Stream networks using R and sf

Stream networks using R and sf

I have a paper in the works that involves data for a few hundred lakes in Nova Scotia, for which I need catchment parameters. That’s a tall order! Automated catchment extraction is possible, but it helps to have a ballpark area to work with. Actually, it’s mission critical to have a ballpark area to work with…650 is just too many lakes to catch all the errors by hand. One of the ways to generate these catchments is using the stream network. I’ll do so using the tidyverse family of packages and sf:

library(tidyverse)
library(sf)

The data I’m using is from Nova Scotia Environment/Nova Scotia Department of Natural Resources' excellent collection of geographic information (the geospatial data directory). Included is a small subset of the water features (lakes) and hydrographic network (rivers) near Lake Major.

lakes <- read_sf("lakes.shp")
rivers <- read_sf("rivers.shp") %>% 
  st_cast("LINESTRING") %>% 
  transmute(river_id = 1:n())

lakes
## Simple feature collection with 6 features and 1 field
## geometry type:  POLYGON
## dimension:      XY
## bbox:           xmin: 456770.4 ymin: 4951163 xmax: 465842.1 ymax: 4964343
## epsg (SRID):    26920
## proj4string:    +proj=utm +zone=20 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs
## # A tibble: 6 x 2
##   feat_id                                                          geometry
##   <chr>                                                       <POLYGON [m]>
## 1 card_set     ((463125.7 4961860, 463140.7 4961858, 463149.7 4961856, 463…
## 2 care_catch   ((459477.3 4964343, 459489.2 4964343, 459495.2 4964340, 459…
## 3 carry_news   ((457335.6 4956697, 457340.5 4956695, 457343.5 4956691, 457…
## 4 carry_result ((460692.9 4957888, 460693.9 4957886, 460696.8 4957880, 460…
## 5 case_contra… ((464473.3 4956212, 464476.1 4956205, 464480.9 4956193, 464…
## 6 case_on      ((458446.9 4958244, 458453.8 4958237, 458456.7 4958233, 458…
rivers
## Simple feature collection with 811 features and 1 field
## geometry type:  LINESTRING
## dimension:      XY
## bbox:           xmin: 455676.1 ymin: 4954527 xmax: 469315.8 ymax: 4966713
## epsg (SRID):    26920
## proj4string:    +proj=utm +zone=20 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs
## # A tibble: 811 x 2
##    river_id                                                        geometry
##  *    <int>                                                <LINESTRING [m]>
##  1        1 (461837.9 4955133, 461835.1 4955126, 461833.9 4955121, 461833.…
##  2        2 (461171.9 4954904, 461167.3 4954905, 461138.1 4954939, 461110.…
##  3        3 (460825 4955149, 460866.6 4955016, 460867.6 4955013, 460868.8 …
##  4        4 (460911.9 4955137, 460909.5 4955137, 460907.7 4955138, 460904 …
##  5        5 (460512.5 4955185, 460493.8 4954909, 460495.1 4954865, 460495.…
##  6        6 (462494.3 4955272, 462489.3 4955271, 462476.3 4955268, 462431 …
##  7        7                            (459961.3 4955396, 459984.1 4955397)
##  8        8 (461711.8 4955615, 461714.6 4955605, 461722.1 4955579, 461728.…
##  9        9 (458104.5 4955291, 458102.6 4955296, 458100.7 4955302, 458100.…
## 10       10 (457870.3 4955693, 457884.6 4955704, 457888.4 4955707, 457888.…
## # … with 801 more rows

An important bit here is that I’ve made sure that rivers is a LINESTRING…(previously it was a MULTILINESTRING). This is important later when we extract the nodes. I’ve given each river an ID as well, which also comes in handy later. Plotted, these look like this:

I’ve highlighted East Lake, which is the lake I’ll use as an example to generate an approximate catchment. The basic approach is: follow the rivers that come into the lake upstream until there are no more rivers!

We’ll start with “the rivers that come into the lake”. Actually, even simpler: “the rivers that touch the edge of the lake”. We can find these with the binary predicate st_touches().

lake <- lakes %>% filter(feat_id == "carry_result")
lake_border_segments <- rivers %>% 
  filter(st_touches(geometry, st_boundary(lake), sparse = FALSE))

plot(lake$geometry)
plot(lake_border_segments$geometry, col = "red", add = T)

An important feature of a hydrographic network is that the features must be ordered in the right direction. That is, the network is only useful if the segments are all defined in the direction of flow. This means that the “first” node in the linestring is always upstream of the “last” node in a segment. We can extract nodes by using st_cast(x, "POINT"), but it’s a little tricky to generalize this to a per-feature basis. For exactly one feature, a function like this works:

extract_node_single <- function(x, n) {
  # extract the nodes
  nodes <- suppressWarnings(st_cast(x, "POINT"))
  
  # lets you specify n = -1 for the last node
  if (n < 0) {
    n <- nrow(nodes) + 1 + n
  }
  
  # ensures that the output is always length(n)
  if (n > nrow(nodes)) {
    sfc <-  st_sfc(st_point(), crs = st_crs(x))
    st_as_sf(tibble(geometry = rep(sfc, length(n))))
  } else {
    nodes[n, ]
  }
}

lake_border_segments_start <- map(
  seq_len(nrow(lake_border_segments)), 
  ~extract_node_single(lake_border_segments[.x, ], 1)
) %>% 
  do.call(rbind, .)

plot(c(lake$geometry, lake_border_segments$geometry))
plot(lake_border_segments$geometry, col = "red", add = T)
plot(lake_border_segments_start$geometry, col = "red", add = T)

I took a few liberties with this function. Notably, I made sure that it always has an output of predictable length. This is important, because when we use it we need to be able to trust that the features will line up. Second, I let negative indices denote “from the end”. This is a bit like stringr::str_sub() and Python indexing, and it’s useful as we also need to know the last node of each feature.

