code refactor

gplately/__init__.py

@@ -183,15 +183,13 @@
     plot,
     ptt,
     pygplates,
-    read_geometries,
     reconstruction,
 )
 from .data import DataCollection
 from .download import DataServer
 from .grids import Raster
 from .oceans import SeafloorGrid
 from .plot import PlotTopologies
-from .read_geometries import get_geometries, get_valid_geometries
 from .reconstruction import (
     PlateReconstruction,
     Points,
@@ -200,6 +198,8 @@
     _ReconstructByTopologies,
 )
 from .tools import EARTH_RADIUS
+from .utils import io_utils
+from .utils.io_utils import get_geometries, get_valid_geometries
 
 __pdoc__ = {
     "data": False,
@@ -218,7 +218,7 @@
     "oceans",
     "plot",
     "pygplates",
-    "read_geometries",
+    "io_utils",
     "reconstruction",
     "plate_model_manager",
     "ptt",

gplately/plot.py

@@ -2,8 +2,7 @@
 
 Methods in `plot.py` reconstruct geological features using 
 [pyGPlates' `reconstruct` function](https://www.gplates.org/docs/pygplates/generated/pygplates.reconstruct.html),
-turns them into plottable Shapely geometries, and plots them onto 
-Cartopy GeoAxes using Shapely and GeoPandas.
+turns them into plottable Shapely geometries, and plots them onto Cartopy GeoAxes using Shapely and GeoPandas.
 
 Classes
 -------
@@ -16,7 +15,6 @@
 
 import cartopy.crs as ccrs
 import geopandas as gpd
-import matplotlib.pyplot as plt
 import numpy as np
 import pygplates
 from shapely.geometry.base import BaseGeometry, BaseMultipartGeometry
@@ -25,24 +23,36 @@
 from . import ptt
 from .gpml import _load_FeatureCollection
 from .pygplates import FeatureCollection as _FeatureCollection
-from .read_geometries import (
-    get_valid_geometries,
-)  # included for backwards compatibility
 from .reconstruction import PlateReconstruction as _PlateReconstruction
 from .tools import EARTH_RADIUS
 from .utils.feature_utils import shapelify_features as _shapelify_features
-from .utils.plot_utils import (
-    _clean_polygons,
-    _meridian_from_ax,
-    _plot_geometries,
-    plot_subduction_teeth,
-)
+from .utils.plot_utils import (_clean_polygons, _meridian_from_ax,
+                               _plot_geometries)
+from .utils.plot_utils import plot_subduction_teeth as _plot_subduction_teeth
 
 logger = logging.getLogger("gplately")
 
-shapelify_features = _shapelify_features
-shapelify_feature_lines = _shapelify_features
-shapelify_feature_polygons = _shapelify_features
+
+def shapelify_features(*args, **kwargs):
+    return _shapelify_features(*args, **kwargs)
+
+
+def shapelify_feature_lines(*args, **kwargs):
+    return _shapelify_features(*args, **kwargs)
+
+
+def shapelify_feature_polygons(*args, **kwargs):
+    return _shapelify_features(*args, **kwargs)
+
+
+def plot_subduction_teeth(*args, **kwargs):
+    return _plot_subduction_teeth(*args, **kwargs)
+
+
+plot_subduction_teeth.__doc__ = _plot_subduction_teeth.__doc__
+shapelify_features.__doc__ = _shapelify_features.__doc__
+shapelify_feature_lines.__doc__ = _shapelify_features.__doc__
+shapelify_feature_polygons.__doc__ = _shapelify_features.__doc__
 
 
 class PlotTopologies(object):
@@ -1689,7 +1699,13 @@ def plot_plate_polygon_by_id(self, ax, plate_id, **kwargs):
 
     # the old function name(plot_plate_id) is bad. we should change the name
     # for backward compatibility, we have to allow users to use the old name
-    plot_plate_id = plot_plate_polygon_by_id
+    def plot_plate_id(self, *args, **kwargs):
+        logger.warn(
+            "The class method plot_plate_id will be deprecated in the future soon. Use plot_plate_polygon_by_id instead."
+        )
+        return self.plot_plate_polygon_by_id(*args, **kwargs)
+
+    plot_plate_id.__doc__ = plot_plate_polygon_by_id.__doc__
 
     def plot_grid(self, ax, grid, extent=[-180, 180, -90, 90], **kwargs):
         """Plot a `MaskedArray` raster or grid onto a standard map Projection.
@@ -3379,26 +3395,10 @@ def plot_all_topologies(self, ax, color="black", **kwargs):
             A standard cartopy.mpl.geoaxes.GeoAxes or cartopy.mpl.geoaxes.GeoAxesSubplot map
             with unclassified features plotted onto the chosen map projection.
         """
-        if "transform" in kwargs.keys():
-            warnings.warn(
-                "'transform' keyword argument is ignored by PlotTopologies",
-                UserWarning,
-            )
-            kwargs.pop("transform")
-        tessellate_degrees = kwargs.pop("tessellate_degrees", 1)
-        central_meridian = kwargs.pop("central_meridian", None)
-        if central_meridian is None:
-            central_meridian = _meridian_from_ax(ax)
 
