hippocampus demo

examples/plot_rat_hippocampus_foraging.py

@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+"""
+Decode location from CA1 activity
+==============================
+
+This is an example of how to decode location in a free field from CA1 activity
+
+"""
+
+from neuroglia.datasets import fetch_rat_hippocampus_foraging
+
+dataset = fetch_rat_hippocampus_foraging()
+
+#########################################
+# Let's plot the path in the free field
+
+import matplotlib.pyplot as plt
+plt.plot(dataset.location['x'], dataset.location['y'], alpha=0.5)
+plt.axis('equal')
+plt.show()
+
+#########################################
+# Create a feature vector for each time point in the location data
+
+from neuroglia.spike import Binner
+
+binner = Binner(sample_times=dataset.location['time'])
+response = binner.fit_transform(dataset.spikes)
+print(response.head())
+
+#########################################
+# create feature
+
+
+from sklearn.linear_model import LinearRegression
+lm = LinearRegression()
+
+split = int(len(response)/2)
+
+X_train = response.values[:split]
+y_train = dataset.location['x'].values[:split]
+
+lm.fit(X_train,y_train)
+
+
+X_test = response.values[split:]
+y_test = dataset.location['x'].values[split:-1]
+y_pred = lm.predict(X_test)
+plt.plot(y_test[:100])
+plt.plot(y_pred[:100])
+plt.show()

setup.py

@@ -33,6 +33,7 @@
  'pandas',
  'xarray',
  'scikit-learn',
+ 'requests',
  ],
  classifiers=[
  'Development Status :: 2 - Pre-Alpha',