R/seabird.db.r

In jae0/bio.snowcrab: Snow crab assessment suite using aegis* and associated projects and data streams.

	# mostly a copy over of the MINILOG functions with variable nemaes being replaced

  seabird.db = function( DS="", Y=NULL, plotdata=FALSE, force_recompute=FALSE ){

    sb.dir = project.datadirectory("bio.snowcrab", "data", "seabird" )
    seabird.rawdata.location = file.path( sb.dir, "archive" )

    if (!is.null(Y)) {
        iY = which( Y>=2012 )  # no historical data prior to 2012
        if (length(iY)==0) return ("No data for specified years")
        Y = Y[iY]
    }


    if ( DS %in% c("basedata", "metadata", "load") ) {

      if (DS=="basedata" ){
        flist = list.files(path=sb.dir, pattern="basedata", full.names=T, recursive=FALSE)
        if (!is.null(Y)) {
          mm = NULL
          for (yy in Y ) {
            ll = grep( yy, flist)
            if (length(ll)==0) return( NULL) # nothing to do
            if (length(ll)>0 ) mm = c( mm, ll)
          }
          if (length(mm) > 0 ) flist= flist[mm]
        }
        out = NULL
        for ( i in flist ) {
          load( i )
          out= rbind( out, basedata )
        }
        return( out )
      }

      if (DS=="metadata" ){
        flist = list.files(path=sb.dir, pattern="metadata", full.names=T, recursive=FALSE)
        if (!is.null(Y)) {
          mm = NULL
          for (yy in Y ) {
            ll = grep( yy, flist)
            if (length(ll)==0) return( NULL) # nothing to do
            if (length(ll)>0 ) mm = c( mm, ll)
          }
          if (length(mm) > 0 ) flist= flist[mm]
        }
        out = NULL
        for ( i in flist ) {
          load( i ) # loads a thing called metadata
          out= rbind( out, metadata )
        }
        return( out )
      }

      # default is to "load"

      dirlist = list.files(path=seabird.rawdata.location, full.names=T, recursive=T)
      nfiles = length(dirlist)
      filelist = matrix( NA, ncol=3, nrow=nfiles)
      for (f in 1:nfiles) {
        yr = seabirdDate( fnSeaBird=dirlist[f] )
        if (is.null(yr) ) next()
        if ( yr %in% Y ) filelist[f,] = c( f, dirlist[f], yr )
      }
      fli = which( !is.na( filelist[,1] ) )
      if (length(fli) == 0) return( "No data found matching the criteria")

      filelist = filelist[ fli , ]

      set = snowcrab.db( DS="setInitial" )

      for ( yr in Y ) {
        print(yr)
        fn.meta = file.path( sb.dir, paste( "seabird", "metadata", yr, "rdata", sep="." ) )
        fn.raw = file.path( sb.dir, paste( "seabird", "basedata", yr, "rdata", sep="." ) )
        fs = filelist[ which( as.numeric(filelist[,3])==yr ) , 2 ]
        if (length(fs)==0) next()
        basedata = NULL
        metadata = NULL
        for (f in 1:length(fs)) {
          j = load.seabird.rawdata( fn=fs, f=f, set=set, plotdata=plotdata )
          if (is.null(j)) next()
          metadata = rbind( metadata, j$metadata)
          basedata = rbind( basedata, j$basedata)
        }

        save( metadata, file=fn.meta, compress=TRUE )
        save( basedata, file=fn.raw, compress=TRUE )
      }

      seabird.db( DS="set.seabird.lookuptable.redo" )

      return ( sb.dir )
    }


    if (DS %in% c("stats", "stats.redo" ) ) {

      dir.create( file.path( sb.dir, "figures" ), recursive=TRUE, showWarnings=FALSE )

      if (DS=="stats") {

        flist = list.files(path=sb.dir, pattern="stats", full.names=T, recursive=FALSE)
        if (!is.null(Y)) {
          mm = NULL
          for (yy in Y ) {
            ll = grep( yy, flist)
            if (length(ll)==0) return( NULL) # nothing to do
            if (length(ll)>0 ) mm = c( mm, ll)
          }
          if (length(mm) > 0 ) flist= flist[mm]
        }

        sb.stat = NULL
        for ( i in 1:length(flist )) {
          load( flist[i] )
          sb.stat = rbind( sb.stat, sbStats )
        }

        sb.meta = seabird.db( DS="metadata", Y=Y )

        res = merge( sb.meta, sb.stat,  by="seabird_uid", all.x=TRUE, all.y=FALSE, sort=FALSE )

        if(any(duplicated(res[,c('trip','set')]))) {
          res = removeDuplicateswithNA(res,cols=c('trip','set'),idvar='dt')
        }

