Chimera Commands Index

topography model-spec options

The topography command creates a surface in which height represents the values in a single plane of volume data. The volume data should first be opened and only a single plane displayed. Model-spec is the model number of the data, preceded by #.

The topographic surface is opened as a new surface model named after the volume data but with the word height appended. Creating or rotating the surface can be slow. Default options for a 512 x 512 data plane create a 1 million-triangle surface. Such a surface took 5 seconds to create and rendered at 2 frames per second on a 2005 Mac G5 PPC. Surface size can be reduced by adjusting the volume plane display beforehand to a larger step size and/or smaller subregion.


Option keywords for topography can be truncated to unique strings and their case does not matter. Synonyms for true: True, 1. Synonyms for false: False, 0. A vertical bar "|" designates mutually exclusive options, and default settings are indicated with bold.

height h
Values will be mapped linearly to surface heights of up to h (in the physical units of the volume data) from the volume data plane. The surface minimum will coincide with the volume data plane. The default h is 10% of the data size along the X axis.
interpolation cubic|none
Cubic interpolation generates additional data points in the plane to make a surface with four times as many triangles. The finer triangulation improves surface appearance but slows rendering.
meshType isotropic|slash|backslash
Whether to represent each data grid cell with four triangles and an added center point (isotropic, default) or with two triangles defined with a diagonal line from bottom left to top right (slash) or from top left to bottom right (backslash) when the axis normal to the data plane is positive towards the user. Using a two-triangle option speeds rendering but can yield anisotropic artifacts.
colorMap rainbow|none
Whether to color the surface by height (default is rainbow coloring from red for the lowest values to blue for the highest) or a uniform gray (none). The surface can be recolored with scolor.
smoothingIterations i
How many cycles of surface smoothing by moving surface vertices toward the average position of neighboring vertices should be performed (default 0, or no smoothing). Smoothing will improve surface appearance but alter its shape, degrading the mapping of values to heights.
smoothingFactor f
What fraction of the distance to the average position of neighboring vertices to move each vertex in a single cycle of smoothing (default 0.3).
replace true|false
Whether to replace any existing topography surfaces with the new one rather than opening an additional model.

See also: volume, scolor, vop tile, Volume Viewer