diff --git a/NAMESPACE b/NAMESPACE
index 9c9f593b412bc9409a914d835c57d4d9d0967625..72481a1d7375a173b8f25c13d23630404684a49f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,7 +1,16 @@
# Generated by roxygen2: do not edit by hand
export(convert_sic_params)
+export(create_section_txt)
+export(create_uniform_reach_txt)
+export(dem_to_reach)
+export(dem_to_reach_txt)
+export(dem_to_section)
+export(extract_reach)
+export(get_section_centers)
export(loadConfig)
+export(merge_reaches)
export(set_initial_conditions)
export(sic_run_export)
export(sic_run_fortran)
+export(split_reach)
diff --git a/R/create_section_txt.R b/R/create_section_txt.R
new file mode 100644
index 0000000000000000000000000000000000000000..8f38a251869d5d95b1c4e5bff00a623df577e3d3
--- /dev/null
+++ b/R/create_section_txt.R
@@ -0,0 +1,43 @@
+#' Export a section in importation SIC format
+#'
+#' @param section_name [character], name of the section
+#' @param abscissa [numeric], abscissa of the section in the reach
+#' @param section_type 1-length [character], type of the section: "T" for Trapezoidal, "A" for Abscissa/Elevation, "L" for Width/Elevation
+#' @param profile [list] or [matrix], profile of the section (See details)
+#' @param distance_majeur [logical] or [numeric], `FALSE` for a minor bed section
+#'
+#' @return [character], section description in SIC text import format.
+#' @export
+#' @examples
+#' # Trapezoidal section
+#' export_section_txt("Trapeze", 0, "T", list(B = 2, S = 1.5, ZF = 100, ZB = 102))
+create_section_txt <- function(section_name, abscissa, section_type, profile, distance_majeur = FALSE) {
+
+ if (section_type == "T") {
+ if (!is.list(profile) || !all(c("B", "S", "ZF", "ZB") %in% names(profile))) {
+ stop("With `section_type = \"T\", `profile` should be a list with the items B, S, ZF and ZB")
+ }
+ sic_profile <- c(paste(profile$B, profile$S, sep = "\t"), paste(profile$ZB, profile$ZF, sep = "\t"))
+ } else if (section_type %in% c("A", "L")) {
+ if (!is.matrix(profile) || ncol(profile) != 2) {
+ stop("With `section_type = \"A\" or \"L\", `profile` should be a matrix with 2 columns")
+ }
+ sic_profile <- capture.output(write.table(profile, sep = "\t", quote = FALSE, col.names = FALSE, row.names = FALSE))
+ } else {
+ stop("section_type ", section_type, " not allowed. Possible choices are: A, L and T")
+ }
+
+ if (!(is.logical(distance_majeur) || is.numeric(distance_majeur)) || length(distance_majeur) != 1) {
+ stop("`distance_majeur` should be a `logical` or a `numeric` of length 1")
+ }
+ bMajorBed <- !is.logical(distance_majeur)
+ section_txt <- c(paste(section_name,
+ abscissa,
+ ifelse(bMajorBed, distance_majeur, ""),
+ ifelse(bMajorBed, "1", "0"),
+ section_type,
+ sep = " $ "),
+ sic_profile)
+ class(section_txt) <- c("SectionTxt", class(section_txt))
+ return(section_txt)
+}
diff --git a/R/create_uniform_reach_txt.R b/R/create_uniform_reach_txt.R
new file mode 100644
index 0000000000000000000000000000000000000000..2594e8cfe0b117f4a41886eb5cc350f2ff6ec269
--- /dev/null
+++ b/R/create_uniform_reach_txt.R
@@ -0,0 +1,55 @@
+#' Generate text export geometry for an uniform reach
+#'
+#' @param abscissas [numeric] vector of section abscissas
+#' @param upstream_bed_elevation [numeric], upstream bed elevation (m)
+#' @param slope [numeric], bed slope of the reach (m/m)
+#' @param names [character] vector of section names
+#' @inheritParams create_section_txt
+#'
+#' @return A [list] from which each item is a section exported by [create_section_txt].
+#' Names of the list are the abscissas with trailing zeros for character sorting.
+#' @export
+#'
+#' @examples
+#' # Trapezoidal section
+#' profT <- list(B = 2,S = 1, ZF = 100, ZB = 100 + 2)
+#'
+#' # Generate a reach with 2 sections at x=1000 and 2000
+#' create_uniform_reach_txt(abscissas = c(1000, 2000),
+#' upstream_bed_elevation = 100,
+#' slope = 0.001,
+#' section_type = "T",
+#' profile = profT)
+create_uniform_reach_txt <- function(abscissas,
+ upstream_bed_elevation,
+ slope,
+ section_type,
+ profile,
+ section_names = paste0("Section x=", abscissas)) {
+
+ sections <- lapply(seq_along(abscissas), function(i) {
+ x <- abscissas[i]
+ bed_elevation <- upstream_bed_elevation - (x - abscissas[1]) * slope
+ shifted_prof <- shift_profile(section_type, profile, bed_elevation)
+ create_section_txt(section_name = section_names[i],
+ abscissa = x,
+ section_type = section_type,
+ profile = shifted_prof)
+ })
+ names(sections) <- sprintf("%08d", abscissas)
+ class(sections) <- c("ReachTxt", class(sections))
+ return(sections)
+}
+
+shift_profile <- function(section_type, profile, bed_elevation) {
+ shifted_prof <- profile
+ if (section_type == "T") {
+ shifted_prof$ZF <- bed_elevation
+ shifted_prof$ZB <- profile$ZB + bed_elevation - profile$ZF
+ } else if (section_type == "L") {
+ shifted_prof[,2] <- shifted_prof[,2] + bed_elevation - min(profile[, 2])
+ } else {
+ stop("section_type ", section_type, " not allowed. Possible choices are: T and L")
+ }
+ return(shifted_prof)
+}
diff --git a/R/dem_to_reach.R b/R/dem_to_reach.R
new file mode 100644
index 0000000000000000000000000000000000000000..173139f94bad9145c9664c17b3907d4375ce2ea6
--- /dev/null
+++ b/R/dem_to_reach.R
@@ -0,0 +1,129 @@
+#' Create SIC geometry sections from a DEM
+#'
+#' The coordinate system of `dem` should be a metric orthonormal coordinate system.
