issue-250-ridge-transforms

gplately/plot.py

@@ -327,6 +327,8 @@ def __init__(
         self.COBs = None
         self._topological_plate_boundaries = None
         self._topologies = None
+        self._ridges = []
+        self._transforms = []
 
         self._anchor_plate_id = self._check_anchor_plate_id(anchor_plate_id)
         self._plot_engine = plot_engine
@@ -399,6 +401,34 @@ def topologies(self):
         self._resolve_both_boundaries_and_networks()
         return self._topologies
 
+    @property
+    def ridges(self):
+        """
+        Mid-ocean ridge features (all the features which are labelled as gpml:MidOceanRidge in the model).
+        """
+        logger.debug(
+            "The 'ridges' property has been changed since GPlately 1.3.0. "
+            "You need to check your workflow to make sure the new 'ridges' property still suits your purpose. "
+            "In earlier releases of GPlately, we used an algorithm to identify the 'ridges' and 'transforms' within the gpml:MidOceanRidge features. "
+            "Unfortunately, the algorithm did not work very well. So we have removed the algorithm and now the 'ridges' property contains all the features "
+            "which are labelled as gpml:MidOceanRidge in the reconstruction model."
+        )  # use logger.debug to make the message less aggressive
+        return self._ridges
+
+    @property
+    def transforms(self):
+        """
+        Transform boundary features (all the features which are labelled as gpml:Transform in the model).
+        """
+        logger.debug(
+            "The 'transforms' property has been changed since GPlately 1.3.0. "
+            "You need to check your workflow to make sure the new 'transforms' property still suits your purpose. "
+            "In earlier releases of GPlately, we used an algorithm to identify the 'ridges' and 'transforms' within the gpml:MidOceanRidge features. "
+            "Unfortunately, the algorithm did not work very well. So we have removed the algorithm and now the 'transforms' property contains all the features "
+            "which are labelled as gpml:Transform in the reconstruction model."
+        )  # use logger.debug to make the message less aggressive
+        return self._transforms
+
     @property
     def time(self):
         """The reconstruction time."""
@@ -438,6 +468,29 @@ def _check_anchor_plate_id(id):
             raise ValueError("Invalid anchor plate ID: {}".format(id))
         return id
 
+    @property
+    def ridge_transforms(self):
+        """
+        Deprecated! DO NOT USE!
+        """
+
+        warnings.warn(
+            "Deprecated! DO NOT USE!"
+            "The 'ridge_transforms' property will be removed in the future GPlately releases. "
+            "Update your workflow to use the 'ridges' and 'transforms' properties instead, "
+            "otherwise your workflow will not work with the future GPlately releases.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        logger.debug(
+            "The 'ridge_transforms' property has been changed since GPlately 1.3.0. "
+            "You need to check your workflow to make sure the new 'ridge_transforms' property still suits your purpose. "
+            "In earlier releases of GPlately, the 'ridge_transforms' property contains only the features "
+            "which are labelled as gpml:MidOceanRidge in the reconstruction model. "
+            "Now, the 'ridge_transforms' property contains both gpml:Transform and gpml:MidOceanRidge features."
+        )
+        return self._ridges + self._transforms
+
     def update_time(self, time):
         """Re-reconstruct features and topologies to the time specified by the `PlotTopologies` `time` attribute
         whenever it or the anchor plate is updated.
@@ -463,8 +516,8 @@ def update_time(self, time):
         self._time = float(time)
         (
             self._topological_plate_boundaries,
-            self.ridges,
-            self._ridges_do_not_use_for_now,
+            self._ridges,
+            self._ridges_do_not_use_for_now,  # the algorithm to separate ridges and transforms has not been ready yet
             self._transforms_do_not_use_for_now,
             self.trenches,
             self.trench_left,
@@ -494,7 +547,6 @@ def update_time(self, time):
         self.extended_continental_crusts = []
         self.passive_continental_boundaries = []
         self.slab_edges = []
-        self.transforms = []
         self.unclassified_features = []
 
         for topol in self.other:
@@ -551,7 +603,7 @@ def update_time(self, time):
                 self.slab_edges.append(topol)
 
             elif topol.get_feature_type() == pygplates.FeatureType.gpml_transform:  # type: ignore
-                self.transforms.append(topol)
+                self._transforms.append(topol)
 
