ReadVTK.jl

With ReadVTK.jl you can read in data from VTK XML files in Julia. It aims to complement the excellent package WriteVTK.jl. ReadVTK is part of the Trixi Framework.

Note: ReadVTK was mainly motivated by wanting to write proper tests for Trixi2Vtk.jl. A lot of useful features are still missing (see below), and community contributions to improve this package are welcome!

Usage

First, load the package with

using ReadVTK

Open a VTK file by creating a VTKFile object and passing the filename to the constructor:

vtk = VTKFile(get_example_file("celldata_appended_binary_compressed.vtu"))

To retrieve information about the cell data, use

cell_data = get_cell_data(vtk)

The return object of type VTKCellData allows access to the individual VTKDataArrays using a dictionary-like syntax:

element_ids = cell_data["element_ids"]

Finally, the actual data can be obtained by executing

data = get_data(element_ids)

Full example including REPL output:

julia> using ReadVTK

julia> vtk = VTKFile(get_example_file("celldata_appended_binary_compressed.vtu"))
VTKFile("celldata_appended_binary_compressed.vtu", <XMLDocument>, "UnstructuredGrid", "1.0.0", "LittleEndian", "vtkZLibDataCompressor", <appended_data>, 4434, 3085)

julia> cell_data = get_cell_data(vtk)
VTKData()

julia> element_ids = cell_data["element_ids"]
VTKDataArray("element_ids")

julia> data = get_data(element_ids)
3085-element reinterpret(Int64, ::Vector{UInt8}):
    1
    2
    3
    ⋮
 3083
 3084
 3085

Further example VTK files can be found in the ReadVTK_examples repository.

What works

• Reading in VTK XML files of type UnstructuredGrid or ImageData
• Extracting cell or point data
• Extracting point coordinates
• Extracting information about cell types
• Only for ImageData files: get origin, spacing, and extent information
• Reading PolyData files containing vortices, lines, and/or polygons

What does not work

• Reading VTK files not stored in the VTK XML format
• Reading VTK files of other type than UnstructuredGrid, ImageData, or PolyData
• Multiblock files, PVD files
• Different byte orders in file and host system
• Probably reading from VTK files that were not created by WriteVTK.jl will fail, specifically since
  • compressed data is assumed to be stored as a single block
  • appended data is assumed to be stored as raw
  • header_type is hardcoded to UInt64
• Extracting primitives from PolyData files other than vortices, lines, and/or polygons
• Likely anything else that is not specifically mentioned under What works

Development

Helpful resources for working with (i.e., reading and writing) VTK XML files:

• VTK file format documentation (incomplete!) as a PDF
• VTK XML formats wiki article
• Blog post on encoding binary data
• Mailing list message on encoding binary data

Authors

ReadVTK is maintained by the Trixi authors. Its principal developers are Michael Schlottke-Lakemper (University of Stuttgart, Germany) and Hendrik Ranocha (University of Hamburg, Germany).

Further contributions to ReadVTK have been made by the following people:

• Jorge Pérez Zerpa (Universidad de la República, Uruguay)
• Ondřej Kincl (Charles University, Czech Republic)

License and contributing

ReadVTK is licensed under the MIT license (see LICENSE.md). Since ReadVTK is an open-source project, we are very happy to accept contributions from the community. Please refer to CONTRIBUTING.md for more details. To get in touch with the developers, join us on Trixi's Slack workspace or create an issue.

Acknowledgments

This package would not exist without the nice work of Juan Ignacio Polanco and his cleanly written and well-documented package WriteVTK.jl.