+#'
+#' @param dem [terra::SpatRaster] object with altitude data (m).
+#' @param node_coords [matrix] with coordinates of starting and ending points of the line to browse
+#' @param space_step 1-length [numeric], distance between each section (m)
+#' @param section_width 1-length [numeric], width of the sections to create
+#' @param nb_points 1-length [numeric], number of points to describe cross-section geometries
+#' @param start 1-length [numeric], starting value for the chainage (i.e. section abscissa) along the reach
+#' @param major_bed [logical], `TRUE` for major bed, `FALSE` for minor-medium bed
+#'
+#' @return
+#' @rdname dem_to_reach
+#' @export
+#'
+#' @examples
+#' ## Inputs preparation
+#' data("floodam_ead_dem")
+#' dem <- terra::rast(floodam_ead_dem)
+#' node_coords <- matrix(c(102550, 102550, 110000, 108000), ncol = 2)
+#' space_step = 100
+#' section_width = 5000
+#'
+#' ## Get section positions
+#' reach_length <- as.numeric(dist(node_coords[1:2,]))
+#' nb_sections <- ceiling(reach_length / space_step) + 1
+#' section_centers <- get_section_centers(node_coords, nb_sections)
+#'
+#' ## Create a section profile and plot it!
+#' profile <- dem_to_section(dem, node_coords, section_centers[5,], section_width)
+#' plot(profile)
+#'
+#' ## Generate cross section profiles for a reach
+#' reach <- dem_to_reach(dem, node_coords, section_centers, section_width)
+#' plot(reach[[5]])
+#'
+#' ## Generate section profiles in SIC import text format
+#' reach_txt <- dem_to_reach_txt(dem, node_coords, space_step, section_width, major_bed = TRUE)
+#' reach_txt[[5]]
+#'
+dem_to_reach_txt <- function(dem, node_coords, space_step, section_width, nb_points = 50, start = 0, major_bed = FALSE) {
+ reach_length <- as.numeric(dist(node_coords[1:2,]))
+ nb_sections <- ceiling(reach_length / space_step) + 1
+ section_centers <- get_section_centers(node_coords, nb_sections)
+ abscissas <- start + sapply(seq_len(nrow(section_centers)), function(i) {as.numeric(dist(section_centers[c(1,i), ]))})
+ reach <- dem_to_reach(dem, node_coords, section_centers, section_width, nb_points)
+ reach_txt <- lapply(seq_along(reach), function(i) {
+ section_name <- paste0(ifelse(major_bed, "Major", "Minor"), " x=", abscissas[i])
+ profile <- reach[[i]]
+ if (major_bed != FALSE) {
+ distance_majeur <- abscissas[i] - abscissas[max(i - 1, 1)]
+ } else {
+ distance_majeur <- FALSE
+ }
+ create_section_txt(section_name, abscissas[i], "A", profile, distance_majeur)
+ })
+ names(reach_txt) <- sprintf("%08d", abscissas)
+ class(reach_txt) <- c("ReachTxt", class(reach_txt))
+ return(reach_txt)
+}
+
+#' @rdname dem_to_reach
+#' @export
+dem_to_reach <- function(dem, node_coords, section_centers, section_width, nb_points = 50) {
+ lapply(seq_len(nrow(section_centers)), function(i) {
+ section_center <- section_centers[i,]
+ dem_to_section(dem, node_coords, section_center, section_width, nb_points)
+ })
+}
+
+
+#' Create a section cross profile from a DEM
+#'
+#' @inheritParams dem_to_reach
+#' @param section_center 2-lenght [numeric], coordinates of the section center
+#'
+#' @return
+#' @export
+#'
+#' @inherit dem_to_reach return examples
+dem_to_section <- function(dem, node_coords, section_center, section_width, nb_points = 50) {
+ if (length(section_center) != 2) {
+ stop("`section_center` should be of lenght 2")
+ }
+ section_bounds <-
+ t(sapply(c(-1, 1), function(direction) {
+ get_section_bound(node_coords, section_center, section_width, direction)
+ }))
+ section_points <-
+ apply(section_bounds, 2, function(x) {
+ seq(x[1], x[2], length.out = nb_points)
+ })
+ z <- terra::extract(dem, section_points, method = "bilinear")$lyr.1
+ x_points <- sapply(seq_len(nrow(section_points)), function(i) {as.numeric(dist(section_points[c(1,i), ]))})
+ m <- matrix(c(x_points, z), ncol = 2)
+ colnames(m) <- c("x", "z")
+ return(m)
+}
+
+get_section_bound <- function(node_coords, section_center, section_width, direction = 1) {
+ theta_reach <- atan2(diff(node_coords[,2]), diff(node_coords[,1]))
+ theta <- theta_reach + direction * pi / 2
+ r <- section_width / 2
+ c(x = section_center[1] + r * cos(theta), y = section_center[2] + r * sin(theta))
+}
+
+#' Get coordinates of section centers
+#'
+#' From the coordinates of a segment, this function returns the coordinates
+#' of equidistant points along the segment given a number of points
+#'
+#' @param node_coords 2-rows [matrix], with coordinates of segment boundaries
+#' @param nb_sections 1-length [numeric], number of points to extract
+#'
+#' @return A [matrix] with the coordinates of the points along the segment
+#' @export
+#'
+#' @examples
+#' node_coords <- matrix(c(102550, 102550, 110000, 108000), ncol = 2)
+#' reach_length <- as.numeric(dist(node_coords[1:2,]))
+#' space_step <- 100
+#' nb_sections <- ceiling(reach_length / space_step) + 1
+#' get_section_centers(node_coords, nb_sections)
+get_section_centers <- function(node_coords, nb_sections) {
+ apply(node_coords, 2, function(x) {
+ seq(x[1], x[2], length.out = nb_sections)
+ })
+}
diff --git a/R/floodam_ead_dem.R b/R/floodam_ead_dem.R
new file mode 100644
index 0000000000000000000000000000000000000000..d3bcc109ebf9d7e5d002ab1560c99a0eb1c80f24
--- /dev/null
+++ b/R/floodam_ead_dem.R
@@ -0,0 +1,13 @@
+#' Default DEM from the floodam-ead package
+#'
+#' This is the default DEM generated by [floodam.ead::generate_DEM] function with default arguments.
