From 366b782152c3897b2786b4d67a2c4a4b9faa3f89 Mon Sep 17 00:00:00 2001
From: rCarto <timothee.giraud@cnrs.fr>
Date: Mon, 27 May 2024 17:17:24 +0200
Subject: [PATCH] feat: add a smooth parameter to osrmIso*() functions, see
 #129

---
 DESCRIPTION                     |   6 ++-
 R/osrmIsochrone.R               |  79 ++++++++++++++++++++++++++------
 R/osrmIsodistance.R             |  55 +++++++++++++++++++++-
 R/utils.R                       |  13 ++++--
 inst/tinytest/fill_grid_out.rds | Bin 7441 -> 9140 bytes
 man/osrmIsochrone.Rd            |   9 ++++
 man/osrmIsodistance.Rd          |   9 ++++
 7 files changed, 150 insertions(+), 21 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b932381..8b02589 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -25,7 +25,11 @@ Imports:
     sf
 Depends:
     R (>= 3.5.0)
-Suggests: mapsf, tinytest, covr
+Suggests: 
+    mapsf, 
+    tinytest, 
+    covr, 
+    terra
 URL: https://github.com/riatelab/osrm
 BugReports: https://github.com/riatelab/osrm/issues
 Encoding: UTF-8
diff --git a/R/osrmIsochrone.R b/R/osrmIsochrone.R
index c3bb69c..a72ef61 100644
--- a/R/osrmIsochrone.R
+++ b/R/osrmIsochrone.R
@@ -19,6 +19,11 @@
 #' grid, the total number of points will be res*res. Increase res to obtain more
 #' detailed isochrones.
 #' @param returnclass deprecated.
+#' @param smooth if TRUE a moving window with a gaussian blur is applied to 
+#' durations. This option may be usefull to remove small patches of hard to 
+#' reach areas. The computed isochrones are less precise but better looking. 
+#' @param k size (sigma) of the gaussian moving window. A reasonable value is 
+#' used by default.
 #' @param osrm.server the base URL of the routing server.
 #' getOption("osrm.server") by default.
 #' @param osrm.profile the routing profile to use, e.g. "car", "bike" or "foot"
@@ -64,27 +69,30 @@
 #' }
 #' }
 osrmIsochrone <- function(loc, breaks = seq(from = 0, to = 60, length.out = 7),
-                          exclude, res = 30, returnclass,
+                          exclude, res = 30, smooth = FALSE, k,
+                          returnclass,
                           osrm.server = getOption("osrm.server"),
                           osrm.profile = getOption("osrm.profile")) {
   opt <- options(error = NULL)
   on.exit(options(opt), add = TRUE)
-
+  
   if (!missing(returnclass)) {
     warning('"returnclass" is deprecated.', call. = FALSE)
   }
-
+  
   # input management
   loc <- input_route(x = loc, id = "loc", single = TRUE)
   oprj <- loc$oprj
   loc <- st_as_sf(data.frame(lon = loc$lon, lat = loc$lat),
-    coords = c("lon", "lat"), crs = 4326
+                  coords = c("lon", "lat"), crs = 4326
   )
   loc <- st_transform(loc, "epsg:3857")
-
+  
   # max distance management to see how far to extend the grid to get measures
   breaks <- unique(sort(breaks))
   tmax <- max(breaks)
+  
+  # gentle sleeptime & param for demo server
   if (osrm.profile %in% c("foot", "walk")) {
     speed <- 10 * 1000 / 60
   }
@@ -95,8 +103,8 @@ osrmIsochrone <- function(loc, breaks = seq(from = 0, to = 60, length.out = 7),
     speed <- 120 * 1000 / 60
   }
   dmax <- tmax * speed
-
-
+  
+  
   # gentle sleeptime & param for demo server
   if (osrm.server != "https://routing.openstreetmap.de/") {
     sleeptime <- 0
@@ -105,7 +113,7 @@ osrmIsochrone <- function(loc, breaks = seq(from = 0, to = 60, length.out = 7),
     sleeptime <- 1
     deco <- 75
   }
-
+  
   # create a grid to obtain measures
   sgrid <- rgrid(loc = loc, dmax = dmax, res = res)
   # slice the grid to make several API calls
@@ -140,19 +148,20 @@ osrmIsochrone <- function(loc, breaks = seq(from = 0, to = 60, length.out = 7),
     listDur[[ltot]] <- dmat$durations
     listDest[[ltot]] <- dmat$destinations
   }
-
+  
   measure <- do.call(c, listDur)
   destinations <- do.call(rbind, listDest)
   # for testing purpose
   # return(list(destinations = destinations, measure = measure,
   #             sgrid = sgrid, res = res, tmax = tmax))
-
+  
   # assign values to the grid
   sgrid <- fill_grid(
     destinations = destinations, measure = measure,
     sgrid = sgrid, res = res, tmax = tmax
   )
-  if (min(sgrid$measure) >= tmax + 1) {
+  
+  if (min(sgrid$measure, na.rm = TRUE) > tmax) {
     warning(
       paste0(
         "An empty object is returned. ",
@@ -169,19 +178,63 @@ osrmIsochrone <- function(loc, breaks = seq(from = 0, to = 60, length.out = 7),
     )
     return(empty_res)
   }
+  
+  if (isFALSE(smooth)) {
+    # All values not within breaks are set to tmax+1 
+    sgrid[is.na(sgrid$measure), "measure"] <- tmax + 1
+    sgrid[is.nan(sgrid$measure), "measure"] <- tmax + 1
+    sgrid[is.infinite(sgrid$measure), "measure"] <- tmax + 1
+    sgrid[sgrid$measure > tmax, "measure"] <- tmax + 1
+  } else {
+    if (!requireNamespace("terra", quietly = TRUE)) {
+      stop(paste0(
+        "'terra' package is needed for this function to work.",
+        "Please install it."
+      ), call. = FALSE)
+    }
+    r <- terra::rast(sgrid[, c("COORDX", "COORDY", "measure"), drop = TRUE], 
+              crs = "epsg:3857")
+    if (missing(k)) {
+      k <- terra::res(r)[1] / 2
+    }
+    mat <- terra::focalMat(x = r, d = k, type = "Gauss")
+    
+    # test for invalid focal matrix
+    if (sum(dim(mat)) < 6){
+      warning(
+        paste0(
+          "An empty object is returned. ",
+          "Select a larger value for 'k'."
+        ),
+        call. = FALSE
+      )
+      empty_res <- st_sf(
