##################    Master script for temperature predictions  #######################################

############################ TMIN AND TMAX predictions ##########################################

#                           

##This script produces intperpolated surface of TMIN and TMAX for specified processing region(s) given sets 

#of inputs and parameters.

#STAGE 1: LST climatology downloading and/or calculation

#STAGE 2: Covariates preparation for study/processing area: calculation of covariates (spect,land cover,etc.) and reprojection

#STAGE 3: Data preparation: meteorological station database query and extraction of covariates values from raster brick

#STAGE 4: Raster prediction: run interpolation method (-- gam fusion, gam CAI, ...) and perform validation 

#STAGE 5: Output analyses: assessment of results for specific dates...

#

#AUTHOR: Benoit Parmentier                                                                       

#DATE: 11/29/2013                                                                                 

#PROJECT: NCEAS INPLANT: Environment and Organisms --TASK#363, TASK$568--   

## TODO:

# Modify code for stage 1 and call python script from R in parallel

# Add options to run only specific stage + additional out_suffix?

# Make master script a function?

# Add log file for master script,add function to collect inputs and outputs

##################################################################################################

###Loading R library and packages  ou 

library(RPostgreSQL)

library(maps)

library(maptools)

library(parallel)

library(gtools)                              # loading some useful tools 

library(mgcv)                                # GAM package by Simon Wood

library(sp)                                  # Spatial pacakge with class definition by Bivand et al.

library(spdep)                               # Spatial pacakge with methods and spatial stat. by Bivand et al.

library(rgdal)                               # GDAL wrapper for R, spatial utilities

library(gstat)                               # Kriging and co-kriging by Pebesma et al.

library(fields)                              # NCAR Spatial Interpolation methods such as kriging, splines

library(raster)                              # Hijmans et al. package for raster processing

library(rasterVis)

library(spgwr)

library(reshape)

library(plotrix)

######## PARAMETERS FOR WORK FLOW #########################

### Need to add documentation ###

#Adding command line arguments to use mpiexec

args<-commandArgs(TRUE)

script_path<-"/nobackupp6/aguzman4/climateLayers/finalCode/environmental-layers/climate/research/oregon/interpolation"

dataHome<-"/nobackupp6/aguzman4/climateLayers/inputLayers/"

script_path2<-"/nobackupp6/aguzman4/climateLayers/finalCode/environmental-layers/climate/research/world/interpolation"

#CALLED FROM MASTER SCRIPT:

modis_download_script <- file.path(script_path,"modis_download.py") # LST modis download python script

clim_script <- file.path(script_path,"climatology.py") # LST climatology python script

grass_setting_script <- file.path(script_path,"grass-setup.R") #Set up system shell environment for python+GRASS

#source(file.path(script_path,"download_and_produce_MODIS_LST_climatology_06112013.R"))

source(file.path(script_path2,"covariates_production_temperature.R"))

source(file.path(script_path2,"Database_stations_covariates_processing_function.R"))

source(file.path(script_path2,"GAM_fusion_analysis_raster_prediction_multisampling.R"))

source(file.path(script_path,"results_interpolation_date_output_analyses.R"))

#source(file.path(script_path,"results_covariates_database_stations_output_analyses_04012013.R")) #to be completed

#FUNCTIONS CALLED FROM GAM ANALYSIS RASTER PREDICTION ARE FOUND IN...

source(file.path(script_path,"sampling_script_functions.R"))

source(file.path(script_path2,"GAM_fusion_function_multisampling.R")) #Includes Fusion and CAI methods

source(file.path(script_path2,"interpolation_method_day_function_multisampling.R")) #Include GAM_day

source(file.path(script_path,"GAM_fusion_function_multisampling_validation_metrics.R"))

#sub sampling of stations

source(file.path(script_path2,"subsampling_data_func.R")) #Include GAM_day

#stages_to_run<-c(0,2,3,4,5) #MRun only raster fitting, prediction and assessemnt (providing lst averages, covar brick and met stations)

#stages_to_run<-c(0,2,3,0,0)

stages_to_run<-c(0,2,3,0,0)

#If stage 2 is skipped then use previous covar object

covar_obj_file<-args[8]

