Revision 70d0063c
Added by Benoit Parmentier over 11 years ago
| climate/research/oregon/interpolation/covariates_production_temperatures.R | ||
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# -MODIS LST: mean and obs |
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#3) The output is a multiband file in tif format with projected covariates for the processing region/tile. |
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#AUTHOR: Benoit Parmentier |
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#DATE: 03/19/2013
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#DATE: 03/21/2013
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#PROJECT: NCEAS INPLANT: Environment and Organisms --TASK#363-- |
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##Comments and TODO: |
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################################################################################################## |
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###Loading R library and packages |
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library(RPostgreSQL) |
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library(sp) # Spatial pacakge with class definition by Bivand et al. |
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library(spdep) # Spatial pacakge with methods and spatial stat. by Bivand et al. |
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library(rgdal) # GDAL wrapper for R, spatial utilities |
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library(raster) |
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library(gtools) |
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library(rasterVis) |
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library(graphics) |
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library(grid) |
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library(lattice) |
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### Parameters and arguments |
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##Paths to inputs and output |
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var<-"TMAX" |
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in_path <- "/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/input_data/" |
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out_path<- "/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/output_data/" |
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lc_path<-"/home/layers/data/land-cover/lc-consensus-global" |
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#elev_path<-"/home/layers/data/terrain/dem-cgiar-srtm-1km-tif" |
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#infile3<-"countries_sinusoidal_world.shp" |
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#infile1<-"worldborder_sinusoidal.shp" |
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infile_modis_grid<-"modis_sinusoidal_grid_world.shp" |
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infile_elev<-"/home/layers/data/terrain/dem-cgiar-srtm-1km-tif/srtm_1km.tif" #this is the global file: replace later with the input produced by the DEM team |
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infile_canheight<-"Simard_Pinto_3DGlobalVeg_JGR.tif" #Canopy height |
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list_tiles_modis = c('h11v08','h11v07','h12v07','h12v08','h10v07','h10v08') #tile for Venezuel and surrounding area
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infile_reg_outline="" #input region outline defined by polygon |
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CRS_interp<-"+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs"; |
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CRS_locs_WGS84<-CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +towgs84=0,0,0") #Station coords WGS84
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out_region_name<-"_venezuela_region" #generated on the fly |
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out_suffix<-"_VE_03182013" |
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ref_rast_name<-"" #local raster name defining resolution, exent, local projection--. set on the fly?? |
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#for the processing tile/region? This is a group fo six tiles for now. |
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#The names of covariates can be changed...these names should be output/input from covar script!!! |
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rnames<-c("x","y","lon","lat","N","E","N_w","E_w","elev","slope","aspect","CANHEIGHT","DISTOC")
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lc_names<-c("LC1","LC2","LC3","LC4","LC5","LC6","LC7","LC8","LC9","LC10","LC11","LC12")
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lst_names<-c("mm_01","mm_02","mm_03","mm_04","mm_05","mm_06","mm_07","mm_08","mm_09","mm_10","mm_11","mm_12",
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"nobs_01","nobs_02","nobs_03","nobs_04","nobs_05","nobs_06","nobs_07","nobs_08", |
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"nobs_09","nobs_10","nobs_11","nobs_12") |
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covar_names<-c(rnames,lc_names,lst_names) |
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list_param_covar_production<-list(var,in_path,out_path,lc_path,infile_modis_grid,infile_elev,infile_canheight, |
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list_tiles_modis,infile_reg_outline,CRS_interp,CRS_locs_WGS84,out_region_name, |
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out_suffix,ref_rast_name,covar_names) |
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names(list_param_covar_production)<-c("var","in_path","out_path","lc_path","infile_modis_grid","infile_elev","infile_canheight",
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"list_tiles_modis","infile_reg_outline","CRS_interp","CRS_locs_WGS84","out_region_name", |
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"out_suffix","ref_rast_name","covar_names") |
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#LST_night_rast<-raster("mean_LST_Night_1km_h11v08_dec_11_03192013.tif")
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#### Functions used in the script ### |
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create_modis_tiles_region<-function(modis_grid,tiles){
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#This functions returns a subset of tiles from the modis grdi. |
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# |
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# |
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# |
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###Loading R library and packages |
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library(RPostgreSQL) |
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library(sp) # Spatial pacakge with class definition by Bivand et al. |
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library(spdep) # Spatial pacakge with methods and spatial stat. by Bivand et al. |
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library(rgdal) # GDAL wrapper for R, spatial utilities |
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library(raster) |
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library(gtools) |
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library(rasterVis) |
