From 1311b4abe859a53bbaea09611fa7abac9861c910 Mon Sep 17 00:00:00 2001
From: Nic <sciurusurbanus@hotmail.it>
Date: Thu, 26 Oct 2023 12:39:02 +0200
Subject: [PATCH 01/22] Update line_segment_detector.R

Adapted the code to work with SpatRaster from the terra package and added the possibility to output the lines as an sf object.
There's a horrible workaround to solve a transpostion of the data along the second axi but couldn't find a better alternative. Overall, it works smoothly and fast even with high resolution aerial images (tested on 1km tiles with 0.15 cm pixels)
---
 .../R/line_segment_detector.R                 | 81 ++++++++++++++++++-
 1 file changed, 77 insertions(+), 4 deletions(-)

diff --git a/image.LineSegmentDetector/R/line_segment_detector.R b/image.LineSegmentDetector/R/line_segment_detector.R
index f3a1025..1c38674 100644
--- a/image.LineSegmentDetector/R/line_segment_detector.R
+++ b/image.LineSegmentDetector/R/line_segment_detector.R
@@ -30,6 +30,7 @@
 #' @param union_ang_th Numeric value with angle threshold in order to union
 #' @param union_use_NFA Logical indicating to use NFA to union
 #' @param union_log_eps Detection threshold to union
+#' @param export_sf Boolean. Set to TRUE to export lines as sf spatial objects (WARNING: process may take several time)
 #' @return an object of class lsd which is a list with the following elements
 #' \itemize{
 #'  \item{n: }{The number of found line segments}
@@ -78,13 +79,27 @@
 #' mat <- drop(mat)
 #' linesegments <- image_line_segment_detector(mat)
 #' plot(linesegments, lwd = 2)
+
+
 image_line_segment_detector <- function(x, scale = 0.8,
-                                  sigma_scale = 0.6, quant = 2.0, ang_th = 22.5, log_eps = 0.0,
-                                  density_th = 0.7, n_bins = 1024,
-                                  union = FALSE, union_min_length = 5, union_max_distance = 5,
-                                  union_ang_th=7, union_use_NFA=FALSE, union_log_eps = 0.0) {
+                                        sigma_scale = 0.6, quant = 2.0, ang_th = 22.5, log_eps = 0.0,
+                                        density_th = 0.7, n_bins = 1024,
+                                        union = FALSE, union_min_length = 5, union_max_distance = 5,
+                                        union_ang_th=7, union_use_NFA=FALSE, union_log_eps = 0.0,
+                                        export_sf=FALSE ){
+  UseMethod("image_line_segment_detector")
+  }
 
 
+#' @export
+image_line_segment_detector.matrix <- function(x, scale = 0.8,
+                                        sigma_scale = 0.6, quant = 2.0, ang_th = 22.5, log_eps = 0.0,
+                                        density_th = 0.7, n_bins = 1024,
+                                        union = FALSE, union_min_length = 5, union_max_distance = 5,
+                                        union_ang_th=7, union_use_NFA=FALSE, union_log_eps = 0.0,
+                                        export_sf=FALSE ) {
+  
+  
   stopifnot(is.matrix(x))
   linesegments <- detect_line_segments(as.numeric(x),
                                        X=nrow(x),
@@ -107,6 +122,64 @@ image_line_segment_detector <- function(x, scale = 0.8,
   linesegments
 }
 
+
+
+#' @export
+image_line_segment_detector.SpatRaster <- function(x, scale = 0.8,
+                                                   sigma_scale = 0.6, quant = 2.0, ang_th = 22.5, log_eps = 0.0,
+                                                   density_th = 0.7, n_bins = 1024,
+                                                   union = FALSE, union_min_length = 5, union_max_distance = 5,
+                                                   union_ang_th=7, union_use_NFA=FALSE, union_log_eps = 0.0,
+                                                   export_sf=FALSE ){
+  requireNamespace("terra")
+  uprightX = terra::ext(x)[2]
+  uprightY = terra::ext(x)[4]  
+  resol = terra::res(x)[1]
+  
+  x = t(terra::as.matrix(x,wide=TRUE))
+  
+  if( anyNA(x) ){
+    x[is.na(x)] = 0
+    warning("NA values found and set to 0") }
+  
+  linesegments = image_line_segment_detector.matrix(x, scale = scale,
+                                                    sigma_scale = sigma_scale, quant = quant, ang_th = ang_th, log_eps = log_eps,
+                                                    density_th = density_th, n_bins = n_bins,
+                                                    union = union, union_min_length = union_min_length, union_max_distance = union_max_distance,
+                                                    union_ang_th=union_ang_th, union_use_NFA=union_use_NFA, union_log_eps = union_log_eps,
+                                                    export_sf=export_sf )
+  
+  linesegments = as.data.frame(linesegments$lines)
+  
+  # assign spatial coordinates
+  linesegments$x1 = linesegments$x1 * -resol + uprightY
+  linesegments$y1 = linesegments$y1 * -resol + uprightX
+  linesegments$x2 = linesegments$x2 * -resol + uprightY
+  linesegments$y2 = linesegments$y2 * -resol + uprightX
+  
+  
+  # export object as sf
+  if(isTRUE(export_sf)){
+    requireNamespace("sf")
+    
+    linesegments = apply(linesegments, 1, function(x) 
+    {
+      v <- as.numeric(x[c(2,4,1,3)])
+      m <- matrix(v, nrow = 2)
+      return(sf::st_sfc(sf::st_linestring(m), crs = NA_crs_))
+    })
+    print("Sf export in progress...")
+    linesegments = do.call(c, linesegments)
+    
+    linesegments = sf::st_sf(linesegments)
+    linesegments$line_ID = 1:nrow(linesegments)
+    linesegments$length_m = sf::st_length(linesegments)
+  }
+  
+  return(linesegments)
+}
+
+
 #' @export
 print.lsd <- function(x, ...){
   cat("Line Segment Detector", sep = "\n")

From c5694f2c38dd070048955c9342e277e684be06fc Mon Sep 17 00:00:00 2001
From: Nic <sciurusurbanus@hotmail.it>
Date: Fri, 3 Nov 2023 18:25:00 +0100
Subject: [PATCH 02/22] Update DESCRIPTION

---
 image.LineSegmentDetector/DESCRIPTION | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/image.LineSegmentDetector/DESCRIPTION b/image.LineSegmentDetector/DESCRIPTION
index 5cb72a4..b3d537b 100644
--- a/image.LineSegmentDetector/DESCRIPTION
+++ b/image.LineSegmentDetector/DESCRIPTION
@@ -15,5 +15,7 @@ Imports: Rcpp (>= 0.12.8), sp
 LinkingTo: Rcpp
 Suggests:
     pixmap,
-    magick
+    magick,
+    sf,
+    terra
 RoxygenNote: 7.1.0

From b6bde8638a7517379906b8484d04ea68a7e12b32 Mon Sep 17 00:00:00 2001
From: Nic <sciurusurbanus@hotmail.it>
Date: Wed, 12 Jun 2024 09:50:23 +0200
Subject: [PATCH 03/22] Update contour_detector.R

added SpatRaster method
---
 image.ContourDetector/R/contour_detector.R | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/image.ContourDetector/R/contour_detector.R b/image.ContourDetector/R/contour_detector.R
index 5d1bee5..96db59d 100644
--- a/image.ContourDetector/R/contour_detector.R
+++ b/image.ContourDetector/R/contour_detector.R
@@ -122,6 +122,25 @@ image_contour_detector.RasterLayer <- function(x, Q=2.0, ...){
   return(contourlines)
 }
 
+#' @export
+image_contour_detector.SpatRaster <- function(x, Q=2.0, ...){
+  requireNamespace("terra")
+  minX = terra::ext(x)[1]
+  minY = terra::ext(x)[3]  
+  resol = terra::res(x)[1]  
+  x = terra::as.matrix(x, wide=TRUE)
+  
+  if( anyNA(x) ){
+    x[is.na(x)] = 0
+    warning("NA values found and set to 0") }
+
+  contourlines = image_contour_detector.matrix(x, Q=Q)
+  
+  contourlines$data$x = contourlines$data$x * resol + minX
+  contourlines$data$y = contourlines$data$y * resol + minY
+  return(contourlines)
+}
+                         
 
