pygmt.xyz2grd

pygmt.xyz2grd(data=None, x=None, y=None, z=None, outgrid=None, **kwargs)

Create a grid file from table data.

Reads one or more tables with x, y, z columns and creates a binary grid file. pygmt.xyz2grd will report if some of the nodes are not filled in with data. Such unconstrained nodes are set to a value specified by the user [Default is NaN]. Nodes with more than one value will be set to the mean value.

Full option list at https://docs.generic-mapping-tools.org/6.5/xyz2grd.html

Aliases:

• A = duplicate

• I = spacing

• J = projection

• R = region

• V = verbose

• Z = convention

• b = binary

• d = nodata

• e = find

• f = coltypes

• h = header

• i = incols

• r = registration

• w = wrap

Parameters:

• data (str, numpy.ndarray, pandas.DataFrame, xarray.Dataset, or geopandas.GeoDataFrame) – Pass in (x, y, z) or (longitude, latitude, elevation) values by providing a file name to an ASCII data table, a 2-D numpy.ndarray, a pandas.DataFrame, an xarray.Dataset made up of 1-D xarray.DataArray data variables, or a geopandas.GeoDataFrame containing the tabular data.

• x/y/z (1-D arrays) – The arrays of x and y coordinates and z data points.

• outgrid (str | None, default: None) – Name of the output netCDF grid file. If not specified, will return an xarray.DataArray object. For writing a specific grid file format or applying basic data operations to the output grid, see https://docs.generic-mapping-tools.org/6.5/gmt.html#grd-inout-full for the available modifiers.

• duplicate (str) – [d|f|l|m|n|r|S|s|u|z]. By default we will calculate mean values if multiple entries fall on the same node. Use duplicate to change this behavior, except it is ignored if convention is given. Append f or s to simply keep the first or last data point that was assigned to each node. Append l or u or d to find the lowest (minimum) or upper (maximum) value or the difference between the maximum and minimum values at each node, respectively. Append m or r or S to compute mean or RMS value or standard deviation at each node, respectively. Append n to simply count the number of data points that were assigned to each node (this only requires two input columns x and y as z is not consulted). Append z to sum multiple values that belong to the same node.

• spacing (float, str, or list) –

  x_inc[+e|n][/y_inc[+e|n]]. x_inc [and optionally y_inc] is the grid spacing.

  • Geographical (degrees) coordinates: Optionally, append an increment unit. Choose among 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, the registration, 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 region=grdfile is used then the grid spacing and the registration have already been initialized; use spacing and registration to override these values.

• projection (str) – projcode[projparams/]width|scale. Select map projection.

• region (str or list) – xmin/xmax/ymin/ymax[+r][+uunit]. Specify the region of interest.

• verbose (bool or str) –

  Select verbosity level [Default is w], which modulates the messages written to stderr. Choose among 7 levels of verbosity:

  • q - Quiet, not even fatal error messages are produced

  • e - Error messages only

  • w - Warnings [Default]

  • t - Timings (report runtimes for time-intensive algorithms)

  • i - Informational messages (same as verbose=True)

  • c - Compatibility warnings

  • d - Debugging messages

• convention (str) –

  [flags]. Read a 1-column ASCII [or binary] table. This assumes that all the nodes are present and sorted according to specified ordering convention contained in flags. If incoming data represents rows, make flags start with T(op) if first row is y = ymax or B(ottom) if first row is y = ymin. Then, append L or R to indicate that first element is at left or right end of row. Likewise for column formats: start with L or R to position first column, and then append T or B to position first element in a row. Note: These two row/column indicators are only required for grids; for other tables they do not apply. For gridline registered grids: If data are periodic in x but the incoming data do not contain the (redundant) column at x = xmax, append x. For data periodic in y without redundant row at y = ymax, append y. Append sn to skip the first n number of bytes (probably a header). If the byte-order or the words needs to be swapped, append w. Select one of several data types (all binary except a):

  • A ASCII representation of one or more floating point values per record

  • a ASCII representation of a single item per record

  • c int8_t, signed 1-byte character

  • u uint8_t, unsigned 1-byte character

  • h int16_t, signed 2-byte integer

  • H uint16_t, unsigned 2-byte integer

  • i int32_t, signed 4-byte integer

  • I uint32_t, unsigned 4-byte integer

  • l int64_t, long (8-byte) integer

  • L uint64_t, unsigned long (8-byte) integer

  • f 4-byte floating point single precision

  • d 8-byte floating point double precision

  [Default format is scanline orientation of ASCII numbers: La]. The difference between A and a is that the latter can decode both dateTclock and ddd:mm:ss[.xx] formats but expects each input record to have a single value, while the former can handle multiple values per record but can only parse regular floating point values. Translate incoming z-values via the incols parameter.