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library(graphics) |
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library(grid) |
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library(lattice) |
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### Parameters and arguments |
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########################################################### |
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############ Main body: BEGIN--START OF THE SCRIPT ################### |
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##### STEP 1: Reading region or tile information to set the study or processing region
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##### STEP 1: PARSING ARGUMENTS
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var<-list_param$var |
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in_path <-list_param$in_path |
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out_path<- list_param$out_path |
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lc_path<-list_param$lc_path |
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#elev_path<-"/home/layers/data/terrain/dem-cgiar-srtm-1km-tif" |
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#infile3<-"countries_sinusoidal_world.shp" |
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#infile1<-"worldborder_sinusoidal.shp" |
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infile_modis_grid<-list_param$infile_modis_grid |
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infile_elev<-list_param$infile_elev #this is the global file: replace later with the input produced by the DEM team |
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infile_canheight<-list_param$infile_canheight #Canopy height |
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list_tiles_modis<-list_param$list_tiles_modis #tile for Venezuel and surrounding area |
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list_tiles_modis<-list_param$list_tiles_modis #tile for Venezuela and surrounding area
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infile_reg_outline<-list_param$infile_reg_outline #input region outline defined by polygon |
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CRS_interp<-list_param$CRS_interp #local projection system |
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CRS_locs_WGS84<-list_param$CRS_locs_WGS84 # |
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out_region_name<-list_param$out_region_name #generated on the fly |
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out_suffix<-list_param$out_suffix |
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ref_rast_name<-list_param$ref_rast_name #local raster name defining resolution, exent, local projection--. set on the fly?? |
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#for the processing tile/region? This is a group fo six tiles for now. |
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covar_names<-list_param$covar_names |
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##### SET UP STUDY AREA #### |
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setwd(in_path) |
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filename<-sub(".shp","",infile_modis_grid) #Removing the extension from file.
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Nw<-sin(r2)*cos(r1) #Adding a variable to the dataframe |
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Ew<-sin(r2)*sin(r1) #Adding variable to the dataframe. |
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#topo_rast<-stack(STRM_reg,N,E,Nw,Ew) |
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###################################### |
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#4) LCC land cover |
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#LC12<-raster(paste("reg_con_1km_class_12_",out_suffix,".tif",sep="")) #this is open water
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LC12<-raster(lc_reg_s,layer=nlayers(lc_reg_s)) #this is open water |
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LC_mask<-LC12 |
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LC_mask[LC_mask==100]<-NA |
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LC_mask <- LC_mask > 100 |
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#lc_reg_s<-mask(x=lc_reg_s,mask=LC_mask,filename=paste("reg_con_1km_all_classes_",out_suffix,".tif",sep=""),
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# bandorder="BSQ",overwrite=TRUE) |
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############################### |
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#5) DISTOC, distance to coast: Would be useful to have a distance to coast layer ready... |
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################################ |
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##Step 3: combine covariates in one stack for the next work flow stage |
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#Create a stack in tif format... |
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#? output name?? |
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r<-stack(x,y,lon,lat,N,E,Nw,Ew,SRTM_reg,terrain_rast,CANHEIGHT,distoc_reg) |
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#rnames<-c("x","y","lon","lat","N","E","N_w","E_w","elev","slope","aspect","CANHEIGHT","DISTOC")
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#names(r)<-rnames |
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s_raster<-r |
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#Add landcover layers |
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#lc_names<-c("LC1","LC2","LC3","LC4","LC5","LC6","LC7","LC8","LC9","LC10","LC11","LC12")
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#names(lc_reg_s)<-lc_names #assign land cover names |
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s_raster<-addLayer(s_raster, lc_reg_s) |
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lst_s<-stack(c(as.character(mean_m_list),as.character(nobs_m_list))) |
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#lst_names<-c("mm_01","mm_02","mm_03","mm_04","mm_05","mm_06","mm_07","mm_08","mm_09","mm_10","mm_11","mm_12",
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# "nobs_01","nobs_02","nobs_03","nobs_04","nobs_05","nobs_06","nobs_07","nobs_08", |
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# "nobs_09","nobs_10","nobs_11","nobs_12") |
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#names(lst_s)<-lst_names |
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s_raster<-addLayer(s_raster, lst_s) |
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#covar_names<-c(rnames,lc_names,lst_names) |
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return(raster_name) |
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} |
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####################################################### |
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################### END OF SCRIPT/FUNCTION ##################### |
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################### END OF SCRIPT/FUNCTION ##################### |
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Also available in: Unified diff
Covariates production raster modifications -transforming scrip into function