 #' @export
 print.cld <- function(x, ...){

From 952d8d07be34497316d1d96c27292482372b61ac Mon Sep 17 00:00:00 2001
From: Nic <sciurusurbanus@hotmail.it>
Date: Wed, 12 Jun 2024 10:03:56 +0200
Subject: [PATCH 04/22] Update DESCRIPTION

---
 image.ContourDetector/DESCRIPTION | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/image.ContourDetector/DESCRIPTION b/image.ContourDetector/DESCRIPTION
index e8c4ccf..8ae99d2 100644
--- a/image.ContourDetector/DESCRIPTION
+++ b/image.ContourDetector/DESCRIPTION
@@ -19,5 +19,7 @@ LinkingTo: Rcpp
 Suggests:
     pixmap,
     magick,
-    raster
+    raster,
+    sf,
+    terra
 RoxygenNote: 7.1.1

From 78d06a3e0a2ea14314e09c6dea476a013007ccd4 Mon Sep 17 00:00:00 2001
From: Nic <sciurusurbanus@hotmail.it>
Date: Wed, 12 Jun 2024 12:06:02 +0200
Subject: [PATCH 05/22] Update contour_detector.R

---
 image.ContourDetector/R/contour_detector.R | 35 +++++++++++++++-------
 1 file changed, 24 insertions(+), 11 deletions(-)

diff --git a/image.ContourDetector/R/contour_detector.R b/image.ContourDetector/R/contour_detector.R
index 96db59d..60fbe6c 100644
--- a/image.ContourDetector/R/contour_detector.R
+++ b/image.ContourDetector/R/contour_detector.R
@@ -11,6 +11,7 @@
 #' an efficient algorithm is derived producing sub-pixel contours.
 #' @param x a matrix of image pixel values in the 0-255 range.
 #' @param Q numeric value with the pixel quantization step
+#' @param export_sf Boolean. Set to TRUE to export lines as sf spatial objects (WARNING: process may take several time)
 #' @param ... further arguments, not used yet
 #' @return an object of class cld which is a list with the following elements
 #' \itemize{
@@ -70,8 +71,8 @@
 #' \{
 #' }
 #' \donttest{
-#' library(raster)
-#' x   <- raster(system.file("extdata", "landscape.tif", package="image.ContourDetector"))
+#' library(terra)
+#' x   <- rast(system.file("extdata", "landscape.tif", package="image.ContourDetector"))
 #' 
 #' contourlines <- image_contour_detector(x)
 #' image(x)
@@ -81,12 +82,12 @@
 #' \}
 #' # End of main if statement running only if the required packages are installed
 #' }
-image_contour_detector <- function(x, Q=2.0, ...){
+image_contour_detector <- function(x, Q=2.0 export_sf=FALSE, ...){
   UseMethod("image_contour_detector")
 }
 
 #' @export
-image_contour_detector.matrix <- function(x, Q=2.0, ...){
+image_contour_detector.matrix <- function(x, Q=2.0, export_sf=FALSE, ...){
   stopifnot(is.matrix(x))
   contourlines <- detect_contours(x, 
                   X=nrow(x),
@@ -104,7 +105,7 @@ image_contour_detector.matrix <- function(x, Q=2.0, ...){
 }
 
 #' @export
-image_contour_detector.RasterLayer <- function(x, Q=2.0, ...){
+image_contour_detector.RasterLayer <- function(x, Q=2.0, export_sf=FALSE, ...){
   requireNamespace("raster")
   minX = raster::extent(x)[1]
   minY = raster::extent(x)[3]  
@@ -115,7 +116,7 @@ image_contour_detector.RasterLayer <- function(x, Q=2.0, ...){
     x[is.na(x)] = 0
     warning("NA values found and set to 0") }
 
-  contourlines = image_contour_detector.matrix(x, Q=Q)
+  contourlines = image_contour_detector.matrix(x, Q=Q, export_sf=export_sf)
   
   contourlines$data$x = contourlines$data$x * resol + minX
   contourlines$data$y = contourlines$data$y * resol + minY
@@ -123,21 +124,33 @@ image_contour_detector.RasterLayer <- function(x, Q=2.0, ...){
 }
 
 #' @export
-image_contour_detector.SpatRaster <- function(x, Q=2.0, ...){
+image_contour_detector.SpatRaster <- function(x, Q=2.0, export_sf=FALSE, ...){
   requireNamespace("terra")
   minX = terra::ext(x)[1]
   minY = terra::ext(x)[3]  
   resol = terra::res(x)[1]  
-  x = terra::as.matrix(x, wide=TRUE)
+  xmat = terra::as.matrix(x, wide=TRUE)
   
-  if( anyNA(x) ){
-    x[is.na(x)] = 0
+  if( anyNA(xmat) ){
+    x[is.na(xmat)] = 0
     warning("NA values found and set to 0") }
 
-  contourlines = image_contour_detector.matrix(x, Q=Q)
+  contourlines = image_contour_detector.matrix(xmat, Q=Q, export_sf=export_sf)
   
   contourlines$data$x = contourlines$data$x * resol + minX
   contourlines$data$y = contourlines$data$y * resol + minY
+
+  # export object as sf
+  if(isTRUE(export_sf)){
+    requireNamespace("sf")
+    
+  contourlines <- contourlines$data %>%
+  sf::st_as_sf(coords = c("x", "y"), crs = sf::st_crs(x) ) %>%
+  dplyr::group_by( curve ) %>%
+  dplyr::summarize(do_union=FALSE) %>%
+  sf::st_cast("LINESTRING")
+  contourlines$length_m = sf::st_length(contourlines)
+  }  
   return(contourlines)
 }
                          

From 795b9d75db92e945dada49c4c74f472660ecb6e9 Mon Sep 17 00:00:00 2001
From: Nic <sciurusurbanus@hotmail.it>
Date: Wed, 12 Jun 2024 12:20:57 +0200
Subject: [PATCH 06/22] Update contour_detector.R

---
 image.ContourDetector/R/contour_detector.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/image.ContourDetector/R/contour_detector.R b/image.ContourDetector/R/contour_detector.R
index 60fbe6c..045305c 100644
--- a/image.ContourDetector/R/contour_detector.R
+++ b/image.ContourDetector/R/contour_detector.R
@@ -64,10 +64,10 @@
 #' }
 #' 
 #' ##
-#' ##  working with a RasterLayer
+#' ##  working with a SpatRaster
 #' ##
 #' \dontshow{
-#' if(require(raster))
+#' if(require(terra))
 #' \{
 #' }
 #' \donttest{

From e373efea6966e1c89b43234b7191abce6a5ea32d Mon Sep 17 00:00:00 2001
From: Nic <sciurusurbanus@hotmail.it>
Date: Wed, 12 Jun 2024 12:21:31 +0200
Subject: [PATCH 07/22] Update line_segment_detector.R

---
 .../R/line_segment_detector.R                 | 21 ++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/image.LineSegmentDetector/R/line_segment_detector.R b/image.LineSegmentDetector/R/line_segment_detector.R
index 1c38674..573edb5 100644
--- a/image.LineSegmentDetector/R/line_segment_detector.R
+++ b/image.LineSegmentDetector/R/line_segment_detector.R
@@ -79,7 +79,26 @@
 #' mat <- drop(mat)
 #' linesegments <- image_line_segment_detector(mat)
 #' plot(linesegments, lwd = 2)
-
+#'
+#' ##
+#' ##  working with a SpatRaster
+#' ##
+#' \dontshow{
+#' if(require(terra))
+#' \{
+#' }
+#' \donttest{
+#' library(terra)
+#' x   <- rast(system.file("extdata", "landscape.tif", package="image.ContourDetector"))
+#' 
+#' linesegments <- image_line_segment_detector(x)
+#' image(x)
+#' plot(linesegments, add = TRUE, col = "blue", lwd = 10)
+#' }
+#' \dontshow{
+#' \}
+#' # End of main if statement running only if the required packages are installed
+#' }
 
 image_line_segment_detector <- function(x, scale = 0.8,
                                         sigma_scale = 0.6, quant = 2.0, ang_th = 22.5, log_eps = 0.0,

