ee_extract() function error

[sooyoung1021]

• rgee version: 1.1.4
• R version: 4.3.2
• Operating System: Windows 11 (22H2)

At submit an issue, please attached the following information of your rgee session:

• [x] You have the Python API installed (from terminal):

  earthengine -h

• [x] You can find the credentials file on your system:

  library(rgee)
  ee_path <- path.expand("~/.config/earthengine/credentials")
  file.exists(ee_path)

  FALSE

• [x] You can run a simple EE command from R:

library(rgee)

# Initialize the Earth Engine module.
ee_Initialize()
ee$Initialize(project='ee-sooyoung1021') # works

# Print metadata for a DEM dataset.
print(ee$Image('USGS/SRTMGL1_003')$getInfo())

$type [1] "Image"

$bands $bands[[1]] $bands[[1]]$id [1] "elevation"

$bands[[1]]$data_type $bands[[1]]$data_type$type [1] "PixelType"

$bands[[1]]$data_type$precision [1] "int"

$bands[[1]]$data_type$min [1] -32768

$bands[[1]]$data_type$max [1] 32767

$bands[[1]]$dimensions [1] 1296001 417601

$bands[[1]]$crs [1] "EPSG:4326"

$bands[[1]]$crs_transform $bands[[1]]$crs_transform[[1]] [1] 0.0002777778

$bands[[1]]$crs_transform[[2]] [1] 0

$bands[[1]]$crs_transform[[3]] [1] -180.0001

$bands[[1]]$crs_transform[[4]] [1] 0

$bands[[1]]$crs_transform[[5]] [1] -0.0002777778

$bands[[1]]$crs_transform[[6]] [1] 60.00014

$version [1] -1

$id [1] "USGS/SRTMGL1_003"

$properties $properties$system:visualization_0_min [1] "0.0"

$properties$type_name [1] "Image"

$properties$keywords [1] "dem" "elevation" "geophysical" "nasa" "srtm" "topography" "usgs"

$properties$thumb [1] "https://mw1.google.com/ges/dd/images/SRTM90_V4_thumb.png"

$properties$description [1] "

The Shuttle Radar Topography Mission (SRTM, see <a href=\"https://onlinelibrary.wiley.com/doi/10.1029/2005RG000183/full\">Farr\net al. 2007)\ndigital elevation data is an international research effort that\nobtained digital elevation models on a near-global scale. This\nSRTM V3 product (SRTM Plus) is provided by NASA JPL\nat a resolution of 1 arc-second (approximately 30m).

This dataset has undergone a void-filling process using open-source data\n(ASTER GDEM2, GMTED2010, and NED), as opposed to other versions that\ncontain voids or have been void-filled with commercial sources.\nFor more information on the different versions see the\n<a href=\"https://lpdaac.usgs.gov/documents/13/SRTM_Quick_Guide.pdf\">SRTM Quick Guide.

Documentation:

• <a href=\"https://lpdaac.usgs.gov/documents/179/SRTM_User_Guide_V3.pdf\">User&#39;s Guide

• <a href=\"https://lpdaac.usgs.gov/documents/13/SRTM_Quick_Guide.pdf\">General Documentation

• <a href=\"https://doi.org/10.1029/2005RG000183\">Algorithm Theoretical Basis Document (ATBD)

Provider: <a href=\"https://cmr.earthdata.nasa.gov/search/concepts/C1000000240-LPDAAC_ECS.html\">NASA / USGS / JPL-Caltech

Bands<table class=\"eecat\"><th scope=\"col\">Name<th scope=\"col\">Descriptionelevation

Elevation

Terms of Use

Unless otherwise noted, images and video on JPL public\nweb sites (public sites ending with a jpl.nasa.gov address) may\nbe used for any purpose without prior permission. For more information\nand exceptions visit the <a href=\"https://www.jpl.nasa.gov/imagepolicy/\">JPL Image Use Policy site.

Suggested citation(s)

• Farr, T.G., Rosen, P.A., Caro, E., Crippen, R., Duren, R., Hensley,\nS., Kobrick, M., Paller, M., Rodriguez, E., Roth, L., Seal, D.,\nShaffer, S., Shimada, J., Umland, J., Werner, M., Oskin, M., Burbank,\nD., and Alsdorf, D.E., 2007, The shuttle radar topography mission:\nReviews of Geophysics, v. 45, no. 2, RG2004, at\n<a href=\"https://doi.org/10.1029/2005RG000183\">https://doi.org/10.1029/2005RG000183.

"

$properties$source_tags [1] "nasa" "usgs"

$properties$visualization_0_max [1] "6000.0"

$properties$title [1] "NASA SRTM Digital Elevation 30m"

$properties$product_tags [1] "srtm" "elevation" "topography" "dem" "geophysical"

$properties$provider [1] "NASA / USGS / JPL-Caltech"

$properties$visualization_0_min [1] "0.0"

$properties$visualization_0_name [1] "Elevation"

$properties$date_range [1] -1 -1

$properties$system:visualization_0_gamma [1] "1.6"

$properties$period [1] 0

$properties$system:visualization_0_bands [1] "elevation"

$properties$provider_url [1] "https://cmr.earthdata.nasa.gov/search/concepts/C1000000240-LPDAAC_ECS.html"

$properties$visualization_0_gamma [1] "1.6"

$properties$sample [1] "https://mw1.google.com/ges/dd/images/SRTM90_V4_sample.png"

$properties$tags [1] "dem" "elevation" "geophysical" "nasa" "srtm" "topography" "usgs"

