Merge 47233d3 into 829cdf3

LFPy · Oct 9, 2020 · 6c8078d · 6c8078d
2 parents 829cdf3 + 47233d3
commit 6c8078d
Show file tree

Hide file tree

Showing 5 changed files with 36 additions and 24 deletions.
diff --git a/LFPy/__init__.py b/LFPy/__init__.py
@@ -60,7 +60,8 @@
 from .version import version as __version__
 from .pointprocess import Synapse, PointProcess, StimIntElectrode
 from lfpykit import RecExtElectrode, RecMEAElectrode, CurrentDipoleMoment, \
-    PointSourcePotential, LineSourcePotential, OneSphereVolumeConductor
+    PointSourcePotential, LineSourcePotential, OneSphereVolumeConductor, \
+    LaminarCurrentSourceDensity
 from .cell import Cell
 from .templatecell import TemplateCell
 from .network import NetworkCell, NetworkPopulation, Network

diff --git a/LFPy/eegmegcalc.py b/LFPy/eegmegcalc.py
@@ -75,7 +75,7 @@ class FourSphereVolumeConductor(lfpykit.eegmegcalc.FourSphereVolumeConductor):
     >>> # current dipole moment
     >>> p = np.array([[10., 10., 10.]]*10) # 10 timesteps [nA µm]
     >>> # compute potential
-    >>> sphere_model.calc_potential(p, rz)  # [mV]
+    >>> sphere_model.get_dipole_potential(p, rz)  # [mV]
     array([[1.06247669e-08, 1.06247669e-08, 1.06247669e-08, 1.06247669e-08,
             1.06247669e-08, 1.06247669e-08, 1.06247669e-08, 1.06247669e-08,
             1.06247669e-08, 1.06247669e-08],
@@ -96,7 +96,7 @@ def __init__(self,
                          sigmas=sigmas,
                          iter_factor=iter_factor)
 
-    def calc_potential_from_multi_dipoles(self, cell, timepoints=None):
+    def get_dipole_potential_from_multi_dipoles(self, cell, timepoints=None):
         """
         Return electric potential from multiple current dipoles from cell.
 
@@ -141,7 +141,7 @@ def calc_potential_from_multi_dipoles(self, cell, timepoints=None):
         >>> MD_4s = FourSphereVolumeConductor(radii,
         >>>                                   sigmas,
         >>>                                   electrode_locs)
-        >>> phi = MD_4s.calc_potential_from_multi_dipoles(cell,
+        >>> phi = MD_4s.get_dipole_potential_from_multi_dipoles(cell,
         >>>                                               timepoints)
         """
         multi_p, multi_p_locs = cell.get_multi_current_dipole_moments(
@@ -150,7 +150,7 @@ def calc_potential_from_multi_dipoles(self, cell, timepoints=None):
         Ni, Nd, Nt = multi_p.shape
         potential = np.zeros((N_elec, Nt))
         for i in range(Ni):
-            pot = self.calc_potential(multi_p[i], multi_p_locs[i])
+            pot = self.get_dipole_potential(multi_p[i], multi_p_locs[i])
             potential += pot
         return potential
 

diff --git a/LFPy/test/test_eegmegcalc.py b/LFPy/test/test_eegmegcalc.py
@@ -366,7 +366,7 @@ def test_calc_zn(self):
         z1 = fs._calc_zn(n)
         np.testing.assert_almost_equal(z1, -2.16574585635359)
 
-    def test_calc_potential(self):
+    def test_get_dipole_potential(self):
         '''test comparison between four-sphere model and model for
         infinite homogeneous space
         when sigma is constant and r4 goes to infinity'''
@@ -384,13 +384,13 @@ def test_calc_potential(self):
                            [0., 40., 0.]])
         four_s = LFPy.FourSphereVolumeConductor(
             r_elec, radii, sigmas)
-        pots_4s = four_s.calc_potential(p, rz)
+        pots_4s = four_s.get_dipole_potential(p, rz)
         inf_s = LFPy.InfiniteVolumeConductor(0.3)
         pots_inf = inf_s.get_dipole_potential(p, r_elec - rz)
 
         np.testing.assert_allclose(pots_4s, pots_inf, rtol=1e-6)
 
-    def test_calc_potential01(self):
+    def test_get_dipole_potential01(self):
         '''test comparison between analytical 4S-model and FEM simulation'''
         # load data
         fem_sim = np.load(
@@ -408,15 +408,15 @@ def test_calc_potential01(self):
         fs = LFPy.FourSphereVolumeConductor(
             ele_coords, radii, sigmas)
         k_mV_to_muV = 1e3
-        pot_analytical = fs.calc_potential(
+        pot_analytical = fs.get_dipole_potential(
             p, rz).reshape(
             (len(ele_coords),)).reshape(
             pot_fem.shape) * k_mV_to_muV
         global_error = np.abs(pot_analytical - pot_fem) / \
             (np.max(np.abs(pot_fem)))
         np.testing.assert_array_less(global_error, 0.01)
 
