Add script to profile

scripts/processing/02-maxwell_filtering.py

@@ -89,4 +89,5 @@ def run_filter(subject_id):
         raw.save(raw_out, overwrite=True)
 
 
-run_filter(subject_id=1)  # Only for sub01.
+if __name__ == '__main__':
+    run_filter(subject_id=1)  # Only for sub01.

scripts/processing/02-python_filtering.py

@@ -66,5 +66,6 @@ def run_filter(subject_id):
         raw.save(raw_out, overwrite=True)
 
 
-parallel, run_func, _ = parallel_func(run_filter, n_jobs=N_JOBS)
-parallel(run_func(subject_id) for subject_id in range(1, 20))
+if __name__ == '__main__':
+    parallel, run_func, _ = parallel_func(run_filter, n_jobs=N_JOBS)
+    parallel(run_func(subject_id) for subject_id in range(1, 20))

scripts/processing/03-run_extract_events.py

@@ -38,5 +38,7 @@ def run_events(subject_id):
         fname_events = op.join(data_path, 'run_%02d_filt_sss-eve.fif' % run)
         mne.write_events(fname_events, events)
 
-parallel, run_func, _ = parallel_func(run_events, n_jobs=N_JOBS)
-parallel(run_func(subject_id) for subject_id in range(1, 20))
+
+if __name__ == '__main__':
+    parallel, run_func, _ = parallel_func(run_events, n_jobs=N_JOBS)
+    parallel(run_func(subject_id) for subject_id in range(1, 20))

scripts/processing/04-run_ica.py

@@ -44,6 +44,7 @@ def run_ica(subject_id, tsss=False):
         ica.save(ica_name)
 
 
-parallel, run_func, _ = parallel_func(run_ica, n_jobs=N_JOBS)
-parallel(run_func(subject_id) for subject_id in range(1, 20))
-run_ica(1, True)
+if __name__ == '__main__':
+    parallel, run_func, _ = parallel_func(run_ica, n_jobs=N_JOBS)
+    parallel(run_func(subject_id) for subject_id in range(1, 20))
+    run_ica(1, True)

scripts/processing/05-make_epochs.py

@@ -129,9 +129,10 @@ def run_epochs(subject_id, tsss=False):
                     % (subject, l_freq)))
 
 
-###############################################################################
-# Let us make the script parallel across subjects
+if __name__ == '__main__':
+    ###########################################################################
+    # Let us make the script parallel across subjects
 
-parallel, run_func, _ = parallel_func(run_epochs, n_jobs=1)
-parallel(run_func(subject_id) for subject_id in range(1, 20))
-run_epochs(1, True)  # run on maxwell filtered data
+    parallel, run_func, _ = parallel_func(run_epochs, n_jobs=1)
+    parallel(run_func(subject_id) for subject_id in range(1, 20))
+    run_epochs(1, True)  # run on maxwell filtered data

scripts/processing/06-make_evoked.py

@@ -65,6 +65,7 @@ def run_evoked(subject_id, tsss=False):
                  % (subject, l_freq)))
 
 
-parallel, run_func, _ = parallel_func(run_evoked, n_jobs=N_JOBS)
-parallel(run_func(subject_id) for subject_id in range(1, 20))
-run_evoked(1, True)  # run on maxwell filtered data
+if __name__ == '__main__':
+    parallel, run_func, _ = parallel_func(run_evoked, n_jobs=N_JOBS)
+    parallel(run_func(subject_id) for subject_id in range(1, 20))
+    run_evoked(1, True)  # run on maxwell filtered data

scripts/processing/07-time_frequency.py

@@ -46,5 +46,6 @@ def run_time_frequency(subject_id):
                        overwrite=True)
 
 
-parallel, run_func, _ = parallel_func(run_time_frequency, n_jobs=N_JOBS)
-parallel(run_func(subject_id) for subject_id in range(1, 20))
+if __name__ == '__main__':
+    parallel, run_func, _ = parallel_func(run_time_frequency, n_jobs=N_JOBS)
+    parallel(run_func(subject_id) for subject_id in range(1, 20))

scripts/processing/08-run_time_decoding.py

@@ -26,7 +26,7 @@
 # Then we write a function to do time decoding on one subject
 
 
-def run_time_decoding(subject_id, condition1, condition2):
+def run_time_decoding(subject_id, condition1='face', condition2='scrambled'):
     subject = "sub%03d" % subject_id
     data_path = os.path.join(meg_dir, subject)
     epochs = mne.read_epochs(os.path.join(data_path,
@@ -72,8 +72,9 @@ def run_time_decoding(subject_id, condition1, condition2):
 #    This may take a large amount of memory because the epochs will be
 #    replicated for each parallel job
 