• binary (bool or str) –

  i|o[ncols][type][w][+l|b]. Select native binary input (using binary="i") or output (using binary="o"), where ncols is the number of data columns of type, which must be one of:

  • c - int8_t (1-byte signed char)

  • u - uint8_t (1-byte unsigned char)

  • h - int16_t (2-byte signed int)

  • H - uint16_t (2-byte unsigned int)

  • i - int32_t (4-byte signed int)

  • I - uint32_t (4-byte unsigned int)

  • l - int64_t (8-byte signed int)

  • L - uint64_t (8-byte unsigned int)

  • f - 4-byte single-precision float

  • d - 8-byte double-precision float

  • x - use to skip ncols anywhere in the record

  For records with mixed types, append additional comma-separated combinations of ncols type (no space). The following modifiers are supported:

  • w after any item to force byte-swapping.

  • +l|b to indicate that the entire data file should be read as little- or big-endian, respectively.

  Full documentation is at https://docs.generic-mapping-tools.org/6.5/gmt.html#bi-full.

• nodata (str) – i|onodata. Substitute specific values with NaN (for tabular data). For example, nodata="-9999" will replace all values equal to -9999 with NaN during input and all NaN values with -9999 during output. Prepend i to the nodata value for input columns only. Prepend o to the nodata value for output columns only.

• find (str) – [~]“pattern” | [~]/regexp/[i]. Only pass records that match the given pattern or regular expressions [Default processes all records]. Prepend ~ to the pattern or regexp to instead only pass data expressions that do not match the pattern. Append i for case insensitive matching. This does not apply to headers or segment headers.

• coltypes (str) – [i|o]colinfo. Specify data types of input and/or output columns (time or geographical data). Full documentation is at https://docs.generic-mapping-tools.org/6.5/gmt.html#f-full.

• header (str) –

  [i|o][n][+c][+d][+msegheader][+rremark][+ttitle]. Specify that input and/or output file(s) have n header records [Default is 0]. Prepend i if only the primary input should have header records. Prepend o to control the writing of header records, with the following modifiers supported:

  • +d to remove existing header records.

  • +c to add a header comment with column names to the output [Default is no column names].

  • +m to add a segment header segheader to the output after the header block [Default is no segment header].

  • +r to add a remark comment to the output [Default is no comment]. The remark string may contain \n to indicate line-breaks.

  • +t to add a title comment to the output [Default is no title]. The title string may contain \n to indicate line-breaks.

  Blank lines and lines starting with # are always skipped.

• incols (str or 1-D array) –

  Specify data columns for primary input in arbitrary order. Columns can be repeated and columns not listed will be skipped [Default reads all columns in order, starting with the first (i.e., column 0)].

  • For 1-D array: specify individual columns in input order (e.g., incols=[1,0] for the 2nd column followed by the 1st column).

  • For str: specify individual columns or column ranges in the format start[:inc]:stop, where inc defaults to 1 if not specified, with columns and/or column ranges separated by commas (e.g., incols="0:2,4+l" to input the first three columns followed by the log-transformed 5th column). To read from a given column until the end of the record, leave off stop when specifying the column range. To read trailing text, add the column t. Append the word number to t to ingest only a single word from the trailing text. Instead of specifying columns, use incols="n" to simply read numerical input and skip trailing text. Optionally, append one of the following modifiers to any column or column range to transform the input columns:

    • +l to take the log10 of the input values.

    • +d to divide the input values by the factor divisor [Default is 1].

    • +s to multiple the input values by the factor scale [Default is 1].

    • +o to add the given offset to the input values [Default is 0].

• registration (str) – g|p. Force gridline (g) or pixel (p) node registration [Default is g(ridline)].

• wrap (str) –

  y|a|w|d|h|m|s|cperiod[/phase][+ccol]. Convert the input x-coordinate to a cyclical coordinate, or a different column if selected via +ccol. The following cyclical coordinate transformations are supported:

  • y - yearly cycle (normalized)

  • a - annual cycle (monthly)

  • w - weekly cycle (day)

  • d - daily cycle (hour)

  • h - hourly cycle (minute)

  • m - minute cycle (second)

  • s - second cycle (second)

  • c - custom cycle (normalized)

  Full documentation is at https://docs.generic-mapping-tools.org/6.5/gmt.html#w-full.

Return type:

DataArray | None

Returns:

ret – Return type depends on whether the outgrid parameter is set:

• xarray.DataArray: if outgrid is not set

• None if outgrid is set (grid output will be stored in file set by outgrid)

Example

>>> import numpy as np
>>> import pygmt
>>> # generate a grid for z=x**2+y**2, with an x-range of 0 to 3,
>>> # and a y-range of 10.5 to 12.5. The x- and y-spacings are 1.0 and 0.5.
>>> x, y = np.meshgrid([0, 1, 2, 3], [10.5, 11.0, 11.5, 12.0, 12.5])
>>> z = x**2 + y**2
>>> xx, yy, zz = x.flatten(), y.flatten(), z.flatten()
>>> grid = pygmt.xyz2grd(
...     x=xx, y=yy, z=zz, spacing=(1.0, 0.5), region=[0, 3, 10, 13]
... )

Examples using pygmt.xyz2grd

Blockmean

Blockmean