grd2cpt

Make linear or histogram-equalized color palette table from grid

Synopsis

gmt grd2cpt grid [ -Atransparency[+a] ] [ -Ccpt ] [ -D[i] ] [ -E[nlevels] ] [ -F[R|r|h|c][+c]] [ -Gzlo/zhi ] [ -H ] [ -I[c][z] ] [ -Lminlimit/maxlimit ] [ -M ] [ -N ] [ -Q[i|o] ] [ -Rregion ] [ -Sh|l|m|u ] [ -Tstart/stop/inc ] [ -V[level] ] [ -W[w] ] [ -Z ] [ --PAR=value ]

Note: No space is allowed between the option flag and the associated arguments.

Description

grd2cpt reads one or more grid files and writes a static color palette (CPT) file. In classic mode we write the CMT to standard output, while under modern mode we simply save the CPT as the current session CPT (but see -H). The CPT is based on an existing dynamic master CPT of your choice, and the mapping from data value to colors is through the data’s cumulative distribution function (CDF), so that the colors are histogram equalized. Thus if the grid(s) and the resulting CPT are used in grdimage with a linear projection, the colors will be uniformly distributed in area on the plot. Let z be the data values in the grid. Define CDF(Z) = (# of z < Z) / (# of z in grid). (NaNs are ignored). These z-values are then normalized to the master CPT and colors are sampled at the desired intervals.

The color palette includes three additional colors beyond the range of z-values. These are the background color (B) assigned to values lower than the lowest z-value, the foreground color (F) assigned to values higher than the highest z-value, and the NaN color (N) painted wherever values are undefined. For color tables beyond the standard GMT offerings, visit cpt-city and Scientific Colour-Maps.

If the master CPT includes B, F, and N entries, these will be copied into the new master file. If not, the parameters COLOR_BACKGROUND, COLOR_FOREGROUND, and COLOR_NAN from the gmt.conf file or the command line will be used. This default behavior can be overruled using the options -D, -M or -N.

The color model (RGB, HSV or CMYK) of the palette created by makecpt will be the same as specified in the header of the master CPT. When there is no COLOR_MODEL entry in the master CPT, the COLOR_MODEL specified in the gmt.conf file or on the command line will be used.

Required Arguments

grid
Names of one or more grid files used to derive the color palette table. All grids need to have the same size and dimensions. (See GRID FILE FORMATS below).

Optional Arguments

-Atransparency[+a]
Sets a constant level of transparency (0-100) for all color slices. Append +a to also affect the fore-, back-, and nan-colors [Default is no transparency, i.e., 0 (opaque)].
-Ccpt
Selects the master color table to use in the interpolation. Choose among the built-in tables (type grd2cpt to see the list) or give the name of an existing CPT [Default gives a rainbow CPT]. Yet another option is to specify -Ccolor1,color2[,color3,…] to build a linear continuous CPT from those colors automatically. In this case colorn can be a r/g/b triplet, a color name, or an HTML hexadecimal color (e.g. #aabbcc ).
-D[i]
Select the back- and foreground colors to match the colors for lowest and highest z-values in the output CPT [Default uses the colors specified in the master file, or those defined by the parameters COLOR_BACKGROUND, COLOR_FOREGROUND, and COLOR_NAN]. Append i to match the colors for the lowest and highest values in the input (instead of the output) CPT.
-E[nlevels]
Create a linear color table by using the grid z-range as the new limits in the CPT. Alternatively, append nlevels and we will resample the color table into nlevels equidistant slices.
-F[R|r|h|c][+c]]
Force output CPT to written with r/g/b codes, gray-scale values or color name (R, default) or r/g/b codes only (r), or h-s-v codes (h), or c/m/y/k codes (c). Optionally or alternatively, append +c to write discrete palettes in categorical format.
-Gzlo/zhi
Truncate the incoming CPT so that the lowest and highest z-levels are to zlo and zhi. If one of these equal NaN then we leave that end of the CPT alone. The truncation takes place before any resampling. See also Manipulating CPTs
-H
Modern mode only: Write the CPT to standard output as well [Default saves the CPT as the session current CPT]. Required for scripts used to make animations via movie where we must pass named CPT files.
-I[c][z]
Append c [Default] to reverse the sense of color progression in the master CPT. Also exchanges the foreground and background colors, including those specified by the parameters COLOR_BACKGROUND and COLOR_FOREGROUND. Append z to reverse the sign of z-values in the color table. Note that this change of z-direction happens before -G and -S values are used so the latter much be compatible with the changed z-range. See also Manipulating CPTs
-Lminlimit/maxlimit
Limit range of CPT to minlimit/maxlimit, and don’t count data outside this range when estimating CDF(Z). [Default uses min and max of data.]
-M
Overrule background, foreground, and NaN colors specified in the master CPT with the values of the parameters COLOR_BACKGROUND, COLOR_FOREGROUND, and COLOR_NAN specified in the gmt.conf file or on the command line. When combined with -D, only COLOR_NAN is considered.
-N
Do not write out the background, foreground, and NaN-color fields [Default will write them].
-Q[i|o]
Selects a logarithmic interpolation scheme [Default is linear]. -Qi expects input z-values to be log10(z), assigns colors, and writes out z [Default]. -Qo takes log10(z) first, assigns colors, and writes out z.
-Rxmin/xmax/ymin/ymax[+r][+uunit] (more …)
Specify the region of interest.
-Sh|l|m|u
Force the color table to be symmetric about zero (from -R to +R). Append flag to set the range R: l for R =|zmin|, u for R = |zmax|, m for R = min(|zmin|, |zmax|), or h for R = max(|zmin|, |zmax|).
-Tstart/stop/inc or -Tn
Set steps in CPT. Calculate entries in CPT from start to stop in steps of (inc). Default chooses arbitrary values by a crazy scheme based on equidistant values for a Gaussian CDF. Use -Tn to select n points from such a cumulative normal distribution [11].
-V
Verbose operation. This will write CDF(Z) estimates to stderr. [Default is silent.]
-W
Do not interpolate the input color table but pick the output colors starting at the beginning of the map. This is particularly useful in combination with a categorical color table. Cannot be used in combination with -Z. Alternatively, use -Ww to produce a wrapped (cyclic) color table that endlessly repeats its range.
-Z
Will create a continuous color palette. [Default is discontinuous, i.e., constant color intervals]
-^ or just -
Print a short message about the syntax of the command, then exits (NOTE: on Windows just use -).
-+ or just +
Print an extensive usage (help) message, including the explanation of any module-specific option (but not the GMT common options), then exits.
-? or no arguments
Print a complete usage (help) message, including the explanation of all options, then exits.
--PAR=value
Temporarily override a GMT default setting; repeatable. See gmt.conf for parameters.

