add plot to notebook

kiriclope · Sep 18, 2023 · 6d42f4a · 6d42f4a
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diff --git a/notebooks/doc.ipynb b/notebooks/doc.ipynb
diff --git a/org/doc.org b/org/doc.org
@@ -146,3 +146,67 @@ Then one just runs the model with
   saving data to /home/leon/tmp/rnn_numba/data/simul/test.h5
   Elapsed (with compilation) = 7.218026272952557s
 #+end_example
+
+
+** analysis
+
+#+begin_src ipython
+import pandas as pd
+from src.analysis.decode import decode_bump
+#+end_src
+
+#+RESULTS:
+
+#+begin_src ipython
+  df = pd.read_hdf("/home/leon/tmp/rnn_numba/data/simul/test.h5", mode="r")
+  print(df.head())
+#+end_src
+
+#+RESULTS:
+:       rates        ff       h_E  neurons   time
+: 0  3.899561  3.440118 -5.947128        0  0.499
+: 1  1.512104 -1.030196 -5.946676        1  0.499
+: 2  4.634333  8.938921 -5.946227        2  0.499
+: 3  3.354177  8.559323 -5.945780        3  0.499
+: 4  1.629222 -2.949507 -5.945335        4  0.499
+
+#+begin_src ipython
+  data = df.groupby(['time'])['rates'].apply(decode_bump).reset_index()
+  data[['m0', 'm1', 'phase']] = pd.DataFrame(data['rates'].tolist(), index=data.index)
+  data = data.drop(columns=['rates'])
+
+  print(data.head())
+#+end_src
+
+#+RESULTS:
+:     time        m0        m1     phase
+: 0  0.499  2.169205  0.090843  5.330103
+: 1  0.999  2.160349  0.099340  1.362622
+: 2  1.499  6.259074  7.082152  3.131938
+: 3  1.999  5.858699  5.441624  3.103535
+: 4  2.499  5.864153  5.443271  3.108716
+
+#+begin_src ipython
+  fig, ax = plt.subplots(1, 3, figsize=[2*width, height])
+
+  sns.lineplot(data=data, x='time', y='m0', legend=False, lw=2, ax=ax[0])
+  ax[0].set_xlabel('Time (s)')
+  ax[0].set_ylabel('$\mathcal{F}_0 (Hz)$')
+  ax[1].set_xticks([0, 1, 2, 3, 4])
+
+  sns.lineplot(x=data['time'], y=data['m1']/data['m0'], legend=False, lw=2, ax=ax[1])
+  ax[1].set_xlabel('Time (s)')
+  ax[1].set_ylabel('$\mathcal{F}_1 / \mathcal{F}_0$')
+  ax[1].set_xticks([0, 1, 2, 3, 4])
+
+  sns.lineplot(x=data['time'], y=data['phase']*180/np.pi, legend=False, lw=2, ax=ax[2])
+  ax[2].set_xlabel('Time (s)')
+  ax[2].set_ylabel('$\phi$ (°)')
+  ax[2].set_xticks([0, 1, 2, 3, 4])
+  ax[2].set_yticks([0, 90, 180, 270, 360])
+  plt.show()
+
+#+end_src
+
+#+RESULTS:
+[[file:./.ob-jupyter/7403f6ea654a97566db3dd1a7c8dffd5322bb6cd.png]]
diff --git a/src/analysis/pev.py b/src/analysis/pev.py
diff --git a/src/loops/bump_I0.py b/src/loops/bump_I0.py
diff --git a/src/loops/bump_I0_J0.py b/src/loops/bump_I0_J0.py
diff --git a/src/loops/bump_I0_S0.py b/src/loops/bump_I0_S0.py
diff --git a/src/loops/bump_J0_J1.py b/src/loops/bump_J0_J1.py
diff --git a/src/loops/bump_diff.py b/src/loops/bump_diff.py
diff --git a/src/loops/bump_drift.py b/src/loops/bump_drift.py
diff --git a/src/loops/bump_gain.py b/src/loops/bump_gain.py