pygmt.binstats

pygmt.binstats(data, *, statistic=None, empty=None, outgrid=None, spacing=None, normalize=None, region=None, search_radius=None, verbose=None, weight=None, aspatial=None, binary=None, header=None, incols=None, registration=None, **kwargs)[source]

Bin spatial data and determine statistics per bin.

Reads arbitrarily located (x,y[,z][,w]) points (2-4 columns) from data and for each node in the specified grid layout determines which points are within the given radius. These point are then used in the calculation of the specified statistic. The results may be presented as is or may be normalized by the circle area to perhaps give density estimates.

Full option list at https://docs.generic-mapping-tools.org/latest/gmtbinstats.html

Aliases:

  • C = statistic

  • E = empty

  • G = outgrid

  • I = spacing

  • N = normalize

  • R = region

  • S = search_radius

  • V = verbose

  • W = weight

  • a = aspatial

  • b = binary

  • h = header

  • i = incols

  • r = registration

Parameters
  • data (str or numpy.ndarray or pandas.DataFrame or xarray.Dataset or geopandas.GeoDataFrame) – A file name of an ASCII data table or a 2D numpy.ndarray, a pandas.DataFrame, an xarray.Dataset made up of 1D xarray.DataArray data variables, or a geopandas.GeoDataFrame containing the tabular data.

  • outgrid (str or None) – The name of the output netCDF file with extension .nc to store the grid in.

  • statistic (str) –

    a|d|g|i|l|L|m|n|o|p|q[quant]|r|s|u|U|z. Choose the statistic that will be computed per node based on the points that are within radius distance of the node. Select one of:

    • a for mean (average)

    • d for median absolute deviation (MAD)

    • g for full (max-min) range

    • i for 25-75% interquartile range

    • l for minimum (low)

    • L for minimum of positive values only

    • m for median

    • n the number of values

    • o for LMS scale

    • p for mode (maximum likelihood)

    • q for selected quantile (append desired quantile in 0-100% range [50])

    • r for the r.m.s.

    • s for standard deviation

    • u for maximum (upper)

    • U for maximum of negative values only

    • z for the sum

  • empty (float or int) – Set the value assigned to empty nodes [Default is NaN].

  • normalize (bool) – Normalize the resulting grid values by the area represented by the search radius [no normalization].

  • search_radius (float or str) – Sets the search_radius that determines which data points are considered close to a node. Append the distance unit. Not compatible with tiling.

  • weight (str) – Input data have an extra column containing observation point weight. If weights are given then weighted statistical quantities will be computed while the count will be the sum of the weights instead of number of points. If the weights are actually uncertainties (one sigma) then append +s and weight = 1/sigma.

  • spacing (str) –

    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.

  • 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

  • aspatial (bool or str) – [col=]name[,…]. Control how aspatial data are handled during input and output. Full documentation is at https://docs.generic-mapping-tools.org/latest/gmt.html#aspatial-full.

  • 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/latest/gmt.html#bi-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 1d 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 1d 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)].

Returns

ret (xarray.DataArray or None) – 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)