Skip Array data when constructing VTKData (#65)

* Skip Array data when constructing VTKData

* Formatting

* Add contribution info

README.md

@@ -125,6 +125,8 @@ Further contributions to ReadVTK have been made by the following people:
   (Johannes-Gutenberg University Mainz, Germany)
 * [Matthew Whisenant](https://volweb2.utk.edu/~mwhisena/)
   (University of Tennessee, Knoxville)
+* [William Davis](https://posgeo.wordpress.com/)
+  (Terra AI, USA)
 
 ## License and contributing
 ReadVTK is licensed under the MIT license (see [LICENSE.md](LICENSE.md)).

src/ReadVTK.jl

@@ -415,14 +415,15 @@ end
 
 
 # Retrieve a data section (should be `CellData` or `PointData`) from the VTK file
+
 function get_data_section(vtk_file::VTKFile, section)
   names = String[]
   data_arrays = XMLElement[]
 
   # Iterate over XML elemens in the section
   for xml_element in child_elements(piece(vtk_file)[section][1])
     # We do not know how to handle anything other than `DataArray`s
-    @assert LightXML.name(xml_element) == "DataArray"
+    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))
@@ -437,6 +438,7 @@ 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)
 """
@@ -446,6 +448,7 @@ get_cell_data(vtk_file::VTKFile) = get_data_section(vtk_file, "CellData")
     get_cell_data(pvtk_file::PVTKFile)
 
 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)
 """
@@ -464,6 +467,7 @@ end
     get_point_data(vtk_file::VTKFile)
 
 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)
 """
@@ -473,6 +477,7 @@ get_point_data(vtk_file::VTKFile) = get_data_section(vtk_file, "PointData")
     get_point_data(pvtk_file::PVTKFile)
 
 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)
 """
@@ -490,6 +495,7 @@ end
     get_coordinate_data(vtk_file::VTKFile)
 
 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)
 """
@@ -499,6 +505,7 @@ get_coordinate_data(vtk_file::VTKFile) = get_data_section(vtk_file, "Coordinates
     get_coordinate_data(pvtk_file::PVTKFile)
 
 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)
 """

test/pvtk_files.jl

@@ -41,6 +41,8 @@ for part in 1:4
     pvtk["Velocity"] = [x + 2y + 3z + v for v in v_global, x in xs, y in ys, z in zs]
     pvtk["Pressure"] = [x + 2y + 3z for x in xs_c, y in ys_c, z in zs_c]
     pvtk["Phase"] = [trunc(Int64, x * 15) for x in xs_c, y in ys_c, z in zs_c]
+    pvtk["Temperature string"] = [x + 2y + 3z > 0.5 ? "high" : "low"
+                                  for x in xs, y in ys, z in zs]
     return nothing
   end
 end
@@ -218,6 +220,14 @@ end
   Phase_read = get_data_reshaped(cell_data["Phase"], cell_data = true)
   @test P_global == P_read
   @test Phase_global == Phase_read
+
+  @testset "error on get string cell data" begin
+    @test_throws KeyError cell_data["Temperature string"]
+  end
+
+  @testset "error on get string point data" begin
+    @test_throws KeyError point_data["Temperature string"]
+  end
 end
 
 # c) PVTU files

test/runtests.jl

@@ -200,16 +200,25 @@ clean_directory(TEST_EXAMPLES_DIR) = @test_nowarn rm(TEST_EXAMPLES_DIR, recursiv
 
     # generate random data
     point_scalar_field = rand(Nx, Ny, Nz)
-    point_data_name = "Point scalar data"
+    point_scalar_name = "Point scalar data"
 
     cell_scalar_field = rand(Nx - 1, Ny - 1, Nz - 1)
-    cell_data_name = "Cell scalar data"
+    cell_scalar_name = "Cell scalar data"
+
+    # generate random string data
+    point_string_field = map(x -> x > 0.5 ? "high" : "low", point_scalar_field)
+    point_string_name = "Point string data"
+
+    cell_string_field = map(x -> x > 0.5 ? "high" : "low", cell_scalar_field)
+    cell_string_name = "Cell string data"
 
