Nothing
#'Clip GEDI Level2B data by Coordinates
#'
#'@description This function extracts GEDI Level1B data a within given bounding coordinates
#'
#'
#'@param level2b A GEDI Level2B object (output of \code{\link[rGEDI:readLevel2B]{readLevel2B}} function).
#'An S4 object of class "gedi.level2b".
#'@param xmin Numeric. West longitude (x) coordinate of the bounding rectangle, in decimal degrees.
#'@param xmax Numeric. East longitude (x) coordinate of the bounding rectangle, in decimal degrees.
#'@param ymin Numeric. South latitude (y) coordinate of the bounding rectangle, in decimal degrees.
#'@param ymax Numeric. North latitude (y) coordinate of the bounding rectangle, in decimal degrees.
#'@param output Optional character path where to save the new hdf5 file. The default stores a temporary file only.
#'
#'@return Returns a list of S4 object of class "gedi.level2b" containing clipped GEDI Level2B data.
#'
#'@seealso https://lpdaac.usgs.gov/products/gedi01_bv001/
#'
#'@examples
#'\donttest{
#'outdir = tempdir()
#'
#'# Specifying the path to GEDI level2B data (zip file)
#'level2B_fp_zip <- system.file("extdata",
#' "GEDI02_B_2019108080338_O01964_T05337_02_001_01_sub.zip",
#' package="rGEDI")
#'
#'# Unzipping GEDI level2A data
#'level2Bpath <- unzip(level2B_fp_zip,exdir = outdir)
#'
#'# Reading GEDI level2B data (h5 file)
#'level2b<-readLevel2B(level2Bpath=level2Bpath)
#'
#'# Bounding rectangle coordinates
#'xmin=-44.13
#'xmax=-44.12
#'ymin=-13.74
#'ymax=-13.73
#'
#'# Specifying output file and path
#'output<-file.path(outdir,"GEDI02_B_2019108080338_O01964_T05337_02_001_01_clip")
#'
#'# Clipping GEDI data by extent boundary box
#'level2b_clip <- clipLevel2B(level2b, xmin, xmax, ymin, ymax)
#'
#'close(level2b)
#'close(level2b_clip)
#'}
#'@export
clipLevel2B = function(level2b, xmin, xmax, ymin, ymax, output=""){
# Get all spatial data as a list of dataframes with spatial information
spData = getSpatialData2B(level2b)
checkClipExtentInputs(level2b, "gedi.level2b", xmin, xmax, ymin, ymax)
masks = clipSpDataByExtentLevelB(spData, xmin, xmax, ymin, ymax)
if (output == "") {
output = tempfile(fileext = ".h5")
}
output = fs::path_ext_set(output, "h5")
newFile = clipByMask2B(level2b,
masks,
output)
output = newFile@h5$filename
close(newFile)
result = readLevel2B(output)
return (result)
}
#'Clip GEDI Level2B data by geometry
#'
#'@description This function extracts GEDI Level1B data within a given geometry
#'
#'@param level2b A GEDI Level2B object (output of \code{\link[rGEDI:readLevel2B]{readLevel2B}} function).
#'An S4 object of class "gedi.level2b".
#'@param polygon_spdf Polygon. An object of class \code{\link[sp]{SpatialPolygonsDataFrame-class}},
#'which can be loaded as an ESRI shapefile using \code{\link[raster:shapefile]{raster::shapefile()}} function in the \emph{raster} package.
#'@param output optional character path where to save the new h5file. Default "" (temporary file).
#'@param split_by Polygon id. If defined, GEDI data will be clipped by each polygon using the attribute specified by \code{split_by} from the attribute table.
#'
#'@return Returns a list of S4 objects of class "gedi.level2b" containing clipped GEDI Level2B data.
#'
#'@seealso https://lpdaac.usgs.gov/products/gedi01_bv001/
#'
#'@examples
#'\donttest{
#'outdir = tempdir()
#'
#'# Specifying the path to GEDI level2B data (zip file)
#'level2B_fp_zip <- system.file("extdata",
#' "GEDI02_B_2019108080338_O01964_T05337_02_001_01_sub.zip",
#' package="rGEDI")
#'
#'# Unzipping GEDI level2A data
#'level2Bpath <- unzip(level2B_fp_zip,exdir = outdir)
#'
#'# Reading GEDI level2B data (h5 file)
#'level2b<-readLevel2B(level2Bpath=level2Bpath)
#'
#'# Specifying the path to shapefile
#'polygon_filepath <- system.file("extdata", "stands_cerrado.shp", package="rGEDI")
#'
#'# Reading shapefile as SpatialPolygonsDataFrame object
#'library(raster)
#'polygon_spdf<-shapefile(polygon_filepath)
#'
#'# Specifying output file and path
#'output<-file.path(outdir,"GEDI02_B_2019108080338_O01964_T05337_02_001_01_clip")
#'
#'# Clipping GEDI data by extent boundary box
#'level2b_clip <- clipLevel2BGeometry(level2b, polygon_spdf = polygon_spdf,
#' output=output,
#' split_by="id")
#'
#'close(level2b)
#'lapply(level2b_clip, close)
#'}
#'@export
clipLevel2BGeometry = function(level2b, polygon_spdf, output="", split_by=NULL) {
output = checkOutput(output)
checkClipGeoInputs(level2b, "gedi.level2b", polygon_spdf, split_by)
spData = getSpatialData2B(level2b)
xmin = polygon_spdf@bbox[1,1]
xmax = polygon_spdf@bbox[1,2]
ymin = polygon_spdf@bbox[2,1]
ymax = polygon_spdf@bbox[2,2]
masks = clipSpDataByExtentLevelB(spData, xmin, xmax, ymin, ymax)
polygon_masks = getPolygonMaskLevelB(spData, masks, polygon_spdf, split_by)
results = clipByMasks(level2b, polygon_masks, output, split_by, clipByMask2B)
return (results)
}
# Helper function to return spatial data within a dataframe
getSpatialData2B = function(level2b) {
level2b.h5<-level2b@h5
groups_id<-grep("BEAM\\d{4}$",gsub("/","",
hdf5r::list.groups(level2b.h5, recursive = F)), value = T)
beams_spdf = list()
for ( i in gsub("/","",groups_id)){
beams_spdf[[i]] = data.frame(
latitude_bin0=level2b.h5[[paste0(i,"/geolocation/latitude_bin0")]][],
latitude_lastbin=level2b.h5[[paste0(i,"/geolocation/latitude_lastbin")]][],
longitude_bin0=level2b.h5[[paste0(i,"/geolocation/longitude_bin0")]][],
longitude_lastbin=level2b.h5[[paste0(i,"/geolocation/longitude_lastbin")]][]
)
}
return (beams_spdf)
}
clipByMask2B = function(level2b, masks, output = "") {
newFile = hdf5r::H5File$new(output, mode="w")
if(length(masks) == 0) {
message("No intersection found!")
