XYZ Files

These are some examples of XYZ files, a very simple format for recording points and lines in 3D space.

An XYZ file has a simple structure:

• Comment lines begin with '#" in column 1, and may appear anywhere;
• Blank lines may appear anywhere.
• The coordinates of a point are written on a single line, separated by spaces;

There is a variation on the format which adds one additional rule:

• If the coordinates for two points are listed consecutively, it is assumed there is a line segment connecting them; to indicate that no such line segment exists, insert a blank line between the two records;

Example XYZ File:

        #  Corners of a tetrahedron
        #
        0.0  0.0  0.0
        1.0  0.0  0.0
        0.0  1.0  0.0
        0.0  0.0  1.0
      

Related Data and Programs:

• The TABLE file format is a more general format which includes XYZ files for the 3D case.
• The XY file format is an analogous format for the 2D case.

XYZ file characteristics:

• ASCII
• 3D
• No compression
• 1 image

Programs to create an XYZ file:

• RANDOM_DATA can produce a set of points that are randomly sampled from a given geometric shape. In cases where this was a 3D shape, the resulting output file is an XYZ file.
• RBOX will produce a random sample of points according to a given distribution, and over a given geometric shape. In cases where this was a 3D shape, then the resulting output file is ALMOST an XYZ file (you just need to delete the two initial records that list the spatial dimension and number of points.)

Programs to process an XYZ file:

Programs to process an XYZ file include all the programs that will handle a TABLE file, including:

• TABLE_QUALITY is a program which reads a TABLE file (in particular, an XYZ file), and returns the "quality" of dispersion. TABLE_QUALITY is available in a C++ version, and a FORTRAN90 version, and a MATLAB version.
• TABLE_UNIFORM_NOISE will read an XYZ file and add uniform noise to it.

Routines to read an XYZ file:

• TABLE_IO is a set of routines that can read a TABLE file, or, in particular, an XYZ file. TABLE_IO is available in a C++ version, and a FORTRAN90 version, and a MATLAB version.

Routines to write an XYZ file:

• TABLE_IO is a set of routines that can write a TABLE file, or, in particular, an XYZ file. TABLE_IO is available in a C++ version, and a FORTRAN90 version, and a MATLAB version.

Programs to convert an XYZ file to another format:

• IVREAD can read an XYZ file and convert it to a number of different formats.
• SXYZ_VORONOI is a FORTRAN90 program which can read an XYZ file of points on a sphere, determine the Delaunay triangulation and Voronoi diagram, and make EPS file images of them.
XYZ_TO_PDB is a FORTRAN90 program which reads an XYZ file and writes the data as atomic coordinates in a PDB file.

Programs to convert a file to XYZ format:

• IVREAD is a FORTRAN90 program which can read a graphics file in a number of formats and write it as an XYZ file.
• PDB_TO_XYZ is a FORTRAN90 program which reads a PDB file and writes the atomic coordinates to an XYZ file.

Programs to display an XYZ file:

• POINTS_DISPLAY_MATLAB can read a file of point coordinates and display an image of the points inside the MATLAB graphics window.

Sample XYZ files:

• block.xyz, the outline of a block;
• bridge.xyz, a line drawing of a bridge;
• cube.xyz, the outline of a cube;
• delaunay_refine.xyz a Delaunay refined mesh on a sphere;
• delaunay_refine2.xyz a Delaunay refined mesh on a sphere;
• helix_201_3d.txt, 201 points on a helix;
• helix_201_3d.png, a PNG image of the data.
• line3d.xyz, a simple demonstration of drawing lines in 3D;
• simplex.xyz, a simplex or tetrahedron;
• spiralpoints.xyz, 700 points spiral around the surface of the unit sphere;
• tetrahedron.xyz, a tetrahedron;

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