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Revision 277a0e97

Added by Benoit Parmentier over 11 years ago

testing workflow for Oregon, fixing problems related to automation for covariates production

View differences:

climate/research/oregon/interpolation/covariates_production_temperatures.R
67 67 
  #Output: spatial grid data frame of the subset of tiles
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  ## Parse input arguments
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  raster_name <- list_param$raster_name[j] #list of raster ot project and crop
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  reg_ref_rast <- list_param$reg_ref_rast
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  raster_name <- list_param$raster_name[[j]] #list of raster ot project and crop, this is a list!!
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  reg_ref_rast <- list_param$reg_ref_rast #This must have a coordinate system defined!!
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  out_rast_name <- list_param$out_rast_name[j]
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  ## Start #
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  layer_rast<-raster(raster_name)
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  new_proj<-proj4string(layer_rast)                  #Extract coordinates reference system in PROJ4 format
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  region_temp_projected<-projectExtent(reg_ref_rast,CRS(new_proj))     #Project from current to region coord. system
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  new_proj<-proj4string(layer_rast)                  #Extract current coordinates reference system in PROJ4 format
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  region_temp_projected<-projectExtent(reg_ref_rast,CRS(new_proj))     #Project from ref to current region coord. system
78 78 
  layer_crop_rast<-crop(layer_rast, region_temp_projected) #crop using the extent from the region tile
79 79 
  #layer_projected_rast<-projectRaster(from=layer_crop_rast,crs=proj4string(reg_outline),method="ngb")
80 80 
  layer_projected_rast<-projectRaster(from=layer_crop_rast,to=reg_ref_rast,method="ngb")
......
314 314 
  ### Now mosaic tiles...Note that function could be improved to use less memory
315 315 
  list_param_mosaic<-list(j,mosaic_list_mean,out_rastnames_mean,out_path)
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  names(list_param_mosaic)<-c("j","mosaic_list","out_rastnames","out_path")
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  mean_m_list <-mclapply(1:12, list_param=list_param_mosaic, mosaic_m_raster_list,mc.preschedule=FALSE,mc.cores = 12) #This is the end bracket from mclapply(...) statement
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  mean_m_list <-mclapply(1:12, list_param=list_param_mosaic, mosaic_m_raster_list,mc.preschedule=FALSE,mc.cores = 6) #This is the end bracket from mclapply(...) statement
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  list_param_mosaic<-list(j,mosaic_list_nobs,out_rastnames_nobs,out_path)
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  names(list_param_mosaic)<-c("j","mosaic_list","out_rastnames","out_path")
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  nobs_m_list <-mclapply(1:12, list_param=list_param_mosaic, mosaic_m_raster_list,mc.preschedule=FALSE,mc.cores = 12) #This is the end bracket from mclapply(...) statement
321 
  nobs_m_list <-mclapply(1:12, list_param=list_param_mosaic, mosaic_m_raster_list,mc.preschedule=FALSE,mc.cores = 6) #This is the end bracket from mclapply(...) statement
322 322
323 323 
  #Use this as ref file for now?? Ok for the time being: this will need to change to be a processing tile.
324 324 
  if (ref_rast_name==""){
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    ref_rast<-raster(mean_m_list[[1]])
325 
    ref_rast<-raster(mean_m_list[[1]])
326 
    #Use one mosaiced modis tile as reference image...We will need to add a function
327 
    #to define a local reference system and reproject later!!
328 
    #Assign new projection system here in the argument CRS_interp (!it is used later)
326 329 
  }else{
327 330 
    ref_rast<-raster(ref_rast_name) #This is the reference image used to define the study/processing area
331 
    proj4string(ref_rast) <- CRS_interp #Assign given reference system
328 332 
  }
329 333
330 334 
  ## Project mosaiced tiles if local projection is provided...
331 335 

  		




  332
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  out_suffix_lst <-paste(out_suffix,".tif",sep="")          


  		




  333
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  mean_lst_list_outnames<-change_names_file_list(mean_m_list,out_suffix_lst,"reg_",".tif",out_path=out_path)     


  		




  334
  
  
    
  nobs_lst_list_outnames<-change_names_file_list(nobs_m_list,out_suffix_lst,"reg_",".tif",out_path=out_path)    


  		




  
  338
  
    
  nobs_lst_list_outnames<-change_names_file_list(nobs_m_list,out_suffix_lst,"reg_",".tif",out_path=out_path)   


  		




  335
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  340
  
    
  # if ref_name!="" need to reproject and clip!!! do this in mclapply for all the list of covar!!!


  		




  336
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  if (ref_rast_name!=""){


  		




  337
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    #list(mean_m_list)


  		




  338
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    list_param_create_region<-list(j,raster_name=mean_m_list,reg_ref_rast=ref_rast,out_rast_name=mean_lst_list_outnames)


  		




  
  344
  
    
    #test<-create__m_raster_region(1,list_param_create_region)


  		




  339
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    mean_m_list <-mclapply(1:12, list_param=list_param_create_region, create__m_raster_region,mc.preschedule=FALSE,mc.cores = 6) #This is the end bracket from mclapply(...) statement


  		




  340
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    list_param_create_region<-list(j,raster_name=nobs_m_list,reg_ref_rast=ref_rast,out_rast_name=nobs_lst_list_outnames)


  		




  341
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    nobs_m_list <-mclapply(1:12, list_param=list_param_create_region, create__m_raster_region,mc.preschedule=FALSE,mc.cores = 6) #This is the end bracket from mclapply(...) statement


  		




  342
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  }


  		




  343
  
  
    
  # if ref_name!="" need to reproject and clip!!! do this in mclapply for all the list of covar!!!


  		




  
  349
  
    

  		




  344
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  345
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  #ref_rast <-raster("mosaiced_dec_lst_mean_VE_03182013.tif")


  		




  346
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  #Modis shapefile tile is slighly shifted:


  		












  

    
      climate/research/oregon/interpolation/master_script_temp.R
    
  





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


  		




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#


  		




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#AUTHOR: Benoit Parmentier                                                                       


  		




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#DATE: 05/30/2013                                                                                 


  		




  
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#DATE: 05/31/2013                                                                                 


  		




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


  		




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  ......




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source(file.path(script_path,"GAM_fusion_function_multisampling_validation_metrics_05062013.R"))


  		




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#stages_to_run<-c(1,2,3,4,5) #May decide on antoher strategy later on...


  		




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stages_to_run<-c(1,2,3,4,5) #May decide on antoher strategy later on...


  		




  
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stages_to_run<-c(0,2,3,4,5) #May decide on antoher strategy later on...


  		




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var<-"TMAX" # variable being interpolated


  		




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out_prefix<-"_365d_GAM_fus_all_lst_05302013"                #User defined output prefix


  		




  76
  
  
    
out_suffix<-"_OR_05302013"


  		




  77
  
  
    
out_suffix_modis <-"_05302013"


  		




  
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out_prefix<-"_365d_GAM_fus_all_lst_05312013"                #User defined output prefix


  		




  
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out_suffix<-"_OR_05312013"


  		




  
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out_suffix_modis <-"_05302013" #use tiles produce previously


  		




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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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