#If stage 3 is skipped then use previous met_stations object

met_stations_outfiles_obj_file<-args[9]

var<-"TMAX" # variable being interpolated

out_prefix<-args[1]

out_suffix<-args[2]                             #Regional suffix

out_suffix_modis<-args[3]                       #pattern to find tiles produced previously     

#interpolation_method<-c("gam_fusion") #other otpions to be added later

interpolation_method<-c("gam_CAI")

out_path <- args[4] #"/nobackup/aguzman4/climateLayers/output/"

out_path <-paste(out_path,out_prefix,sep="")

if (!file.exists(out_path)){

  dir.create(out_path)

  #} else{

  #  out_path <-paste(out_path..)

}

lc_path<-paste(dataHome,"lc-consensus-global_combined",sep="")

infile_modis_grid<-paste(dataHome,"/modis_grid/modis_sinusoidal_grid_world.shp",sep="") #modis grid tiling system, global

infile_elev<-paste(dataHome,"/GMTED2010/elevation_md_GMTED2010_md.tif",sep="")  #elevation at 1km, global extent to be replaced by the new fused product 

infile_canheight<-paste(dataHome,"treeheight-simard2011/Simard_Pinto_3DGlobalVeg_JGR.tif",sep="")#Canopy height, global extent

infile_distoc <- paste(dataHome,"distance_to_coast/GMT_intermediate_coast_distance_01d_rev.tif",sep="") #distance to coast, global extent at 0.01 deg

infile_reg_outline <- args[5]  #input region outline defined by polygon

ref_rast_name<- args[6]

buffer_dist<-0 #not in use yet, must change climatology step to make sure additional tiles are downloaded and LST averages

               #must also be calculated for neighbouring tiles.

list_tiles_modis <- "" 

CRS_interp<-"+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs";

#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";

CRS_locs_WGS84<-CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +towgs84=0,0,0") #Station coords WGS84

out_region_name<-""

#The names of covariates can be changed...these names should be output/input from covar script!!!

rnames<-c("x","y","lon","lat","N","E","N_w","E_w","elev_s","slope","aspect","CANHGHT","DISTOC")

lc_names<-c("LC1","LC2","LC3","LC4","LC5","LC6","LC7","LC8","LC9","LC10","LC11","LC12")

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",

               "nobs_01","nobs_02","nobs_03","nobs_04","nobs_05","nobs_06","nobs_07","nobs_08",

               "nobs_09","nobs_10","nobs_11","nobs_12")

covar_names<-c(rnames,lc_names,lst_names)

#list_val_range <-c("lon,-180,180","lat,-90,90","N,-1,1","E,-1,1","N_w,-1,1","E_w,-1,1","elev_s,0,6000","slope,0,90",

#                   "aspect,0,360","DISTOC,-0,10000000","CANHGHT,0,255","LC1,0,100","LC5,0,100","mm_01,-15,50",

#                   "mm_02,-15,50","mm_03,-15,50","mm_04,-15,50","mm_05,-15,50","mm_06,-15,50","mm_07,-15,50",

#                   "mm_08,-15,50","mm_09,-15,50","mm_10,-15,50","mm_11,-15,50","mm_12,-15,50")

list_val_range <-c("lon,-180,180","lat,-90,90","N,-1,1","E,-1,1","N_w,-1,1","E_w,-1,1","elev_s,-400,9000","slope,0,90",

                   "aspect,0,360","DISTOC,-0,10000000","CANHGHT,0,255","LC1,0,100","LC5,0,100","mm_01,-60,70",

                   "mm_02,-60,70","mm_03,-60,70","mm_04,-60,70","mm_05,-60,70","mm_06,-60,70","mm_07,-60,70",

                   "mm_08,-60,70","mm_09,-60,70","mm_10,-60,70","mm_11,-60,70","mm_12,-60,70")

############ STAGE 1: LST Climatology ###############

#Parameters,Inputs from R to Python??

start_year = "2001"

end_year = "2010"

hdfdir <- "" #path directory to MODIS data

download=0 #download MODIS product if 1

clim_calc=1 #calculate lst averages/climatology if 1

list_param_download_clim_LST_script <- list(list_tiles_modis,start_year,end_year,hdfdir,

