Merge pull request #118 from martinfleis/kde

ci/envs/310-latest.yaml

@@ -13,9 +13,11 @@ dependencies:
   - scikit-learn
   - shapely
   - geopandas
+  - statsmodels
   - pytest
   - pytest-cov
   - codecov
   - pip
   - pip:
       - opencv-contrib-python
+      - KDEpy

ci/envs/311-dev.yaml

@@ -23,3 +23,5 @@ dependencies:
       - git+https://github.com/pysal/libpysal.git
       - scipy
       - scikit-learn
+      - statsmodels
+      - KDEpy

ci/envs/311-latest.yaml

@@ -13,12 +13,14 @@ dependencies:
   - scikit-learn
   - shapely
   - geopandas
+  - statsmodels
   - pytest
   - pytest-cov
   - codecov
   - pip
   - pip:
       - opencv-contrib-python
+      - KDEpy
   # for docs build action (this env only)
   - nbsphinx
   - numpydoc

ci/envs/39-latest.yaml

@@ -13,9 +13,11 @@ dependencies:
   - scikit-learn
   - shapely
   - geopandas
+  - statsmodels
   - pytest
   - pytest-cov
   - codecov
   - pip
   - pip:
       - opencv-contrib-python
+      - KDEpy

docs/api.rst

@@ -46,6 +46,17 @@ Centrography
     skyum
     dtot
 
+
+.. _density_api:
+
+Density
+-------
+
+.. autosummary::
+   :toctree: generated/
+
+    plot_density
+
 .. _quadrat_api:
 
 Quadrat Based Statistics

docs/conf.py

@@ -288,6 +288,8 @@ def setup(app):
                        'pandas': ('https://pandas.pydata.org/pandas-docs/stable/', None),
                        'matplotlib':("https://matplotlib.org/", None),
                        'opencv-contrib-python':("https://docs.opencv.org/3.4/index.html", None),
+                       'KDEpy':("https://kdepy.readthedocs.io/en/latest/", None),
+                       'statsmodels':("https://www.statsmodels.org/stable/", None),
                        }
 
 

pointpats/__init__.py

@@ -8,3 +8,4 @@
 from .quadrat_statistics import *
 from .distance_statistics import *
 from .spacetime import *
+from .kde import *

pointpats/kde.py

@@ -0,0 +1,149 @@
+import numpy as np
+
+
+def plot_density(
+    data,
+    bandwidth,
+    kernel=None,
+    resolution=100,
+    levels=10,
+    fill=False,
+    margin=0.1,
+    **kwargs,
+):
+    """Plot kernel density of a given point pattern
+
+    The KDE can be done either using :class:`statsmodels.nonparametric.KDEMultivariate`,
+    which is used when ``kernel=None``, or using :class:`KDEpy.FFTKDE` when kernel is
+    set. :class:`~KDEpy.FFTKDE` tends to be generally faster in most cases but may need
+    different than ``"gaussian"`` kernel to resolve in some cases. For small data of up
+    to 10 000 points, the difference is not noticeable. For larger data, specify
+    ``bandwidth`` to enforce the use of :class:`~KDEpy.FFTKDE`. Note that while being
+    faster, :class:`~KDEpy.FFTKDE` may in some case result in erroneous KDE.
+
+    KDE is plotted using matplotlib's :meth:`~matplotlib.pyplot.contour` or
+    :meth:`~matplotlib.pyplot.contourf` function to plot the density.
+
+    If MultiPoints are given, each point is treated as separate observation.
+
+    Parameters
+    ----------
+    data : array or geopandas object
+        Array with a shape (2, n) containing coordinates of points
+        or a geopandas object with (Multi)Point geometry. Assumes
+        projected coordinates, geographical coordinates (latitude, longitude)
+        are not supported.
+    bandwidth : float
+        bandwidth in the units of CRS in which data is
+    kernel : str | None, optional
+        The kernel function. If None, defaults to the Gaussian kernel and statsmodels
+        implementation. If set, uses KDEpy implementation. See
+        :meth:`KDEpy.FFTKDE._available_kernels.keys()` for choices.
+    resolution : int | tuple(int, int), optional
+        resolution of the grid used to evaluate the probability density
+        function. If tuple, each dimension of the grid is specified separately.
+        By default 100
+    levels : int or array-like, optional
+        Determines the number and positions of the contour lines / regions.
+        See the documentation of :meth:`~matplotlib.pyplot.contour` for details.
+        By default 10
+    fill : bool, optional
+        Fill the area between contour lines, by default False
+    margin : float, optional
+        The factor of the margin by which the extent of the data will be expanded when
+        creating the grid. 0.1 means 10% on each side, by default 0.1. Only used
+        with the ``statsmodels`` implementation.
+    **kwargs
+        Keyword arguments passed to :meth:`~matplotlib.pyplot.contour` or
+        :meth:`~matplotlib.pyplot.contourf` used for further
+        styling of the plot, for example ``cmap``, ``linewidths``, ``linestyles``,
+        or `alpha`. See the documentation of :meth:`~matplotlib.pyplot.contour` for
+        details.
+
+    Returns
+    -------
+    matplotlib.pyplot.QuadContourSet
+        plot
+    """
+    if kernel is None:
+        try:
+            import statsmodels.api as sm
+        except ImportError as err:
+            raise ImportError(
+                "statsmodels is required for `plot_density` when kernel"
+                "is not specified."
+            ) from err
+
+        engine = "sm"
+    else:
+        try:
+            from KDEpy import FFTKDE
+        except ImportError as err:
+            raise ImportError(
+                "KDEpy is required for `plot_density` when kernel is not None."
+            ) from err
+
+        engine = "kdepy"
+
+    try:
+        import matplotlib.pyplot as plt
+    except ImportError as err:
+        raise ImportError("matplotlib is required for `plot_density`") from err
+
+    if isinstance(data, np.ndarray):
+        pass
+    else:  # geopandas
+        if not data.geom_type.str.contains("Point").all():
+            raise ValueError(
+                "data contain non-point geometries. "
+                "Only (Multi)Points are supported."
+            )
+        data = data.get_coordinates().values
+
+    if engine == "sm":
+        dens_u = sm.nonparametric.KDEMultivariate(
+            data=[data[:, 0], data[:, 1]],
+            var_type="cc",
+            bw=[bandwidth, bandwidth],
+        )
+
+        xmax = data[:, 0].max()
+        xmin = data[:, 0].min()
+        ymax = data[:, 1].max()
+        ymin = data[:, 1].min()
+
+        # get margin to go beyond the extent to avoid cutting of countour lines
+        x_margin = (xmax - xmin) * margin
+        y_margin = (ymax - ymin) * margin
+
+        if isinstance(resolution, tuple):
+            x_res, y_res = resolution
+        elif isinstance(resolution, (float, int)):
+            x_res = resolution
+            y_res = resolution
+        elif resolution is None:
+            x_res = 100
+            y_res = 100
+        else:
+            raise ValueError("Unsupported option for `resolution`.")
+
+        # create mesh for predicting KDE on with more space around the points
+        x_mesh, y_mesh = np.meshgrid(
+            np.linspace(xmin - x_margin, xmax + x_margin, x_res),
+            np.linspace(ymin - y_margin, ymax + y_margin, y_res),
+        )
+
+        # get the prediction
+        pred = dens_u.pdf(np.vstack([x_mesh.flatten(), y_mesh.flatten()]).T)
+        z = pred.reshape(x_mesh.shape)
+
+    else:
+        kde = FFTKDE(bw=bandwidth, kernel=kernel)
+        grid, points = kde.fit(data).evaluate(resolution)
+        x_mesh, y_mesh = np.unique(grid[:, 0]), np.unique(grid[:, 1])
+        z = points.reshape(resolution, resolution).T
+
+    if fill:
+        return plt.contourf(x_mesh, y_mesh, z, levels=levels, **kwargs)
+    else:
+        return plt.contour(x_mesh, y_mesh, z, levels=levels, **kwargs)