From 5726149caf5edc2aac188676e7de065474a2b061 Mon Sep 17 00:00:00 2001
From: Nic <sciurusurbanus@hotmail.it>
Date: Wed, 12 Jun 2024 12:23:20 +0200
Subject: [PATCH 08/22] Update DESCRIPTION

---
 image.ContourDetector/DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/image.ContourDetector/DESCRIPTION b/image.ContourDetector/DESCRIPTION
index 8ae99d2..2f1a3e0 100644
--- a/image.ContourDetector/DESCRIPTION
+++ b/image.ContourDetector/DESCRIPTION
@@ -9,7 +9,7 @@ Authors@R: c(
     person("BNOSAC", role = "cph", comment = "R wrapper"), 
     person("Rafael Grompone von Gioi", role = c("ctb", "cph"), email = "grompone@gmail.com", comment = "src/smooth_contours"), 
     person("Gregory Randall", role = c("ctb", "cph"), email = "randall@fing.edu.uy", comment = "src/smooth_contours"),
-    person("Niccolò Marchi", role = "ctb", email = "niccolo.marchi@unipd.it"))
+    person("Niccolò Marchi", role = "ctb", email = "sciurusurbanus@hotmail.it"))
 Encoding: UTF-8
 License: AGPL-3
 Version: 0.1.1
@@ -17,6 +17,7 @@ URL: https://github.com/bnosac/image
 Imports: Rcpp (>= 0.12.8), sp
 LinkingTo: Rcpp
 Suggests:
+    dplyr,
     pixmap,
     magick,
     raster,

From f2eba9aa3f049e94431bf2f6aa15055e4708703f Mon Sep 17 00:00:00 2001
From: Nic <sciurusurbanus@hotmail.it>
Date: Wed, 12 Jun 2024 12:23:48 +0200
Subject: [PATCH 09/22] Update DESCRIPTION

---
 image.LineSegmentDetector/DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/image.LineSegmentDetector/DESCRIPTION b/image.LineSegmentDetector/DESCRIPTION
index b3d537b..636d174 100644
--- a/image.LineSegmentDetector/DESCRIPTION
+++ b/image.LineSegmentDetector/DESCRIPTION
@@ -7,7 +7,8 @@ Maintainer: Jan Wijffels <jwijffels@bnosac.be>
 Authors@R: c(
     person("Jan", "Wijffels", role = c("aut", "cre", "cph"), email = "jwijffels@bnosac.be", comment = "R wrapper"), 
     person("BNOSAC", role = "cph", comment = "R wrapper"), 
-    person("Rafael Grompone von Gioi", role = c("ctb", "cph"), email = "grompone@gmail.com", comment = "src/lsd"))
+    person("Rafael Grompone von Gioi", role = c("ctb", "cph"), email = "grompone@gmail.com", comment = "src/lsd")),
+    person("Niccolò Marchi", role = "ctb", email = "sciurusurbanus@hotmail.it"))
 License: AGPL-3
 Version: 0.1.0
 URL: https://github.com/bnosac/image

From f42ce79e4bbdcd230ffec248585bdcf99be0b06c Mon Sep 17 00:00:00 2001
From: Nic <sciurusurbanus@hotmail.it>
Date: Mon, 17 Jun 2024 16:22:59 +0200
Subject: [PATCH 10/22] Update line_segment_detector.R

changed "export_sf" parameter to "as_sf"
---
 image.LineSegmentDetector/R/line_segment_detector.R | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/image.LineSegmentDetector/R/line_segment_detector.R b/image.LineSegmentDetector/R/line_segment_detector.R
index 573edb5..e70208c 100644
--- a/image.LineSegmentDetector/R/line_segment_detector.R
+++ b/image.LineSegmentDetector/R/line_segment_detector.R
@@ -30,7 +30,7 @@
 #' @param union_ang_th Numeric value with angle threshold in order to union
 #' @param union_use_NFA Logical indicating to use NFA to union
 #' @param union_log_eps Detection threshold to union
-#' @param export_sf Boolean. Set to TRUE to export lines as sf spatial objects (WARNING: process may take several time)
+#' @param as_sf Boolean. Set to TRUE to export lines as sf spatial objects (WARNING: process may take several time)
 #' @return an object of class lsd which is a list with the following elements
 #' \itemize{
 #'  \item{n: }{The number of found line segments}
@@ -105,7 +105,7 @@ image_line_segment_detector <- function(x, scale = 0.8,
                                         density_th = 0.7, n_bins = 1024,
                                         union = FALSE, union_min_length = 5, union_max_distance = 5,
                                         union_ang_th=7, union_use_NFA=FALSE, union_log_eps = 0.0,
-                                        export_sf=FALSE ){
+                                        as_sf=FALSE ){
   UseMethod("image_line_segment_detector")
   }
 
@@ -116,7 +116,7 @@ image_line_segment_detector.matrix <- function(x, scale = 0.8,
                                         density_th = 0.7, n_bins = 1024,
                                         union = FALSE, union_min_length = 5, union_max_distance = 5,
                                         union_ang_th=7, union_use_NFA=FALSE, union_log_eps = 0.0,
-                                        export_sf=FALSE ) {
+                                        as_sf=FALSE ) {
   
   
   stopifnot(is.matrix(x))
@@ -149,7 +149,7 @@ image_line_segment_detector.SpatRaster <- function(x, scale = 0.8,
                                                    density_th = 0.7, n_bins = 1024,
                                                    union = FALSE, union_min_length = 5, union_max_distance = 5,
                                                    union_ang_th=7, union_use_NFA=FALSE, union_log_eps = 0.0,
-                                                   export_sf=FALSE ){
+                                                   as_sf=FALSE ){
   requireNamespace("terra")
   uprightX = terra::ext(x)[2]
   uprightY = terra::ext(x)[4]  
@@ -166,7 +166,7 @@ image_line_segment_detector.SpatRaster <- function(x, scale = 0.8,
                                                     density_th = density_th, n_bins = n_bins,
                                                     union = union, union_min_length = union_min_length, union_max_distance = union_max_distance,
                                                     union_ang_th=union_ang_th, union_use_NFA=union_use_NFA, union_log_eps = union_log_eps,
-                                                    export_sf=export_sf )
+                                                    as_sf=as_sf )
   
   linesegments = as.data.frame(linesegments$lines)
   
@@ -178,7 +178,7 @@ image_line_segment_detector.SpatRaster <- function(x, scale = 0.8,
   
   
   # export object as sf
-  if(isTRUE(export_sf)){
+  if(isTRUE(as_sf)){
     requireNamespace("sf")
     
     linesegments = apply(linesegments, 1, function(x) 

From a19672c4826130949b94ce6cdf266ba637422a35 Mon Sep 17 00:00:00 2001
From: Nic <sciurusurbanus@hotmail.it>
Date: Mon, 17 Jun 2024 16:23:11 +0200
Subject: [PATCH 11/22] Update contour_detector.R

changed "export_sf" parameter to "as_sf"
---
 image.ContourDetector/R/contour_detector.R | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/image.ContourDetector/R/contour_detector.R b/image.ContourDetector/R/contour_detector.R
index 045305c..78333ac 100644
--- a/image.ContourDetector/R/contour_detector.R
+++ b/image.ContourDetector/R/contour_detector.R
@@ -11,7 +11,7 @@
 #' an efficient algorithm is derived producing sub-pixel contours.
 #' @param x a matrix of image pixel values in the 0-255 range.
 #' @param Q numeric value with the pixel quantization step
-#' @param export_sf Boolean. Set to TRUE to export lines as sf spatial objects (WARNING: process may take several time)
+#' @param as_sf Boolean. Set to TRUE to export lines as sf spatial objects (WARNING: process may take several time)
 #' @param ... further arguments, not used yet
 #' @return an object of class cld which is a list with the following elements
 #' \itemize{
@@ -82,12 +82,12 @@
 #' \}
 #' # End of main if statement running only if the required packages are installed
 #' }
-image_contour_detector <- function(x, Q=2.0 export_sf=FALSE, ...){
+image_contour_detector <- function(x, Q=2.0 as_sf=FALSE, ...){
   UseMethod("image_contour_detector")
 }
 
