Revision ca012182
Added by Benoit Parmentier about 8 years ago
| climate/research/oregon/interpolation/global_product_assessment_part2.R | ||
|---|---|---|
| 4 | 4 |
#This part 2 of the assessment focuses on graphics to explore the spatial patterns of raster times series as figures and movie |
| 5 | 5 |
#AUTHOR: Benoit Parmentier |
| 6 | 6 |
#CREATED ON: 10/03/2016 |
| 7 |
#MODIFIED ON: 10/19/2016
|
|
| 7 |
#MODIFIED ON: 10/20/2016
|
|
| 8 | 8 |
#Version: 1 |
| 9 | 9 |
#PROJECT: Environmental Layers project |
| 10 | 10 |
#COMMENTS: Initial commit, script based on part NASA biodiversity conferenc |
| ... | ... | |
| 18 | 18 |
#source /nobackupp6/aguzman4/climateLayers/sharedModules2/etc/environ.sh |
| 19 | 19 |
# |
| 20 | 20 |
#setfacl -Rm u:aguzman4:rwx /nobackupp6/aguzman4/climateLayers/LST_tempSpline/ |
| 21 |
#COMMIT: moving check missing function and testing it
|
|
| 21 |
#COMMIT: checking missing files for region 5 with check_missing function
|
|
| 22 | 22 |
|
| 23 | 23 |
################################################################################################# |
| 24 | 24 |
|
| ... | ... | |
| 127 | 127 |
#in_dir <- "/data/project/layers/commons/NEX_data/climateLayers/out/reg5/assessment" |
| 128 | 128 |
#in_dir_mosaic <- "/data/project/layers/commons/NEX_data/climateLayers/out/reg5/mosaic/mosaic" |
| 129 | 129 |
in_dir <- "/data/project/layers/commons/NEX_data/climateLayers/out/reg6/assessment" |
| 130 |
in_dir_mosaic <- "/data/project/layers/commons/NEX_data/climateLayers/out/reg6/mosaics/mosaic" #predicted mosaic |
|
| 131 |
#/data/project/layers/commons/NEX_data/climateLayers/out/reg4/mosaic/mosaic
|
|
| 130 |
#in_dir_mosaic <- "/data/project/layers/commons/NEX_data/climateLayers/out/reg6/mosaics/mosaic" #predicted mosaic
|
|
| 131 |
in_dir_mosaic <- "/data/project/layers/commons/NEX_data/climateLayers/out/reg4/mosaic/mosaic"
|
|
| 132 | 132 |
|
| 133 |
region_name <- c("reg6") #param 6, arg 3
|
|
| 134 |
out_suffix <- "global_assessment_reg6_10102016"
|
|
| 133 |
region_name <- c("reg4") #param 6, arg 3
|
|
| 134 |
out_suffix <- "global_assessment_reg4_10102016"
|
|
| 135 | 135 |
|
| 136 | 136 |
create_out_dir_param <- TRUE #param 9, arg 6 |
| 137 | 137 |
|
| 138 | 138 |
|
| 139 |
out_dir <- "/data/project/layers/commons/NEX_data/climateLayers/out/reg6/assessment"
|
|
| 139 |
out_dir <- "/data/project/layers/commons/NEX_data/climateLayers/out/reg4/assessment"
|
|
| 140 | 140 |
|
| 141 | 141 |
#run_figure_by_year <- TRUE # param 10, arg 7 |
| 142 | 142 |
|
| ... | ... | |
| 156 | 156 |
|
| 157 | 157 |
#infile_mask <- "/nobackupp8/bparmen1/NEX_data/regions_input_files/r_mask_LST_reg4.tif" |
| 158 | 158 |
#infile_mask <- "/data/project/layers/commons/NEX_data/regions_input_files/r_mask_LST_reg5.tif" |
| 159 |
infile_mask <- "/data/project/layers/commons/NEX_data/regions_input_files/r_mask_LST_reg6.tif"
|
|
| 159 |
infile_mask <- "/data/project/layers/commons/NEX_data/regions_input_files/r_mask_LST_reg4.tif"
