Update cmap function in example notebooks

examples/dvh_analysis.ipynb

@@ -23,6 +23,7 @@
     "    !pip install platipy\n",
     "    import platipy\n",
     "\n",
+    "import matplotlib\n",
     "import matplotlib.pyplot as plt\n",
     "import SimpleITK as sitk\n",
     "\n",
@@ -103,7 +104,7 @@
    "source": [
     "vis = ImageVisualiser(ct_image, cut=get_com(structures[\"PTV60\"]))\n",
     "\n",
-    "vis.add_scalar_overlay(dose, discrete_levels=20, colormap=plt.cm.get_cmap(\"inferno\"), name=\"Dose (Gy)\")\n",
+    "vis.add_scalar_overlay(dose, discrete_levels=20, colormap=matplotlib.colormaps.get_cmap(\"inferno\"), name=\"Dose (Gy)\")\n",
     "vis.add_contour(structures)\n",
     "\n",
     "fig = vis.show()"
@@ -160,7 +161,7 @@
     "\n",
     "# Plot the DVH\n",
     "fig, ax = plt.subplots()\n",
-    "plt_dvh.plot(ax=ax, kind=\"line\", colormap=plt.cm.get_cmap(\"rainbow\"), legend=False)\n",
+    "plt_dvh.plot(ax=ax, kind=\"line\", colormap=matplotlib.colormaps.get_cmap(\"rainbow\"), legend=False)\n",
     "\n",
     "# Add labels and show plot\n",
     "plt.legend(loc='best')\n",
@@ -226,8 +227,8 @@
     "    d_cc_points=[10],\n",
     "    structure_for_limits=dose>5,\n",
     "    expansion_for_limits=40,\n",
-    "    contour_cmap=plt.cm.get_cmap(\"rainbow\"),\n",
-    "    dose_cmap=plt.cm.get_cmap(\"inferno\"),\n",
+    "    contour_cmap=matplotlib.colormaps.get_cmap(\"rainbow\"),\n",
+    "    dose_cmap=matplotlib.colormaps.get_cmap(\"inferno\"),\n",
     "    title=\"TCGA_CV_5977 Dose Metrics\")"
    ]
   },

examples/visualise.ipynb

@@ -32,10 +32,11 @@
     "# Function to grab some test data\n",
     "from platipy.imaging.tests.data import get_lung_nifti\n",
     "\n",
-    "# Usual suspects\n",
+    "# Import some common libraries which we need\n",
     "import numpy as np\n",
     "import SimpleITK as sitk\n",
     "from pathlib import Path\n",
+    "import matplotlib\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
     "# Some utilities we use for generating interesting data\n",
@@ -153,7 +154,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "image_visualiser = ImageVisualiser(ct_image, window=(-900, 1100), colormap=plt.cm.get_cmap(\"terrain\"), figure_size_in=6)\n",
+    "image_visualiser = ImageVisualiser(ct_image, window=(-900, 1100), colormap=matplotlib.colormaps.get_cmap(\"terrain\"), figure_size_in=6)\n",
     "\n",
     "image_visualiser.set_limits_from_label(contours[\"LUNG_L\"] + contours[\"LUNG_R\"])\n",
     "\n",
@@ -238,7 +239,7 @@
     "image_visualiser.add_vector_overlay(\n",
     "    dvf_expansion,\n",
     "    name=\"DVF magnitude [mm]\",\n",
-    "    colormap=plt.cm.get_cmap(\"gnuplot2\"),\n",
+    "    colormap=matplotlib.colormaps.get_cmap(\"gnuplot2\"),\n",
     "    alpha=0.75,\n",
     "    arrow_scale=1,\n",
     "    arrow_width=1,\n",
@@ -314,7 +315,7 @@
     "image_visualiser.add_vector_overlay(\n",
     "    dvf_expansion,\n",
     "    name=\"DVF magnitude [mm]\",\n",
-    "    colormap=plt.cm.get_cmap(\"gnuplot2\"),\n",
+    "    colormap=matplotlib.colormaps.get_cmap(\"gnuplot2\"),\n",
     "    alpha=0.5,\n",
     "    arrow_scale=1,\n",
     "    arrow_width=1,\n",