                                            var,grass_setting_script,modis_download_script, clim_script,

                                            download,clim_calc,out_suffix_modis)

names(list_param_download_clim_LST_script)<-c("list_tiles_modis","start_year","end_year","hdfdir",

                                              "var","grass_setting_script","modis_download_script","clim_script",

                                              "download","clim_calc","out_suffix_modis")

no_tiles <- length(unlist(strsplit(list_tiles_modis,",")))  # transform string into separate element in char vector

if (stages_to_run[1]==1){

  #clim_production_obj <-mclapply(1:2, list_param=list_param_download_clim_LST_script, download_calculate_MODIS_LST_climatology,mc.preschedule=FALSE,mc.cores = 2) #This is the end bracket from mclapply(...) statement

  clim_production_obj <-lapply(1:no_tiles, list_param=list_param_download_clim_LST_script, download_calculate_MODIS_LST_climatology) #,mc.preschedule=FALSE,mc.cores = 2) #This is the end bracket from mclapply(...) statement

}

#Collect LST climatology list as output???

############ STAGE 2: Covariate production ################

#If tiles are already in wgs84 grid

process_LST<-args[7] #FALSE

#list of 18 parameters

list_param_covar_production<-list(var,out_path,lc_path,infile_modis_grid,infile_elev,infile_canheight,

                                  infile_distoc,list_tiles_modis,infile_reg_outline,CRS_interp,CRS_locs_WGS84,out_region_name,

                                  buffer_dist,list_val_range,out_suffix,out_suffix_modis,ref_rast_name,hdfdir,covar_names,process_LST) 

names(list_param_covar_production)<-c("var","out_path","lc_path","infile_modis_grid","infile_elev","infile_canheight",

                                      "infile_distoc","list_tiles_modis","infile_reg_outline","CRS_interp","CRS_locs_WGS84","out_region_name",

                                   "buffer_dist","list_val_range","out_suffix","out_suffix_modis","ref_rast_name","hdfdir","covar_names","process_LST") 

## Modify to store infile_covar_brick in output folder!!!

if (stages_to_run[2]==2){

  covar_obj <- covariates_production_temperature(list_param_covar_production)

  infile_covariates <- covar_obj$infile_covariates

  infile_reg_outline <- covar_obj$infile_reg_outline

  covar_names<- covar_obj$covar_names

}else{

  covar_obj <-load_obj(covar_obj_file)

  infile_covariates <- covar_obj$infile_covariates

  infile_reg_outline <- covar_obj$infile_reg_outline

  covar_names<- covar_obj$covar_names

}  

#Note that if stages_to_run[2]!=2, then use values defined at the beginning of the script for infile_covariates and infile_reg_outline

############# STAGE 3: Data preparation ###############

#specific to this stage

#db.name <- "ghcn_subset"       # name of the Postgres database

db.name <- "ghcn_gssd_90to01.db"       # name of the Postgres database

range_years<-c("1992","1993") #right bound not included in the range!!

range_years_clim<-c("1990","2001") #right bound not included in the range!!

infile_ghncd_data <-paste(dataHome,"ghcn/v2.92-upd-2012052822/ghcnd_gssd_station_list.txt",sep="") #This is the textfile of station locations from GHCND

qc_flags_stations<-c("0","S")    #flags allowed for screening after the query from the GHCND??

#qc_flags_stations<-c("0")    #flags allowed for screening after the query from the GHCND??

#infile_covariates and infile_reg_outline defined in stage 2 or at the start of script...

#Add subsampling parameters

sub_sampling <- TRUE  #if TRUE then monthly stations data are resampled

sub_sample_rnd <- TRUE #if  TRUE use random sampling  in addition to spatial  sub-sampling

target_range_nb <- c(600,700) # number of stations desired as min and max, convergence to  min  for  now

dist_range <- c(0,0.04165) #distance range  for pruning,  usually (0,5) in km or 0,0.009*5 for  degreee

step_dist <- 0.00833

#daily

sub_sampling_day <- TRUE

target_range_daily_nb <- c(600,700) # number of stations desired as min and max, convergence to  min  for  now

#list of 12 parameters for input in the function...

