Mercurial > repos > siwaa > redelac_stics_t

comparison redelacSticsTool.R @ 0:7f8f474a7bd7 draft

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"planemo upload for repository https://forgemia.inra.fr/redelac commit 29a2aee3b41d8da4d056600ea5cf4af978c714b9"
author siwaa
date Tue, 06 Feb 2024 09:21:00 +0000
parents
children ed9c49c6c6e1
comparison
equal deleted inserted replaced
-1:000000000000 0:7f8f474a7bd7
1 library(SticsRFiles)
2 library(SticsOnR)
3 library(dplyr)
4 library(lubridate)
5 library(parallel)
6 library(doParallel)
7 library(doFuture)
8 library(stringr)
9 library(readxl)
10 library(data.table)
11 library(readr)
12 library(tidyr)
13
14 sessionInfo()
15
16 args = commandArgs(trailingOnly = TRUE)
17
18 startTime <- Sys.time()
19
20 workspace <- paste0(getwd(), "/WS")
21 javastics_path <- getwd()
22 default_config_path <- paste0(javastics_path, "/config")
23
24 txt_path <- paste0(getwd(), "/WS/txt_files")
25 dir.create(txt_path, recursive = T)
26
27 USMsFile <- "USMs.csv"
28 TecFile <- "Tec.csv"
29 IniFile <- "Ini.csv"
30 StationFile <- "Station.csv"
31
32 redelac <- (args[1] == "optim")
33 parallel <- (args[2] == "parallel")
34 print(paste("parallel:", parallel, args[2]))
35 nbSlots <- as.integer(args[3])
36 print(paste("nbslots:", nbSlots))
37 scenario <- args[4]
38
39 # USMs file loading
40
41 usms_param <- read_params_table(file.path(workspace, USMsFile)) %>%
42 select(
43 usm_name,
44 datedebut,
45 datefin,
46 finit,
47 nomsol,
48 fstation,
49 fclim1,
50 fclim2,
51 culturean,
52 nbplantes,
53 codesimul,
54 fplt_1,
55 ftec_1,
56 flai_1,
57 fplt_2,
58 ftec_2,
59 flai_2
60 )
61
62 # Tec files loading and generating xml
63
64 tec_param <- read_params_table(file.path(workspace, TecFile))
65 columnToRemove <-
66 names(tec_param[grep("juleclair|nbinfloecl", names(tec_param))])
67 columnToKeep <-
68 names(tec_param)[names(tec_param) %in% columnToRemove == FALSE]
69
70 tec_param <- subset(tec_param, select = columnToKeep)
71
72 gen_tec_xml(param_df = tec_param, out_dir = workspace)
73
74 # Ini files loading and generating xml
75
76 ini_param <- read_params_table(file.path(workspace, IniFile))
77
78 gen_ini_xml(param_df = ini_param, out_dir = workspace)
79
80 # Station files loading and generating xml
81
82 sta_param <- read_params_table(file.path(workspace, StationFile))
83
84 gen_sta_xml(param_df = sta_param, out_dir = workspace)
85
86 if (parallel) {
87 doFuture::registerDoFuture()
88 future::plan(multisession, workers = nbSlots)
89 `%dordopar%` <- `%dofuture%`
90 } else {
91 `%dordopar%` <- `%do%`
92 }
93
94 beforeGenXmlTime <- Sys.time()
95
96 #gen_usms_xml(file = file.path(workspace, "usms.xml"),
97 # param_df = usms_param)
98
99 chunckSize <- 1000
100 nbUSMs <- nrow(usms_param)
101
102 ids <- seq(1, nbUSMs, chunckSize)
103
104 foreach (i = ids,
105 .options.future = list(packages = c("foreach", "SticsRFiles"))) %dordopar% {
106 gen_usms_xml(file = file.path(workspace, paste0("usms__", i, ".xml")),
107 param_df = usms_param[i:min(i + chunckSize - 1, nbUSMs),])
108 }
109
110 afterGenXmlTime <- Sys.time()
111 durGenX <-
112 lubridate::as.duration(lubridate::interval(beforeGenXmlTime,
113 afterGenXmlTime))
114
115 beforeGenTxtTime <- Sys.time()
116
117 foreach (i = ids,
118 .options.future = list(packages = c("foreach", "SticsRFiles"))) %dordopar% {
119 gen_usms_xml2txt(
120 javastics = javastics_path,
121 workspace = workspace,
122 out_dir = txt_path,
123 usms_file = paste0("usms__", i, ".xml"),
124 redelac = redelac,
125 parallel = parallel,
126 verbose = FALSE
127 )
128 }
129
130 afterGenTxtTime <- Sys.time()
131 durGenT <-
132 lubridate::as.duration(lubridate::interval(beforeGenTxtTime, afterGenTxtTime))
133
134 afterGenTxtTime <- Sys.time()
135 durGenT <-
136 lubridate::as.duration(lubridate::interval(beforeGenTxtTime, afterGenTxtTime))
