Unable to import various VTK and VTU file types

[2pt0]

vtkio is unable to parse VTK and VTU files generated by pygmsh which internally uses meshio for generation of VTK and VTU files.

I have tested the following file types:

• VTK ASCII (Legacy)
• VTK XML Binary
• VTU ASCII
• VTU XML Binary - No compression
• VTU XML Binary - LZMA compression
• VTU XML Binary - zlib compression

Paraview is able to visualize each file without problem. The spreadsheet view for each file shows the appropriate data.

Here is the script used to generate the VTK and VTU files:

import pygmsh

with pygmsh.geo.Geometry() as geom:
    p = geom.add_polygon(
        [
            [0.0, 0.0],
            [1.0, -0.2],
            [1.1, 1.2],
            [0.1, 0.7],
        ],
        mesh_size=0.4,
    )
    geom.add_physical(p.lines[0], label="bottom")
    geom.add_physical(p.lines[1], label="right")
    geom.add_physical(p.lines[2], label="top")
    geom.add_physical(p.lines[3], label="left")

    mesh = geom.generate_mesh()

mesh.write("no-compression.vtu", compression=None)
mesh.write("lzma.vtu", compression="lzma")
mesh.write("zlib.vtu", compression="zlib")
mesh.write("ascii.vtu", binary=False)
mesh.write("binary.vtk")
mesh.write("ascii.vtk", binary=False)

Here is the file I am using to test the import of these files:

use std::path::Path;
use vtkio::model::Vtk;

fn main() -> Result<(), Box<dyn std::error::Error>> {
    let inputs = &[
        "ascii.vtk",
        "binary.vtk",
        "ascii.vtu",
        "no-compression.vtu",
        "lzma.vtu",
        "zlib.vtu",
    ];

    let vtks = inputs
        .iter()
        .map(|input| Vtk::import(input));

    for (input, vtk) in inputs.iter().zip(vtks) {
        print!("{}.. ", input);

        match vtk {
            Ok(_) => println!("parsed!"),
            Err(e) => println!("{}", e),
        };
    }

    Ok(())
}

And the output

ascii.vtk.. Parse error: Alt
binary.vtk.. Parse error: Alt
ascii.vtu.. XML error: Validation error: InvalidDataFormat
no-compression.vtu.. XML error: Validation error: DataArraySizeMismatch { name: "types", expected: 38, actual: 37 }
lzma.vtu.. XML error: Validation error: Base64Decode(InvalidByte(22, 61))
zlib.vtu.. XML error: Validation error: Base64Decode(InvalidByte(22, 61))

I'm not sure if the problem is with vtkio or mehsio. I have opened an issue here since Kitware's Paraview (which also develops VTK) reports no problems with these files.

Thanks for your help!

[elrnv]

Thank you for the issue! It is definitely a goal to support files accepted by VTK or ParaView as much as possible.

[2pt0]

Thanks for the library! Is there a path forward to fix this or any obvious reasons why the parsing is failing?

[elrnv]

I took a quick look at the ascii.vtk file, and noticed there are two additional fields titled "CONNECTIVITY" and "OFFSETS", which aren't documented (https://kitware.github.io/vtk-examples/site/VTKFileFormats/) unfortunately.
I think these use the same format as the xml files use, which means vtkio can already represent this data in a straightforward way, we just need to add some parsing functions for those extra fields.

I haven't yet looked at the other files. It's possible they are failing for different reasons.

I have been adding these undocumented fields/extensions to the vtk formats previously. I think these are inevitable, but I simply don't know what they are until someone finds files which don't work with vtkio, so thank you for bringing it up. I think these can serve as great test examples that we can add to assets and add more tests for these files in particular.

It might be a while until I have time to dig into these myself, but I'm willing to help out if you have time trying to fix some of these failures :)

[brioglade]

Dear developer,could you please updata this script to Houdini 19 ? Thank you very much.