Complete documentation for grdtrack (#1190)

Finish up aliasing parameters for `grdtrack`
as per upstream GMT docs at
https://docs.generic-mapping-tools.org/6.1/grdtrack.
Begin by adding long aliases for resample (A),
crossprofile (C), profile (E), and common aliases
region (R), verbose (V), coltypes (f), distcalc (j),
and interpolation (n).

* Alias no_skip (N) and z_only (Z) for grdtrack
* Alias dfile (D) for grdtrack
* Alias critical (F) for grdtrack
* Alias stack (S) for grdtrack
* Alias radius (T) for grdtrack
* Alias incols (i) for grdtrack

Co-authored-by: Meghan Jones <[email protected]>

Author: weiji14

pygmt/src/grdtrack.py

@@ -9,22 +9,44 @@
     build_arg_string,
     data_kind,
     fmt_docstring,
+    kwargs_to_strings,
     use_alias,
 )
 
 
 @fmt_docstring
-@use_alias(V="verbose", f="coltypes", n="interpolation")
+@use_alias(
+    A="resample",
+    C="crossprofile",
+    D="dfile",
+    E="profile",
+    F="critical",
+    R="region",
+    N="no_skip",
+    S="stack",
+    T="radius",
+    V="verbose",
+    Z="z_only",
+    f="coltypes",
+    i="incols",
+    j="distcalc",
+    n="interpolation",
+)
+@kwargs_to_strings(R="sequence", S="sequence")
 def grdtrack(points, grid, newcolname=None, outfile=None, **kwargs):
-    """
+    r"""
     Sample grids at specified (x,y) locations.
 
-    Grdtrack reads one or more grid files and a table with (x,y) [or (lon,lat)]
-    positions in the first two columns (more columns may be present). It
-    interpolates the grid(s) at the positions in the table and writes out the
-    table with the interpolated values added as (one or more) new columns. A
-    bicubic [Default], bilinear, B-spline or nearest-neighbor interpolation is
-    used, requiring boundary conditions at the limits of the region (see
+    Reads one or more grid files and a table (from file or an array input; but
+    see ``profile`` for exception) with (x,y) [or (lon,lat)] positions in the
+    first two columns (more columns may be present). It interpolates the
+    grid(s) at the positions in the table and writes out the table with the
+    interpolated values added as (one or more) new columns. Alternatively
+    (``crossprofile``), the input is considered to be line-segments and we
+    create orthogonal cross-profiles at each data point or with an equidistant
+    separation and sample the grid(s) along these profiles. A bicubic
+    [Default], bilinear, B-spline or nearest-neighbor interpolation is used,
+    requiring boundary conditions at the limits of the region (see
     ``interpolation``; Default uses "natural" conditions (second partial
     derivative normal to edge is zero) unless the grid is automatically
     recognized as periodic.)
@@ -51,8 +73,169 @@ def grdtrack(points, grid, newcolname=None, outfile=None, **kwargs):
     outfile : str
         The file name for the output ASCII file.
 
