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test_kcsd.py
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test_kcsd.py
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# -*- coding: utf-8 -*-
"""
Unit tests for the kCSD methods
This was written by :
Chaitanya Chintaluri,
Laboratory of Neuroinformatics,
Nencki Institute of Exprimental Biology, Warsaw.
:license: Modified BSD, see LICENSE.txt for details.
"""
import unittest
import neo
import numpy as np
import quantities as pq
from elephant import current_source_density as CSD
import elephant.current_source_density_src.utility_functions as utils
class KCSD1D_TestCase(unittest.TestCase):
def setUp(self):
self.ele_pos = utils.generate_electrodes(dim=1).reshape(5, 1)
self.csd_profile = utils.gauss_1d_dipole
pots = CSD.generate_lfp(self.csd_profile, self.ele_pos)
self.pots = np.reshape(pots, (-1, 1))
self.test_method = 'KCSD1D'
self.test_params = {'h': 50.}
temp_signals = []
for ii in range(len(self.pots)):
temp_signals.append(self.pots[ii])
self.an_sigs = neo.AnalogSignal(np.array(temp_signals).T * pq.mV,
sampling_rate=1000 * pq.Hz)
self.an_sigs.annotate(coordinates=self.ele_pos * pq.mm)
def test_kcsd1d_estimate(self, cv_params={}):
self.test_params.update(cv_params)
result = CSD.estimate_csd(self.an_sigs, method=self.test_method,
**self.test_params)
self.assertEqual(result.t_start, 0.0 * pq.s)
self.assertEqual(result.sampling_rate, 1000 * pq.Hz)
self.assertEqual(result.times, [0.] * pq.s)
self.assertEqual(len(result.annotations.keys()), 1)
true_csd = self.csd_profile(result.annotations['x_coords'])
rms = np.linalg.norm(np.array(result[0, :]) - true_csd)
rms /= np.linalg.norm(true_csd)
self.assertLess(rms, 0.5, msg='RMS between trueCSD and estimate > 0.5')
def test_valid_inputs(self):
self.test_method = 'InvalidMethodName'
self.assertRaises(ValueError, self.test_kcsd1d_estimate)
self.test_method = 'KCSD1D'
self.test_params = {'src_type': 22}
self.assertRaises(KeyError, self.test_kcsd1d_estimate)
self.test_method = 'KCSD1D'
self.test_params = {'InvalidKwarg': 21}
self.assertRaises(TypeError, self.test_kcsd1d_estimate)
cv_params = {'InvalidCVArg': np.array((0.1, 0.25, 0.5))}
self.assertRaises(TypeError, self.test_kcsd1d_estimate, cv_params)
class KCSD2D_TestCase(unittest.TestCase):
def setUp(self):
xx_ele, yy_ele = utils.generate_electrodes(dim=2, res=9,
xlims=[0.05, 0.95],
ylims=[0.05, 0.95])
self.ele_pos = np.vstack((xx_ele, yy_ele)).T
self.csd_profile = utils.large_source_2D
pots = CSD.generate_lfp(
self.csd_profile,
xx_ele,
yy_ele,
resolution=100)
self.pots = np.reshape(pots, (-1, 1))
self.test_method = 'KCSD2D'
self.test_params = {'gdx': 0.25, 'gdy': 0.25, 'R_init': 0.08,
'h': 50., 'xmin': 0., 'xmax': 1.,
'ymin': 0., 'ymax': 1.}
temp_signals = []
for ii in range(len(self.pots)):
temp_signals.append(self.pots[ii])
self.an_sigs = neo.AnalogSignal(np.array(temp_signals).T * pq.mV,
sampling_rate=1000 * pq.Hz)
self.an_sigs.annotate(coordinates=self.ele_pos * pq.mm)
def test_kcsd2d_estimate(self, cv_params={}):
self.test_params.update(cv_params)
result = CSD.estimate_csd(self.an_sigs, method=self.test_method,
**self.test_params)
self.assertEqual(result.t_start, 0.0 * pq.s)
