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Fixes due to changes in LFPy interface #155

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Merged
ccluri merged 1 commit into from
Dec 22, 2023
Merged

Fixes due to changes in LFPy interface #155

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25 changes: 14 additions & 11 deletions figures/sKCSD_paper/run_LFP.py
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Original file line number Diff line number Diff line change
Expand Up @@ -182,13 +182,14 @@ def save_morphology_to_file(self):
segments = self.cell.get_idx()
nseg = len(segments)
self.morphology = np.zeros((nseg+1, 7))
coords = np.array((self.cell.xstart,
self.cell.ystart,
self.cell.zstart)).T
ends = np.array((self.cell.xend,
self.cell.yend,
self.cell.zend)).T
segdiam = self.cell.diam
print(self.cell.x.shape)
coords = np.array((self.cell.x[:, 0],
self.cell.y[:, 0],
self.cell.z[:, 0])).T
ends = np.array((self.cell.x[:, 1],
self.cell.y[:, 1],
self.cell.z[:, 1])).T
segdiam = self.cell.d
parents = {}
self.morphology[0, 0] = 1
self.morphology[0, 1] = 1
Expand Down Expand Up @@ -253,7 +254,8 @@ def add_electrodes(self):
self.electrode_parameters['y'] = self.ele_coordinates[:, 1],
self.electrode_parameters['z'] = self.ele_coordinates[:, 2],
self.electrode_parameters['sigma'] = self.sigma
electrode = LFPy.RecExtElectrode(**self.electrode_parameters)
electrode = LFPy.RecExtElectrode(self.cell,
**self.electrode_parameters)
self.simulation_parameters['electrode'] = electrode

def setup_LFPy_2D_grid(self,
Expand Down Expand Up @@ -465,13 +467,14 @@ def simulate(self, stimulus=None):
self.cell.simulate(**self.simulation_parameters)

def save_LFP(self, directory=''):
self.simulation_parameters['electrode'].calc_lfp()
M = self.simulation_parameters['electrode'].get_transformation_matrix()
V_ex = M @ self.cell.imem
LFP_path = os.path.join(self.new_path, directory)
if not os.path.exists(LFP_path):
print("Creating", LFP_path)
os.makedirs(LFP_path)
fname = os.path.join(LFP_path, 'MyLFP')
np.savetxt(fname, self.simulation_parameters['electrode'].LFP)
np.savetxt(fname, V_ex)

def save_electrode_pos(self, directory=''):
electr = np.hstack((self.ele_coordinates[:, 0],
Expand Down Expand Up @@ -527,7 +530,7 @@ def save_for_R_kernel(self, directory=''):
np.savetxt(os.path.join(new_path, 'coordsend_x_y_z'),
coordsend)
# diameter of the segments
segdiam = np.hstack((self.cell.diam))
segdiam = np.hstack((self.cell.d))
np.savetxt(os.path.join(new_path, 'segdiam_x_y_z'),
segdiam)
# time in the simulation
Expand Down