+#'
+#' @format A `PackedSpatRaster` object, use 'terra::rast()' to unpack it.
+#' @source https://gitlab.irstea.fr/flood-appraisal/floodam/floodam-ead
+#'
+#' @examples
+#' data("floodam_ead_dem", package = "rsic2")
+#' floodam_ead_dem
+#' terra::rast(floodam_ead_dem)
+"floodam_ead_dem"
+
diff --git a/R/merge_reaches.R b/R/merge_reaches.R
new file mode 100644
index 0000000000000000000000000000000000000000..dd3b31753f1de4b639ad7e1b8493ffa22c9ea667
--- /dev/null
+++ b/R/merge_reaches.R
@@ -0,0 +1,42 @@
+#' Merge several ReachTxt objects into one
+#'
+#' @param ... ReachTxt objects
+#'
+#' @return
+#' @export
+#'
+#' @examples
+#' # Minor bed generation
+#' profT <- list(
+#' B = 2,
+#' S = (6 - 2) / 2 / 2,
+#' ZF = 100,
+#' ZB = 100 + 2
+#' )
+#' min_reach <- create_uniform_reach_txt(abscissas = seq(0, 10000, 100),
+#' upstream_bed_elevation = 10 + 2000 * 0.002,
+#' slope = 0.002,
+#' section_type = "T",
+#' profile = profT)
+#'
+#' # Major bed generation
+#' data("floodam_ead_dem")
+#' dem <- terra::rast(floodam_ead_dem)
+#' node_coords <- matrix(c(102550, 102550, 110000, 100000), ncol = 2)
+#' space_step = 100
+#' section_width = 5000
+#' maj_reach <- dem_to_reach_txt(dem, node_coords, space_step, section_width, major_bed = TRUE)
+#'
+#' # Merge reaches into one
+#' reach <- merge_reaches(min_reach, maj_reach)
+merge_reaches <- function(...) {
+ reaches <- list(...)
+ lapply(reaches, function(reach) {
+ if (!inherits(reach, "ReachTxt")) stop("Parameters must be of class ReachTxt")
+ })
+ if (length(reaches) == 1) return(reaches[[1]])
+ merged_reach <- do.call(c, reaches)
+ merged_reach <- merged_reach[order(names(merged_reach))]
+ class(merged_reach) <- c("ReachTxt", class(merged_reach))
+ return(merged_reach)
+}
diff --git a/R/sic_import_reaches.R b/R/sic_import_reaches.R
new file mode 100644
index 0000000000000000000000000000000000000000..d363252820e53d2b2f70e24e7f20f7145467d20f
--- /dev/null
+++ b/R/sic_import_reaches.R
@@ -0,0 +1,33 @@
+sic_import_reaches <- function(reaches, import_mode = "ImportXml_UPDATE", cfg = loadConfig()) {
+ # Create reach files
+ import_path <- dirname(cfg$project$path)
+ reach_files <- sapply(seq_along(reaches), function(i) {
+ file <- file.path(import_path, sprintf("reach_%04d.txt", i))
+ write_reach_txt(file, reaches[[i]])
+ return(shQuote(basename(file), type = "cmd"))
+ })
+
+ # Import files with EdiSic https://sic.g-eau.fr/Import-sections-in-text-format?lang=en
+ project_name <- basename(tools::file_path_sans_ext(cfg$project$path))
+ cmd_line <- shQuote(
+ paste(
+ file.path(cfg$sic$path, cfg$sic$edisic),
+ shQuote(dirname(cfg$project$path), type = "cmd"),
+ import_mode,
+ shQuote(project_name, type = "cmd"),
+ paste(reach_files, collapse = " ")
+ ),
+ type = "cmd2"
+ )
+ logger::log_debug(cmd_line)
+ shell(
+ cmd_line,
+ wait = T,
+ translate = T
+ )
+}
+
+write_reach_txt <- function(file, reach) {
+ s <- unlist(reach)
+ writeLines(s, file)
+}
diff --git a/R/split_reach.R b/R/split_reach.R
new file mode 100644
index 0000000000000000000000000000000000000000..e6850990aa4c84384dd99acf7b0ab4e05e33e76b
--- /dev/null
+++ b/R/split_reach.R
@@ -0,0 +1,32 @@
+#' Split a reach into a list of reaches
+#'
+#' @param reach A ReachTxt object
+#' @param x_limits Chainage (i.e. abscissas along the reach) of splitting points
+#'
+#' @return A [list] of ReachTxt objects
+#' @export
+#'
+#' @examples
+split_reach <- function(reach, x_limits) {
+ if(length(x_limits) < 2) {
+ stop("`x_limits` length must be greater or equal to 2")
+ }
+ lapply(seq_len(length(x_limits) - 1), function(i) extract_reach(reach, x_limits[i:(i+1)]))
+}
+
+#' Select portion of a reach between two chainages
+#'
+#' @param reach A ReachTxt object
+#' @param x_limits 2-length [numeric], min and max chainage
+#'
+#' @return A ReachTxt object containing the selected sections.