             elif (
                 topol.get_feature_type()
@@ -737,7 +789,7 @@ def _plot_feature(self, ax, get_feature_func, **kwargs) -> None:
             )
 
         if len(gdf) == 0:
-            logger.warning("No feature found for plotting. Do nothing and return.")
+            logger.debug("No feature found for plotting. Do nothing and return.")
             return ax
 
         self._plot_engine.plot_geo_data_frame(ax, gdf, **kwargs)
@@ -845,7 +897,15 @@ def get_ridges(
         central_meridian=0.0,
         tessellate_degrees=1,
     ):
-        """Create a geopandas.GeoDataFrame object containing geometries of reconstructed mid-ocean ridge lines(gpml:MidOceanRidge)."""
+        """Create a geopandas.GeoDataFrame object containing the geometries of reconstructed mid-ocean ridge lines (gpml:MidOceanRidge)."""
+        logger.debug(
+            "The 'get_ridges' function has been changed since GPlately 1.3.0. "
+            "You need to check your workflow to make sure the new 'get_ridges' function still suits your purpose. "
+            "In earlier releases of GPlately, we used an algorithm to identify the 'ridges' and 'transforms' within the gpml:MidOceanRidge features. "
+            "Unfortunately, the algorithm did not work very well. So we have removed the algorithm and now the 'get_ridges' function returns all the features "
+            "which are labelled as gpml:MidOceanRidge in the reconstruction model."
+        )  # use logger.debug to make the message less aggressive
+
         return self.get_feature(
             self.ridges,
             central_meridian=central_meridian,
@@ -873,9 +933,18 @@ def plot_ridges(self, ax, color="black", **kwargs):
         Point features near the poles (-89 & 89 degree latitude) are also clipped to ensure
         compatibility with Cartopy.
         """
+
+        logger.debug(
+            "The 'plot_ridges' function has been changed since GPlately 1.3.0. "
+            "You need to check your workflow to make sure the new 'plot_ridges' function still suits your purpose. "
+            "In earlier releases of GPlately, we used an algorithm to identify the 'ridges' and 'transforms' within the gpml:MidOceanRidge features. "
+            "Unfortunately, the algorithm did not work very well. So we have removed the algorithm and now the 'plot_ridges' function plots all the features "
+            "which are labelled as gpml:MidOceanRidge in the reconstruction model."
+        )  # use logger.debug to make the message less aggressive
+
         return self.plot_feature(
             ax,
-            self.ridges,
+            self._ridges,
             feature_name="ridges",
             facecolor="none",
             edgecolor=color,
@@ -892,6 +961,32 @@ def get_trenches(self, central_meridian=0.0, tessellate_degrees=1):
             tessellate_degrees=tessellate_degrees,
         )
 
+    @validate_reconstruction_time
+    def get_ridges_and_transforms(self, central_meridian=0.0, tessellate_degrees=1):
+        """
+        Deprecated! DO NOT USE.
+        """
+        warnings.warn(
+            "Deprecated! The 'get_ridges_and_transforms' function will be removed in the future GPlately releases. "
+            "Update your workflow to use the 'get_ridges' and 'get_transforms' functions instead, "
+            "otherwise your workflow will not work with the future GPlately releases.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        logger.debug(
+            "The 'get_ridges_and_transforms' function has been changed since GPlately 1.3.0. "
+            "You need to check your workflow to make sure the new 'get_ridges_and_transforms' function still suits your purpose. "
+            "In earlier releases of GPlately, we used an algorithm to identify the 'ridges' and 'transforms' within the gpml:MidOceanRidge features. "
+            "Unfortunately, the algorithm did not work very well. So we have removed the algorithm and now the 'get_ridges_and_transforms' function returns all the features "
+            "which are labelled as gpml:MidOceanRidge or gpml:Transform in the reconstruction model."
+        )  # use logger.debug to make the message less aggressive
+
+        return self.get_feature(
+            self._ridges + self._transforms,
+            central_meridian=central_meridian,
+            tessellate_degrees=tessellate_degrees,
+        )
+
     @validate_topology_availability("trenches")
     @append_docstring(PLOT_DOCSTRING.format("trenches"))
     def plot_trenches(self, ax, color="black", **kwargs):
@@ -1722,23 +1817,62 @@ def get_transforms(
         tessellate_degrees=None,
     ):
         """Create a geopandas.GeoDataFrame object containing geometries of reconstructed transform lines(gpml:Transform)."""
+        logger.debug(
+            "The 'get_transforms' function has been changed since GPlately 1.3.0. "
+            "You need to check your workflow to make sure the new 'get_transforms' function still suits your purpose. "
+            "In earlier releases of GPlately, we used an algorithm to identify the 'ridges' and 'transforms' within the gpml:MidOceanRidge features. "
+            "Unfortunately, the algorithm did not work very well. So we have removed the algorithm and now the 'get_transforms' function returns all the features "
+            "which are labelled as gpml:Transform in the reconstruction model."
+        )  # use logger.debug to make the message less aggressive
+
         return self.get_feature(
-            self.transforms,
+            self._transforms,
             central_meridian=central_meridian,
             tessellate_degrees=tessellate_degrees,
         )
 
