bug fix on calc_flux: be careful of approx(), it can flip the order o…

…f xycoord and cause bug. missing scal added in. inherit dots arguments in more explicit way.

R/calc_flux.R

@@ -1,14 +1,16 @@
 calc_flux <- function(FUN = get_fluxln, vf_path,
                       side = c('right', 'left'),
-                      refv = 0, width, ...) {
+                      refv = 0, width, scal, ...) {
   side <- match.arg(side)
   fluxlnpts <- FUN(...)
   projected_v <- proj_v(fluxlnpts, vf_path = vf_path, side = side)
 
   # return sum of vectors * width they represent, after adjustment by relative
   # velocity
-  if (as.character(substitute(FUN)) == 'get_fluxln')
-    width <- ln_width*scal*ln_width_scal
+  if (as.character(substitute(FUN)) == 'get_fluxln') {
+    dot_args <- list(...)
+    width <- dot_args$ln_width*scal*dot_args$ln_width_scal
+  }  
   return((mean(projected_v)+refv) * width)
 }
 
@@ -32,7 +34,7 @@ tcalc_flux <-function(body_land_array, vf_dir, id, vect_scal,
     refv <- calc_refv(body_land_array, type = type, scal = scal,
                       t_stamp = t_stamp)
   } else {
-    refv = 0
+    refv = rep(0, length(id))
   }
 
   # calc flux
@@ -42,9 +44,9 @@ tcalc_flux <-function(body_land_array, vf_dir, id, vect_scal,
                            vf_path = file.path(vf_dir, get_file(id[i])),
                            refv = refv[i],
                            vect_scal = vect_scal,
-                           ln_width, ln_width_scal = ln_width_scal,
+                           ln_width = ln_width, ln_width_scal = ln_width_scal,
                            side = side,
-                           body_land = body_land_array[, , i])
+                           body_land = body_land_array[, , i], scal = scal)
   }
 
   return(result)
@@ -61,7 +63,7 @@ proj_v <- function(xycoord, vf_path, nseg = 8, side = c('right', 'left')) {
   # get the xycoords of these 17 points
   approx_out <- approx(xycoord, n = nseg*2+1)  # in/output in xy.coords format
   # from the indices, get the center points of each segment
-  flux_ln <- lapply(approx_out, `[`, cell_idx)
+  flux_ln <- lapply(approx_out, `[`, cell_idx)  
 
   ## interpolate vector field on flux line
   # get the vector field
@@ -77,8 +79,8 @@ proj_v <- function(xycoord, vf_path, nseg = 8, side = c('right', 'left')) {
   ## projection
   # let's make flux line a vector
   flux_ln_mat <- xycoords2mat(flux_ln)  # just change format
-  flux_ln_vec <- unitv(flux_ln_mat[2, ] - flux_ln_mat[1, ])
-
+  flux_ln_vec <- unitv(xycoords2mat(xycoord)[2, ] -xycoords2mat(xycoord)[1, ] )
+  
   # unit normal vector, have two in either direction
   # find normal vector by swapping x and y, and minus to either one
   unormv1 <- c(flux_ln_vec[2], -flux_ln_vec[1])  # clockwise (right)

man/calc_flux.Rd

@@ -37,7 +37,7 @@ proj_v(xycoord, vf_path, nseg = 8, side = c('right', 'left'))
   \item{ln_width}{passed to \code{\link{get_fluxln}}, single value}
   \item{ln_width_scal}{passed to \code{\link{get_fluxln}}, single value}
   \item{t_stamp}{passed to \code{\link{calc_refv}}}
-  \item{scal}{passed to \code{\link{get_fluxln}}}
+  \item{scal}{scale in length/ pixel to scale \code{width}}
   \item{xycoord}{xy coordinates of two points defining the line segment to 
     calculate flux, should in \code{R \link{xy.coords}} format}
   \item{nseg}{(int) how many segments the flux line consists of, arbitrarily set}