Merge pull request #19 from PKU-NIP-Lab/develop

update doc

README.rst

@@ -156,11 +156,11 @@ Neurodynamics simulation
     </table>
 
 
-More neuron examples please see `neurons <https://github.com/PKU-NIP-Lab/BrainPy/tree/master/examples/neurons>`_.
+More neuron examples please see `examples/neurons <https://github.com/PKU-NIP-Lab/BrainPy/tree/master/examples/neurons>`_.
 
-More synapse examples please see `synapses <https://github.com/PKU-NIP-Lab/BrainPy/tree/master/examples/synapses>`_.
+More synapse examples please see `examples/synapses <https://github.com/PKU-NIP-Lab/BrainPy/tree/master/examples/synapses>`_.
 
-More network examples please see `networks <https://github.com/PKU-NIP-Lab/BrainPy/tree/master/examples/networks>`_.
+More network examples please see `examples/networks <https://github.com/PKU-NIP-Lab/BrainPy/tree/master/examples/networks>`_.
 
 
 Neurodynamics analysis
@@ -173,7 +173,7 @@ Neurodynamics analysis
         <tr>
             <td border="0" width="30%">
                 <a href="examples/dynamics_analysis/phase_portrait_of_NaK_model.py">
-                <img src="docs/images/phase_plane_analysis.png">
+                <img src="docs/images/phase_plane_analysis1.png">
                 </a>
             </td>
             <td border="0" valign="top">
@@ -210,6 +210,6 @@ Neurodynamics analysis
 
 
 More examples please see
-`dynamics analysis <https://github.com/PKU-NIP-Lab/BrainPy/tree/master/examples/dynamics_analysis>`_.
+`examples/dynamics_analysis <https://github.com/PKU-NIP-Lab/BrainPy/tree/master/examples/dynamics_analysis>`_.
 
 

examples/dynamics_analysis/phase_portrait_of_NaK_model.py

@@ -23,7 +23,6 @@
 
 import brainpy as bp
 import brainpy.numpy as np
-from brainpy.dynamics import PhasePortraitAnalyzer
 
 bp.profile.set(dt=0.01)
 
@@ -113,16 +112,16 @@ def update(ST, _t_):
 
 NaK_neuron = get_NaK_model()
 
-group = bp.NeuGroup(NaK_neuron, 1, monitors=['V'])
-group.run(50., inputs=('ST.inp', 50.))
-bp.visualize.line_plot(group.mon.ts, group.mon.V, ylabel='Potential (mV)', show=True)
-
-pp = PhasePortraitAnalyzer(model=NaK_neuron,
-                           target_vars=OrderedDict(V=[-90, 20], n=[0., 1.]),
-                           fixed_vars={'input': 50., 'inp': 50.})
-pp.plot_nullcline()
-pp.plot_vector_filed()
-pp.plot_fixed_point()
-pp.plot_trajectory([(-10, 0.2, 100.), (-80, 0.4, 100.)],
-                   show=True)
-
+# group = bp.NeuGroup(NaK_neuron, 1, monitors=['V'])
+# group.run(50., inputs=('ST.inp', 50.))
+# bp.visualize.line_plot(group.mon.ts, group.mon.V, ylabel='Potential (mV)', show=True)
+
+analyzer = bp.PhasePortraitAnalyzer(
+    model=NaK_neuron,
+    target_vars=OrderedDict(V=[-90, 20], n=[0., 1.]),
+    fixed_vars={'input': 50., 'inp': 50.})
+analyzer.plot_nullcline()
+analyzer.plot_vector_filed()
+analyzer.plot_fixed_point()
+analyzer.plot_trajectory([(-10, 0.2, 100.), (-80, 0.4, 100.)],
+                         show=True)