Reinstall R et renv avant test Rix Nix

DESCRIPTION

@@ -9,7 +9,7 @@ Description: This lczexplore package automatize the comparison of sets of local
 License: LGPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Imports: RColorBrewer,
           cowplot,
           dplyr,
@@ -31,7 +31,6 @@ Suggests:
     png,
     markdown
 Config/testthat/edition: 3
-VignetteBuilder: knitr
 LazyData: true
 Depends: 
     R (>= 2.10)

R/createIntersect.R

@@ -0,0 +1,39 @@
+createIntersec<-function(sfList, columns, refCrs=NULL, sfWf=NULL){
+  echInt<-sfList[[1]] %>% select(columns[1])
+  if (is.null(refCrs)){refCrs<-st_crs(echInt)}
+  for (i in 2:length(sfList)){
+    sfProv<-sfList[[i]] %>% select(columns[i])
+    if (st_crs(sfProv) != refCrs ) {sfProv<-st_transform(sfProv, crs=refCrs)}
+    echInt<-st_intersection(echInt,sfProv)
+  }
+  if (!is.null(sfWf) & length(sfWf) == length(sfList)){
+    names(echInt)[1:(ncol(echInt)-1)]<-paste0("LCZ",sfWf)
+  } else { names(echInt)[1:(ncol(echInt)-1)]<-paste0("LCZ",1:length(sfList)) }
+  echInt 
+}
+
+# sfBDT_11_78030<-importLCZvect(dirPath="/home/gousseff/Documents/0_DocBiblioTutosPublis/0_ArticlesScientEtThèses/ArticleComparaisonLCZGCWUDAPTEXPERTS/BDT/2011/bdtopo_2_78030",
+#                    file="rsu_lcz.fgb", column="LCZ_PRIMARY")
+# class(sfBDT_11_78030)
+# sfBDT_22_78030<-importLCZvect(dirPath="/home/gousseff/Documents/0_DocBiblioTutosPublis/0_ArticlesScientEtThèses/ArticleComparaisonLCZGCWUDAPTEXPERTS/BDT/2022/bdtopo_3_78030",
+#                               file="rsu_lcz.fgb", column="LCZ_PRIMARY")
+# sf_OSM_11_Auffargis<-importLCZvect(dirPath="/home/gousseff/Documents/0_DocBiblioTutosPublis/0_ArticlesScientEtThèses/ArticleComparaisonLCZGCWUDAPTEXPERTS/OSM/2011/osm_Auffargis/",
+#                                    file="rsu_lcz.fgb", column="LCZ_PRIMARY")
+# sf_OSM_22_Auffargis<-importLCZvect(dirPath="/home/gousseff/Documents/0_DocBiblioTutosPublis/0_ArticlesScientEtThèses/ArticleComparaisonLCZGCWUDAPTEXPERTS/OSM/2022/osm_Auffargis/",
+#                                    file="rsu_lcz.fgb", column="LCZ_PRIMARY")
+# sf_WUDAPT_78030<-importLCZvect("/home/gousseff/Documents/0_DocBiblioTutosPublis/0_ArticlesScientEtThèses/ArticleComparaisonLCZGCWUDAPTEXPERTS/WUDAPT", 
+#                                file ="wudapt_78030.geojson", column="lcz_primary")
+# 
+# sfList<-list(BDT11 = sfBDT_11_78030, BDT22 = sfBDT_22_78030, OSM11= sf_OSM_11_Auffargis, OSM22 = sf_OSM_22_Auffargis, 
+#              WUDAPT = sf_WUDAPT_78030)
+# showLCZ(sfList[[1]])
+# 
+# 
+# 
+# intersected<-createIntersec(sfList = sfList, columns = c(rep("LCZ_PRIMARY",4),"lcz_primary"), 
+#                             sfWf = c("BDT11","BDT22","OSM11","OSM22","WUDAPT"))
+# 
+# 
+# test_list<-list(a=c(1,2),b="top",c=TRUE)
+# length(test_list)
+# for (i in test_list[2:3]) print(str(i))

