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Command: topography

topography  volume-model  [ height  h ] [ interpolation  cubic | none ] [ meshType  isotropic | slash | backslash ] [ replace  true | false ] [ smoothingIterations  N ] [ smoothingFactor  f ] [ color  colorname ]  palette-options 

The topography command creates a surface in which height represents the values in a single plane of volume data. The volume data should already be open and displayed as a single plane. See also: shape, surface operations, volume operations

Values will be mapped linearly to surface heights up to a maximum of height h from the volume data plane, with a zero value coinciding with the volume data plane. The default h is 10% of the data size along the X axis.

The resulting surface may contain a very large number of triangles; if response time becomes an issue, ways to reduce the size of the surface are to adjust the volume plane display beforehand to a larger step size and/or smaller region. Using interpolation cubic has the opposite effect, making the surface larger by using cubic interpolation to make a surface with four times as many triangles (default none, no interpolation). The meshType option indicates 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.

The replace option indicates whether to replace any existing topography surfaces with the new one (default) rather than opening an additional model.

The smoothingIterations option indicates how many cycles of surface smoothing by moving surface vertices toward the average position of neighboring vertices should be performed (default 0, no smoothing). Smoothing will improve surface appearance but alter its shape, degrading the mapping of values to heights. The smoothingFactor option gives 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).

Surface multicoloring can be specified with the palette options palette and range, or a single color can be given with the color option (default #b4b4b4

UCSF Resource for Biocomputing, Visualization, and Informatics / November 2022