Help downloading MODIS data in R

[Avtober]

Hi, I am trying to download NDVI from MODIS and used the following code but am having issues:

devtools::install_github("MatMatt/MODIS", ref = "develop") library(MODIS)

MODIS = runGdal("MOD13Q1", collection = "006", tileH = 20, tileV = 11, begin = "2000.02.18", end = "2010.03.10", job = "MOD13Q1", SDSstring = "110000000000") # extract NDVI and EVI

I get the following error message: ######################## outProj = asIn pixelSize = asIn resamplingType = near Output directory = C:/Users/avtob/AppData/Local/Temp/RtmpKeYFk0/MODIS_ARC/PROCESSED/MOD13Q1.006_20210816171601 (no 'job' name specified, generated (date/time based)) ######################## Downloading structure on 'LPDAAC' for: MOD13Q1.006 Hm, I have to search for the file. Next time provide the full path and I'll be very fast! Error in strsplit(x, ":") : non-character argument

Please help, I am not sure what it means by provide the full path, how do I do this?

Thanks Anya

[fdetsch]

@Avtober Can you have a look at https://github.com/MatMatt/MODIS/issues/111#issuecomment-902473477 (similar issue) and try to provide the required information?

[Avtober]

Hi @fdetsch, If I run the traceback i get the following:

> traceback()
7: strsplit(x, ":")
6: getSdsNames(SDSnames)
5: gsub("\"", "", getSdsNames(SDSnames))
4: getSds(HdfName = y, SDSstring = SDSstring)
3: FUN(X[[i]], ...)
2: lapply(files, function(y) {
       getSds(HdfName = y, SDSstring = SDSstring)
   })
1: runGdal("MOD13Q1", collection = "006", tileH = 20, tileV = 11, 
       begin = "2000.02.18", end = "2010.03.10", job = "MOD13Q1", 
       SDSstring = "110000000000")

Not sure if that is helpful. Thanks Anya

[fdetsch]

I deleted everything that is not relevant at this stage from your answer – hope that's okay.

From your first post, it looks like you are attempting to download to a temporary folder, which I would not recommend for such big data. Can you do me a favor and set localArcPath to a permanent folder on your hard drive? Then verify if the downloaded .hdf file is several 100 MB large or if you're seeing empty files (i.e. something close to 0 kB) only. For example, do the following (remember to change lap that defines the local download folder):

library(MODIS)

## enable permanent file storage
lap = "~/Documents/data/MODIS_ARC"
MODISoptions(
  localArcPath = lap
  , outDirPath = file.path(
    lap
    , "PROCESSED"
  )
)

## download data for most recent collection
product = "MOD13Q1"

clc = getCollection(
  product
  , forceCheck = TRUE
)

tfs = runGdal(
  product
  , collection = clc
  , tileH = 20
  , tileV = 11
  , begin = "2000.02.18"
  , end = "2000.02.18"
  , job = "MOD13Q1"
  , SDSstring = "11" # ndvi, evi
)

[Avtober]

Hi @fdetsch,

Thanks, I tried that and it created the folder but the folder was empty. I have copied the outcome and the error message below:

Setting 'localArcPath' to 'C:/Users/avtob/OneDrive/Documents/Documents/data/MODIS_ARC' If you already have downloaded some HDF files, you can use '?orgStruc' to rearrange them. 'outDirPath' has been changed from 'C:/Users/avtob/AppData/Local/Temp/RtmpS2IFWF/MODIS_ARC/PROCESSED/' to 'C:/Users/avtob/OneDrive/Documents/Documents/data/MODIS_ARC/PROCESSED'. File '~/.MODIS_Opts.R' does not exist. Create it now to make settings permanent? [y/n]: n

STORAGE:

---

localArcPath : C:/Users/avtob/OneDrive/Documents/Documents/data/MODIS_ARC outDirPath : C:/Users/avtob/OneDrive/Documents/Documents/data/MODIS_ARC/PROCESSED

DOWNLOAD:

---

MODISserverOrder : LPDAAC, LAADS dlmethod : auto stubbornness : high wait : 0.5 quiet : TRUE

PROCESSING:

---

GDAL : 3.2.1 MRT : Enabled pixelSize : asIn outProj : asIn resamplingType : NN dataFormat : GTiff cellchunk : 1

product = "MOD13Q1" clc = getCollection(

• product
• , forceCheck = TRUE) tfs = runGdal(
• product
• , collection = clc
• , tileH = 20
• , tileV = 11
• , begin = "2000.02.18"
• , end = "2000.02.18"
• , job = "MOD13Q1"
• , SDSstring = "11" # ndvi, evi
• ) ######################## outProj = asIn pixelSize = asIn resamplingType = near Output Directory = C:/Users/avtob/OneDrive/Documents/Documents/data/MODIS_ARC/PROCESSED/MOD13Q1 ######################## Downloading structure on 'LPDAAC' for: MOD13Q1.061 Hm, I have to search for the file. Next time provide the full path and I'll be very fast! Error in strsplit(x, ":") : non-character argument

Thanks Anya

[fdetsch]

Is a file ~/.netrc present and are the credentials therein correct? In RStudio, you can easily find out with file.edit("~/.netrc").

[Avtober]

It brings up the file but it looks like its empty.

[fdetsch]

One step closer, I guess. Please run EarthdataLogin() and enter your Earthdata credentials (see ?EarthdataLogin for details). Afterwards, try again the code from https://github.com/MatMatt/MODIS/issues/114#issuecomment-903875483.

[Avtober]

I think that worked, I now have a HDF file of around 200,00KB and two Tiff files (NDVI and EVI) in the processed folder! I guess I can try this with the larger data now?

Thanks for your help! Anya

[fdetsch]

Happy to help. Let me know if you encounter other problems. Closing this once the availability of Earthdata credentials can be verified through the package, see https://github.com/MatMatt/MODIS/pull/115.