I had similar issue too.
I modified the runMrt to make it work, you will find attached a
working script that you can source to replace MODIS::runMrt before the
authors fix this bug (source('runMrt.R').
Hope it helps.
On Wed, Jul 15, 2015 at 12:12 AM, Roberto Horn <[email protected]> wrote:
> Hello
>
> Im having trouble with function runMrt from the package MODIS. I've
> already looked for help in forums, with no success. Any help would be
> useful!
>
> runMrt(product="MOD09GA",tileH="13",tileV="11" ,begin="2014.01.01",
> end="2014.01.02", SDSstring="000000000000100001000",
> job="mod09ga/safra14.15", outProj="GEO", datum="WGS84",
> pixelSize="0.0045", mosaic="FALSE")
>
> All suggested packages are installed
> Output projection: Geographic
> Output pixel size: 0.0045
> Resampling method: nn
> No output projection parameters specified. Reprojecting with no Parameters!
> Error in runMrt(product = "MOD09GA", tileH = "13", tileV = "11", begin
> = "2014.01.01", :
> object 'ftpdirs' not found
>
> -----------------------------------------------------
> System info:
> Win 7 32-bit
> R version 3.2.1 (2015-06-18)
> MODIS version: 0.10-29
> MRT directory: D:/MRT/MRT
> raster version: 2.4-15
> rgdal 1.0-4
> rgeos 0.3-11
> XML 3.98-1.3
> RCurl 1.95-4.7
>
>
> Thank you!
>
> _______________________________________________
> R-sig-Geo mailing list
> [email protected]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
--
Ahmadou H. DICKO
statistician economist (Ingénieur Statisticien Économiste)
PhD candidate in Climate change economics
Faculty of economics and managment - Cheikh Anta Diop University
West African Science Service Center on Climate Change and Adaptated
Land Use (WASCAL)
Center for Development Research (ZEF) - University of Bonn
email : [email protected]
twitter : @dickoah
github : github/dickoa
tel : +221 33 827 55 16
portable: +221 77 123 81 69
runMrt <- function (...)
{
MODISoptions(save = FALSE, quiet = TRUE)
opts <- MODIS:::combineOptions(...)
if (!opts$mrtOk) {
stop("MRT path not set or MRT not installed on your system!")
}
opts$product <- MODIS:::getProduct(opts$product, quiet = TRUE)
opts$product$CCC <- MODIS:::getCollection(opts$product, collection = opts$collection)
tLimits <- transDate(begin = opts$begin, end = opts$end)
opts$localArcPath <- MODIS:::setPath(opts$localArcPath)
opts$outDirPath <- MODIS:::setPath(opts$outDirPath)
if (!tolower(opts$dataFormat) %in% c("raw binary", "hdf-eos",
"hdf4image", "gtiff", "geotiff")) {
stop("dataFormat='", opts$dataFormat, "' is not supported by MRT (only 'raw binary', 'HDF-EOS' or 'GeoTiff')")
}
ext <- MODIS:::getExtension(opts$dataFormat)
if (is.null(opts$quiet)) {
opts$quiet <- FALSE
}
if (is.null(opts$mosaic)) {
opts$mosaic <- TRUE
}
if (is.null(opts$anonym)) {
opts$anonym <- TRUE
}
opts$resamplingType <- MODIS:::checkResamplingType(opts$resamplingType,
tool = "mrt", quiet = TRUE)
opts$outProj <- MODIS:::checkOutProj(opts$outProj, tool = "mrt",
quiet = TRUE)
if (opts$outProj[1] == "asIn") {
if (as.numeric(opts$product$CCC) > 3) {
opts$outProj <- list(short = "SIN", long = "Sinusoidal")
}
else {
opts$outProj <- list(short = "ISIN", long = "Integerized Sinusoidal")
}
}
cat("Output projection:", opts$outProj$long, "\n")
if (opts$outProj$short == "UTM") {
if (is.null(opts$zone)) {
cat("No UTM zone specified using MRT autodetection.\n")
}
else {
cat("Using UTM zone:", opts$zone, "\n")
}
}
cat("Output pixel size:", opts$pixelSize, "\n")
cat("Resampling method:", opts$resamplingType, "\n")
if (is.null(opts$datum)) {
