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WriteVTK

Julia package for writing VTK XML files

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WriteVTK

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This package allows to write VTK XML files for visualisation of multidimensional datasets using tools such as ParaView.

The supported VTK file formats include rectilinear (.vtr) and structured grids (.vts), image data (.vti), unstructured grids (.vtu) and polygonal data (.vtp). Multiblock files (.vtm), which can point to multiple VTK files, can also be exported; as well as ParaView collection files (.pvd), which can be used to visualise time series of VTK files.

Contents

Installation

From the Julia REPL:

]add WriteVTK

Then load the package in Julia with:

using WriteVTK

Quick start

The vtk_grid function is the entry point for creating different kinds of VTK files. In the simplest cases, one just passes coordinate information to this function. WriteVTK then decides on the VTK format that is more adapted for the provided data.

For instance, it is natural in Julia to describe a 3D uniform grid, with regularly spaced increments, as a list of ranges:

x = 0:0.1:1
y = 0:0.2:1
z = -1:0.05:1

This specific way of specifying coordinates is compatible with the image data VTK format (.vti files). The following creates such a file, with some scalar data attached to each point:

vtk_grid("my_dataset", x, y, z) do vtk
    vtk["my_point_data"] = rand(length(x), length(y), length(z))
end

This will save a my_dataset.vti file with the data. Note that the file extension should not be included in the filename, as it will be attached automatically according to the dataset type.

By changing the coordinate specifications, the above can be naturally generalised to non-uniform grid spacings and to curvilinear and unstructured grids. In each case, the correct kind of VTK file will be generated.

Rectilinear and structured meshes

Define a grid

The function vtk_grid initialises the VTK file. This function requires a filename with no extension, and the grid coordinates. Depending on the shape of the arrays x, y and z, either a rectilinear or structured grid is created.

vtkfile = vtk_grid("my_vtk_file", x, y, z) # 3-D
vtkfile = vtk_grid("my_vtk_file", x, y)    # 2-D

Required array shapes for each grid type:

  • Rectilinear grid: x, y, z are 1-D arrays with different lengths in general (Ni, Nj and Nk respectively).
  • Structured grid: x, y, z are 3-D arrays with the same shape: (Ni, Nj, Nk). For the two dimensional case, x and y are 2-D arrays with shape (Ni, Nj)

Alternatively, in the case of structured grids, the grid points can be defined from a single 4-D array xyz, of dimensions (3, Ni, Nj, Nk). For the two dimensional case xy is a 3-D array, with dimensions (2, Ni, Nj):

vtkfile = vtk_grid("my_vtk_file", xyz) # 3-D
vtkfile = vtk_grid("my_vtk_file", xy)  # 2-D

This is actually more efficient than the previous formulation.

Add some data to the file

In a VTK file, data can be associated to grid points or to data cells (see Defining cells for details on cells). Data is written to a VTK file object using the syntax

vtkfile["Velocity"] = vel
vtkfile["Pressure"] = p
vtkfile["Concentration"] = C

where the "index" is the name of the dataset in the VTK file.

It is also possible to write datasets whose dimensions are independent of the discrete geometry. In VTK this is called "field data", and can be used to write metadata such as time information or strings:

vtkfile["Time"] = 42.0
vtkfile["Date"] = "30/05/2020"
vtkfile["Distances"] = [2.0, 4.0, 8.0]

For convenience, the input data is automatically associated either to grid points or data cells, or interpreted as field data, according to the input data dimensions. If more control is desired, one can explicitly pass a VTKPointData, a VTKCellData or a VTKFieldData instance as a second index:

vtkfile["Velocity", VTKPointData()] = vel
vtkfile["Pressure", VTKCellData()] = p
vtkfile["Time", VTKFieldData()] = 42.0

Note that in rectilinear and structured meshes, the cell dimensions are always (Ni - 1, Nj - 1, Nk - 1), and the dimensions of the data arrays associated to cells should be consistent with these dimensions.

The input array can represent either scalar or vectorial data. The shape of the array should be (Ni, Nj, Nk) for scalars, and (Nc, Ni, Nj, Nk) for vectors, where Nc is the number of components of the vector.

Vector datasets can also be given as a tuple of scalar datasets, where each scalar represents a component of the vector field. Example:

acc = (acc_x, acc_y, acc_z)  # acc_x, acc_y and acc_z have size (Ni, Nj, Nk)
vtkfile["Acceleration"] = acc

This can be useful to avoid copies of data in some cases.

Save the file

Finally, close and save the file with vtk_save:

outfiles = vtk_save(vtkfile)

outfiles is an array of strings with the paths to the generated files. In this case, the array is of length 1, but that changes when working with multiblock files.