+        crs = ifelse(is.na(oprj), 4326, oprj),
+        id = integer(),
+        isomin = numeric(),
+        isomax = numeric(),
+        geometry = st_sfc()
+      )
+      return(empty_res)
+    }
+    sgrid <- terra::focal(x = r, w = mat, fun = mean, na.rm = TRUE)
+    sgrid[is.na(sgrid)] <- tmax + 1
+  }
+  
+  
   # computes isopolygones
   iso <- mapiso(x = sgrid, breaks = breaks, var = "measure")
   # get rid of out of breaks polys
   iso <- iso[-nrow(iso), ]
   # fisrt line always start at 0
   iso[1, "isomin"] <- 0
-
+  
   # proj mgmnt
   if (!is.na(oprj)) {
     iso <- st_transform(x = iso, oprj)
   } else {
     iso <- st_transform(x = iso, 4326)
   }
-
+  
   return(iso)
 }
diff --git a/R/osrmIsodistance.R b/R/osrmIsodistance.R
index bb3b897..30e6712 100644
--- a/R/osrmIsodistance.R
+++ b/R/osrmIsodistance.R
@@ -19,6 +19,11 @@
 #' square grid, the total number of points will be res*res. Increase res to
 #' obtain more detailed isodistances.
 #' @param returnclass deprecated.
+#' @param smooth if TRUE a moving window with a gaussian blur is applied to 
+#' distances. This option may be usefull to remove small patches of hard to 
+#' reach areas. The computed isodistances are less precise but better looking. 
+#' @param k size (sigma) of the gaussian moving window. A reasonable value is 
+#' used by default.
 #' @param osrm.server the base URL of the routing server.
 #' getOption("osrm.server") by default.
 #' @param osrm.profile the routing profile to use, e.g. "car", "bike" or "foot"
@@ -62,7 +67,8 @@
 #' }
 #' }
 osrmIsodistance <- function(loc, breaks = seq(from = 0, to = 10000, length.out = 4),
-                            exclude, res = 30, returnclass,
+                            exclude, res = 30, smooth = FALSE, k,
+                            returnclass,
                             osrm.server = getOption("osrm.server"),
                             osrm.profile = getOption("osrm.profile")) {
   opt <- options(error = NULL)
@@ -138,7 +144,9 @@ osrmIsodistance <- function(loc, breaks = seq(from = 0, to = 10000, length.out =
     destinations = destinations, measure = measure,
     sgrid = sgrid, res = res, tmax = tmax
   )
-  if (min(sgrid$measure) >= tmax + 1) {
+  
+  
+  if (min(sgrid$measure, na.rm = TRUE) >= tmax) {
     warning(
       paste0(
         "An empty object is returned. ",
@@ -155,6 +163,49 @@ osrmIsodistance <- function(loc, breaks = seq(from = 0, to = 10000, length.out =
     )
     return(empty_res)
   }
+  
+  if (isFALSE(smooth)) {
+    # All values not within breaks are set to tmax+1 
+    sgrid[is.na(sgrid$measure), "measure"] <- tmax + 1
+    sgrid[is.nan(sgrid$measure), "measure"] <- tmax + 1
+    sgrid[is.infinite(sgrid$measure), "measure"] <- tmax + 1
+    sgrid[sgrid$measure > tmax, "measure"] <- tmax + 1
+  } else {
+    if (!requireNamespace("terra", quietly = TRUE)) {
+      stop(paste0(
+        "'terra' package is needed for this function to work.",
+        "Please install it."
+      ), call. = FALSE)
+    }
+    r <- terra::rast(sgrid[, c("COORDX", "COORDY", "measure"), drop = TRUE], 
+                     crs = "epsg:3857")
+    if (missing(k)) {
+      k <- terra::res(r)[1] / 2
+    }
+    mat <- terra::focalMat(x = r, d = k, type = "Gauss")
+    
+    # test for invalid focal matrix
+    if (sum(dim(mat)) < 6){
+      warning(
+        paste0(
+          "An empty object is returned. ",
+          "Select a larger value for 'k'."
+        ),
+        call. = FALSE
+      )
+      empty_res <- st_sf(
+        crs = ifelse(is.na(oprj), 4326, oprj),
+        id = integer(),
+        isomin = numeric(),
+        isomax = numeric(),
+        geometry = st_sfc()
+      )
+      return(empty_res)
+    }
+    sgrid <- terra::focal(x = r, w = mat, fun = mean, na.rm = TRUE)
+    sgrid[is.na(sgrid)] <- tmax + 1
+  }
+  
   # computes isopolygones
   iso <- mapiso(x = sgrid, breaks = breaks, var = "measure")
   # get rid of out of breaks polys
diff --git a/R/utils.R b/R/utils.R
index 16e50f3..841fca5 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -372,16 +372,19 @@ fill_grid <- function(destinations, measure, sgrid, res, tmax) {
     n = c(res, res)
   )
   ag_pt <- function(x) {
-    if (length(x > 0)) {
+    if (length(x) > 0) {
       min(rpt[["measure"]][x], na.rm = TRUE)
     } else {
-      tmax + 1
+      NA
     }
   }
   inter <- st_intersects(xx, rpt)
   sgrid$measure <- unlist(lapply(inter, ag_pt))
-  sgrid[is.infinite(sgrid$measure), "measure"] <- tmax + 1
-  sgrid[is.nan(sgrid$measure), "measure"] <- tmax + 1
-  sgrid[sgrid$measure > tmax, "measure"] <- tmax + 1
+  sgrid[is.infinite(sgrid$measure), "measure"] <- NA
+  sgrid[is.nan(sgrid$measure), "measure"] <- NA
   sgrid
 }
+
+
+
+
diff --git a/inst/tinytest/fill_grid_out.rds b/inst/tinytest/fill_grid_out.rds
index bbae8e02dffcc68bf67a3839082975c5f8ea7987..5b62bfcfbe55ab87169174912b15fbe30081f966 100644
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diff --git a/man/osrmIsochrone.Rd b/man/osrmIsochrone.Rd
index a190ef5..3bf4882 100644
--- a/man/osrmIsochrone.Rd
+++ b/man/osrmIsochrone.Rd
@@ -9,6 +9,8 @@ osrmIsochrone(
   breaks = seq(from = 0, to = 60, length.out = 7),
   exclude,
   res = 30,
+  smooth = FALSE,
+  k,
   returnclass,
   osrm.server = getOption("osrm.server"),
   osrm.profile = getOption("osrm.profile")
@@ -34,6 +36,13 @@ in minutes.}
 grid, the total number of points will be res*res. Increase res to obtain more
 detailed isochrones.}
 
