Jonathan V. Solórzano
Reputation: 5620
How to plot an image from a `sits` cube
I recently tried to use the sits package to do some classifications based on image time-series in R. Following the instructions in the SITS book (https://e-sensing.github.io/sitsbook/earth-observation-data-cubes.html) I ran the following code, but I am unable to plot an image. I am using the open data collection in AWS to get the data, so there should be no problem to obtain the data. Anyone knows if this is a bug or I am missing something in my code?
library(sits)
# Get data
s2_15QYU_cube <- sits_cube(
source = "AWS",
collection = "SENTINEL-S2-L2A-COGS",
tiles = "15QYU",
bands = c("B08", "B04", "B03", "CLOUD"),
start_date = "2019-02-01",
end_date = "2019-02-28"
)
# see dates in time series
sits_timeline(s2_15QYU_cube)
# See an image
s2_15QYU_cube |>
# dplyr::filter(tile == "15QYU") |>
plot(red = "B08",
green = "B04",
blue = "B03",
date = "2019-02-12")
This is the error I am obtaining after running the final line.
Error in CPL_read_gdal(as.character(x), as.character(options), as.character(driver), :
trying to read a band that is not present
In addition: Warning messages:
1: In FUN(X[[i]], ...) :
st_apply on x/y dimensions applied to downsampled image(s)
2: In CPL_read_gdal(as.character(x), as.character(options), as.character(driver), :
GDAL Error 5: /vsicurl/https://sentinel-cogs.s3.us-west-2.amazonaws.com/sentinel-s2-l2a-cogs/15/Q/YU/2019/2/S2B_15QYU_20190212_0_L2A/B04.tif: GDALDataset::GetRasterBand(2) - Illegal band #
The same code seems to work in @aldo_tapia session (thanks for the test) and I am sure I have an active connection to internet, so I am posting my session info to see if the error might be caused by some package version issues.
─ Session info ───────────────────────────────────────────────
setting value
version R version 4.2.2 (2022-10-31 ucrt)
os Windows 10 x64 (build 22621)
system x86_64, mingw32
ui RStudio
language (EN)
collate Spanish_Mexico.utf8
ctype Spanish_Mexico.utf8
tz America/Mexico_City
date 2023-01-20
rstudio 2022.12.0+353 Elsbeth Geranium (desktop)
pandoc NA
─ Packages ───────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.2.0)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.2)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.2.0)
class 7.3-20 2022-01-16 [2] CRAN (R 4.2.2)
classInt 0.4-8 2022-09-29 [1] CRAN (R 4.2.2)
cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.2)
clipr 0.8.0 2022-02-22 [1] CRAN (R 4.2.2)
codetools 0.2-18 2020-11-04 [2] CRAN (R 4.2.2)
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.2)
crosstalk 1.2.0 2021-11-04 [1] CRAN (R 4.2.2)
curl 5.0.0 2023-01-12 [1] CRAN (R 4.2.2)
data.table 1.14.6 2022-11-16 [1] CRAN (R 4.2.2)
DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.2)
dichromat 2.0-0.1 2022-05-02 [1] CRAN (R 4.2.0)
digest 0.6.31 2022-12-11 [1] CRAN (R 4.2.2)
dplyr 1.0.10 2022-09-01 [1] CRAN (R 4.2.2)
e1071 1.7-12 2022-10-24 [1] CRAN (R 4.2.2)
fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.2)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.2)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.2)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.2)
htmltools 0.5.4 2022-12-07 [1] CRAN (R 4.2.2)
htmlwidgets 1.6.1 2023-01-07 [1] CRAN (R 4.2.2)
httr 1.4.4 2022-08-17 [1] CRAN (R 4.2.2)
jsonlite 1.8.4 2022-12-06 [1] CRAN (R 4.2.2)
KernSmooth 2.23-20 2021-05-03 [2] CRAN (R 4.2.2)
lattice 0.20-45 2021-09-22 [2] CRAN (R 4.2.2)
leafem 0.2.0 2022-04-16 [1] CRAN (R 4.2.2)
leaflet 2.1.1 2022-03-23 [1] CRAN (R 4.2.2)
leafsync 0.1.0 2019-03-05 [1] CRAN (R 4.2.2)
lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.2)
lubridate 1.9.0 2022-11-06 [1] CRAN (R 4.2.2)
lwgeom 0.2-11 2023-01-14 [1] CRAN (R 4.2.2)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.2)
pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.2)
png 0.1-8 2022-11-29 [1] CRAN (R 4.2.2)
proxy 0.4-27 2022-06-09 [1] CRAN (R 4.2.2)
