mapcmd

var Command = &command.Command{
	Usage: `map [-c|--columns <value>] [--key <key-file>] [--gray]
	[--bound <value>] [--richness]
	[--unrot] [--present] [--contour <image-file>]
	-i|--input <file> [-o|--output <file-prefix>] <project-file>`,
	Short: "draw a map reconstruction",
	Long: `
Command map reads a file with a probability reconstruction for the nodes of
one or more trees in a project and draws the reconstruction as an image map
using a plate carrée (equirectangular) projection.

The argument of the command is the name of the project file.

The flag --input, or -i, is required and indicates the input file. The input
file is a pixel probability file.

By default, when reading a KDE reconstruction, it will only map the pixels in
the 0.95 of the CDF. Use the flag --bound to change this bound value.

By default, the reconstructions will be mapped using their respective time
stages. If the flag --unrot is given, then the reconstructions will be drawn
at the present time. By default, the landscape of the time stage will be used
for the background; if the flag --present is given, the present landscape will
be used for the background. If the --contour flag is defined with a file, the
given image will be used as a contour of the output map. The contour map will
set the size of the output image and should be fully transparent, except for
the contour, which will always be drawn in black.

By default, it will output the results of each node. If the flag --richness is
defined, then it will output the relative richness over time, that is, the
number of lineages alive at the end of each time stage. This number is
calculated using the scaled pixel values of each node alive at each time (so
each pixel can add a number between 1 and 0). For each map, the output is
scaled to the maximum value at that time stage.

By default, the output image will have the input file name as a prefix. To
change the prefix, use the flag --output or -o. The suffix of the file will be
the tree name, the node ID, and the time stage.

By default, the resulting image will be 3600 pixels wide. Use the flag
--column, or -c, to define a different number of columns. By default, the
images will have a gray background. Use the flag --key to define the landscape
colors of the image. If the flag --gray is set, then gray colors will be used.
	`,
	SetFlags: setFlags,
	Run:      run,
}