-    def test_calc_potential02(self):
+    def test_get_dipole_potential02(self):
         '''Test radial and tangential parts of dipole sums to dipole'''
         radii = [88000, 90000, 95000, 100000]
         sigmas = [0.3, 1.5, 0.015, 0.3]
@@ -445,7 +445,7 @@ def test_calc_potential02(self):
         for i in range(len(p_locs)):
             fs = LFPy.FourSphereVolumeConductor(
                 el_locs[i], radii, sigmas)
-            phi = fs.calc_potential(dips[i].T, p_locs[i])
+            phi = fs.get_dipole_potential(dips[i].T, p_locs[i])
             if i == 0:
                 phi0 = phi[0][0]
             else:
@@ -480,12 +480,12 @@ def test_get_transformation_matrix_00(self):
         for i in range(len(p_locs)):
             fs = LFPy.FourSphereVolumeConductor(
                 el_locs[i], radii, sigmas)
-            phi = fs.calc_potential(dips[i].T, p_locs[i])
+            phi = fs.get_dipole_potential(dips[i].T, p_locs[i])
 
             M = fs.get_transformation_matrix(p_locs[i])
             np.testing.assert_allclose(M @ dips[i].T, phi)
 
-    def test_calc_potential_from_multi_dipoles00(self):
+    def test_get_dipole_potential_from_multi_dipoles00(self):
         """test comparison between multi-dipoles and single dipole approach"""
         neuron.h('forall delete_section()')
         soma = neuron.h.Section(name='soma')
@@ -511,7 +511,7 @@ def test_calc_potential_from_multi_dipoles00(self):
         p, dipole_locs = cell.get_multi_current_dipole_moments(t_point)
         Np, Nt, Nd = p.shape
         Ne = electrode_locs.shape[0]
-        pot_MD = MD_4s.calc_potential_from_multi_dipoles(cell, t_point)
+        pot_MD = MD_4s.get_dipole_potential_from_multi_dipoles(cell, t_point)
 
         cell.__del__()
 
@@ -521,13 +521,13 @@ def test_calc_potential_from_multi_dipoles00(self):
             dip_loc = dipole_locs[i]
             fs = LFPy.FourSphereVolumeConductor(
                 electrode_locs, radii, sigmas)
-            pot = fs.calc_potential(dip, dip_loc)
+            pot = fs.get_dipole_potential(dip, dip_loc)
             pot_sum += pot
 
         np.testing.assert_almost_equal(pot_MD, pot_sum)
         np.testing.assert_allclose(pot_MD, pot_sum, rtol=1E-4)
 
-    def test_calc_potential_from_multi_dipoles01(self):
+    def test_get_dipole_potential_from_multi_dipoles01(self):
         """test comparison between multi-dipoles and single dipole approach"""
         neuron.h('forall delete_section()')
         soma = neuron.h.Section(name='soma')
@@ -555,7 +555,7 @@ def test_calc_potential_from_multi_dipoles01(self):
         p, dipole_locs = cell.get_multi_current_dipole_moments(t_point)
         Np, Nt, Nd = p.shape
         Ne = electrode_locs.shape[0]
-        pot_MD = MD_4s.calc_potential_from_multi_dipoles(cell, t_point)
+        pot_MD = MD_4s.get_dipole_potential_from_multi_dipoles(cell, t_point)
 
         cell.__del__()
 
@@ -565,7 +565,7 @@ def test_calc_potential_from_multi_dipoles01(self):
             dip_loc = dipole_locs[i]
             fs = LFPy.FourSphereVolumeConductor(
                 electrode_locs, radii, sigmas)
-            pot = fs.calc_potential(dip, dip_loc)
+            pot = fs.get_dipole_potential(dip, dip_loc)
             pot_sum += pot
 
         np.testing.assert_almost_equal(pot_MD, pot_sum)

diff --git a/README.md b/README.md
@@ -90,12 +90,12 @@ but a simpler point-source method is also available. The calculations assume tha
 independent conductivity, and compartments are assumed to be at least at a minimal distance from the electrode (which can be specified by the user). For more information on
 the biophysics underlying the numerical framework used see this coming book chapter:
 
