Create mask grid from polygons or point coverage
gmt grdmask pathfiles -Gmask_grd_file -Iincrement -Rregion [ -A[m|p|x|y] ] [ -N[z|Z|p|P]values ] [ -Ssearch_radius[unit] |xlim/ylim ] [ -V[level] ] [ -bibinary ] [ -dinodata ] [ -eregexp ] [ -fflags ] [ -ggaps ] [ -hheaders ] [ -iflags ] [ -jflags ] [ -nflags ] [ -rreg ] [ -x[[-]n] ] [ -:[i|o] ] [ --PAR=value ]
Note: No space is allowed between the option flag and the associated arguments.
grdmask can operate in two different modes. 1. It reads one or more pathfiles that each define a closed polygon. The nodes defined by the specified region and lattice spacing will be set equal to one of three possible values depending on whether the node is outside, on the polygon perimeter, or inside the polygon. The resulting mask may be used in subsequent operations involving grdmath to mask out data from polygonal areas. 2. The pathfiles simply represent data point locations and the mask is set to the inside or outside value depending on whether a node is within a maximum distance from the nearest data point. If the distance specified is zero then only the nodes nearest each data point are considered “inside”.
- The name of 1 or more ASCII [or binary, see -bi] files holding the polygon(s) or data points.
- Name of resulting output mask grid file. (See GRID FILE FORMATS below).
- x_inc [and optionally y_inc] is the grid spacing. Optionally, append a suffix modifier. Geographical (degrees) coordinates: Append m to indicate arc minutes or s to indicate arc seconds. If one of the units e, f, k, M, n or u is appended instead, the increment is assumed to be given in meter, foot, km, Mile, nautical mile or US survey foot, respectively, and will be converted to the equivalent degrees longitude at the middle latitude of the region (the conversion depends on PROJ_ELLIPSOID). If y_inc is given but set to 0 it will be reset equal to x_inc; otherwise it will be converted to degrees latitude. All coordinates: If +e is appended then the corresponding max x (east) or y (north) may be slightly adjusted to fit exactly the given increment [by default the increment may be adjusted slightly to fit the given domain]. Finally, instead of giving an increment you may specify the number of nodes desired by appending +n to the supplied integer argument; the increment is then recalculated from the number of nodes and the domain. The resulting increment value depends on whether you have selected a gridline-registered or pixel-registered grid; see GMT File Formats for details. Note: if -Rgrdfile is used then the grid spacing has already been initialized; use -I to override the values.
- -Rxmin/xmax/ymin/ymax[+r][+uunit] (more …)
- Specify the region of interest.
- If the input data are geographic (as indicated by -f) then the sides in the polygons will be approximated by great circle arcs. When using the -A sides will be regarded as straight lines. Alternatively, append m to have sides first follow meridians, then parallels. Or append p to first follow parallels, then meridians. For Cartesian data, points are simply connected, unless you append x or y to construct stair-case paths whose first move is along x or y, respectively.
- Sets the out/edge/in that will be assigned to nodes that are outside the polygons, on the edge, or inside. Values can be any number, including the textstring NaN [Default is 0/0/1]. Optionally, use Nz to set polygon insides to the z-value obtained from the data (either segment header -Zzval, -Lheader or via -aZ=name); use -NZ to consider the polygon boundary as part of the inside. Alternatively, use -Np to use a running number as polygon ID; optionally append start of the sequence . Here, -NP includes the polygon perimeter as inside. Note: -Nz|Z|p|P cannot be used in conjunction with -S; they also all optionally accept /out .
- -Ssearch_radius[unit] |xlim/ylim
- Set nodes to inside, on edge, or outside depending on their distance to the nearest data point. Nodes within radius  from the nearest data point are considered inside; append a distance unit (see Units). If radius is given as z then we instead read individual radii from the 3rd input column. Unless Cartesian data, specify the unit of these radii by appending it after -Sz. If -S is not set then we consider the input data to define one or more closed polygon(s) instead. For Cartesian data with different units you can instead append xlim/ylim which will perform a rectangular search where all nodes within ±xlim and ±ylim of a data point will be considered inside. One can also achieve the rectangular selection effect by using the -Sn_cellsc form. Here n_cells means the number of cells around each data point. As an example, -S0c means that only the cell where point lies is masked, -S1c masks one cell beyond that (i.e. makes a 3x3 neighborhood), and so on.
- -V[level] (more …)
- Select verbosity level [c].
- -bi[ncols][t] (more …)
- Select native binary format for primary input. [Default is 2 input columns (3 with -Sz)].
- -dinodata (more …)
- Replace input columns that equal nodata with NaN.
- -e[~]”pattern” | -e[~]/regexp/[i] (more …)
- Only accept data records that match the given pattern.
- -f[i|o]colinfo (more …)
- Specify data types of input and/or output columns.
- -g[a]x|y|d|X|Y|D|[col]zgap[u][+n|p] (more …)
- Determine data gaps and line breaks.
