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4 |
#Different options to explore mosaicing are tested. This script only contains functions.
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5 |
#AUTHOR: Benoit Parmentier
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| 6 |
6 |
#CREATED ON: 04/14/2015
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#MODIFIED ON: 07/05/2016
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7 |
#MODIFIED ON: 08/16/2016
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8 |
#Version: 2
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#PROJECT: Environmental Layers project
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#COMMENTS: Bug solved for reg5, problem in matching rmse val and number of files in predictions by tiles
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| ... | ... | |
| 221 |
221 |
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222 |
#### end of function
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223 |
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mosaic_python_merge <- function(NA_flag_val,module_path,module_name,input_file,out_mosaic_name){
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#out_mosaic_name <- r_weights_sum_raster_name <- file.path(out_dir,paste("r_weights_sum_m_",method_str,"_weighted_mean_",out_suffix,".tif",sep=""))
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cmd_str <- paste("python", file.path(module_path,module_name),
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mosaic_python_merge <- function(NA_flag_val,module_path,module_name,input_file,out_mosaic_name,raster_ref_name=NULL){
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#Inputs:
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#NA_falg_val: NA value to use in the output
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#module_path: python module to be used with path
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#module_name: name of the module
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#input_file: input file as text file containing a list of files to mosaic
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#out_mosaic_name: output file for the mosaic
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#rast_ref_name: reference file with extent and resolution to be used in the mosaicing
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|
232 |
#
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233 |
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#### Start script ###
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235 |
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236 |
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if(is.null(raster_ref_name)){
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|
238 |
|
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#out_mosaic_name <- r_weights_sum_raster_name <- file.path(out_dir,paste("r_weights_sum_m_",method_str,"_weighted_mean_",out_suffix,".tif",sep=""))
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|
240 |
cmd_str <- paste("python", file.path(module_path,module_name),
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| 227 |
241 |
"--config GDAL_CACHEMAX=1500",
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| 228 |
242 |
"--overwrite=TRUE",
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| 229 |
243 |
paste("-o",out_mosaic_name,sep=" "),
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| 230 |
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paste("--optfile", input_file,sep=" "),
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| 231 |
245 |
paste("-n",NA_flag_val,sep=" "))
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| 232 |
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system(cmd_str)
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246 |
system(cmd_str)
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|
247 |
}
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|
248 |
if(!is.null(raster_ref_name)){
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|
249 |
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250 |
#lf_files <- c(r_m_weighted_mean_raster_name) #match to mask
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|
251 |
#rast_ref_name <- r_mask_raster_name
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|
252 |
r_ref <- raster(raster_ref_name)
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|
253 |
extent_r_ref <- as.numeric(as.matrix(extent(r_ref)))
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|
254 |
res_pix <- res(r_mask)
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|
255 |
#c(xmin,ymax,xmax,ymin)
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|
256 |
#c(ulx,uly,lrx,lry)
|
|
257 |
extent_str <- c(extent_r_ref[1],extent_r_ref[4],extent_r_ref[3],extent_r_ref[2])
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|
258 |
#-ps 0.00833349 0.008333229 -ul_lr -187.143383752 81.744912045 -5.073165638 14.554089652
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|
259 |
#out_mosaic_name <- r_weights_sum_raster_name <- file.path(out_dir,paste("r_weights_sum_m_",method_str,"_weighted_mean_",out_suffix,".tif",sep=""))
|
|
260 |
cmd_str <- paste("python", file.path(module_path,module_name),
|
|
261 |
"--config GDAL_CACHEMAX=1500",
|
|
262 |
"--overwrite=TRUE",
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|
263 |
paste("-o",out_mosaic_name,sep=" "),
|
|
264 |
paste("-ps", res_pix[1],res_pix[2],sep=" "), #pixel size
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|
265 |
paste("-ul_lr", extent_str[1],extent_str[2],extent_str[3],extent_str[4],sep=" "), #extent
|
|
266 |
paste("--optfile", input_file,sep=" "),
|
|
267 |
paste("-n",NA_flag_val,sep=" "))
|
|
268 |
system(cmd_str)
|
|
269 |
|
|
270 |
}
|
| 233 |
271 |
#list(out_mosaic_name,cmd_str)
|
| 234 |
272 |
mosaic_python_merge_obj <- list(out_mosaic_name,cmd_str)
|
| 235 |
273 |
names(mosaic_python_merge_obj) <- c("out_mosaic_name","cmd_str")
|
| ... | ... | |
| 721 |
759 |
#browser()
|
| 722 |
760 |
#python /nobackupp6/aguzman4/climateLayers/sharedCode/gdal_merge_sum.py
|
| 723 |
761 |
#--config GDAL_CACHEMAX=1500 --overwrite=TRUE -o outputname.tif --optfile input.txt
|
|
762 |
if(!is.null(r_mask_raster_name)){
|
|
763 |
#d
|
|
764 |
#different extent between mask and output if match extent is false!!
