added a repath function to save in a different directory

R/repath_EVdir_flex2.R

@@ -0,0 +1,146 @@
+#' repath_EVdir_flex.R
+#'
+#' @description Function to take a directory of EV files and reset the path.
+#' This works for EV files that have an ek5 sub-directory too.
+#' The ek5 subdirectory must be named 'ek5 EV'.  The EK5_Dir_Flag must be
+#' set appropriately in the excel file. This version saves to the directory in
+#' Post_EV_Dir
+#' Written by RT 2022, modified 2024.
+#' Requires an excel file input that says what the paths are
+#' Each row is a survey (survey_name), and each column is a path or file name
+#'
+#' @param SurveyName name of survey as in excel file
+#' @param DirNameFile excel file name of paths
+#' Excel file has the following columns (with header names)
+#' Cal_File: calibration file name
+#' Base_Path:
+#' Orig_EV_Dir:
+#' Raw_Dir
+#' EK5_Dir_Flag
+#' EK5_Raw_Dir
+#' @param ni is an optional argument for which file to start with (default ni=1 is the first file).
+#' @param sheet is an optional argument to denote which sheet of the DirNameFile
+#'
+#' @examples
+#'  \dontrun{
+#' DirNameFile="C:/rthomas/R/Rcode/EK60_EK80 conversion/EK60_Ek80_conv_updated/Directory Structure EK60 EK80 conversion updated.xlsx"
+#' SurveyName='2019_US'
+#' repath_EVdir_flex(SurveyName,DirNameFile, ni, sheet)
+#'}
+#' @export
+repath_EVdir_flex <- function(SurveyName, DirNameFile, ni=1,sheet,...) {
+
+###
+# uses functions from
+# RDCOMClient
+# readxl
+
+  ###############################################
+  #           Set Paths                         #
+  ###############################################
+
+  DirTable <- readxl::read_excel(DirNameFile, sheet)
+  DirTableSurvey<- subset(DirTable, Survey == SurveyName)
+  DirTableSurvey[] <- lapply(DirTableSurvey, function(x) if(is.factor(x)) factor(x) else x)  #to ensure dataframe actually removed other variables in subset
+  BasePath<-DirTableSurvey$Base_Path
+  BaseJudgePath<-DirTableSurvey$Orig_EV_Dir
+  Post_EV_Dir<-DirTableSurvey$Post_EV_Dir
+
+  #calibration
+  if (DirTableSurvey$Mult_Cal_Flag==0){  #multiple calibration flag off
+       CALfileName<-DirTableSurvey$Cal_File
+       CALfileName_EK5<-DirTableSurvey$EK5_Cal_File
+     }else{  #multiple calibrations for the survey, look in the excel sheet
+       CALsheetname<-paste0(SurveyName,"_cal")
+       CALsheet<-readxl::read_excel(DirNameFile, sheet=CALsheetname)
+       CALfileName_EK5<-DirTableSurvey$EK5_Cal_File
+       CALfileName<-NA
+     }
+  #location of .raw files
+  RAWdir<-DirTableSurvey$Raw_Dir
+  RAWdir2<-DirTableSurvey$Raw_Dir2 #possible second raw directory -used in 2011 for .ek6 files
+  RAWdir_EK5<-DirTableSurvey$EK5_Raw_Dir
+
+  #Get ek_flag
+  EK_flag<-DirTableSurvey$EK5_Dir_Flag
+
+  #location of transect EV files
+  Transectdir<-DirTableSurvey$Orig_EV_Dir
+  TransectEK5dir<-file.path(DirTableSurvey$Orig_EV_Dir, 'ek5 EV')
+
+  ###############################################
+  #         Update paths in Echoview            #
+  ###############################################
+
+  # list the EV files
+  #EVfile.list <- list.files(file.path(Transectdir), pattern="*.(?i)EV$")
+  EVfileEK5.list<- list.files(file.path(TransectEK5dir), pattern="*.(?i)EV$")
+  EVfile.list<-setdiff(list.files(file.path(Transectdir), pattern="*.(?i)EV$"), list.dirs(file.path(Transectdir),recursive = FALSE, full.names = FALSE)) #don't include directories
+  # create COM connection between R and Echoview
+  EVApp <- RDCOMClient::COMCreate("EchoviewCom.EvApplication")
+
+  if (EK_flag==1){
+       EVlists<-list(EVfile.list,EVfileEK5.list)
+       Transectlistdir<-list(Transectdir,TransectEK5dir)
+       Callist<-list(CALfileName, CALfileName_EK5)
+       RAWlist<-list(RAWdir,RAWdir_EK5)
+  }else{
+       EVlists<-list(EVfile.list)
+       Transectlistdir<-list(Transectdir)
+       Callist<-list(CALfileName)
+       RAWlist<-list(RAWdir)
+  }
+  #Will need another case in here if ever have multiple calibrations as well as using ek5 files as well as .raw files
+  ## ------------- start loop
+  for (j in 1:length(EVlists)){  #put back to j=1
+       Thisfile.list<-EVlists[[j]]
+       ThisTransectdir<-Transectlistdir[[j]]
+       ThisCal<-Callist[[j]]
+       ThisRAW<-RAWlist[[j]]
+       ni<-1 #reset ni
+       nfiles=length(Thisfile.list)  #number of EV files
+       for (i in Thisfile.list[ni:nfiles]){
+         ni=which(Thisfile.list==i)
+         print(ni)
+         EVfileName <- file.path(ThisTransectdir, i)
+         print(EVfileName)
+         Transect<-getTnumv2(EVfileName)
+         # open EV file
+         EVfile <- EVApp$OpenFile(EVfileName)
+
+         #set the first fileset object
+         filesetObj <- EVfile[["Filesets"]]$Item(0)  #RAW
+
+         # set data properties object and input new datafiles folder location
+         evPropObj <- EVfile[["Properties"]]
+         evPropObj[["DataPaths"]]$Clear()
+         #evPropObj[["DataPaths"]]$Add(file.path(ThisRAW))
+         evPropObj[["DataPaths"]]$Insert(file.path(RAWdir2),0) #better to do it like this where the new datapath is above the default data path. #add in second data path
+         evPropObj[["DataPaths"]]$Insert(file.path(ThisRAW),0) #better to do it like this where the new datapath is above the default data path.
+         print(paste("data path:", evPropObj[["DataPaths"]]$Item(0)))
+         # set calibration file
+         if (DirTableSurvey$Mult_Cal_Flag==0){  #multiple calibration flag off, Calfilename is already set above
+         }else{  #multiple calibrations for the survey, look in the excel sheet
+              Bounds<-as.matrix(CALsheet[,c("x_low_bound","x_up_bound")])
+              for (ri in 1:nrow(Bounds)){
+                   if (between(Transect,Bounds[ri,1],Bounds[ri,2])){  #If the transect is within the bounds of that row
+                        CALfileName<-as.character(CALsheet[ri,3])
+                        ThisCal<-CALfileName
+                   }
+              }
+         }
+         add.calibration <- filesetObj$SetCalibrationFile(ThisCal)
+         print(paste("calibration added: ",add.calibration))
+
+         # save EV file
+         EVfile$SaveAs(file.path(Post_EV_Dir,i))
+
+         #close EV file
+         EVApp$CloseFile(EVfile)
+
+       }
+  }
+  ##########################################
+
+  EVApp$Quit()  #quit echoview
+}