Revision 55408bb4
Added by Benoit Parmentier over 11 years ago
| climate/research/oregon/interpolation/master_script_temp.R | ||
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#STAGE 5: Output analyses-visualization of results for specific dates... |
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# |
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#AUTHOR: Benoit Parmentier |
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#DATE: 05/14/2013
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#DATE: 05/17/2013
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#PROJECT: NCEAS INPLANT: Environment and Organisms --TASK#363, TASK$568-- |
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### Need to add documentation ### |
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script_path<-"/home/parmentier/Data/IPLANT_project/env_layers_scripts/" |
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#script_path<-"/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/" |
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#list_script_files<- |
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##SCRIPT USED FOR THE PREDICTIONS: Source all scripts here to avoid confusion on versions being run!!!! |
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##SCRIPT USED FOR THE PREDICTIONS: Source or list all scripts here to avoid confusion on versions being run!!!!
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#source(file.path(script_path,"master_script_temp_05132013.R")) #Master script can be run directly...
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#source(file.path(script_path,"master_script_temp_05162013.R")) #Master script can be run directly...
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#CALLED FROM MASTER SCRIPT: |
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#modis_download_script <- file.path(script_path,"modis_download_05132013.py") # LST modis download python script |
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modis_download_script <- file.path(script_path,"modis_download_05142013.py") # LST modis download python script |
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clim_script <- file.path(script_path,"climatology_05132013.py") # LST climatology python script |
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grass_setting_script <- file.path(script_path,"grass-setup.R") |
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clim_script <- file.path(script_path,"climatology_05142013.py") # LST climatology python script |
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grass_setting_script <- file.path(script_path,"grass-setup.R") #Set up system shell environment for python+GRASS |
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source(file.path(script_path,"download_and_produce_MODIS_LST_climatology_05162013.R")) |
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source(file.path(script_path,"covariates_production_temperatures_05132013.R")) |
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source(file.path(script_path,"Database_stations_covariates_processing_function_05062013.R")) |
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source(file.path(script_path,"GAM_fusion_analysis_raster_prediction_multisampling_05062013.R")) |
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stages_to_run<-c(0,0,3,4,5) #May decide on antoher strategy later on... |
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var<-"TMAX" # variable being interpolated |
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out_prefix<-"_365d_GAM_CAI_all_lst_05132013" #User defined output prefix
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out_prefix<-"_365d_GAM_CAI_all_lst_05172013" #User defined output prefix
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#interpolation_method<-c("gam_fusion","gam_CAI") #other otpions to be added later
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interpolation_method<-c("gam_CAI") #other otpions to be added later
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#interpolation_method<-c("gam_fusion") #other otpions to be added later
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} |
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lc_path<-"/home/layers/data/land-cover/lc-consensus-global" |
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infile_modis_grid<-"modis_sinusoidal_grid_world.shp" #Give path!!! NEED TO CHANGE THIS... |
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infile_modis_grid<-"/home/layers/commons/modis/modis_sinusoidal/modis_sinusoidal_grid_world.shp" #Give path!!! NEED TO CHANGE THIS...
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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<-"/home/layers/data/land-cover/treeheight-simard2011/Simard_Pinto_3DGlobalVeg_JGR.tif" #Canopy height |
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list_tiles_modis <- c("h11v08,h11v07,h12v07,h12v08,h10v07,h10v08") #tile for Venezuela and surrounding area
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#CRS_interp <-"+proj=lcc +lat_1=43 +lat_2=45.5 +lat_0=41.75 +lon_0=-120.5 +x_0=400000 +y_0=0 +ellps=GRS80 +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_05092013"
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out_suffix<-"_VE_05172013"
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ref_rast_name<-"" #local raster name defining resolution, exent, local projection--. set on the fly?? |
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#ref_rast_name<-"mean_day244_rescaled.rst" #local raster name defining resolution, exent: oregon |
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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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############ STAGE 1: LST Climatology ############### |
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#Parameters,Inputs from R to Python?? |
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#tiles = ['h11v08','h11v07','h12v07','h12v08','h10v07','h10v08'] #These tiles correspond to Venezuela. |
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list_tiles_modis <- c("h11v08,h11v07,h12v07,h12v08,h10v07,h10v08") #tile for Venezuel and surrounding area
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#list_tiles_modis <- c("h08v04,h09v04") #tiles for Oregon #defined above...
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start_year = "2001" |
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end_year = "2010" |
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#end_year = "2002" #for testing (year included?) |
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end_month= "12" |
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start_month= "1" |
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hdfdir = '/home/layers/commons/modis/MOD11A1_tiles' #destination file where hdf files are stored locally after download. |
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if (!file.exists(hdfdir)){
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dir.create(hdfdir) |
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#} else{
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# out_path <-paste(out_path..) |
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} |
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if (var=="TMIN") {
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night="1" # if 1 then produce night climatology |
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} else{
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night="0" # if 0 then produce day climatology |
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} |
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download="1" # if 1 then download modis files before calculating averages |
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#hdfdir = '/home/layers/commons/modis/MOD11A1_tiles' #destination file where hdf files are stored locally after download. |
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hdfdir = '/home/parmentier/Data/IPLANT_project/MOD11A1_tiles' |
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download=1 |
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clim_calc=0 |
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out_suffix_modis="_05132013" |
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#end_month= "12" |
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#start_month= "1" |
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list_param_python_script <- list(list_tiles_modis,start_year,end_year,start_month,end_month,hdfdir, |
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night,download,out_suffix_modis) |
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names(list_param_python_script)<-c("list_tiles_modis","start_year","end_year","start_month","end_month","hdfdir",
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"night","download","out_suffix_modis") |
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list_param_python_script_str <- paste(unlist(list_param_python_script), collapse=" ") |
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#command_str<-"python /home/parmentier/Data/test5.py h01v05,h02v05 2001 2005 12 1 /benoit 1 test_out 1" |
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#paste(toString(list_param_python_script),collapse=",",sep=" ") |
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list_param_download_clim_LST_script <- list(list_tiles_modis,start_year,end_year,hdfdir, |
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var,grass_setting_script,modis_download_script, clim_script, |
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download,clim_calc,out_suffix_modis) |
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names(list_param_download_clim_LST_script)<-c("list_tiles_modis","start_year","end_year","hdfdir",
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"var","grass_setting_script","modis_download_script","clim_script", |
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"download","clim_calc","out_suffix_modis") |
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if (stages_to_run[1]==1){
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##Run download if necessary |
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if (download==1){
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command_str <- paste("python",modis_download_script, list_param_python_script_str,sep=" ")
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#command_str <- paste("python","/home/parmentier/Data/benoit_test/test5.py", list_param_python_script_str,sep=" ")
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system(command_str) |
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} |
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##Now run climatology |
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source(grass_setting_script) |
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command_str <- paste("python",clim_script, list_param_python_script_str,sep=" ")
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system(command_str) |
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#/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/climatology_05132013.py |
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download_calculate_MODIS_LST_climatology(1,list_param_download_clim_LST_script) |
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} |
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#Collect LST climatology list as output??? |
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############ STAGE 2: Covariate production ################ |
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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,hdfdir,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","hdfdir","covar_names") |
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## Modify to store infile_covar_brick in output folder!!! |
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if (stages_to_run[2]==2){
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Also available in: Unified diff
master script, calling python scripts from R function