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mukey.wcs(): fix areas containing all NoData and resolution for AOI at edge of WCS extent #306

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merged 6 commits into from
Oct 27, 2023
Merged

mukey.wcs(): fix areas containing all NoData and resolution for AOI at edge of WCS extent #306

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b957c55
fix for #304
brownag Sep 30, 2023
3f79d36
set layer name first
brownag Sep 30, 2023
3cc97a9
Fix for slight resolution offsets due to non-integer extent for #304
brownag Sep 30, 2023
b596292
Merge branch 'master' into fix304
brownag Oct 1, 2023
e83b7a3
extend to input geometry, downgrade warnings
brownag Oct 1, 2023
1e9521f
Merge branch 'master' into fix304
brownag Oct 3, 2023
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43 changes: 27 additions & 16 deletions R/mukey-WCS.R
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Original file line number Diff line number Diff line change
Expand Up @@ -172,6 +172,8 @@ mukey.wcs <- function(aoi, db = c('gNATSGO', 'gSSURGO', 'RSS', 'STATSGO', 'PR_SS
silent = TRUE
)

if (!quiet) cat("\n")

if (inherits(dl.try, 'try-error')) {
message('bad WCS request')
return(dl.try)
Expand All @@ -185,20 +187,34 @@ mukey.wcs <- function(aoi, db = c('gNATSGO', 'gSSURGO', 'RSS', 'STATSGO', 'PR_SS
stop('result is not a valid GeoTIFF', call. = FALSE)
}

# warn about requested v.s. received grid dimensions
if (round((ymax2 - ymin) / res) != nrow(r))
warning("expected ", (ymax2 - ymin) / res, " rows, received ", nrow(r), "; Y resolution may be affected. Try requesting a smaller extent.", call. = FALSE)
if (round((xmax2 - xmin) / res) != ncol(r))
warning("expected ", (xmax2 - xmin) / res, " columns, received ", ncol(r), "; X resolution may be affected. Try requesting a smaller extent.", call. = FALSE)
test_y <- round((ymax2 - ymin) / res) != nrow(r)
test_x <- round((xmax2 - xmin) / res) != ncol(r)

# fix requested vs. received grid dimensions
if (test_x || test_y) {
if (test_x)
message("Request partially outside boundary of coverage source data: expected ",
(xmax2 - xmin) / res, " columns, received ", ncol(r))
if (test_y)
message("Request partially outside boundary of coverage source data: expected ",
(ymax2 - ymin) / res, " rows, received ", nrow(r))

# fix extent of result due to rounding error/incomplete pixels at edges of map
rex <- terra::ext(r)
terra::ext(r) <- terra::ext(c(rex[1], rex[1] + ncol(r) * res, rex[3], rex[3] + nrow(r) * res))

# extend to input extent
r <- terra::extend(r, terra::ext(c(xmin, xmax2, ymin, ymax2)))
}

## TODO: is this needed?
## TODO: is this needed? (yes, still needed; AGB 2023/09/30)
## '0' is returned by the WCS sometimes -- never valid for MUKEY
r <- terra::classify(r, matrix(c(0, var.spec$na,
NA, var.spec$na,
NaN, var.spec$na), ncol = 2, byrow = TRUE), include.lowest = TRUE)


# load all values into memory
terra::values(r) <- terra::values(r)
terra::set.values(r)

# specification of NODATA
# this doesn't make it through the WCS
Expand All @@ -209,17 +225,12 @@ mukey.wcs <- function(aoi, db = c('gNATSGO', 'gSSURGO', 'RSS', 'STATSGO', 'PR_SS
# remove tempfile
unlink(tf)

## TODO: use terra::as.factor()
# build RAT
# NB: unique() takes na.rm argument on terra >1.5-21 <https://github.com/rspatial/terra/issues/561>
uids <- na.omit(terra::unique(r)[[1]])
rat <- data.frame(ID = uids,
mukey = uids)
levels(r)[[1]] <- rat

# set layer name in object
names(r) <- 'mukey'

# build RAT
r <- terra::as.factor(r)

# and as an attribute
attr(r, 'layer name') <- var.spec$desc

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