137
138 endTime <- Sys.time()
139
140 dur <-
141 lubridate::as.period(lubridate::as.duration(lubridate::interval(startTime, endTime)))
142 durGenXP <- lubridate::as.period(durGenX)
143 durGenTP <- lubridate::as.period(durGenT)
144
145 print("REDELACSticsInputGenerator Report")
146 print("=================================")
147 print(paste("number of usms: ", nrow(usms_param)))
148 print(paste("redelac optimization:", redelac))
149 print(paste("process in parallel:", parallel))
150 print(paste("nbslots:", nbSlots))
151
152 sprintf(
153 'overall duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
154 lubridate::day(dur),
155 lubridate::hour(dur),
156 lubridate::minute(dur),
157 lubridate::second(dur)
158 )
159
160 sprintf(
161 'inside gen_usms_xml duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
162 lubridate::day(durGenXP),
163 lubridate::hour(durGenXP),
164 lubridate::minute(durGenXP),
165 lubridate::second(durGenXP)
166 )
167
168 sprintf(
169 'inside gen_usms_xml2txt duration: %g jour(s) %g heure(s) %g minute(s) %g seconde(s)',
170 lubridate::day(durGenTP),
171 lubridate::hour(durGenTP),
172 lubridate::minute(durGenTP),
173 lubridate::second(durGenTP)
174 )
175 print(
176 "==================================================================================="
177 )
178
179
180 #
181 # Simulation part
182 #
183
184 # List of successive USMs
185 successive_usms_file <- ("successionPlan.csv")
186 successive_usms_tab <-
187 read.csv(file = file.path(workspace, successive_usms_file),
188 sep = ";")
189
190 # from succesions to simulate retrieving upcSol Cases
191
192 successRef <- successive_usms_tab["Treatment"]
193
194 successRef <- successRef %>%
195 separate(
196 col = Treatment,
197 into = c("upc", "sol", "systeme", "rotation", "tete_rotation", "horizon"),
198 sep = "-",
199 remove = FALSE
200 )
201
202 successRef$upcSol <- paste0(successRef$upc, "-", successRef$sol)
203
204 casesUpcSol <- unique(successRef$upcSol)
205
206 systeme <- successRef$systeme[1]
207 rotation <- successRef$rotation[1]
208
209 successive_usms_tab_split <- list()
210
211 for (j in 1:length(casesUpcSol)) {
212 splited <- strsplit(casesUpcSol[j], split = "-")[[1]]
213
214 upc <- splited[1]
215
216 sol <- splited[2]
217
218 successive_usms_tab_split[[j]] <-
219 successive_usms_tab[successRef$upcSol == casesUpcSol[j],]
220 }
221
222 result <- foreach(j = 1:length(casesUpcSol)) %:%
223 foreach(
224 i = 1:nrow(successive_usms_tab_split[[j]]),
225 .options.future = list(packages =c("foreach", "SticsRFiles", "SticsOnR"))
226
227 ) %dordopar% {
228
229 nusms <- as.numeric(successive_usms_tab_split[[j]][i, 2])
230
231 vec <-
232 as.character(successive_usms_tab_split[[j]][i, c(3:(2 + nusms))])
233
234 list_successive_usms <- list(vec)
235
236 sim_options <- stics_wrapper_options(
237 javastics = javastics_path,
238 stics_exe = paste0(javastics_path, "/bin/stics_modulo"),
239 workspace = txt_path,
240 verbose = TRUE,
241 successive = list_successive_usms
242 )
243
244 list_usms <- vec
245
246 cat(paste0("--> succession : ", successive_usms_tab_split[[j]][i, 1], " launched\n"))
247
248 return(stics_wrapper(model_options = sim_options, situation = list_usms))
249
250 }
251
252 for (j in 1:length(casesUpcSol)) {
253 splited <- strsplit(casesUpcSol[j], split = "-")[[1]]
254
255 upc <- splited[1]
256
257 sol <- splited[2]
258
259 for (i in 1:nrow(successive_usms_tab_split[[j]])) {
260 #i=1
261 if (i == 1) {
262 simPCP <- result[[j]][[i]]
263 } else {
264 simPCP$sim_list <- c(simPCP$sim_list, result[[j]][[i]]$sim_list)
265 }
266
267 }
268
269 #agregation des sorties dans un dataframe
270 sim_df <-
271 rbindlist(simPCP$sim_list, use.names = TRUE, idcol = "usm")
272
273 #ajout des colonnes explicatives + de l'horizon temporel
274 sim_df <- sim_df %>%
275 separate(
276 col = usm,