     # write vti file using WriteVTK
     path = joinpath(TEST_EXAMPLES_DIR, "grid")
     vtk_grid(path, x, y, z) do vtk
-      vtk[point_data_name, VTKPointData()] = point_scalar_field # scalar field attached to points
-      vtk[cell_data_name, VTKCellData()] = cell_scalar_field    # scalar field attached to cells
+      vtk[point_scalar_name, VTKPointData()] = point_scalar_field # scalar field attached to points
+      vtk[cell_scalar_name, VTKCellData()] = cell_scalar_field    # scalar field attached to cells
+      vtk[point_string_name, VTKPointData()] = point_string_field # string field attached to points
+      vtk[cell_string_name, VTKCellData()] = cell_string_field    # string field attached to cells
       return nothing
     end
 
@@ -230,33 +239,41 @@ clean_directory(TEST_EXAMPLES_DIR) = @test_nowarn rm(TEST_EXAMPLES_DIR, recursiv
     end
 
     @testset "get scalar cell data" begin
-      cell_data_raw = get_data(get_cell_data(vtk)[cell_data_name])
+      cell_data_raw = get_data(get_cell_data(vtk)[cell_scalar_name])
       cell_data_reshaped = reshape(cell_data_raw, ((Nx - 1), (Ny - 1), (Nz - 1)))
-      cell_data_reshaped1 = get_data_reshaped(get_cell_data(vtk)[cell_data_name],
+      cell_data_reshaped1 = get_data_reshaped(get_cell_data(vtk)[cell_scalar_name],
                                               cell_data = true)
 
       @test cell_data_reshaped == cell_scalar_field
       @test cell_data_reshaped1 == cell_scalar_field
     end
 
     @testset "get scalar point data" begin
-      point_data_raw = get_data(get_point_data(vtk)[point_data_name])
+      point_data_raw = get_data(get_point_data(vtk)[point_scalar_name])
       point_data_reshaped = reshape(point_data_raw, (Nx, Ny, Nz))
-      point_data_reshaped1 = get_data_reshaped(get_point_data(vtk)[point_data_name])
+      point_data_reshaped1 = get_data_reshaped(get_point_data(vtk)[point_scalar_name])
 
       @test point_data_reshaped == point_scalar_field
       @test point_data_reshaped1 == point_scalar_field
     end
 
+    @testset "error on get string cell data" begin
+      @test_throws KeyError get_cell_data(vtk)[cell_string_name]
+    end
+
+    @testset "error on get string point data" begin
+      @test_throws KeyError get_point_data(vtk)[point_string_name]
+    end
+
     # generate random 2D data
     point_scalar_field = rand(Nx, Ny)
     cell_scalar_field = rand(Nx - 1, Ny - 1)
 
     # write 2D vti file using WriteVTK
     path = joinpath(TEST_EXAMPLES_DIR, "grid_2D")
     vtk_grid(path, x, y) do vtk
-      vtk[point_data_name, VTKPointData()] = point_scalar_field # scalar field attached to points
-      vtk[cell_data_name, VTKCellData()] = cell_scalar_field    # scalar field attached to cells
+      vtk[point_scalar_name, VTKPointData()] = point_scalar_field # scalar field attached to points
+      vtk[cell_scalar_name, VTKCellData()] = cell_scalar_field    # scalar field attached to cells
       return nothing
     end
 
@@ -275,13 +292,13 @@ clean_directory(TEST_EXAMPLES_DIR) = @test_nowarn rm(TEST_EXAMPLES_DIR, recursiv
     end
 
     @testset "get 2D scalar cell data" begin
-      cell_data_raw = get_data(get_cell_data(vtk)[cell_data_name])
+      cell_data_raw = get_data(get_cell_data(vtk)[cell_scalar_name])
       cell_data_reshaped = reshape(cell_data_raw, ((Nx - 1), (Ny - 1)))
       @test cell_data_reshaped == cell_scalar_field
     end
 
     @testset "get 2D scalar point data" begin
-      point_data_raw = get_data(get_point_data(vtk)[point_data_name])
+      point_data_raw = get_data(get_point_data(vtk)[point_scalar_name])
       point_data_reshaped = reshape(point_data_raw, (Nx, Ny))
       @test point_data_reshaped == point_scalar_field
     end