Type: Package
Title: Extraction of Bands from MODIS Surface Reflectance Product MOD09 NRT
Version: 0.14
Author: Rishabh Gupta <rishabh.uk@gmail.com>, Nicholas J. Matzke, Dept. of Integrative Biology, U.C. Berkeley
Maintainer: Rishabh Gupta <rishabh.uk@gmail.com>
Description: Package for processing downloaded MODIS Surface reflectance Product HDF files. Specifically, MOD09 surface reflectance product files, and the associated MOD03 geolocation files (for MODIS-TERRA). The package will be most effective if the user installs MRTSwath (MODIS Reprojection Tool for swath products; https://lpdaac.usgs.gov/tools/modis_reprojection_tool_swath, and adds the directory with the MRTSwath executable to the default R PATH by editing ~/.Rprofile.
SystemRequirements: MRTSwath
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-24 11:48:00 UTC; 500028930
Repository: CRAN
Date/Publication: 2016-07-24 13:55:50

Convert to data.frame, without factors

Description

Shortcut for: as.data.frame(x, row.names=NULL, stringsAsFactors=FALSE)

Usage

adf(x)

Arguments

x

matrix or other object transformable to data.frame

Details

This function is useful for dealing with errors due to automatic conversion of some columns to factors. Another solution may be to prepend options(stringsAsFactors = FALSE) at the start of one's script, to turn off all default stringsAsFactors silliness.

Value

data.frame

Author(s)

Nicholas J. Matzke matzke@berkeley.edu

Examples

x = matrix(c(1,2,3,4,5,6), nrow=3, ncol=2)
adf(x)

Checks that every MODIS surface reflectance project HDF has a matching MOD03 file

Description

Each MOD09 surface reflectance product file requires a corresponding MOD03 geolocation file to be successfully processed with the MRTSwath tool.

Usage

check_for_matching_geolocation_files_mod09nrt(moddir = getwd(),
  modtxt = "MOD09", geoloctxt = "MOD03", return_geoloc = FALSE,
  return_product = FALSE)

Arguments

moddir

the string describing the directory containing the MOD09 and MOD03 files; both must be in the same directory. Default: getwd(), which gives the present working directory.

modtxt

the text string indicating which HDF files are the MODIS surface reflectance product (or hypothetically, other product). Default: MOD09 (MODIS surface reflectance product)

geoloctxt

the text string indicating which HDF files are the MODIS geolocation files (or hypothetically, another set of files). Default: MOD03

return_geoloc

if TRUE, return the list of unmatched geolocation files (e.g. MOD03 )

return_product

if TRUE, return the list of unmatched product files (e.g. MOD09)

Details

MRTSwath is the MRT (MODIS Reprojection Tool) for the MODIS

E.g. this surface reflectance file:

MOD09.A2016204.0500.005.2016204062219.NRT.hdf

...goes with this corresponding geolocation file:

MOD03.A2016204.0500.005.2016204060250.NRT.hdf

...which is a large file (~30 MB) containing detailed information on the position, tilt, etc. of the MODIS satellite. MRTSwath tool needs one of each, however.

Value

data.frame of matching files; or a list of non-matching files, if return_geoloc or return_product are TRUE.

Author(s)

Rishabh Gupta rishabh.uk@gmail.com

Examples

# Check your working directory
moddir = getwd()

# Here are some example MODIS files in mod09nrt/extdata/
# Code excluded from CRAN check because it depends on modiscdata
## Not run: 
library(devtools)
library(modiscdata)
moddir = system.file("extdata/2002raw/", package="modiscdata")

# You need to have some e.g. MOD files in it (from the MODIS-TERRA platform)
list.files(path=moddir, pattern="MOD")
list.files(path=moddir, pattern="MOD")

# Check for matches (for MODIS-TERRA platform)
check_for_matching_geolocation_files_mod09nrt(moddir=moddir, modtxt="MOD09", geoloctxt="MOD03", 
return_geoloc=FALSE, return_product=FALSE)

## End(Not run)

Get the filename from a path

Description

The filename is split on slashes, and the last item is taken; this should be just the filename.

