extracting data cube values along a trajectory

edzer commented 3 years ago

Here is a nice use case: https://github.com/r-spatial/stars/issues/352

I will look into how to modify st_extract to do this, when the second argument is an sf_time object. Building upon the example referenced, there's something odd with the print method for sftime:

> st_sf_time(traj, traj$time)
Spatiotemporal feature collection with 5 features and 2 fields
geometry type:  POINT
dimension:      XY
bbox:           xmin: -4.852793 ymin: -30.65914 xmax: 9.145356 ymax: -21.05251
CRS:            NA
[1] "1981-09-02" "1981-09-03" "1981-09-04" "1981-09-06" "1981-09-08"
Simple feature collection with 5 features and 3 fields
geometry type:  POINT
dimension:      XY
bbox:           xmin: -4.852793 ymin: -30.65914 xmax: 9.145356 ymax: -21.05251
CRS:            NA
# A tibble: 5 x 4
       x     y time                     geometry
*  <dbl> <dbl> <date>                    <POINT>
1 -0.433 -30.7 1981-09-02 (-0.4329524 -30.65914)
2 -4.85  -21.1 1981-09-03  (-4.852793 -21.05251)
3 -1.06  -30.1 1981-09-04  (-1.061405 -30.11632)
4 -0.880 -26.2 1981-09-06 (-0.8799466 -26.21402)
5  9.15  -23.4 1981-09-08   (9.145356 -23.38446)
> st_extract(z, st_sf_time(traj, traj$time))
stars object with 2 dimensions and 4 attributes
attribute(s):
   sst [°*C]       anom [°*C]        err [°*C]      ice [percent]
 Min.   :16.83   Min.   :-0.1500   Min.   :0.1100   Min.   : NA  
 1st Qu.:17.08   1st Qu.: 0.1200   1st Qu.:0.1200   1st Qu.: NA  
 Median :17.32   Median : 0.3700   Median :0.1600   Median : NA  
 Mean   :17.33   Mean   : 0.3811   Mean   :0.1867   Mean   :NaN  
 3rd Qu.:17.55   3rd Qu.: 0.6100   3rd Qu.:0.2200   3rd Qu.: NA  
 Max.   :17.93   Max.   : 0.9700   Max.   :0.3300   Max.   : NA  
 NA's   :36      NA's   :36        NA's   :36       NA's   :45   
dimension(s):
         from to         offset  delta  refsys point
geometry    1  5             NA     NA      NA  TRUE
time        1  9 1981-09-01 UTC 1 days POSIXct    NA
                                                              values
geometry POINT (-0.4329524 -30.65914),...,POINT (9.145356 -23.38446)
time                                                            NULL

henningte commented 2 years ago

Yes, this now also works for sftime objects! Can we close this issue? Shall I post this also in the sf issue you linked?

library(stars)
#> Loading required package: abind
#> Loading required package: sf
#> Linking to GEOS 3.9.1, GDAL 3.3.2, PROJ 7.2.1; sf_use_s2() is TRUE
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(abind)
library(lubridate)
#> 
#> Attaching package: 'lubridate'
#> The following objects are masked from 'package:base':
#> 
#>     date, intersect, setdiff, union
library(sftime)

# spatiotemporal data from the oceans,
# adapted from a stars vignette
x = c(
  "avhrr-only-v2.19810901.nc",
  "avhrr-only-v2.19810902.nc",
  "avhrr-only-v2.19810903.nc",
  "avhrr-only-v2.19810904.nc",
  "avhrr-only-v2.19810905.nc",
  "avhrr-only-v2.19810906.nc",
  "avhrr-only-v2.19810907.nc",
  "avhrr-only-v2.19810908.nc",
  "avhrr-only-v2.19810909.nc"
)

# see the second vignette:
# install.packages("starsdata", repos = "http://pebesma.staff.ifgi.de", type = "source")
file_list = system.file(paste0("netcdf/", x), package = "starsdata")
(y = read_stars(file_list, quiet = TRUE))
#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".

#> Warning in CPL_read_gdal(as.character(x), as.character(options),
#> as.character(driver), : GDAL Message 1: Recode from UTF-8 to CP_ACP failed with
#> the error: "Invalid argument".
#> stars object with 4 dimensions and 4 attributes
#> attribute(s), summary of first 1e+05 cells:
#>                Min. 1st Qu. Median       Mean 3rd Qu. Max.  NA's
#> sst [°*C]     -1.80   -1.19  -1.05 -0.3201670   -0.20 9.36 13360
#> anom [°*C]    -4.69   -0.06   0.52  0.2299385    0.71 3.70 13360
#> err [°*C]      0.11    0.30   0.30  0.2949421    0.30 0.48 13360
#> ice [percent]  0.01    0.73   0.83  0.7657695    0.87 1.00 27377
#> dimension(s):
#>      from   to         offset  delta  refsys point values x/y
#> x       1 1440              0   0.25      NA    NA   NULL [x]
#> y       1  720             90  -0.25      NA    NA   NULL [y]
#> zlev    1    1          0 [m]     NA      NA    NA   NULL    
#> time    1    9 1981-09-01 UTC 1 days POSIXct    NA   NULL

