Differences

This shows you the differences between two versions of the page.

--- manual:python_binary_toolkit [2016/08/10 18:14] – created zenke
+++ manual:python_binary_toolkit [2016/08/30 18:19] – [Auryn Python binary tools] zenke
@@ Line 1: / Line 1: @@
-====== Auryn Python toolkit ======
+====== Auryn Python binary tools ======
 Auryn v0.8.0 is the first version to come with a set of Python tools which allow decoding from binary files generated with [[BinarySpikeMonitor]] or [[BinaryStateMonitor]]. You can find the Python code in the ''tools/python'' directory.
+To use the Auryn tools point your Python path to the ''auryn/tools/python'' directory. For instance by
+<code>
+export PYTHONPATH=$PYTHONPATH:<path_to_auryn_src_directory>/tools/python
+</code>
 ===== Example: Plot spikes from spk file =====
@@ Line 12: / Line 16: @@
 import numpy as np
 import pylab as pl
-from auryn_binary_tools import *
+from auryntools import *
 filename  =  "/tmp/coba.0.e.spk"
@@ Line 38: / Line 42: @@
 import numpy as np
 import pylab as pl
-from auryn_binary_tools import *
+from auryntools import *
 num_mpi_ranks = 4
@@ Line 67: / Line 71: @@
 import numpy as np
 import pylab as pl
-from auryn_binary_tools import *
+from auryntools import *
 datadir = "/home/zenke/data/sim" # Set this to your local data path
@@ Line 99: / Line 103: @@
 {{ :manual:python_receptive_fields.png?500 |}}
 as you can see the neuron here is torn between being selective to a square and a triangle.
+===== Example: Get membrane potential from BinaryStateMonitor file =====
+Finally, here is an example of howto read binary state monitor files:
+<code python>
+import numpy as np
+import pylab as pl
+from auryntools import *
+# This code snipped assumes that you have run the example simulation
+# sim_epsp_binmon with default parameters and adjusted the below
+# filename to its output.
+filename  =  "../../build/release/examples/out_epsp.0.bmem"
+t_from=0.2
+t_to  =2.5
+sf = AurynBinaryStateFile(filename)
+mem = np.array(sf.get_data(t_from, t_to))
+pl.plot(mem[:,0], mem[:,1])
+pl.xlabel("Time [s]")
+pl.ylabel("Membrane potential [V]")
+pl.show()
+</code>
+{{ :manual:python_membrane.png?500 |}}