fix allen errors

NeuromatchAcademy · Jul 8, 2024 · e17bbe4 · e17bbe4
1 parent 6c32c6a
commit e17bbe4
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Showing 3 changed files with 19 additions and 8 deletions.
diff --git a/projects/neurons/load_Allen_Visual_Behavior_from_SDK.ipynb b/projects/neurons/load_Allen_Visual_Behavior_from_SDK.ipynb
@@ -99,7 +99,8 @@
     "\n",
     "pd.set_option('display.max_columns', 500)\n",
     "# this line may be needed if you run into Error in pandas query function\n",
-    "pd.DataFrame.query = lambda self, expr, **kwargs: self.query(expr, engine='python', **kwargs) "
+    "# Otherwise set the engine to python in queries made throught the book\n",
+    "# pd.DataFrame.query = lambda self, expr, **kwargs: self.query(expr, engine='python', **kwargs) "
    ]
   },
   {
@@ -606,7 +607,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "stimulus_table.query('omitted').head(10)"
+    "stimulus_table.query('omitted', engine='python').head(10)"
    ]
   },
   {
@@ -637,7 +638,7 @@
     "    data=neural_data.query('cell_specimen_id == @cell_id'),\n",
     "    t='timestamps',\n",
     "    y='dff',\n",
-    "    event_times=stimulus_table.query('omitted')['start_time'],\n",
+    "    event_times=stimulus_table.query('omitted', engine='python')['start_time'],\n",
     "    t_before=3,\n",
     "    t_after=3,\n",
     "    output_sampling_rate=50,\n",
@@ -747,7 +748,7 @@
     "      data=df,\n",
     "      t='timestamps',\n",
     "      y=y,\n",
-    "      event_times=stimulus_table.query(event_query)['start_time'],\n",
+    "      event_times=stimulus_table.query(event_query, engine='python')['start_time'],\n",
     "      t_before=t_before,\n",
     "      t_after=t_before,\n",
     "      output_sampling_rate=50,\n",
@@ -1322,6 +1323,13 @@
    },
    "outputs": [],
    "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -1338,7 +1346,7 @@
    "name": "python3"
   },
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -1352,7 +1360,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.3"
+   "version": "3.9.16"
   }
  },
  "nbformat": 4,

diff --git a/projects/neurons/load_Allen_Visual_Behavior_from_pre_processed_file.ipynb b/projects/neurons/load_Allen_Visual_Behavior_from_pre_processed_file.ipynb
@@ -634,7 +634,7 @@
    "name": "python3"
   },
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -648,7 +648,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.3"
+   "version": "3.9.16"
   }
  },
  "nbformat": 4,

diff --git a/requirements.txt b/requirements.txt
@@ -10,3 +10,6 @@ pathlib
 pandas
 xkcd
 decorator==5.0.9
+h5py
+opencv-python
+torchvision