Changeset 455 for trunk

Timestamp:

08/24/10 18:28:25 (21 months ago)

Author:

mpereira

Message:

removed dependency of signals/analogs.py on analysis. added support for SpikeTrain objects to analysis.crosscorrelate()

Location:

trunk

Files:

• src/analysis.py (modified) (4 diffs)
• src/signals/analogs.py (modified) (1 diff)
• test/test_analysis.py (modified) (1 diff)

trunk/src/analysis.py

@@ -16 +16 @@
 
 ccf                       - fast cross correlation function based on fft
+crosscorrelate            - cross-correlation between two series of discrete
+                            events (e.g. spikes)
 simple_frequency_spectrum - Simple frequencxy spectrum
 arrays_almost_equal       - comparison of two arrays
+make_kernel               - creates kernel functions for convolution
 """
 
 import os, numpy
-from NeuroTools import check_dependency
+from NeuroTools import check_dependency, signals
 
 def arrays_almost_equal(a, b, threshold):
@@ -96 +99 @@
      
     Inputs:
-        sua1      - array of event times. Can be either a column/row vector.
-        sua2      - array of event times. Can be either a column/row vector.
+        sua1      - array of event times. Can be either a column/row vector or a
+                    member of the SpikeTrain class.
+        sua2      - array of event times. Can be either a column/row vector or a
+                    member of the SpikeTrain class.
                     If sua2 == sua1 the result is the
                     autocorrelogram.
@@ -134 +139 @@
     Examples:
         >> crosscorrelate(numpy_array1, numpy_array2)
-        >> crosscorrelate(spike_train1.spike_times, spike_train2.spike_times)
-        >> crosscorrelate(spike_train1.spike_times, spike_train2.spike_times,
-                          lag = 150.0)
-        >> crosscorrelate(spike_train1.spike_times, spike_train2.spike_times,
-                          display=True, kwargs={'bins':100})
+        >> crosscorrelate(spike_train1, spike_train2)
+        >> crosscorrelate(spike_train1, spike_train2, lag = 150.0)
+        >> crosscorrelate(spike_train1, spike_train2, display=True,
+                          kwargs={'bins':100})
             
     See also:
@@ -149 +153 @@
     sua = []
     for x in (sua1, sua2):
-        if x.ndim == 1:
+        if isinstance(x, signals.SpikeTrain):
+            sua.append(x.spike_times)
+        elif x.ndim == 1:
             sua.append(x)
         elif x.ndim == 2 and (x.shape[0] == 1 or x.shape[1] == 1):

trunk/src/signals/analogs.py

@@ -32 +32 @@
 
 import os, re, numpy
-from NeuroTools import check_dependency, check_numpy_version, analysis
+from NeuroTools import check_dependency, check_numpy_version
 from NeuroTools.io import *
 from NeuroTools.plotting import get_display, set_axis_limits, set_labels, SimpleMultiplot

trunk/test/test_analysis.py

@@ -29 +29 @@
         #Used for the testcases of the crosscorrelate function
         spk = signals.load_spikelist('analysis/crosscorrelate/spike_data')
-        self.spk0 = spk[0].spike_times
-        self.spk1 = spk[1].spike_times
+        self.spk0 = spk[0]
+        self.spk1 = spk[1]
 
     def testSimpleFrequencySpectrum(self):