        #tzone = "UTC"
        #res$t0 = as.POSIXct( lubridate::ymd_hms(res$t0), origin=lubridate::origin, tz=tzone )
        #res$t1 = as.POSIXct( lubridate::ymd_hms(res$t1), origin=lubridate::origin, tz=tzone )
        # res$timestamp = lubridate::ymd_hms( res$timestamp)

        return(res)
      }

      # bad.list = c(
      #  "seabird.S06112014.8.210.18.44.9",
      #  "seabird.S06112014.1.37.7.45.13" )
      bad.list = NULL
      bad.list = unique( c(bad.list, p$netmensuration.problems) )

      # default action  is "stats.redo"
      for ( yr in Y ) {
        print (yr )

        fn = file.path( sb.dir, paste( "seabird.stats", yr, "rdata", sep=".") )
        sbRAW = mta = sbStats = NULL

        sbRAW = seabird.db( DS="basedata", Y=yr )
        mta = seabird.db( DS="metadata", Y=yr )

        if (is.null(sbRAW) | is.null(mta)) next()

        rid = seabird.db( DS="set.seabird.lookuptable" )
        rid = data.frame( seabird_uid=rid$seabird_uid, stringsAsFactors=FALSE )
        rid = merge( rid, mta, by="seabird_uid", all.x=TRUE, all.y=FALSE )
        rid = rid[ which(rid$yr== yr) ,]

        if (nrow(rid) == 0 ) next()

        for ( i in 1:nrow(rid) ) {
     
          print(i)

          id = rid$seabird_uid[i]
          if (id %in% bad.list) next()

          sso.trip = rid$trip[i]
          sso.set = rid$set[i]
          sso.station = rid$station[i]

          Mi = which( sbRAW$seabird_uid == id )
          if (length( Mi) == 0 ) next()
          if (length( Mi) < 30 ) next()

          M = sbRAW[ Mi, ]

          ### BC Trying to add netmind metrics for better manual touchdown determination
          
          
          nmRAW = netmind.db( DS="basedata", Y=yr )
          nid = netmind.db( DS="set.netmind.lookuptable" )
          nuid = nid[which(nid$trip == sso.trip & nid$set == sso.set),]$netmind_uid
          Ni = nmRAW[which(nmRAW$netmind_uid == nuid),]
          Ni = Ni[which(Ni$timestamp>=M$timestamp[1] & Ni$timestamp<=M$timestamp[length(M$timestamp)]),]

          Ni = merge(Ni, M, by = "timestamp", all.x = TRUE)
          jj = which( names(Ni) %in% c("timestamp", "temperature", "depth.y", "lat", "lon", "primary", "doorspread" ) )
          if (!(length(jj) == 7)) { 
            jj = which( names(Ni) %in% c("timestamp", "temperature.y", "depth.y", "lat", "lon", "primary", "doorspread" ) )
          }
          if (!(length(jj) == 7)) {
            message( jj)
            message("No of vars incorrect: verify this .. ")
            message( head(Ni) )
            next()
          }

          Ni = Ni[, jj]
          names(Ni) = c("timestamp", "latitude", "longitude", "opening", "wingspread", "temperature", "depth")
          M = Ni

          ##End of Netmind metrics merger
          
          settimestamp= rid$timestamp[i]

          # default, empty container
          res = data.frame(z=NA, t=NA, zsd=NA, tsd=NA, n=NA, t0=NA, t1=NA, dt=NA)
          # initial estimate of z, t in case bottom contact fails
          time.gate0 =  list( t0=settimestamp, t1=settimestamp + dminutes(5) )  # expected bottom
          ii0 = which( M$timestamp > time.gate0[1] & M$timestamp < time.gate0[2]  )
          if (length(ii0) > 30) {
            res$z = mean(M$depth[ii0], na.rm=TRUE)
            res$zsd = sd(M$depth[ii0], na.rm=TRUE)
            res$t = mean(M$temperature[ii0], na.rm=TRUE)
            res$tsd = sd(M$temperature[ii0], na.rm=TRUE)
          }

          time.gate =  list( t0=settimestamp - dminutes(6), t1=settimestamp + dminutes(12) )
          # tdiff.max can be large if there is a current ... speed can be reduced
          bcp = list(id=id, nr=nrow(M), YR=yr, trip = sso.trip, tdif.min=3, tdif.max=15, time.gate=time.gate,
                     depth.min=20,depth.range=c(-25,30), eps.depth=1.5,
                     smooth.windowsize=5, modal.windowsize=5,
                     noisefilter.trim=0.025, noisefilter.target.r2=0.85, noisefilter.quants=c(0.025, 0.975),
                     user.interaction = TRUE, datasource = "snowcrab")

          bcp = bottom.contact.parameters( bcp ) # add other default parameters

          #BC: Determine if this station was done yet, if not then we want user interaction.
          if(file.exists(file.path(bcp$from.manual.archive, "clicktouchdown_all.csv"))){
            manualclick = read.csv(file.path(bcp$from.manual.archive, "clicktouchdown_all.csv"), as.is=TRUE)
            station = unlist(strsplit(bcp$id, "\\."))[4]
            sta.ind = which(manualclick$station == station & manualclick$year == bcp$YR)
            if(length(sta.ind) == 1) bcp$user.interaction = FALSE
            else bcp$user.interaction = TRUE
          }
          