 #' @export
-image_contour_detector.matrix <- function(x, Q=2.0, export_sf=FALSE, ...){
+image_contour_detector.matrix <- function(x, Q=2.0, as_sf=FALSE, ...){
   stopifnot(is.matrix(x))
   contourlines <- detect_contours(x, 
                   X=nrow(x),
@@ -105,7 +105,7 @@ image_contour_detector.matrix <- function(x, Q=2.0, export_sf=FALSE, ...){
 }
 
 #' @export
-image_contour_detector.RasterLayer <- function(x, Q=2.0, export_sf=FALSE, ...){
+image_contour_detector.RasterLayer <- function(x, Q=2.0, as_sf=FALSE, ...){
   requireNamespace("raster")
   minX = raster::extent(x)[1]
   minY = raster::extent(x)[3]  
@@ -116,7 +116,7 @@ image_contour_detector.RasterLayer <- function(x, Q=2.0, export_sf=FALSE, ...){
     x[is.na(x)] = 0
     warning("NA values found and set to 0") }
 
-  contourlines = image_contour_detector.matrix(x, Q=Q, export_sf=export_sf)
+  contourlines = image_contour_detector.matrix(x, Q=Q, as_sf=as_sf)
   
   contourlines$data$x = contourlines$data$x * resol + minX
   contourlines$data$y = contourlines$data$y * resol + minY
@@ -124,7 +124,7 @@ image_contour_detector.RasterLayer <- function(x, Q=2.0, export_sf=FALSE, ...){
 }
 
 #' @export
-image_contour_detector.SpatRaster <- function(x, Q=2.0, export_sf=FALSE, ...){
+image_contour_detector.SpatRaster <- function(x, Q=2.0, as_sf=FALSE, ...){
   requireNamespace("terra")
   minX = terra::ext(x)[1]
   minY = terra::ext(x)[3]  
@@ -135,13 +135,13 @@ image_contour_detector.SpatRaster <- function(x, Q=2.0, export_sf=FALSE, ...){
     x[is.na(xmat)] = 0
     warning("NA values found and set to 0") }
 
-  contourlines = image_contour_detector.matrix(xmat, Q=Q, export_sf=export_sf)
+  contourlines = image_contour_detector.matrix(xmat, Q=Q, as_sf=as_sf)
   
   contourlines$data$x = contourlines$data$x * resol + minX
   contourlines$data$y = contourlines$data$y * resol + minY
 
   # export object as sf
-  if(isTRUE(export_sf)){
+  if(isTRUE(as_sf)){
     requireNamespace("sf")
     
   contourlines <- contourlines$data %>%

From 0d21434a35038c9dc576aa2645c2c56b0e1b3956 Mon Sep 17 00:00:00 2001
From: Nic <sciurusurbanus@hotmail.it>
Date: Mon, 1 Jul 2024 21:53:46 +0200
Subject: [PATCH 12/22] Update DESCRIPTION

---
 image.LineSegmentDetector/DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/image.LineSegmentDetector/DESCRIPTION b/image.LineSegmentDetector/DESCRIPTION
index 636d174..5f7c262 100644
--- a/image.LineSegmentDetector/DESCRIPTION
+++ b/image.LineSegmentDetector/DESCRIPTION
@@ -7,8 +7,9 @@ Maintainer: Jan Wijffels <jwijffels@bnosac.be>
 Authors@R: c(
     person("Jan", "Wijffels", role = c("aut", "cre", "cph"), email = "jwijffels@bnosac.be", comment = "R wrapper"), 
     person("BNOSAC", role = "cph", comment = "R wrapper"), 
-    person("Rafael Grompone von Gioi", role = c("ctb", "cph"), email = "grompone@gmail.com", comment = "src/lsd")),
+    person("Rafael Grompone von Gioi", role = c("ctb", "cph"), email = "grompone@gmail.com", comment = "src/lsd"),
     person("Niccolò Marchi", role = "ctb", email = "sciurusurbanus@hotmail.it"))
+Encoding: UTF-8
 License: AGPL-3
 Version: 0.1.0
 URL: https://github.com/bnosac/image

From 2d93e56a3beebb9d0413e058fe636eefb375db68 Mon Sep 17 00:00:00 2001
From: Nic <sciurusurbanus@hotmail.it>
Date: Mon, 1 Jul 2024 22:40:23 +0200
Subject: [PATCH 13/22] Update contour_detector.R

---
 image.ContourDetector/R/contour_detector.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/image.ContourDetector/R/contour_detector.R b/image.ContourDetector/R/contour_detector.R
index 78333ac..18805e8 100644
--- a/image.ContourDetector/R/contour_detector.R
+++ b/image.ContourDetector/R/contour_detector.R
@@ -82,7 +82,7 @@
 #' \}
 #' # End of main if statement running only if the required packages are installed
 #' }
-image_contour_detector <- function(x, Q=2.0 as_sf=FALSE, ...){
+image_contour_detector <- function(x, Q=2.0, as_sf=FALSE, ...){
   UseMethod("image_contour_detector")
 }
 

From 8379a37fa25ac9642678df92bb4fa4c9ea04a3fb Mon Sep 17 00:00:00 2001
From: Nic <sciurusurbanus@hotmail.it>
Date: Mon, 1 Jul 2024 23:38:42 +0200
Subject: [PATCH 14/22] removed dependency on dplyr

---
 image.ContourDetector/R/contour_detector.R | 25 ++++++++++++++++------
 1 file changed, 19 insertions(+), 6 deletions(-)

diff --git a/image.ContourDetector/R/contour_detector.R b/image.ContourDetector/R/contour_detector.R
index 18805e8..48cf011 100644
--- a/image.ContourDetector/R/contour_detector.R
+++ b/image.ContourDetector/R/contour_detector.R
@@ -144,12 +144,25 @@ image_contour_detector.SpatRaster <- function(x, Q=2.0, as_sf=FALSE, ...){
   if(isTRUE(as_sf)){
     requireNamespace("sf")
     
-  contourlines <- contourlines$data %>%
-  sf::st_as_sf(coords = c("x", "y"), crs = sf::st_crs(x) ) %>%
-  dplyr::group_by( curve ) %>%
-  dplyr::summarize(do_union=FALSE) %>%
-  sf::st_cast("LINESTRING")
-  contourlines$length_m = sf::st_length(contourlines)
+  # contourlines <- contourlines$data %>%
+  # sf::st_as_sf(coords = c("x", "y"), crs = sf::st_crs(x) ) %>%
+  # dplyr::group_by( curve ) %>%
+  # dplyr::summarize(do_union=FALSE) %>%
+  # sf::st_cast("LINESTRING")
+
+    contourlines <- contourlines$data
+    contourlines = sf::st_as_sf( contourlines, coords = c("x", "y"), crs = sf::st_crs(x) )
+    
+    out = list()
+    
+    for( i in unique(contourlines$curve) ){
+      ss = subset(contourlines, curve == i )
+      ss = sf::st_combine(ss)      
+      out[[length(out)+1]] = sf::st_cast( st_sf(ss), "LINESTRING")
+    }
+    
+    contourlines = do.call(rbind,out)    
+    contourlines$length_m = sf::st_length(contourlines)    
   }  
   return(contourlines)
 }

From 9713cdde987637a929bf0331f88fbe8a6027512b Mon Sep 17 00:00:00 2001
From: Jan Wijffels <jwijffels@bnosac.be>
Date: Tue, 2 Jul 2024 23:28:30 +0200
Subject: [PATCH 15/22] documentation changes