- -h[i|o][n][+c][+d][+rremark][+rtitle] (more …)
- Skip or produce header record(s).
- -icols[+l][+sscale][+ooffset][,…][,t[word]] (more …)
- Select input columns and transformations (0 is first column, t is trailing text, append word to read one word only).
- -je|f|g (more …)
- Determine how spherical distances are calculated.
- Append +bBC to set any boundary conditions to be used, adding g for geographic, p for periodic, or n for natural boundary conditions. For the latter two you may append x or y to specify just one direction, otherwise both are assumed. [Default is geographic if grid is geographic].
- -r[g|p] (more …)
- Set node registration [gridline].
- -x[[-]n] (more …)
- Limit number of cores used in multi-threaded algorithms (OpenMP required).
- -^ 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.
- Temporarily override a GMT default setting; repeatable. See gmt.conf for parameters.
For map distance unit, append unit d for arc degree, m for arc minute, and s for arc second, or e for meter [Default], f for foot, k for km, M for statute mile, n for nautical mile, and u for US survey foot. By default we compute such distances using a spherical approximation with great circles (-jg) using the authalic radius (see PROJ_MEAN_RADIUS). You can use -jf to perform “Flat Earth” calculations (quicker but less accurate) or -je to perform exact geodesic calculations (slower but more accurate; see PROJ_GEODESIC for method used).
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. To specify the precision, scale and offset, the user should add the suffix =ID[+sscale][+ooffset][+ninvalid], where ID is a two-letter identifier of the grid type and precision, and scale and offset are optional scale factor and offset to be applied to all grid values, and invalid is the value used to indicate missing data. See grdconvert and Section Grid file format specifications of the GMT Technical Reference and Cookbook for more information.
When writing a netCDF file, the grid is stored by default with the variable name “z”. To specify another variable name varname, append ?varname to the file name. Note that you may need to escape the special meaning of ? in your shell program by putting a backslash in front of it, or by placing the filename and suffix between quotes or double quotes.
Geographical And Time Coordinates¶
When the output grid type is netCDF, the coordinates will be labeled “longitude”, “latitude”, or “time” based on the attributes of the input data or grid (if any) or on the -f or -R options. For example, both -f0x -f1t and -R90w/90e/0t/3t will result in a longitude/time grid. When the x, y, or z coordinate is time, it will be stored in the grid as relative time since epoch as specified by TIME_UNIT and TIME_EPOCH in the gmt.conf file or on the command line. In addition, the unit attribute of the time variable will indicate both this unit and epoch.
To determine if a point is inside, outside, or exactly on the boundary of a polygon we need to balance the complexity (and execution time) of the algorithm with the type of data and shape of the polygons. For any Cartesian data we use a non-zero winding algorithm, which is quite fast. For geographic data we will also use this algorithm as long as (1) the polygons do not include a geographic pole, and (2) the longitude extent of the polygons is less than 360. If this is the situation we also carefully adjust the test point longitude for any 360 degree offsets, if appropriate. Otherwise, we employ a full spherical ray-shooting method to determine a points status.
A grid produced by grdmask is a categorical dataset. As such, one has to be careful not to interpolate it with standard methods, such as splines. However, if you make a map of this grid using a map projection the grid will be reprojected to yield a rectangular matrix in the projected coordinates. This interpolation is done using splines by default and thus may yield artifacts in your map. We recommend you use grdimage -nn to instead use a nearest neighbor interpolation for such cases.
Save storage space¶
Since most uses of grdmask revolves around creating mask grids that hold just a few integer values (and perhaps NaN), we choose to write them to disk as byte grids by appending the suffix =nb to the desired grid filename. Some situations may store integers that exceed the range available in a byte and for those we specify a short integer grid with =ns. For larger integers you may consider =ni, otherwise use the default float grid format.
Note: Below are some examples of valid syntax for this module.
The examples that use remote files (file names starting with
can be cut and pasted into your terminal for testing.
Other commands requiring input files are just dummy examples of the types
of uses that are common but cannot be run verbatim as written.
To set all nodes inside and on the polygons coastline_*.xy to 0, and outside points to 1, do
gmt grdmask coastline_*.xy -R-60/-40/-40/-30 -I5m -N1/0/0 -Gland_mask.nc=nb -V
To set nodes within 50 km of data points to 1 and other nodes to NaN, do
gmt grdmask data.xyz -R-60/-40/-40/-30 -I5m -NNaN/1/1 -S50k -Gdata_mask.nc=nb -V
To assign polygon IDs to the gridnodes using the insides of the polygons in plates.gmt, based on the attribute POL_ID, do
gmt grdmask plates.gmt -R-40/40/-40/40 -I2m -Nz -Gplate_IDs.nc=ns -aZ=POL_ID -V
Same exercise, but instead compute running polygon IDs starting at 100, do
gmt grdmask plates.gmt -R-40/40/-40/40 -I2m -Np100 -Gplate_IDs.nc=ns -V