-- K.H. Pettersen, H. Linden, A.M. Dale and G.T. Einevoll: Extracellular spikes and current-source density, in *Handbook of Neural Activity Measurement*, edited by R. Brette and A. Destexhe, Cambridge, to appear (preprint PDF, 5.7MB http://arken.umb.no/~gautei/forskning/PettersenLindenDaleEinevoll-BookChapter-revised.pdf
+- K.H. Pettersen, H. Linden, A.M. Dale and G.T. Einevoll: Extracellular spikes and current-source density, in *Handbook of Neural Activity Measurement*, edited by R. Brette and A. Destexhe, Cambridge, to appear (preprint PDF, 5.7MB http://www.csc.kth.se/~helinden/PettersenLindenDaleEinevoll-BookChapter-revised.pdf
 
 The first release of LFPy (v1.x) was mainly designed for simulation extracellular potentials of single neurons, described in our paper on the package in Frontiers in Neuroinformatics entitled "LFPy: A tool for biophysical simulation of extracellular potentials generated by detailed model neurons".
-The article can be found at http://dx.doi.org/10.3389%2Ffninf.2013.00041.
+The article can be found at https://dx.doi.org/10.3389/fninf.2013.00041.
 Since version 2 (LFPy v2.x), the tool also facilitates simulations of extracellular potentials and current dipole moment from ongoing activity in recurrently connected networks of multicompartment neurons, prediction of EEG scalp surface potentials,
-MEG scalp surface magnetic fields, as described in the bioRXiv preprint "Multimodal modeling of neural network activity: computing LFP, ECoG, EEG and MEG signals with LFPy2.0" by Espen Hagen, Solveig Naess, Torbjoern V Ness, Gaute T Einevoll, found at https://doi.org/10.1101/281717.
+MEG scalp surface magnetic fields, as described in the publication "Multimodal modeling of neural network activity: computing LFP, ECoG, EEG and MEG signals with LFPy2.0" by Espen Hagen, Solveig Naess, Torbjoern V Ness, Gaute T Einevoll, found at https://dx.doi.org/10.3389/fninf.2018.00092.
 
 Citing LFPy
 -----------
@@ -117,8 +117,8 @@ For updated information on LFPy and online documentation, see the LFPy homepage
 Tutorial slides on LFPy
 -----------------------
 
-- Slides for OCNS 2019 meeting tutorial `T8: Biophysical modeling of extracellular potentials (using LFPy).` <https://www.cnsorg.org/cns-2019-tutorials#T8>_ hosted in Barcelona, Spain on LFPy: `CNS2019_LFPy_tutorial` <https://LFPy.github.io/downloads/CNS2019_LFPy_tutorial.pdf>_
-- Older tutorial slides can be found at `https://LFPy.github.io/downloads` <https://github.com/LFPy/LFPy.github.io/tree/master/downloads>_
+- Slides for OCNS 2019 meeting tutorial [T8: Biophysical modeling of extracellular potentials (using LFPy)](https://www.cnsorg.org/cns-2019-tutorials#T8) hosted in Barcelona, Spain on LFPy: [CNS2019 LFPy tutorial slides](https://LFPy.github.io/downloads/CNS2019_LFPy_tutorial.pdf "slides")
+- Older tutorial slides can be found at [https://github.com/LFPy/LFPy.github.io/tree/master/downloads](https://github.com/LFPy/LFPy.github.io/tree/master/downloads)
 
 
 Related projects
@@ -269,7 +269,7 @@ m2r2, Numpydoc and the Sphinx ReadTheDocs theme may be needed:
 Physical units in LFPy
 ----------------------
 
-Units follow the NEURON conventions found `here <https://www.neuron.yale.edu/neuron/static/docs/units/unitchart.html>`_.
+Physical units follow the NEURON conventions found [here](https://www.neuron.yale.edu/neuron/static/docs/units/unitchart.html).
 The units in LFPy for given quantities are:
 
 | Quantity                   | Symbol    | Unit      |
@@ -285,6 +285,7 @@ The units in LFPy for given quantities are:
 | Current dipole moment      | P         | [nA µm]   |
 | Magnetic field             | H         | [nA/µm]   |
 | Magnetic permeability      | µ, mu     | [T m/A]   |
+| Current Source Density     | CSD       | [nA/µm3]  |  
 
 Note: resistance, conductance and capacitance are usually specific values, i.e per membrane area (lowercase r_m, g, c_m)
 Depending on the mechanism files, some may use different units altogether, but this should be taken care of internally by NEURON.
diff --git a/doc/classes.rst b/doc/classes.rst
@@ -149,6 +149,16 @@ class :class:`MEG`
     :undoc-members:
 
 
+Current Source Density (CSD)
+============================
+
+class :class:`LaminarCurrentSourceDensity`
+------------------------------------------
+.. autoclass:: LaminarCurrentSourceDensity
+    :members:
+    :show-inheritance:
+    :undoc-members:
+
 Misc.
 =====