|
|
| 160 | 160 |
|
| 161 | 161 |
#run_figure_by_year <- TRUE # param 10, arg 7 |
| 162 | 162 |
list_year_predicted <- "1984,2014" |
| 163 | 163 |
scaling <- 0.01 #was scaled on 100 |
| 164 | 164 |
#if scaling is null then perform no scaling!! |
| 165 | 165 |
|
| 166 |
#df_centroids_fname <- "/data/project/layers/commons/NEX_data/climateLayers/out/reg4/mosaic/output_reg5_1999/df_centroids_19990701_reg5_1999.txt"
|
|
| 167 |
df_centroids_fname <- "/data/project/layers/commons/NEX_data/climateLayers/out/reg6/mosaic/output_reg6_1984/df_centroids_19840101_reg6_1984.txt" |
|
| 166 |
df_centroids_fname <- "/data/project/layers/commons/NEX_data/climateLayers/out/reg4/mosaic/output_reg4_1999/df_centroids_19990701_reg4_1999.txt"
|
|
| 167 |
#df_centroids_fname <- "/data/project/layers/commons/NEX_data/climateLayers/out/reg6/mosaic/output_reg6_1984/df_centroids_19840101_reg6_1984.txt"
|
|
| 168 | 168 |
#/nobackupp6/aguzman4/climateLayers/out/reg1/assessment//output_reg1_1984/df_assessment_files_reg1_1984_reg1_1984.txt |
| 169 | 169 |
|
| 170 | 170 |
#dates to plot and analyze |
| ... | ... | |
| 233 | 233 |
function_product_assessment_part2_functions <- "global_product_assessment_part2_functions_10192016b.R" |
| 234 | 234 |
source(file.path(script_path,function_product_assessment_part2_functions)) #source all functions used in this script |
| 235 | 235 |
|
| 236 |
#Using default values for parameters |
|
| 237 |
debug(check_missing) |
|
| 236 |
#Using default values for parameters exectpt for num_cores=11 instead of 1
|
|
| 237 |
#debug(check_missing)
|
|
| 238 | 238 |
test_missing <- check_missing(lf=lf_raster, |
| 239 | 239 |
pattern_str=NULL, |
| 240 |
in_dir=".", |
|
| 240 |
in_dir=".", #this is not used if lf is given
|
|
| 241 | 241 |
date_start="1984101", |
| 242 | 242 |
date_end="20141231", |
| 243 | 243 |
item_no=13, |
| 244 | 244 |
out_suffix="", |
| 245 |
num_cores=1,
|
|
| 245 |
num_cores=num_cores,
|
|
| 246 | 246 |
out_dir=".") |
| 247 | 247 |
|
| 248 | 248 |
##Run this on reg4 and reg5 after |
| 249 |
#Add report by year in text file? |
|
| 249 | 250 |
#Using specified values for parameters |
| 250 | 251 |
test_missing <- check_missing(lf=lf_raster, |
| 251 | 252 |
pattern_str=NULL, |
| 252 |
in_dir=".",
|
|
| 253 |
in_dir=in_dir_mosaic,
|
|
| 253 | 254 |
date_start="1984101", |
| 254 | 255 |
date_end="20141231", |
| 255 | 256 |
item_no=13, |
| 256 |
out_suffix="") |
|
| 257 |
out_suffix=out_suffix, |
|
| 258 |
num_cores=num_cores, |
|
| 259 |
out_dir=".") |
|
| 260 |
|
|
| 261 |
df_time_series <- test_missing$df_time_series |
|
| 262 |
head(df_time_series) |
|
| 263 |
|
|
| 264 |
table(df_time_series$missing) |
|
| 265 |
table(df_time_series$year) |
|
| 257 | 266 |
|
| 258 | 267 |
############################# |
| 259 | 268 |
##### Creating animation based on prediction |
Also available in: Unified diff
checking missing files for region 5 with check_missing function