Skip to content

Commit

Permalink
522 speed up rnet merge (#550)
Browse files Browse the repository at this point in the history 
* Remove comments

* Format

* Simplify use_rsgeo

Heads-up @JosiahParry, I think it works fine on projected data, as long as not too far to the poles?

* Speed-up by vectorisation, close #522

* Tidy up

* Fixes to line_segment()

* Debug edge case error

* Fix edge case issue, re-test

* Add browser() for debugging

* Debugging for #551

* Use geosphere, fix #551

* Document

* Make line_bearing work for projected data

* Format rnet_join()

* Document
  • Loading branch information
@Robinlovelace
Robinlovelace authored Oct 5, 2023
1 parent a85cfd4 commit 1f31f69
Show file tree
Hide file tree
Showing 25 changed files with 285 additions and 257 deletions.
1 change: 1 addition & 0 deletions DESCRIPTION
View file
Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@ Imports:
curl (>= 3.2),
data.table,
dplyr (>= 0.7.6),
geosphere,
httr (>= 1.3.1),
jsonlite (>= 1.5),
lwgeom (>= 0.1.4),
Expand Down
1 change: 1 addition & 0 deletions NAMESPACE
View file
Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,7 @@ export(line_segment)
export(line_segment1)
export(line_via)
export(mats2line)
export(n_segments)
export(n_vertices)
export(od2line)
export(od2odf)
Expand Down
212 changes: 108 additions & 104 deletions R/linefuns.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
#' @family lines
#' @export
#' @examples
#' l = routes_fast_sf
#' l <- routes_fast_sf
#' n_vertices(l)
#' n_vertices(zones_sf)
n_vertices <- function(l) {
Expand Down Expand Up @@ -59,21 +59,21 @@ is_linepoint <- function(l) {
#' @family lines
#' @export
#' @examples
#' lib_versions <- sf::sf_extSoftVersion()
#' lib_versions
#' # fails on some systems (with early versions of PROJ)
#' if (lib_versions[3] >= "6.3.1") {
#' bearings_sf_1_9 <- line_bearing(flowlines_sf[1:5, ])
#' bearings_sf_1_9 # lines of 0 length have NaN bearing
#' line_bearing(flowlines_sf[1:5, ], bidirectional = TRUE)
#' }
#' l <- flowlines_sf[1:5, ]
#' bearings_sf_1_9 <- line_bearing(l)
#' bearings_sf_1_9 # lines of 0 length have NaN bearing
#' line_bearing(l, bidirectional = TRUE)
line_bearing <- function(l, bidirectional = FALSE) {
p <- sf::st_geometry(line2points(l))
i_s <- seq_along(sf::st_geometry(l)) * 2 - 1

bearing_radians <- sapply(i_s, function(i) lwgeom::st_geod_azimuth(p[i:(i + 1)]))

bearing <- bearing_radians * 180 / pi
# Convert to lon/lat data if not already
is_longlat <- sf::st_is_longlat(l)
if (!is_longlat) {
l <- sf::st_transform(l, "EPSG:4326")
}
odc <- od::od_coordinates(l)
bearing <- geosphere::bearing(
p1 = odc[, 1:2],
p2 = odc[, 3:4]
)
if (bidirectional) {
bearing <- make_bidirectional(bearing)
}
Expand Down Expand Up @@ -133,22 +133,25 @@ angle_diff <- function(l, angle, bidirectional = FALSE, absolute = TRUE) {
#' @family lines
#' @export
#' @examples
#' l = routes_fast_sf[2:5, ]
#' l <- routes_fast_sf[2:5, ]
#' plot(l$geometry, col = 2:5)
#' midpoints = line_midpoint(l)
#' midpoints <- line_midpoint(l)
#' plot(midpoints, add = TRUE)
line_midpoint <- function(l, tolerance = NULL) {
if(is.null(tolerance)) {
sub = lwgeom::st_linesubstring(x = l, from = 0, to = 0.5)
if (is.null(tolerance)) {
sub <- lwgeom::st_linesubstring(x = l, from = 0, to = 0.5)
} else {
sub = lwgeom::st_linesubstring(x = l, from = 0, to = 0.5, tolerance = tolerance)
sub <- lwgeom::st_linesubstring(x = l, from = 0, to = 0.5, tolerance = tolerance)
}
lwgeom::st_endpoint(sub)
}

