#'CST_Analogs
#' 
#'@author Carmen Alvarez-Castro, \email{carmen.alvarez-castro@cmcc.it}
#'        adapted version of the method of Yiou et al 2013 
#'        
#'@references Yiou, P., T. Salameh, P. Drobinski, L. Menut, R. Vautard, and M. Vrac, 2013 : 
#'           Ensemble reconstruction of the atmospheric column from surface pressure using analogues. 
#'           Clim. Dyn., 41, 1419-1437. \email{pascal.yiou@lsce.ipsl.fr}
#'           
#'@description search for days with similar atmospheric conditions based on the large scale slp (or geopotential height)
#              and the local scale (precipitation or Temperature)
#'
#'@param month      month of the analog day
#'       day        day of the analog day
#'       yr         year of the analog day
#'       mAnalog    month or list of months to search for analogs
#'@import 
#'
#'@return list      best.corr.time.ana,best.dist.time.ana,selec.dist.time,selec.corr.time 
#'        list      file.dat with a list of days with the format yyyymmdd ordered by best analog with the dist (minima) and corr (maxima) 
#'        plot      preliminary plot of the best analog selected
#'        yr1       first year of the total period of study
#'        yr2       last year of the total period of study
#'        ical       number of days per year in the calendar (360,365,366)
#'@example

# Analogs <- function(exp, obs) {
#   if (!all(c('member', 'sdate') %in% names(dim(exp)))) {
#     stop("Parameter 'exp' must have the dimensions 'member' and 'sdate'.")
#   }
#   
#   if (!all(c('sdate') %in% names(dim(obs)))) {
#     stop("Parameter 'obs' must have the dimension 'sdate'.")
#   }
#   
#   if (any(is.na(exp)))  {
#     warning("Parameter 'exp' contains NA values.")
#   }
#   
#   if (any(is.na(obs))) {
#     warning("Parameter 'obs' contains NA values.")
#   }
#   
#   target_dims_obs <- 'sdate'
#   if ('member' %in% names(dim(obs))) {
#     target_dims_obs <- c('member', target_dims_obs)
#   }
#   
#   Analogs <- Apply(data = list(var_obs = obs, var_exp = exp),
#                       target_dims = list(target_dims_obs, c('member', 'sdate')),
#                       fun = .select)$output1
#   
#   return(Analogs)
# }

time_obsL <- as.Date(c("2005-01-01", "2005-02-01", "2005-03-01",
                       "2005-04-01", "2005-05-01"))
Analogs <- function(expL, obsL, time_obsL, expVar = NULL, obsVar = NULL, 
                    criteria = "Large_dist",
                    lon_local = NULL, lat_local = NULL, region = NULL, 
                    nAnalogs = 1, return_list = FALSE) {
  # checks
  metric <- Select(expL = expL, obsL = obsL,  expVar = expVar, obsVar = obsVar, 
                   criteria = criteria, lon_local = lon_local, lat_local = lat_local,
                   region = region)
  best <- Apply(list(metric), target_dims = 'time', fun = BestAnalog,
                criteria = criteria, return = return_list)
}
#'@example
#'met <- Select(expL = expL, obsL = obsL)
#'pos <- BestAnalog(met)
BestAnalog <- function(metric, criteria = 'Large_dist', return_list = FALSE, 
                       nAnalogs = 1)
    if (criteria == 'Large_dist') {
      metric1 <- metric$metric1
      pos1 <- metric$pos1
       if (return_list == FALSE) {
          pos <- pos1[1]
       } else {
           pos <- pos1[1 : nAnalogs]
       }
  } else if (criteria== 'Local_dist') {
    # pos1 <- c(7, 13, 5, 3, 6, 12, 10, 1, 8, 9, 11, 4, 2, 14)
    # pos2 <- c(4, 8, 13, 6, 3, 1, 12, 5, 9, 7, 10, 2, 11, 14)
    pos1 <- pos1[1 : nAnalogs]
    pos2 <- pos2[1 : nAnalogs]
    best <- match(pos1, pos2)
    pos <- pos1[as.logical(best)]
    pos <- pos[which(!is.na(pos))]
       if (return_list == FALSE) {
         pos <- pos[1]
       }
  } else if (criteria == 'Local_cor') {
    pos1 <- pos1[1 : nAnalogs]
    pos2 <- pos2[1 : nAnalogs]
    best <- match(pos1, pos2)
    pos <- pos1[as.logical(best)]
    pos <- pos[which(!is.na(pos))]
    # pos3 <- c(6, 11, 14, 3, 13, 7, 2, 5, 1, 12, 10, 9, 8, 4) 
    pos3 <- pos3[1 : nAnalogs]
    best <- match(pos, pos3)
    pos <- pos[order(best, decreasing = F)]
    pos <- pos[which(!is.na(pos))]
      if (return_list == FALSE) {
          pos[1]
      } 
    return(pos)
}