---
 image.ContourDetector/NAMESPACE               |  1 +
 image.ContourDetector/R/contour_detector.R    | 26 ++++++++++++++-----
 .../man/image_contour_detector.RasterLayer.Rd | 26 +++++++++++++++++++
 .../man/image_contour_detector.Rd             | 10 +++----
 .../man/image_contour_detector.SpatRaster.Rd  | 26 +++++++++++++++++++
 5 files changed, 78 insertions(+), 11 deletions(-)
 create mode 100644 image.ContourDetector/man/image_contour_detector.RasterLayer.Rd
 create mode 100644 image.ContourDetector/man/image_contour_detector.SpatRaster.Rd

diff --git a/image.ContourDetector/NAMESPACE b/image.ContourDetector/NAMESPACE
index 97f0294..1c90b27 100644
--- a/image.ContourDetector/NAMESPACE
+++ b/image.ContourDetector/NAMESPACE
@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(image_contour_detector,RasterLayer)
+S3method(image_contour_detector,SpatRaster)
 S3method(image_contour_detector,matrix)
 S3method(plot,cld)
 S3method(print,cld)
diff --git a/image.ContourDetector/R/contour_detector.R b/image.ContourDetector/R/contour_detector.R
index 48cf011..1300114 100644
--- a/image.ContourDetector/R/contour_detector.R
+++ b/image.ContourDetector/R/contour_detector.R
@@ -11,8 +11,7 @@
 #' an efficient algorithm is derived producing sub-pixel contours.
 #' @param x a matrix of image pixel values in the 0-255 range.
 #' @param Q numeric value with the pixel quantization step
-#' @param as_sf Boolean. Set to TRUE to export lines as sf spatial objects (WARNING: process may take several time)
-#' @param ... further arguments, not used yet
+#' @param ... further arguments passed on to \code{image_contour_detector.matrix}, \code{\link{image_contour_detector.RasterLayer}} or \code{\link{image_contour_detector.SpatRaster}}.
 #' @return an object of class cld which is a list with the following elements
 #' \itemize{
 #'  \item{curves: }{The number of contour lines found}
@@ -82,12 +81,12 @@
 #' \}
 #' # End of main if statement running only if the required packages are installed
 #' }
-image_contour_detector <- function(x, Q=2.0, as_sf=FALSE, ...){
+image_contour_detector <- function(x, Q=2.0, ...){
   UseMethod("image_contour_detector")
 }
 
 #' @export
-image_contour_detector.matrix <- function(x, Q=2.0, as_sf=FALSE, ...){
+image_contour_detector.matrix <- function(x, Q=2.0, ...){
   stopifnot(is.matrix(x))
   contourlines <- detect_contours(x, 
                   X=nrow(x),
@@ -104,6 +103,14 @@ image_contour_detector.matrix <- function(x, Q=2.0, as_sf=FALSE, ...){
   return(contourlines)
 }
 
+#' @title Unsupervised Smooth Contour Lines Detection for RasterLayer objects
+#' @description Unsupervised Smooth Contour Detection
+#' @param x a RasterLayer object
+#' @param Q numeric value with the pixel quantization step
+#' @param as_sf Boolean. Set to TRUE to export lines as sf spatial objects
+#' @param ... further arguments passed on to \code{image_contour_detector.matrix}
+#' @return an object of class cld which as described in \code{\link{image_contour_detector}}
+#' @seealso \code{\link{image_contour_detector}}
 #' @export
 image_contour_detector.RasterLayer <- function(x, Q=2.0, as_sf=FALSE, ...){
   requireNamespace("raster")
@@ -116,13 +123,20 @@ image_contour_detector.RasterLayer <- function(x, Q=2.0, as_sf=FALSE, ...){
     x[is.na(x)] = 0
     warning("NA values found and set to 0") }
 
-  contourlines = image_contour_detector.matrix(x, Q=Q, as_sf=as_sf)
+  contourlines = image_contour_detector.matrix(x, Q=Q, ...)
   
   contourlines$data$x = contourlines$data$x * resol + minX
   contourlines$data$y = contourlines$data$y * resol + minY
   return(contourlines)
 }
 
+#' @title Unsupervised Smooth Contour Lines Detection for SpatRaster objects
+#' @param x a SpatRaster object
+#' @param Q numeric value with the pixel quantization step
+#' @param as_sf Boolean. Set to TRUE to export lines as sf spatial objects
+#' @param ... further arguments passed on to \code{image_contour_detector.matrix}
+#' @return an object of class cld which as described in \code{\link{image_contour_detector}}
+#' @seealso \code{\link{image_contour_detector}}
 #' @export
 image_contour_detector.SpatRaster <- function(x, Q=2.0, as_sf=FALSE, ...){
   requireNamespace("terra")
@@ -135,7 +149,7 @@ image_contour_detector.SpatRaster <- function(x, Q=2.0, as_sf=FALSE, ...){
     x[is.na(xmat)] = 0
     warning("NA values found and set to 0") }
 
-  contourlines = image_contour_detector.matrix(xmat, Q=Q, as_sf=as_sf)
+  contourlines = image_contour_detector.matrix(xmat, Q=Q, ...)
   
   contourlines$data$x = contourlines$data$x * resol + minX
   contourlines$data$y = contourlines$data$y * resol + minY
diff --git a/image.ContourDetector/man/image_contour_detector.RasterLayer.Rd b/image.ContourDetector/man/image_contour_detector.RasterLayer.Rd
new file mode 100644
index 0000000..d577d6e
--- /dev/null
+++ b/image.ContourDetector/man/image_contour_detector.RasterLayer.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/contour_detector.R
+\name{image_contour_detector.RasterLayer}
+\alias{image_contour_detector.RasterLayer}
+\title{Unsupervised Smooth Contour Lines Detection for RasterLayer objects}
+\usage{
+\method{image_contour_detector}{RasterLayer}(x, Q = 2, as_sf = FALSE, ...)
+}
+\arguments{
+\item{x}{a RasterLayer object}
+
+\item{Q}{numeric value with the pixel quantization step}
+
+\item{as_sf}{Boolean. Set to TRUE to export lines as sf spatial objects}
+
+\item{...}{further arguments passed on to \code{image_contour_detector.matrix}}
+}
+\value{
+an object of class cld which as described in \code{\link{image_contour_detector}}
+}
+\description{
+Unsupervised Smooth Contour Detection
+}
+\seealso{
+\code{\link{image_contour_detector}}
+}
diff --git a/image.ContourDetector/man/image_contour_detector.Rd b/image.ContourDetector/man/image_contour_detector.Rd
index fc13ad0..c977c57 100644
--- a/image.ContourDetector/man/image_contour_detector.Rd
+++ b/image.ContourDetector/man/image_contour_detector.Rd
@@ -11,7 +11,7 @@ image_contour_detector(x, Q = 2, ...)
 
 \item{Q}{numeric value with the pixel quantization step}
 
-\item{...}{further arguments, not used yet}
+\item{...}{further arguments passed on to \code{image_contour_detector.matrix}, \code{\link{image_contour_detector.RasterLayer}} or \code{\link{image_contour_detector.SpatRaster}}.}
 }
 \value{
 an object of class cld which is a list with the following elements
@@ -75,15 +75,15 @@ plot(contourlines)
 }
 
 ##
-##  working with a RasterLayer
+##  working with a SpatRaster
 ##
 \dontshow{
-if(require(raster))
+if(require(terra))
 \{
 }
 \donttest{
-library(raster)
-x   <- raster(system.file("extdata", "landscape.tif", package="image.ContourDetector"))
+library(terra)
+x   <- rast(system.file("extdata", "landscape.tif", package="image.ContourDetector"))
 
 contourlines <- image_contour_detector(x)
 image(x)
diff --git a/image.ContourDetector/man/image_contour_detector.SpatRaster.Rd b/image.ContourDetector/man/image_contour_detector.SpatRaster.Rd
new file mode 100644
index 0000000..a0a8105
--- /dev/null
+++ b/image.ContourDetector/man/image_contour_detector.SpatRaster.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/contour_detector.R
+\name{image_contour_detector.SpatRaster}
+\alias{image_contour_detector.SpatRaster}
+\title{Unsupervised Smooth Contour Lines Detection for SpatRaster objects}
+\usage{
+\method{image_contour_detector}{SpatRaster}(x, Q = 2, as_sf = FALSE, ...)
+}
+\arguments{
+\item{x}{a SpatRaster object}
+
+\item{Q}{numeric value with the pixel quantization step}
+
+\item{as_sf}{Boolean. Set to TRUE to export lines as sf spatial objects}
+
+\item{...}{further arguments passed on to \code{image_contour_detector.matrix}}
+}
+\value{
+an object of class cld which as described in \code{\link{image_contour_detector}}
+}
+\description{
+Unsupervised Smooth Contour Lines Detection for SpatRaster objects
+}
+\seealso{
+\code{\link{image_contour_detector}}
+}