newFile$close_all()
newFile = hdf5r::H5File$new(output, mode="r")
result = new("gedi.level2b", h5 = newFile)
return(result)
}
for (attr in hdf5r::list.attributes(level2b@h5)) {
hdf5r::h5attr(newFile, attr) = hdf5r::h5attr(level2b@h5, attr)
}
all_groups = hdf5r::list.groups(level2b@h5)
beams_with_value = sapply(masks, length)>0
beams_with_value = names(which(beams_with_value))
beams_with_value = c(beams_with_value, "METADATA")
which_groups = gsub("([^/]*).*","\\1",all_groups) %in% beams_with_value
groups_with_value = all_groups[which_groups]
# Setup progress bar
all_datasets = hdf5r::list.datasets(level2b@h5)
which_datasets = gsub("([^/]*).*","\\1",all_datasets) %in% beams_with_value
datasets_with_value = all_datasets[which_datasets]
total = length(datasets_with_value)
pb = utils::txtProgressBar(min = 0, max = total, style = 3)
progress = 0
for (group in groups_with_value) {
beam_id = strsplit(group, "/")[[1]][1]
mask = masks[[beam_id]]
mask_size = length(mask)
hdf5r::createGroup(newFile,group)
createAttributesWithinGroup(level2b@h5, newFile, group)
for (dt in hdf5r::list.datasets(level2b@h5[[group]], recursive = FALSE, full.names = T)) {
beam_shot_n = level2b@h5[[beam_id]][["shot_number"]]$dims
h5_dt = level2b@h5[[dt]]
dt_dim = h5_dt$dims
dtype = h5_dt$get_type()
if (is.na(all(h5_dt$chunk_dims))) {
chunkdims = NULL
} else {
chunkdims = h5_dt$chunk_dims
}
if (length(dt_dim) == 1) {
if (dt_dim == 1) {
hdf5r::createDataSet(newFile,dt,h5_dt[], dtype=dtype, chunk_dim=chunkdims)
} else if (dt_dim == beam_shot_n) {
hdf5r::createDataSet(newFile,dt,h5_dt[mask], dtype=dtype, chunk_dim=chunkdims)
} else if ((dt_dim %% beam_shot_n) == 0) {
n_waveforms = h5_dt$dims / beam_shot_n
v.seq = Vectorize(seq.default,vectorize.args = c("from"), SIMPLIFY=T)
mask_init = mask*n_waveforms - (n_waveforms - 1)
mask_waveform = matrix(v.seq(mask_init, len=n_waveforms), nrow=1)[1,]
total_size = n_waveforms*mask_size
chunk_part = 1
dt_res=hdf5r::createDataSet(newFile, dt, dtype=dtype, chunk_dim=chunkdims, dims=total_size)
while (chunk_part < total_size) {
end = chunk_part+chunkdims-1
if (end > total_size) {
end = total_size
}
get_part = mask_waveform[(chunk_part):(end)]
dt_res[get_part] = h5_dt[get_part]
chunk_part = end+1
}
}
} else if (length(dt_dim) == 2 && dt_dim[1] == beam_shot_n) {
if (length(mask) == 1) {
chunkdims = chunkdims[[2]]
}
hdf5r::createDataSet(newFile,dt,h5_dt[mask,], dtype=dtype, chunk_dim=chunkdims)
} else if (length(dt_dim) == 2 && dt_dim[2] == beam_shot_n){
if (length(mask) == 1) {
chunkdims = chunkdims[[1]]
}
hdf5r::createDataSet(newFile,dt,h5_dt[,mask], dtype=dtype, chunk_dim=chunkdims)
} else {
stop(paste0("Don't know how to handle dataset: ", dt, "\nContact the maintainer of the package!"))
}
#Update progress
progress = progress + 1
utils::setTxtProgressBar(pb, progress)
}
}
newFile$close_all()
newFile = hdf5r::H5File$new(output, mode="r")
result = new("gedi.level2b", h5 = newFile)
close(pb)
#spatial = level2b2dt(level2b)
return (result)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.