expL <- (1  + 2): (4 * 3 * 2 + 2)
dim(expL) <- c(lat = 4, lon = 3, time = 2)
obsL <- 1 : c(4 * 3 * 5)
dim(obsL) <- c(lat = 4, lon = 3, time = 5)
res = Select(expL, obsL)
expL <- (1  + 2): (8 * 10 * 2 + 2)
dim(expL) <- c(lat = 8, lon = 10, time = 2)
obsL <- 1 : c(8 * 10 * 5)
dim(obsL) <- c(lat = 8, lon = 10, time = 5)
lat_local <- lat <- seq(0, 19, 2.5)
lon_local <- lon <- seq(0, 23, 2.5)
res = Select(expL, obsL, criteria = "Local_dist", lon_local = lon, 
             lat_local = lat,
             region = c(lonmin = 0, lonmax = 5, latmin = 0, latmax = 5 ))
# probar mas ejemplos con diferentes criterios, latitudes, longitudes
Select <- function(expL, obsL,  expVar = NULL, obsVar = NULL, criteria = "Large_dist",
                   lon_local = NULL, lat_local = NULL, region = NULL) {
  #check expL
  #check obsL
  #check obsVar
  metric1 <- Apply(list(obsL), target_dims = list(c('lat', 'lon')), 
                   fun = .select, expL, metric = "dist",
                   output_dims = c('time_exp'))$output1
  pos1 <- apply(metric1, 1, order)
  metric1 <-  apply(metric1, 1, sort)

  if (criteria == "Large_dist") {
    return(list(metric1 = metric1, pos1 = pos1))
  }
  if (criteria == "Local_dist" | criteria == "Local_cor") {
    obs <- SelBox(obsL, lon = lon_local, lat = lat_local, region = region)$data
    exp <- SelBox(expL, lon = lon_local, lat = lat_local, region = region)$data
    metric2 <- Apply(list(obs), target_dims = list(c('lat', 'lon')), 
                     fun = .select, exp, metric = "dist")$output1
    pos2 <- apply(metric2, 1, order)
    metric2 <-  apply(metric2, 1, sort)
      if (criteria == "Local_dist") {
        return(list(metric1 = metric1, metric2 = metric2, 
                    pos1 = pos1, pos2 = pos2))
      }   
   }
  if (criteria == "Local_cor") {
    obs <- SelBox(obsVar, lon = lon_local, lat = lat_local, region = region)$data
    exp <- SelBox(expVar, lon = lon_local, lat = lat_local, region = region)$data
    metric3 <- Apply(list(obs), target_dims = list(c('lat', 'lon')), 
                     fun = .select, exp, metric = "cor")$output1
    pos3 <- apply(metric3, 1, order, decreasing = TRUE)
    metric3 <-  apply(metric3, 1, sort)
      return(list(metric1 = metric1, metric2 = metric2, metric3 = metric3, 
                  pos1 = pos1, pos2 = pos2, pos3 = pos3))
    }
  else {
    stop("Parameter 'criteria' must to be one of the: 'Large_dist', ",
         "'Local_dist','Local_cor'.")
  }
}
  
# data <- 1:(20 * 3 * 2 * 4)
# dim(data) <- c(lon = 20, lat = 3, time = 2, model = 4)
# lon <- seq(2, 40, 2)
# lat <- c(1, 5, 10)
# a <- SelBox(data = data, lon = lon, lat = lat, region = c(2, 20, 1, 5),
#             londim = 1, latdim = 2, mask = NULL)
# str(a)
  
#'@example
exp <- (1  + 2): (4 * 3 + 2)
dim(exp) <- c(lat = 4, lon = 3)
obs <- 1 : c(5 * 4 * 3)
dim(obs) <- c(time = 5, lat = 4, lon = 3)
res <- .select(exp, obs)
res
res <- .select(exp, obs, metric = 'cor')
dim(res)
.select <- function(exp, obs, metric = "dist") {
  if (metric == "dist") {
    #metric <- sum((obs - exp) ^ 2)
    #metric <- apply(obs, "time", function(x) {sum((x - exp) ^ 2)})
    result <- Apply(list(obs), target_dims = list(c('lat', 'lon')), 
                    fun = function(x) {sum((x - exp) ^ 2)})$output1
  } else if (metric == "cor") {
    result <- Apply(list(obs), target_dims = list(c('lat', 'lon')), 
                    fun = function(x) {cor(as.vector(x), as.vector(exp))})$output1
  } 
  result
}