Grid File Formats

By default GMT writes out grid as single precision floats in a COARDS-complaint netCDF file format. However, GMT is able to produce grid files in many other commonly used grid file formats and also facilitates so called “packing” of grids, writing out floating point data as 1- or 2-byte integers. (more …)

Notes on Transparency

The PostScript language originally had no accommodation for transparency. However, Adobe added an extension that allows developers to encode some forms of transparency using the PostScript language model but it is only realized when converting the PostScript to PDF (and via PDF to any raster image format). GMT uses this model but there are some limitations: Transparency can only be controlled on a per-object or per-layer basis. This means that a color specifications (such as those in CPTs of given via command-line options) only apply to vector graphic items (i.e., text, lines, polygon fills) or to an entire layer (which could include items such as PostScript images). This limitation rules out any mechanism of controlling transparency in such images on a pixel level.

Color Aliasing

For best result when -E is used we recommend you do no append a specific nlevels. This way the original CPT is used exactly as is but the z boundaries are adjusted to match the grid limits. Otherwise you may, depending on the nature of the input CPT, miss aspects of the color changes by aliasing the signal.

Examples

Sometimes you don’t want to make a CPT (yet) but would find it helpful to know that 90% of your data lie between z1 and z2, something you cannot learn from grdinfo. So you can do this to see some points on the CDF(Z) curve (use -V option to see more):

gmt grd2cpt mydata.nc -V > /dev/null

To make a CPT with entries from 0 to 200 in steps of 20, and ignore data below zero in computing CDF(Z), and use the built-in master cpt file relief, run

gmt grd2cpt mydata.nc -Crelief -L0/10000 -T0/200/20 > mydata.cpt

Note on CPTs in Modern Mode

In modern mode, CPTs are rarely needed to be named explicitly. Instead, when a module that may create a CPT, such as grd2cpt and makecpt (or even grdimage when no color table is available), the behavior under modern mode is to write that CPT to a hidden file in the session directory. When a module requires a CPT (e.g., grdimage not given -C or plot given -C with no name) then we read this hidden CPT (if it exists). This file is called the current CPT. In fact, there are several levels of current CPTs that may all be different, and some may not be present. If you create a CPT within an inset operation then that CPT is only accessible during the inset plotting; it thus only has the inset as its scope. If you create a CPT while positioned into a specific subplot, then that CPT is likewise only accessible to that subplot. If, on the other hand, you make a CPT after subplot begin but before any plotting then that CPT is available to all the subplots (but can be locally overridden by a subplot-specific CPT mention above). Finally, each call to figure means you may have a figure-specific CPT, should you create them. If none exists then the session CPT is used. The rule gmt follows is to always get the CPT with the most restricted scope that is visible from where you are in the plotting hierarchy. If not found we go up the hierarchy to CPTs with broader scope, and if none is ultimately found (and the module, unlike grdimage, cannot create a CPT by itself), then you have likely made a scripting error. There are cases in modern mode when you must explicitly create a named CPT using the -H option. One such case is when making movies with movie since you will want to create the CPT once and have movie access it again and again. Since each movie frame is a separate session there is no cross-session sharing of current CPTs.

References

Crameri, F., (2018). Scientific colour-maps. Zenodo. http://doi.org/10.5281/zenodo.1243862

Crameri, F. (2018), Geodynamic diagnostics, scientific visualisation and StagLab 3.0, Geosci. Model Dev., 11, 2541-2562, doi:10.5194/gmd-11-2541-2018.