[R] Hdf files Download
I am triing one more time since my first message was rejected by the filter: Dear all, I need to download and process large amounts of MODIS surface reflectance imagery. I have adapted a script written by T. Hengl ( http://www.spatial-analyst.net/wiki/?title=Download_and_resampling_of_MODIS _images http://www.spatial-analyst.net/wiki/?title=Download_and_resampling_of_MODIS_ images) for download from the new HTTP (since FTP is no longer available). The downloaded .HDF files however have no headers and it is impossible to work with them. If I download directly from the webpage everything is fine. Does anyone know what the problem might be, please? I am attaching my code Please it is urgent. Thanks a lot. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Hdf files Download
Your script didn't make it. There are restrictions on the mail list for attached files. You might try putting the script directly into the email. -Roy On Oct 22, 2013, at 9:40 AM, Tereza Smejkalova terka...@gmail.com wrote: I am triing one more time since my first message was rejected by the filter: Dear all, I need to download and process large amounts of MODIS surface reflectance imagery. I have adapted a script written by T. Hengl ( http://www.spatial-analyst.net/wiki/?title=Download_and_resampling_of_MODIS _images http://www.spatial-analyst.net/wiki/?title=Download_and_resampling_of_MODIS_ images) for download from the new HTTP (since FTP is no longer available). The downloaded .HDF files however have no headers and it is impossible to work with them. If I download directly from the webpage everything is fine. Does anyone know what the problem might be, please? I am attaching my code Please it is urgent. Thanks a lot. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ** The contents of this message do not reflect any position of the U.S. Government or NOAA. ** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center 1352 Lighthouse Avenue Pacific Grove, CA 93950-2097 e-mail: roy.mendelss...@noaa.gov (Note new e-mail address) voice: (831)-648-9029 fax: (831)-648-8440 www: http://www.pfeg.noaa.gov/ Old age and treachery will overcome youth and skill. From those who have been given much, much will be expected the arc of the moral universe is long, but it bends toward justice -MLK Jr. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Hdf files Download
On Oct 22, 2013, at 11:34 AM, Roy Mendelssohn - NOAA Federal wrote:
Your script didn't make it. There are restrictions on the mail list for
attached files. You might try putting the script directly into the email.
Thinking that the rejection might have be due to a Nabble posting I located it
there and here include it. I'm hoping to use the method as well.
#
# title : MODIS_download_HTTP.R
# purpose : Download of MODIS EVI images for the British Colombia;
# reference :
http://spatial-analyst.net/wiki/index.php?title=Download_and_resampling_of_MODIS_images
# producer : Prepared by T. Hengl (addapted by T. Smejkalova)
# last update : Southampton, UK, 18 October 2013.
# inputs: Coordinates of the area of interest; proj4 parameters; ftp
addresses etc.;
# outputs : a series of EVI images (geoTIFF) projected in the local
coordinate system;
# remarks 1 : To run this script, you need to obtain and install the MODIS
resampling tool from
[https://lpdaac.usgs.gov/lpdaac/tools/modis_reprojection_tool];
# remarks 2 : You should also obtain the WGET from
[http://users.ugent.be/~bpuype/wget/] --- simply copy the wget exe to windows
system folder;
# remarks 3 : make sure you disable your antivirus tools such as Norton or
McAfee otherwise it might block wget from running!
