# -MODIS LST: mean and obs

#3) The output is a multiband file in tif format with projected covariates for the processing region/tile.             

#AUTHOR: Benoit Parmentier                                                                       

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

##Comments and TODO:

  return(rast_list)

}

covariates_production_temperature<-function(list_param){

  #This functions produce covariates used in the interpolation of temperature.

  #It requires 15 arguments:

    lst_pat<-"LST_Day_1km" #for the time being change at later stage...

  }

  #Get list of files containing the LST averages

  #pat_str2 <- glob2rx(paste("nobs","*",lst_pat,"*.tif",sep=""))

  pat_str2 <- glob2rx(paste("nobs","*",lst_pat,"*",out_suffix_modis,"*.tif",sep=""))

  #mixedsort(list.files(path=hdfdir,pattern=".*tif"))

  out_rastnames<-paste(list_date_names,out_rastnames,sep="")

  #reproject and crop if necessary

  #nobs_m_list<-list.files(pattern='mosaiced_.*._lst_nobs_VE_03182013.tif')

  ##Now mosaic for mean: should reorder files!!

  pat_str1 <- glob2rx(paste("mean","*.tif",sep=""))

  tmp_str1<- mixedsort(list.files(pattern=pat_str1))

  list_date_names<-c("jan","feb","mar","apr","may","jun","jul","aug","sep","oct","nov","dec")

  mosaic_list<-split(tmp_str1,list_date_names)

  new_list<-vector("list",length(mosaic_list))

    names(mosaic_list)[j]<-list_date_names[i]

    new_list[i]<-mosaic_list[j]

  }

  #mean_m_list<-list.files(pattern='mosaiced_.*._lst_mean_VE_03182013.tif')

  #Use this as ref file for now?? Ok for the time being: this will need to change to be a processing tile.

  #ref_rast <-raster("mosaiced_dec_lst_mean_VE_03182013.tif")

  #Modis shapefile tile is slighly shifted:

  # +proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6370997 +b=6370997 +units=m +no_defs for ref_rast

  #min_val<-(-15+273.16) #if values less than -15C then screen out (note the Kelvin units that will need to be changed later in all datasets)

  #LST[LST < (min_val)]<-NA

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

  ##2) Crop and reproject Canopy height data

  #Make it a function?

  #canopy_rast<-raster("Simard_Pinto_3DGlobalVeg_JGR.tif")

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

  #3) Creating elev, aspect, slope from STRM

  lc_list<-list.files(pattern="con_1km_class_.*.tif")

  #lc<-raster(file.path(lc_path,lc_names))

  lc_reg_list<-vector("list",length(lc_list))

  for (i in 1:length(lc_list)){

    lc_name<-lc_list[[i]]

    lc_reg<-create_raster_region(lc_name,ref_rast)

    data_name<-paste("reg_",sub(".tif","",lc_name),"_",sep="") #can add more later...

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

#

#AUTHOR: Benoit Parmentier                                                                       

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

stages_to_run<-c(0,0,3,4,5) #May decide on antoher strategy later on...

var<-"TMAX" # variable being interpolated

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

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

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

#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<-"_venezuela_region" #generated on the fly

ref_rast_name<-""  #local raster name defining resolution, exent, local projection--. set on the fly??

#ref_rast_name<-"mean_day244_rescaled.rst"  #local raster name defining resolution, exent: oregon

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

download=1

clim_calc=0

#end_month= "12"

#start_month= "1"

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

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

#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")