As written, it only works for a one-row sf object. We can generalize it using purrr::map2() so that we can pass any size of sf object in. Because purrr::map2() recycles x and n to a common length, extract_node() is properly vectorized on both.

extract_node <- function(x, n) {
  nodes_single <- map2(
    seq_len(nrow(x)), n, 
    ~extract_node_single(x[.x, ], n = .y)
  )
  do.call(rbind, nodes_single)
}

With this, we can extract the end nodes more readily:

lake_border_segments_end <- extract_node(lake_border_segments, -1)

plot(c(lake$geometry, lake_border_segments$geometry))
plot(lake_border_segments$geometry, col = "red", add = T)
plot(lake_border_segments_end$geometry, col = "red", add = T)

From here, we can at the very least find the outlet of the lake. I happen to know it’s at the south, but from a “segments in hydrographic network” standpoint, it’s a segment outside the lake boundary that is touching the lake boundary whose first point intersects the lake boundary (note that this works because the water layer and the hydrographic network were generated together, so segments are already broken along the lake boundary). I use st_difference() to remove the segments inside the lake.

outlet <- lake_border_segments %>% 
  st_difference(lake) %>% 
  extract_node(1) %>% 
  st_intersection(st_boundary(lake))

plot(lake$geometry)
plot(outlet$geometry, col = "red", add = T)

We’re getting there! The outlet is important because all the other segments must therefore be inlets, which is what we want to follow. The act of “following” requires a heavy amount of lookup: for each segment, we’ll need to find all the other segments in the network that also touch that segment. The lookup doesn’t take long with this tiny dataset, but for the whole province this is incredibly time-consuming. To make this as efficient as possible, we can cache which segments touch which other segments using a unary st_touches(obj). It generates a list of indices, so that for any index i we can use obj[result[[i]], ] to find all the neighbouring segments of obj[i, ].

neighbouring_segment_lookup <- st_touches(rivers, sparse = TRUE)
neighbouring_segment_lookup[[1]]
## [1] 6 8

Finally, we have all the pieces to make an upstream segments function. I’m using a recursive approach…I’m sure there’s a more efficient way, but this seems to perform reasonably well for the whole province (650 lakes in about an hour), so I didn’t bother to optimise.

upstream_segments <- function(x, recursion_limit = 100) {
  if (recursion_limit == 0) {
    message("Recursion limit reached!")
    return(x)
  }
  
  touching_segs <- rivers[neighbouring_segment_lookup[[x$river_id]], ]
  is_upstream <- st_intersects(
    extract_node(x, 1), 
    extract_node(touching_segs, -1), 
    sparse = FALSE
  )
  upstream_segs <- touching_segs[is_upstream, ]
  
  if (nrow(upstream_segs) == 0) {
    x
  } else {
    upstream_of_upstream <- map(
      seq_len(nrow(upstream_segs)), 
      ~upstream_segments(upstream_segs[.x, ], recursion_limit - 1)
    )

    do.call(rbind, c(list(x), upstream_of_upstream))
  }
}

The general approach is (1) locate all the touching segments, (2) only use touching segments whose last node intersects the first node of the input, and (3) for all of those, locate the upstream segments and bind the result together. I keep track of the recursion_limit in case I did something wrong (likely when constructing the function), and because it helped me make an animation of the process below.

Let’s see it in action! Picking one of the segments, does it work!?

lake_upstream <- upstream_segments(lake_border_segments[6, ])
plot(lake_upstream$geometry)
plot(lake$geometry, add = T)
plot(lake_border_segments[6, ], col = "red", add = T)

Cool! To generate the whole network, we need to do this for both inlets, which we can find by st_difference()ing out the lake and removing the outlet.

lake_inlets <- lake_border_segments %>% 
  st_difference(lake) %>% 
  select(-feat_id) %>% 
  filter(st_disjoint(geometry, outlet, sparse = FALSE)) 

lake_upstream_all <- map(
  seq_len(nrow(lake_inlets)), 
  ~upstream_segments(lake_inlets[.x, ])
) %>% 
  do.call(rbind, .)

plot(lake_upstream_all$geometry)
plot(lake$geometry, add = T)

It takes about a second, but it works! This is a few kilometers wide and finished in 100 levels of recursion…for reference, the largest network in the province took about 10 seconds and took about 2,000 levels of recursion.

We can use the recursion limit to visualize the process. Using animation.hook='gifski' in my knitr chunk options, this is reasonably straightforward:

for (i in 0:50) {
  plot(lake_upstream_all$geometry, main = paste("recursion limit:", i))
  plot(lake$geometry, add = T)
  
  map(
    seq_len(nrow(lake_inlets)), 
    ~upstream_segments(lake_inlets[.x, ], recursion_limit = i)
  ) %>% 
    do.call(rbind, .) %>% 
    pull(geometry) %>% 
    plot(col = "red", add = T)
}

There is definitely room for optimization, but it’s a whole lot easier than doing it by hand!

Avatar
Dewey Dunnington
Geoscientist, Programmer, Educator