Usage

extract_fn_from_path(fn_with_path)

Arguments

fn_with_path

The filename, with partial or full path

Value

fn The extracted filename

Author(s)

Nicholas J. Matzke matzke@berkeley.edu

See Also

strsplit

Examples

fn_with_path = "/Library/Frameworks/R.framework/Versions/2.15/Resources/library/modiscloud/extdata
/2002raw/MYD35_L2.A2002185.1910.005.2007206043609.hdf"
extract_fn_from_path(fn_with_path)

Run MRTSwath swath2grid tool

Description

MRTSwath is the "MODIS Reprojection Tool for swath products". See: https://lpdaac.usgs.gov/tools/modis_reprojection_tool_swath).

Usage

run_swath2grid_mod09nrt(mrtpath = "swath2grid", prmfn = "tmpMRTparams.prm",
  tifsdir, modfn, geoloc_fn, ul_lon, ul_lat, lr_lon, lr_lat)

Arguments

mrtpath

This is the path to the MRTSwath executable swath2grid. If your ~/.Rprofile file has the location of swath2grid in the PATH, then you can just use mrtpath="swath2grid". Otherwise, the user must provide the full path to swath2grid.

prmfn

The name of the parameter/control file which will be the input to MRTSwath's swath2grid function.

tifsdir

The directory to save the output TIF files in

modfn

The filename of the MODIS data

geoloc_fn

The filename of the corresponding geolocation file (annoyingly, this is a much larger file than the data file!)

ul_lon

Upper left (ul) longitude (x-coordinate) for subsetting

ul_lat

Upper left (ul) latitude (y-coordinate) for subsetting

lr_lon

Lower right (lr) longitude (x-coordinate) for subsetting

lr_lat

Lower right (lr) latitude (y-coordinate) for subsetting

Details

If you want this function to use MRTSwath tool successfully, you should add the directory with the MRTSwath executable to the default R PATH by editing ~/.Rprofile.

Value

cmdstr The string giving the system command that ran swath2grid

Author(s)

Nicholas J. Matzke matzke@berkeley.edu

See Also

write_MRTSwath_param_file_mod09nrt

http://landweb.nascom.nasa.gov/cgi-bin/QA_WWW/newPage.cgi?fileName=hdf_filename @cite NASA2001

Examples

#######################################################
# Run MRTSwath tool "swath2grid"
#######################################################

# Source MODIS files (both data and geolocation)
# Code excluded from CRAN check because it depends on modiscdata
## Not run: 
library(devtools)
library(modiscdata)
moddir = system.file("extdata/2002raw/", package="modiscdata")

# Get the matching data/geolocation file pairs
fns_df = check_for_matching_geolocation_files(moddir, modtxt="MOD09", geoloctxt="MOD03")
fns_df

# Resulting TIF files go in this directory
tifsdir = getwd()


# Box to subset
ul_lat = 13
ul_lon = -87
lr_lat = 8
lr_lon = -82

for (i in 1:nrow(fns_df))
	{
	
prmfn = write_MRTSwath_param_file_mod09nrt(prmfn="tmpMRTparams.prm", tifsdir=tifsdir,
 modfn=fns_df$mod09_fns[i], geoloc_fn=fns_df$mod03_fns[i], ul_lon=ul_lon, ul_lat=ul_lat, 
 lr_lon=lr_lon, lr_lat=lr_lat)
print(scan(file=prmfn, what="character", sep="\n"))
	
run_swath2grid_mod09nrt(mrtpath="swath2grid", prmfn="tmpMRTparams.prm", tifsdir=tifsdir,
 modfn=fns_df$mod309_fns[i], geoloc_fn=fns_df$mod03_fns[i], ul_lon=ul_lon, ul_lat=ul_lat,
 lr_lon=lr_lon, lr_lat=lr_lat)

	}

list.files(tifsdir, pattern=".tif", full.names=TRUE)

## End(Not run)

Remove double slash (slash a slash)

Description

Shortcut for: gsub(pattern="//", replacement="/", x=tmpstr)

Usage

slashslash(tmpstr)

Arguments

tmpstr

a path that you want to remove double slashes from

Details

This function is useful for removing double slashes that can appear in full pathnames due to inconsistencies in trailing slashes in working directories etc.