#list_param_prep<-list(db.name,var,range_years,range_years_clim,infile_reg_outline,infile_ghncd_data,infile_covariates,CRS_locs_WGS84,out_path,covar_names,qc_flags_stations,out_prefix)

#cnames<-c("db.name","var","range_years","range_years_clim","infile_reg_outline","infile_ghncd_data","infile_covariates","CRS_locs_WGS84","out_path","covar_names","qc_flags_stations","out_prefix")

list_param_prep<-list(db.name,var,range_years,range_years_clim,infile_reg_outline,infile_ghncd_data,infile_covariates,CRS_locs_WGS84,out_path,covar_names,qc_flags_stations,out_prefix,

 sub_sampling,sub_sample_rnd,target_range_nb,dist_range,step_dist,target_range_daily_nb,sub_sampling_day)

cnames<-c("db.name","var","range_years","range_years_clim","infile_reg_outline","infile_ghncd_data","infile_covariates","CRS_locs_WGS84","out_path","covar_names",

 "qc_flags_stations","out_prefix","sub_sampling","sub_sample_rnd","target_range_nb","dist_range","step_dist","target_range_daily_nb","sub_sampling_day")

names(list_param_prep)<-cnames

##### RUN SCRIPT TO GET STATION DATA WITH COVARIATES #####

if (stages_to_run[3]==3){

  list_outfiles<-database_covariates_preparation(list_param_prep)

  print("Done 3")

}

if ((stages_to_run[4]==4) | (stages_to_run[5]==5)){

    list_outfiles <-load_obj(met_stations_outfiles_obj_file)

}else{

    quit()

  }

############### STAGE 4: RASTER PREDICTION #################

#Prepare parameters for for raster prediction... 

#Collect parameters from the previous stage: data preparation stage

#3 parameters from output

infile_monthly<-list_outfiles$monthly_covar_ghcn_data #outile4 from database_covar script

infile_daily<-list_outfiles$daily_covar_ghcn_data  #outfile3 from database_covar script

infile_locs<- list_outfiles$loc_stations_ghcn #outfile2? from database covar script

#names(outfiles_obj)<- c("loc_stations","loc_stations_ghcn","daily_covar_ghcn_data","monthly_covar_ghcn_data")

list_param_data_prep <- list(infile_monthly,infile_daily,infile_locs,infile_covariates,covar_names,var,out_prefix,CRS_locs_WGS84)

names(list_param_data_prep) <- c("infile_monthly","infile_daily","infile_locs","infile_covariates","covar_names","var","out_prefix","CRS_locs_WGS84")

#Set additional parameters

#Input for sampling function...need to reorganize inputs!!!

seed_number<- 100  #if seed zero then no seed?     

nb_sample<-1           #number of time random sampling must be repeated for every hold out proportion

#step<- 0.1         

step<- 0         

constant<-0             #if value 1 then use the same samples as date one for the all set of dates

prop_minmax<-c(0.3,0.3)  #if prop_min=prop_max and step=0 then predictions are done for the number of dates...

#prop_minmax<-c(0.1,0.7)  #if prop_min=prop_max and step=0 then predictions are done for the number of dates...

seed_number_month <- 100

nb_sample_month <-1           #number of time random sampling must be repeated for every hold out proportion

step_month <-0         

#step_month <-0.1

constant_month <- 0             #if value 1 then use the same samples as date one for the all set of dates

prop_minmax_month <-c(0,0)  #if prop_min=prop_max and step=0 then predictions are done for the number of dates...

#dates_selected<-c("20100101","20100102","20100103","20100901") # Note that the dates set must have a specific format: yyymmdd

#dates_selected<-c("20100101","20100102","20100301","20100302","20100501","20100502","20100701","20100702","20100901","20100902","20101101","20101102")

dates_selected<-"" # if empty string then predict for the full year specified earlier

#dates_selected <- 2 # if integer then predict for the evert n dat in the year specified earlier

screen_data_training<- FALSE #screen training data for NA and use same input training for all models fitted

use_clim_image <- TRUE # use predicted image as a base...rather than average Tmin at the station for delta

join_daily <- FALSE # join monthly and daily station before calucating delta

#Models to run...this can be changed for each run

#LC1: Evergreen/deciduous needleleaf trees

#list_models<-c("y_var ~ lat*lon + elev_s + N_w*E_w",

#               "y_var ~ lat*lon + elev_s + DISTOC",

#               "y_var ~ lat*lon + elev_s + LST",

#               "y_var ~ lat*lon + elev_s + LST + I(LST*LC1)")

#list_models2<-c("y_var ~ s(lat,lon) + s(DISTOC)")

list_models2 <- NULL

interp_method2 <- NULL #other options are "gwr" and "kriging"

