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Commit c3e744a8 authored by Ruben Heinrich's avatar Ruben Heinrich
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[feature] Refactored .vtu class, added .pvd wrapper class

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1 merge request!6Merge branch 7 fixed functionality into master
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R/vtu.R
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− 65
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......@@ -22,7 +22,7 @@ OGS6_pvd <- R6::R6Class(
private$.datasets <- lapply(dataset_nodes,
node_to_object)
private$.OGS6_vtus <- lapply(self$abs_vtu_paths,
read_in_vtu)
OGS6_vtu$new)
},
......@@ -31,11 +31,11 @@ OGS6_pvd <- R6::R6Class(
#'@param timestep string: Timestep
get_vtu_path_by_timestep = function(timestep){
assertthat::assert_that(assertthat::is.string(timestep))
assertthat::assert_that(assertthat::is.number(timestep))
for(i in seq_len(length(private$.datasets))){
if(private$.datasets[[i]][["timestep"]] == timestep){
return(private$.datasets[[i]][["file"]])
for(i in seq_len(length(self$timesteps))){
if(self$timesteps[[i]] == timestep){
return(self$vtu_paths[[i]])
}
}
......@@ -50,9 +50,9 @@ OGS6_pvd <- R6::R6Class(
assertthat::assert_that(assertthat::is.string(vtu_path))
for(i in seq_len(length(private$.datasets))){
if(private$.datasets[[i]][["file"]] == vtu_path){
return(private$.datasets[[i]][["timestep"]])
for(i in seq_len(length(self$vtu_paths))){
if(self$vtu_paths[[i]] == vtu_path){
return(self$timesteps[[i]])
}
}
......@@ -62,28 +62,75 @@ OGS6_pvd <- R6::R6Class(
#'@description
#'Creates a tibble object from PointData
#'@param point_ids numeric: Optional: IDs of the points of interest.
#' Will default to all point IDs if not defined.
#'@param Names character: `Name` attributes of `DataArray` elements
get_PointData_time_tibble = function(Names){
#'@param start_at_timestep number: Timestep to start at
#'@param end_at_timestep number: Timestep to end at
get_PointData_time_tibble = function(point_ids,
Names,
start_at_timestep,
end_at_timestep){
if(missing(point_ids)){
max_point_id <- self$OGS6_vtus[[1]]$get_number_of_points() - 1
point_ids <- seq(0, max_point_id)
}
assertthat::assert_that(is.character(Names))
assertthat::assert_that(is.numeric(point_ids))
if(missing(start_at_timestep)){
start_at_timestep <- self$timesteps[[1]]
}
if(missing(end_at_timestep)){
end_at_timestep <- self$timesteps[[length(self$timesteps)]]
}
assertthat::assert_that(assertthat::is.number(start_at_timestep))
assertthat::assert_that(assertthat::is.number(end_at_timestep))
relevant_vtus <- list()
for(i in seq_len(length(self$OGS6_vtus))){
timestep <- self$get_timestep_by_vtu_path(self$vtu_paths[[i]])
if(timestep >= start_at_timestep &&
timestep <= end_at_timestep){
relevant_vtus <- c(relevant_vtus, list(self$OGS6_vtus[[i]]))
}
}
time_list <- list()
# For each .vtu file referenced in pvd_path...
for(i in seq_len(length(self$OGS6_vtus))){
for(i in seq_len(length(relevant_vtus))){
new_row <- list()
timestep_name <- paste0("t", i)
# ... get all rows of PointData or get rows by Name
if(missing(Names)){
Names <- names(relevant_vtus[[i]]$get_PointData())
}
# ... get row of PointData by Name
for(j in seq_len(length(Names))){
assertthat::assert_that(is.character(Names))
for (j in seq_len(length(point_ids))) {
point_data <-
self$OGS6_vtus[[i]]$get_PointData_DataArray(Names[[j]])
new_row <- c(new_row, list(list(point_data)))
names(new_row)[[length(new_row)]] <- Names[[j]]
relevant_vtus[[i]]$get_PointData_for_point(
point_ids[[j]],
Names)
new_row <- c(new_row,
list(list(point_data)))
names(new_row[[length(new_row)]]) <- timestep_name
names(new_row)[[length(new_row)]] <- paste0("p", (j - 1))
}
time_list <- c(time_list,
list(tibble::as_tibble_row(new_row)))
names(time_list)[[length(time_list)]] <- timestep_name
}
# Combine into tibble
......@@ -92,30 +139,21 @@ OGS6_pvd <- R6::R6Class(
return(time_tibble)