library(rgdal)
library(RCurl)
setInternet2(use = TRUE)
# Obtain the MODIS tool from:
http://lpdaac.usgs.gov/landdaac/tools/modis/index.asp
# setwd(E:/PineBeetleBC/MODIS)
# location of the MODIS 1 km monthly blocks:
MOD09GQ - http://e4ftl01.cr.usgs.gov/MOLT/MOD09GQ.005/;
MOD09GQa - http://anonymous:t...@e4ftl01.cr.usgs.gov/MOLT/MOD09GQ.005/;
product = MOD09GQ
year = 2000
# location of the mosaicing tool:
MRT - 'D:\\MRT\\MRT_Win\\bin\\'
workd - 'D:\\R_Modis\\'
setwd('D:\\R_Modis\\')
options(download.file.method=auto)
# get the list of directories (thanks to Barry Rowlingson):
items1 - strsplit(getURL(MOD09GQ), \n)[[1]]
# get the directory names and create a new data frame:
dates=data.frame(dirname=substr(items1[20:length(items1)],52,62))
# get the list of *.hdf files:
dates$BLOCK1 - rep(NA, length(dates))
dates$BLOCK2 - rep(NA, length(dates))
#dates$BLOCK3 - rep(NA, length(dates))
#dates$BLOCK4 - rep(NA, length(dates))
for (i in 1:1)#length(dates))# for each date per year
{
getlist - strsplit(getURL(paste(MOD09GQ, dates$dirname[i], sep=)),
)[[1]]
getlist=getlist[grep(product,getlist)]
getlist=getlist[grep(.hdf,getlist)]
filenames=substr(getlist,1,nchar(getlist[1])-3)
BLOCK1 - filenames[grep(filenames,pattern=MOD09GQ.*.h18v02.*.hdf)[1]]
BLOCK2 - filenames[grep(filenames,pattern=MOD09GQ.*.h19v02.*.hdf)[1]]
# write up the file names back to the dates.txt:
for(j in 2:3){
dates[i,j] - get(paste(BLOCK, j-1, sep=))
}
# Download all blocks from the list to a local drive:
#
while(!is.na(dates[i,2])!is.na(dates[i,3])!is.na(dates[i,4])!is.na(dates[i,5])!is.na(dates[i,6])!is.na(dates[i,7])!is.na(dates[i,8])!is.na(dates[i,9])!is.na(dates[i,10])){
download.file(paste(MOD09GQa, dates$dirname[i],
dates$BLOCK1[i],sep=),destfile=paste(getwd(), /, BLOCK1, sep=))
download.file(paste(MOD09GQ, dates$dirname[i],
dates$BLOCK2[i],sep=),destfile=paste(getwd(), /, BLOCK2, sep=),
cacheOK=FALSE, )
# remove . from the file name:
dirname1 - sub(sub(pattern=\\., replacement=_, dates$dirname[[i]]),
pattern=\\., replacement=_, dates$dirname[[i]])
# mosaic the blocks:
mosaicname = file(paste(MRT, TmpMosaic.prm, sep=), open=wt)
write(paste(workd, BLOCK1, sep=), mosaicname)
write(paste(workd, BLOCK2, sep=), mosaicname, append=T)
#write(paste(workd, BLOCK3, sep=), mosaicname, append=T)
#write(paste(workd, BLOCK4, sep=), mosaicname, append=T)
close(mosaicname)
# generate temporary mosaic:
shell(cmd=paste(MRT, 'mrtmosaic -i ', MRT, 'TmpMosaic.prm -s 0 1 0 0 0 0 0 0
0 0 0 -o ', workd, 'TmpMosaic.hdf', sep=))
# resample to epsg=3005:
filename = file(paste(MRT, mrt, dirname1, .prm, sep=), open=wt)
write(paste('INPUT_FILENAME = ', workd, 'TmpMosaic.hdf', sep=), filename)
# write(paste('INPUT_FILENAMES = ( ', workd, BLOCK1, ' ', workd, BLOCK2, ' ',
workd, BLOCK3, ' ', workd, BLOCK4, ' ', workd, BLOCK5, ' ', workd, BLOCK6, ' ',
workd, BLOCK7, ' ', workd, BLOCK8, ' ', workd, BLOCK9, ' )', sep=), filename)
# unfortunatelly does not work via command line :(
write(' ', filename, append=TRUE)
# write('SPECTRAL_SUBSET = ( 0 1 0 0 0 0 0 0 0 0 0 )', filename, append=TRUE)
write('SPECTRAL_SUBSET = ( 1 )', filename, append=TRUE)
write(' ', filename, append=TRUE)
write('SPATIAL_SUBSET_TYPE = OUTPUT_PROJ_COORDS', filename, append=TRUE)
write(' ', filename, append=TRUE)
write('SPATIAL_SUBSET_UL_CORNER = ( 50.0 -180.0 )', filename,
append=TRUE)
write('SPATIAL_SUBSET_LR_CORNER = ( 160.0 -270.0 )', filename,
append=TRUE)
write(' ', filename, append=TRUE)
write(paste('OUTPUT_FILENAME = ', workd,
[R] hdf-files