pointpats/tests/test_kde.py

@@ -0,0 +1,98 @@
+import numpy as np
+import pytest
+
+from pointpats import plot_density
+
+matplotlib = pytest.importorskip("matplotlib")
+statsmodels = pytest.importorskip("statsmodels")
+KDEpy = pytest.importorskip("KDEpy")
+
+
+class TestDensity:
+    def setup_method(self):
+        self.points = np.array(
+            [
+                [66.22, 32.54],
+                [22.52, 22.39],
+                [31.01, 81.21],
+                [9.47, 31.02],
+                [30.78, 60.10],
+                [75.21, 58.93],
+                [79.26, 7.68],
+                [8.23, 39.93],
+                [98.73, 77.17],
+                [89.78, 42.53],
+                [65.19, 92.08],
+                [54.46, 8.48],
+            ]
+        )
+
+    def test_default(self):
+        qm = plot_density(self.points, 10)
+        collections = list(qm.collections)
+        assert len(collections) == 12
+        for col in collections:
+            assert col.get_linewidths() == np.array(1.5)
+        np.testing.assert_array_equal(
+            collections[5].get_edgecolor(),
+            np.array([[0.143343, 0.522773, 0.556295, 1.0]]),
+        )
+
+    def test_bandwidth(self):
+        qm = plot_density(self.points, 1)
+        collections = list(qm.collections)
+        assert len(collections) == 10
+
+    def test_resolution(self):
+        qm = plot_density(self.points, 10, resolution=200)
+        collections = list(qm.collections)
+        assert len(collections) == 12
+
+    def test_margin(self):
+        qm = plot_density(self.points, 10, margin=.3)
+        collections = list(qm.collections)
+        assert len(collections) == 12
+
+    def test_kdepy(self):
+        qm = plot_density(self.points, 10, kernel="gaussian")
+        collections = list(qm.collections)
+        assert len(collections) == 12
+        for col in collections:
+            assert col.get_linewidths() == np.array(1.5)
+
+    def test_levels(self):
+        qm = plot_density(self.points, 10, levels=5)
+        collections = list(qm.collections)
+        assert len(collections) == 7
+
+    def test_fill(self):
+        qm = plot_density(self.points, 10, fill=True)
+        collections = list(qm.collections)
+        assert collections[0].get_edgecolor().shape == (0, 4)
+        np.testing.assert_array_equal(
+            collections[0].get_facecolor(),
+            np.array([[0.279566, 0.067836, 0.391917, 1.0]]),
+        )
+
+    def test_geopandas(self):
+        geopandas = pytest.importorskip("geopandas")
+
+        gs = geopandas.GeoSeries.from_xy(*self.points.T)
+        qm = plot_density(gs, 10)
+        collections = list(qm.collections)
+        assert len(collections) == 12
+        for col in collections:
+            assert col.get_linewidths() == np.array(1.5)
+
+    def test_kwargs(self):
+        qm = plot_density(
+            self.points, 10, cmap="magma", linewidths=0.5, linestyles="-."
+        )
+        collections = list(qm.collections)
+        assert len(collections) == 12
+        for col in collections:
+            assert col.get_linewidths() == np.array(0.5)
+        np.testing.assert_array_equal(
+            collections[5].get_edgecolor(),
+            np.array([[0.639216, 0.189921, 0.49415, 1.0]]),
+        )