Get_all_Ocean_Prod: Download all SeaWiFS or MODIS HDF4 file from Ocean...

In chihlinwei/OceanData: Tools to download and extract oceanographic data from various sources

Download all SeaWiFS or MODIS HDF4 file from Ocean Productivity Web page

Description

Download SeaWiFS or MODIS HDF4 file from Ocean Productivity Web page and then convert to a raster object

Usage

Get_all_Ocean_Prod(url_list, ts, x = NULL, outdir = NULL, plot = FALSE)

Arguments

url_list	A list string for each variable naming the time-series URLs of HDF4 file to be downloaded. The names of the url_list (names(url_list)) should be given as a vector of variable names.
ts	The number of urls to be download in url_list
x	Raster* object defining the spatial extent, resolution and projection of climatology data to be retrived. If not provide, returning full data set.
outdir	output directory to write raster file
plot	Logical, whether or not to plot the output raster

Details

This function dowloads multiple HDF4 files from Ocean Productivity Web page http://www.science.oregonstate.edu/ocean.productivity/

Value

a raster object

Author(s)

Chih-Lin Wei <[e-mail]>

Examples

#### Get data from 1998-01 to 2007-12 (using SeaWiFS) and 2008-01 to 2012-12 (using MODIS)
# Take serveral hours; best to leave it overnight

# Raster template of Canadian Arctic
data(tmp)

# Create a folder to output raster bricks 
folder <- "../Arctic_ocean_data/Ocean_Productivity"
dir.create(folder)

# Year and day of year by month from 1998-01-01 to 2012-12-0
seawifs <- Year_Day("1998-01-01", "2007-12-01", by="month") # SEAWiFS time series
modis <- Year_Day("2008-01-01", "2012-12-01", by="month") # MODIS time series

# URLs for each variable
# The url path may change depending on the NASA Ocean Color reprocessing version
# Check http://www.science.oregonstate.edu/ocean.productivity/ before using the following examplea

# Paticle Backscattering
bbp <- c(paste("http://orca.science.oregonstate.edu/data/2x4/monthly/bbp.r2010.gsm.v6.s/hdf/bbp", seawifs, "hdf.gz", sep="."), 
         paste("http://orca.science.oregonstate.edu/data/2x4/monthly/bbp.r2013.gsm.v7.m/hdf/bbp", modis, "hdf.gz", sep="."))
         
# Carbon concentration
carbon <- c(paste("http://orca.science.oregonstate.edu/data/2x4/monthly/carbon.s.r2010.gsm.v6/hdf/carbon", seawifs, "hdf.gz", sep="."), 
            paste("http://orca.science.oregonstate.edu/data/2x4/monthly/carbon.m.r2013.gsm.v7/hdf/carbon", modis, "hdf.gz", sep="."))
            
# Carbon-based primary production model
cbpm <- c(paste("http://orca.science.oregonstate.edu/data/2x4/monthly/cbpm2.s.r2010.gsm.v6/hdf/cbpm", seawifs, "hdf.gz", sep="."), 
          paste("http://orca.science.oregonstate.edu/data/2x4/monthly/cbpm2.m.r2013.gsm.v7/hdf/cbpm", modis, "hdf.gz", sep="."))
          
# Chlorophyll concentration
chl <- c(paste("http://orca.science.oregonstate.edu/data/2x4/monthly/chl.r2010.seawifs/hdf/chl", seawifs, "hdf.gz", sep="."), 
         paste("http://orca.science.oregonstate.edu/data/2x4/monthly/chl.modis.r2013/hdf/chl", modis, "hdf.gz", sep="."))
         
# Eppley variation of VGPM primary production
eppley <- c(paste("http://orca.science.oregonstate.edu/data/2x4/monthly/eppley.r2010.s.chl.a.sst/hdf/eppley", seawifs, "hdf.gz", sep="."), 
            paste("http://orca.science.oregonstate.edu/data/2x4/monthly/eppley.r2013.m.chl.m.sst4/hdf/eppley", modis, "hdf.gz", sep="."))
            
# Phytoplankton growth rate
growth <- c(paste("http://orca.science.oregonstate.edu/data/2x4/monthly/growth.s.r2010.gsm.v6/hdf/growth", seawifs, "hdf.gz", sep="."),
            paste("http://orca.science.oregonstate.edu/data/2x4/monthly/growth.m.r2013.gsm.v7/hdf/growth", modis, "hdf.gz", sep="."))
            
# Photosynthetically available radiation
par <- c(paste("http://orca.science.oregonstate.edu/data/2x4/monthly/par.r2010.seawifs/hdf/par", seawifs, "hdf.gz", sep="."), 
         paste("http://orca.science.oregonstate.edu/data/2x4/monthly/par.modis.r2013/hdf/par", modis, "hdf.gz", sep="."))
         
# Vertical General Production model
vgpm <- c(paste("http://orca.science.oregonstate.edu/data/2x4/monthly/vgpm.r2010.s.chl.a.sst/hdf/vgpm", seawifs, "hdf.gz", sep="."), 
          paste("http://orca.science.oregonstate.edu/data/2x4/monthly/vgpm.r2013.m.chl.m.sst4/hdf/vgpm", modis, "hdf.gz", sep="."))
          
# Sea surface temperature
sst <- c(paste("http://orca.science.oregonstate.edu/data/2x4/monthly/sst.avhrr/hdf/sst", seawifs, "hdf.gz", sep="."), 
         paste("http://orca.science.oregonstate.edu/data/2x4/monthly/sst4.modis.r2013/hdf/sst4", modis, "hdf.gz", sep="."))
         
# Mixed layer depth
soda <- paste("http://orca.science.oregonstate.edu/data/1x2/monthly/mld.soda/hdf/mld", Year_Day("1998-01-01", "2004-12-01", by="month"), "hdf.gz", sep=".")
tops <- paste("http://orca.science.oregonstate.edu/data/1x2/monthly/ild.fnmoc_tops/hdf/ild", Year_Day("2005-01-01", "2005-06-01", by="month"), "hdf.gz", sep=".")
fnmoc <- paste("http://orca.science.oregonstate.edu/data/1x2/monthly/mld.fnmoc_highres/hdf/mld", Year_Day("2005-07-01", "2008-09-01", by="month"), "hdf.gz", sep=".")
hycom <- paste("http://orca.science.oregonstate.edu/data/1x2/monthly/mld.hycom/hdf/mld", Year_Day("2008-10-01", "2012-12-01"), "hdf.gz", sep=".")
mld <- c(soda, tops, fnmoc, hycom)

url_list <- list(bbp, carbon, cbpm, chl, eppley, growth, par, vgpm, mld, sst)
names(url_list) <- c("bbp", "carbon", "cbpm", "chl", "eppley", "growth", "par", "vgpm", "mld", "sst")

# Use August 1998 as example
Get_all_Ocean_Prod(url_lis=url_list, ts=8, x=tmp, plot=TRUE)

# Download the entire time series 

library(foreach)
library(doSNOW)

cl<-makeCluster(4) # change 4 to your number of CPU cores
registerDoSNOW(cl) # register the SNOW parallel backend with the foreach package
foreach(i=1:2, .packages="OceanData") %dopar% Get_all_Ocean_Prod(url_list, ts=i, x=tmp, outdir=folder)
stopCluster(cl) # stop a SNOW cluster

chihlinwei/OceanData documentation built on Jan. 17, 2025, 4:24 a.m.