+#' @export
+#'
+#' @examples
+extract_reach <- function(reach, x_limits) {
+ reach_names <- names(reach)
+ x_limits <- sprintf("%08d", x_limits)
+ sel_reach <- reach[reach_names >= min(x_limits) & reach_names <= max(x_limits)]
+ class(sel_reach) <- c("ReachTxt", class(sel_reach))
+ return(sel_reach)
+}
diff --git a/data-raw/floodam_ead_DEM.R b/data-raw/floodam_ead_DEM.R
new file mode 100644
index 0000000000000000000000000000000000000000..e86c2c920fb722f586825fa03719ee7c713a163d
--- /dev/null
+++ b/data-raw/floodam_ead_DEM.R
@@ -0,0 +1,138 @@
+## code to prepare `floodam-ead_DEM`
+
+# Prior to run this script, install all suggested packages with `remotes::install_deps(dependencies = TRUE)`
+
+# Function exported from floodam-ead 2022-02-03
+#' @title Generate floodplain DEM including streams
+#'
+#' @param min_elevation numeric, floodplain minimum elevation
+#' @param D numeric, lateral floodplain elevation range (across floodplain)
+#' @param rad numeric, x and y extent for a cell in pixels
+#' @param n_y numeric, number of cells along y axis
+#' @param r numeric, raster resolution in m
+#' @param slope numeric, upstream-downstream slope
+#' @param epsg, integer, EPSG Geodetic Parameter. Default value corresponding
+#' Chaco area in Argentina (Def :UTM Zone 19S)
+#' @param lower_left numeric, lower left, i.e. floodplain origin in metric
+#' geodesic system
+#' @param s_depth numeric, stream depth in m
+#' @param s_up_width numeric, upper riverbed width in m (assuming symetric and
+#' trapezoidal crosssection)
+#' @param s_down_width numeric, lower riverbed width in m (assuming symetric
+#' and trapezoidal crosssection)
+#' @param ridge_ratio numeric, width ratio for ridge position
+#' @param lambda numeric, sigmoid exponent controling bank slope
+#' @param bank_width numeric, sigmoid width in pixels
+#' @param random_microtopo logical, addition of random microtopo
+#' @param seed integer, seed for generation of random microtopo
+#' @param microtopo_sill numeric, square of macrotopo / microtopo ratio
+#' (default 0.05)
+#' @param microtopo_range numeric, microtopo spatial range in pixels
+#'
+#' @return Raster object
+#'
+#' @export
+#'
+#' @examples
+#' DEM <- generate_DEM()
+#'
+#' @encoding UTF-8
+#' @author Jean-Stéphane BAILLY, \email{bailly@agroparistech.fr}
+#' @author Frédéric Grelot, \email{frederic.grelot@inrae.fr}
+
+generate_DEM = function(
+ min_elevation = 10,
+ D = 20,
+ rad = 100,
+ n_y = 4,
+ r = 25,
+ slope = 0.002,
+ epsg = 32719,
+ lower_left = c(100000, 100000),
+ s_depth = 2,
+ s_up_width = 100,
+ s_down_width = 75,
+ ridge_ratio = 1 / 3,
+ lambda = 1,
+ bank_width = rad / 5,
+ random_microtopo = "FALSE",
+ seed = 123,
+ microtopo_sill = (0.02)^2,
+ microtopo_range = rad / 10
+) {
+
+ # Cell design
+ x <- matrix(1:rad, nrow = rad, ncol = rad, byrow = TRUE)
+ y <- matrix(rad:1, nrow = rad, ncol = rad)
+ # ridge shoulder location along x axis (in pixels)
+ ridge_x <- (1 + sin(seq(pi / 2, 5 * pi / 2, length.out = rad))) / 2
+ ridge_x <- round(1 + (ridge_x * ((ridge_ratio * rad)-1)))
+ sigm <- function(xi, lambda, bank_width) {
+ 1 / (1 + exp(lambda * (xi[-length(xi)] - xi[length(xi)]) / bank_width))
+ }
+ prov <- cbind(x, ridge_x)
+ z0 <- t(apply(prov, 1, sigm, lambda = lambda, bank_width = bank_width))
+
+ # Cell replication
+ z0 <- cbind(z0, z0[ , ncol(z0):1])
+ z0 <- do.call(rbind, mget(paste0("z", rep(0, n_y))))
+
+ # Adding local microtopo from spatial random realization
+ if (random_microtopo == "TRUE") {
+ set.seed(seed)
+ mt <- as.matrix(
+ RandomFields::RFsimulate(
+ x = 1:(rad * n_y),
+ y = 1:(rad * 2),
+ model = RandomFields::RMgauss(
+ var = microtopo_sill,
+ scale = microtopo_range
+ ),
+ grid = TRUE
+ )
+ )
+ z0 <- z0 + mt
+ }
+
+ # Elevation scaling
+ z0 <- (z0 * D) + min_elevation
+
+ # Stream concatenation
+ s <- seq(0, (s_up_width / 2), by = r)
+ zs <- rep(0, length(s))
+ zs[s <= s_down_width / 2] <- - s_depth
+ zs[s > s_down_width / 2] <-
+ - s_depth +
+ 2 * s_depth *
+ (s[s > s_down_width / 2] - s_down_width / 2) /
+ (s_up_width - s_down_width)
+ zs <- c(rev(zs[-1]), zs)
+ zs <- as.matrix(do.call(rbind, mget(rep("zs", nrow(z0)))))
+ zs <- zs + min_elevation
+ z0 <- cbind(
+ z0[ , 1:(ncol(z0) / 2)],
+ zs,
+ z0[ , (1 + ncol(z0) / 2):ncol(z0)]
+ )
+
+ # Upstream-downstream slopping
+ z0 <- z0 + (nrow(z0) + 1 - row(z0)) * r * slope
+
+ # Shape result
+ result <- terra::rast(
+ z0,
+ extent = terra::ext(
+ lower_left[1],
+ lower_left[1] + (r * (rad * 2 + ncol(zs))),
+ lower_left[2],
+ lower_left[2] + (r * rad * n_y)
+ ),
+ crs = sprintf("epsg:%s", epsg)
+ )
+
+ invisible(return(result))
+}
+
+floodam_ead_dem <- terra::wrap(generate_DEM())