#' Divide an sf object with LINESTRING geometry into regular segments
#'
#' This function keeps the attributes
#' This function keeps the attributes.
#' Note: results differ when `use_rsgeo` is `TRUE`:
#' the `{rsgeo}` implementation is faster and more reliably
#' keeps returned linestrings below a the `segment_length` value.
#'
#' @inheritParams line2df
#' @param segment_length The approximate length of segments in the output (overides n_segments if set)
Expand All @@ -159,75 +162,83 @@ line_midpoint <- function(l, tolerance = NULL) {
#' @family lines
#' @export
#' @examples
#' library(sf)
#' l <- routes_fast_sf[2:4, ]
#' l_seg_multi = line_segment(l, segment_length = 1000)
#' l_seg_multi <- line_segment(l, segment_length = 1000, use_rsgeo = FALSE)
#' plot(l_seg_multi, col = seq_along(l_seg_multi), lwd = 5)
#' round(st_length(l_seg_multi))
#' # Test rsgeo implementation:
#' # rsmulti = line_segment(l, segment_length = 1000, use_rsgeo = TRUE)
#' # plot(rsmulti, col = seq_along(l_seg_multi), lwd = 5)
#' # round(st_length(rsmulti))
#' # waldo::compare(l_seg_multi, rsmulti)
line_segment <- function(
l,
segment_length = NA,
use_rsgeo = NULL,
debug_mode = FALSE
) {
l,
segment_length = NA,
use_rsgeo = NULL,
debug_mode = FALSE) {
UseMethod("line_segment")
}
#' @export
line_segment.sf <- function(
l,
segment_length = NA,
use_rsgeo = NULL,
debug_mode = FALSE
) {
l,
segment_length = NA,
use_rsgeo = NULL,
debug_mode = FALSE) {
if (is.na(segment_length)) {
rlang::abort(
"`segment_length` must be set.",
call = rlang::caller_env()
)
}
n_row_l = nrow(l)
# browser()
# Decide whether to use rsgeo or lwgeom, if not set:
if (is.null(use_rsgeo)) {
use_rsgeo <- use_rsgeo(l)
}
if (use_rsgeo) {
# If using rsgeo, we can do the whole thing in one go:
segment_lengths <- as.numeric(sf::st_length(l))
n_segments <- n_segments(segment_lengths, segment_length)
res <- line_segment_rsgeo(l, n_segments = n_segments)
return(res)
}
n_row_l <- nrow(l)
if (n_row_l > 1) {
res_list = pbapply::pblapply(seq(n_row_l), function(i) {
res_list <- pbapply::pblapply(seq(n_row_l), function(i) {
if (debug_mode) {
message(paste0("Processing row ", i, " of ", n_row_l))
}
# if( i == 108) {
# browser()
# }
l_segmented = line_segment1(l[i, ], n_segments = NA, segment_length = segment_length, use_rsgeo)
l_segmented <- line_segment1(l[i, ], n_segments = NA, segment_length = segment_length)
res_names <- names(sf::st_drop_geometry(l_segmented))
# Work-around for https://github.com/ropensci/stplanr/issues/531
if (i == 1) {
res_names <<- names(sf::st_drop_geometry(l_segmented))
}
l_segmented = l_segmented[res_names]
l_segmented <- l_segmented[res_names]
l_segmented
})
res = bind_sf(res_list)
})
res <- bind_sf(res_list)
} else {
# If there's only one row:
res = line_segment1(l, n_segments = NA, segment_length = segment_length, use_rsgeo)
res <- line_segment1(l, n_segments = NA, segment_length = segment_length)
}
res
}


#' @export
line_segment.sfc_LINESTRING <- function(
l,
segment_length = NA,
use_rsgeo = NULL,
debug_mode = FALSE
) {
l,
segment_length = NA,
use_rsgeo = NULL,
debug_mode = FALSE) {
l <- sf::st_as_sf(l)
res = line_segment(l, segment_length = segment_length, use_rsgeo, debug_mode)
res <- line_segment(l, segment_length = segment_length, use_rsgeo, debug_mode)
sf::st_geometry(res)
}

#' Segment a single line, using lwgeom or rsgeo
#'
#'
#' @inheritParams line_segment
#' @param n_segments The number of segments to divide the line into
#' @family lines
Expand All @@ -236,7 +247,7 @@ line_segment.sfc_LINESTRING <- function(
#' l <- routes_fast_sf[2, ]
#' l_seg2 <- line_segment1(l = l, n_segments = 2)
#' # Test with rsgeo (must be installed):
#' # l_seg2_rsgeo = line_segment1(l = l, n_segments = 2, use_rsgeo = TRUE)
#' # l_seg2_rsgeo = line_segment1(l = l, n_segments = 2)
#' # waldo::compare(l_seg2, l_seg2_rsgeo)
#' l_seg3 <- line_segment1(l = l, n_segments = 3)
#' l_seg_100 <- line_segment1(l = l, segment_length = 100)
Expand All @@ -246,21 +257,17 @@ line_segment.sfc_LINESTRING <- function(
#' plot(sf::st_geometry(l_seg_100), col = seq(nrow(l_seg_100)), lwd = 5)
#' plot(sf::st_geometry(l_seg_1000), col = seq(nrow(l_seg_1000)), lwd = 5)
line_segment1 <- function(
l,
n_segments = NA,
segment_length = NA,
use_rsgeo = NULL
) {
l,
n_segments = NA,
segment_length = NA) {
UseMethod("line_segment1")
}

#' @export
line_segment1.sf <- function(
l,
n_segments = NA,
segment_length = NA,
use_rsgeo = NULL
) {
l,
n_segments = NA,
segment_length = NA) {
if (is.na(n_segments) && is.na(segment_length)) {
rlang::abort(
"`n_segment` or `segment_length` must be set.",
Expand All @@ -275,27 +282,17 @@ line_segment1.sf <- function(
return(l)
}

