Re: [R-sig-Geo] Issue with st_warp, gdal and NAs
Dear Julian, you can do that by passing a non-NA value as no_data_value, e.g. by ag3 <- st_warp(src = s1, dest = st_as_stars(st_bbox(s1), dx = 1, dy = 1), use_gdal = TRUE, method = "average", no_data_value = -) On 16/07/2021 12:17, Julian M. Burgos wrote: Dear list, My apologies for posting this again. I am not sure if it went through the first time. I am having a bit of trouble using st_warp() to aggregate star objects with the option "use_gdal = TRUE". I am using the "average" method, and I want cells with NA values to be ignored when computing the averages. To demonstrate, I will make a small raster for testing, and will include cells with NA values: #- library(raster) # Create raster for testing myfile <- "~/myraster.tif" myraster <- raster(xmn = 0, ymn = 0, xmx = 10, ymx = 10, resolution = 0.1, crs = 4326, vals = sample(1:20, size = 1, replace = TRUE)) myraster[sample(1:1, 200)] <- NA writeRaster(myraster, filename = myfile, overwrite = TRUE) #- With the raster package, I can aggregate the cells ignoring the NA values like this: r1 <- raster(myfile) ag1 <- raster::aggregate(x = raster(myfile), fact = 10, fun = mean, na.rm = TRUE) ...which is what I want. I can also aggregate the cells including the NAs, like this: ag2 <- raster::aggregate(x = raster(myfile), fact = 10, fun = mean, na.rm = FALSE) which produces a raster with a lots of gaps. Now, to do a similar aggregation with the stars package I can do this: s1 <- read_stars(myfile) ag3 <- st_warp(src = s1, dest = st_as_stars(st_bbox(s1), dx = 1, dy = 1), use_gdal = TRUE, method = "average") The resulting raster (ag3) has gaps like ag2, which means that the NAs are not being ignored when computing the averages. With use_gdal_TRUE and method="average" we are using gdalwarp with the average resampling method, which according to the documentation "computes the weighted average of all non-NODATA contributing pixels.". So I guess the problem is that the NAs are not being recognized as NODATA pixels. Does anybody know how to solve this? Many thanks, Julian -- Edzer Pebesma Institute for Geoinformatics Heisenbergstrasse 2, 48151 Muenster, Germany Phone: +49 251 8333081 ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
[R-sig-Geo] Issue with st_warp, gdal and NAs
Dear list, My apologies for posting this again. I am not sure if it went through the first time. I am having a bit of trouble using st_warp() to aggregate star objects with the option "use_gdal = TRUE". I am using the "average" method, and I want cells with NA values to be ignored when computing the averages. To demonstrate, I will make a small raster for testing, and will include cells with NA values: #- library(raster) # Create raster for testing myfile <- "~/myraster.tif" myraster <- raster(xmn = 0, ymn = 0, xmx = 10, ymx = 10, resolution = 0.1, crs = 4326, vals = sample(1:20, size = 1, replace = TRUE)) myraster[sample(1:1, 200)] <- NA writeRaster(myraster, filename = myfile, overwrite = TRUE) #- With the raster package, I can aggregate the cells ignoring the NA values like this: r1 <- raster(myfile) ag1 <- raster::aggregate(x = raster(myfile), fact = 10, fun = mean, na.rm = TRUE) ...which is what I want. I can also aggregate the cells including the NAs, like this: ag2 <- raster::aggregate(x = raster(myfile), fact = 10, fun = mean, na.rm = FALSE) which produces a raster with a lots of gaps. Now, to do a similar aggregation with the stars package I can do this: s1 <- read_stars(myfile) ag3 <- st_warp(src = s1, dest = st_as_stars(st_bbox(s1), dx = 1, dy = 1), use_gdal = TRUE, method = "average") The resulting raster (ag3) has gaps like ag2, which means that the NAs are not being ignored when computing the averages. With use_gdal_TRUE and method="average" we are using gdalwarp with the average resampling method, which according to the documentation "computes the weighted average of all non-NODATA contributing pixels.". So I guess the problem is that the NAs are not being recognized as NODATA pixels. Does anybody know how to solve this? Many thanks, Julian -- Julian Mariano Burgos, PhD Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/ Marine and Freshwater Research Institute Botnsjávarsviðs / Demersal Division Fornubúðir 5, IS-220 Hafnarfjörður, Iceland www.hafogvatn.is Sími/Telephone : +354-5752037 Netfang/Email: julian.bur...@hafogvatn.is ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
[R-sig-Geo] Issue with st_warp, gdal and NAs
Dear list, I am having a bit of trouble using st_warp() to aggregate star objects with the option "use_gdal = TRUE". I am using the "average" method, and I want cells with NA values to be ignored. To demonstrate, I will make a small raster for testing, and will include cells with NA values: #- library(raster) # Create raster for testing myfile <- "~/myraster.tif" myraster <- raster(xmn = 0, ymn = 0, xmx = 10, ymx = 10, resolution = 0.1, crs = 4326, vals = sample(1:20, size = 1, replace = TRUE)) myraster[sample(1:1, 200)] <- NA writeRaster(myraster, filename = myfile, overwrite = TRUE) #- With the raster package, I can aggergate the cells ignoring the NA values like this: r1 <- raster(myfile) ag1 <- raster::aggregate(x = raster(myfile), fact = 10, fun = mean, na.rm = TRUE) ...which is what I want. I can also aggregate the cells including the NAs, like this: ag2 <- raster::aggregate(x = raster(myfile), fact = 10, fun = mean, na.rm = FALSE) which produces a raster with a lots of gaps. Now, to do a similar aggregation with the stars package I can do this: s1 <- read_stars(myfile) ag3 <- st_warp(src = s1, dest = st_as_stars(st_bbox(s1), dx = 1, dy = 1), use_gdal = TRUE, method = "average") The resulting raster (ag3) has gaps like ag2, which means that the NAs are not being ignored when computing the averages. With use_gdal_TRUE and method="average" we are using gdalwarp with the average resampling method, which according to the documentation "computes the weighted average of all non-NODATA contributing pixels.". So I guess the problem is that the NAs are not being recognized as NODATA pixels. Does anybody know how to solve this? Many thanks, Julian -- Julian Mariano Burgos, PhD Hafrannsóknastofnun, rannsókna- og ráðgjafarstofnun hafs og vatna/ Marine and Freshwater Research Institute Botnsjávarsviðs / Demersal Division Fornubúðir 5, IS-220 Hafnarfjörður, Iceland www.hafogvatn.is Sími/Telephone : +354-5752037 Netfang/Email: julian.bur...@hafogvatn.is ___ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