Dear All, I have data in HDF file format and would like to read it into R. I have tried the package hdf5 without success. Any ideas and suggestions?? Kind regards, Katrin -- Katrin Fleischer Vrije Universiteit Amsterdam Faculty of Earth and Life Sciences Subdepartment Hydrolgy and Geo-Environmental Sciences Room E-360 De Boelelaan 1085 1081 HV AMSTERDAM Tel: +31 20 59 87391 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] hdf files
Dear All, I want to upload data in HDF-file format into R. I have tried the package 'hdf5' without success. I presume that my files are in the hdf4 format and therefore are not readable with this package. I understand that its possible to convert hdf4 into hdf5 format using C, but I was wondering whether there is an alternative option for importing hdf4 files into R? kind regards, Katrin -- Katrin Fleischer Vrije Universiteit Amsterdam Faculty of Earth and Life Sciences Subdepartment Hydrolgy and Geo-Environmental Sciences Room E-360 De Boelelaan 1085 1081 HV AMSTERDAM Tel: +31 20 59 87391 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] hdf-files
Hi, On Thu, Sep 23, 2010 at 7:13 AM, Katrin Fleischer katrin.fleisc...@falw.vu.nl wrote: Dear All, I have data in HDF file format and would like to read it into R. I have tried the package hdf5 without success. What type of errors are you getting? Any ideas and suggestions?? Sure, from: http://cran.r-project.org/doc/manuals/R-data.html Packages hdf5, RNetCDF and ncdf on CRAN provide interfaces to NASA's HDF5 ... I'm not familiar with the differences between hdf5 and netCDF, but perhaps those other packages can help (I see that they've been more recently updated, anyway ...). -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] hdf-files
Hi Katrin, (don't forget to reply-all to R-help messages -- by default they are only sent to the recipient, and not back to the list). On Thu, Sep 23, 2010 at 10:03 AM, Katrin Fleischer katrin.fleisc...@falw.vu.nl wrote: The error message is Error in hdf5load(Jan2006.HDF) : unable to open HDF file: Jan2006.HDF Dumb question, but is that the correct path to the file? If you call `dir()` in your R session, is Jan2006.HDF one of the elements returned? Maybe try the absolute path to the file if not. I have also seen these other packages, but Im afraid that the data I have might be in hdf4 (thats would be an explanation to why hdf5load isnt working), so I was wondering whether there is a package for R dealing with hdf4 files.. Perhaps you could try converting it to hdf5 format, if that's the case. It looks like there is a utility you can use to do so here: http://www.hdfgroup.org/h4toh5/ -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] hdf files
hello,
I have a problem to open an hdf file. i have downloaded the package 'hdf5' as
it was advised on R seek. But when i try to load the file, the R console sends
me an eror message:
setwd(C:/Documents and Settings/Karine/Bureau/data/)
#install.packages('hdf5')
library(hdf5)
sea_ice - hdf5load(asi-s6250-20090704-v5i.hdf, load = TRUE, verbosity = 3,
tidy = FALSE)
Grid_ice - hdf5load(LongitudeLatitudeGrid-s6250-Antarctic.hdf, load = TRUE,
verbosity = 3, tidy = FALSE)
sea_ice - hdf5load(asi-s6250-20090704-v5i.hdf, load = TRUE, verbosity =
3, tidy = FALSE)
hdf5_global_verbosity=3 load=1
Erreur dans hdf5load(asi-s6250-20090704-v5i.hdf, load = TRUE, verbosity = 3,
:
unable to open HDF file: asi-s6250-20090704-v5i.hdf
Grid_ice - hdf5load(LongitudeLatitudeGrid-s6250-Antarctic.hdf, load =
TRUE, verbosity = 3, tidy = FALSE)
hdf5_global_verbosity=3 load=1
Erreur dans hdf5load(LongitudeLatitudeGrid-s6250-Antarctic.hdf, load = TRUE,
:
unable to open HDF file: LongitudeLatitudeGrid-s6250-Antarctic.hdf
Thanks a lot,
Karine HEERAH
Master 2 mention océanographie et environnements marins, parcours océanique
42 rue Salvador Allende
92000 Nanterre
06.61.50.97.47
Faites une bonne action avec Bing Solidaire ! C'est ici !