          
          
          print(id)
         
          ds.out.range = which(M$wingspread < 2 | M$wingspread > 18)
          if(length(ds.out.range)>0){
            M$wingspread[ds.out.range] = NA
          }
          op.out.range = which(M$opening < .1 | M$opening > 10)
          if(length(op.out.range)>0){
            M$opening[op.out.range] = NA
          }
          M$doorspread = M$wingspread# hack to force SA to run
          
          bc = NULL
          bc = bottom.contact( x=M, bcp=bcp )
          #browser()

          if ( is.null(bc) || ( !is.null(bc$res)  && ( ( !is.finite(bc$res$t0 ) || !is.finite(bc$res$t1 ) ) ) )) {
             bcp$noisefilter.target.r2=0.75
             bc = bottom.contact( x=M, bcp=bcp )
          }
          if ( is.null(bc) || ( !is.null(bc$res) && ( ( !is.finite(bc$res$t0 ) || !is.finite(bc$res$t1 ) ) ) )) {
            M$depth = jitter( M$depth, amount = bcp$eps.depth/10 )
            bcp$noisefilter.inla.h = 0.1
            bc = bottom.contact( x=M, bcp=bcp )
          }
          if ( is.null(bc) || ( !is.null(bc$res) && ( ( !is.finite(bc$res$t0 ) || !is.finite(bc$res$t1 ) ) ) )) {
            M$depth = jitter( M$depth, amount = bcp$eps.depth/10 )
            bcp$noisefilter.inla.h = 0.25
            bc = bottom.contact( x=M, bcp=bcp )
          }

          if ( !is.null(bc) && !is.null( bc$res ) ) res = bc$res

          if ( !is.null(bc) ) {
            if (plotdata) {
              bottom.contact.plot( bc )
              plotfn = file.path( sb.dir, "figures", paste(id, "pdf", sep="." ) )
              print (plotfn)
              dev.flush()
              #dev.copy2pdf( file=plotfn )
              graphics.off()
            }
          }
          sbStats = rbind( sbStats, cbind( seabird_uid=id, res ) )
        }
        sbStats$seabird_uid =  as.character(sbStats$seabird_uid)
        sbStats$t0 = as.POSIXct(sbStats$t0,origin=lubridate::origin, tz="UTC" )
        sbStats$t1 = as.POSIXct(sbStats$t1,origin=lubridate::origin, tz="UTC")
        sbStats$dt = difftime( sbStats$t1, sbStats$t0 )
        save( sbStats, file=fn, compress=TRUE)
      }

      return ( sb.dir )
    }


    # ----------------------

    if ( DS %in% c("set.seabird.lookuptable", "set.seabird.lookuptable.redo" ) ) {

      fn = file.path( sb.dir, "set.seabird.lookuptable.rdata" )

      if ( DS=="set.seabird.lookuptable" ) {
        B = NULL
        if ( file.exists( fn) ) load (fn)

        return (B)
      }

      B = seabird.db( DS="metadata" )

      # duplicates are created when datafiles are not reset completely
      # and the same data is reloaded during the survey ... cleanup at this stage

      # seabird_uid cannot be used as it has a file number attached
      # to make each one unique, even with duplicated data streams
      uuid = paste( B$trip, B$set, sep="." )
      dups = which( duplicated( uuid) )

      if (length(dups > 0 ) ) {
        toremove =NULL
        for (i in dups) {
          di = which( uuid == uuid[i] )

          tdiff = difftime( B$set_timestamp[di],  B$timestamp[di] )
          oo = which.min( abs( tdiff) )
          toremove = c(toremove, di[-oo] )
          print("----")
          print( "Matching based upon closest time stamps")
          print(B[di, ])
          print( "Choosing: ")
          print(B[di[oo], ])
          print("")
          toremove = c(toremove, di[-oo] )
        }
        B = B[ -toremove, ]
      }

      B =  B[, c("trip", "set", "seabird_uid" )]
      save(B, file=fn, compress=TRUE )
      return(fn)

    }

	}

  # --------------------