+
+usethis::use_data(floodam_ead_dem, overwrite = TRUE)
diff --git a/data/floodam_ead_dem.rda b/data/floodam_ead_dem.rda
new file mode 100644
index 0000000000000000000000000000000000000000..4b38496243e9d81dd3e1fd211b7839ddc6b3f80b
Binary files /dev/null and b/data/floodam_ead_dem.rda differ
diff --git a/man/create_section_txt.Rd b/man/create_section_txt.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..cd02ce1b2d7cc5467c1f085432653c477936510d
--- /dev/null
+++ b/man/create_section_txt.Rd
@@ -0,0 +1,35 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/create_section_txt.R
+\name{create_section_txt}
+\alias{create_section_txt}
+\title{Export a section in importation SIC format}
+\usage{
+create_section_txt(
+ section_name,
+ abscissa,
+ section_type,
+ profile,
+ distance_majeur = FALSE
+)
+}
+\arguments{
+\item{section_name}{\link{character}, name of the section}
+
+\item{abscissa}{\link{numeric}, abscissa of the section in the reach}
+
+\item{section_type}{1-length \link{character}, type of the section: "T" for Trapezoidal, "A" for Abscissa/Elevation, "L" for Width/Elevation}
+
+\item{profile}{\link{list} or \link{matrix}, profile of the section (See details)}
+
+\item{distance_majeur}{\link{logical} or \link{numeric}, \code{FALSE} for a minor bed section}
+}
+\value{
+\link{character}, section description in SIC text import format.
+}
+\description{
+Export a section in importation SIC format
+}
+\examples{
+# Trapezoidal section
+export_section_txt("Trapeze", 0, "T", list(B = 2, S = 1.5, ZF = 100, ZB = 102))
+}
diff --git a/man/create_uniform_reach_txt.Rd b/man/create_uniform_reach_txt.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..f47a6405f510c7dafba40ecfe942730cfaccfcda
--- /dev/null
+++ b/man/create_uniform_reach_txt.Rd
@@ -0,0 +1,46 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/create_uniform_reach_txt.R
+\name{create_uniform_reach_txt}
+\alias{create_uniform_reach_txt}
+\title{Generate text export geometry for an uniform reach}
+\usage{
+create_uniform_reach_txt(
+ abscissas,
+ upstream_bed_elevation,
+ slope,
+ section_type,
+ profile,
+ section_names = paste0("Section x=", abscissas)
+)
+}
+\arguments{
+\item{abscissas}{\link{numeric} vector of section abscissas}
+
+\item{upstream_bed_elevation}{\link{numeric}, upstream bed elevation (m)}
+
+\item{slope}{\link{numeric}, bed slope of the reach (m/m)}
+
+\item{section_type}{1-length \link{character}, type of the section: "T" for Trapezoidal, "A" for Abscissa/Elevation, "L" for Width/Elevation}
+
+\item{profile}{\link{list} or \link{matrix}, profile of the section (See details)}
+
+\item{names}{\link{character} vector of section names}
+}
+\value{
+A \link{list} from which each item is a section exported by \link{create_section_txt}.
+Names of the list are the abscissas with trailing zeros for character sorting.
+}
+\description{
+Generate text export geometry for an uniform reach
+}
+\examples{
+# Trapezoidal section
+profT <- list(B = 2,S = 1, ZF = 100, ZB = 100 + 2)
+
+# Generate a reach with 2 sections at x=1000 and 2000
+create_uniform_reach_txt(abscissas = c(1000, 2000),
+ upstream_bed_elevation = 100,
+ slope = 0.001,
+ section_type = "T",
+ profile = profT)
+}
diff --git a/man/dem_to_reach.Rd b/man/dem_to_reach.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..0cbfdd85a49f2bf752e49380292b36390bfd6247
--- /dev/null
+++ b/man/dem_to_reach.Rd
@@ -0,0 +1,66 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/dem_to_reach.R
+\name{dem_to_reach_txt}
+\alias{dem_to_reach_txt}
+\alias{dem_to_reach}
+\title{Create SIC geometry sections from a DEM}
+\usage{
+dem_to_reach_txt(
+ dem,
+ node_coords,
+ space_step,
+ section_width,
+ nb_points = 50,
+ start = 0,
+ major_bed = FALSE
+)
+
+dem_to_reach(dem, node_coords, section_centers, section_width, nb_points = 50)
+}
+\arguments{
+\item{dem}{\link[terra:SpatRaster-class]{terra::SpatRaster} object with altitude data (m).}
+
+\item{node_coords}{\link{matrix} with coordinates of starting and ending points of the line to browse}
+
+\item{space_step}{1-length \link{numeric}, distance between each section (m)}
+
+\item{section_width}{1-length \link{numeric}, width of the sections to create}
+
+\item{nb_points}{1-length \link{numeric}, number of points to describe cross-section geometries}
+
+\item{start}{1-length \link{numeric}, starting value for the chainage (i.e. section abscissa) along the reach}
+
+\item{major_bed}{\link{logical}, \code{TRUE} for major bed, \code{FALSE} for minor-medium bed}
+}
+\value{
+
+}
+\description{
+The coordinate system of \code{dem} should be a metric orthonormal coordinate system.
