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Let us first describe how a map/surface is drawn. The input data come from an evaluated function or from an splot data file. Each surface consists of a sequence of separate scans (isolines). The pm3d algorithm fills the region between two neighbouring points in one scan with another two points in the next scan by a gray (or color) according to z-values (or according to an additional 'color' column, see help for using) of these 4 corners; by default the 4 corner values are averaged, but this can be changed by the option corners2color. In order to get a reasonable surface, the neighbouring scans should not cross and the number of points in the neighbouring scans should not differ too much; of course, the best plot is with scans having same number of points. There are no other requirements (e.g. the data need not be gridded). Another advantage is that the pm3d algorithm does not draw anything outside of the input (measured or calculated) region.
Surface coloring works with the following input data:
1. splot of function or of data file with one or three data columns: The gray/color scale is obtained by mapping the averaged (or corners2color) z-coordinate of the four corners of the above-specified quadrangle into the range [min_color_z,max_color_z] of zrange or cbrange providing a gray value in the range [0:1]. This value can be used directly as the gray for gray maps. The normalized gray value can be further mapped into a color---see set palette for the complete description.
2. splot of data file with two or four data columns: The gray/color value is obtained by using the last-column coordinate instead of the z-value, thus allowing the color and the z-coordinate be mutually independent. This can be used for 4d data drawing.
Other notes:
1. The term 'scan' referenced above is used more among physicists than the term 'iso_curve' referenced in gnuplot documentation and sources. You measure maps recorded one scan after another scan, that's why.
2. The 'gray' or 'color' scale is a linear mapping of a continuous variable onto a smoothly varying palette of colors. The mapping is shown in a rectangle next to the main plot. This documentation refers to this as a "colorbox", and refers to the indexing variable as lying on the colorbox axis. See set colorbox, set cbrange.