+    resample : str
+        **f**\|\ **p**\|\ **m**\|\ **r**\|\ **R**\ [**+l**]
+        For track resampling (if ``crossprofile`` or ``profile`` are set) we
+        can select how this is to be performed. Append **f** to keep original
+        points, but add intermediate points if needed [Default], **m** as
+        **f**, but first follow meridian (along y) then parallel (along x),
+        **p** as **f**, but first follow parallel (along y) then meridian
+        (along x), **r** to resample at equidistant locations; input points are
+        not necessarily included in the output, and **R** as **r**, but adjust
+        given spacing to fit the track length exactly. Finally, append
+        **+l** if geographic distances should be measured along rhumb lines
+        (loxodromes) instead of great circles. Ignored unless ``crossprofile``
+        is used.
+    crossprofile : str
+        *length*/\ *ds*\ [*/spacing*][**+a**\|\ **+v**][**l**\|\ **r**].
+        Use input line segments to create an equidistant and (optionally)
+        equally-spaced set of crossing profiles along which we sample the
+        grid(s) [Default simply samples the grid(s) at the input locations].
+        Specify two length scales that control how the sampling is done:
+        *length* sets the full length of each cross-profile, while *ds* is
+        the sampling spacing along each cross-profile. Optionally, append
+        **/**\ *spacing* for an equidistant spacing between cross-profiles
+        [Default erects cross-profiles at the input coordinates]; see
+        ``resample`` for how resampling the input track is controlled. By
+        default, all cross-profiles have the same direction (left to right
+        as we look in the direction of the input line segment). Append **+a**
+        to alternate the direction of cross-profiles, or **v** to enforce
+        either a "west-to-east" or "south-to-north" view. By default the entire
+        profiles are output. Choose to only output the left or right halves
+        of the profiles by appending **+l** or **+r**, respectively.  Append
+        suitable units to *length*; it sets the unit used for *ds* [and
+        *spacing*] (See :gmt-docs:`Units <grdtrack.html#units>`). The default
+        unit for geographic grids is meter while Cartesian grids implies the
+        user unit.  The output columns will be *lon*, *lat*, *dist*, *azimuth*,
+        *z1*, *z2*, ..., *zn* (The *zi* are the sampled values for each of the
+        *n* grids).
+    dfile : str
+        In concert with ``crossprofile`` we can save the (possibly resampled)
+        original lines to *dfile* [Default only saves the cross-profiles]. The
+        columns will be *lon*, *lat*, *dist*, *azimuth*, *z1*, *z2*, ...
+        (sampled value for each grid).
+    profile : str
+        *line*\ [,\ *line*,...][**+a**\ *az*][**+c**][**+d**][**+g**]\
+        [**+i**\ *inc*][**+l**\ *length*][**+n**\ *np*][**+o**\ *az*]\
+        [**+r**\ *radius*].
+        Instead of reading input track coordinates, specify profiles via
+        coordinates and modifiers. The format of each *line* is
+        *start*/*stop*, where *start* or *stop* are either *lon*/*lat* (*x*/*y*
+        for Cartesian data) or a 2-character XY key that uses the
+        :gmt-docs:`text <text.html>`-style justification format to specify
+        a point on the map as [LCR][BMT]. Each line will be a separate segment
+        unless **+c** is used which will connect segments with shared joints
+        into a single segment. In addition to line coordinates, you can use Z-,
+        Z+ to mean the global minimum and maximum locations in the grid (only
+        available if a single grid is given via **outfile**). You may append
+        **+i**\ *inc* to set the sampling interval; if not given then we
+        default to half the minimum grid interval. For a *line* along parallels
+        or meridians you can add **+g** to report degrees of longitude or
+        latitude instead of great circle distances starting at zero. Instead of
+        two coordinates you can specify an origin and one of **+a**, **+o**, or
+        **+r**. The **+a** sets the azimuth of a profile of given length
+        starting at the given origin, while **+o** centers the profile on the
+        origin; both require **+l**. For circular sampling specify **+r** to
+        define a circle of given radius centered on the origin; this option
+        requires either **+n** or **+i**.  The **+n**\ *np* modifier sets the
+        desired number of points, while **+l**\ *length* gives the total length
+        of the profile. Append **+d** to output the along-track distances after
+        the coordinates. **Note**: No track file will be read. Also note that
+        only one distance unit can be chosen. Giving different units will
+        result in an error. If no units are specified we default to great
+        circle distances in km (if geographic). If working with geographic data
+        you can use ``distcalc`` to control distance calculation mode [Default
+        is Great Circle]. **Note**: If ``crossprofile`` is set and *spacing* is
