Mercurial > repos > siwaa > redelac_stics_g

comparison redelacSticsInputGenerator.R @ 17:4d0807472ad3 draft default tip

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"planemo upload for repository https://forgemia.inra.fr/redelac commit 9c5802d9b947f1e59bd5df610ebe5dfc89745be6"
author siwaa
date Tue, 23 Jan 2024 18:51:34 +0000
parents f2fe11a20371
children
comparison
equal deleted inserted replaced
16:f2fe11a20371 17:4d0807472ad3
76 76
77 gen_sta_xml(param_df = sta_param, out_dir = workspace) 77 gen_sta_xml(param_df = sta_param, out_dir = workspace)
78 78
79 if (parallel) { 79 if (parallel) {
80 doFuture::registerDoFuture() 80 doFuture::registerDoFuture()
81 81 future::plan(multisession, workers = nbSlots)
82 future::plan(multicore, workers = nbSlots) 82 `%dordopar%` <- `%dofuture%`
83 } else {
84 `%dordopar%` <- `%do%`
83 } 85 }
84 86
85 beforeGenXmlTime <- Sys.time() 87 beforeGenXmlTime <- Sys.time()
86 88
87 #gen_usms_xml(file = file.path(workspace, "usms.xml"), 89 #gen_usms_xml(file = file.path(workspace, "usms.xml"),
91 nbUSMs <- nrow(usms_param) 93 nbUSMs <- nrow(usms_param)
92 94
93 ids <- seq(1, nbUSMs, chunckSize) 95 ids <- seq(1, nbUSMs, chunckSize)
94 96
95 foreach (i = ids, 97 foreach (i = ids,
96 .options.future = list(packages = c("foreach", "SticsRFiles"))) %dofuture% { 98 .options.future = list(packages = c("foreach", "SticsRFiles"))) %dordopar% {
97 gen_usms_xml(file = file.path(workspace, paste0("usms__", i, ".xml")), 99 gen_usms_xml(file = file.path(workspace, paste0("usms__", i, ".xml")),
98 param_df = usms_param[i:min(i + chunckSize - 1, nbUSMs),]) 100 param_df = usms_param[i:min(i + chunckSize - 1, nbUSMs),])
99 } 101 }
100 102
101 afterGenXmlTime <- Sys.time() 103 afterGenXmlTime <- Sys.time()
104 afterGenXmlTime)) 106 afterGenXmlTime))
105 107
106 beforeGenTxtTime <- Sys.time() 108 beforeGenTxtTime <- Sys.time()
107 109
108 foreach (i = ids, 110 foreach (i = ids,
109 .options.future = list(packages = c("foreach", "SticsRFiles"))) %dofuture% { 111 .options.future = list(packages = c("foreach", "SticsRFiles"))) %dordopar% {
110 gen_usms_xml2txt( 112 gen_usms_xml2txt(
111 javastics = javastics_path, 113 javastics = javastics_path,
112 workspace = workspace, 114 workspace = workspace,
113 out_dir = txt_path, 115 out_dir = txt_path,
114 usms_file = paste0("usms__", i, ".xml"), 116 usms_file = paste0("usms__", i, ".xml"),