Image data

The points and cells of an image data file are defined by the number of points in each direction, (Nx, Ny, Nz). In addition, the origin of the dataset and the spacing in each direction can be optionally specified. Example:

Nx, Ny, Nz = 10, 12, 42
origin = (3.0, 4.0, -3.2)
spacing = (0.1, 0.2, 0.3)
vtk = vtk_grid("my_vti_file", Nx, Ny, Nz, origin=origin, spacing=spacing)
vtk_save(vtk)

Coordinates may also be specified using ranges (any subtype of AbstractRange works). Some examples:

# Using StepRangeLen objects
vtk_grid("vti_file_1", 0:0.1:10, 0:0.2:10, 1:0.3:4)

# Using LinRange objects
vtk_grid("vti_file_2", LinRange(0, 4.2, 10), LinRange(1, 3.1, 42), LinRange(0.2, 12.1, 32))

Unstructured meshes

An unstructured mesh is defined by a set of points in space and a set of cells that connect those points.

Defining cells

In WriteVTK, a cell is defined using the MeshCell type:

cell = MeshCell(cell_type, connectivity)
  • cell_type is of type VTKCellType which contains the name and an integer value that determines the type of the cell, as defined in the VTK specification (see figures 2 and 3 in that document). For convenience, WriteVTK includes a VTKCellTypes module that contains these definitions. For instance, a triangle is associated to the value cell_type = VTKCellTypes.VTK_TRIANGLE. Cell types may also be constructed from their associated integer identifier. For instance, VTKCellType(5) also returns a VTK_TRIANGLE cell type.

  • connectivity is a vector of indices that determine the mesh points that are connected by the cell. In the case of a triangle, this would be an integer array of length 3.

Note that the connectivity indices are one-based (as opposed to zero-based), following the convention in Julia.

Generating an unstructured VTK file

First, initialise the file:

vtkfile = vtk_grid("my_vtk_file", points, cells)
  • points is an array with the point locations, of dimensions (dim, num_points) where dim is the dimension (1, 2 or 3) and num_points the number of points.

  • cells is a MeshCell array that contains all the cells of the mesh. For example:

    # Suppose that the mesh is made of 5 points:
    cells = [MeshCell(VTKCellTypes.VTK_TRIANGLE, [1, 4, 2]),
           MeshCell(VTKCellTypes.VTK_QUAD,     [2, 4, 3, 5])]
    

Alternatively, the grid points can be defined from 1-D arrays x, y, z with equal lengths num_points:

vtkfile = vtk_grid("my_vtk_file", x, y, z, cells) # 3D
vtkfile = vtk_grid("my_vtk_file", x, y, cells)    # 2D
vtkfile = vtk_grid("my_vtk_file", x, cells)       # 1D

or from a 4-D array points, with dimension [dim, Ni, Nj, Nk] where dim is the dimension and Ni,Nj,Nk the number of points in each direction x,y,z:

vtkfile = vtk_grid("my_vtk_file", points, cells)

These two last methods are less efficient though.

Now add some data to the file. It is possible to add both point data and cell data:

vtkfile["my_point_data", VTKPointData()] = pdata
vtkfile["my_cell_data", VTKCellData()] = cdata

The pdata and cdata arrays must have sizes consistent with the number of points and cells in the mesh, respectively. Note that, as discussed above, the second argument (VTKPointData() or VTKCellData()) can be generally omitted. In this case, its value will be automatically determined from the input data dimensions.

Finally, close and save the file:

outfiles = vtk_save(vtkfile)

Polyhedron cells

WriteVTK also supports the creation of unstructured VTK files containing polyhedron cells. The specificity of polyhedron cells is that they require the specification not only of a connectivity vector, but also of a list of faces constituting the polyhedron. To specify a polyhedron cell, instead of using the MeshCell type, one should create an instance of VTKPolyhedron.

The following simple example creates a cube as a polyhedron cell (see also test/polyhedron_cube.jl for an example with two cubes):

# Vertices of the cube
points = permutedims(Float32[
    -1 -1 -1;
     1 -1 -1;
     1  1 -1;
    -1  1 -1;
    -1 -1  1;
     1 -1  1;
     1  1  1;
    -1  1  1;
])

# Create a single polyhedron cell describing the cube
cells = [
    VTKPolyhedron(
        1:8,           # connectivity vector
        (1, 4, 3, 2),  # face 1
        (1, 5, 8, 4),  # face 2
        (5, 6, 7, 8),  # etc...
        (6, 2, 3, 7),
        (1, 2, 6, 5),
        (3, 4, 8, 7),
    ),
]

# Finally, create a simple VTK file
vtk_grid("polyhedron_cube", points, cells; compress = false) do vtk
    # one can add point and cell data here...
end

Polygonal data

Polygonal datasets are a special type of unstructured grids, in which the cell types are restricted to vertices, lines, triangle strips and polygons. In WriteVTK, these shapes are respectively identified by the singleton types PolyData.Verts, PolyData.Lines, PolyData.Strips and PolyData.Polys.

The specification of points is the same as for unstructured grids. Cells are specified by passing one of the above types to MeshCell. For instance, the following specifies a line passing by 4 points of the grid:

line = MeshCell(PolyData.Lines(), [3, 4, 7, 2])

Similarly to unstructured grids, a VTK file is created by passing vectors of cells to vtk_grid. The difference is that one can pass multiple vectors (one for each cell type), and that each vector may only contain a single cell type.