cat("No Datum specified, using 'NODATUM'!\n")
opts$datum <- "NODATUM"
}
else if (!toupper(opts$datum) %in% c("NAD27", "NAD83", "WGS66",
"WGS72", "WGS84", "NODATUM")) {
stop("\"datum\" must be one of: \"NAD27\", \"NAD83\", \"WGS66\", \"WGS72\", \"WGS84\" or \"NODATUM\"")
}
if (is.null(opts$projPara)) {
if (opts$outProj$short == "SIN") {
opts$projPara <- "6371007.18 0.00 0.00 0.00 0.00 0.00 0.00 0.00 86400.00 0.00 0.00 0.00 0.00 0.00 0.00"
}
else {
cat("No output projection parameters specified. Reprojecting with no Parameters!\n")
opts$projPara <- "0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0"
}
}
else {
cat("Output projection parameters specified!\nUsing:\n ",
opts$projPara, "\n")
}
for (z in 1:length(opts$product$PRODUCT)) {
if (opts$product$TYPE[z] == "CMG") {
tileID = "GLOBAL"
ntiles = 1
}
else {
opts$extent <- MODIS:::getTile(extent = opts$extent, tileH = opts$tileH,
tileV = opts$tileV, buffer = opts$buffer)
ntiles <- length(opts$extent$tile)
}
todo <- paste(opts$product$PRODUCT[z], ".", opts$product$CCC[[opts$product$PRODUCT[z]]],
sep = "")
for (u in 1:length(todo)) {
if (is.null(opts$job)) {
opts$job <- paste(todo[u], "_", format(Sys.time(),
"%Y%m%d%H%M%S"), sep = "")
cat("No 'job' name specified, generated (date/time based)):",
opts$job, "\n")
}
outDir <- file.path(opts$outDirPath, opts$job, fsep = "/")
dir.create(outDir)
ftpdirs <- list()
ftpdirs[[1]] <- as.Date(MODIS:::getStruc(product = strsplit(todo[u],
"\\.")[[1]][1], collection = strsplit(todo[u],
"\\.")[[1]][2], begin = opts$begin, end = opts$end)$dates)
avDates <- ftpdirs[[1]]
avDates <- avDates[!is.na(avDates)]
sel <- as.Date(avDates, format = "%Y.%m.%d")
us <- sel >= tLimits$begin & sel <= tLimits$end
if (sum(us, na.rm = TRUE) > 0) {
avDates <- avDates[us]
for (l in 1:length(avDates)) {
files <- unlist(MODIS:::getHdf(product = opts$product$PRODUCT[z],
collection = strsplit(todo[u], "\\.")[[1]][2],
begin = avDates[l], end = avDates[l], tileH = opts$extent$tileH,
tileV = opts$extent$tileV, stubbornness = opts$stubbornness))
if (length(files) != 0) {
mos <- opts$mosaic
if (mos) {
if (sum(file.exists(files)) < length(opts$extent$tile)) {
mos <- FALSE
}
else {
mos <- TRUE
}
}
else {
mos <- FALSE
}
if (mos) {
v <- 1
}
else {
v <- seq_along(files)
}
for (q in v) {
w <- options("warn")
options(warn = -1)
if (is.null(opts$SDSstring)) {
opts$SDSstring <- rep(1, length(MODIS:::getSds(HdfName = files[q],
method = "mrt")$SDSnames))
}
SDSstringIntern <- MODIS:::getSds(HdfName = files[q],
SDSstring = opts$SDSstring, method = "mrt")
options(warn = w$warn)
if (!opts$quiet && u == 1 && l == 1) {
cat("\n#############################\nExtracing SDS:",
SDSstringIntern$SDSnames, "#############################\n",
sep = "\n")
}
if (mos) {
TmpMosNam <- paste("TmpMosaic", MODIS:::makeRandomString(),
".hdf", sep = "")
paraname <- file.path(outDir, "/MRTgMosaic.prm",
fsep = "/")
filename = file(paraname, open = "wt")
write(paste("\"", files, "\"", sep = "",
collapse = " "), filename)
close(filename)
if (.Platform$OS == "unix") {
system(paste("mrtmosaic -i ", paraname,
" -o ", outDir, "/", TmpMosNam, " -s '",
SDSstringIntern$SDSstring, "'", sep = ""))
}
else {
shell(paste("mrtmosaic -i \"", paraname,
"\" -o \"", normalizePath(outDir),
"\\", TmpMosNam, "\" -s \"", SDSstringIntern$SDSstring,
"\"", sep = ""))
}
unlink(paraname)
Sys.sleep(0.5)
}
basenam <- strsplit(files[q], "/")[[1]]
basenam <- basenam[length(basenam)]
if (mos) {
basenam <- paste(strsplit(basenam, "\\.")[[1]][c(1,
2, 4)], collapse = ".")
