Move LFP tests to separate file

hnn_core/lfp.py

@@ -129,6 +129,8 @@ class _LFPElectrode:
         Extracellular conductivity in mS/cm (uniform for simplicity)
     pc : instance of h.ParallelContext()
         ParallelContext instance for running in parallel
+    cvode : instanse of h.CVode
+        Multi order variable time step integration method.
     method : str
         'psa' (default), i.e., point source approximation or line source
         approximation, i.e., 'lsa'

hnn_core/tests/test_lfp.py

@@ -0,0 +1,57 @@
+# Authors: Nick Tolley <nicholas_tolley@brown.edu>
+
+from copy import deepcopy
+import os.path as op
+import pytest
+
+import hnn_core
+from hnn_core import read_params, Network
+
+
+def test_lfp():
+    """Test LFP recording API."""
+    hnn_core_root = op.dirname(hnn_core.__file__)
+    params_fname = op.join(hnn_core_root, 'param', 'default.json')
+    params = read_params(params_fname)
+    # add rhythmic inputs (i.e., a type of common input)
+    params.update({'input_dist_A_weight_L2Pyr_ampa': 5.4e-5,
+                   'input_dist_A_weight_L5Pyr_ampa': 5.4e-5,
+                   't0_input_dist': 50,
+                   'input_prox_A_weight_L2Pyr_ampa': 5.4e-5,
+                   'input_prox_A_weight_L5Pyr_ampa': 5.4e-5,
+                   't0_input_prox': 50})
+    net = Network(deepcopy(params), add_drives_from_params=True)
+
+    # Test LFP electrodes
+    kwargs_default = {
+        'electrode_pos': (2, 2, 400),
+        'sigma': 3.0, 'method': 'psa'}
+    net.add_electrode(**kwargs_default)
+    kwargs_default['electrode_pos'] = [(2, 2, 400), (6, 6, 800)]
+    net.add_electrode(**kwargs_default)
+    assert len(net.lfp) == 3
+    with pytest.raises(AssertionError):
+        kwargs = kwargs_default.copy()
+        kwargs['electrode_pos'] = [(2, 2), (6, 6, 800)]
+        net.add_electrode(**kwargs)
+    with pytest.raises(AssertionError):
+        kwargs = kwargs_default.copy()
+        kwargs['sigma'] = -1.0
+        net.add_electrode(**kwargs)
+
+    match = "Invalid value for the 'method' parameter"
+    with pytest.raises(ValueError, match=match):
+        kwargs = kwargs_default.copy()
+        kwargs['method'] = 'LSA'
+        net.add_electrode(**kwargs)
+
+    bad_kwargs = [
+        ('electrode_pos', '[(2, 2, 400), (6, 6, 800)]'),
+        ('electrode_pos', (2, '2', 400)),
+        ('sigma', '3.0'), ('method', 3.0)]
+    for arg, item in bad_kwargs:
+        kwargs = kwargs_default.copy()
+        kwargs[arg] = item
+        match = 'must be an instance of'
+        with pytest.raises(TypeError, match=match):
+            net.add_electrode(**kwargs)

hnn_core/tests/test_network.py

@@ -210,40 +210,6 @@ def test_network():
     net.clear_connectivity()
     assert len(net.connectivity) == 0
 
-    # Test LFP electrodes
-    kwargs_default = {
-        'electrode_pos': (2, 2, 400),
-        'sigma': 3.0, 'method': 'psa'}
-    net.add_electrode(**kwargs_default)
-    kwargs_default['electrode_pos'] = [(2, 2, 400), (6, 6, 800)]
-    net.add_electrode(**kwargs_default)
-    assert len(net.lfp) == 3
-    with pytest.raises(AssertionError):
-        kwargs = kwargs_default.copy()
-        kwargs['electrode_pos'] = [(2, 2), (6, 6, 800)]
-        net.add_electrode(**kwargs)
-    with pytest.raises(AssertionError):
-        kwargs = kwargs_default.copy()
-        kwargs['sigma'] = -1.0
-        net.add_electrode(**kwargs)
-
-    match = "Invalid value for the 'method' parameter"
-    with pytest.raises(ValueError, match=match):
-        kwargs = kwargs_default.copy()
-        kwargs['method'] = 'LSA'
-        net.add_electrode(**kwargs)
-
-    bad_kwargs = [
-        ('electrode_pos', '[(2, 2, 400), (6, 6, 800)]'),
-        ('electrode_pos', (2, '2', 400)),
-        ('sigma', '3.0'), ('method', 3.0)]
-    for arg, item in bad_kwargs:
-        kwargs = kwargs_default.copy()
-        kwargs[arg] = item
-        match = 'must be an instance of'
-        with pytest.raises(TypeError, match=match):
-            net.add_electrode(**kwargs)
-
 
 def test_tonic_biases():
     """Test tonic biases."""