Added spike train example

miladh · Nov 30, 2018 · b7965a1 · b7965a1
1 parent c35bbd8
commit b7965a1
Show file tree

Hide file tree

Showing 6 changed files with 42 additions and 5 deletions.
diff --git a/docs/images/generate_spiketrain.gif b/docs/images/generate_spiketrain.gif
diff --git a/docs/images/raster.png b/docs/images/raster.png
diff --git a/docs/source/examples.rst b/docs/source/examples.rst
@@ -20,3 +20,4 @@ Natural scenes
     :maxdepth: 1
 
     examples/natural_stimulus
+    examples/generate_spiketrain
diff --git a/docs/source/examples/generate_spiketrain.rst b/docs/source/examples/generate_spiketrain.rst
@@ -0,0 +1,32 @@
+.. _generate_spiketrain:
+
+Generate spike trains
+=====================
+
+In this example a static image is shown in 80 ms after a 40 ms delay.
+
+.. literalinclude:: ../../../examples/generate_spiketrain.py
+    :language: python
+    :lines: 1-26
+
+The calculated rates can be converted to spikes via a nonstationary Poisson process:
+
+.. literalinclude:: ../../../examples/generate_spiketrain.py
+    :language: python
+    :lines: 28-42
+
+In the animation below the generated spikes at each location are shown as dots:
+
+.. figure:: ../../images/generate_spiketrain.gif
+      :scale: 100 %
+      :align: center
+
+A simple raster plot of individual locations can be created using:
+
+.. literalinclude:: ../../../examples/generate_spiketrain.py
+    :language: python
+    :lines: 44
+
+.. figure:: ../../images/raster.png
+      :scale: 100 %
+      :align: center
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -33,6 +33,7 @@ Examples
   * :ref:`einevoll_2012`.
 
   * :ref:`natural_stimulus`.
+  * :ref:`generate_spiketrain`.
 
 
 

diff --git a/examples/generate_spiketrain.py b/examples/generate_spiketrain.py
@@ -1,14 +1,13 @@
 import pylgn
 import pylgn.kernels.spatial as spl
 import pylgn.kernels.temporal as tpl
-import pylgn.tools as tls
 import quantities as pq
 
 # create network
 network = pylgn.Network()
 
 # create integrator
-integrator = network.create_integrator(nt=7, nr=7, dt=1*pq.ms, dr=1*pq.deg)
+integrator = network.create_integrator(nt=7, nr=7, dt=2*pq.ms, dr=0.4*pq.deg)
 
 # create kernels
 Wg_r = spl.create_dog_ft()
@@ -19,15 +18,17 @@
 
 # create stimulus
 stimulus = pylgn.stimulus.create_natural_image(filenames="natural_scene.png",
-                                               delay=10*pq.ms,
-                                               duration=50*pq.ms)
+                                               delay=40*pq.ms,
+                                               duration=80*pq.ms)
 network.set_stimulus(stimulus, compute_fft=True)
 
 # compute
 network.compute_response(ganglion)
-rates = ganglion.response
+
+import pylgn.tools as tls
 
 # apply static nonlinearity and scale rates
+rates = ganglion.response
 rates = tls.heaviside_nonlinearity(rates)
 rates = tls.scale_rates(rates, 60*pq.Hz)
 
@@ -39,3 +40,5 @@
                                   times=integrator.times,
                                   positions=integrator.positions,
                                   title="Spike activity")
+
+pylgn.plot.raster_plot(spike_trains.flatten()[::200])