Refactor _validate_data_input to simplify the codes

pygmt/clib/session.py

@@ -1836,23 +1836,25 @@ def virtualfile_in(  # noqa: PLR0912
             )
             ncols = 3
 
+        # Specify either data or x/y/z.
+        if data is not None and any(v is not None for v in (x, y, z)):
+            msg = "Too much data. Use either data or x/y/z."
+            raise GMTInvalidInput(msg)
+
+        # Determine the kind of data.
         kind = data_kind(data, required=required_data)
-        _validate_data_input(
-            data=data,
-            x=x,
-            y=y,
-            z=z,
-            ncols=ncols,
-            required_data=required_data,
-            kind=kind,
-        )
 
+        # Check if the kind of data is valid.
         if check_kind:
             valid_kinds = ("file", "arg") if required_data is False else ("file",)
-            if check_kind == "raster":
-                valid_kinds += ("grid", "image")
-            elif check_kind == "vector":
-                valid_kinds += ("empty", "matrix", "vectors", "geojson")
+            match check_kind:
+                case "raster":
+                    valid_kinds += ("grid", "image")
+                case "vector":
+                    valid_kinds += ("empty", "matrix", "vectors", "geojson")
+                case _:
+                    msg = f"Invalid value for check_kind: '{check_kind}'."
+                    raise GMTInvalidInput(msg)
             if kind not in valid_kinds:
                 msg = f"Unrecognized data type for {check_kind}: {type(data)}."
                 raise GMTInvalidInput(msg)
@@ -1886,6 +1888,7 @@ def virtualfile_in(  # noqa: PLR0912
                 _data = [x, y]
                 if z is not None:
                     _data.append(z)
+                # TODO(PyGMT>=0.20.0): Remove the deprecated parameter 'extra_arrays'.
                 if extra_arrays:
                     msg = (
                         "The parameter 'extra_arrays' will be removed in v0.20.0. "
@@ -1911,6 +1914,9 @@ def virtualfile_in(  # noqa: PLR0912
                 _virtualfile_from = self.virtualfile_from_vectors
                 _data = data.T
 
+        # Check if _data to be passed to the virtualfile_from_ function is valid.
+        _validate_data_input(data=_data, kind=kind, ncols=ncols)
+
         # Finally create the virtualfile from the data, to be passed into GMT
         file_context = _virtualfile_from(_data)
         return file_context

pygmt/helpers/utils.py

@@ -40,102 +40,95 @@
     "ISO-8859-15",
     "ISO-8859-16",
 ]
+# Type hints for the list of possible data kinds.
+Kind = Literal[
+    "arg", "empty", "file", "geojson", "grid", "image", "matrix", "stringio", "vectors"
+]
 
 
-def _validate_data_input(  # noqa: PLR0912
-    data=None, x=None, y=None, z=None, ncols=2, required_data=True, kind=None
-) -> None:
+def _validate_data_input(data: Any, kind: Kind, ncols=2) -> None:
     """
-    Check if the combination of data/x/y/z is valid.
+    Check if the data to be passed to the virtualfile_from_ functions is valid.
 
     Examples
     --------
-    >>> _validate_data_input(data="infile")
-    >>> _validate_data_input(x=[1, 2, 3], y=[4, 5, 6])
-    >>> _validate_data_input(x=[1, 2, 3], y=[4, 5, 6], z=[7, 8, 9])
-    >>> _validate_data_input(data=None, required_data=False)
-    >>> _validate_data_input()
+    The "empty" kind means the data is given via a series of vectors like x/y/z.
+
+    >>> _validate_data_input(data=[[1, 2, 3], [4, 5, 6]], kind="empty")
+    >>> _validate_data_input(data=[[1, 2, 3], [4, 5, 6], [7, 8, 9]], kind="empty")
+    >>> _validate_data_input(data=[None, [4, 5, 6]], kind="empty")
     Traceback (most recent call last):
         ...
-    pygmt.exceptions.GMTInvalidInput: No input data provided.
-    >>> _validate_data_input(x=[1, 2, 3])
+    pygmt.exceptions.GMTInvalidInput: Must provide both x and y.
+    >>> _validate_data_input(data=[[1, 2, 3], None], kind="empty")
     Traceback (most recent call last):
         ...
     pygmt.exceptions.GMTInvalidInput: Must provide both x and y.
-    >>> _validate_data_input(y=[4, 5, 6])
+    >>> _validate_data_input(data=[None, None], kind="empty")
     Traceback (most recent call last):
         ...
     pygmt.exceptions.GMTInvalidInput: Must provide both x and y.
+    >>> _validate_data_input(data=[[1, 2, 3], [4, 5, 6]], kind="empty", ncols=3)
     >>> _validate_data_input(x=[1, 2, 3], y=[4, 5, 6], ncols=3)
     Traceback (most recent call last):
         ...
     pygmt.exceptions.GMTInvalidInput: Must provide x, y, and z.
+
+    The "matrix" kind means the data is given via a 2-D numpy.ndarray.
+
     >>> import numpy as np
     >>> import pandas as pd
     >>> import xarray as xr
     >>> data = np.arange(8).reshape((4, 2))
     >>> _validate_data_input(data=data, ncols=3, kind="matrix")
     Traceback (most recent call last):
         ...
-    pygmt.exceptions.GMTInvalidInput: data must provide x, y, and z columns.
+    pygmt.exceptions.GMTInvalidInput: Need at least 3 columns but 2 column(s) are given.
+
+    The "vectors" kind means the original data is either dictionary, list, tuple,
+    pandas.DataFrame, pandas.Series, xarray.Dataset, or xarray.DataArray.
+
     >>> _validate_data_input(
     ...     data=pd.DataFrame(data, columns=["x", "y"]),
     ...     ncols=3,
     ...     kind="vectors",
     ... )
     Traceback (most recent call last):
         ...
-    pygmt.exceptions.GMTInvalidInput: data must provide x, y, and z columns.
+    pygmt.exceptions.GMTInvalidInput: Need at least 3 columns but 2 column(s) are given.
     >>> _validate_data_input(
     ...     data=xr.Dataset(pd.DataFrame(data, columns=["x", "y"])),
     ...     ncols=3,
     ...     kind="vectors",
     ... )
     Traceback (most recent call last):
         ...
-    pygmt.exceptions.GMTInvalidInput: data must provide x, y, and z columns.
-    >>> _validate_data_input(data="infile", x=[1, 2, 3])
-    Traceback (most recent call last):
-        ...
-    pygmt.exceptions.GMTInvalidInput: Too much data. Use either data or x/y/z.
-    >>> _validate_data_input(data="infile", y=[4, 5, 6])
-    Traceback (most recent call last):
-        ...
-    pygmt.exceptions.GMTInvalidInput: Too much data. Use either data or x/y/z.
-    >>> _validate_data_input(data="infile", x=[1, 2, 3], y=[4, 5, 6])
-    Traceback (most recent call last):
-        ...
-    pygmt.exceptions.GMTInvalidInput: Too much data. Use either data or x/y/z.
-    >>> _validate_data_input(data="infile", z=[7, 8, 9])
-    Traceback (most recent call last):
-        ...
-    pygmt.exceptions.GMTInvalidInput: Too much data. Use either data or x/y/z.
+    pygmt.exceptions.GMTInvalidInput: Need at least 3 columns but 2 column(s) are given.
 
