govtk

GoVTK

A Go package to write data to VTK XML files.

Note: not all feature are implemented yet. Basic VTK XML files and ParaViewData (PVD) collections are availabe.

The package supports a variety of VTK XML styles to be written, i.e. image data (.vti), rectilinear grids (.vtr), structured grids (.vts), and unstructured grids (*.vtu). Each format allows to write the XML using ascii, base64, or binary encoding. The data can be compressed using zlib by means of the Go standard library compress/zlib.

Usage

Four different formats are supported by their constructor:

• Image() for .vti files
• Rectilinear() for .vtr files
• Structured() for .vts files
• Unstructured() for .vtu files

These support three types of encoding: Ascii(), Base64(), and Raw() (binary data). The latter two result in significantly smaller files. Note, Base64() does maintain valid XML, while Raw() does not. Additionally, Base64() and Raw() encoding allow to compress the data before encoding by passing Compressed(), to further reduces file size.

Data is added by Add(). Point/Cell data can be inserted as Add(Data("fieldname", data)), which infers if the data should be place on the points or cells. Alternatively, the CellData and PointData allow to directly write data to either points or cells. Global, generic data fields can be added by FieldData.

The file is written to disk by either Save(filename string) or Write(w io.Writer). For each file type a small example is presented.

Image data

vti, err := govtk.Image(govtk.WholeExtend(0, nx, 0, ny, 0, nz))
data := make([]float64, (nx+1)*(ny+1)*(nz+1))
vti.Add(govtk.Data("fieldname", data))
vti.Save("image.vti") 

Rectilinear

vtr, err := govtk.Rectilinear(govtk.WholeExtend(0, nx, 0, ny, 0, nz)) 

// store x, y, z coordinates a 1D vectors 
x := make([]float64, nx+1)
y := make([]float64, ny+1)
z := make([]float64, nz+1)

// fill x, y, z accordingly 
// ... 

// store coordinates
vtr.Add(govtk.Points(x, y, z)) 
vtr.Add(govtk.Data(...)) 
vtr.Save("rectilinear.vtr") 

Structured grid

vts, err := govtk.Structured(govtk.WholeExtend(0, nx, 0, ny, 0, nz)) 

// store all x,y,z tuples for each node
xyz := make([]float64, 3*(nx+1)*(ny+1)*(nz+1))

// fill xyz with each coordinate 
// ... 

vts.Add(govtk.Points(xyz))
vts.Add(govtk.Data(...))
vts.Save("structured.vts") 

Unstructured grid

vtu, err := govtk.Unstructured() 

// store all x,y,z tuples for each node 
vtu.Add(Points(...))

// provide cell connectivity, e.g. two tet elements 
conn := []int{0, 1, 2, 3, 0, 4, 5, 6}
offset := []int{0, 4, 6} // start of each element in conn 
labels := []int{20, 20} // VTK labels 

vtu.Add(govtk.Cells(conn, offset, labels))

// store data and save 
vtu.Add(govtk.Data(...))
vtk.Save("unstructured.vtu" 

Paraview data file format (PVD)

The package also allows to write PVD collections. These ParaviewData files allow to store references to multiple VTK XML files, which might be located anywhere on disk. Each file can save a time step, part id, and group name as attribute. The time steps are directly available in ParaView, which is beneficial for data of transient time series.

For example to store a time series:

pvd, err := govtk.NewPVD(govtk.Directory("./mypvd")) 

// some time series 
for t := 0; t < 100; t++ {

    // generate output data 
    vti, err := govtk.Image(govtk.WholeExtend(0, nx, 0, ny, 0, nz), govkt.Raw()) 
    vti.Add(govtk.Data(...))
    
    // attach to PVD collection
    pvd.Add(vti, govtk.Time(float64(t))
}

// save PVD main file
pvd.Save(filepath.Join(pvd.Dir(), "pvd.pvd"))

Provides the following directory

myvpd/
    file_000.vti 
    file_001.vti
    ...
    file_099.vti
    pvd.pvd

Legacy format

Not yet supported

Encoding and compression settings

Basic encoding and compression is controlled by:

govtk.Ascii()     // plain ascii 
govtk.Binary()    // base64 encoding 
govtk.Raw()       // plain binary 

// compression only applies to `govtk.Binary()` and `govtk.Raw()`
govtk.Compressed()               // applies govtk.DefaultCompression
govtk.CompressedLevel(level int) // applies received compression level 

// compression levels are directly taken from `compress/zlib`
const ( 
    govtk.NoCompression      = zlib.NoCompression 
    govtk.BestSpeed          = zlib.BestSpeed
    govtk.BestCompression    = zlib.BestCompression
    govtk.DefaultCompression = zlib.DefaultCompression
    govtk.HuffmanOnly        = zlib.HuffmanOnly
) 

Command-line tools

to be implemented

Installation

Install the package

go get -u -v github.com/maxvdkolk/govtk/...

References

• https://vtk.org/Wiki/VTK_XML_Formats
• https://vtk.org/wp-content/uploads/2015/04/file-formats.pdf
• https://github.com/jipolanco/WriteVTK.jl