From a14225bf9d6594e65d5d77e243578907cc504986 Mon Sep 17 00:00:00 2001
From: Martin Kim <46072231+martinkim0@users.noreply.github.com>
Date: Thu, 7 Dec 2023 11:05:02 -0800
Subject: [PATCH] Fix stereoscope tutorial (#196)

---
 spatial/stereoscope_heart_LV_tutorial.ipynb | 39 +++++++--------------
 1 file changed, 12 insertions(+), 27 deletions(-)

diff --git a/spatial/stereoscope_heart_LV_tutorial.ipynb b/spatial/stereoscope_heart_LV_tutorial.ipynb
index ff7facb..d1c3d5d 100644
--- 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": {