Add support for field data (#66)

* Introduced functions 'get_field' and 'field_data'
in order to be able to read FieldData from VTK files.

* Introduced suggested changes in pull request

* Indented docstring

* Export the `get_field_data` function

* Add test for field data

* Update docstring references on `get_field_data`

* Ignore non DataArray elements

Co-authored-by: Hendrik Ranocha <[email protected]>

* Format field data test

* Add field data support to documentation

* format

---------

Co-authored-by: andresegido <[email protected]>
Co-authored-by: Hendrik Ranocha <[email protected]>

Author: 3 people

README.md

@@ -71,6 +71,7 @@ Further example VTK files can be found in the
 ### What works
 * Reading in VTK XML files of type `UnstructuredGrid`, `StructuredGrid`, `RectilinearGrid`,`ImageData`, `PUnstructuredGrid`,`PStructuredGrid` `PRectilinearGrid`,`PImageData`, or `PolyData`
 * Extracting cell or point data
+* Extracting field data
 * Extracting point coordinates
 * Extracting information about cell types
 * Only for `ImageData`,`PImageData` files: get origin, spacing, and extent information

docs/src/index.md

@@ -80,6 +80,7 @@ Further example VTK files can be found in the
 ### What works
 * Reading in VTK XML files of type `UnstructuredGrid`, `StructuredGrid`, `RectilinearGrid`,`ImageData`, `PUnstructuredGrid`, `PStructuredGrid`, `PRectilinearGrid`,`PImageData`, or `PolyData`
 * Extracting cell or point data
+* Extracting field data
 * Extracting point coordinates
 * Extracting information about cell types
 * Only for `ImageData`,`PImageData` files: get origin, spacing, and extent information

src/ReadVTK.jl

@@ -13,7 +13,8 @@ using Reexport: @reexport
 
 export VTKFile, VTKData, VTKDataArray, VTKCells, VTKPrimitives,           # structs
        PVTKFile, PVTKData, PVTKDataArray, PVDFile,
-       get_point_data, get_cell_data, get_data, get_data_reshaped,        # get data functions
+       get_point_data, get_cell_data, get_field_data, get_data,           # get data functions
+       get_data_reshaped,
        get_points, get_cells, get_origin, get_spacing, get_primitives,    # get geometry functions
        get_coordinates, get_coordinate_data,                              # get geometry functions
        get_example_file,                                                  # other functions
@@ -184,6 +185,11 @@ function piece(vtk_file::VTKFile)
   return LightXML.root(vtk_file.xml_file)[vtk_file.file_type][1]["Piece"][1]
 end
 
+# Return `FieldData` XML element that contains all VTK field data
+function field_data(vtk_file::VTKFile)
+  return LightXML.root(vtk_file.xml_file)[vtk_file.file_type][1]["FieldData"][1]
+end
+
 """
     isstructured(xml_file)
 
@@ -433,14 +439,37 @@ function get_data_section(vtk_file::VTKFile, section)
   return VTKData(names, data_arrays, vtk_file)
 end
 
+"""
+    get_field_data(vtk_file::VTKFile)
+
+Retrieve a lightweight `VTKData` object with the field data of the given VTK file.
+
+See also: [`VTKData`](@ref), [`get_point_data`](@ref), [`get_cell_data`](@ref)
+"""
+function get_field_data(vtk_file::VTKFile)
+  names = String[]
+  data_arrays = XMLElement[]
+
+  # Iterate over XML elemens in the section
+  for xml_element in child_elements(field_data(vtk_file))
+    # We do not know how to handle anything other than `DataArray`s
+    LightXML.name(xml_element) != "DataArray" && continue
+
+    # Store the name and the XML element for each found data array
+    push!(names, attribute(xml_element, "Name", required = true))
+    push!(data_arrays, xml_element)
+  end
+
+  return VTKData(names, data_arrays, vtk_file)
+end
 
 """
     get_cell_data(vtk_file::VTKFile)
 
 Retrieve a lightweight `VTKData` object with the cell data of the given VTK file.
 Only numeric data (i.e., `DataArray`) elements will be read.
 
-See also: [`VTKData`](@ref), [`get_point_data`](@ref)
+See also: [`VTKData`](@ref), [`get_point_data`](@ref), [`get_field_data`](@ref)
 """
 get_cell_data(vtk_file::VTKFile) = get_data_section(vtk_file, "CellData")
 
@@ -450,7 +479,7 @@ get_cell_data(vtk_file::VTKFile) = get_data_section(vtk_file, "CellData")
 Retrieve a lightweight vector with `PVTKData` objects with the cell data of the given PVTK files.
 Only numeric data (i.e., `DataArray`) elements will be read.
 