-parallel, run_func, _ = parallel_func(run_time_decoding, n_jobs=N_JOBS)
-parallel(run_func(subject_id, 'face', 'scrambled')
-         for subject_id in range(1, 20))
-parallel(run_func(subject_id, 'face/famous', 'face/unfamiliar')
-         for subject_id in range(1, 20))
+if __name__ == '__main__':
+    parallel, run_func, _ = parallel_func(run_time_decoding, n_jobs=N_JOBS)
+    parallel(run_func(subject_id, 'face', 'scrambled')
+             for subject_id in range(1, 20))
+    parallel(run_func(subject_id, 'face/famous', 'face/unfamiliar')
+             for subject_id in range(1, 20))

scripts/processing/09-group_average_sensors.py

@@ -15,10 +15,10 @@
 
 exclude = [1, 5, 16]  # Excluded subjects
 
-for run in range(1, 20):
-    if run in exclude:
+for subject_id in range(1, 20):
+    if subject_id in exclude:
         continue
-    subject = "sub%03d" % run
+    subject = "sub%03d" % subject_id
     print("processing subject: %s" % subject)
     data_path = op.join(meg_dir, subject)
 

scripts/processing/12-make_forward.py

@@ -47,5 +47,6 @@ def run_forward(subject_id):
     mne.write_forward_solution(fname_fwd, fwd, overwrite=True)
 
 
-parallel, run_func, _ = parallel_func(run_forward, n_jobs=N_JOBS)
-parallel(run_func(subject_id) for subject_id in range(1, 20))
+if __name__ == '__main__':
+    parallel, run_func, _ = parallel_func(run_forward, n_jobs=N_JOBS)
+    parallel(run_func(subject_id) for subject_id in range(1, 20))

scripts/processing/14-group_average_source.py

@@ -41,10 +41,12 @@ def morph_stc(subject_id):
     return morphed
 
 
-parallel, run_func, _ = parallel_func(morph_stc, n_jobs=N_JOBS)
-stcs = parallel(run_func(subject_id) for subject_id in range(1, 20)
-                if subject_id not in exclude)
-
-data = np.average([s.data for s in stcs], axis=0)
-stc = mne.SourceEstimate(data, stcs[0].vertices, stcs[0].tmin, stcs[0].tstep)
-stc.save(op.join(meg_dir, 'contrast-average'))
+if __name__ == '__main__':
+    parallel, run_func, _ = parallel_func(morph_stc, n_jobs=N_JOBS)
+    stcs = parallel(run_func(subject_id) for subject_id in range(1, 20)
+                    if subject_id not in exclude)
+
+    data = np.average([s.data for s in stcs], axis=0)
+    stc = mne.SourceEstimate(data, stcs[0].vertices, stcs[0].tmin,
+                             stcs[0].tstep)
+    stc.save(op.join(meg_dir, 'contrast-average'))

scripts/processing/15-lcmv_beamformer.py

@@ -35,5 +35,6 @@ def run_inverse(subject_id):
     stc.save(op.join(data_path, 'mne_LCMV_inverse-contrast'))
 
 
-parallel, run_func, _ = parallel_func(run_inverse, n_jobs=N_JOBS)
-parallel(run_func(subject_id) for subject_id in range(1, 20))
+if __name__ == '__main__':
+    parallel, run_func, _ = parallel_func(run_inverse, n_jobs=N_JOBS)
+    parallel(run_func(subject_id) for subject_id in range(1, 20))

scripts/processing/profile.py

@@ -0,0 +1,23 @@
+import time
+from importlib import import_module
+from memory_profiler import memory_usage
+
+subject_id = 1
+
+filenames = ['02-python_filtering', '03-run_extract_events',
+             '04-run_ica', '05-make_epochs', '06-make_evoked',
+             '07-time_frequency', '08-run_time_decoding',
+             '12-make_forward', '13-make_inverse', '14-group_average_source']
+
+funcs = ['run_filter', 'run_events', 'run_ica', 'run_epochs',
+         'run_evoked', 'run_time_frequency', 'run_time_decoding',
+         'run_forward', 'run_inverse', 'morph_stc']
+
+times, memory = list(), list()
+for fname, func in zip(filenames, funcs):
+    t1 = time.time()
+    mod = import_module(fname)
+    func, args, kwargs = getattr(mod, func), (subject_id, ), {}
+    mem = memory_usage((func, args, kwargs), max_usage=True)
+    times.append(t1 - time.time())
+    memory.append(mem)