Merge pull request #33 from alejoe91/small-changes

Small changes

Author: alejoe91

bluepyopt/ephys/efeatures.py

@@ -316,14 +316,15 @@ def __init__(
                 of channels
             stim_start (float): stimulation start time (ms)
             stim_end (float): stimulation end time (ms)
-            exp_mean (float): experimental mean of this eFeature
-            exp_std(float): experimental standard deviation of this eFeature
-            threshold(float): spike detection threshold (mV)
+            exp_mean (list of floats): experimental mean of this eFeature
+            exp_std (list of floats): experimental standard deviation
+                of this eFeature
+            threshold (float): spike detection threshold (mV)
             comment (str): comment
-            interp_step(float): interpolation step (ms)
-            double_settings(dict): dictionary with efel double settings that
+            interp_step (float): interpolation step (ms)
+            double_settings (dict): dictionary with efel double settings that
                 should be set before extracting the features
-            int_settings(dict): dictionary with efel int settings that
+            int_settings (dict): dictionary with efel int settings that
                 should be set before extracting the features
         """
 
@@ -421,7 +422,6 @@ def calculate_feature(
             responses,
             raise_warnings=False,
             return_waveforms=False,
-            verbose=False,
     ):
         from .extra_features_utils import calculate_features
 
@@ -445,21 +445,18 @@ def calculate_feature(
                 np.diff(response["time"])
         ):
             assert self.fs is not None
-            if verbose:
-                print("interpolate")
+            logger.info("extraFELFeature.calculate_feature: interpolate")
             response_interp = _interpolate_response(response, fs=self.fs)
         else:
             response_interp = response
 
         if self.fcut is not None:
-            if verbose:
-                print("filter enabled")
+            logger.info("extraFELFeature.calculate_feature: enabled")
             response_filter = _filter_response(response_interp,
                                                fcut=self.fcut,
                                                filt_type=self.filt_type)
         else:
-            if verbose:
-                print("filter disabled")
+            logger.info("extraFELFeature.calculate_feature: filter disabled")
             response_filter = response_interp
 
         ewf = _get_waveforms(response_filter, peak_times, self.ms_cut)

bluepyopt/tests/test_ephys/test_features.py

@@ -326,3 +326,34 @@ def test_extraFELFeature():
 
     assert efeature.name == name
     assert extrafel_feature_name in str(efeature)
+
+
+@pytest.mark.unit
+def test_masked_cosine_distance():
+    """ephys.efeatures: Testing masked_cosine_distance"""
+    from scipy.spatial import distance
+
+    exp = numpy.array([0.5, 0.5, 0.5])
+    model = numpy.array([0.7, 0.8, 0.4])
+
+    score = efeatures.masked_cosine_distance(exp, model)
+    assert score == distance.cosine(exp, model)
+
+    # test nan in model feature values
+    model = numpy.array([0.7, numpy.nan, 0.4])
+    score = efeatures.masked_cosine_distance(exp, model)
+    assert score == distance.cosine([0.5, 0.5], [0.7, 0.4])
+
+    # test nan in experimental feature values
+    exp = numpy.array([0.5, 0.5, numpy.nan])
+    model = numpy.array([0.7, 0.8, 0.4])
+
+    score = efeatures.masked_cosine_distance(exp, model)
+    assert score == distance.cosine([0.5, 0.5], [0.7, 0.8]) * 2. / 3.
+
+    # test na in both exp and model feature values
+    exp = numpy.array([0.5, 0.5, numpy.nan])
+    model = numpy.array([0.7, numpy.nan, 0.4])
+
+    score = efeatures.masked_cosine_distance(exp, model)
+    assert score == distance.cosine([0.5], [0.7]) * 2. / 3.

bluepyopt/tests/test_ephys/test_stimuli.py

@@ -250,7 +250,7 @@ def test_LFPySquarePulse_instantiate():
 
     lfpy_sim = ephys.simulators.LFPySimulator()
     dummy_cell = dummycells.DummyLFPyCellModel1()
-    _, lfpycell = dummy_cell.instantiate(sim=lfpy_sim)
+    _, lfpy_cell = dummy_cell.instantiate(sim=lfpy_sim)
 
     soma_loc = ephys.locations.NrnSeclistCompLocation(
         name=None,
@@ -266,8 +266,12 @@ def test_LFPySquarePulse_instantiate():
         total_duration=300
     )
 
-    stim.instantiate(sim=lfpy_sim, lfpy_cell=lfpycell)
-    lfpy_sim.run(stim.total_duration)
+    stim.instantiate(sim=lfpy_sim, lfpy_cell=lfpy_cell)
+    lfpy_sim.run(
+        lfpy_cell=lfpy_cell,
+        lfpy_electrode=dummy_cell.lfpy_electrode,
+        tstop=stim.total_duration
+    )
 
     stim.destroy(sim=lfpy_sim)
     dummy_cell.destroy(sim=lfpy_sim)

setup.py

@@ -29,8 +29,7 @@
 ]
 
 EXTRA_LFP = [
-    'MEAutility',
-    'LFPy>=2.2.0',
+    'LFPy @ git+https://github.com/LFPy/LFPy.git@mpi_optional',
 ]
 
 setuptools.setup(

tox.ini

@@ -15,12 +15,12 @@ envdir =
     py27{-unit,-functional,-style,-syntax}: {toxworkdir}/py27
     py3{5,6,7,8,9,10,}{-unit,-functional,-style,-syntax}: {toxworkdir}/py3
     docs: {toxworkdir}/docs
+extras = lfpy
 deps =
     coverage
     flake8
     mock
     neuron-nightly
-    git+https://github.com/LFPy/LFPy.git@mpi_optional
     sh
     pytest-cov
 download = true