Hi all, I would like to access and subset following OpeNDAP files. server: http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/ file name: tmax.01.2014040312.daily.grb2 <http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/catalog.html?dataset=modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/tmax.01.2014040312.daily.grb2> I would like to access and subset the file. Any help will be appreciated. with regards -Deb
OPeNDAP access / OPeNDAP subsetting with R
7 messages · Debasish Pai Mazumder, Roy Mendelssohn - NOAA Federal, Michael Sumner
Look at the package ncdf4. You can use an OPeNDAP URL in place of the file name to perform subsets., -Roy
On Sep 27, 2016, at 9:06 AM, Debasish Pai Mazumder <pai1981 at gmail.com> wrote: Hi all, I would like to access and subset following OpeNDAP files. server: http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/ file name: tmax.01.2014040312.daily.grb2 <http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/catalog.html?dataset=modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/tmax.01.2014040312.daily.grb2> I would like to access and subset the file. Any help will be appreciated. with regards -Deb [[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 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 ***Note new address and phone*** 110 Shaffer Road Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: Roy.Mendelssohn at noaa.gov 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.
Hi Roy, Thanks for your response. I have tried according your suggestion but it doesn't work. the OPeNDAP link of the data http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_ forecast_ts_9mon/2014/201404/20140403/2014040312/ datafile: tmax.01.2014040312.daily.grb2 Thanks -Deb On Tue, Sep 27, 2016 at 11:51 AM, Roy Mendelssohn - NOAA Federal <
roy.mendelssohn at noaa.gov> wrote:
Look at the package ncdf4. You can use an OPeNDAP URL in place of the file name to perform subsets., -Roy
On Sep 27, 2016, at 9:06 AM, Debasish Pai Mazumder <pai1981 at gmail.com>
wrote:
Hi all, I would like to access and subset following OpeNDAP files. server: http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_
forecast_ts_9mon/2014/201404/20140403/2014040312/
file name: tmax.01.2014040312.daily.grb2 <http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_
forecast_ts_9mon/2014/201404/20140403/2014040312/catalog. html?dataset=modeldata/cfsv2_forecast_ts_9mon/2014/201404/ 20140403/2014040312/tmax.01.2014040312.daily.grb2>
I would like to access and subset the file. Any help will be appreciated.
with regards
-Deb
[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 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 ***Note new address and phone*** 110 Shaffer Road Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: Roy.Mendelssohn at noaa.gov 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.
Please post the code of what you tried, as I have no idea otherwise what did or did not work for you. -Roy
On Sep 27, 2016, at 12:44 PM, Debasish Pai Mazumder <pai1981 at gmail.com> wrote: Hi Roy, Thanks for your response. I have tried according your suggestion but it doesn't work. the OPeNDAP link of the data http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/ datafile: tmax.01.2014040312.daily.grb2 Thanks -Deb On Tue, Sep 27, 2016 at 11:51 AM, Roy Mendelssohn - NOAA Federal <roy.mendelssohn at noaa.gov> wrote: Look at the package ncdf4. You can use an OPeNDAP URL in place of the file name to perform subsets., -Roy
On Sep 27, 2016, at 9:06 AM, Debasish Pai Mazumder <pai1981 at gmail.com> wrote: Hi all, I would like to access and subset following OpeNDAP files. server: http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/ file name: tmax.01.2014040312.daily.grb2 <http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/catalog.html?dataset=modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/tmax.01.2014040312.daily.grb2> I would like to access and subset the file. Any help will be appreciated. with regards -Deb [[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 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 ***Note new address and phone*** 110 Shaffer Road Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: Roy.Mendelssohn at noaa.gov 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.
********************** "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 ***Note new address and phone*** 110 Shaffer Road Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: Roy.Mendelssohn at noaa.gov 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.
Opendap won't work on Windows CRAN build of ncdf4, though the rgdal build does work directly on grib. Summary: download the files wholus for use on Windows, or set your own system on Linux. Building ncdf4 on Windows is not too hard if you know about doing that. Cheers, Mike On Wed, 28 Sep 2016, 06:49 Roy Mendelssohn - NOAA Federal <
roy.mendelssohn at noaa.gov> wrote:
Please post the code of what you tried, as I have no idea otherwise what did or did not work for you. -Roy
On Sep 27, 2016, at 12:44 PM, Debasish Pai Mazumder <pai1981 at gmail.com>
wrote:
Hi Roy, Thanks for your response. I have tried according your suggestion but it
doesn't work.
