Fix stereoscope tutorial (#196)

scverse · Dec 7, 2023 · a14225b · a14225b
1 parent 84636ee
commit a14225b
Showing 1 changed file with 12 additions and 27 deletions.
diff --git a/spatial/stereoscope_heart_LV_tutorial.ipynb b/spatial/stereoscope_heart_LV_tutorial.ipynb
@@ -488,15 +488,12 @@
    },
    "outputs": [],
    "source": [
-    "train = True\n",
-    "if train:\n",
-    "    sc_model = RNAStereoscope(sc_adata)\n",
-    "    sc_model.train(max_epochs=100)\n",
-    "    sc_model.history[\"elbo_train\"][10:].plot()\n",
-    "    sc_model.save(\"scmodel\", overwrite=True)\n",
-    "else:\n",
-    "    sc_model = RNAStereoscope.load(\"scmodel\", adata=sc_adata)\n",
-    "    print(\"Loaded RNA model from file!\")"
+    "sc_model_path = os.path.join(save_dir.name, \"sc_model\")\n",
+    "\n",
+    "sc_model = RNAStereoscope(sc_adata)\n",
+    "sc_model.train(max_epochs=100)\n",
+    "sc_model.history[\"elbo_train\"][10:].plot()\n",
+    "sc_model.save(sc_model_path, overwrite=True)"
    ]
   },
   {
@@ -546,15 +543,12 @@
    },
    "outputs": [],
    "source": [
-    "train = True\n",
-    "if train:\n",
-    "    spatial_model = SpatialStereoscope.from_rna_model(st_adata, sc_model)\n",
-    "    spatial_model.train(max_epochs=2000)\n",
-    "    spatial_model.history[\"elbo_train\"][10:].plot()\n",
-    "    spatial_model.save(\"stmodel\", overwrite=True)\n",
-    "else:\n",
-    "    spatial_model = SpatialStereoscope.load(\"stmodel\", adata=st_adata)\n",
-    "    print(\"Loaded Spatial model from file!\")"
+    "spatial_model_path = os.path.join(save_dir.name, \"spatial_model\")\n",
+    "\n",
+    "spatial_model = SpatialStereoscope.from_rna_model(st_adata, sc_model)\n",
+    "spatial_model.train(max_epochs=2000)\n",
+    "spatial_model.history[\"elbo_train\"][10:].plot()\n",
+    "spatial_model.save(spatial_model_path, overwrite=True)"
    ]
   },
   {
@@ -619,15 +613,6 @@
     "    color_map=\"inferno\",\n",
     ")"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "id": "WfEk_qy0f2tA"
-   },
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {