merged with Caio

azh2 · Mar 9, 2020 · 6e99b20 · 6e99b20
1 parent dd00d48
commit 6e99b20
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Showing 49 changed files with 263 additions and 256 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,4 +1,4 @@
-# Generated by roxygen2: do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 export(LPDAACDataPool)
 export(clipLevel1B)

diff --git a/R/C_processExtractMetrics.R b/R/C_processExtractMetrics.R
@@ -113,7 +113,7 @@
 #'
 #'# Unzipping ALS data
 #'alsfile_Amazon_filepath <- unzip(alsfile_Amazon_zip,exdir = dirname(alsfile_Amazon_zip))
-#'alsfile_Savanna_filepath <- unzip(alsfile_Smazon_zip,exdir = dirname(alsfile_Savanna_zip))
+#'alsfile_Savanna_filepath <- unzip(alsfile_Savanna_zip,exdir = dirname(alsfile_Savanna_zip))
 #'
 #'# Reading and plot ALS file (las file)
 #'als_Amazon<-readLAS(alsfile_Amazon_filepath)
@@ -135,14 +135,14 @@
 #'                            coords = c(xcenter_Savanna, ycenter_Savanna))
 #'
 #'# Extracting GEDI feull-waveform derived metrics
-#'wf_amazon_metrics<-gediWFMetrics(input=wf_amazon,outRoot=file.path(getwd(), "amazon"))
-#'wf_cerrado_metrics<-gediWFMetrics(input=wf_cerrado,outRoot=file.path(getwd(), "cerrado"))
+#'wf_amazon_metrics<-gediWFMetrics(input=wf_Amazon,outRoot=file.path(getwd(), "amazon"))
+#'wf_savanna_metrics<-gediWFMetrics(input=wf_Savanna,outRoot=file.path(getwd(), "cerrado"))
 #'
-#'close(wf_amazon)
-#'close(wf_cerrado)
+#'close(wf_Amazon)
+#'close(wf_Savanna)
 #'
-#'metrics<-rbind(wf_amazon_metrics,wf_cerrado_metrics)
-#'rownames(metrics)<-c("Amazon","Cerrado")
+#'metrics<-rbind(wf_amazon_metrics,wf_savanna_metrics)
+#'rownames(metrics)<-c("Amazon","Savanna")
 #'head(metrics)
 #'}
 #'
@@ -301,7 +301,7 @@ gediWFMetrics = function(
   inputInList = list(NULL, NULL)
   if (class(input)=="list") {
     files = sapply(input, function(x) {
-      x@h5$close_all()
+      close(x)
       return (x@h5$filename)
     })
     inList = tempfile(fileext=".txt")
@@ -310,7 +310,7 @@ gediWFMetrics = function(
     close(fileHandle)
     inputInList[[2]] = inList
   } else {
-    input@h5$close_all()
+    close(input)
     inputInList[[1]] = input@h5$filename
   }
 

diff --git a/R/C_simulateFullWaveform.R b/R/C_simulateFullWaveform.R
@@ -88,7 +88,7 @@
 #'
 #'# Unzipping ALS data
 #'alsfile_Amazon_filepath <- unzip(alsfile_Amazon_zip,exdir = dirname(alsfile_Amazon_zip))
-#'alsfile_Savanna_filepath <- unzip(alsfile_Smazon_zip,exdir = dirname(alsfile_Savanna_zip))
+#'alsfile_Savanna_filepath <- unzip(alsfile_Savanna_zip,exdir = dirname(alsfile_Savanna_zip))
 #'
 #'# Reading and plot ALS file (las file)
 #'als_Amazon<-readLAS(alsfile_Amazon_filepath)
@@ -132,9 +132,9 @@
 #'plot(wf_Savanna, relative=TRUE, polygon=TRUE, type="l", lwd=2, col="green",
 #'     xlab="Waveform Amplitude (%)", ylab="Elevation (m)", ylim=c(815,835))
 #'grid()
-#' 
-#'close(wf_Amazon)
+#'
 #'close(wf_Amazon)
+#'close(wf_Savanna)
 #'}
 #'
 #' @import hdf5r

diff --git a/R/clipLevel1B.R b/R/clipLevel1B.R
@@ -53,7 +53,7 @@ clipLevel1B = function(level1b, xmin, xmax, ymin, ymax, output=""){
                          masks,
                          output)
   output = newFile@h5$filename
-  newFile@h5$close_all()
+  close(newFile)
   result = readLevel1B(output)
 
   return (result)

diff --git a/R/clipLevel1BGeo.R b/R/clipLevel1BGeo.R
@@ -37,12 +37,12 @@
 #'ymax = -13.71244
 #'
 #'# clip by boundary box coordinates
-#'level1bGeo_clip <- clipLevel1BGeo(level1BGeo,xmin, xmax, ymin, ymax)
+#'level1BGeo_clip <- clipLevel1BGeo(level1BGeo,xmin, xmax, ymin, ymax)
 #'
 #'library(leaflet)
 #'leaflet() %>%
-#'  addCircleMarkers(level1bGeo_clip$longitude_bin0,
-#'                   level1bGeo_clip$latitude_bin0,
+#'  addCircleMarkers(level1BGeo_clip$longitude_bin0,
+#'                   level1BGeo_clip$latitude_bin0,
 #'                   radius = 1,
 #'                   opacity = 1,
 #'                   color = "red")  %>%
@@ -106,9 +106,9 @@ clipLevel1BGeo = function(level1BGeo,xmin, xmax, ymin, ymax){
 #'
 #'# Reading shapefile as SpatialPolygonsDataFrame object
 #'library(raster)
-#'polygon_spdf<-shapefile(polygons_filepath)
+#'polygon_spdf<-shapefile(polygon_filepath)
 #'
-#'level1bGeo_clip = clipLevel1BGeometry(level1bGeo, polygon_spdf, split_by="id")
+#'level1BGeo_clip = clipLevel1BGeometry(level1BGeo, polygon_spdf, split_by="id")
 #'
 #'library(leaflet)
 #'leaflet() %>%

diff --git a/R/clipLevel2A.R b/R/clipLevel2A.R
@@ -55,7 +55,7 @@ clipLevel2A = function(level2a, xmin, xmax, ymin, ymax, output=""){
                          masks,
                          output)
   output = newFile@h5$filename
-  newFile@h5$close_all()
+  close(newFile)
   result = readLevel2A(output)
 
   return (result)
@@ -94,7 +94,7 @@ clipLevel2A = function(level2a, xmin, xmax, ymin, ymax, output=""){
 #'
 #'# Reading shapefile as SpatialPolygonsDataFrame object
 #'library(raster)
-#'polygon_spdf<-shapefile(polygons_filepath)
+#'polygon_spdf<-shapefile(polygon_filepath)
 #'
 #'# Spepecifing output file and path
 #'output<-paste0(getwd(),"//GEDI02_A_2019108080338_O01964_T05337_02_001_01_clip")

diff --git a/R/clipLevel2AM.R b/R/clipLevel2AM.R
@@ -94,7 +94,7 @@ clipLevel2AM = function(level2AM,xmin, xmax, ymin, ymax){
 #'
 #'# Reading shapefile as SpatialPolygonsDataFrame object
 #'library(raster)
-#'polygon_spdf<-shapefile(polygons_filepath)
+#'polygon_spdf<-shapefile(polygon_filepath)
 #'
 #'level2AM_clip = clipLevel2AMGeometry(level2AM, polygon_spdf, split_by="id")
 #'

diff --git a/R/clipLevel2B.R b/R/clipLevel2B.R
@@ -67,7 +67,7 @@ clipLevel2B = function(level2b, xmin, xmax, ymin, ymax, output=""){
                          masks,
                          output)
   output = newFile@h5$filename
-  newFile@h5$close_all()
+  close(newFile)
   result = readLevel2B(output)
 
   return (result)
@@ -104,7 +104,7 @@ clipLevel2B = function(level2b, xmin, xmax, ymin, ymax, output=""){
 #'
 #'# Reading shapefile as SpatialPolygonsDataFrame object
 #'library(raster)
-#'polygon_spdf<-shapefile(polygons_filepath)
+#'polygon_spdf<-shapefile(polygon_filepath)
 #'
 #'# Spepecifing output file and path
 #'output<-paste0(getwd(),"//GEDI02_B_2019108080338_O01964_T05337_02_001_01_clip")

diff --git a/R/clipLevel2BPAIProfile.R b/R/clipLevel2BPAIProfile.R
@@ -95,7 +95,7 @@ clipLevel2BPAIProfile = function(level2BPAIProfile,xmin, xmax, ymin, ymax){
 #'
 #'# Reading shapefile as SpatialPolygonsDataFrame object
 #'library(raster)
-#'polygon_spdf<-shapefile(polygons_filepath)
+#'polygon_spdf<-shapefile(polygon_filepath)
 #'
 #'# clip level2BPAIProfile by geometry
 #'level2b_clip_geometry <- clipLevel2BPAIProfileGeometry(

diff --git a/R/clipLevel2BPAVDProfile.R b/R/clipLevel2BPAVDProfile.R
@@ -94,7 +94,7 @@ clipLevel2BPAVDProfile = function(level2BPAVDProfile,xmin, xmax, ymin, ymax){
 #'
 #'# Reading shapefile as SpatialPolygonsDataFrame object
 #'library(raster)
-#'polygon_spdf<-shapefile(polygons_filepath)
+#'polygon_spdf<-shapefile(polygon_filepath)
 #'
 #'# clip level2BPAIProfile by geometry
 #'level2BPAVDProfile_clip <- clipLevel2BPAVDProfileGeometry(

diff --git a/R/clipLevel2BVPM.R b/R/clipLevel2BVPM.R
@@ -119,7 +119,7 @@ clipLevel2BVPM = function(level2BVPM,xmin, xmax, ymin, ymax){
 #'
 #'# Reading shapefile as SpatialPolygonsDataFrame object
 #'library(raster)
-#'polygon_spdf<-shapefile(polygons_filepath)
+#'polygon_spdf<-shapefile(polygon_filepath)
 #'
 #'# clip level2BVPM by geometry
 #'level2b_clip_geometry <- clipLevel2BVPMGeometry(level2BVPM,polygon_spdf,split_by="id")

diff --git a/R/getLevel1bGeo.R b/R/getLevel1bGeo.R
@@ -110,8 +110,8 @@
 #'level1b<-readLevel1B(level1Bpath=level1Bpath)
 #'
 #'# Get GEDI level1B geolocations
-#'level1bGeo<-getLevel1BGeo(level1b,select=c("elevation_bin0", "elevation_lastbin"))
-#'head(level1bGeo)
+#'level1BGeo<-getLevel1BGeo(level1b,select=c("elevation_bin0", "elevation_lastbin"))
+#'head(level1BGeo)
 #'
 #'
 #'@export

diff --git a/R/getLevel2AM.R b/R/getLevel2AM.R
@@ -12,7 +12,7 @@
 #'@seealso https://lpdaac.usgs.gov/products/gedi02_av001/
 #'
 #'@examples
-#'\dontrun{
+#'
 #'# specify the path to GEDI level2A data (zip file)
 #'level2A_fp_zip <- system.file("extdata",
 #'                   "GEDI02_A_2019108080338_O01964_T05337_02_001_01_sub.zip",
@@ -27,7 +27,7 @@
 #'# Get GEDI Elevation and Height Metrics
 #'level2AM<-getLevel2AM(level2a)
 #'head(level2AM)
-#'}
+#'
 #'@export
 getLevel2AM<-function(level2a){
   level2a<-level2a@h5

diff --git a/R/gridStatsLevel2AM.R b/R/gridStatsLevel2AM.R
@@ -14,7 +14,7 @@
 #'@seealso https://lpdaac.usgs.gov/products/gedi02_av001/
 #'
 #'@examples
-#'\dontrun{
+#'\donttest{
 #'# specify the path to GEDI level2A data (zip file)
 #'level2A_fp_zip <- system.file("extdata",
 #'                   "GEDI02_A_2019108080338_O01964_T05337_02_001_01_sub.zip",

diff --git a/R/polyStatsLevel2AM.R b/R/polyStatsLevel2AM.R
@@ -31,7 +31,7 @@
 #'
 #'# Reading shapefile as SpatialPolygonsDataFrame object
 #'library(raster)
-#'polygon_spdf<-shapefile(polygons_filepath)
+#'polygon_spdf<-shapefile(polygon_filepath)
 #'
 #'# Get GEDI Eleveation and Relative Metrics (level2A)
 #'level2AM<-getLevel2AM(level2a)

diff --git a/R/polyStatsLevel2BVPM.R b/R/polyStatsLevel2BVPM.R
@@ -31,7 +31,7 @@
 #'
 #'# Reading shapefile as SpatialPolygonsDataFrame object
 #'library(raster)
-#'polygon_spdf<-shapefile(polygons_filepath)
+#'polygon_spdf<-shapefile(polygon_filepath)
 #'
 #'# Get GEDI Canopy Cover and Vertical Profile Metrics
 #'level2BVPM<-getLevel2BVPM(level2b)

diff --git a/R/readLevel2A.R b/R/readLevel2A.R
@@ -12,7 +12,7 @@
 #'@seealso https://lpdaac.usgs.gov/products/gedi02_av001/
 #'
 #'@examples
-#'\dontrun{
+#'\donttest{
 #'# specify the path to GEDI level2A data (zip file)
 #'level2A_fp_zip <- system.file("extdata",
 #'                   "GEDI02_A_2019108080338_O01964_T05337_02_001_01_sub.zip",

diff --git a/R/zzz.R b/R/zzz.R
@@ -4,9 +4,27 @@
   classes = classes[classes %in% objs]
   objNames = names(classes)
   for (o in objNames) {
-    try(close(get(o)), silent=T)
+    try(close(get(o, envir = .GlobalEnv)), silent=T)
   }
-  rm(list=as.vector(objNames))
   library.dynam.unload("rGEDI", libpath)
   invisible()
 }
+
+.onLoad <- function(libname, pkgname){
+  objs = c("gedi.level1a", "gedi.level1b", "gedi.level2a", "gedi.level1bSim")
+  classes = sapply(ls(.GlobalEnv), function(x) class(get(x)))
+  classes = classes[classes %in% objs]
+  objNames = names(classes)
+  for (i in 1:length(objNames)) {
+    if (length(classes) > 0) {
+      assign(
+        objNames[i], 
+        new(
+          classes[i][[1]],
+          h5=hdf5r::h5file(get(objNames[i])@h5$filename)), 
+        envir=.GlobalEnv)
+    }
+  }
+
+  invisible()
+}
diff --git a/inst/extdata/GEDI01_B_2019108080338_O01964_T05337_02_003_01_sub.zip b/inst/extdata/GEDI01_B_2019108080338_O01964_T05337_02_003_01_sub.zip
diff --git a/inst/extdata/GEDI02_A_2019108080338_O01964_T05337_02_001_01_sub.zip b/inst/extdata/GEDI02_A_2019108080338_O01964_T05337_02_001_01_sub.zip
diff --git a/inst/extdata/GEDI02_B_2019108080338_O01964_T05337_02_001_01_sub.zip b/inst/extdata/GEDI02_B_2019108080338_O01964_T05337_02_001_01_sub.zip
diff --git a/inst/extdata/Savanna.zip b/inst/extdata/Savanna.zip
diff --git a/man/LPDAACDataPool.Rd b/man/LPDAACDataPool.Rd
diff --git a/man/clipLevel1BGeo.Rd b/man/clipLevel1BGeo.Rd
diff --git a/man/clipLevel1BGeoGeometry.Rd b/man/clipLevel1BGeoGeometry.Rd
diff --git a/man/clipLevel2AGeometry.Rd b/man/clipLevel2AGeometry.Rd
diff --git a/man/clipLevel2AMGeometry.Rd b/man/clipLevel2AMGeometry.Rd
diff --git a/man/clipLevel2BGeometry.Rd b/man/clipLevel2BGeometry.Rd
diff --git a/man/clipLevel2BPAIProfileGeometry.Rd b/man/clipLevel2BPAIProfileGeometry.Rd
diff --git a/man/clipLevel2BPAVDProfileGeometry.Rd b/man/clipLevel2BPAVDProfileGeometry.Rd
diff --git a/man/clipLevel2BVPMGeometry.Rd b/man/clipLevel2BVPMGeometry.Rd