Add import_dipole function

hnn_core/__init__.py

@@ -2,7 +2,7 @@
 
 load_custom_mechanisms()
 
-from .dipole import simulate_dipole
+from .dipole import simulate_dipole, import_dipole
 from .feed import ExtFeed
 from .params import Params, read_params
 from .network import Network

hnn_core/dipole.py

@@ -133,6 +133,24 @@ def simulate_dipole(net, n_trials=1, n_jobs=1):
     net.spikegids = spikegids
     return dpl
 
+def import_dipole(fname, units='nAm'):
+    """Read dipole values from a file and create a Dipole instance.
+
+    Parameters
+    ----------
+    fname : str
+        Full path to the input file (.txt)
+
+    Returns
+    -------
+    dpl : Dipole
+        The instance of Dipole class
+    """
+    dpl_data = np.loadtxt(fname, dtype=float)
+    dpl = Dipole(dpl_data[:, 0], dpl_data[:, 1:4])
+    if units=='nAm':
+        dpl.units = units
+    return dpl
 
 class Dipole(object):
     """Dipole class.
@@ -277,7 +295,7 @@ def write(self, fname):
         Outputs
         -------
         txt file at fname where rows correspond to samples
-            and columns, delimited by \\t, correspond to 
+            and columns, delimited by \\t, correspond to
             1) time (s),
             2) aggregate current dipole (scaled nAm),
             3) L2/3 current dipole (scaled nAm), and

hnn_core/network.py

@@ -557,23 +557,22 @@ def write_spikes(self, fname, trial_idx=None):
         with open(fname, 'w') as f:
             for spk_idx in range(len(spiketimes)):
                 f.write('{:.3f}\t{}\t{}\n'.format(spiketimes[spk_idx],
-                    int(spikegids[spk_idx]), gidtypes[spk_idx]))
+                        int(spikegids[spk_idx]), gidtypes[spk_idx]))
 
     def read_spikes(self, fname, append_trial=True):
         """Read spike times from a file.
 
         Parameters
         ----------
         fname : str
-            Full path to the output file (.txt)
+            Full path to the input file (.txt)
         append_trials : bool
             If True, append the contents of fname
             (i.e., as a trial) to the spike-related
             attributes of Network instance. If False,
             all spikes of the Network instance will
             be overwritten.
         """
-
         spike_data = np.loadtxt(fname, dtype=str)
         spiketimes = spike_data[:,0].astype(float)
         spikegids = spike_data[:,1].astype(float)