ESA Landcover tile mapping issue

[karpfen]

I encountered a bug when calculating the ESA Landcover indicator for a portfolio that spans multiple tiles and years. The package downloads the correct tifs and builds the tileindex GPKG as expected, but upon reading the tiles within calc_indicators, it selects the wrong ones. Then it reports that the polygons and tiles do not overlap and returns NA rather than the expected landcovers.

I managed to trace the error back to this code block:

mapme.biodiversity/R/calc_indicators.R

Lines 150 to 175 in babe3d0

	} else { # some tiles share the same bboxes, and others do not, needs proper merging
	# We assume here that the tiles present in tileindex have a temporal dimension.
	# Thus each timestep should end up in its own layer. Different tiles from
	# the same timestep should be spatially merged. We want to avoid merging
	# different tile from different timesteps. We thus assume some regularity
	# in how the name of a raster file expresses its temporal dimension.
	# With this assumption, we can expect the files in tindex to be ordered.
	# Thus we retrive the index of all files sharing the same bbox and assume
	# that they belong to different timesteps. The files in between these
	# indices thus belong to the previous timestep and we can merge these
	# as a vrt and later join the bands. We always assign the name of the
	# first file as the layername.
	unique_bboxes <- unique(unlist(all_bboxes))
	layer_index <- which(all_bboxes == unique_bboxes[[1]])
	temporal_gap <- layer_index[2] - layer_index[1] - 1
	out <- lapply(layer_index, function(j) {
	target_files <- tindex$location[j:(j + temporal_gap)]
	org_filename <- basename(target_files[1])
	filename <- tools::file_path_sans_ext(org_filename)
	vrt_name <- tempfile(pattern = sprintf("vrt_%s.vrt", filename))
	tmp <- terra::vrt(target_files, filename = vrt_name)
	names(tmp) <- org_filename
	tmp
	})
	out <- do.call(c, out)
	}

However, I was not able to fix it yet. I'm also afraid to break something else in the process, so I'd prefer to look at this together once you're back in business, @goergen95.

Heres a reprex of what I mean:

library(sf)
library(mapme.biodiversity)

polys <- data.frame (
  id = 1:2,
  geom = c("Polygon ((20.62472622642718889 -17.96824385542232605, 20.62496802397372875 -17.98457342071599641, 20.63657430620789413 -17.98411345363312464, 20.6416520546853377 -17.96709382912841946, 20.62472622642718889 -17.96824385542232605))",
           "Polygon ((-80.95285139309206102 34.04564701142924577, -80.95140060781277214 34.02841503501579723, -80.93785994520627014 34.0312204790189341, -80.94172870595097891 34.04404418455595049, -80.95285139309206102 34.04564701142924577))"
           )
)

polys <- st_as_sf(polys, wkt = "geom", crs = 4326)

pf <- init_portfolio(
    polys,
    2015:2016,
    outdir = "location1",
    verbose = TRUE) %>%
  get_resources("esalandcover")

inds <- calc_indicators(pf, "landcover")
inds$landcover # landcover for one polygon is missing

pf2 <- init_portfolio(
    polys,
    2015,
    outdir = "location2",
    verbose = TRUE) %>%
  get_resources("esalandcover")

inds2 <- calc_indicators(pf2, "landcover")
inds2$landcover # correct result

sessionInfo()

R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: Europe/Berlin
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] purrr_1.0.2              mapme.biodiversity_0.4.0 sf_1.0-14               

loaded via a namespace (and not attached):
 [1] s2_1.1.4           future_1.33.0      tidyr_1.3.0        utf8_1.2.4         generics_0.1.3     class_7.3-22       KernSmooth_2.23-22 stringi_1.7.12     SPEI_1.8.1        
[10] lattice_0.21-9     listenv_0.9.0      digest_0.6.33      magrittr_2.0.3     lmomco_2.4.11      grid_4.3.1         timechange_0.2.0   plyr_1.8.9         e1071_1.7-13      
[19] backports_1.4.1    reshape_0.8.9      DBI_1.1.3          httr_1.4.7         fansi_1.0.5        scales_1.2.1       codetools_0.2-19   cli_3.6.1          rlang_1.1.1       
[28] units_0.8-4        parallelly_1.36.0  munsell_0.5.0      withr_2.5.2        Lmoments_1.3-1     parallel_4.3.1     tools_4.3.1        lmom_3.0           checkmate_2.2.0   
[37] dplyr_1.1.3        colorspace_2.1-0   ggplot2_3.4.3      globals_0.16.2     curl_5.1.0         vctrs_0.6.3        R6_2.5.1           zoo_1.8-12         proxy_0.4-27      
[46] lifecycle_1.0.4    lubridate_1.9.3    classInt_0.4-10    stringr_1.5.0      MASS_7.3-60        furrr_0.3.1        pkgconfig_2.0.3    progressr_0.14.0   terra_1.7-55      
[55] pillar_1.9.0       TLMoments_0.7.5.3  gtable_0.3.4       glue_1.6.2         Rcpp_1.0.11        tibble_3.2.1       tidyselect_1.2.0   rstudioapi_0.15.0  goftest_1.2-3     
[64] wk_0.9.0           compiler_4.3.1