+        given then that sampling scheme overrules any modifier set in
+        ``profile``.
+    critical : str
+        [**+b**][**+n**][**+r**][**+z**\ *z0*].
+        Find critical points along each cross-profile as a function of
+        along-track distance. Requires ``crossprofile`` and a single input grid
+        (*z*). We examine each cross-profile generated and report (*dist*,
+        *lonc*, *latc*, *distc*, *azimuthc*, *zc*) at the center peak of
+        maximum *z* value, (*lonl*, *latl*, *distl*) and (*lonr*, *latr*,
+        *distr*) at the first and last non-NaN point whose *z*-value exceeds
+        *z0*, respectively, and the *width* based on the two extreme points
+        found. Here, *dist* is the distance along the original input
+        ``points`` and the other 12 output columns are a function of that
+        distance.  When searching for the center peak and the extreme first and
+        last values that exceed the threshold we assume the profile is positive
+        up. If we instead are looking for a trough then you must use **+n** to
+        temporarily flip the profile to positive. The threshold *z0* value is
+        always given as >= 0; use **+z** to change it [Default is 0].
+        Alternatively, use **+b** to determine the balance point and standard
+        deviation of the profile; this is the weighted mean and weighted
+        standard deviation of the distances, with *z* acting as the weight.
+        Finally, use **+r** to obtain the weighted rms about the cross-track
+        center (*distc* == 0). **Note**: We round the exact results to the
+        nearest distance nodes along the cross-profiles. We write 13 output
+        columns per track: *dist, lonc, latc, distc, azimuthc, zc, lonl, latl,
+        distl, lonr, latr, distr, width*.
+    {R}
+    no_skip : bool
+        Do *not* skip points that fall outside the domain of the grid(s)
+        [Default only output points within grid domain].
+    stack : str or list
+        *method*/*modifiers*.
+        In conjunction with ``crossprofile``, compute a single stacked profile
+        from all profiles across each segment. Choose how stacking should be
+        computed [Default method is **a**]:
+
+        - **a** = mean (average)
+        - **m** = median
+        - **p** = mode (maximum likelihood)
+        - **l** = lower
+        - **L** = lower but only consider positive values
+        - **u** = upper
+        - **U** = upper but only consider negative values.
+
+        The *modifiers* control the output; choose one or more among these
+        choices:
+
+        - **+a** : Append stacked values to all cross-profiles.
+        - **+d** : Append stack deviations to all cross-profiles.
+        - **+r** : Append data residuals (data - stack) to all cross-profiles.
+        - **+s**\ [*file*] : Save stacked profile to *file* [Default filename
+          is grdtrack_stacked_profile.txt].
+        - **+c**\ *fact* : Compute envelope on stacked profile as
+          ±\ *fact* \*\ *deviation* [Default fact value is 2].
+
+        Notes:
+
+        1. Deviations depend on *method* and are st.dev (**a**), L1 scale,
+           i.e., 1.4826 \* median absolute deviation (MAD) (for **m** and
+           **p**), or half-range (upper-lower)/2.
+        2. The stacked profile file contains a leading column plus groups of
+           4-6 columns, with one group for each sampled grid. The leading
+           column holds cross distance, while the first four columns in a group
+           hold stacked value, deviation, min value, and max value,
+           respectively. If *method* is one of **a**\|\ **m**\|\ **p** then we
+           also write the lower and upper confidence bounds (see **+c**). When
+           one or more of **+a**, **+d**, and **+r** are used then we also
+           append the stacking results to the end of each row, for all
+           cross-profiles. The order is always stacked value (**+a**), followed
+           by deviations (**+d**) and finally residuals (**+r**). When more
+           than one grid is sampled this sequence of 1-3 columns is repeated
+           for each grid.
+    radius : bool or int or float or str
+        [*radius*][**+e**\|\ **p**].
+        To be used with normal grid sampling, and limited to a single, non-IMG
+        grid. If the nearest node to the input point is NaN, search outwards
+        until we find the nearest non-NaN node and report that value instead.
+        Optionally specify a search radius which limits the consideration to
+        points within this distance from the input point. To report the
+        location of the nearest node and its distance from the input point,
+        append **+e**. The default unit for geographic grid distances is
+        spherical degrees. Use *radius* to change the unit and give *radius* =
+        0 if you do not want to limit the radius search. To instead replace the
+        input point with the coordinates of the nearest node, append **+p**.
     {V}
+    z_only : bool
+        Only write out the sampled z-values [Default writes all columns].
     {f}
+    {i}
+    {j}
     {n}
 
     Returns