+}
+\examples{
+## Inputs preparation
+data("floodam_ead_dem")
+dem <- terra::rast(floodam_ead_dem)
+node_coords <- matrix(c(102550, 102550, 110000, 108000), ncol = 2)
+space_step = 100
+section_width = 5000
+
+## Get section positions
+reach_length <- as.numeric(dist(node_coords[1:2,]))
+nb_sections <- ceiling(reach_length / space_step) + 1
+section_centers <- get_section_centers(node_coords, nb_sections)
+
+## Create a section profile and plot it!
+profile <- dem_to_section(dem, node_coords, section_centers[5,], section_width)
+plot(profile)
+
+## Generate cross section profiles for a reach
+reach <- dem_to_reach(dem, node_coords, section_centers, section_width)
+plot(reach[[5]])
+
+## Generate section profiles in SIC import text format
+reach_txt <- dem_to_reach_txt(dem, node_coords, space_step, section_width, major_bed = TRUE)
+reach_txt[[5]]
+
+}
diff --git a/man/dem_to_section.Rd b/man/dem_to_section.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..f3dcd7ec1de8c5b77e0e323a239874e3da02572e
--- /dev/null
+++ b/man/dem_to_section.Rd
@@ -0,0 +1,51 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/dem_to_reach.R
+\name{dem_to_section}
+\alias{dem_to_section}
+\title{Create a section cross profile from a DEM}
+\usage{
+dem_to_section(dem, node_coords, section_center, section_width, nb_points = 50)
+}
+\arguments{
+\item{dem}{\link[terra:SpatRaster-class]{terra::SpatRaster} object with altitude data (m).}
+
+\item{node_coords}{\link{matrix} with coordinates of starting and ending points of the line to browse}
+
+\item{section_center}{2-lenght \link{numeric}, coordinates of the section center}
+
+\item{section_width}{1-length \link{numeric}, width of the sections to create}
+
+\item{nb_points}{1-length \link{numeric}, number of points to describe cross-section geometries}
+}
+\value{
+
+}
+\description{
+Create a section cross profile from a DEM
+}
+\examples{
+## Inputs preparation
+data("floodam_ead_dem")
+dem <- terra::rast(floodam_ead_dem)
+node_coords <- matrix(c(102550, 102550, 110000, 108000), ncol = 2)
+space_step = 100
+section_width = 5000
+
+## Get section positions
+reach_length <- as.numeric(dist(node_coords[1:2,]))
+nb_sections <- ceiling(reach_length / space_step) + 1
+section_centers <- get_section_centers(node_coords, nb_sections)
+
+## Create a section profile and plot it!
+profile <- dem_to_section(dem, node_coords, section_centers[5,], section_width)
+plot(profile)
+
+## Generate cross section profiles for a reach
+reach <- dem_to_reach(dem, node_coords, section_centers, section_width)
+plot(reach[[5]])
+
+## Generate section profiles in SIC import text format
+reach_txt <- dem_to_reach_txt(dem, node_coords, space_step, section_width, major_bed = TRUE)
+reach_txt[[5]]
+
+}
diff --git a/man/extract_reach.Rd b/man/extract_reach.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..7b62ec508798c4676e1518f47bf286a30f3408a2
--- /dev/null
+++ b/man/extract_reach.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/split_reach.R
+\name{extract_reach}
+\alias{extract_reach}
+\title{Select portion of a reach between two chainages}
+\usage{
+extract_reach(reach, x_limits)
+}
+\arguments{
+\item{reach}{A ReachTxt object}
+
+\item{x_limits}{2-length \link{numeric}, min and max chainage}
+}
+\value{
+A ReachTxt object containing the selected sections.
+}
+\description{
+Select portion of a reach between two chainages
+}
diff --git a/man/floodam_ead_dem.Rd b/man/floodam_ead_dem.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..5e30065d2936919adc5cb78657a132c7ffdb9acc
--- /dev/null
+++ b/man/floodam_ead_dem.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/floodam_ead_dem.R
+\docType{data}
+\name{floodam_ead_dem}
+\alias{floodam_ead_dem}
+\title{Default DEM from the floodam-ead package}
+\format{
+A \code{PackedSpatRaster} object, use 'terra::rast()' to unpack it.
+}
+\source{
+https://gitlab.irstea.fr/flood-appraisal/floodam/floodam-ead
+}
+\usage{
+floodam_ead_dem
+}
+\description{
+This is the default DEM generated by \link[floodam.ead:generate_DEM]{floodam.ead::generate_DEM} function with default arguments.
