dsa-helpers 1.0.7.dev0__tar.gz → 1.0.8.dev0__tar.gz

{dsa_helpers-1.0.7.dev0/dsa_helpers.egg-info → dsa_helpers-1.0.8.dev0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dsa_helpers
-Version: 1.0.7.dev0
+Version: 1.0.8.dev0
 Summary: Utility functions for working with the DSA girder client.
 Author-email: "Juan C. Vizcarra" <jvizcar@emory.edu>
 Maintainer-email: "Juan C. Vizcarra" <jvizcar@emory.edu>

dsa_helpers-1.0.8.dev0/dsa_helpers/gpd_utils.py

@@ -0,0 +1,172 @@
+"""
+Utility functions for working with GeoPandas.
+
+"""
+
+import geopandas as gpd
+from shapely.geometry import Polygon
+
+import matplotlib.patches as mpatches
+import matplotlib.pyplot as plt
+
+
+def count_polygon_points(polygon: Polygon) -> int:
+    """
+    Count the total number of points in a Shapely polygon, including
+    exterior and interior rings.
+
+    Args:
+        polygon (shapely.geometry.Polygon): A Shapely polygon object.
+
+    Returns:
+        int: The total number of points in the polygon.
+
+    """
+    # Count exterior points.
+    exterior_points = len(polygon.exterior.coords)
+
+    # Count interior points (holes).
+    interior_points = sum(
+        len(interior.coords) for interior in polygon.interiors
+    )
+
+    # Total points.
+    return exterior_points + interior_points
+
+
+def total_points_in_gdf(gdf: gpd.GeoDataFrame) -> int:
+    """
+    Calculate the total number of points in all polygons in a GeoDataFrame.
+
+    Args:
+        gdf (geopandas.GeoDataFrame): GeoDataFrame containing polygons.
+
+    Returns:
+        int: The total number of points in all polygons.
+
+    """
+    return int(gdf.geometry.apply(count_polygon_points).sum())
+
+
+def plot_gdf(
+    gdf: gpd.GeoDataFrame,
+    figsize: int | tuple[int, int] | None = None,
+    label2color: dict | None = None,
+):
+    """Plot a geopandas dataframe.
+
+    Args:
+        gdf (geopandas.GeoDataFrame): A GeoDataFrame containing
+            polygons. Must have a 'label' column.
+        figsize (int | tuple[int, int] | None): The size of the figure.
+            If None, the figure size will be (5, 5).
+        label2color (dict | None): A dictionary mapping labels to
+            colors. If None then a legend will not be included and the
+            colors will be random. Colors should be an accepted
+            matplotlib color.
+
+    """
+    if figsize is None:
+        figsize = (5, 5)
+    elif isinstance(figsize, int):
+        figsize = (figsize, figsize)
+
+    gdf = gdf.copy()
+
+    # Blow up any multi-polygons.
+    gdf = gdf.explode(index_parts=False).reset_index(drop=True)
+
+    total_points = total_points_in_gdf(gdf)
+
+    if label2color is not None:
+        gdf["color"] = gdf["label"].map(label2color)
+
+        # Remove rows where color is nan.
+        gdf = gdf.dropna(subset=["color"])
+
+    # # Create the plot
+    ax = plt.subplots(figsize=figsize)[1]
+    gdf.plot(color=gdf["color"], ax=ax)
+
+    if label2color is not None:
+        # Add legend.
+        handles = [
+            mpatches.Patch(color=color, label=key)
+            for key, color in label2color.items()
+        ]
+
+        ax.legend(
+            handles=handles,
+            title="Legend",
+            loc="upper left",
+            bbox_to_anchor=(
+                1.02,
+                1,
+            ),  # x > 1 pushes it to the right, y = 1 keeps it top-aligned
+            borderaxespad=0,
+        )
+    plt.title(f"Total points: {total_points:,}")
+    plt.show()
+
+
+def remove_gdf_overlaps(
+    gdf: gpd.GeoDataFrame,
+    columns: str | list[str],
+    ascending: bool | list[bool] = True,
+    is_notebook: bool = False,
+) -> gpd.GeoDataFrame:
+    """Remove overlaps from a GeoDataFrame.
+
+    Args:
+        gdf (geopandas.GeoDataFrame): The GeoDataFrame to remove
+            overlaps from.
+        columns (str | list[str]): The columns to sort dataframe by. The
+            order determines the order of removal overlapping polygon
+            regions.
+        ascending (bool): Whether to remove overlaps in ascending order.
+        is_notebook (bool): Switch which tqdm bar to use. Default is
+            False, which uses the terminal progress bar.
+
+    Returns:
+        gpd.GeoDataFrame: The GeoDataFrame with overlaps removed.
+
+    """
+    if isinstance(columns, str):
+        columns = [columns]
+
+    if isinstance(ascending, bool):
+        ascending = [ascending] * len(columns)
+
+    # Remove multi-polygons.
+    gdf = gdf.explode(index_parts=False).reset_index(drop=True)
+
+    # Sort the GeoDataFrame by the columns and ascending order.
+    gdf = gdf.sort_values(by=columns, ascending=ascending).reset_index(
+        drop=True
+    )
+
+    if is_notebook:
+        from tqdm.notebook import tqdm
+    else:
+        from tqdm import tqdm
+
+    # Loop through each row in the GeoDataFrame.
+    for i, row in tqdm(gdf.iterrows(), total=len(gdf)):
+        # Check overlap with all following rows.
+        other_gdf = gdf[i + 1 :]
+
+        if len(other_gdf):
+            # Get the rows that overlap.
+            overlap = row.geometry.overlaps(other_gdf.geometry)
+
+            # Get the rows that overlap.
+            other_rows = other_gdf[overlap]
+
+            other_gdf.loc[:, "geometry"] = other_gdf.geometry.difference(
+                row.geometry
+            )
+
+    # This could have created multiple polygons, explode them.
+    gdf = gdf.explode(index_parts=False).reset_index(drop=True)
+
+    return gdf

{dsa_helpers-1.0.7.dev0 → dsa_helpers-1.0.8.dev0/dsa_helpers.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dsa_helpers
-Version: 1.0.7.dev0
+Version: 1.0.8.dev0
 Summary: Utility functions for working with the DSA girder client.
 Author-email: "Juan C. Vizcarra" <jvizcar@emory.edu>
 Maintainer-email: "Juan C. Vizcarra" <jvizcar@emory.edu>

{dsa_helpers-1.0.7.dev0 → dsa_helpers-1.0.8.dev0}/dsa_helpers.egg-info/SOURCES.txt

@@ -10,6 +10,7 @@ docs/source/index.rst
 dsa_helpers/__init__.py
 dsa_helpers/cli_utils.py
 dsa_helpers/girder_utils.py
+dsa_helpers/gpd_utils.py
 dsa_helpers/image_utils.py
 dsa_helpers/imread.py
 dsa_helpers/imwrite.py

{dsa_helpers-1.0.7.dev0 → dsa_helpers-1.0.8.dev0}/pyproject.toml

@@ -35,7 +35,7 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
 ]
 keywords = ["dsa", "girder", "girder_client"]
-version = "v1.0.7.dev0"
+version = "v1.0.8.dev0"
 
 [project.urls]
 Repository = "https://github.com/Gutman-Lab/dsa-python-utils"