the OPeNDAP link of the data
datafile: tmax.01.2014040312.daily.grb2 Thanks -Deb On Tue, Sep 27, 2016 at 11:51 AM, Roy Mendelssohn - NOAA Federal <
roy.mendelssohn at noaa.gov> wrote:
Look at the package ncdf4. You can use an OPeNDAP URL in place of the
file name to perform subsets.,
-Roy
On Sep 27, 2016, at 9:06 AM, Debasish Pai Mazumder <pai1981 at gmail.com>
wrote:
Hi all, I would like to access and subset following OpeNDAP files. server:
file name: tmax.01.2014040312.daily.grb2 <
I would like to access and subset the file. Any help will be
appreciated.
with regards
-Deb
[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 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 ***Note new address and phone*** 110 Shaffer Road Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: Roy.Mendelssohn at noaa.gov 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. ********************** "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 ***Note new address and phone*** 110 Shaffer Road Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: Roy.Mendelssohn at noaa.gov 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 at r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
Dr. Michael Sumner Software and Database Engineer Australian Antarctic Division 203 Channel Highway Kingston Tasmania 7050 Australia [[alternative HTML version deleted]]
2 days later
Hi
Now I am using netcdfSubset and I am able to download the file but not sure
how to read the files. here my scripts
library("ncdf4")
gribfile<-"
http://thredds.ucar.edu/thredds/ncss/grib/NCEP/GFS/Pacific_40km/best/dataset.html
"
download.file(gribfile,basename(gribfile),mode = "wb")
x<-nc_open(gribfile)
gribfile<-"
http://thredds.ucar.edu/thredds/ncss/grib/NCEP/GFS/Global_0p5deg/best?north=47.0126&west=-114.841&east=-112.641&south=44.8534&time_start=present&time_duration=PT3H&accept=netcdf&var=v-component_of_wind_height_above_ground,u-component_of_wind_height_above_ground"
download.file(gribfile,basename(gribfile),mode = "wb")
x<-nc_open(gribfile)
nc_open doesn't work.
which command should I use?
with regards
-Deb
On Tue, Sep 27, 2016 at 9:30 PM, Michael Sumner <mdsumner at gmail.com> wrote:
Opendap won't work on Windows CRAN build of ncdf4, though the rgdal build does work directly on grib. Summary: download the files wholus for use on Windows, or set your own system on Linux. Building ncdf4 on Windows is not too hard if you know about doing that. Cheers, Mike On Wed, 28 Sep 2016, 06:49 Roy Mendelssohn - NOAA Federal < roy.mendelssohn at noaa.gov> wrote:
Please post the code of what you tried, as I have no idea otherwise what did or did not work for you. -Roy
On Sep 27, 2016, at 12:44 PM, Debasish Pai Mazumder <pai1981 at gmail.com>
wrote:
Hi Roy, Thanks for your response. I have tried according your suggestion but it
doesn't work.
the OPeNDAP link of the data http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_
forecast_ts_9mon/2014/201404/20140403/2014040312/
datafile: tmax.01.2014040312.daily.grb2 Thanks -Deb On Tue, Sep 27, 2016 at 11:51 AM, Roy Mendelssohn - NOAA Federal <
roy.mendelssohn at noaa.gov> wrote:
Look at the package ncdf4. You can use an OPeNDAP URL in place of the
file name to perform subsets.,
-Roy
On Sep 27, 2016, at 9:06 AM, Debasish Pai Mazumder <pai1981 at gmail.com>
wrote:
Hi all, I would like to access and subset following OpeNDAP files. server: http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_
forecast_ts_9mon/2014/201404/20140403/2014040312/
file name: tmax.01.2014040312.daily.grb2 <http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_
forecast_ts_9mon/2014/201404/20140403/2014040312/catalog. html?dataset=modeldata/cfsv2_forecast_ts_9mon/2014/201404/ 20140403/2014040312/tmax.01.2014040312.daily.grb2>
I would like to access and subset the file. Any help will be
appreciated.
with regards
-Deb
[[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 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 ***Note new address and phone*** 110 Shaffer Road Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: Roy.Mendelssohn at noaa.gov 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.