-        gdf = self.get_all_topologies(
-            central_meridian=central_meridian,
-            tessellate_degrees=tessellate_degrees,
+        return _plot_geometries(
+            ax, self.base_projection, color, self.get_all_topologies, **kwargs
         )
-        if hasattr(ax, "projection"):
-            gdf = _clean_polygons(data=gdf, projection=ax.projection)
-        else:
-            kwargs["transform"] = self.base_projection
-        return gdf.plot(ax=ax, facecolor="none", edgecolor=color, **kwargs)
 
     def get_all_topological_sections(
         self,
@@ -3530,26 +3530,10 @@ def plot_all_topological_sections(self, ax, color="black", **kwargs):
             A standard cartopy.mpl.geoaxes.GeoAxes or cartopy.mpl.geoaxes.GeoAxesSubplot map
             with unclassified features plotted onto the chosen map projection.
         """
-        if "transform" in kwargs.keys():
-            warnings.warn(
-                "'transform' keyword argument is ignored by PlotTopologies",
-                UserWarning,
-            )
-            kwargs.pop("transform")
-        tessellate_degrees = kwargs.pop("tessellate_degrees", 1)
-        central_meridian = kwargs.pop("central_meridian", None)
-        if central_meridian is None:
-            central_meridian = _meridian_from_ax(ax)
 
-        gdf = self.get_all_topological_sections(
-            central_meridian=central_meridian,
-            tessellate_degrees=tessellate_degrees,
+        return _plot_geometries(
+            ax, self.base_projection, color, self.get_all_topological_sections, **kwargs
         )
-        if hasattr(ax, "projection"):
-            gdf = _clean_polygons(data=gdf, projection=ax.projection)
-        else:
-            kwargs["transform"] = self.base_projection
-        return gdf.plot(ax=ax, color=color, **kwargs)
 
     def get_ridges(self, central_meridian=0.0, tessellate_degrees=1):
         """Create a geopandas.GeoDataFrame object containing geometries of reconstructed ridge lines.
@@ -3647,7 +3631,7 @@ def plot_ridges(self, ax, color="black", **kwargs):
             logger.warn(
                 "Plate model does not have topology features. Unable to plot_ridges."
             )
-            return
+            return ax
 
         return _plot_geometries(
             ax, self.base_projection, color, self.get_ridges, **kwargs

gplately/utils/log_utils.py

@@ -7,7 +7,9 @@
 
 # configurate the logging utility
 def setup_logging():
-    cfg_file_path = f"{os.path.dirname(os.path.realpath(__file__))}/logging_config.yaml"
+    cfg_file_path = (
+        f"{os.path.dirname(os.path.realpath(__file__))}/../logging_config.yaml"
+    )
     if os.path.isfile(cfg_file_path):
         with open(cfg_file_path, "rt") as f:
             config = yaml.safe_load(f.read())

gplately/utils/plot_utils.py

@@ -9,7 +9,7 @@
 from shapely.geometry.base import BaseGeometry, BaseMultipartGeometry
 from shapely.ops import linemerge, substring
 
-from ..read_geometries import get_geometries as _get_geometries
+from .io_utils import get_geometries as _get_geometries
 
 logger = logging.getLogger("gplately")
 
@@ -513,6 +513,11 @@ def _plot_geometries(ax, projection, color, get_data_func, **kwargs):
         central_meridian=central_meridian,
         tessellate_degrees=tessellate_degrees,
     )
+
+    if len(gdf) == 0:
+        logger.warn("No geometry found for plotting. Do nothing and return.")
+        return ax
+
     if hasattr(ax, "projection"):
         gdf = _clean_polygons(data=gdf, projection=ax.projection)
     else:

tests-dir/unittest/test_plot.py

@@ -44,17 +44,42 @@ def main(show=True):
     fig = plt.figure(figsize=(10, 5), dpi=96)
     ax = fig.add_subplot(111, projection=ccrs.Robinson(central_longitude=180))
 
-    gplot.plot_continent_ocean_boundaries(ax, color="cornflowerblue")
-    gplot.plot_coastlines(ax, color="black")
-    gplot.plot_ridges_and_transforms(ax, color="red")
-    gplot.plot_trenches(ax, color="orange")
-    gplot.plot_subduction_teeth(ax, color="orange")
-    gplot.plot_ridges(ax, color="green")
+    plot_flag = {
+        "continent_ocean_boundaries": 1,
+        "coastlines": 1,
+        "ridges_and_transforms": 1,
+        "trenches": 1,
+        "subduction_teeth": 1,
+        "ridges": 1,
+        "all_topologies": 1,
+        "all_topological_sections": 1,
+        "plot_plate_polygon_by_id": 1,
+    }
+
+    if plot_flag["continent_ocean_boundaries"]:
+        gplot.plot_continent_ocean_boundaries(ax, color="cornflowerblue")
+    if plot_flag["coastlines"]:
+        gplot.plot_coastlines(ax, color="black")
+    if plot_flag["ridges_and_transforms"]:
+        gplot.plot_ridges_and_transforms(ax, color="red")
+    if plot_flag["trenches"]:
+        gplot.plot_trenches(ax, color="orange")
+    if plot_flag["subduction_teeth"]:
+        gplot.plot_subduction_teeth(ax, color="orange")
+    if plot_flag["ridges"]:
+        gplot.plot_ridges(ax, color="green")
+    if plot_flag["all_topologies"]:
+        gplot.plot_all_topologies(ax, color="red")
+    if plot_flag["all_topological_sections"]:
+        gplot.plot_all_topological_sections(ax, color="red")
     ax.set_global()
 
     ids = set([f.get_reconstruction_plate_id() for f in gplot.topologies])
     for id in ids:
-        gplot.plot_plate_id(ax, id, facecolor="None", edgecolor="lightgreen")
+        if plot_flag["plot_plate_polygon_by_id"]:
+            gplot.plot_plate_polygon_by_id(
+                ax, id, facecolor="None", edgecolor="lightgreen"
+            )
     plt.title(f"{age} Ma")
 
     if show: