Correct colour maps in dose vis

pyplati · Feb 22, 2023 · e50dfc8 · e50dfc8
1 parent 437d8ab
commit e50dfc8
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Showing 2 changed files with 19 additions and 6 deletions.
diff --git a/examples/dvh_analysis.ipynb b/examples/dvh_analysis.ipynb
@@ -128,6 +128,15 @@
     "dvh = calculate_dvh_for_labels(dose, structures)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dvh"
+   ]
+  },
   {
    "attachments": {},
    "cell_type": "markdown",
@@ -146,13 +155,12 @@
    "source": [
     "# Reshape the DVH\n",
     "plt_dvh = dvh\n",
-    "plt_dvh.set_index(\"label\")\n",
-    "plt_dvh.transpose()\n",
+    "plt_dvh = plt_dvh.set_index(\"label\")\n",
     "plt_dvh = plt_dvh.iloc[:,3:].transpose()\n",
     "\n",
     "# Plot the DVH\n",
     "fig, ax = plt.subplots()\n",
-    "plt_dvh.plot(ax=ax, kind=\"line\", colormap=plt.cm.get_cmap(\"viridis\"), legend=False)\n",
+    "plt_dvh.plot(ax=ax, kind=\"line\", colormap=plt.cm.get_cmap(\"rainbow\"), legend=False)\n",
     "\n",
     "# Add labels and show plot\n",
     "plt.legend(loc='best')\n",
@@ -218,6 +226,8 @@
     "    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",
     "    title=\"TCGA_CV_5977 Dose Metrics\")"
    ]
   },

diff --git a/platipy/imaging/visualisation/dose.py b/platipy/imaging/visualisation/dose.py
@@ -58,7 +58,8 @@ def visualise_dose(
     structure_for_limits=None,
     expansion_for_limits=10,
     title="",
-    contour_cmap=plt.cm.get_cmap("inferno"),
+    contour_cmap=plt.cm.get_cmap("rainbow"),
+    dose_cmap=plt.cm.get_cmap("inferno"),
     structure_name_dict=None,
     img_vis_kw=None,
 ):
@@ -86,6 +87,8 @@ def visualise_dose(
             to 10.
         title (str, optional): Title to display on visualisation. Defaults to "".
         contour_cmap (plt.cm.colormap, optional): Matplotlib color map to use for contour colors.
+            Defaults to plt.cm.get_cmap("rainbow").
+        dose_cmap (plt.cm.colormap, optional): Matplotlib color map to use for dose colors.
             Defaults to plt.cm.get_cmap("inferno").
         structure_name_dict (dict, optional): Dictionary to map alternative structure names.
             Defaults to None.
@@ -158,12 +161,12 @@ def visualise_dose(
     vis.add_scalar_overlay(
         dose,
         discrete_levels=int(max_val / round_to_nearest),
-        colormap=contour_cmap,
+        colormap=dose_cmap,
         alpha=0.5,
         max_value=max_val,
         name="Dose (Gy)",
     )
-    vis.add_contour(structures, show_legend=False)
+    vis.add_contour(structures, show_legend=False, colormap=contour_cmap)
 
     if structure_for_limits is not None:
         vis.set_limits_from_label(structure_for_limits, expansion=expansion_for_limits)