Fix deprecated matplotlib get_cmap

Author: elbeejay

dorado/routines.py

@@ -1304,7 +1304,11 @@ def show_nourishment_area(visit_freq, grid=None, walk_data=None,
     alphas = Normalize(0, amax, clip=True)(visit_freq)  # Normalize alphas
     alphas = np.clip(alphas, min_alpha, 1)
     colors = Normalize(np.nanmin(visit_freq), 1)(visit_freq)  # Normalize color
-    cmap = plt.cm.get_cmap(cmap)
+    if isinstance(cmap, str):
+        try:
+            cmap = matplotlib.colormaps[cmap]
+        except AttributeError:
+            cmap = plt.cm.get_cmap(cmap)
     colors = cmap(colors)
     colors[..., -1] = alphas
 
@@ -1390,7 +1394,11 @@ def show_nourishment_time(mean_times, grid=None, walk_data=None,
     alphas = np.clip(alphas, min_alpha, 1)
     colors = Normalize(np.nanmin(mean_times),
                        np.nanmax(mean_times))(mean_times)  # Normalize colors
-    cmap = plt.cm.get_cmap(cmap)
+    if isinstance(cmap, str):
+        try:
+            cmap = matplotlib.colormaps[cmap]
+        except AttributeError:
+            cmap = plt.cm.get_cmap(cmap)
     colors = cmap(colors)
     colors[..., -1] = alphas
 

examples/spatial_exposure_time_example_Delft3DFM.ipynb

@@ -41,6 +41,7 @@
     "import json\n",
     "from pathlib import Path\n",
     "import dorado\n",
+    "import matplotlib\n",
     "from matplotlib import pyplot as plt\n",
     "import dorado.spatial as spat\n",
     "import dorado.particle_track as pt"
@@ -423,7 +424,7 @@
    "outputs": [],
    "source": [
     "title = 'System-wide exposure time (days)'\n",
-    "cmap = plt.get_cmap('plasma_r')\n",
+    "cmap = matplotlib.colormaps['plasma_r'] if hasattr(matplotlib, 'colormaps') else plt.get_cmap('plasma_r')\n",
     "max_exposure = 30 # max time in model\n",
     "cbar_levels = 7"
    ]
@@ -563,7 +564,7 @@
    "outputs": [],
    "source": [
     "title_local = 'Localized exposure time (days)'\n",
-    "cmap_local = plt.get_cmap('viridis_r')\n",
+    "cmap_local = matplotlib.colormaps['viridis_r'] if hasattr(matplotlib, 'colormaps') else plt.get_cmap('viridis_r')\n",
     "max_exposure_local = 7\n",
     "cbar_levels_local = 6"
    ]
@@ -655,4 +656,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

tests/test_spatial.py

@@ -4,6 +4,7 @@
 
 @author: cturn
 """
+import matplotlib
 from matplotlib import pyplot as plt
 import numpy as np
 import pytest
@@ -100,7 +101,7 @@ def test_plot_spatial(test_grid, walk_data):
         elevation=elevation,
         max_exposure=7,
         cbar_levels=7,
-        cmap=plt.get_cmap("plasma_r"),
+        cmap=matplotlib.colormaps["plasma_r"] if hasattr(matplotlib, "colormaps") else plt.get_cmap("plasma_r"),
         title="Test System-Wide (s)")
     plt.close("all")
 
@@ -112,6 +113,6 @@ def test_plot_spatial(test_grid, walk_data):
         elevation=elevation,
         max_exposure=7,
         cbar_levels=7,
-        cmap=plt.get_cmap("viridis_r"),
+        cmap=matplotlib.colormaps["viridis_r"] if hasattr(matplotlib, "colormaps") else plt.get_cmap("viridis_r"),
         title="Test Localized (s)")
     plt.close("all")