From d217bf3dc93864577e8ebff930b6f91704456d46 Mon Sep 17 00:00:00 2001
From: Jan Wijffels <jwijffels@bnosac.be>
Date: Tue, 2 Jul 2024 23:33:04 +0200
Subject: [PATCH 16/22] no need to bring in dplyr dependency

---
 image.ContourDetector/DESCRIPTION | 1 -
 1 file changed, 1 deletion(-)

diff --git a/image.ContourDetector/DESCRIPTION b/image.ContourDetector/DESCRIPTION
index 2f1a3e0..999ea98 100644
--- a/image.ContourDetector/DESCRIPTION
+++ b/image.ContourDetector/DESCRIPTION
@@ -17,7 +17,6 @@ URL: https://github.com/bnosac/image
 Imports: Rcpp (>= 0.12.8), sp
 LinkingTo: Rcpp
 Suggests:
-    dplyr,
     pixmap,
     magick,
     raster,

From 5e07b0910c4f69ed9beb832db7af3a4b3c65048a Mon Sep 17 00:00:00 2001
From: Jan Wijffels <jwijffels@bnosac.be>
Date: Tue, 2 Jul 2024 23:33:24 +0200
Subject: [PATCH 17/22] fix R CMD check notes

---
 image.ContourDetector/R/contour_detector.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/image.ContourDetector/R/contour_detector.R b/image.ContourDetector/R/contour_detector.R
index 1300114..8a6b86f 100644
--- a/image.ContourDetector/R/contour_detector.R
+++ b/image.ContourDetector/R/contour_detector.R
@@ -170,9 +170,9 @@ image_contour_detector.SpatRaster <- function(x, Q=2.0, as_sf=FALSE, ...){
     out = list()
     
     for( i in unique(contourlines$curve) ){
-      ss = subset(contourlines, curve == i )
+      ss = subset(contourlines, contourlines$curve == i )
       ss = sf::st_combine(ss)      
-      out[[length(out)+1]] = sf::st_cast( st_sf(ss), "LINESTRING")
+      out[[length(out)+1]] = sf::st_cast( sf::st_sf(ss), "LINESTRING")
     }
     
     contourlines = do.call(rbind,out)    

From 4f7f60c2219ef2cb382682992ab5c3a7f3776d35 Mon Sep 17 00:00:00 2001
From: Jan Wijffels <jwijffels@bnosac.be>
Date: Tue, 2 Jul 2024 23:52:27 +0200
Subject: [PATCH 18/22] replace NA with 0 in matrix, not in SpatRaster

---
 image.ContourDetector/R/contour_detector.R | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/image.ContourDetector/R/contour_detector.R b/image.ContourDetector/R/contour_detector.R
index 8a6b86f..cccaac7 100644
--- a/image.ContourDetector/R/contour_detector.R
+++ b/image.ContourDetector/R/contour_detector.R
@@ -145,9 +145,10 @@ image_contour_detector.SpatRaster <- function(x, Q=2.0, as_sf=FALSE, ...){
   resol = terra::res(x)[1]  
   xmat = terra::as.matrix(x, wide=TRUE)
   
-  if( anyNA(xmat) ){
-    x[is.na(xmat)] = 0
-    warning("NA values found and set to 0") }
+  if(anyNA(xmat)){
+    xmat[is.na(xmat)] = 0
+    warning("NA values found and set to 0") 
+  }
 
   contourlines = image_contour_detector.matrix(xmat, Q=Q, ...)
   

From 56f133a2cbb63d360d409cb6b4fc4b171e719fef Mon Sep 17 00:00:00 2001
From: Jan Wijffels <jwijffels@bnosac.be>
Date: Tue, 2 Jul 2024 23:55:08 +0200
Subject: [PATCH 19/22] move example to SpatRaster method

---
 image.ContourDetector/R/contour_detector.R    | 37 +++++++++----------
 .../man/image_contour_detector.Rd             | 20 ----------
 .../man/image_contour_detector.SpatRaster.Rd  | 18 +++++++++
 3 files changed, 35 insertions(+), 40 deletions(-)

diff --git a/image.ContourDetector/R/contour_detector.R b/image.ContourDetector/R/contour_detector.R
index cccaac7..c175db1 100644
--- a/image.ContourDetector/R/contour_detector.R
+++ b/image.ContourDetector/R/contour_detector.R
@@ -61,26 +61,6 @@
 #' \}
 #' # End of main if statement running only if the required packages are installed
 #' }
-#' 
-#' ##
-#' ##  working with a SpatRaster
-#' ##
-#' \dontshow{
-#' if(require(terra))
-#' \{
-#' }
-#' \donttest{
-#' library(terra)
-#' x   <- rast(system.file("extdata", "landscape.tif", package="image.ContourDetector"))
-#' 
-#' contourlines <- image_contour_detector(x)
-#' image(x)
-#' plot(contourlines, add = TRUE, col = "blue", lwd = 10)
-#' }
-#' \dontshow{
-#' \}
-#' # End of main if statement running only if the required packages are installed
-#' }
 image_contour_detector <- function(x, Q=2.0, ...){
   UseMethod("image_contour_detector")
 }
@@ -138,6 +118,23 @@ image_contour_detector.RasterLayer <- function(x, Q=2.0, as_sf=FALSE, ...){
 #' @return an object of class cld which as described in \code{\link{image_contour_detector}}
 #' @seealso \code{\link{image_contour_detector}}
 #' @export
+#' @examples 
+#' \dontshow{
+#' if(require(terra))
+#' \{
+#' }
+#' \donttest{
+#' library(terra)
+#' x   <- rast(system.file("extdata", "landscape.tif", package="image.ContourDetector"))
+#' 
+#' contourlines <- image_contour_detector(x)
+#' image(x)
+#' plot(contourlines, add = TRUE, col = "blue", lwd = 10)
+#' }
+#' \dontshow{
+#' \}
+#' # End of main if statement running only if the required packages are installed
+#' }
 image_contour_detector.SpatRaster <- function(x, Q=2.0, as_sf=FALSE, ...){
   requireNamespace("terra")
   minX = terra::ext(x)[1]
diff --git a/image.ContourDetector/man/image_contour_detector.Rd b/image.ContourDetector/man/image_contour_detector.Rd
index c977c57..602bfbb 100644
--- a/image.ContourDetector/man/image_contour_detector.Rd
+++ b/image.ContourDetector/man/image_contour_detector.Rd
@@ -73,26 +73,6 @@ plot(contourlines)
 \}
 # End of main if statement running only if the required packages are installed
 }
-
-##
-##  working with a SpatRaster
-##
-\dontshow{
-if(require(terra))
-\{
-}
-\donttest{
-library(terra)
-x   <- rast(system.file("extdata", "landscape.tif", package="image.ContourDetector"))
-
-contourlines <- image_contour_detector(x)
-image(x)
-plot(contourlines, add = TRUE, col = "blue", lwd = 10)
-}
-\dontshow{
-\}
-# End of main if statement running only if the required packages are installed
-}
 }
 \references{
 Rafael Grompone von Gioi, and Gregory Randall, Unsupervised Smooth Contour Detection, 
diff --git a/image.ContourDetector/man/image_contour_detector.SpatRaster.Rd b/image.ContourDetector/man/image_contour_detector.SpatRaster.Rd
index a0a8105..bb09dcf 100644
--- a/image.ContourDetector/man/image_contour_detector.SpatRaster.Rd
+++ b/image.ContourDetector/man/image_contour_detector.SpatRaster.Rd
@@ -21,6 +21,24 @@ an object of class cld which as described in \code{\link{image_contour_detector}
 \description{
 Unsupervised Smooth Contour Lines Detection for SpatRaster objects
 }
+\examples{
+\dontshow{
+if(require(terra))
+\{
+}
+\donttest{
+library(terra)
+x   <- rast(system.file("extdata", "landscape.tif", package="image.ContourDetector"))
+
+contourlines <- image_contour_detector(x)
+image(x)
+plot(contourlines, add = TRUE, col = "blue", lwd = 10)
+}
+\dontshow{
+\}
+# End of main if statement running only if the required packages are installed
+}
+}
 \seealso{
 \code{\link{image_contour_detector}}
 }