#list_models<-c("y_var ~ s(lat,lon,k=4) + s(elev_s,k=4)",

#               "y_var ~ s(lat,lon,k=4) + s(elev_s,k=4) + s(LST,k=4)") #,

               #"y_var ~ s(lat,lon) + s(elev_s) + s(N_w,E_w) + s(LST) + ti(LST,LC1) + s(LC1)")

#list_models<-c("y_var ~ s(lat,lon,k=5) + s(elev_s,k=3)",

#               "y_var ~ s(lat,lon,k=5) + s(elev_s,k=3) + s(LST,k=3)")

list_models<-c("y_var ~ s(lat,lon,k=5) + s(elev_s,k=3) + s(LST,k=3)")

#Default name of LST avg to be matched               

lst_avg<-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")  

#Add num_cores for doing global runs

num_cores<-args[10]

#max number of cells to read in memory

max_mem<-args[11]

#rasterOptions(maxmemory=1e+07,timer=TRUE)

#Collect all parameters in a list

list_param_raster_prediction<-list(list_param_data_prep,screen_data_training,

                                seed_number,nb_sample,step,constant,prop_minmax,dates_selected,

                                seed_number_month,nb_sample_month,step_month,constant_month,prop_minmax_month,

                                list_models,list_models2,interp_method2,lst_avg,out_path,script_path,use_clim_image,join_daily,

                                interpolation_method,num_cores,max_mem)

names(list_param_raster_prediction)<-c("list_param_data_prep","screen_data_training",

                                "seed_number","nb_sample","step","constant","prop_minmax","dates_selected",

                                "seed_number_month","nb_sample_month","step_month","constant_month","prop_minmax_month",

                                "list_models","list_models2","interp_method2","lst_avg","out_path","script_path","use_clim_image","join_daily",

                                "interpolation_method","num_cores","max_mem")

#debug(raster_prediction_fun)

#debug(debug_fun_test)

#debug_fun_test(list_param_raster_prediction)

if (stages_to_run[4]==4){

  raster_prediction_obj <- raster_prediction_fun(list_param_raster_prediction)

}

############## STAGE 5: OUTPUT ANALYSES ##################

if ((stages_to_run[4]==0)&(stages_to_run[5]==5)){

   #Load from previous

   if (var=="TMAX"){

      y_var_name<-"dailyTmax"

      y_var_month<-"TMax"

   }

   if (var=="TMIN"){

     y_var_name<-"dailyTmin"

     y_var_month <-"TMin"

   }

   raster_prediction_obj<-load_obj(file.path(out_path,paste("raster_prediction_obj_",interpolation_method,"_", y_var

_name,out_prefix,".RData",sep="")))

}

date_selected_results<-c("20100101") 

list_param_results_analyses<-list(out_path,script_path,raster_prediction_obj,interpolation_method,

                                  covar_obj,date_selected_results,var,out_prefix)

names(list_param_results_analyses)<-c("out_path","script_path","raster_prediction_obj","interpolation_method",

                     "covar_obj","date_selected_results","var","out_prefix")

#plots_assessment_by_date<-function(j,list_param){

if (stages_to_run[5]==5){

  #source(file.path(script_path,"results_interpolation_date_output_analyses_08052013.R"))

  #Use lapply or mclapply

  summary_v_day <-plots_assessment_by_date(1,list_param_results_analyses)

  #Call as function...

}

###############   END OF SCRIPT   ###################

#####################################################

# #LAND COVER INFORMATION

# LC1: Evergreen/deciduous needleleaf trees

# LC2: Evergreen broadleaf trees

# LC3: Deciduous broadleaf trees

# LC4: Mixed/other trees

# LC5: Shrubs

# LC6: Herbaceous vegetation

# LC7: Cultivated and managed vegetation

# LC8: Regularly flooded shrub/herbaceous vegetation

# LC9: Urban/built-up

# LC10: Snow/ice

# LC11: Barren lands/sparse vegetation

# LC12: Open water