z <- y %>% adrop()
attr(z, "dimensions")$time$point <- FALSE ## points can't be used for interpolation, set to interval
z
#> stars object with 3 dimensions and 4 attributes
#> attribute(s), summary of first 1e+05 cells:
#>                Min. 1st Qu. Median       Mean 3rd Qu. Max.  NA's
#> sst [°*C]     -1.80   -1.19  -1.05 -0.3201670   -0.20 9.36 13360
#> anom [°*C]    -4.69   -0.06   0.52  0.2299385    0.71 3.70 13360
#> err [°*C]      0.11    0.30   0.30  0.2949421    0.30 0.48 13360
#> ice [percent]  0.01    0.73   0.83  0.7657695    0.87 1.00 27377
#> dimension(s):
#>      from   to         offset  delta  refsys point values x/y
#> x       1 1440              0   0.25      NA    NA   NULL [x]
#> y       1  720             90  -0.25      NA    NA   NULL [y]
#> time    1    9 1981-09-01 UTC 1 days POSIXct FALSE   NULL

### same location but at different times (now with sftime object)
traj <- dplyr::tibble(x = 181,
                      y = 2,
                      ts = c(lubridate::ymd_h("19810901 00") + days(c(1,2,3, 7,8)),
                             lubridate::ymd_h("19810901 00") + days(c(1,2,7,8)) + hours(12))) %>%
  arrange(ts) %>%
  sf::st_as_sf(coords = c("x", "y"), remove = F) %>%
  sftime::st_as_sftime(time_column_name = "ts")

st_extract(z, traj, bilinear = T, interpolate_time = T)
#> Simple feature collection with 9 features and 6 fields
#> Geometry type: POINT
#> Dimension:     XY
#> Bounding box:  xmin: 181 ymin: 2 xmax: 181 ymax: 2
#> CRS:           NA
#>       sst   anom    err ice       time                  ts      geometry
#> 1 28.8725 0.1050 0.1200 NaN 1981-09-02 1981-09-02 00:00:00 POINT (181 2)
#> 2 28.8725 0.1050 0.1200 NaN 1981-09-02 1981-09-02 12:00:00 POINT (181 2)
#> 3 29.1825 0.4150 0.1200 NaN 1981-09-03 1981-09-03 00:00:00 POINT (181 2)
#> 4 29.1825 0.4150 0.1200 NaN 1981-09-03 1981-09-03 12:00:00 POINT (181 2)
#> 5 28.9100 0.1375 0.1275 NaN 1981-09-04 1981-09-04 00:00:00 POINT (181 2)
#> 6 29.4000 0.6200 0.3050 NaN 1981-09-08 1981-09-08 00:00:00 POINT (181 2)
#> 7 29.4000 0.6200 0.3050 NaN 1981-09-08 1981-09-08 12:00:00 POINT (181 2)
#> 8 29.4000 0.6200 0.3050 NaN 1981-09-08 1981-09-09 00:00:00 POINT (181 2)
#> 9      NA     NA     NA  NA       <NA> 1981-09-09 12:00:00 POINT (181 2)

attr(z, "dimensions")$time$point <- TRUE ## time points: are used for interpolation
st_extract(z, traj, bilinear = T, time_column = "ts", interpolate_time = T)
#> Simple feature collection with 9 features and 6 fields
#> Geometry type: POINT
#> Dimension:     XY
#> Bounding box:  xmin: 181 ymin: 2 xmax: 181 ymax: 2
#> CRS:           NA
#>        sst    anom     err ice       time                  ts      geometry
#> 1 28.87250 0.10500 0.12000 NaN 1981-09-02 1981-09-02 00:00:00 POINT (181 2)
#> 2 29.02750 0.26000 0.12000 NaN 1981-09-02 1981-09-02 12:00:00 POINT (181 2)
#> 3 29.18250 0.41500 0.12000 NaN 1981-09-03 1981-09-03 00:00:00 POINT (181 2)
#> 4 29.04625 0.27625 0.12375 NaN 1981-09-03 1981-09-03 12:00:00 POINT (181 2)
#> 5 28.91000 0.13750 0.12750 NaN 1981-09-04 1981-09-04 00:00:00 POINT (181 2)
#> 6 29.40000 0.62000 0.30500 NaN 1981-09-08 1981-09-08 00:00:00 POINT (181 2)
#> 7 29.38250 0.60375 0.43250 NaN 1981-09-08 1981-09-08 12:00:00 POINT (181 2)
#> 8 29.36500 0.58750 0.56000 NaN 1981-09-09 1981-09-09 00:00:00 POINT (181 2)
#> 9       NA      NA      NA  NA       <NA> 1981-09-09 12:00:00 POINT (181 2)

