Wrap blockmean (GenericMappingTools#1092)

* Rename blockmedian.py to blockm.py
* Refactor blockmedian to support mean and mode
* Wrap method blockmean
* Add tests for blockmean method

Co-authored-by: Dongdong Tian <[email protected]>
Co-authored-by: Wei Ji <[email protected]>

Author: 3 people

doc/api/index.rst

@@ -67,6 +67,7 @@ Operations on tabular data:
 .. autosummary::
     :toctree: generated
 
+    blockmean
     blockmedian
     surface
 

pygmt/__init__.py

@@ -29,6 +29,7 @@
 from pygmt.session_management import begin as _begin
 from pygmt.session_management import end as _end
 from pygmt.src import (
+    blockmean,
     blockmedian,
     config,
     grd2cpt,

pygmt/src/__init__.py

@@ -3,7 +3,7 @@
 """
 # pylint: disable=import-outside-toplevel
 from pygmt.src.basemap import basemap
-from pygmt.src.blockmedian import blockmedian
+from pygmt.src.blockm import blockmean, blockmedian
 from pygmt.src.coast import coast
 from pygmt.src.colorbar import colorbar
 from pygmt.src.config import config

pygmt/src/blockmedian.py renamed to pygmt/src/blockm.py

@@ -1,5 +1,5 @@
 """
-blockmedian - Block average (x,y,z) data tables by median estimation.
+blockm - Block average (x,y,z) data tables by mean or median estimation.
 """
 import pandas as pd
 from pygmt.clib import Session
@@ -15,6 +15,122 @@
 )
 
 
+def _blockm(block_method, table, outfile, **kwargs):
+    r"""
+    Block average (x,y,z) data tables by mean or median estimation.
+
+    Reads arbitrarily located (x,y,z) triples [or optionally weighted
+    quadruples (x,y,z,w)] from a table and writes to the output a mean or
+    median (depending on ``block_method``) position and value for every
+    non-empty block in a grid region defined by the ``region`` and ``spacing``
+    parameters.
+
+    Parameters
+    ----------
+    block_method : str
+        Name of the GMT module to call. Must be "blockmean" or "blockmedian".
+
+    Returns
+    -------
+    output : pandas.DataFrame or None
+        Return type depends on whether the ``outfile`` parameter is set:
+
+        - :class:`pandas.DataFrame` table with (x, y, z) columns if ``outfile``
+          is not set
+        - None if ``outfile`` is set (filtered output will be stored in file
+          set by ``outfile``)
+    """
+
+    kind = data_kind(table)
+    with GMTTempFile(suffix=".csv") as tmpfile:
+        with Session() as lib:
+            if kind == "matrix":
+                if not hasattr(table, "values"):
+                    raise GMTInvalidInput(f"Unrecognized data type: {type(table)}")
+                file_context = lib.virtualfile_from_matrix(table.values)
+            elif kind == "file":
+                if outfile is None:
+                    raise GMTInvalidInput("Please pass in a str to 'outfile'")
+                file_context = dummy_context(table)
+            else:
+                raise GMTInvalidInput(f"Unrecognized data type: {type(table)}")
+
+            with file_context as infile:
+                if outfile is None:
+                    outfile = tmpfile.name
+                arg_str = " ".join([infile, build_arg_string(kwargs), "->" + outfile])
+                lib.call_module(module=block_method, args=arg_str)
+
+        # Read temporary csv output to a pandas table
+        if outfile == tmpfile.name:  # if user did not set outfile, return pd.DataFrame
+            result = pd.read_csv(tmpfile.name, sep="\t", names=table.columns)
+        elif outfile != tmpfile.name:  # return None if outfile set, output in outfile
+            result = None
+
+    return result
+
+
+@fmt_docstring
+@use_alias(
+    I="spacing",
+    R="region",
+    V="verbose",
+    a="aspatial",
+    f="coltypes",
+    r="registration",
+)
+@kwargs_to_strings(R="sequence")
+def blockmean(table, outfile=None, **kwargs):
+    r"""
+    Block average (x,y,z) data tables by mean estimation.
+
+    Reads arbitrarily located (x,y,z) triples [or optionally weighted
+    quadruples (x,y,z,w)] from a table and writes to the output a mean
+    position and value for every non-empty block in a grid region defined by
+    the ``region`` and ``spacing`` parameters.
+
+    Full option list at :gmt-docs:`blockmean.html`
+
+    {aliases}
+
+    Parameters
+    ----------
+    table : pandas.DataFrame or str
+        Either a pandas dataframe with (x, y, z) or (longitude, latitude,
+        elevation) values in the first three columns, or a file name to an
+        ASCII data table.
+
+    spacing : str
+        *xinc*\[\ *unit*\][**+e**\|\ **n**]
+        [/*yinc*\ [*unit*][**+e**\|\ **n**]].
+        *xinc* [and optionally *yinc*] is the grid spacing.
+
+    region : str or list
+        *xmin/xmax/ymin/ymax*\[\ **+r**\][**+u**\ *unit*].
+        Specify the region of interest.
+
+    outfile : str
+        Required if ``table`` is a file. The file name for the output ASCII
+        file.
+
+    {V}
+    {a}
+    {f}
+    {r}
+
+    Returns
+    -------
+    output : pandas.DataFrame or None
+        Return type depends on whether the ``outfile`` parameter is set:
+
+        - :class:`pandas.DataFrame` table with (x, y, z) columns if ``outfile``
+          is not set
+        - None if ``outfile`` is set (filtered output will be stored in file
+          set by ``outfile``)
+    """
+    return _blockm(block_method="blockmean", table=table, outfile=outfile, **kwargs)
+
+
 @fmt_docstring
 @use_alias(
     I="spacing",
@@ -73,30 +189,4 @@ def blockmedian(table, outfile=None, **kwargs):
         - None if ``outfile`` is set (filtered output will be stored in file
           set by ``outfile``)
     """
-    kind = data_kind(table)
-    with GMTTempFile(suffix=".csv") as tmpfile:
-        with Session() as lib:
-            if kind == "matrix":
-                if not hasattr(table, "values"):
-                    raise GMTInvalidInput(f"Unrecognized data type: {type(table)}")
-                file_context = lib.virtualfile_from_matrix(table.values)
-            elif kind == "file":
-                if outfile is None:
-                    raise GMTInvalidInput("Please pass in a str to 'outfile'")
-                file_context = dummy_context(table)
-            else:
-                raise GMTInvalidInput(f"Unrecognized data type: {type(table)}")
-
-            with file_context as infile:
-                if outfile is None:
-                    outfile = tmpfile.name
-                arg_str = " ".join([infile, build_arg_string(kwargs), "->" + outfile])
-                lib.call_module(module="blockmedian", args=arg_str)
-
-        # Read temporary csv output to a pandas table
-        if outfile == tmpfile.name:  # if user did not set outfile, return pd.DataFrame
-            result = pd.read_csv(tmpfile.name, sep="\t", names=table.columns)
-        elif outfile != tmpfile.name:  # return None if outfile set, output in outfile
-            result = None
-
-    return result
+    return _blockm(block_method="blockmedian", table=table, outfile=outfile, **kwargs)