self.assertEqual(result.sampling_rate, 1000 * pq.Hz)
self.assertEqual(result.times, [0.] * pq.s)
self.assertEqual(len(result.annotations.keys()), 2)
true_csd = self.csd_profile(result.annotations['x_coords'],
result.annotations['y_coords'])
rms = np.linalg.norm(np.array(result[0, :]) - true_csd)
rms /= np.linalg.norm(true_csd)
self.assertLess(rms, 0.5, msg='RMS ' + str(rms) +
'between trueCSD and estimate > 0.5')
def test_moi_estimate(self):
result = CSD.estimate_csd(self.an_sigs, method='MoIKCSD',
MoI_iters=10, lambd=0.0,
gdx=0.2, gdy=0.2)
self.assertEqual(result.t_start, 0.0 * pq.s)
self.assertEqual(result.sampling_rate, 1000 * pq.Hz)
self.assertEqual(result.times, [0.] * pq.s)
self.assertEqual(len(result.annotations.keys()), 2)
def test_valid_inputs(self):
self.test_method = 'InvalidMethodName'
self.assertRaises(ValueError, self.test_kcsd2d_estimate)
self.test_method = 'KCSD2D'
self.test_params = {'src_type': 22}
self.assertRaises(KeyError, self.test_kcsd2d_estimate)
self.test_params = {'InvalidKwarg': 21}
self.assertRaises(TypeError, self.test_kcsd2d_estimate)
cv_params = {'InvalidCVArg': np.array((0.1, 0.25, 0.5))}
self.assertRaises(TypeError, self.test_kcsd2d_estimate, cv_params)
class KCSD3D_TestCase(unittest.TestCase):
def setUp(self):
xx_ele, yy_ele, zz_ele = utils.generate_electrodes(dim=3, res=5,
xlims=[0.15, 0.85],
ylims=[0.15, 0.85],
zlims=[0.15, 0.85])
self.ele_pos = np.vstack((xx_ele, yy_ele, zz_ele)).T
self.csd_profile = utils.gauss_3d_dipole
pots = CSD.generate_lfp(self.csd_profile, xx_ele, yy_ele, zz_ele)
self.pots = np.reshape(pots, (-1, 1))
self.test_method = 'KCSD3D'
self.test_params = {'gdx': 0.05, 'gdy': 0.05, 'gdz': 0.05,
'lambd': 5.10896977451e-19, 'src_type': 'step',
'R_init': 0.31, 'xmin': 0., 'xmax': 1., 'ymin': 0.,
'ymax': 1., 'zmin': 0., 'zmax': 1.}
temp_signals = []
for ii in range(len(self.pots)):
temp_signals.append(self.pots[ii])
self.an_sigs = neo.AnalogSignal(np.array(temp_signals).T * pq.mV,
sampling_rate=1000 * pq.Hz)
self.an_sigs.annotate(coordinates=self.ele_pos * pq.mm)
def test_kcsd3d_estimate(self, cv_params={}):
self.test_params.update(cv_params)
result = CSD.estimate_csd(self.an_sigs, method=self.test_method,
**self.test_params)
self.assertEqual(result.t_start, 0.0 * pq.s)
self.assertEqual(result.sampling_rate, 1000 * pq.Hz)
self.assertEqual(result.times, [0.] * pq.s)
self.assertEqual(len(result.annotations.keys()), 3)
true_csd = self.csd_profile(result.annotations['x_coords'],
result.annotations['y_coords'],
result.annotations['z_coords'])
rms = np.linalg.norm(np.array(result[0, :]) - true_csd)
rms /= np.linalg.norm(true_csd)
self.assertLess(rms, 0.5, msg='RMS ' + str(rms) +
' between trueCSD and estimate > 0.5')
def test_valid_inputs(self):
self.test_method = 'InvalidMethodName'
self.assertRaises(ValueError, self.test_kcsd3d_estimate)
self.test_method = 'KCSD3D'
self.test_params = {'src_type': 22}
self.assertRaises(KeyError, self.test_kcsd3d_estimate)
self.test_params = {'InvalidKwarg': 21}
self.assertRaises(TypeError, self.test_kcsd3d_estimate)
cv_params = {'InvalidCVArg': np.array((0.1, 0.25, 0.5))}
self.assertRaises(TypeError, self.test_kcsd3d_estimate, cv_params)
if __name__ == '__main__':
unittest.main()