purrr 1.0.1 2023-01-10 [1] CRAN (R 4.2.2)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.2)
raster 3.6-14 2023-01-16 [1] CRAN (R 4.2.2)
RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.2.0)
Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.1)
rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.2)
rstac 0.9.2 2023-01-20 [1] CRAN (R 4.2.2)
rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.2)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.2)
sf 1.0-9 2022-11-08 [1] CRAN (R 4.2.2)
sits * 1.2.0 2022-11-16 [1] CRAN (R 4.2.2)
slider 0.3.0 2022-11-16 [1] CRAN (R 4.2.2)
sp 1.6-0 2023-01-19 [1] CRAN (R 4.2.2)
stars 0.6-0 2022-11-21 [1] CRAN (R 4.2.2)
terra 1.6-53 2023-01-17 [1] CRAN (R 4.2.2)
tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.2)
tidyr 1.2.1 2022-09-08 [1] CRAN (R 4.2.2)
tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.2)
timechange 0.2.0 2023-01-11 [1] CRAN (R 4.2.2)
tmap 3.3-3 2022-03-02 [1] CRAN (R 4.2.2)
tmaptools 3.1-1 2021-01-19 [1] CRAN (R 4.2.2)
units 0.8-1 2022-12-10 [1] CRAN (R 4.2.2)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.2)
vctrs 0.5.0 2022-10-22 [1] CRAN (R 4.2.2)
viridisLite 0.4.1 2022-08-22 [1] CRAN (R 4.2.2)
warp 0.2.0 2020-10-21 [1] CRAN (R 4.2.2)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.2)
XML 3.99-0.13 2022-12-04 [1] CRAN (R 4.2.2)
yaml 2.3.6 2022-10-18 [1] CRAN (R 4.2.2)
───────────────────────────────────────────────────────────────────────
Upvotes: 0
Views: 110
Answers (2)
Jonathan V. Solórzano
Reputation: 5620
This was indeed a bug. I wrote to the developers and it is now fixed in version v1.2.0-3. To install this version, use: devtools::install_github("e-sensing/sits").
Upvotes: 0
aldo_tapia
Reputation: 1228
It should be a connection error. It's working fine:
library(sits)
# Get data
s2_15QYU_cube <- sits_cube(
source = "AWS",
collection = "SENTINEL-S2-L2A-COGS",
tiles = "15QYU",
bands = c("B08", "B04", "B03", "CLOUD"),
start_date = "2019-02-01",
end_date = "2019-02-28"
)
# see dates in time series
sits_timeline(s2_15QYU_cube)
# See an image
s2_15QYU_cube |>
# dplyr::filter(tile == "15QYU") |>
plot(red = "B08",
green = "B04",
blue = "B03",
date = "2019-02-12")
Session info:
─ Session info ───────────────────────────────────────────────────────
setting value
version R version 4.2.0 (2022-04-22)
os macOS Monterey 12.5
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Santiago
date 2023-01-20
rstudio 2022.12.0+353 Elsbeth Geranium (desktop)
pandoc 2.18 @ /usr/local/bin/pandoc
─ Packages ───────────────────────────────────────────────────────────
package * version date (UTC) lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.0)
cli 3.6.0 2023-01-09 [1] CRAN (R 4.2.0)
colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.0)
data.table 1.14.6 2022-11-16 [1] CRAN (R 4.2.0)
DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0)
dplyr 1.0.9 2022-04-28 [1] CRAN (R 4.2.0)
fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.0)
lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.0)
lubridate 1.8.0 2021-10-07 [1] CRAN (R 4.2.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0)
pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.0)
rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.0)
rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.0)
scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
sits * 1.2.0 2022-11-16 [1] CRAN (R 4.2.0)
tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.0)
tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.2.0)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0)
vctrs 0.5.1 2022-11-16 [1] CRAN (R 4.2.0)
writexl 1.4.0 2021-04-20 [1] CRAN (R 4.2.0)
yaml 2.3.6 2022-10-18 [1] CRAN (R 4.2.0)
zoo 1.8-11 2022-09-17 [1] CRAN (R 4.2.0)
[1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
──────────────────────────────────────────────────────────────────────
Upvotes: 1
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