pygmt/tests/test_blockmean.py

@@ -0,0 +1,78 @@
+"""
+Tests for blockmean.
+"""
+import os
+
+import numpy.testing as npt
+import pandas as pd
+import pytest
+from pygmt import blockmean
+from pygmt.datasets import load_sample_bathymetry
+from pygmt.exceptions import GMTInvalidInput
+from pygmt.helpers import GMTTempFile, data_kind
+
+
+def test_blockmean_input_dataframe():
+    """
+    Run blockmean by passing in a pandas.DataFrame as input.
+    """
+    dataframe = load_sample_bathymetry()
+    output = blockmean(table=dataframe, spacing="5m", region=[245, 255, 20, 30])
+    assert isinstance(output, pd.DataFrame)
+    assert all(dataframe.columns == output.columns)
+    assert output.shape == (5849, 3)
+    npt.assert_allclose(output.iloc[0], [245.888877, 29.978707, -384.0])
+
+    return output
+
+
+def test_blockmean_wrong_kind_of_input_table_matrix():
+    """
+    Run blockmean using table input that is not a pandas.DataFrame but still a
+    matrix.
+    """
+    dataframe = load_sample_bathymetry()
+    invalid_table = dataframe.values
+    assert data_kind(invalid_table) == "matrix"
+    with pytest.raises(GMTInvalidInput):
+        blockmean(table=invalid_table, spacing="5m", region=[245, 255, 20, 30])
+
+
+def test_blockmean_wrong_kind_of_input_table_grid():
+    """
+    Run blockmean using table input that is not a pandas.DataFrame or file but
+    a grid.
+    """
+    dataframe = load_sample_bathymetry()
+    invalid_table = dataframe.bathymetry.to_xarray()
+    assert data_kind(invalid_table) == "grid"
+    with pytest.raises(GMTInvalidInput):
+        blockmean(table=invalid_table, spacing="5m", region=[245, 255, 20, 30])
+
+
+def test_blockmean_input_filename():
+    """
+    Run blockmean by passing in an ASCII text file as input.
+    """
+    with GMTTempFile() as tmpfile:
+        output = blockmean(
+            table="@tut_ship.xyz",
+            spacing="5m",
+            region=[245, 255, 20, 30],
+            outfile=tmpfile.name,
+        )
+        assert output is None  # check that output is None since outfile is set
+        assert os.path.exists(path=tmpfile.name)  # check that outfile exists at path
+        output = pd.read_csv(tmpfile.name, sep="\t", header=None)
+        assert output.shape == (5849, 3)
+        npt.assert_allclose(output.iloc[0], [245.888877, 29.978707, -384.0])
+
+    return output
+
+
+def test_blockmean_without_outfile_setting():
+    """
+    Run blockmean by not passing in outfile parameter setting.
+    """
+    with pytest.raises(GMTInvalidInput):
+        blockmean(table="@tut_ship.xyz", spacing="5m", region=[245, 255, 20, 30])