Value

outstr a string of the fixed path

Author(s)

Nicholas J. Matzke matzke@berkeley.edu

See Also

gsub

Examples

tmpstr = "/Library/Frameworks/R.framework/Versions/2.15/Resources/library/modiscloud/extdata/
2002raw//MYD03.A2002185.0645.005.2009192031332.hdf"

outstr = slashslash(tmpstr)
outstr

Write a parameter control file for MRTSwath

Description

MRTSwath is the "MODIS Reprojection Tool for swath products". See: https://lpdaac.usgs.gov/tools/modis_reprojection_tool_swath).

Usage

write_MRTSwath_param_file_mod09nrt(prmfn = "tmpMRTparams.prm", tifsdir, modfn,
  geoloc_fn, ul_lon, ul_lat, lr_lon, lr_lat)

Arguments

prmfn

The name of the parameter/control file which will be the input to MRTSwath's swath2grid function.

tifsdir

The directory to save the output TIF files in

modfn

The filename of the MODIS data

geoloc_fn

The filename of the corresponding geolocation file (annoyingly, this is a much larger file than the data file!)

ul_lon

Upper left (ul) longitude (x-coordinate) for subsetting

ul_lat

Upper left (ul) latitude (y-coordinate) for subsetting

lr_lon

Lower right (lr) longitude (x-coordinate) for subsetting

lr_lat

Lower right (lr) latitude (y-coordinate) for subsetting

Details

If you want this function to use MRTSwath tool successfully, you should add the directory with the MRTSwath executable to the default R PATH by editing ~/.Rprofile.

This function hard-codes these options into the parameter file:
* all the bands are extracted
* the output file is a GeoTIFF
* the output projection is Geographic (plain unprojected Latitude/Longitude)
* the resampling is Nearest Neighbor (NN), which of course is the only one which makes sense when the pixels encode bytes that encode bits that encode discrete classification results, 0/1 error flags, etc.

MRTswath can do many other projections and output formats; users can modify this function to run those options.

Value

prmfn The name of the temporary parameter file

Author(s)

Rishabh Gupta rishabh.uk@gmail.com

See Also

run_swath2grid_mod09nrt

http://landweb.nascom.nasa.gov/cgi-bin/QA_WWW/newPage.cgi?fileName=hdf_filename @cite NASA2001

Examples


# Source MODIS files (both data and geolocation)
# Code excluded from CRAN check because it depends on modiscdata
## Not run: 
library(devtools)
library(modiscdata)
moddir = system.file("extdata/2002raw/", package="modiscdata")

# Get the matching data/geolocation file pairs
fns_df = check_for_matching_geolocation_files_mod09nrt(moddir, modtxt="MOD09", geoloctxt="MOD03")
fns_df

# Resulting TIF files go in this directory
tifsdir = getwd()


# Box to subset
ul_lat = 13
ul_lon = -87
lr_lat = 8
lr_lon = -82

for (i in 1:nrow(fns_df))
	{
	
	prmfn = write_MRTSwath_param_file_mod09nrt(prmfn="tmpMRTparams.prm", tifsdir=tifsdir,
	modfn=fns_df$mod09_fns[i], geoloc_fn=fns_df$mod03_fns[i], ul_lon=ul_lon, ul_lat=ul_lat,
	lr_lon=lr_lon, lr_lat=lr_lat)
	print(scan(file=prmfn, what="character", sep="\n"))
	
	}

## End(Not run)