     @append_docstring(PLOT_DOCSTRING.format("transforms"))
     def plot_transforms(self, ax, color="black", **kwargs):
         """Plot transform boundaries(gpml:Transform) onto a map."""
+
+        logger.debug(
+            "The 'plot_transforms' function has been changed since GPlately 1.3.0. "
+            "You need to check your workflow to make sure the new 'plot_transforms' function still suits your purpose. "
+            "In earlier releases of GPlately, we used an algorithm to identify the 'ridges' and 'transforms' within the gpml:MidOceanRidge features. "
+            "Unfortunately, the algorithm did not work very well. So we have removed the algorithm and now the 'plot_transforms' function plots all the features "
+            "which are labelled as gpml:Transform in the reconstruction model."
+        )  # use logger.debug to make the message less aggressive
+
         return self.plot_feature(
             ax,
-            self.transforms,
+            self._transforms,
             feature_name="transforms",
             edgecolor=color,
             **kwargs,
         )
 
+    def plot_ridges_and_transforms(self, ax, color="black", **kwargs):
+        """
+        Deprecated! DO NOT USE!
+        """
+        warnings.warn(
+            "Deprecated! The 'plot_ridges_and_transforms' function will be removed in the future GPlately releases. "
+            "Update your workflow to use the 'plot_ridges' and 'plot_transforms' functions instead, "
+            "otherwise your workflow will not work with the future GPlately releases.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        logger.debug(
+            "The 'plot_ridges_and_transforms' function has been changed since GPlately 1.3.0. "
+            "You need to check your workflow to make sure the new 'plot_ridges_and_transforms' function still suits your purpose. "
+            "In earlier releases of GPlately, we used an algorithm to identify the 'ridges' and 'transforms' within the gpml:MidOceanRidge features. "
+            "Unfortunately, the algorithm did not work very well. So we have removed the algorithm and now the 'plot_ridges_and_transforms' function plots all the features "
+            "which are labelled as gpml:Transform or gpml:MidOceanRidge in the reconstruction model."
+        )  # use logger.debug to make the message less aggressive
+
+        self.plot_ridges(ax, color=color, **kwargs)
+        self.plot_transforms(ax, color=color, **kwargs)
+
     @validate_reconstruction_time
     @append_docstring(GET_DATE_DOCSTRING.format("unclassified features"))
     def get_unclassified_features(
@@ -1927,3 +2061,49 @@ def plot_topological_plate_boundaries(self, ax, color="black", **kwargs):
             color=color,
             **kwargs,
         )
+
+    @property
+    def misc_transforms(self):
+        """
+        Deprecated! DO NOT USE.
+        """
+        warnings.warn(
+            "Deprecated! The 'misc_transforms' property will be removed in the future GPlately releases. "
+            "Update your workflow to use the 'transforms' property instead, "
+            "otherwise your workflow will not work with the future GPlately releases.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        return self._transforms
+
+    def plot_misc_transforms(self, ax, color="black", **kwargs):
+        """
+        Deprecated! DO NOT USE.
+        """
+        warnings.warn(
+            "Deprecated! The 'plot_misc_transforms' function will be removed in the future GPlately releases. "
+            "Update your workflow to use the 'plot_transforms' function instead, "
+            "otherwise your workflow will not work with the future GPlately releases.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        self.plot_transforms(ax=ax, color=color, **kwargs)
+
+    def get_misc_transforms(
+        self,
+        central_meridian=0.0,
+        tessellate_degrees=None,
+    ):
+        """
+        Deprecated! DO NOT USE.
+        """
+        warnings.warn(
+            "Deprecated! The 'get_misc_transforms' function will be removed in the future GPlately releases. "
+            "Update your workflow to use the 'get_transforms' function instead, "
+            "otherwise your workflow will not work with the future GPlately releases.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        return self.get_transforms(
+            central_meridian=central_meridian, tessellate_degrees=tessellate_degrees
+        )