     Raises
     ------
     GMTInvalidInput
         If the data input is not valid.
     """
-    required_z = ncols >= 3
-    if data is None:  # data is None
-        if x is None and y is None:  # both x and y are None
-            if required_data:  # data is not optional
-                msg = "No input data provided."
+    match kind:
+        case "empty":  # data = [x, y], [x, y, z], [x, y, z, ...]
+            if len(data) < 2 or any(v is None for v in data[:2]):
+                msg = "Must provide both x and y."
                 raise GMTInvalidInput(msg)
-        elif x is None or y is None:  # either x or y is None
-            msg = "Must provide both x and y."
-            raise GMTInvalidInput(msg)
-        if required_z and z is None:  # both x and y are not None, now check z
-            msg = "Must provide x, y, and z."
-            raise GMTInvalidInput(msg)
-    else:  # data is not None
-        if x is not None or y is not None or z is not None:
-            msg = "Too much data. Use either data or x/y/z."
-            raise GMTInvalidInput(msg)
-        # check if data has the required z column
-        if required_z:
-            msg = "data must provide x, y, and z columns."
-            if kind == "matrix" and data.shape[1] < 3:
+            if ncols >= 3 and (len(data) < 3 or data[:3] is None):
+                msg = "Must provide x, y, and z."
+                raise GMTInvalidInput(msg)
+        case "matrix":  # 2-D numpy.ndarray
+            if (actual_cols := data.shape[1]) < ncols:
+                msg = f"Need at least {ncols} columns but {actual_cols} column(s) are given."
+                raise GMTInvalidInput(msg)
+        case "vectors":
+            # "vectors" means the original data is either dictionary, list, tuple,
+            # pandas.DataFrame, pandas.Series, xarray.Dataset, or xarray.DataArray.
+            # The original data is converted to a list of vectors or a 2-D numpy.ndarray
+            # in the virtualfile_in function.
+            if (actual_cols := len(data)) < ncols:
+                msg = f"Need at least {ncols} columns but {actual_cols} column(s) are given."
                 raise GMTInvalidInput(msg)
             if kind == "vectors":
                 if hasattr(data, "shape") and (
@@ -145,15 +138,15 @@ def _validate_data_input(  # noqa: PLR0912
                     raise GMTInvalidInput(msg)
                 if hasattr(data, "data_vars") and len(data.data_vars) < 3:  # xr.Dataset
                     raise GMTInvalidInput(msg)
-        if kind == "vectors" and isinstance(data, dict):
-            # Iterator over the up-to-3 first elements.
-            arrays = list(islice(data.values(), 3))
-            if len(arrays) < 2 or any(v is None for v in arrays[:2]):  # Check x/y
-                msg = "Must provide x and y."
-                raise GMTInvalidInput(msg)
-            if required_z and (len(arrays) < 3 or arrays[2] is None):  # Check z
-                msg = "Must provide x, y, and z."
-                raise GMTInvalidInput(msg)
+            if kind == "vectors" and isinstance(data, dict):
+                # Iterator over the up-to-3 first elements.
+                arrays = list(islice(data.values(), 3))
+                if len(arrays) < 2 or any(v is None for v in arrays[:2]):  # Check x/y
+                    msg = "Must provide x and y."
+                    raise GMTInvalidInput(msg)
+                if required_z and (len(arrays) < 3 or arrays[2] is None):  # Check z
+                    msg = "Must provide x, y, and z."
+                    raise GMTInvalidInput(msg)
 
 
 def _is_printable_ascii(argstr: str) -> bool:
@@ -272,11 +265,7 @@ def _check_encoding(argstr: str) -> Encoding:
     return "ISOLatin1+"
 
 
-def data_kind(
-    data: Any, required: bool = True
-) -> Literal[
-    "arg", "empty", "file", "geojson", "grid", "image", "matrix", "stringio", "vectors"
-]:
+def data_kind(data: Any, required: bool = True) -> Kind:
     r"""
     Check the kind of data that is provided to a module.