R/shinyGC/BDTproduction.R

@@ -0,0 +1,97 @@
+# Villes à produire
+# # 78
+# nom de commune, insee
+# Conflans-Sainte-Honorine,	78172
+# Saint-Rémy-lès-Chevreuse,	78575
+# Les Mureaux,	78440
+# Freneuse,	78255
+# Auffargis,	78030
+# Les Essarts-le-Roi,	78220
+# Orgeval,	78466
+# Rosny-sur-Seine,	78531
+# Saint-Léger-en-Yvelines,	78562
+# Poigny-la-Forêt,	78497
+# Blaru,	78068
+# Paray-Douaville,	78478
+# Le Tartre-Gaudran,	78606
+
+# Test conflans 2011 : OK
+
+test<-geoClimateConfigFile(wf = "BDT",
+   date="2011",
+   BDTinFolder="/home/gousseff/Documents/3_data/BDTOPO/2011/",
+   locations="78172",
+   outConfigFile="",
+   outConfigDir = "/home/gousseff/Documents/0_DocBiblioTutosPublis/0_ArticlesScientEtThèses/ArticleComparaisonLCZGCWUDAPTEXPERTS",
+   outFolder = "/home/gousseff/Documents/0_DocBiblioTutosPublis/0_ArticlesScientEtThèses/ArticleComparaisonLCZGCWUDAPTEXPERTS",
+   rsuIndics = c("LCZ"),
+   writeNow = TRUE,
+   forceSRID=TRUE)
+
+geoClimateCall(
+  jarFilePath= "/home/gousseff/Documents/2_CodesSources/GeoClimate/Release1.0/geoclimate-1.0.0.jar",
+  configFilePath="/home/gousseff/Documents/0_DocBiblioTutosPublis/0_ArticlesScientEtThèses/ArticleComparaisonLCZGCWUDAPTEXPERTS/78172BDT2011.json",
+  wf="BDTOPO_V2")
+
+# Test conflans 2022 :
+
+test<-geoClimateConfigFile(wf = "BDT",
+                           date="2022",
+                           BDTinFolder="/home/gousseff/Documents/3_data/BDTOPO/2022/",
+                           locations="78172",
+                           outConfigFile="",
+                           outConfigDir = "/home/gousseff/Documents/0_DocBiblioTutosPublis/0_ArticlesScientEtThèses/ArticleComparaisonLCZGCWUDAPTEXPERTS",
+                           outFolder = "/home/gousseff/Documents/0_DocBiblioTutosPublis/0_ArticlesScientEtThèses/ArticleComparaisonLCZGCWUDAPTEXPERTS",
+                           rsuIndics = c("LCZ"),
+                           writeNow = TRUE,
+                           forceSRID=TRUE)
+
+geoClimateCall(
+  jarFilePath= "/home/gousseff/Documents/2_CodesSources/GeoClimate/Release1.0/geoclimate-1.0.0.jar",
+  configFilePath="/home/gousseff/Documents/0_DocBiblioTutosPublis/0_ArticlesScientEtThèses/ArticleComparaisonLCZGCWUDAPTEXPERTS/78172BDT2022.json",
+  wf="BDTOPO_V3")
+
+city_code_78_93<-c("78172", "78575", "78440", "78255",	"78030", "78220", "78466",
+                 "78531", "78562", "78497", "78068", "78478", "78606", "93029",	"93066",	"93048")
+
+configDir<-"/home/gousseff/Documents/0_DocBiblioTutosPublis/0_ArticlesScientEtThèses/ArticleComparaisonLCZGCWUDAPTEXPERTS"
+for (i in city_code_78){
+  # 2011
+  geoClimateConfigFile(wf = "BDT",
+                       date="2011",
+                       BDTinFolder="/home/gousseff/Documents/3_data/BDTOPO/2011/78/",
+                       locations=i,
+                       outConfigFile="",
+                       outConfigDir = configDir,
+                       outFolder = configDir,
+                       rsuIndics = c("LCZ"),
+                       writeNow = TRUE,
+                       forceSRID=TRUE)
+
+  confFile<-paste0(configDir, "/", i, "BDT2011.json")
+
+  geoClimateCall(
+    jarFilePath= "/home/gousseff/Documents/2_CodesSources/GeoClimate/Release1.0/geoclimate-1.0.0.jar",
+    configFilePath=confFile,
+    wf="BDTOPO_V2")
+
+
+  # 2022
+  geoClimateConfigFile(wf = "BDT",
+                       date="2022",
+                       BDTinFolder="/home/gousseff/Documents/3_data/BDTOPO/2022/78/",
+                       locations=i,
+                       outConfigFile="",
+                       outConfigDir = configDir,
+                       outFolder = configDir,
+                       rsuIndics = c("LCZ"),
+                       writeNow = TRUE,
+                       forceSRID=TRUE)
+
+  confFile<-paste0(configDir, "/", i, "BDT2022.json")
+
+  geoClimateCall(
+    jarFilePath= "/home/gousseff/Documents/2_CodesSources/GeoClimate/Release1.0/geoclimate-1.0.0.jar",
+    configFilePath=confFile,
+    wf="BDTOPO_V3")
+  }