+\item{smooth}{if TRUE a moving window with a gaussian blur is applied to 
+durations. This option may be usefull to remove small patches of hard to 
+reach areas. The computed isochrones are less precise but better looking.}
+
+\item{k}{size (sigma) of the gaussian moving window. A reasonable value is 
+used by default.}
+
 \item{returnclass}{deprecated.}
 
 \item{osrm.server}{the base URL of the routing server.
diff --git a/man/osrmIsodistance.Rd b/man/osrmIsodistance.Rd
index aa72acb..a463b0b 100644
--- a/man/osrmIsodistance.Rd
+++ b/man/osrmIsodistance.Rd
@@ -9,6 +9,8 @@ osrmIsodistance(
   breaks = seq(from = 0, to = 10000, length.out = 4),
   exclude,
   res = 30,
+  smooth = FALSE,
+  k,
   returnclass,
   osrm.server = getOption("osrm.server"),
   osrm.profile = getOption("osrm.profile")
@@ -34,6 +36,13 @@ in meters.}
 square grid, the total number of points will be res*res. Increase res to
 obtain more detailed isodistances.}
 
+\item{smooth}{if TRUE a moving window with a gaussian blur is applied to 
+distances. This option may be usefull to remove small patches of hard to 
+reach areas. The computed isodistances are less precise but better looking.}
+
+\item{k}{size (sigma) of the gaussian moving window. A reasonable value is 
+used by default.}
+
 \item{returnclass}{deprecated.}
 
 \item{osrm.server}{the base URL of the routing server.