Merge branch 'master' into remove_lmfit

brian2modelfitting/metric.py

@@ -7,7 +7,7 @@
 except ImportError:
     warnings.warn('eFEL package not found.')
 from itertools import repeat
-from brian2 import Hz, second, Quantity, ms, us, get_dimensions
+from brian2 import Hz, second, Quantity, ms, us, get_dimensions, mV
 from brian2.units.fundamentalunits import check_units, in_unit, DIMENSIONLESS
 from numpy import (array, sum, abs, amin, digitize, rint, arange, inf, NaN,
                    clip, mean)
@@ -101,7 +101,7 @@ def calc_eFEL(traces, inp_times, feat_list, dt):
         time = arange(0, len(trace))*dt/ms
         temp_trace = {}
         temp_trace['T'] = time
-        temp_trace['V'] = array(trace, copy=False)
+        temp_trace['V'] = trace/mV
         temp_trace['stim_start'] = [inp_times[i][0]]
         temp_trace['stim_end'] = [inp_times[i][1]]
         out_traces.append(temp_trace)

brian2modelfitting/tests/test_metric.py

@@ -226,8 +226,8 @@ def test_calc_EFL():
     results = calc_eFEL(voltage, inp_times, ['voltage_base'], dt=dt)
     assert len(results) == 2
     assert all(res.keys() == {'voltage_base'} for res in results)
-    assert_almost_equal(results[0]['voltage_base'], float(-60*mV))
-    assert_almost_equal(results[1]['voltage_base'], float(-70*mV))
+    assert_almost_equal(results[0]['voltage_base'], -60)
+    assert_almost_equal(results[1]['voltage_base'], -70)
 
 
 def test_get_features_feature_metric():
@@ -251,9 +251,9 @@ def test_get_features_feature_metric():
     assert len(results) == 3
     assert all(isinstance(r, dict) for r in results)
     assert all(r.keys() == {'voltage_base'} for r in results)
-    assert_almost_equal(results[0]['voltage_base'], np.array([2.5*mV, 5*mV]))
+    assert_almost_equal(results[0]['voltage_base'], [2.5, 5])
     assert_almost_equal(results[1]['voltage_base'], [0, 0])
-    assert_almost_equal(results[2]['voltage_base'], np.array([2.5*mV, 5*mV]))
+    assert_almost_equal(results[2]['voltage_base'], [2.5, 5])
 
     # Custom comparison: squared difference
     feature_metric = FeatureMetric(inp_times, ['voltage_base'],
@@ -262,9 +262,9 @@ def test_get_features_feature_metric():
     assert len(results) == 3
     assert all(isinstance(r, dict) for r in results)
     assert all(r.keys() == {'voltage_base'} for r in results)
-    assert_almost_equal(results[0]['voltage_base'], np.array([(2.5*mV)**2, (5*mV)**2]))
+    assert_almost_equal(results[0]['voltage_base'], [2.5**2, 5**2])
     assert_almost_equal(results[1]['voltage_base'], [0, 0])
-    assert_almost_equal(results[2]['voltage_base'], np.array([(2.5*mV)**2, (5*mV)**2]))
+    assert_almost_equal(results[2]['voltage_base'], [2.5**2, 5**2])
 
 
 def test_get_errors_feature_metric():