R/shinyGC/geoClimateCall.R

@@ -0,0 +1,43 @@
+#' Calls GeoClimate and feeds it a configuration file by building a command an using system (only tested on linux)
+#' @param jarFilePath tells where the geoclimate jar file is, default points to the embedded jar file,
+#' i.e. the latest snapshot version when the package was built.
+#' Versions can be downloaded from https://github.com/orbisgis/geoclimate/wiki/Download
+#' @param configFilePath points to the configuration JSON file for GeoClimate, typically a file created with the
+#' geoClimateConfigFile function
+#' @param wf is the workflow to use with GeoClimate, the default is OSM for OpenStreetMap.
+#' The other possible value is "BDTOPO_V2". Other values will be added (e.g. for BDTOPO_V3) when tested.
+#' @return returns nothing but files will be created by GeoClimate in the folder specified in the
+#' JSON configuration file.
+#' @export
+#' @examples
+#' test<-geoClimateConfigFile(outFile="", wf="osm",outFolder="/tmp",locations="Redon",
+#' rsuIndics = c("LCZ","TEB","UTRF"),
+#' gridIndics = c("BUILDING_FRACTION","BUILDING_HEIGHT","WATER_FRACTION","VEGETATION_FRACTION","ROAD_FRACTION",
+#' "IMPERVIOUS_FRACTION","LCZ_PRIMARY","LCZ_FRACTION","UTRF"))
+#' geoClimateCall(
+#' jarFilePath= "/home/gousseff/Documents/2_CodesSources/GeoClimate/GeoClimateDefaultCaseV2/geoclimate-0.0.2-SNAPSHOT.jar",
+#' configFilePath="/tmp/Redonosm.json",w="osm")
+#' test
+geoClimateCall<-function(jarFilePath, configFilePath, wf="OSM") {
+  command<-paste0(
+    "java -jar ", jarFilePath, " -f ", configFilePath, " -w ", toupper(wf))
+  print(command)
+  system(command)
+}
+
+# test<-geoClimateConfigFile(outFile="", wf="osm",outFolder="/tmp",locations="Allaire",
+#                            rsuIndics = c("LCZ","TEB","UTRF"),
+#                            gridIndics = c("BUILDING_FRACTION",
+#                                           "BUILDING_HEIGHT",
+#                                           "WATER_FRACTION",
+#                                           "VEGETATION_FRACTION",
+#                                           "ROAD_FRACTION",
+#                                           "IMPERVIOUS_FRACTION",
+#                                           "LCZ_PRIMARY",
+#                                           "LCZ_FRACTION",
+#                                           "UTRF"))
+#
+#  geoClimateCall(
+#  jarFilePath= "/home/gousseff/Documents/2_CodesSources/GeoClimate/GeoClimateDefaultCaseV2/geoclimate-0.0.2-SNAPSHOT.jar",
+#  configFilePath="/tmp/Redonosm.json", wf="osm")
+#  test

