TopologyException: side location conflict with st_overlaps
mem48 opened this issue · 4 comments
Describe the bug
I am getting an error with the attached data
example.zip
I think this is due to bad data, but I wanted to raise it as an issue because it it a little odd. The error message suggests that something is wrong with the data, but st_is_valid returns TRUE. It also only affects some of the binary predicates but not all.
I think the error is related to a polygon having duplicated coordinates, but I have not been able to recreate the error except with my real data.
This is a plot of the two polygons with the red dot showing the location of the error
To Reproduce
polys = st_read("example.geojson")
st_overlaps(polys)
Error in scan(text = lst[[length(lst)]], quiet = TRUE) :
scan() expected 'a real', got '554110.83121316193.'
Error in (function (msg) :
TopologyException: side location conflict at 210668.20566749386 554110.83121316193. This can occur if the input geometry is invalid.
The only fix I could find is to use st_simplify(polys, dTolerance = 0.0001) It also seems to be sensitive to rounding as converting to text and back again also fixes the error.
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.utf8 LC_CTYPE=English_United Kingdom.utf8 LC_MONETARY=English_United Kingdom.utf8
[4] LC_NUMERIC=C LC_TIME=English_United Kingdom.utf8
time zone: Europe/London
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] targets_1.6.0 sf_1.0-16
loaded via a namespace (and not attached):
[1] utf8_1.2.4 future_1.33.2 generics_0.1.3 class_7.3-22 KernSmooth_2.23-22 lattice_0.22-5
[7] listenv_0.9.1 digest_0.6.35 magrittr_2.0.3 grid_4.3.3 processx_3.8.4 e1071_1.7-14
[13] backports_1.4.1 secretbase_0.4.0 DBI_1.2.2 ps_1.7.6 purrr_1.0.2 fansi_1.0.6
[19] codetools_0.2-19 cli_3.6.2 rlang_1.1.3 units_0.8-5 parallelly_1.37.1 withr_3.0.0
[25] yaml_2.3.8 tools_4.3.3 raster_3.6-26 parallel_4.3.3 dplyr_1.1.4 base64url_1.4
[31] nngeo_0.4.7 globals_0.16.3 exactextractr_0.10.0 vctrs_0.6.5 R6_2.5.1 proxy_0.4-27
[37] lifecycle_1.0.4 classInt_0.4-10 furrr_0.3.1 pkgconfig_2.0.3 callr_3.7.6 terra_1.7-71
[43] pillar_1.9.0 data.table_1.15.4 glue_1.7.0 Rcpp_1.0.12 xfun_0.43 tibble_3.2.1
[49] tidyselect_1.2.1 rstudioapi_0.16.0 knitr_1.46 igraph_2.0.3 compiler_4.3.3 sp_2.1-3
sf::sf_extSoftVersion()
GEOS GDAL proj.4 GDAL_with_GEOS USE_PROJ_H PROJ
"3.11.2" "3.8.2" "9.3.1" "true" "true" "9.3.1"
This is rather issue with input data or GEOS than sf.
library("geos")
polys = sf::read_sf("example.geojson")
v = as_geos_geometry(polys)
geos_is_valid(v)
#> [1] TRUE TRUE
geos_overlaps(v[1], v[2])
#> Error in geos_overlaps(v[1], v[2]) :
#> [1] TopologyException: side location conflict at 210668.20566749386 554110.83121316193.
#> This can occur if the input geometry is invalid.It seems that if we use buffer with a very small value, it also works ok.
Setting precision helps in such cases:
library(sf)
# Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.3.1; sf_use_s2() is TRUE
polys = st_read("example.geojson") |> st_set_precision(1e8)
# Reading layer `example' from data source `/home/edzer/Downloads/example.geojson' using driver `GeoJSON'
# Simple feature collection with 2 features and 0 fields
# Geometry type: POLYGON
# Dimension: XY
# Bounding box: xmin: 210659 ymin: 554065.2 xmax: 210747.8 ymax: 554155.8
# Projected CRS: OSGB36 / British National Grid
st_overlaps(polys)
# Sparse geometry binary predicate list of length 2, where the predicate
# was `overlaps'
# 1: (empty)
# 2: (empty)