277 into = c(
278 "upc",
279 "sol",
280 "systeme",
281 "rotation",
282 "tete_rotation",
283 "horizon",
284 "annee",
285 "culture"
286 ),
287 sep = "-",
288 remove = FALSE
289 )
290
291 #sauvegarde sous la forme d'un fichier rds
292
293 if (dir.exists(paste0(
294 workspace,
295 "/analyse_simulations_STICS/",
296 systeme,
297 "/",
298 rotation
299 )) == FALSE) {
300 dir.create(
301 paste0(
302 workspace,
303 "/analyse_simulations_STICS/",
304 systeme,
305 "/",
306 rotation
307 ),
308 recursive = TRUE
309 )
310 }
311
312 saveRDS(
313 sim_df,
314 paste0(
315 workspace,
316 "/analyse_simulations_STICS/",
317 systeme,
318 "/",
319 rotation,
320 "/outputs-",
321 rotation,
322 "-",
323 upc,
324 "-",
325 sol,
326 "-",
327 scenario,
328 ".rds"
329 )
330 )
331
332 successive_usms_tab_split[[j]]$Treatment <- NULL
333 successive_usms_tab_split[[j]]$Number_USM <- NULL
334
335 list_usms <-
336 unlist(unname(as.list(
337 transpose(successive_usms_tab_split[[j]])
338 )))
339 list_usms <- list_usms[!is.na(list_usms)]
340 list_usms <- list_usms[list_usms != '']
341
342 list_usms_yr1 <- successive_usms_tab_split[[j]]$USM_1
343
344 for (i in 1:length(list_usms)) {
345 if (i == 1) {
346 #ajout d'une condition sur l'existence du fichier "mod_rapport.sti" pour la concatenation
347 #en attendant que toutes les simulations tournent correctement
348 #if(exists(file.path(txt_path, list_usms[i], "mod_rapport.sti"))==TRUE){
349 rap_1 <-
350 read_delim(file.path(txt_path, list_usms[i], "mod_rapport.sti"),
351 col_names = TRUE)
352 names_col <- colnames(rap_1)
353
354 rap_string <-
355 read_lines(file = file.path(txt_path, list_usms[i], "mod_rapport.sti"),
356 skip = 1)
357
358 rap <- as_tibble(rap_string) %>%
359 separate(col = value,
360 sep = ";",
361 into = names_col) %>%
362 mutate(USM = list_usms[i])
363 # }
364
365 } else {
366 #if (list_usms[i] %in% list_usms_yr1) {
367 #ajout d'une condition sur l'existence du fichier "mod_rapport.sti" pour la concatenation
368 #en attendant que toutes les simulations tournent correctement
369 #if(exists(file.path(txt_path, list_usms[i], "mod_rapport.sti"))==TRUE){
370 rap_string <-
371 read_lines(file = file.path(txt_path, list_usms[i], "mod_rapport.sti"),
372 skip = 1,)#}
373
374 # } else {
375 #ajout d'une condition sur l'existence du fichier "mod_rapport.sti" pour la concatenation
376 #en attendant que toutes les simulations tournent correctement
377 #if(exists(file.path(txt_path, list_usms[i], "mod_rapport.sti"))==TRUE){
378 # rap_string <-
379 # read_file(file = file.path(txt_path, list_usms[i], "mod_rapport.sti"))#}
380 # }
381 rap_i <- as_tibble(rap_string) %>%
382 separate(col = value,
383 sep = ";",
384 into = names_col) %>%
385 mutate(USM = list_usms[i])
386
387 rap <- bind_rows(rap, rap_i)
388
389 }
390
391 }
392 rm(rap_1, names_col, rap_string, rap_i)
393
394 rap <- rap %>%
395 select(USM, everything()) %>%
396 mutate(P_usm = str_replace_all(P_usm, " ", "")) %>%
397 mutate(wlieu = str_replace_all(wlieu, " ", "")) %>%
398 mutate(stade = str_replace_all(stade, " ", "")) %>%
399 mutate(nomversion = str_replace_all(nomversion, " ", "")) %>%
400 mutate(across(3:9, as.numeric)) %>%
401 mutate(across(13:ncol(rap), as.numeric)) %>%
402 #separate(col=P_usm,into=c("upc","sol","systeme","rotation","tete_rotation","horizon","annee","culture"),sep="-",remove = FALSE)
403 separate(
404 col = USM,
405 into = c(
406 "upc",
407 "sol",
408 "systeme",
409 "rotation",
410 "tete_rotation",
411 "horizon",
412 "annee",
413 "culture"
414 ),
415 sep = "-",
416 remove = FALSE
417 )
418
419 write_delim(
420 x = rap,
421 file = paste0(
422 workspace,
423 "/analyse_simulations_STICS/",
424 systeme,
425 "/",
426 rotation,
427 "/report-",
428 rotation,
429 "-",
430 upc,
431 "-",
432 sol,
433 "-",
434 scenario,
435 ".csv"
436 ),
437 delim = ";"
438 )
439
440 }