From e0d346d2c62da28b46c2a507dfdb6b2fbca25566 Mon Sep 17 00:00:00 2001
From: Jan Wijffels <jwijffels@bnosac.be>
Date: Wed, 3 Jul 2024 00:04:46 +0200
Subject: [PATCH 20/22] docs

---
 image.ContourDetector/R/contour_detector.R                | 8 ++++++--
 .../man/image_contour_detector.SpatRaster.Rd              | 7 +++++--
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/image.ContourDetector/R/contour_detector.R b/image.ContourDetector/R/contour_detector.R
index c175db1..6f013fc 100644
--- a/image.ContourDetector/R/contour_detector.R
+++ b/image.ContourDetector/R/contour_detector.R
@@ -115,12 +115,14 @@ image_contour_detector.RasterLayer <- function(x, Q=2.0, as_sf=FALSE, ...){
 #' @param Q numeric value with the pixel quantization step
 #' @param as_sf Boolean. Set to TRUE to export lines as sf spatial objects
 #' @param ... further arguments passed on to \code{image_contour_detector.matrix}
-#' @return an object of class cld which as described in \code{\link{image_contour_detector}}
+#' @return 
+#' In case \code{as_sf} is \code{FALSE}: an object of class cld which as described in \code{\link{image_contour_detector}}\cr
+#' In case \code{as_sf} is \code{TRUE}: an object of class sf with columns ss and length_m
 #' @seealso \code{\link{image_contour_detector}}
 #' @export
 #' @examples 
 #' \dontshow{
-#' if(require(terra))
+#' if(require(terra) && require(sf))
 #' \{
 #' }
 #' \donttest{
@@ -130,6 +132,8 @@ image_contour_detector.RasterLayer <- function(x, Q=2.0, as_sf=FALSE, ...){
 #' contourlines <- image_contour_detector(x)
 #' image(x)
 #' plot(contourlines, add = TRUE, col = "blue", lwd = 10)
+#' 
+#' contourlines <- image_contour_detector(x, as_sf = TRUE)
 #' }
 #' \dontshow{
 #' \}
diff --git a/image.ContourDetector/man/image_contour_detector.SpatRaster.Rd b/image.ContourDetector/man/image_contour_detector.SpatRaster.Rd
index bb09dcf..6e136d9 100644
--- a/image.ContourDetector/man/image_contour_detector.SpatRaster.Rd
+++ b/image.ContourDetector/man/image_contour_detector.SpatRaster.Rd
@@ -16,14 +16,15 @@
 \item{...}{further arguments passed on to \code{image_contour_detector.matrix}}
 }
 \value{
-an object of class cld which as described in \code{\link{image_contour_detector}}
+In case \code{as_sf} is \code{FALSE}: an object of class cld which as described in \code{\link{image_contour_detector}}\cr
+In case \code{as_sf} is \code{TRUE}: an object of class sf with columns ss and length_m
 }
 \description{
 Unsupervised Smooth Contour Lines Detection for SpatRaster objects
 }
 \examples{
 \dontshow{
-if(require(terra))
+if(require(terra) && require(sf))
 \{
 }
 \donttest{
@@ -33,6 +34,8 @@ x   <- rast(system.file("extdata", "landscape.tif", package="image.ContourDetect
 contourlines <- image_contour_detector(x)
 image(x)
 plot(contourlines, add = TRUE, col = "blue", lwd = 10)
+
+contourlines <- image_contour_detector(x, as_sf = TRUE)
 }
 \dontshow{
 \}

From 84bb8e3909f4317420986835a40889304f0bdebf Mon Sep 17 00:00:00 2001
From: Nic <sciurusurbanus@hotmail.it>
Date: Wed, 3 Jul 2024 10:49:08 +0200
Subject: [PATCH 21/22] Update contour_detector.R

- added curve_ID
- fixed '@return' description
- fixed minor issues
---
 image.ContourDetector/R/contour_detector.R | 46 ++++++++++++++++------
 1 file changed, 35 insertions(+), 11 deletions(-)

diff --git a/image.ContourDetector/R/contour_detector.R b/image.ContourDetector/R/contour_detector.R
index 6f013fc..9f7aa07 100644
--- a/image.ContourDetector/R/contour_detector.R
+++ b/image.ContourDetector/R/contour_detector.R
@@ -89,7 +89,9 @@ image_contour_detector.matrix <- function(x, Q=2.0, ...){
 #' @param Q numeric value with the pixel quantization step
 #' @param as_sf Boolean. Set to TRUE to export lines as sf spatial objects
 #' @param ... further arguments passed on to \code{image_contour_detector.matrix}
-#' @return an object of class cld which as described in \code{\link{image_contour_detector}}
+#' @return
+#' In case \code{as_sf} is \code{FALSE}: an object of class cld which as described in \code{\link{image_contour_detector}}\cr
+#' In case \code{as_sf} is \code{TRUE}: an object of class sf containing the detected lines, a curve ID and its length (in the same units as the SpatRaster's CRS)
 #' @seealso \code{\link{image_contour_detector}}
 #' @export
 image_contour_detector.RasterLayer <- function(x, Q=2.0, as_sf=FALSE, ...){
@@ -97,16 +99,37 @@ image_contour_detector.RasterLayer <- function(x, Q=2.0, as_sf=FALSE, ...){
   minX = raster::extent(x)[1]
   minY = raster::extent(x)[3]  
   resol = raster::res(x)[1]  
-  x = raster::as.matrix(x)
+  xmat = raster::as.matrix(x)
   
-  if( anyNA(x) ){
-    x[is.na(x)] = 0
+  if( anyNA(xmat) ){
+    x[is.na(xmat)] = 0
     warning("NA values found and set to 0") }
 
-  contourlines = image_contour_detector.matrix(x, Q=Q, ...)
+  contourlines = image_contour_detector.matrix( xmat, Q=Q )
   
   contourlines$data$x = contourlines$data$x * resol + minX
   contourlines$data$y = contourlines$data$y * resol + minY
+
+  # export object as sf
+  if(isTRUE(as_sf)){
+    requireNamespace("sf")
+    
+    contourlines <- contourlines$data
+    contourlines = sf::st_as_sf( contourlines, coords = c("x", "y"), crs = sf::st_crs(x) )
+    
+    out = list()
+    
+    for( i in unique(contourlines$curve) ){
+      ss = subset(contourlines, curve == i )
+      ss = sf::st_combine(ss)      
+      out[[length(out)+1]] = sf::st_cast( sf::st_sf(ss), "LINESTRING")
+    }
+    
+    contourlines = do.call(rbind,out)    
+    contourlines$curve_ID = 1:nrow(contourlines)
+    contourlines$length = round( sf::st_length(contourlines), 3)
+  }
+  
   return(contourlines)
 }
 
