7.3 Text-based File Formats

SCIRun's reader and writer modules read and write text files containing the following data:

• Node coordinates
• Node connectivities
• Structured mesh parameters
• Column matrices
• Dense matrices
• Sparse row matrices
• Color map parameters

SCIRun unstructured field types are stored in two or three text files. Curve, hex volume, quad surface, tet volume, and tri surface fields each require three files: a node coordinate, a connectivity, and a column matrix file. Point cloud fields require no connectivity file.

Note that field readers read node coordinate and connectivity files only. Therefore, to construct a complete field from text-based files a FieldReader module is used to read node coordinate and connectivity data and a MatrixReader module is used to read field data from a matrix file. Outputs from modules FieldReader and FieldReader are sent to module ManageFieldData, which combines their outputs to create complete field object. See Using Readers for more information.

When writing a field, use module ManageFieldData to split a field into a geometry stream and a data stream. Send the geometry stream to module FieldWriter, which writes node coordinate and connectivity files, and send the data stream to module MatrixWriter, which writes field data to a matrix file. See Using Writers for more information.

The structured (curve, quad surface, and hex volume) field types each require only a node coordinate file.

SCIRun column matrix, dense matrix, and sparse row matrix data are stored in column matrix, dense matrix and sparse matrix files respectively.

A Colormap is stored in a colormap file.

7.3.1 Node Coordinate File

Node coordinate files have the extension .pts. A node coordinate file contains the coordinates of every node in a mesh.

Field reader and writer modules import/export pts files.

The format is as follows:

N
x0 y0 z0
x1 y1 z1
    .
    .
    .
xN yN zN

N is the number of nodes in the file. Each remaining line defines the coordinates of one mesh node.

7.3.2 Connectivity Files

SCIRun supports five unstructured mesh types. Each mesh type is described by a corresponding type of node connectivity file. Curve meshes are made up of edge elements contained in edge files. Surface meshes composed of triangular elements are stored in fac files. Surface meshes composed of quadrilateral elements are stored in quad files. Volume meshes composed of tetrahedral elements are stored in tet files. Volume meshes composed of hexahedral elements are stored in hex file.

Edge files have the file extension .edge. Fac files have the extension .fac. Likewise for quad, tet, and hex files.

Field reader and writer modules import/export edge, fac, quad, tet, and hex connectivity files.

Connectivity files are formatted as follows:

N
Node indicies of element 0
Node indicies of element 1
            .
            .
            .
Node indicies of element N

N specifies the number of elements in a file.

Each remaining line specifies node indices of one element. Node indices are assumed to be zero-based.

Edge files have two node indices per line, fac files have three, quad and tet files have four, and hex files have eight node indices per line. For example, a fac file looks like the following:

N
i0 j0 k0
i1 j1 k0
    .
    .
    .
iN jN kN

7.3.3 Structured Meshes

Structured meshes are stored in node coordinate (pts) files. Only node coordinates are needed. Connectivities are implicit because node coordinates are stored in scan-line order.

For example, in a structured hexahedral mesh, the list of nodes comprising element e_{i, j, k} mathend000# is {n_{i, j, k}, n_{i, j, k+1}, n_{i, j+1, k+1}, n_{i, j+1, k}, n_{i+1, j, k}, n_{i+1, j, k+1}, n_{i+1, j+1, k+1}, n_{i+1, j+1, k}} mathend000#

The formats of node coordinate files for structured meshes differ slightly from node coordinate files described in Node Coordinate File Format. Node coordinate files for structured meshes specify the number of indices in each dimension of the mesh.

A structured curve field node coordinate file looks like this:

NI
x0 y0 z0
x1 y1 z1
    .
    .
    .
xN yN zN

The node coordinate file for a structured quadrilateral surface field looks like this:

NI NJ
x0 y0 z0
x1 y1 z1
    .
    .
    .
xN yN zN

The node coordinate file for a structured hexahedral volume field looks like this:

NI NJ NK
x0 y0 z0
x1 y1 z1
    .
    .
    .
xN yN zN

7.3.4 Column Matrix

The column matrix file format is:

N
v0 
v1
.
.
.
vN

N specifies the number of matrix rows. N is followed by a list of data values.

7.3.5 Dense Matrix

The dense matrix file format is:

N M
v(0,0) v(0,1)...v(0,M)
v(1,0) v(1,1)...v(1,M)
        .
        .
        .
v(N,0) v(N,1)...v(N,M)

N, M are the number of matrix rows and columns respectively. Following N and M is a list of data values given in row major order.

7.3.6 Sparse Row Matrix

The sparse row matrix file format is:

NR NC NE
r0 c0 v0
r1 c1 v1
   .
   .
   .
rNE cNE vNE

NR, NC, and NE specify the number of rows, number of columns, and number of matrix entries respectively.

Remaining lines are matrix entries. Each entry consists of a row index, a column index, and a data value. Entries must have ascending row indices. Column indices must be in ascending order for rows with multiple entries.

7.3.7 Color Map

The color map file format is:

N
r1 g1 b1 a1 v1
r2 g2 b2 a2 v2
      .
      .
      .
rN gN bN aN vN

N specifies the number of color map entries in the file.

Each line following N is a color map entry consisting of an RGB color entry, an alpha value, and a data value. All RGB, alpha, and data values are in the range 0.0 to 1.0 inclusive.