^{Created on 2022-04-29 by the reprex package (v2.0.1)}

Session info

``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.2.0 (2022-04-22 ucrt) #> os Windows 10 x64 (build 19044) #> system x86_64, mingw32 #> ui RTerm #> language (EN) #> collate German_Germany.utf8 #> ctype German_Germany.utf8 #> tz Europe/Berlin #> date 2022-04-29 #> pandoc 2.17.1.1 @ C:/Program Files/RStudio/bin/quarto/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> abind * 1.4-5 2016-07-21 [1] CRAN (R 4.2.0) #> class 7.3-20 2022-01-16 [2] CRAN (R 4.2.0) #> classInt 0.4-3 2020-04-07 [1] CRAN (R 4.2.0) #> cli 3.3.0 2022-04-25 [1] CRAN (R 4.2.0) #> crayon 1.5.1 2022-03-26 [1] CRAN (R 4.2.0) #> DBI 1.1.2 2021-12-20 [1] CRAN (R 4.2.0) #> digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.0) #> dplyr * 1.0.8 2022-02-08 [1] CRAN (R 4.2.0) #> e1071 1.7-9 2021-09-16 [1] CRAN (R 4.2.0) #> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0) #> evaluate 0.15 2022-02-18 [1] CRAN (R 4.2.0) #> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0) #> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0) #> fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.0) #> generics 0.1.2 2022-01-31 [1] CRAN (R 4.2.0) #> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0) #> highr 0.9 2021-04-16 [1] CRAN (R 4.2.0) #> htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.2.0) #> KernSmooth 2.23-20 2021-05-03 [2] CRAN (R 4.2.0) #> knitr 1.38 2022-03-25 [1] CRAN (R 4.2.0) #> lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.2.0) #> lubridate * 1.8.0 2021-10-07 [1] CRAN (R 4.2.0) #> lwgeom 0.2-8 2021-10-06 [1] CRAN (R 4.2.0) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0) #> pillar 1.7.0 2022-02-01 [1] CRAN (R 4.2.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0) #> proxy 0.4-26 2021-06-07 [1] CRAN (R 4.2.0) #> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.0) #> R.cache 0.15.0 2021-04-30 [1] CRAN (R 4.2.0) #> R.methodsS3 1.8.1 2020-08-26 [1] CRAN (R 4.2.0) #> R.oo 1.24.0 2020-08-26 [1] CRAN (R 4.2.0) #> R.utils 2.11.0 2021-09-26 [1] CRAN (R 4.2.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0) #> Rcpp 1.0.8.3 2022-03-17 [1] CRAN (R 4.2.0) #> reprex 2.0.1 2021-08-05 [1] CRAN (R 4.2.0) #> rlang 1.0.2 2022-03-04 [1] CRAN (R 4.2.0) #> rmarkdown 2.13 2022-03-10 [1] CRAN (R 4.2.0) #> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.2.0) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0) #> sf * 1.0-8 2022-04-29 [1] Github (r-spatial/sf@1281482) #> sftime * 0.2.0.9000 2022-04-29 [1] local #> stars * 0.5-5 2021-12-19 [1] CRAN (R 4.2.0) #> stringi 1.7.6 2021-11-29 [1] CRAN (R 4.2.0) #> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.2.0) #> styler 1.7.0 2022-03-13 [1] CRAN (R 4.2.0) #> tibble 3.1.6 2021-11-07 [1] CRAN (R 4.2.0) #> tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.2.0) #> units 0.8-0 2022-02-05 [1] CRAN (R 4.2.0) #> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0) #> vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.0) #> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0) #> xfun 0.30 2022-03-02 [1] CRAN (R 4.2.0) #> yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.0) #> #> [1] C:/Users/henni/AppData/Local/R/win-library/4.2 #> [2] C:/Program Files/R/R-4.2.0/library #> #> ────────────────────────────────────────────────────────────────────────────── ```

edzer commented 2 years ago

Nice! We can also directly pipe the result of st_extract() into sftime:

st_extract(z, traj, bilinear = T, time_column = "ts", interpolate_time = T) |> st_as_sftime()

edzer commented 2 years ago

Shall I post this also in the sf issue you linked?

Please do.

r-spatial / sftime

extracting data cube values along a trajectory #3