################################ DOWNLOAD AND PRODUCE LST CLIMATOLOGY  #######################################

############################ Production of spatial average from MODIS ##########################################

#This script downloads modis tiles and computes monthly average over a given time period.

#Part 1: Download given list of tiles...

#Part 2: Compute climatology using monhtly average method over 10 years 

#

# This R script calls python scripts. 

#

#AUTHORS: Benoit Parmentier    

#         Using python scripts started by J. Regetz and modified by B.Parmentier.

#DATE: 05/30/2013                                                                                 

#To Do:

#-collect list of LST files created

#-solve issue realted to parallelization of python script: GRASS problem?

#PROJECT: NCEAS INPLANT: Environment and Organisms --TASK#???--   

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

download_calculate_MODIS_LST_climatology <-function(j,list_param){

  ###Function to download and calculate LST climatology from MODIS tiles

  #AUTHOR: Benoit Parmentier                                                                       

  #DATE: 05/30/2013                                                                                 

  #PROJECT: NCEAS INPLANT: Environment and Organisms --TASK#363--   

  #1) var 

  #2) list_tiles_modis 

  #3) start_year 

  #4) end_year 

  #5) hdfdir: destination file where hdf files are stored locally after download.

  #6) grass_setting_script 

  #7) modis_download_script 

  #8) clim_script

  #9) download  if 1 then download modis files before calculating averages

  #10) clim_calc

  #11) out_suffix_modis

  ###Loading R library and packages   

  #...

  #PARSING OUT input parameters

  var <- list_param$var

  list_tiles_modis <- list_param$list_tiles_modis

  start_year <- list_param$start_year 

  end_year <- list_param$end_year 

  hdfdir <- list_param$hdfdir #destination file where hdf files are stored locally after download.

  grass_setting_script <- list_param$grass_setting_script

  modis_download_script <- list_param$modis_download_script

  clim_script <- list_param$clim_script

  download <- list_param$download #"1"  # if 1 then download modis files before calculating averages

  clim_calc <- list_param$clim_calc #"1"  # if 1 then download modis files before calculating averages

  out_suffix_modis <- list_param$out_suffix_modis

  #j to be used later...parallelization??

  #Additional parameters

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

  list_tiles_modis <- list_tiles_modis[j]

  end_month= "12"

  start_month= "1"

  ### Create output directory if it does not exist

  if (!file.exists(hdfdir)){

    dir.create(hdfdir)

    #} else{

    #  out_path <-paste(out_path..)

  }

  ### CALCULATE NIGHT OR DAY CLIMATOLOGY?

  if (var=="TMIN") {

    night="1" # if 1 then produce night climatology

  } else{

    night="0" # if 0 then produce day climatology

  }  

  ## Prepare list of arguments for python script

  list_param_python_script <- list(list_tiles_modis,start_year,end_year,start_month,end_month,hdfdir,

                                   night,download,out_suffix_modis)

  names(list_param_python_script)<-c("list_tiles_modis","start_year","end_year","start_month","end_month","hdfdir",

                                     "night","download","out_suffix_modis")

  list_param_python_script_str <- paste(unlist(list_param_python_script), collapse=" ")

  #command_str<-"python /home/parmentier/Data/test5.py h01v05,h02v05 2001 2005 12 1 /benoit 1 test_out 1"

  #paste(toString(list_param_python_script),collapse=",",sep=" ")

  command_download_str <- paste("python",modis_download_script, list_param_python_script_str,sep=" ")

  command_clim_str <- paste("python",clim_script, list_param_python_script_str,sep=" ") #preparing shell command

  ##Downownload files if necessary...

  if (download==1){

    system(command_download_str)

  }

  if (clim_calc==1){

    ##Now run climatology: Can add other climatology scripts or method to produce climatology later on...

    source(grass_setting_script) #Setting to access GRASS (current setting valid for Atlas at nceas)  

    system(command_clim_str)

  }

#   ## return list of files???, may be modified later to return clim list and list of downloaded files + missing.

#   if (clim_calc==1){

#     list_output_obj <-list(command_download_str,command_clim_str)

#     names(list_output_obj) <- c("command_download_str", "command_clim_str")

#   } else{

#     list_output_obj <-list(command_download_str)

#     names(list_output_obj) <- c("command_download_str")

#   }

  #Add function to list files created or modify in python...

  list_output_obj <-list(command_download_str,command_clim_str)

  names(list_output_obj) <- c("command_download_str", "command_clim_str")

  return(list_output_obj)

}

## Run function:

#list_tiles_modis <- c("h19v12,h20v12,h20v11,h21v11,h19v10,h20v10,h21v10") #Africa, S. Africa and more

#list_tiles_modis <- c("h09v02,h10v02,h11v02,h12v02,h13v02,h14v02,h15v02") #tiles for Northenr America, Northern US...

#list_tiles_modis <- c("h10v04,h11v04,h12v04,h13v04,h14v04,h07v06") #tiles for Northenr America, Northern US...

list_tiles_modis <- c("h12v04,h13v04,h14v04,h07v06") #tiles for Northenr America, Northern US...

#list_tiles_modis <- c("h11v08,h11v07,h12v07,h12v08,h10v07,h10v08") #tile for Venezuela and surrounding area

#list_tiles_modis <- c("h08v04,h09v04") #tiles for Oregon #defined above...

#list_tiles_modis <- c("h09v04,h09v04") #tiles for Oregon #defined above...

#list_tiles_modis <- c("h09v04,h09v04") #tiles for Oregon #defined above...

#list_tiles_modis <- c("h09v08,h09v07,h08v07,h0706,h08v06,h09v06,h10v06,h08v05,h09v05,h10v05,h11v05,h12v05") #tiles for Central America and Mexico Southern US...

#list_tiles_modis <- c("h09v09,h10v09,h11v09,h12v09,h13v09,h14v09")

#list_tiles_modis <-c("h30v10,h31v10,h32v10,h30v11,h31v11") #list("Queensland")

script_path<-"/home/parmentier/Data/IPLANT_project/env_layers_scripts/"

modis_download_script <- file.path(script_path,"modis_download_05142013.py") # LST modis download python script

clim_script <- file.path(script_path,"climatology_06092013.py") # LST climatology python script

grass_setting_script <- file.path(script_path,"grass-setup.R")

var="TMAX"

start_year = "2001"

end_year = "2010"

#end_year = "2002"

#path on Jupiter

hdfdir =  '/data/project/layers/commons/modis/MOD11A1_tiles' #destination file where hdf files are stored locally after download.

#hdfdir =  '/home/parmentier/Data/IPLANT_project/MOD11A1_tiles'

download=0

clim_calc=1

out_suffix_modis="_05242013"

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")

#debug(download_calculate_MODIS_LST_climatology)

#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

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

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

#download_calculate_MODIS_LST_climatology(1,list_param_download_clim_LST_script)

#source(file.path(script_path,"covariates_production_temperatures_05312013.R"))

### END OF SCRIPT