Enable netcdf file input for grdtrack

Enable passing in netcdf file as input into grdtrack, instead of just xarray.DataArray. Also fix bug with kwargs being overwritten instead of appended to...

Author: weiji14

pygmt/sampling.py

@@ -5,7 +5,13 @@
 import xarray as xr
 
 from .clib import Session
-from .helpers import build_arg_string, fmt_docstring, GMTTempFile, data_kind
+from .helpers import (
+    build_arg_string,
+    fmt_docstring,
+    GMTTempFile,
+    data_kind,
+    dummy_context,
+)
 from .exceptions import GMTInvalidInput
 
 
@@ -27,7 +33,7 @@ def grdtrack(table: pd.DataFrame, grid: xr.DataArray, newcolname: str = "z_", **
         Table with (x, y) or (lon, lat) values in the first two columns. More columns
         may be present.
 
-    grid: xarray.DataArray
+    grid: xarray.DataArray or file (netcdf)
         Gridded array from which to sample values from.
 
     newcolname: str
@@ -51,13 +57,15 @@ def grdtrack(table: pd.DataFrame, grid: xr.DataArray, newcolname: str = "z_", **
             # Store the xarray.DataArray grid in virtualfile
             if data_kind(grid) == "grid":
                 grid_context = lib.virtualfile_from_grid(grid)
+            elif data_kind(grid) == "file":
+                grid_context = dummy_context(grid)
             else:
                 raise GMTInvalidInput(f"Unrecognized data type {type(grid)}")
 
             # Run grdtrack on the temporary (csv) table and (netcdf) grid virtualfiles
             with table_context as csvfile:
                 with grid_context as grdfile:
-                    kwargs = {"G": grdfile}
+                    kwargs.update({"G": grdfile})
                     arg_str = " ".join(
                         [csvfile, build_arg_string(kwargs), "->" + tmpfile.name]
                     )

pygmt/tests/test_grdtrack.py

@@ -6,6 +6,7 @@
 import pytest
 
 from .. import grdtrack
+from .. import which
 from ..datasets import load_east_pacific_rise_grid, load_ocean_ridge_points
 from ..exceptions import GMTInvalidInput
 from ..helpers import data_kind
@@ -26,6 +27,20 @@ def test_grdtrack_input_dataframe_and_dataarray():
     return output
 
 
+def test_grdtrack_input_dataframe_and_ncfile():
+    """
+    Run grdtrack by passing in a pandas.DataFrame and netcdf file as inputs
+    """
+    dataframe = load_ocean_ridge_points()
+    ncfile = which("@spac_33.nc", download="c")
+
+    output = grdtrack(table=dataframe, grid=ncfile)
+    assert isinstance(output, pd.DataFrame)
+    assert output.columns.to_list() == ["longitude", "latitude", "z_"]
+
+    return output
+
+
 def test_grdtrack_input_wrong_kind_of_table():
     """
     Run grdtrack using table input that is not a pandas.DataFrame (matrix)
@@ -41,7 +56,7 @@ def test_grdtrack_input_wrong_kind_of_table():
 
 def test_grdtrack_input_wrong_kind_of_grid():
     """
-    Run grdtrack using grid input that is not an xarray.DataArray (grid)
+    Run grdtrack using grid input that is not as xarray.DataArray (grid) or file
     """
     dataframe = load_ocean_ridge_points()
     dataarray = load_east_pacific_rise_grid()