gplately/utils/plot_utils.py

@@ -387,8 +387,9 @@ def _clean_polygons(data, projection):
         rects = gpd.GeoDataFrame(
             {"geometry": rects},
             geometry="geometry",
-            crs=ccrs.PlateCarree(),
-        )
+            # crs=ccrs.PlateCarree(),
+            crs="EPSG:4326",  # Michael Chin changed this to avoid "CRS mismatch" warning. More investigation is needed. what's the difference between EPSG:4326 and ccrs.PlateCarree()?
+        )  # type: ignore
         data = data.overlay(rects, how="difference")
 
     projected = data.to_crs(projection)

tests-dir/unittest/test_issue_250.py

@@ -0,0 +1,72 @@
+#!/usr/bin/env python3
+import sys, os
+
+os.environ["GPLATELY_DEBUG"] = "1"
+
+
+import cartopy.crs as ccrs
+import matplotlib.pyplot as plt
+from common import MODEL_REPO_DIR, save_fig
+from plate_model_manager import PlateModelManager
+
+import gplately
+
+print(gplately.__file__)
+
+# https://github.com/GPlates/gplately/issues/250
+
+
+def main(show=True):
+    # Call GPlately's PlateModelManager object and request data from the Müller et al. 2019 study
+    pm_manager = PlateModelManager()
+    muller2019_model = pm_manager.get_model("Muller2019", data_dir=MODEL_REPO_DIR)
+    if not muller2019_model:
+        raise Exception("Failed to get reconstruction model!")
+    rotation_model = muller2019_model.get_rotation_model()
+    topology_features = muller2019_model.get_topologies()
+    static_polygons = muller2019_model.get_static_polygons()
+
+    model = gplately.PlateReconstruction(
+        rotation_model, topology_features, static_polygons
+    )
+
+    # Obtain features for the PlotTopologies object with PlateModelManager
+    coastlines = muller2019_model.get_layer("Coastlines")
+    continents = muller2019_model.get_layer("ContinentalPolygons")
+    COBs = muller2019_model.get_layer("COBs")
+
+    # Call the PlotTopologies object
+    gplot = gplately.plot.PlotTopologies(
+        model, coastlines=coastlines, continents=continents, COBs=COBs
+    )
+
+    gplot.time = 100  # Ma
+
+    fig = plt.figure(figsize=(8, 4))
+    ax = fig.add_subplot(111, projection=ccrs.Mollweide(190))
+    ax.set_global()  # type: ignore
+    gplot.plot_ridges_and_transforms(ax, color="red")
+    gplot.plot_ridges(ax, color="black")
+    gplot.plot_transforms(ax, color="black")
+    gplot.plot_misc_transforms(ax, color="black")
+
+    print(gplot.ridges)
+    print(gplot.transforms)
+    print(gplot.get_ridges_and_transforms())
+    print(gplot.get_misc_transforms())
+    print(gplot.get_ridges())
+    print(gplot.get_transforms())
+
+    plt.title(f"{gplot.time} Ma")
+
+    if show:
+        plt.show()
+    else:
+        save_fig(__file__)
+
+
+if __name__ == "__main__":
+    if len(sys.argv) == 2 and sys.argv[1] == "save":
+        main(show=False)
+    else:
+        main(show=True)

tests-dir/unittest/test_plot_with_raster.py

@@ -15,6 +15,8 @@ def main(show=True):
     # Call GPlately's PlateModelManager object and request data from the Müller et al. 2019 study
     pm_manager = PlateModelManager()
     muller2019_model = pm_manager.get_model("Muller2019", data_dir=MODEL_REPO_DIR)
+    if not muller2019_model:
+        raise Exception("Failed to get reconstruction model!")
     rotation_model = muller2019_model.get_rotation_model()
     topology_features = muller2019_model.get_topologies()
     static_polygons = muller2019_model.get_static_polygons()