runMrt() returns nothing #137
Description
Hello Florian and Matteo @MatMatt !
Here is Corrado.
I've been having issues with the complete download of requested images through runGdal(): sometimes it downloads less images than those requested (both in "raw" and "processed" folders), probably due to my slow connection. I found a workaround by using getHdf(), which is able (I guess) to download only those .hdf files that are missing in the "raw" folder.
After that, as far as I understand, 'runMtr()' is needed to process these .hdf files into geoTIFFs. Sadly, it returns empty characters (as many as the selected SDS layers), while printing something about "mrtmosaic" and "resample".
Here is a reproducible code:
library(raster)
library(terra)
library(MODIS)
## setting modis options
lap <- file.path(tempdir(), "MODIS")
MODISoptions(
localArcPath = lap,
outDirPath = file.path(lap, "PROCESSED"),
dlmethod = "auto", MODISserverOrder = c("LPDAAC", "LAADS", "NSIDC"))
MODIS:::checkEarthdataLogin() ## TRUE
getCollection("MOD10A1F", forceCheck = TRUE) ##"061" ok
## setting the scene
limits <- c(5.9 , 6.2, 44.6 , 44.8)
start <- "2003-01-04"
end <- "2003-01-11"
## downloading HDF files
getHdf(product=c('MOD10A1F'), collection = "061",
extent=extent(limits),
begin=start, end=end,
outProj= "EPSG:4326")
## importing them
hdf_files <- list.files(path= file.path(lap, "MODIS/MOD10A1F.061"), pattern =".hdf$", full.names=T, recursive = T)
## from hdf to GeoTIFF
runMrt(product=c('MOD10A1F'), collection = "061",
extent=extent(limits),
begin=start,
end=end,
job="loop", SDSstring = "11100", ## selecting only the first 3 layers
datum="WGS84")
this last function returns:
Output projection: Sinusoidal
Output pixel size: asIn
Resampling method: nn
Datum conversion: WGS84
Local structure is up-to-date. Using offline information!
"mrtmosaic" is not recognized as an internal or external command, as an executable program, or as a batch file.
"resample" is not recognized as an internal or external command, as an executable program, or as a batch file.
"mrtmosaic" is not recognized as an internal or external command, as an executable program, or as a batch file.
"resample" is not recognized as an internal or external command, as an executable program, or as a batch file.
It keeps printing these two lines for each .hdf file in the "raw" folder.
Finally, it prints:
$MOD10A1F.061
$MOD10A1F.061$`2003-01-04`
[1] "character(0)" "character(0)" "character(0)"
$MOD10A1F.061$`2003-01-05`
[1] "character(0)" "character(0)" "character(0)"
$MOD10A1F.061$`2003-01-06`
[1] "character(0)" "character(0)" "character(0)"
$MOD10A1F.061$`2003-01-07`
[1] "character(0)" "character(0)" "character(0)"
$MOD10A1F.061$`2003-01-08`
[1] "character(0)" "character(0)" "character(0)"
$MOD10A1F.061$`2003-01-09`
[1] "character(0)" "character(0)" "character(0)"
$MOD10A1F.061$`2003-01-10`
[1] "character(0)" "character(0)" "character(0)"
$MOD10A1F.061$`2003-01-11`
[1] "character(0)" "character(0)" "character(0)"
And nothing happens, nor in the environment, nor in the folders.
I also tried setting different outProj ("GEO" and "UTM"), but nothing changes.
Btw, I also tried to process these .hdf files using terra::rast() and terra::sds(), but I find no way to set the proper crs out from them.
A final thought...
Would it be efficient to add this same "update" possibility that is implemented in runMrt() directly into runGdal()?
So that - when requested - it can download only those dates that are missing from the local archive ("localArcPath" folder). If this feature is already implemented, I would suggest a printout to make the user aware of it (just as runMrt() that prints Local structure is up-to-date. Using offline information!).
Thanks a lot for providing this package, and for keeping working on it!
Much much much appreciated!!!
Cheers :)
Finally, here is my session info:
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=Italian_Italy.utf8 LC_CTYPE=Italian_Italy.utf8 LC_MONETARY=Italian_Italy.utf8 LC_NUMERIC=C
[5] LC_TIME=Italian_Italy.utf8
time zone: Europe/Rome
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] beepr_1.3 data.table_1.14.10 forcats_1.0.0 stringr_1.5.1 purrr_1.0.2 readr_2.1.5
[7] tidyr_1.3.1 tibble_3.2.1 ggplot2_3.4.4 tidyverse_2.0.0 dplyr_1.1.4 lubridate_1.9.3
[13] exactextractr_0.10.0 sf_1.0-15 rts_1.1-14 xts_0.13.2 zoo_1.8-12 terra_1.7-65
[19] MODIS_1.2.11.9000 mapdata_2.3.1 maps_3.4.2 units_0.8-5 raster_3.6-26 sp_2.1-2
loaded via a namespace (and not attached):
[1] tidyselect_1.2.0 bitops_1.0-7 fastmap_1.1.1 RCurl_1.98-1.14 promises_1.2.1 digest_0.6.34 timechange_0.3.0
[8] mime_0.12 lifecycle_1.0.4 ellipsis_0.3.2 ptw_1.9-16 magrittr_2.0.3 compiler_4.3.1 rlang_1.1.3
[15] tools_4.3.1 utf8_1.2.4 corrplot_0.92 htmlwidgets_1.6.4 pkgbuild_1.4.3 classInt_0.4-10 curl_5.2.0
[22] pkgload_1.3.4 KernSmooth_2.23-22 miniUI_0.1.1.1 foreign_0.8-86 withr_3.0.0 grid_4.3.1 fansi_1.0.6
[29] urlchecker_1.0.1 profvis_0.3.8 mapedit_0.6.0 xtable_1.8-4 e1071_1.7-14 colorspace_2.1-0 scales_1.3.0
[36] cli_3.6.2 generics_0.1.3 remotes_2.4.2.1 rstudioapi_0.15.0 RcppDE_0.1.7 tzdb_0.4.0 sessioninfo_1.2.2
[43] DBI_1.2.1 cachem_1.0.8 proxy_0.4-27 audio_0.1-11 parallel_4.3.1 vctrs_0.6.5 devtools_2.4.5
[50] hms_1.1.3 maptools_1.1-6 glue_1.7.0 codetools_0.2-19 stringi_1.8.3 gtable_0.3.4 later_1.3.2
[57] munsell_0.5.0 pillar_1.9.0 htmltools_0.5.7 R6_2.5.1 shiny_1.8.0 lattice_0.22-5 memoise_2.0.1
[64] httpuv_1.6.14 class_7.3-22 Rcpp_1.0.12 fs_1.6.3 usethis_2.2.2 pkgconfig_2.0.3