each traces_times value has to be a Quantity now, fixed time array in…

… eFEL calc + docs

brian2modelfitting/modelfitting/metric.py

@@ -1,8 +1,8 @@
 import abc
 import efel
 from itertools import repeat
-from brian2 import Hz, second, Quantity
-from brian2.units.fundamentalunits import check_units
+from brian2 import Hz, second, Quantity, ms, us
+from brian2.units.fundamentalunits import check_units, in_unit
 from numpy import (array, sum, square, reshape, abs, amin, digitize,
                    rint, arange, atleast_2d, NaN, float64, split, shape,)
 
@@ -73,7 +73,7 @@ def get_gamma_factor(model, data, delta, time, dt):
 def calc_eFEL(traces, inp_times, feat_list, dt):
     out_traces = []
     for i, trace in enumerate(traces):
-        time = arange(0, len(trace)*dt, dt)
+        time = arange(0, len(trace))*dt/ms
         temp_trace = {}
         temp_trace['T'] = time
         temp_trace['V'] = trace
@@ -82,7 +82,6 @@ def calc_eFEL(traces, inp_times, feat_list, dt):
         out_traces.append(temp_trace)
 
     results = efel.getFeatureValues(out_traces, feat_list)
-
     return results
 
 
@@ -257,6 +256,13 @@ def feat_to_err(self, d1, d2):
         return err
 
     def get_features(self, traces, output, n_traces, dt):
+        if self.traces_times[0][0] is Quantity:
+            for n, trace in enumerate(self.traces_times):
+                t_start, t_end = trace[0], trace[1]
+                t_start = t_start / ms
+                t_end = t_end / ms
+                self.traces_times[n] = [t_start, t_end]
+
         n_times = shape(self.traces_times)[0]
 
         if (n_times != (n_traces)):
@@ -279,7 +285,7 @@ def get_features(self, traces, output, n_traces, dt):
         for ii in arange(sl):
             temp_trace = temp_traces[ii]
             temp_feat = calc_eFEL(temp_trace, self.traces_times,
-                                  self.feat_list)
+                                  self.feat_list, dt)
             self.check_values(temp_feat)
             features.append(temp_feat)
 

docs_sphinx/metric/index.rst

@@ -87,22 +87,22 @@ To get all of the eFEL features you can run the following code:
 
 To define the :py:class:`~brian2modelfitting.modelfitting.metric.FeatureMetric`, user has to define following input parameters:
 
-- ``traces_times`` - list of times indicating start and end of input current, has to be specified for each of input traces
+- ``traces_times`` - list of times indicating start and end of input current, has to be specified for each of input traces, each value has to be a :py:class:`~brian2.units.fundamentalunits.Quantity`
 - ``feat_list`` - list of strings with names of features to be used
 - ``combine`` - function to be used to compare features between output and simulated traces, (for `combine=None`, subtracts the features)
 
 Example code usage:
 
 .. code:: python
 
-  traces_times = [[50, 100], [50, 100], [50, 100], [50, 100]]
+  traces_times = [[50*ms, 100*ms], [50*ms, 100*ms], [50*ms, 100*ms], [50, 100*ms]]
   feat_list = ['voltage_base', 'time_to_first_spike', 'Spikecount']
   metric = FeatureMetric(traces_times, feat_list, combine=None)
 
 .. note::
 
   If times of stimulation are same for all of the traces, user can specify a single list that will be replicated for
-  ``eFEL`` library: ``traces_times = [[50, 100]]``.
+  ``eFEL`` library: ``traces_times = [[50*ms, 100*ms]]``.
 
 
 

examples/hh_nevergrad_eFEL.py

@@ -42,8 +42,8 @@
 ## Optimization and Metric Choice
 n_opt = NevergradOptimizer()
 
-# traces_times = [[50, 100], [50, 100], [50, 100], [50, 100]]
-traces_times = [[50, 100]]
+# traces_times = [[5*ms, 10*ms]]
+traces_times = [[0.005*second, 0.010*second]]
 feat_list = ['voltage_base', 'time_to_first_spike', 'Spikecount', ]
 metric = FeatureMetric(traces_times, feat_list)
 
@@ -54,7 +54,7 @@
                      param_init={'v': -65*mV},
                      method='exponential_euler',)
 
-res, error = fitter.fit(n_rounds=5,
+res, error = fitter.fit(n_rounds=1,
                         optimizer=n_opt, metric=metric,
                         callback='progressbar',
                         gl = [1e-09 *siemens, 1e-07 *siemens],
@@ -70,10 +70,13 @@
 ## Visualization of the results
 start_scope()
 fits = fitter.generate_traces(params=None, param_init={'v': -65*mV})
+trace = out_traces[0]
+time = arange(0, len(trace)*dt/ms, dt/ms)
+# print(time[-1])
 
 fig, ax = plt.subplots(ncols=4, figsize=(20,5))
-ax[0].plot(out_traces[0].transpose())
-ax[0].plot(fits[0].transpose()/mV)
+ax[0].plot(time, out_traces[0].transpose())
+ax[0].plot(time,fits[0].transpose()/mV)
 
 ax[1].plot(out_traces[1].transpose())
 ax[1].plot(fits[1].transpose()/mV)