d_%H%M%S"),".wav",sep="") | |
| cl<-makeCluster(8,type="SOCK") | |
| clusterExport(cl,list("goodFiles","writeDirectory","waveSegmentation","readWave","writeWave")) | |
| parSapply(cl=cl,goodFiles,waveSegmentation,writeDirectory=writeDirectory) | |
| gc() | |
| stopCluster(cl) | |
| send.mail("dfrancomano@gmail.com","dfrancomano@gmail.com","PPA 02 complete","Let's see if it actually worked...",smtp=list(host.name="smtp.gmail.com",port=465,user.name="dfrancomano",passwd="*****",ssl=TRUE),authenticate=TRUE,send=TRUE) | |
| # PPA 03 | |
| setwd("J:/Dante/Pinguinos/Datos_Acusticos/Isla_de_los_Estados/Raw_Data/PPA_03/S4A00466_20181113_144627") | |
| writeDirectory<-"J:/Dante/Pinguinos/Datos_Acusticos/Isla_de_los_Estados/Trimmed_Data/PPA_03/" | |
| firstGood<-"S4A00466_20181207_130000.wav" | |
| lastGood<-"S4A00466_20181217_170000.wav" | |
| goodFiles<-paste(substr(firstGood,1,9),strftime(seq.POSIXt(strptime(substr(firstGood,10,24),"%Y%m%d_%H%M%S"),strptime(substr(lastGood,10,24),"%Y%m%d_%H%M%S"),"hour"),"%Y%m%d_%H%M%S"),".wav",sep="") | |
| cl<-makeCluster(8,type="SOCK") | |
| clusterExport(cl,list("goodFiles","writeDirectory","waveSegmentation","readWave","writeWave")) | |
| parSapply(cl=cl,goodFiles,waveSegmentation,writeDirectory=writeDirectory) | |
| gc() | |
| stopCluster(cl) | |
| send.mail("dfrancomano@gmail.com","dfrancomano@gmail.com","PPA 03 complete","Let's see if it actually worked...",smtp=list(host.name="smtp.gmail.com",port=465,user.name="dfrancomano",passwd="*****",ssl=TRUE),authenticate=TRUE,send=TRUE) | |
| # PPA 05 | |
| setwd("J:/Dante/Pinguinos/Datos_Acusticos/Isla_de_los_Estados/Raw_Data/PPA_05/S4A03852_20181113_144215") | |
| writeDirectory<-"J:/Dante/Pinguinos/Datos_Acusticos/Isla_de_los_Estados/Trimmed_Data/PPA_05/" | |
| firstGood<-"S4A03852_20181208_230000.wav" | |
| lastGood<-"S4A03852_20181218_090000.wav" | |
| goodFiles<-paste(substr(firstGood,1,9),strftime(seq.POSIXt(strptime(substr(firstGood,10,24),"%Y%m%d_%H%M%S"),strptime(substr(lastGood,10,24),"%Y%m%d_%H%M%S"),"hour"),"%Y%m%d_%H%M%S"),".wav",sep="") | |
| cl<-makeCluster(8,type="SOCK") | |
| clusterExport(cl,list("goodFiles","writeDirectory","waveSegmentation","readWave","writeWave")) | |
| parSapply(cl=cl,goodFiles,waveSegmentation,writeDirectory=writeDirectory) | |
| gc() | |
| stopCluster(cl) | |
| send.mail("dfrancomano@gmail.com","dfrancomano@gmail.com","PPA 05 complete","Let's see if it actually worked...",smtp=list(host.name="smtp.gmail.com",port=465,user.name="dfrancomano",passwd="*****",ssl=TRUE),authenticate=TRUE,send=TRUE) | |
| # PPA 06 | |
| setwd("J:/Dante/Pinguinos/Datos_Acusticos/Isla_de_los_Estados/Raw_Data/PPA_06/S4A00436_20181113_144328") | |
| writeDirectory<-"J:/Dante/Pinguinos/Datos_Acusticos/Isla_de_los_Estados/Trimmed_Data/PPA_06/" | |
| firstGood<-"S4A00436_20181207_150000.wav" | |
| lastGood<-"S4A00436_20181217_160000.wav" | |
| goodFiles<-paste(substr(firstGood,1,9),strftime(seq.POSIXt(strptime(substr(firstGood,10,24),"%Y%m%d_%H%M%S"),strptime(substr(lastGood,10,24),"%Y%m%d_%H%M%S"),"hour"),"%Y%m%d_%H%M%S"),".wav",sep="") | |
| cl<-makeCluster(8,type="SOCK") | |
| clusterExport(cl,list("goodFiles","writeDirectory","waveSegmentation","readWave","writeWave")) | |
| parSapply(cl=cl,goodFiles,waveSegmentation,writeDirectory=writeDirectory) | |
| gc() | |
| stopCluster(cl) | |
| send.mail("dfrancomano@gmail.com","dfrancomano@gmail.com","PPA 06 complete","Let's see if it actually worked...",smtp=list(host.name="smtp.gmail.com",port=465,user.name="dfrancomano",passwd="*****",ssl=TRUE),authenticate=TRUE,send=TRUE) | |
| # PPA 07 | |
| setwd("J:/Dante/Pinguinos/Datos_Acusticos/Isla_de_los_Estados/Raw_Data/PPA_07/S4A00433_20181113_144512") | |
| writeDirectory<-"J:/Dante/Pinguinos/Datos_Acusticos/Isla_de_los_Estados/Trimmed_Data/PPA_07/" | |
| firstGood<-"S4A00433_20181208_120000.wav" | |
| lastGood<-"S4A00433_20181218_080000.wav" | |
| goodFiles<-paste(substr(firstGood,1,9),strftime(seq.POSIXt(strptime(substr(firstGood,10,24),"%Y%m%d_%H%M%S"),strptime(substr(lastGood,10,24),"%Y%m%d_%H%M%S"),"hour"),"%Y%m%d_%H%M%S"),".wav",sep="") | |
| cl<-makeCluster(8,type="SOCK") | |
| clusterExport(cl,list("goodFiles","writeDirectory","waveSegmentation","readWave","writeWave")) | |
| parSapply(cl=cl,goodFiles,waveSegmentation,writeDirectory=writeDirectory) | |
| gc() | |
| stopCluster(cl) | |
| send.mail("dfrancomano@gmail.com","dfrancomano@gmail.com","PPA 07 complete","Let's see if it actually worked...",smtp=list(host.name="smtp.gmail.com",port=465,user.name="dfrancomano",passwd="*****",ssl=TRUE),authenticate=TRUE,send=TRUE) |