Discute avec tes amis partout, grâce à Messenger sur ton mobile. Cliquez ici !
_
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R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] hdf files
hello,
I have a problem to open an hdf file. i have downloaded the package 'hdf5' as
it was advised on R seek. But when i try to load the file, the R console sends
me an eror message:
setwd(C:/Documents and Settings/Karine/Bureau/data/)
#install.packages('hdf5')
library(hdf5)
sea_ice - hdf5load(asi-s6250-20090704-v5i.hdf, load = TRUE, verbosity = 3,
tidy = FALSE)
Grid_ice - hdf5load(LongitudeLatitudeGrid-s6250-Antarctic.hdf, load = TRUE,
verbosity = 3, tidy = FALSE)
sea_ice - hdf5load(asi-s6250-20090704-v5i.hdf, load = TRUE, verbosity =
3, tidy = FALSE)
hdf5_global_verbosity=3 load=1
Erreur dans hdf5load(asi-s6250-20090704-v5i.hdf, load = TRUE, verbosity = 3,
:
unable to open HDF file: asi-s6250-20090704-v5i.hdf
Grid_ice - hdf5load(LongitudeLatitudeGrid-s6250-Antarctic.hdf, load =
TRUE, verbosity = 3, tidy = FALSE)
hdf5_global_verbosity=3 load=1
Erreur dans hdf5load(LongitudeLatitudeGrid-s6250-Antarctic.hdf, load = TRUE,
:
unable to open HDF file: LongitudeLatitudeGrid-s6250-Antarctic.hdf
Thanks a lot,
Karine HEERAH
Master 2 mention océanographie et environnements marins, parcours océanique
42 rue Salvador Allende
92000 Nanterre
06.61.50.97.47
Faites une bonne action avec Bing Solidaire ! C'est ici !
_
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] hdf files
hello,
I have a problem to open an hdf file. i have downloaded the package 'hdf5' as
it was advised on R seek. But when i try to load the file, the R console sends
me an eror message:
setwd(C:/Documents and Settings/Karine/Bureau/data/)
#install.packages('hdf5')
library(hdf5)
sea_ice - hdf5load(asi-s6250-20090704-v5i.hdf, load = TRUE, verbosity = 3,
tidy = FALSE)
Grid_ice - hdf5load(LongitudeLatitudeGrid-s6250-Antarctic.hdf, load = TRUE,
verbosity = 3, tidy = FALSE)
sea_ice - hdf5load(asi-s6250-20090704-v5i.hdf, load = TRUE, verbosity =
3, tidy = FALSE)
hdf5_global_verbosity=3 load=1
Erreur dans hdf5load(asi-s6250-20090704-v5i.hdf, load = TRUE, verbosity = 3,
:
unable to open HDF file: asi-s6250-20090704-v5i.hdf
Grid_ice - hdf5load(LongitudeLatitudeGrid-s6250-Antarctic.hdf, load =
TRUE, verbosity = 3, tidy = FALSE)
hdf5_global_verbosity=3 load=1
Erreur dans hdf5load(LongitudeLatitudeGrid-s6250-Antarctic.hdf, load = TRUE,
:
unable to open HDF file: LongitudeLatitudeGrid-s6250-Antarctic.hdf
Thanks a lot,
Karine HEERAH
Master 2 mention océanographie et environnements marins, parcours océanique
42 rue Salvador Allende
92000 Nanterre
06.61.50.97.47
_
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__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