********************** "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 ***Note new address and phone*** 110 Shaffer Road Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: Roy.Mendelssohn at noaa.gov 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 at r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
-- Dr. Michael Sumner Software and Database Engineer Australian Antarctic Division 203 Channel Highway Kingston Tasmania 7050 Australia
Hi Deb:
gribfile <- 'http://thredds.ucar.edu/thredds/ncss/grib/NCEP/GFS/Global_0p5deg/best?north=47.0126&west=-114.841&east=-112.641&south=44.8534&time_start=present&time_duration=PT3H&accept=netcdf&var=v-component_of_wind_height_above_ground,u-component_of_wind_height_above_ground' download.file(gribfile,'junk.nc',mode = "wb")
trying URL 'http://thredds.ucar.edu/thredds/ncss/grib/NCEP/GFS/Global_0p5deg/best?north=47.0126&west=-114.841&east=-112.641&south=44.8534&time_start=present&time_duration=PT3H&accept=netcdf&var=v-component_of_wind_height_above_ground,u-component_of_wind_height_above_ground' Content type 'application/x-netcdf' length unknown .... downloaded 4360 bytes
library(ncdf4)
junkFile <- nc_open('junk.nc')
str(junkFile)
List of 14 $ filename : chr "junk.nc" $ writable : logi FALSE $ id : int 65536 $ safemode : logi FALSE $ format : chr "NC_FORMAT_CLASSIC" $ is_GMT : logi FALSE $ groups :List of 1 ..$ :List of 7 .. ..$ id : int 65536 .. ..$ name : chr "" .. ..$ ndims: int 4 .. ..$ nvars: int 7 .. ..$ natts: int 13 .. ..$ dimid: int [1:4(1d)] 0 1 2 3 .. ..$ fqgn : chr "" .. ..- attr(*, "class")= chr "ncgroup4" $ fqgn2Rindex:List of 1 ..$ : int 1 $ ndims : num 4 $ natts : num 13 $ dim :List of 4
<snip> I cut off the rest as that is not important for your question. HTH, -Roy
On Sep 30, 2016, at 4:21 PM, Debasish Pai Mazumder <pai1981 at gmail.com> wrote:
Hi
Now I am using netcdfSubset and I am able to download the file but not sure how to read the files. here my scripts
library("ncdf4")
gribfile<-"http://thredds.ucar.edu/thredds/ncss/grib/NCEP/GFS/Pacific_40km/best/dataset.html"
download.file(gribfile,basename(gribfile),mode = "wb")
x<-nc_open(gribfile)
gribfile<-"http://thredds.ucar.edu/thredds/ncss/grib/NCEP/GFS/Global_0p5deg/best?north=47.0126&west=-114.841&east=-112.641&south=44.8534&time_start=present&time_duration=PT3H&accept=netcdf&var=v-component_of_wind_height_above_ground,u-component_of_wind_height_above_ground"
download.file(gribfile,basename(gribfile),mode = "wb")
x<-nc_open(gribfile)
nc_open doesn't work.
which command should I use?
with regards
-Deb
On Tue, Sep 27, 2016 at 9:30 PM, Michael Sumner <mdsumner at gmail.com> wrote:
Opendap won't work on Windows CRAN build of ncdf4, though the rgdal build does work directly on grib.
Summary: download the files wholus for use on Windows, or set your own system on Linux.
Building ncdf4 on Windows is not too hard if you know about doing that.
Cheers, Mike
On Wed, 28 Sep 2016, 06:49 Roy Mendelssohn - NOAA Federal <roy.mendelssohn at noaa.gov> wrote:
Please post the code of what you tried, as I have no idea otherwise what did or did not work for you.
-Roy
On Sep 27, 2016, at 12:44 PM, Debasish Pai Mazumder <pai1981 at gmail.com> wrote: Hi Roy, Thanks for your response. I have tried according your suggestion but it doesn't work. the OPeNDAP link of the data http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/ datafile: tmax.01.2014040312.daily.grb2 Thanks -Deb On Tue, Sep 27, 2016 at 11:51 AM, Roy Mendelssohn - NOAA Federal <roy.mendelssohn at noaa.gov> wrote: Look at the package ncdf4. You can use an OPeNDAP URL in place of the file name to perform subsets., -Roy
On Sep 27, 2016, at 9:06 AM, Debasish Pai Mazumder <pai1981 at gmail.com> wrote: Hi all, I would like to access and subset following OpeNDAP files. server: http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/ file name: tmax.01.2014040312.daily.grb2 <http://nomads.ncdc.noaa.gov/thredds/dodsC/modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/catalog.html?dataset=modeldata/cfsv2_forecast_ts_9mon/2014/201404/20140403/2014040312/tmax.01.2014040312.daily.grb2> I would like to access and subset the file. Any help will be appreciated. with regards -Deb [[alternative HTML version deleted]]
______________________________________________ R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see 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 ***Note new address and phone*** 110 Shaffer Road Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: Roy.Mendelssohn at noaa.gov 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.
********************** "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 ***Note new address and phone*** 110 Shaffer Road Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: Roy.Mendelssohn at noaa.gov 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 at r-project.org mailing list -- To UNSUBSCRIBE and more, see 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. -- Dr. Michael Sumner Software and Database Engineer Australian Antarctic Division 203 Channel Highway Kingston Tasmania 7050 Australia
********************** "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 ***Note new address and phone*** 110 Shaffer Road Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: Roy.Mendelssohn at noaa.gov 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.