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) chidx = neo.ChannelIndex(range(len(self.pots))) chidx.analogsignals.append(self.an_sigs) chidx.coordinates = self.ele_pos * pq.mm chidx.create_relationship()
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) chidx = neo.ChannelIndex(range(len(self.pots))) chidx.analogsignals.append(self.an_sigs) chidx.coordinates = self.ele_pos * pq.mm chidx.create_relationship()
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(temp_signals * pq.mV, sampling_rate=1000 * pq.Hz) chidx = neo.ChannelIndex(range(len(self.pots))) chidx.analogsignals.append(self.an_sigs) chidx.coordinates = self.ele_pos * pq.mm chidx.create_relationship()
def setUp(self): xx_ele, yy_ele, zz_ele = utils.generate_electrodes(dim=3) self.lfp = csd.generate_lfp(utils.gauss_3d_dipole, xx_ele, yy_ele, zz_ele) self.params = {} self.params['KCSD3D'] = {'gdx': 0.1, 'gdy': 0.1, 'gdz': 0.1, 'src_type': 'step', 'Rs': np.array((0.1, 0.25, 0.5))}
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 setUp(self): self.ele_pos = utils.generate_electrodes(dim=1).reshape(5, 1) self.lfp = csd.generate_lfp(utils.gauss_1d_dipole, self.ele_pos) self.csd_method = csd.estimate_csd self.params = {} # Input dictionaries for each method self.params['DeltaiCSD'] = {'sigma_top': 0. * pq.S / pq.m, 'diam': 500E-6 * pq.m} self.params['StepiCSD'] = {'sigma_top': 0. * pq.S / pq.m, 'tol': 1E-12, 'diam': 500E-6 * pq.m} self.params['SplineiCSD'] = {'sigma_top': 0. * pq.S / pq.m, 'num_steps': 201, 'tol': 1E-12, 'diam': 500E-6 * pq.m} self.params['StandardCSD'] = {} self.params['KCSD1D'] = {'h': 50., 'Rs': np.array((0.1, 0.25, 0.5))}
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.} self.an_sigs = [] for ii in range(len(self.pots)): rc = neo.RecordingChannel() rc.coordinate = self.ele_pos[ii] * pq.mm asig = neo.AnalogSignal(self.pots[ii] * pq.mV, sampling_rate=1000 * pq.Hz) rc.analogsignals = [asig] rc.create_relationship() self.an_sigs.append(asig)
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(temp_signals * pq.mV, sampling_rate=1000 * pq.Hz) chidx = neo.ChannelIndex(range(len(self.pots))) chidx.analogsignals.append(self.an_sigs) chidx.coordinates = self.ele_pos * pq.mm chidx.create_relationship()
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, res=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.} self.an_sigs = [] for ii in range(len(self.pots)): rc = neo.RecordingChannel() rc.coordinate = self.ele_pos[ii] * pq.mm asig = neo.AnalogSignal(self.pots[ii] * pq.mV, sampling_rate=1000 * pq.Hz) rc.analogsignals = [asig] rc.create_relationship() self.an_sigs.append(asig)
def test_lfp3d_electrodes(self): ele_pos = utils.generate_electrodes(dim=3, res=3) xx_ele, yy_ele, zz_ele = ele_pos lfp = csd.generate_lfp(utils.gauss_3d_dipole, xx_ele, yy_ele, zz_ele) self.assertEqual(len(ele_pos), 3) self.assertEqual(xx_ele.shape[0], len(lfp))
def test_lfp3d_electrodes(self): ele_pos = utils.generate_electrodes(dim=3, res=3) xx_ele, yy_ele, zz_ele = ele_pos lfp = csd.generate_lfp(utils.gauss_3d_dipole, xx_ele, yy_ele, zz_ele) self.assertEqual(len(ele_pos), 3) self.assertEqual(xx_ele.shape[0], lfp.shape[1])
def test_lfp2d_electrodes(self): ele_pos = utils.generate_electrodes(dim=2) xx_ele, yy_ele = ele_pos lfp = csd.generate_lfp(utils.large_source_2D, xx_ele, yy_ele) self.assertEqual(len(ele_pos), 2) self.assertEqual(xx_ele.shape[0], lfp.shape[1])
def test_lfp1d_electrodes(self): ele_pos = utils.generate_electrodes(dim=1).reshape(5, 1) lfp = csd.generate_lfp(utils.gauss_1d_dipole, ele_pos) self.assertEqual(ele_pos.shape[1], 1) self.assertEqual(ele_pos.shape[0], lfp.shape[1])
def setUp(self): xx_ele, yy_ele = utils.generate_electrodes(dim=2) self.lfp = csd.generate_lfp(utils.large_source_2D, xx_ele, yy_ele) self.params = {} # Input dictionaries for each method self.params['KCSD2D'] = {'sigma': 1., 'Rs': np.array((0.1, 0.25, 0.5))}
def test_lfp2d_electrodes(self): ele_pos = utils.generate_electrodes(dim=2) xx_ele, yy_ele = ele_pos lfp = csd.generate_lfp(utils.large_source_2D, xx_ele, yy_ele) self.assertEqual(len(ele_pos), 2) self.assertEqual(xx_ele.shape[0], len(lfp))
def test_lfp1d_electrodes(self): ele_pos = utils.generate_electrodes(dim=1).reshape(5, 1) lfp = csd.generate_lfp(utils.gauss_1d_dipole, ele_pos) self.assertEqual(ele_pos.shape[1], 1) self.assertEqual(ele_pos.shape[0], len(lfp))