$properties$system:visualization_0_max [1] "6000.0"

$properties$system:visualization_0_name [1] "Elevation"

$properties$system:asset_size [1] -1

$properties$visualization_0_bands [1] "elevation" Attach your Python (reticulate) configuration:

library(reticulate)
py_config()

python: C:/Users/SooyoungKim/AppData/Local/r-miniconda/envs/rgee/python.exe libpython: C:/Users/SooyoungKim/AppData/Local/r-miniconda/envs/rgee/python38.dll pythonhome: C:/Users/SooyoungKim/AppData/Local/r-miniconda/envs/rgee version: 3.8.19 | packaged by conda-forge | (default, Mar 20 2024, 12:38:07) [MSC v.1929 64 bit (AMD64)] Architecture: 64bit numpy: C:/Users/SooyoungKim/AppData/Local/r-miniconda/envs/rgee/Lib/site-packages/numpy numpy_version: 1.24.4 ee: C:\Users\SOOYOU~1\AppData\Local\R-MINI~1\envs\rgee\lib\site-packages\ee__init__.p

NOTE: Python version was forced by RETICULATE_PYTHON

Description

I am trying to extract daily climate variables per administrative area ("ADM2_EN") in the shapefile from ERA5_LAND/DAILY_AGGR image collection between May1 - 30, 2024. The following code used to work perfectly in the past (like until a month ago?) but now it produces an error. It seems to do with the lines within the function ee_extract() that uses create_triplets() on the Image collections. I can't get my head around why this happened. HelP!

What I Did

start <- "2024-05-01"
end <- "2024-05-30"

# Load the ERA5 image collection
era5 <- ee$ImageCollection('ECMWF/ERA5_LAND/DAILY_AGGR')$filterDate(start, end)
#print(era5)

# Select the variables of interest
era5_dat <- era5 %>%   # data range
  ee$ImageCollection$map(function(x) x$select(c('temperature_2m_min', 
                                                'temperature_2m_max', 
                                                'temperature_2m',
                                                'total_precipitation_sum'))) %>% 
  ee$ImageCollection$toBands()  # from ImageCollection to Image

#bandNames <- era5_dat$bandNames()
#cat("Band names: ",paste(bandNames$getInfo(),collapse=",")) 

# Load nigeria shapefile as sf
nigeria <- read_sf(dsn = here::here("nga_adm_osgof_20190417", 
                                    "nga_admbnda_adm2_osgof_20190417.shp"))
names(nigeria)
plot(nigeria)

crs(nigeria) # WGS 84

# Extract the time series from Image Collection usign the shapefile
ee_ng_era <- ee_extract(x=era5_dat,
                        y=nigeria["ADM2_EN"],
                        sf = F)

Error in ee$Image$reduceRegions(image = img, collection = ee_y, reducer = fun, : RuntimeError: unused argument (image = img) Run `reticulate::py_last_error()` for details.

9. | stop(structure(list(message = "RuntimeError: unused argument (image = img)\n\033[90mRun \033]8;;rstudio:run:reticulate::py_last_error()\a`reticulate::py_last_error()`\033]8;;\a for details.\033[39m", call = ee$Image$reduceRegions(image = img, collection = ee_y, reducer = fun, scale = scale, ...)), class = c("python.builtin.RuntimeError", "python.builtin.Exception", "python.builtin.BaseException", "python.builtin.object", ... -- | --

 Where I think the error happened (within ee_extract()) ```` create_tripplets <- function(img) { img_reduce_regions <- ee$Image$reduceRegions(image = img, collection = ee_y, reducer = fun, scale = scale, ...) ee$FeatureCollection$map(img_reduce_regions, function(f) { ee$Feature$set(f, "imageId", ee$Image$get(img, "system:index")) }) } triplets <- x_ic %>% ee$ImageCollection$map(create_tripplets) %>% ee$ImageCollection$flatten() ```

[ambarja]

@sooyoung1021 please here I have edited some of your script 👇

library(rgee)
library(sf)
ee_Initialize()

# Defined date of extracting data
start <- "2024-05-01"
end <- "2024-05-30"

# Load the ERA5 image collection
variables <- c(
  'temperature_2m_min',
  'temperature_2m_max',
  'temperature_2m',
  'total_precipitation_sum'
  )

# Define the dataset with variables
era5 <- ee$ImageCollection('ECMWF/ERA5_LAND/DAILY_AGGR')$
  filterDate(start, end)$
  select(variables)

# Load nigeria shapefile as sf (https://data.humdata.org/dataset/nigeria-admin-level-2)
nigeria <- read_sf("C:/Users/USER/Downloads/nigeria_admin_level_2/Nigeria_Admin_Level_2.shp")

# Extract the time series from Image Collection usign the shapefile
ee_ng_era <- ee_extract(
  x=era5,
  y=nigeria["StateCode"],
  sf = F)

[sooyoung1021]

Same error still happens. Any idea why? :/

[sooyoung1021]

I asked my other colleague to try and same error happens for him too.

[ambarja]

I asked my other colleague to try and same error happens for him too.

@sooyoung1021 Please, You can share some script reproducible with example data?

[sooyoung1021]

I copy-pasted your script and downloaded the shapefile you used in your example and ran the code. That's when the error got produced.

[ambarja]

I'm closing this issue because there is no clear reproducible example.

[sooyoung1021]

Well I think it's clearly a bug that happens to some people and since it doesn't happen on your end, I don't know how else to provide examples or proof. If you'd like to see the live demo of it happening, would be more than happy to connect virtually and show you.