R/shinyGC/geoClimateConfigFile.R

@@ -0,0 +1,145 @@
+#' Builds a JSON configuration file for GeoClimate workflow
+#' @param locations is either the town or the coordinates of the bounding box of the area on which GeoClimate will run.
+#' If a town name, it will be fed to the Nominoe API, through the overpass API of OpenStreetMap.
+#' @param wf is the workflow used by GeoClimate. For now, only OSM" is available, for OpenStreetMap, but "BDT" for
+#' BDTOPO of IGN should be added when an online database is available.
+#' @param date is the date of the data we extract from OpenStreetMap. The format is "yyyy:mm:ddThh:mm:ssZ"
+#' (for BDTOPO the version depends from the input data folder)
+#' @param outFolder indicates where the results of GeoClimate will be put
+#' @param rsuIndics is a vector with the indicators one wants to compute at the RSU scale. The default is c("LCZ","TEB","UTRF"),
+#' @param svfSimplified uses the simplified method to calculate skyview factor, default = TRUE
+#' @param estimatedHeight uses an algorithm to estimate the missing building height, default = TRUE
+#' @param grid_x_size is the x size for the grid if some grid indicators are to be computed, default=100
+#' @param grid_y_size is the x size for the grid if some grid indicators are to be computed, default=100
+#' @param rowCol if grid_x_size and grid_y_size are not set, one cal set the number of rows and cols throug rowCol,
+#' but the recommended and default is FALSE
+#' @param outputType is the format of GeoClimate outputs, default="geojson",
+#' @param gridIndics is a vector containing the indicators to compute at the grid scale. Default is
+#' c("BUILDING_FRACTION",
+#' "BUILDING_HEIGHT",
+#' "WATER_FRACTION",
+#' "VEGETATION_FRACTION",
+#' "ROAD_FRACTION",
+#' "IMPERVIOUS_FRACTION","LCZ_PRIMARY","LCZ_FRACTION","UTRF")
+#' @param outConfigDir is the folder were the resulting JSON file will be put, the folder where GeoClimate will read it from
+#' (different from out outFolder, where GeoClimates will put its geoJSON ouputs), default is "/tmp"
+#' @param outConfigFile is the name of your configuration file, if and empty string, a name will be created from location
+#' and workflow parameters.
+#' @param forceSRID some BD TOPO input file may not have an srid, this forces srid to be 2154
+#' @importFrom jsonlite unbox toJSON
+#' @return returns a JSON configuration file to be fed to GeoClimate
+#' @export
+#' @examples
+#' test<-geoClimateConfigFile(outConfigFile="", wf="osm",outFolder="/tmp",locations="Redon",
+#' rsuIndics = c("LCZ","TEB","UTRF"),
+#' gridIndics = c("BUILDING_FRACTION","BUILDING_HEIGHT","WATER_FRACTION","VEGETATION_FRACTION","ROAD_FRACTION",
+#' "IMPERVIOUS_FRACTION","LCZ_PRIMARY","LCZ_FRACTION","UTRF"))
+#' test
+geoClimateConfigFile<-function(wf, locations, forceSRID=FALSE,
+                               outFolder="/tmp",
+                               date,
+                               rsuIndics=c("LCZ","TEB","UTRF"),
+                               svfSimplified = TRUE,
+                               estimatedHeight = TRUE,
+                               grid_x_size=0,
+                               grid_y_size=0,
+                               rowCol = FALSE,
+                               outputType = "geojson",
+                               gridIndics="",
+                               outConfigDir = "/tmp",
+                               outConfigFile = "configFile",
+                               BDTinFolder = "", BDTinseeCode=29301,
+                               writeNow = FALSE) {
+  # description<-"Test de description unique"
+
+  if (wf=="OSM"){description<-"Processing OSM data"} else {
+    if (wf=="BDTOPO_V2") {description<-"Processing BDTopo v2 data"} else {
+      if (wf=="BDTOPO_V3") {
+        description<-"Processing BDTopo v3 data"}
+      else { description<-paste0("Processing on an unrecognized workflow: ", wf)
+      }
+    }
+  }
+
+  outFolder<-tryCatch( # This hideous tryCatch deals with weird shinyDirChoose behavior
+    {
+      list(folder=jsonlite::unbox(paste0(jsonlite::unbox(outFolder),
+                               "/",wf,"/", substr(date,1,4)))) },
+    error=function(e){
+      list(folder="\tmp")
+    }
+  )
+
+
+  if (wf == "OSM"){
+    input<-list(locations=locations, date=jsonlite::unbox(date))
+  } else { if (grep("BDT",wf)==1) {
+    if (forceSRID==FALSE){
+      input<-
+        list(
+          folder= tryCatch(
+            jsonlite::unbox(BDTinFolder),
+            error=function(e){
+              list(folder="\tmp")
+            }),
+          locations=locations
+        )
+    } else { if (forceSRID==TRUE) {
+      input<-
+        list(
+          folder= tryCatch(
+            jsonlite::unbox(BDTinFolder),
+            error=function(e){
+              list(folder="\tmp")
+            })
+          ,
+          locations=locations,
+          srid=jsonlite::unbox(2154))
+    }}
+  }}
+
+
+if(grid_x_size!=0 & grid_y_size!=0){
+  parameters<-list(
+    rsu_indicators = list(
+      indicatorUse = rsuIndics,
+      svSimplified = jsonlite::unbox(svfSimplified),
+      estimatedHeight = jsonlite::unbox(estimatedHeight)),
+    grid_indicators = list(
+      x_size = jsonlite::unbox(grid_x_size), y_size = jsonlite::unbox(grid_y_size),
+      rowCol = jsonlite::unbox(rowCol),
+      output = jsonlite::unbox(outputType),
+      indicators = gridIndics
+    )
+  )
+} else {
+  parameters<-list(
+    rsu_indicators = list(
+      indicatorUse = rsuIndics,
+      svSimplified = jsonlite::unbox(svfSimplified),
+      estimatedHeight = jsonlite::unbox(estimatedHeight)))
+}
+
+  listJSON <- list(description=jsonlite::unbox(description), input=input, output=outFolder, parameters=parameters)
+
+  output<-toJSON(x=listJSON,
+                 pretty=TRUE)
+
+
+
+  if (outConfigFile=="") { outConfigFile<-paste0(locations,wf) }
+
+  if (writeNow == TRUE){
+    write(output,file=paste0(outConfigDir,"/",outConfigFile,substr(date,1,4),".json"))
+  }
+
+  return(output)
+
+}
+#
+# library(jsonlite)
+# test<-geoClimateConfigFile(outConfigFile="", wf="BDTOPO_V2.2",outFolder=list(folder="/tmp",srid=2154),locations="Allaire",
+#  rsuIndics = c("LCZ","TEB","UTRF"),
+#  gridIndics = c("BUILDING_FRACTION","BUILDING_HEIGHT","WATER_FRACTION","VEGETATION_FRACTION","ROAD_FRACTION",
+#  "IMPERVIOUS_FRACTION","LCZ_PRIMARY","LCZ_FRACTION","UTRF"))
+#  test