FIX: use cleaner import for joblib

README.rst

@@ -20,6 +20,7 @@ Dependencies
 * scipy
 * numpy
 * matplotlib
+* joblib (optional for parallel processing)
 
 Installation
 ============
@@ -28,6 +29,10 @@ We recommend the `Anaconda Python distribution <https://www.continuum.io/downloa
 
 	$ conda install numpy matplotlib scipy
 
+For joblib, you can do::
+
+	$ pip install joblib
+
 Additionally, you would need Neuron which is available here: `https://neuron.yale.edu/neuron/ <https://neuron.yale.edu/neuron/>`_
 
 If you want to install the latest version of the code (nightly) use::

examples/plot_simulate_evoked.py

@@ -33,14 +33,16 @@
 
 ###############################################################################
 # Now let's simulate the dipole
+# You can simulate multiple trials in parallel by using n_jobs > 1
 net = Network(params)
-dpl = simulate_dipole(net, n_jobs=3, n_trials=3)
+dpls = simulate_dipole(net, n_jobs=1, n_trials=2)
 
 ###############################################################################
 # and then plot it
 import matplotlib.pyplot as plt
 fig, axes = plt.subplots(2, 1, sharex=True, figsize=(6, 6))
-dpl.plot(ax=axes[0])
+for dpl in dpls:
+    dpl.plot(ax=axes[0])
 
 ###############################################################################
 # Finally, we can also plot the spikes.

mne_neuron/dipole.py

@@ -6,7 +6,7 @@
 import numpy as np
 from numpy import convolve, hamming
 
-from joblib import Parallel, delayed
+from .parallel import _parallel_func
 
 
 def _hammfilt(x, winsz):
@@ -87,6 +87,11 @@ def prsimtime():
     pc.gid_clear()
     pc.done()
     dpl = Dipole(np.array(t_vec.to_python()), dpl_data)
+    if rank == 0:
+        dpl.baseline_renormalize(net.params)
+        dpl.convert_fAm_to_nAm()
+        dpl.scale(net.params['dipole_scalefctr'])
+        dpl.smooth(net.params['dipole_smooth_win'] / h.dt)
     return dpl
 
 
@@ -105,12 +110,11 @@ def simulate_dipole(net, n_trials=1, n_jobs=1):
 
     Returns
     -------
-    dpl: instance of Dipole
-        The dipole object
+    dpl: list | instance of Dipole
+        The dipole object or list of dipole objects if n_trials > 1
     """
-    dpl = Parallel(n_jobs=n_jobs)(
-        delayed(_simulate_single_trial)(net.params)
-        for i in range(n_trials))
+    parallel, myfunc = _parallel_func(_simulate_single_trial, n_jobs=n_jobs)
+    dpl = parallel(myfunc(net.params) for _ in range(n_trials))
 
     return dpl
 

mne_neuron/parallel.py

@@ -2,6 +2,8 @@
 
 # Authors: Blake Caldwell <blake_caldwell@brown.edu>
 
+from warnings import warn
+
 from neuron import h
 
 rank = 0
@@ -18,3 +20,21 @@ def create_parallel_context(n_jobs=1):
 
     if rank == 0:
         pc.gid_clear()
+
+
+def _parallel_func(func, n_jobs):
+    if n_jobs != 1:
+        try:
+            from joblib import Parallel, delayed
+        except ImportError:
+            warn('joblib not installed. Cannot run in parallel.')
+            n_jobs = 1
+    if n_jobs == 1:
+        n_jobs = 1
+        my_func = func
+        parallel = list
+    else:
+        parallel = Parallel(n_jobs)
+        my_func = delayed(func)
+
+    return parallel, my_func