|
|
765 |
#match resolution and extent first
|
|
766 |
|
|
767 |
#lf_files <- c(r_m_weighted_mean_raster_name) #file(s) to be matched
|
|
768 |
#lf_files <- c(r_m_weighted_mean_raster_name) #match to mask
|
|
769 |
rast_ref_name <- r_mask_raster_name
|
|
770 |
#r_mask <- raster(rast_ref)
|
|
771 |
#extent_r_mask <- as.numeric(as.matrix(extent(r_mask)))
|
|
772 |
#res_pix <- res(r_mask)
|
|
773 |
#c(xmin,ymax,xmax,ymin)
|
|
774 |
#c(ulx,uly,lrx,lry)
|
|
775 |
#extent_str <- c(extent_r_mask[1],extent_r_mask[4],extent_r_mask[3],extent_r_mask[2])
|
|
776 |
}else{
|
|
777 |
rast_ref_name <- NULL
|
|
778 |
}
|
|
779 |
#cmd_mosaic_gam_CAI_dailyTmax_19840101_reg1_1984.txt
|
|
780 |
#python /nobackupp6/aguzman4/climateLayers/sharedCode//gdal_merge_sum.py --config GDAL_CACHEMAX=1500 --overwrite=TRUE -o /nobackupp8/bparmen1/climateLayers/out
|
| 724 |
781 |
mosaic_weights_obj <- mosaic_python_merge(NA_flag_val=NA_flag_val,
|
| 725 |
782 |
module_path=mosaic_python,
|
| 726 |
783 |
module_name="gdal_merge_sum.py",
|
| 727 |
784 |
input_file=filename_list_mosaics_weights_m,
|
| 728 |
|
out_mosaic_name=out_mosaic_name_weights_m)
|
|
785 |
out_mosaic_name=out_mosaic_name_weights_m,
|
|
786 |
raster_ref_name = rast_ref_name) ##if NA, not take into account
|
| 729 |
787 |
r_weights_sum_raster_name <- mosaic_weights_obj$out_mosaic_name
|
| 730 |
788 |
cmd_str1 <- mosaic_weights_obj$cmd_str
|
| 731 |
789 |
#r_prod_sum_raster_name <- mosaic_python_merge(module_path=mosaic_python,
|
| ... | ... | |
| 737 |
795 |
module_path=mosaic_python,
|
| 738 |
796 |
module_name="gdal_merge_sum.py",
|
| 739 |
797 |
input_file=filename_list_mosaics_prod_weights_m,
|
| 740 |
|
out_mosaic_name=out_mosaic_name_prod_weights_m)
|
|
798 |
out_mosaic_name=out_mosaic_name_prod_weights_m,
|
|
799 |
raster_ref_name = rast_ref_name)
|
| 741 |
800 |
r_prod_sum_raster_name <- mosaic_prod_weights_obj$out_mosaic_name
|
| 742 |
801 |
cmd_str2 <- mosaic_prod_weights_obj$cmd_str
|
| 743 |
802 |
#write out python command used for mosaicing
|
| ... | ... | |
| 842 |
901 |
#lf_files <- c(r_m_weighted_mean_raster_name) #file(s) to be matched
|
| 843 |
902 |
lf_files <- c(r_m_weighted_mean_raster_name) #match to mask
|
| 844 |
903 |
rast_ref <- r_mask_raster_name
|
|
904 |
raster(rast_ref)
|
|
905 |
extent_r_mask <- extent(r_mask)
|
| 845 |
906 |
##Maching resolution is probably only necessary for the r mosaic function
|
| 846 |
907 |
#Modify later to take into account option R or python...
|
| 847 |
908 |
list_param_raster_match <- list(lf_files,rast_ref,file_format,python_bin,out_suffix,out_dir)
|
modifying mosaic function script to use reference raster as output