Example:

# Create lists of lines and polygons connecting different points in space
points = rand(3, 100)  # (x, y, z) locations
lines = [MeshCell(PolyData.Lines(), (i, i + 1, i + 4)) for i in (3, 5, 42)]
polys = [MeshCell(PolyData.Polys(), i:(i + 6)) for i = 1:3:20]
vtk = vtk_grid("my_vtp_file", points, lines, polys)

Note that the order of lines and polys is not important. More generally, one can pass any combination of the four polygonal primitives mentioned above.

Once the grid is created, point and cell data can be added to the file just like for unstructured grids.

⚠️ Known issue: when the polygonal dataset contains multiple kinds of cells (e.g. both lines and polygons), cell data is not correctly parsed by the VTK libraries, and as a result it cannot be visualised in ParaView. The problem doesn't happen with point data. This seems to be a very old VTK issue.

Visualising Julia arrays

A convenience function is provided to quickly save Julia arrays as image data:

A = rand(100, 100, 100)
vtk_write_array("my_vti_file", A, "my_property_name")

Multiblock files

Multiblock files (.vtm) are XML VTK files that can point to multiple other VTK files. They can be useful when working with complex geometries that are composed of multiple sub-domains. In order to generate multiblock files, the vtk_multiblock function must be used. The functions introduced above are then used with some small modifications.

First, a multiblock file must be initialised:

vtmfile = vtk_multiblock("my_vtm_file")

Then, each sub-grid can be generated with vtk_grid using the vtmfile object as the first argument:

# First block.
vtkfile = vtk_grid(vtmfile, x1, y1, z1)
vtkfile["Pressure"] = p1

# Second block.
vtkfile = vtk_grid(vtmfile, x2, y2, z2)
vtkfile["Pressure"] = p2

Additional blocks can also be added to the multiblock file with multiblock_add_block, which can contain any of the VTK files that WriteVTK supports:

# Create a block named my_multiblock and add it to vtmfile.
block = multiblock_add_block(vtmfile, "my_multiblock")

# Add a VTK file to `block`.
vtkfile = vtk_grid(block, "another_file", x3, y3, z3)

Blocks can be nested arbitrarily:

# Add more blocks.
another_block = multiblock_add_block(block, "my_multiblock-block")
yet_another_block = multiblock_add_block(another_block, "my_multiblock-block-block")

And more VTK files may be added to the sub-blocks:

vtkfile = vtk_grid(yet_another_block, "my_deeply_nested_file", x4, y4, z4)

Finally, only the multiblock file needs to be saved explicitly:

outfiles = vtk_save(vtmfile)

WriteVTK will write out a multiblock VTK file that looks like something like this (in addition to all the VTK files contained in the multiblock file):



  
    
    
    
      
      
        
          
        
      
    
  

Paraview Data (PVD) file format

A pvd file is a collection of VTK files, typically for holding results at different time steps in a simulation. A pvd file is initialised with:

pvd = paraview_collection("my_pvd_file")

By default this overwrites existent pvd files. To append new datasets to an existent pvd file, set the append option to true:

pvd = paraview_collection("my_pvd_file", append=true)

VTK files are then added to the pvd file with

pvd[time] = vtkfile

Here, time is a real number that represents the current time (or timestep) in the simulation.

When all the files are added to the pvd file, it can be saved using:

vtk_save(pvd)

Do-block syntax

Do-block syntax is supported by vtk_grid, vtk_multiblock and paraview_collection. At the end of the do-block, vtk_save is called implicitly on the generated VTK object. Example:

# Image data, rectilinear or structured grid
outfiles = vtk_grid("my_vtk_file", x, y, z) do vtk
    vtk["Pressure"] = p
    vtk["Velocity"] = vel
end

# Multiblock file
outfiles = vtk_multiblock("my_vtm_file") do vtm
    vtk = vtk_grid(vtm, x1, y1, z1)
    vtk["Velocity"] = vel1

    vtk = vtk_grid(vtm, x2, y2, z2)
    vtk["Velocity"] = vel2
end

Additional options

By default, numerical data is written to the XML files as compressed raw binary data. This can be changed using the optional keyword arguments of vtk_grid.

For instance, to disable both compressing and appending raw data in the case of unstructured meshes:

vtk = vtk_grid("my_vtk_file", points, cells; compress = false, append = false, ascii = false)
  • If append is true (default), data is written appended at the end of the XML file as raw binary data. Note that this violates the XML specification, although it is allowed by VTK.

Otherwise, if append is false, data is written inline. By default, inline data is written base-64 encoded, but may also be written in ASCII format (see below). Writing inline data is usually slower than writing raw binary data, and also results in larger files, but is valid according to the XML specification.

  • If ascii is true, then appended data is written in ASCII format instead of base64-encoded. This is not the default. This option is ignored if append is true.

  • If compress is true (default), data is first compressed using zlib. Its value may also be a compression level between 1 (fast compression) and 9 (best compression). This option is ignored when writing inline data in ASCII format.

Examples

See some examples in the test/ directory.

First Commit

03/22/2015

Last Touched

5 days ago

Commits

408 commits

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