# Decide whether to use rsgeo or lwgeom, if not set:
if (is.null(use_rsgeo)) {
use_rsgeo <- use_rsgeo(l)
}
res <- line_segment_lwgeom(l, n_segments)

if (use_rsgeo) {
res <- line_segment_rsgeo(l, n_segments)
} else {
res <- line_segment_lwgeom(l, n_segments)
}
res
}
#' @export
line_segment1.sfc_LINESTRING <- function(
l,
n_segments = NA,
segment_length = NA,
use_rsgeo = NULL
) {
l,
n_segments = NA,
segment_length = NA) {
l <- sf::st_as_sf(l)
res <- line_segment1(l, n_segments, segment_length = segment_length, use_rsgeo)
res <- line_segment1(l, n_segments, segment_length = segment_length)
sf::st_geometry(res)
}

Expand All @@ -313,59 +310,52 @@ make_bidirectional <- function(bearing) {
#' @param x List of sf objects to combine
#' @return An sf data frame
#' @family geo
bind_sf = function(x) {
bind_sf <- function(x) {
if (length(x) == 0) stop("Empty list")
geom_name = attr(x[[1]], "sf_column")
# browser()
x = data.table::rbindlist(x, use.names = FALSE)
geom_name <- attr(x[[1]], "sf_column")
x <- data.table::rbindlist(x, use.names = FALSE)
# x = collapse::unlist2d(x, idcols = FALSE, recursive = FALSE)
x[[geom_name]] = sf::st_sfc(x[[geom_name]], recompute_bbox = TRUE)
x = sf::st_as_sf(x)
x[[geom_name]] <- sf::st_sfc(x[[geom_name]], recompute_bbox = TRUE)
x <- sf::st_as_sf(x)
x
}

use_rsgeo <- function(shp) {
rsgeo_installed <- rlang::is_installed("rsgeo", version = "0.1.6")
crs <- sf::st_crs(shp)
is_projected <- !crs$IsGeographic
# if its NA set false
if (is.na(is_projected)) {
warning("CRS is NA, assuming projected")
is_projected <- TRUE
if (!rsgeo_installed) {
warning("rsgeo not installed, using lwgeom")
return(FALSE)
}
should_use_rsgeo <- rsgeo_installed & is_projected
should_use_rsgeo
TRUE
}

line_segment_rsgeo <- function(l, n_segments, segment_length) {
line_segment_rsgeo <- function(l, n_segments) {

crs <- sf::st_crs(l)

# extract geometry and convert to rsgeo
geo <- rsgeo::as_rsgeo(sf::st_geometry(l))

# if n_segments is missing it needs to be calculated
if (is.na(n_segments)) {
l_length <- rsgeo::length_euclidean(geo)
n_segments <- max(round(l_length / segment_length), 1)
}

# segmentize the line strings
res <- rsgeo::line_segmentize(geo, n_segments)
res_rsgeo <- rsgeo::line_segmentize(geo, n_segments)

# make them into sfc_LINESTRING
res <- sf::st_cast(sf::st_as_sfc(res), "LINESTRING")
res <- sf::st_cast(sf::st_as_sfc(res_rsgeo), "LINESTRING")

# give them them CRS
res <- sf::st_set_crs(res, crs)

# calculate the number of original geometries
n <- length(geo)
n_lines <- length(geo)
# create index ids to grab rows from
ids <- rep.int(1:n, rep(n_segments, n))
ids <- rep.int(seq_len(n_lines), n_segments)

# index the original sf object
res_tbl <- sf::st_drop_geometry(l)[ids, ]
res_tbl <- sf::st_drop_geometry(l)[ids, , drop = FALSE]

# assign the geometry column
nrow(res_tbl)

res_tbl[[attr(l, "sf_column")]] <- res

# convert to sf and return
Expand All @@ -374,9 +364,9 @@ line_segment_rsgeo <- function(l, n_segments, segment_length) {
}

line_segment_lwgeom <- function(l, n_segments) {
from_to_sequence = seq(from = 0, to = 1, length.out = n_segments + 1)
from_to_sequence <- seq(from = 0, to = 1, length.out = n_segments + 1)
suppressWarnings({
line_segment_list = lapply(seq(n_segments), function(i) {
line_segment_list <- lapply(seq(n_segments), function(i) {
lwgeom::st_linesubstring(
x = l,
from = from_to_sequence[i],
Expand All @@ -387,3 +377,17 @@ line_segment_lwgeom <- function(l, n_segments) {
res <- bind_sf(line_segment_list)
res
}

#' Vectorised function to calculate number of segments given a max segment length
#' @param line_length The length of the line
#' @param max_segment_length The maximum length of each segment
#' @family lines
#' @export
#' @examples
#' n_segments(50, 10)
#' n_segments(50.1, 10)
#' n_segments(1, 10)
#' n_segments(1:9, 2)
n_segments <- function(line_length, max_segment_length) {
pmax(ceiling(line_length / max_segment_length), 1)
}
Loading

0 comments on commit 1f31f69

Please sign in to comment.