}
else {
basenam <- paste(strsplit(basenam, "\\.")[[1]][c(1,
2, 3, 4)], collapse = ".")
}
if (!opts$anonym) {
basenam <- paste(basenam, opts$job, sep = ".")
}
paraname <- paste(outDir, "/MRTgResample.prm",
sep = "")
filename = file(paraname, open = "wt")
if (mos) {
write(paste("INPUT_FILENAME = \"", outDir,
"/", TmpMosNam, "\"", sep = ""), filename)
}
else {
write(paste("SPECTRAL_SUBSET = ( ", SDSstringIntern$SDSstring,
" )", sep = ""), filename)
write(paste("INPUT_FILENAME = \"", files[q],
"\"", sep = ""), filename)
}
write("SPATIAL_SUBSET_TYPE = INPUT_LAT_LONG",
filename)
if (!is.null(opts$extent$extent)) {
write(paste("SPATIAL_SUBSET_UL_CORNER = (",
opts$extent$extent@ymax, " ", opts$extent$extent@xmin,
")", sep = ""), filename)
write(paste("SPATIAL_SUBSET_LR_CORNER = (",
opts$extent$extent@ymin, " ", opts$extent$extent@xmax,
")", sep = ""), filename)
}
if (opts$pixelSize != "asIn") {
write(paste("OUTPUT_PIXEL_SIZE = ", opts$pixelSize,
sep = ""), filename)
}
write(paste("OUTPUT_FILENAME = ", outDir,
"/", basenam, ext, sep = ""), filename)
write(paste("RESAMPLING_TYPE = ", opts$resamplingType,
sep = ""), filename)
write(paste("OUTPUT_PROJECTION_TYPE = ",
opts$outProj$short, sep = ""), filename)
if (opts$outProj$short == "UTM" && !is.null(opts$zone)) {
write(paste("UTM_ZONE = ", opts$zone,
sep = ""), filename)
}
if (!is.null(opts$projPara)) {
write(paste("OUTPUT_PROJECTION_PARAMETERS = ( ",
opts$projPara, " )", sep = ""), filename)
}
if (!is.null(opts$datum)) {
write(paste("DATUM =", opts$datum, sep = ""),
filename)
}
close(filename)
if (.Platform$OS == "unix") {
system(paste("resample -p ", paraname,
sep = ""))
}
else {
shell(paste("resample -p \"", paraname,
"\" -o \"", outDir, "/", basenam, ext,
sep = ""))
}
unlink(paraname)
if (mos) {
unlink(paste(outDir, TmpMosNam, sep = "/"))
}
}
}
else {
cat("Missing files on", avDates[l], "jumping to the next date",
sep = "\n")
}
}
}
else {
cat("No files found for", todo[u], "within the date range\n")
}
}
}
}
environment(runMrt) <- as.environment("package:MODIS")_______________________________________________
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