+}
+\examples{
+data("floodam_ead_dem", package = "rsic2")
+floodam_ead_dem
+terra::rast(floodam_ead_dem)
+}
+\keyword{datasets}
diff --git a/man/get_section_centers.Rd b/man/get_section_centers.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..584d51d15681b739bed06775c2557a18d5c6727d
--- /dev/null
+++ b/man/get_section_centers.Rd
@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/dem_to_reach.R
+\name{get_section_centers}
+\alias{get_section_centers}
+\title{Get coordinates of section centers}
+\usage{
+get_section_centers(node_coords, nb_sections)
+}
+\arguments{
+\item{node_coords}{2-rows \link{matrix}, with coordinates of segment boundaries}
+
+\item{nb_sections}{1-length \link{numeric}, number of points to extract}
+}
+\value{
+A \link{matrix} with the coordinates of the points along the segment
+}
+\description{
+From the coordinates of a segment, this function returns the coordinates
+of equidistant points along the segment given a number of points
+}
+\examples{
+node_coords <- matrix(c(102550, 102550, 110000, 108000), ncol = 2)
+reach_length <- as.numeric(dist(node_coords[1:2,]))
+space_step <- 100
+nb_sections <- ceiling(reach_length / space_step) + 1
+get_section_centers(node_coords, nb_sections)
+}
diff --git a/man/merge_reaches.Rd b/man/merge_reaches.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..fa030e3e039bb72077bbf7428055310b2a90845e
--- /dev/null
+++ b/man/merge_reaches.Rd
@@ -0,0 +1,42 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/merge_reaches.R
+\name{merge_reaches}
+\alias{merge_reaches}
+\title{Merge several ReachTxt objects into one}
+\usage{
+merge_reaches(...)
+}
+\arguments{
+\item{...}{ReachTxt objects}
+}
+\value{
+
+}
+\description{
+Merge several ReachTxt objects into one
+}
+\examples{
+# Minor bed generation
+profT <- list(
+ B = 2,
+ S = (6 - 2) / 2 / 2,
+ ZF = 100,
+ ZB = 100 + 2
+)
+min_reach <- create_uniform_reach_txt(abscissas = seq(0, 10000, 100),
+ upstream_bed_elevation = 10 + 2000 * 0.002,
+ slope = 0.002,
+ section_type = "T",
+ profile = profT)
+
+# Major bed generation
+data("floodam_ead_dem")
+dem <- terra::rast(floodam_ead_dem)
+node_coords <- matrix(c(102550, 102550, 110000, 100000), ncol = 2)
+space_step = 100
+section_width = 5000
+maj_reach <- dem_to_reach_txt(dem, node_coords, space_step, section_width, major_bed = TRUE)
+
+# Merge reaches into one
+reach <- merge_reaches(min_reach, maj_reach)
+}
diff --git a/man/split_reach.Rd b/man/split_reach.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..fe18d7eca4062dbf16e9f0e11ea5d9b5f5c1f6f6
--- /dev/null
+++ b/man/split_reach.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/split_reach.R
+\name{split_reach}
+\alias{split_reach}
+\title{Split a reach into a list of reaches}
+\usage{
+split_reach(reach, x_limits)
+}
+\arguments{
+\item{reach}{A ReachTxt object}
+
+\item{x_limits}{Chainage (i.e. abscissas along the reach) of splitting points}
+}
+\value{
+A \link{list} of ReachTxt objects
+}
+\description{
+Split a reach into a list of reaches
+}
diff --git a/tests/testthat/test-create_section_txt.R b/tests/testthat/test-create_section_txt.R
new file mode 100644
index 0000000000000000000000000000000000000000..b014043213a0a9080cb58aceac6030351968d646
--- /dev/null
+++ b/tests/testthat/test-create_section_txt.R
@@ -0,0 +1,41 @@
+profT <- list(
+ B = 2,
+ S = (6 - 2) / 2 / 2,
+ ZF = 100,
+ ZB = 100 + 2
+)
+
+test_that("Trapezoidale minor section", {
+ expect_equal(
+ create_section_txt("toto", 1000, "T", profT, distance_majeur = FALSE),
+ c("toto $ 1000 $ $ 0 $ T", "2\t1", "102\t100")
+ )
+ profT_wrong <- profT
+ profT_wrong$ZB <- NULL
+ expect_error(
+ create_section_txt("toto", 1000, "T", profT_wrong, distance_majeur = FALSE)
+ )
+})
+
+test_that("X/Z minor section", {
+ expect_error(
+ create_section_txt("toto", 1000, "A", profT, distance_majeur = FALSE)
+ )
+ profA <- matrix(c(0, 2, 4, 6, 102, 100, 100, 102), ncol = 2)
+ expect_equal(
+ create_section_txt("toto", 1000, "A", profA, distance_majeur = FALSE),
+ c("toto $ 1000 $ $ 0 $ A", "0\t102", "2\t100", "4\t100", "6\t102")
+ )
+})
+
+
+test_that("Major section", {
+ expect_equal(
+ create_section_txt("toto", 1000, "T", profT, distance_majeur = 100)[1],
+ "toto $ 1000 $ 100 $ 1 $ T"
+ )
+ expect_equal(
+ create_section_txt("toto", 1000, "T", profT, distance_majeur = 0)[1],
+ "toto $ 1000 $ 0 $ 1 $ T"
+ )
+})
diff --git a/tests/testthat/test-create_uniform_reach_txt.R b/tests/testthat/test-create_uniform_reach_txt.R