@@ -115,9 +138,9 @@ image_contour_detector.RasterLayer <- function(x, Q=2.0, as_sf=FALSE, ...){
 #' @param Q numeric value with the pixel quantization step
 #' @param as_sf Boolean. Set to TRUE to export lines as sf spatial objects
 #' @param ... further arguments passed on to \code{image_contour_detector.matrix}
-#' @return 
+#' @return
 #' In case \code{as_sf} is \code{FALSE}: an object of class cld which as described in \code{\link{image_contour_detector}}\cr
-#' In case \code{as_sf} is \code{TRUE}: an object of class sf with columns ss and length_m
+#' In case \code{as_sf} is \code{TRUE}: an object of class sf containing the detected lines, a curve ID and its length (in the same units as the SpatRaster's CRS)
 #' @seealso \code{\link{image_contour_detector}}
 #' @export
 #' @examples 
@@ -130,7 +153,7 @@ image_contour_detector.RasterLayer <- function(x, Q=2.0, as_sf=FALSE, ...){
 #' x   <- rast(system.file("extdata", "landscape.tif", package="image.ContourDetector"))
 #' 
 #' contourlines <- image_contour_detector(x)
-#' image(x)
+#' plot(x)
 #' plot(contourlines, add = TRUE, col = "blue", lwd = 10)
 #' 
 #' contourlines <- image_contour_detector(x, as_sf = TRUE)
@@ -151,7 +174,7 @@ image_contour_detector.SpatRaster <- function(x, Q=2.0, as_sf=FALSE, ...){
     warning("NA values found and set to 0") 
   }
 
-  contourlines = image_contour_detector.matrix(xmat, Q=Q, ...)
+  contourlines = image_contour_detector.matrix( xmat, Q=Q )
   
   contourlines$data$x = contourlines$data$x * resol + minX
   contourlines$data$y = contourlines$data$y * resol + minY
@@ -172,13 +195,14 @@ image_contour_detector.SpatRaster <- function(x, Q=2.0, as_sf=FALSE, ...){
     out = list()
     
     for( i in unique(contourlines$curve) ){
-      ss = subset(contourlines, contourlines$curve == i )
+      ss = subset(contourlines, curve == i )
       ss = sf::st_combine(ss)      
       out[[length(out)+1]] = sf::st_cast( sf::st_sf(ss), "LINESTRING")
     }
     
     contourlines = do.call(rbind,out)    
-    contourlines$length_m = sf::st_length(contourlines)    
+    contourlines$curve_ID = 1:nrow(contourlines)
+    contourlines$length = round( sf::st_length(contourlines), 3)
   }  
   return(contourlines)
 }

From c179f5fcd1b4430aaabcef4be1d5aabf52d9ed82 Mon Sep 17 00:00:00 2001
From: Nic <sciurusurbanus@hotmail.it>
Date: Wed, 3 Jul 2024 11:54:40 +0200
Subject: [PATCH 22/22] Update line_segment_detector.R

- refined sf objects creation
- removed dependency on sp and moving it to sf
- updated plot.lsd
---
 .../R/line_segment_detector.R                 | 63 +++++++++++--------
 1 file changed, 38 insertions(+), 25 deletions(-)

diff --git a/image.LineSegmentDetector/R/line_segment_detector.R b/image.LineSegmentDetector/R/line_segment_detector.R
index e70208c..a365965 100644
--- a/image.LineSegmentDetector/R/line_segment_detector.R
+++ b/image.LineSegmentDetector/R/line_segment_detector.R
@@ -91,8 +91,8 @@
 #' library(terra)
 #' x   <- rast(system.file("extdata", "landscape.tif", package="image.ContourDetector"))
 #' 
-#' linesegments <- image_line_segment_detector(x)
-#' image(x)
+#' linesegments <- image_line_segment_detector(x, as_sf=TRUE)
+#' plot(x)
 #' plot(linesegments, add = TRUE, col = "blue", lwd = 10)
 #' }
 #' \dontshow{
@@ -155,44 +155,47 @@ image_line_segment_detector.SpatRaster <- function(x, scale = 0.8,
   uprightY = terra::ext(x)[4]  
   resol = terra::res(x)[1]
   
-  x = t(terra::as.matrix(x,wide=TRUE))
+  xmat = t(terra::as.matrix(x,wide=TRUE))
   
-  if( anyNA(x) ){
-    x[is.na(x)] = 0
+  if( anyNA(xmat) ){
+    xmat[is.na(xmat)] = 0
     warning("NA values found and set to 0") }
   
-  linesegments = image_line_segment_detector.matrix(x, scale = scale,
+  linesegments = image_line_segment_detector.matrix(xmat, scale = scale,
                                                     sigma_scale = sigma_scale, quant = quant, ang_th = ang_th, log_eps = log_eps,
                                                     density_th = density_th, n_bins = n_bins,
                                                     union = union, union_min_length = union_min_length, union_max_distance = union_max_distance,
                                                     union_ang_th=union_ang_th, union_use_NFA=union_use_NFA, union_log_eps = union_log_eps,
                                                     as_sf=as_sf )
   
-  linesegments = as.data.frame(linesegments$lines)
-  
   # assign spatial coordinates
-  linesegments$x1 = linesegments$x1 * -resol + uprightY
-  linesegments$y1 = linesegments$y1 * -resol + uprightX
-  linesegments$x2 = linesegments$x2 * -resol + uprightY
-  linesegments$y2 = linesegments$y2 * -resol + uprightX
-  
+  linesegments$lines[,1] = linesegments$lines[,1] * -resol + uprightY
+  linesegments$lines[,2] = linesegments$lines[,2] * -resol + uprightX
+  linesegments$lines[,3] = linesegments$lines[,3] * -resol + uprightY
+  linesegments$lines[,4] = linesegments$lines[,4] * -resol + uprightX
+  linesegments$lines[,5] = linesegments$lines[,5] * resol # width parameter
   
   # export object as sf
   if(isTRUE(as_sf)){
     requireNamespace("sf")
+
+    linesegments = as.data.frame(linesegments$lines)
     
     linesegments = apply(linesegments, 1, function(x) 
     {
       v <- as.numeric(x[c(2,4,1,3)])
       m <- matrix(v, nrow = 2)
-      return(sf::st_sfc(sf::st_linestring(m), crs = NA_crs_))
+      return(sf::st_sfc(sf::st_linestring(m)))
     })
     print("Sf export in progress...")
     linesegments = do.call(c, linesegments)
     
     linesegments = sf::st_sf(linesegments)
+    if( !is.na(sf::st_crs(x)) ){ sf::st_crs(linesegments) = sf::st_crs(x)}
+    st_geometry(linesegments) = 'geometry'
+    
     linesegments$line_ID = 1:nrow(linesegments)
-    linesegments$length_m = sf::st_length(linesegments)
+    linesegments$length = round( sf::st_length(linesegments), 3)
   }
   
   return(linesegments)
@@ -210,7 +213,7 @@ print.lsd <- function(x, ...){
 #' @description Plot the detected lines from the image_line_segment_detector
 #' @param x an object of class lsd as returned by \code{\link{image_line_segment_detector}}
 #' @param ... further arguments passed on to plot
-#' @return invisibly a SpatialLines object with the lines
+#' @return invisibly an sf object with the lines
 #' @export 
 #' @method plot lsd
 #' @examples 
@@ -221,13 +224,23 @@ print.lsd <- function(x, ...){
 #' plot(image)
 #' plot(linesegments, add = TRUE, col = "red")
 plot.lsd <- function(x, ...){
-  requireNamespace("sp")
-  out <- sp::SpatialLines(lapply(seq_len(x$n), FUN=function(i){
-    l <- rbind(
-      x$lines[i, c("x1", "y1")],
-      x$lines[i, c("x2", "y2")])
-    sp::Lines(sp::Line(l), ID = i)
-  }))
-  sp::plot(out, ...)
-  invisible(out)
+  requireNamespace("sf")
+  
+  out = as.data.frame(x$lines)
+  
+  out = apply(out, 1, function(x) 
+  {
+    v <- as.numeric(x[c(2,4,1,3)])
+    m <- matrix(v, nrow = 2)
+    return( sf::st_sfc(sf::st_linestring(m) ) )
+  })
+  print("Loading in progress...")
+  out = do.call(c, out)
+  
+  out = sf::st_sf(out, crs = 'NA_crs_')
+  if( !is.na(sf::st_crs(x)) ){ sf::st_crs(out) = sf::st_crs(x)}
+  st_geometry(out) = 'geometry'
+  
+  plot(out$geometry, ...)
+  invisible(out$geometry)
 }