},
get_PointData_timeline = function(point_id,
Name,
starting_from_timestep,
ending_on_timestep){
# ...
},
#'@description
#'Gets PointData at specified timestep. Calls `get_PointData_timeline`
#' internally with `starting_from_timestep` and `ending_on_timestep`
#' both being `timestep`
#'@param point_id number: Point ID
#'@param Name string: `Name` attribute of `DataArray` element
#'Gets PointData at specified timestep. Calls
#' `get_PointData_time_tibble` internally with `start_at_timestep` and
#' `end_at_timestep` both being `timestep`
#'@param point_ids number: Point IDs
#'@param Names character: `Name` attributes of `DataArray` elements
#'@param timestep string: Timestep
get_PointData_at_timestep = function(point_id,
Name,
get_PointData_at_timestep = function(point_ids,
Names,
timestep){
self$get_PointData_timeline(point_id = point_id,
Name = Name,
starting_from_timestep = timestep,
ending_on_timestep = timestep)
self$get_PointData_time_tibble(point_ids = point_ids,
Names = Names,
start_at_timestep = timestep,
end_at_timestep = timestep)
}
),
......@@ -135,8 +173,6 @@ OGS6_pvd <- R6::R6Class(
#'@field vtu_paths
#'Getter for `datasets` `file`
#'@return character: .vtu paths as referenced in `pvd_path`, for
#' absolute paths use `abs_vtu_paths`
vtu_paths = function() {
vtu_paths <- lapply(private$.datasets, function(x){
......@@ -146,7 +182,6 @@ OGS6_pvd <- R6::R6Class(
#'@field abs_vtu_paths
#'Gets absolute .vtu paths, e.g. `dirname(pvd_path)` + `datasets` `file`
#'@return character: Absolute .vtu paths
abs_vtu_paths = function() {
abs_vtu_paths <- lapply(self$vtu_paths, function(x){
......@@ -160,7 +195,7 @@ OGS6_pvd <- R6::R6Class(
timesteps = function() {
timesteps <- lapply(private$.datasets, function(x){
x[["timestep"]]
as.double(x[["timestep"]])
})
},
......@@ -191,13 +226,49 @@ OGS6_vtu <- R6::R6Class(
#'@description
#'Creates new OGS6_vtu object
#'@param vtkUnstructuredGrid
initialize = function(vtu_path,
vtkUnstructuredGrid) {
self$vtkUnstructuredGrid <- vtkUnstructuredGrid
#'@param vtu_path string: Path to .vtu file
initialize = function(vtu_path) {
vtk_xml_ugr <- vtk$vtkXMLUnstructuredGridReader()
vtk_xml_ugr$SetFileName(vtu_path)
vtk_xml_ugr$Update()
private$.vtu_path <- vtu_path
self$vtkUnstructuredGrid <- vtk_xml_ugr$GetOutput()
},
get_PointData_DataArray = function(Name){
#'@description
#'Gets PointData for point with ID `point_id`
#'@param point_id number: Point ID
#'@param Names character: Optional: `Name` attributes of `DataArray`
#' elements, defaults to all in `PointData`
get_PointData_for_point = function(point_id,
Names){
if(missing(Names)){
Names <- names(self$get_PointData())
}
assertthat::assert_that(assertthat::is.number(point_id))
assertthat::assert_that(is.character(Names))
point_data <- list()
for(i in seq_len(length(Names))){
point_data <-
c(point_data,
list(self$get_PointData(Names[[i]])[[(point_id + 1)]]))
names(point_data)[[length(point_data)]] <- Names[[i]]
}
return(point_data)
},
#'@description
#'Gets PointData of `DataArray` element with `Name` attribute
#'@param Name string: Optional: `Name` attribute of `DataArray`
#' elements, defaults to all in `PointData`
get_PointData = function(Name){
if(missing(Name)){
return(self$dsa_wrapped_vtkUnstructuredGrid$PointData)
......@@ -205,12 +276,24 @@ OGS6_vtu <- R6::R6Class(
assertthat::assert_that(assertthat::is.string(Name))
return(self$dsa_wrapped_vtkUnstructuredGrid$PointData[[Name]])
}
},
#'@description
#'Gets number of points
#'@return number: The number of points
get_number_of_points = function(){
return(self$vtkUnstructuredGrid$GetNumberOfPoints())
}
),
active = list(
#'@field vtu_path
#'Getter for private parameter '.vtu_path'
vtu_path = function() {
private$.vtu_path
},
#'@field vtkUnstructuredGrid
#'Access to private parameter '.vtkUnstructuredGrid'
vtkUnstructuredGrid = function(value) {
......@@ -232,29 +315,13 @@ OGS6_vtu <- R6::R6Class(
),
private = list(
.vtu_path = NULL,
.vtkUnstructuredGrid = NULL,
.dsa_wrapped_vtkUnstructuredGrid = NULL
)
)
#'read_in_vtu
#'@description Reads in .vtu file via `vtkXMLUnstructuredGridReader` from the
#' python `vtk` library
#'@param vtu_path string: Path to .vtu file
#'@return vtkUnstructuredGrid*: Unstructured Grid
#'@export
read_in_vtu <- function(vtu_path) {
vtk_xml_ugr <- vtk$vtkXMLUnstructuredGridReader()
vtk_xml_ugr$SetFileName(vtu_path)
vtk_xml_ugr$Update()
return(invisible(OGS6_vtu$new(vtu_path,
vtk_xml_ugr$GetOutput())))
}
#===== generate_structured_mesh =====
......@@ -263,10 +330,12 @@ read_in_vtu <- function(vtu_path) {
#' (VTK mesh generator). For full documentation see
#'https://www.opengeosys.org/docs/tools/meshing/structured-mesh-generation/
#'@param args_str string: The arguments the script will be called with
#'@param ogs_bin_path string: Optional: Path to OpenGeoSys6 bin folder.
#' Defaults to options("r2ogs6.default_ogs_bin_path").
#'@return string: .vtu file path
#'@export
generate_structured_mesh = function(ogs_bin_path,
args_str) {
generate_structured_mesh = function(args_str,
ogs_bin_path) {
if(missing(ogs_bin_path)){
ogs_bin_path <- unlist(options("r2ogs6.default_ogs_bin_path"))
......
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