-See also: [`PVTKData`](@ref), [`get_cell_data`](@ref)
+See also: [`PVTKData`](@ref), [`get_point_data`](@ref), [`get_field_data`](@ref)
 """
 function get_cell_data(pvtk_file::PVTKFile)
   n_files = length(pvtk_file)
@@ -469,7 +498,7 @@ end
 Retrieve a lightweight `VTKData` object with the point data of the given VTK file.
 Only numeric data (i.e., `DataArray`) elements will be read.
 
-See also: [`VTKData`](@ref), [`get_cell_data`](@ref)
+See also: [`VTKData`](@ref), [`get_cell_data`](@ref), [`get_field_data`](@ref)
 """
 get_point_data(vtk_file::VTKFile) = get_data_section(vtk_file, "PointData")
 
@@ -479,7 +508,7 @@ get_point_data(vtk_file::VTKFile) = get_data_section(vtk_file, "PointData")
 Retrieve a lightweight vector with `PVTKData` objects with the point data of the given PVTK files.
 Only numeric data (i.e., `DataArray`) elements will be read.
 
-See also: [`PVTKData`](@ref), [`get_cell_data`](@ref)
+See also: [`PVTKData`](@ref), [`get_cell_data`](@ref), [`get_field_data`](@ref)
 """
 function get_point_data(pvtk_file::PVTKFile)
   n_files = length(pvtk_file)
@@ -497,7 +526,7 @@ end
 Retrieve a lightweight `VTKData` object with the coordinate data of the given VTK file.
 Only coordinates of numeric data (i.e., `DataArray`) elements will be read.
 
-See also: [`VTKData`](@ref), [`get_point_data`](@ref),  [`get_cell_data`](@ref)
+See also: [`VTKData`](@ref), [`get_point_data`](@ref), [`get_cell_data`](@ref), [`get_field_data`](@ref)
 """
 get_coordinate_data(vtk_file::VTKFile) = get_data_section(vtk_file, "Coordinates")
 
@@ -507,7 +536,7 @@ get_coordinate_data(vtk_file::VTKFile) = get_data_section(vtk_file, "Coordinates
 Retrieve a lightweight `{VTKData` object with the coordinate data of the given VTK file.
 Only coordinates of numeric data (i.e., `DataArray`) elements will be read.
 
-See also: [`PVTKData`](@ref), [`get_point_data`](@ref),  [`get_cell_data`](@ref)
+See also: [`PVTKData`](@ref), [`get_point_data`](@ref), [`get_cell_data`](@ref), [`get_field_data`](@ref)
 """
 function get_coordinate_data(pvtk_file::PVTKFile)
   return get_data_section.(pvtk_file.vtk_files, "Coordinates")

test/fielddata.jl

@@ -0,0 +1,23 @@
+# Create some cells
+points = rand(3, 5)
+cells = [
+  MeshCell(VTKCellTypes.VTK_TRIANGLE, [1, 4, 2]),
+  MeshCell(VTKCellTypes.VTK_QUAD, [2, 4, 3, 5]),
+]
+
+scalar = 5.0
+vector = [1.0, 2.0, 3.0]
+
+path = joinpath(TEST_EXAMPLES_DIR, "fields")
+
+vtk_grid(path, points, cells, append = false) do vtk
+  vtk["scalar"] = scalar
+  return vtk["vector"] = vector
+end
+
+vtk_read = VTKFile(path * ".vtu")
+fielddata = get_field_data(vtk_read)
+
+@test only(get_data(fielddata["scalar"])) == scalar
+
+@test get_data(fielddata["vector"]) == vector

test/runtests.jl

@@ -445,4 +445,13 @@ clean_directory(TEST_EXAMPLES_DIR) = @test_nowarn rm(TEST_EXAMPLES_DIR, recursiv
     clean_directory(TEST_EXAMPLES_DIR)
   end
 
+  @testset "Field data" begin
+    # Start with a clean environment: remove example file directory if it exists
+    create_directory(TEST_EXAMPLES_DIR)
+
+    include("fielddata.jl")
+
+    # Clean up afterwards: delete example file directory
+    clean_directory(TEST_EXAMPLES_DIR)
+  end
 end