new file mode 100644
index 0000000000000000000000000000000000000000..c6eaa3442adbd6652aab15dba749d70d8e739500
--- /dev/null
+++ b/tests/testthat/test-create_uniform_reach_txt.R
@@ -0,0 +1,20 @@
+profT <- list(
+ B = 2,
+ S = (6 - 2) / 2 / 2,
+ ZF = 100,
+ ZB = 100 + 2
+)
+
+test_that("Trapezoidal minor section", {
+ expect_equal(
+ create_uniform_reach_txt(abscissas = c(1000, 2000),
+ upstream_bed_elevation = 100,
+ slope = 0.001,
+ section_type = "T",
+ profile = profT),
+ list(
+ "00001000" = c("Section x=1000 $ 1000 $ $ 0 $ T", "2\t1", "102\t100"),
+ "00002000" = c("Section x=2000 $ 2000 $ $ 0 $ T", "2\t1", "101\t99")
+ )
+ )
+})
diff --git a/tests/testthat/test-dem_to_reach.R b/tests/testthat/test-dem_to_reach.R
new file mode 100644
index 0000000000000000000000000000000000000000..8b137891791fe96927ad78e64b0aad7bded08bdc
--- /dev/null
+++ b/tests/testthat/test-dem_to_reach.R
@@ -0,0 +1 @@
+
diff --git a/tests/testthat/test-merge_reaches.R b/tests/testthat/test-merge_reaches.R
new file mode 100644
index 0000000000000000000000000000000000000000..ac7a2a1fd6efe93bee6e855702b69b91dd1d57e8
--- /dev/null
+++ b/tests/testthat/test-merge_reaches.R
@@ -0,0 +1,26 @@
+# Minor bed generation
+profT <- list(
+ B = 2,
+ S = (6 - 2) / 2 / 2,
+ ZF = 100,
+ ZB = 100 + 2
+)
+min_reach <- create_uniform_reach_txt(abscissas = seq(0, 10000, 100),
+ upstream_bed_elevation = 10 + 2000 * 0.002,
+ slope = 0.002,
+ section_type = "T",
+ profile = profT)
+
+# Major bed generation
+data("floodam_ead_dem")
+dem <- terra::rast(floodam_ead_dem)
+node_coords <- matrix(c(102550, 102550, 110000, 100000), ncol = 2)
+space_step = 100
+section_width = 5000
+maj_reach <- dem_to_reach_txt(dem, node_coords, space_step, section_width, major_bed = TRUE)
+
+test_that("merge_reaches should work", {
+ reach <- merge_reaches(min_reach, maj_reach)
+ expect_s3_class(reach, "ReachTxt")
+ expect_length(reach, length(min_reach) + length(maj_reach))
+})
diff --git a/tests/testthat/test-sic_import_reaches.R b/tests/testthat/test-sic_import_reaches.R
new file mode 100644
index 0000000000000000000000000000000000000000..4ac55c863d71a2a63c5ae50f29152c00da6c29d4
--- /dev/null
+++ b/tests/testthat/test-sic_import_reaches.R
@@ -0,0 +1,27 @@
+skip_on_ci()
+
+cfg <- loadLocalConfig()
+
+# Minor bed generation
+profT <- matrix(c(2, 6, 0, 2), ncol = 2)
+min_reach <- create_uniform_reach_txt(abscissas = seq(0, 10000, 100),
+ upstream_bed_elevation = 8 + 2000 * 0.002,
+ slope = 0.002,
+ section_type = "L",
+ profile = profT)
+
+# Major bed generation
+data("floodam_ead_dem")
+dem <- terra::rast(floodam_ead_dem)
+node_coords <- matrix(c(102550, 102550, 110000, 100000), ncol = 2)
+space_step = 100
+section_width = 5000
+maj_reach <- dem_to_reach_txt(dem, node_coords, space_step, section_width, major_bed = TRUE)
+
+# Merge minor and major beds and split into 2 reaches
+reach <- merge_reaches(min_reach, maj_reach)
+reaches <- split_reach(reach, seq(0, 10000, 5000))
+
+test_that("Geometry Import works", {
+ sic_import_reaches(reaches, cfg = cfg)
+})
diff --git a/tests/testthat/test-sic_run_export.R b/tests/testthat/test-sic_run_export.R
index d2b413da70ac8de7a524058162390344d60e3fd1..45e6a50d82e1d3097ece670d28e54d6d7260e69c 100644
--- a/tests/testthat/test-sic_run_export.R
+++ b/tests/testthat/test-sic_run_export.R
@@ -2,7 +2,7 @@ skip_on_ci()
cfg <- loadLocalConfig()
-test_that("multiplication works", {
+test_that("RunExport on Fluvia run works", {
sic_run_fortran("fluvia", list(SCE = 1), cfg = cfg)
m <- sic_run_export(scenario = 1, params = list(t = 0), cfg = cfg)
expect_type(m, "double")
diff --git a/tests/testthat/test-split_reach.R b/tests/testthat/test-split_reach.R
new file mode 100644
index 0000000000000000000000000000000000000000..baea982190d17f9806c8ed725e7020797e2ef624
--- /dev/null
+++ b/tests/testthat/test-split_reach.R
@@ -0,0 +1,24 @@
+# Minor bed generation
+profT <- list(
+ B = 2,
+ S = (6 - 2) / 2 / 2,
+ ZF = 100,
+ ZB = 100 + 2
+)
+min_reach <- create_uniform_reach_txt(abscissas = seq(0, 10000, 100),
+ upstream_bed_elevation = 10 + 2000 * 0.002,
+ slope = 0.002,
+ section_type = "T",
+ profile = profT)
+
+test_that("extract_reach works", {
+ sel_reach <- extract_reach(min_reach, c(2000, 4000))
+ expect_s3_class(sel_reach, "ReachTxt")
+ expect_s3_class(sel_reach[[1]], "SectionTxt")
+ expect_length(sel_reach, 21)
+})
+
+test_that("split_reach works", {
+ reaches <- split_reach(min_reach, seq(0, 10000, 2000))
+ expect_length(reaches, 5)
+})