Fix errors provided by lint

Author: asiaszmek

figures/npx/Neuropixels_with_fitted_dipoles_model.py

@@ -1,10 +1,12 @@
+from pathlib import Path
 import kCSD2D_reconstruction_from_npx as npx
 import matplotlib.pyplot as plt
 import matplotlib.cm as cm
 import scipy
 import numpy as np
+from numpy.linalg import LinAlgError
 from scipy.signal import filtfilt, butter
-
+import DemoReadSGLXData.readSGLX as readSGLX
 
 def set_axis(ax, x, y, letter=None):
     ax.text(
@@ -198,4 +200,4 @@ def gauss2d(x, y, p):
     make_plot(ax4, k.estm_x, k.estm_y, projection.reshape(true_csd.shape), ele_pos,
                   title='Projection', cmap='bwr')
     plt.tight_layout()
-    plt.savefig('Neuropixels_with_fitted_model.png', dpi=300)
+    plt.savefig('Neuropixels_with_fitted_model.png', dpi=300)

figures/sKCSD_paper/make_fig_5.py

@@ -122,7 +122,8 @@
             utils.save_sim(path, ker)
             est_skcsd = ker.values(estimate='CSD')
         except NameError:
-            skcsd, pot, cell_obj = utils.load_sim(path)
+            skcsd, pot, morphology, ele_pos, n_src = utils.load_sim(path)
+            cell_obj =  sKCSDcell(morphology, ele_pos, n_src
             est_skcsd = cell_itself[i].transform_to_3D(skcsd)
 
         xmin = cell_itself[i].xmin

figures/sKCSD_paper/make_fig_9.py

@@ -5,7 +5,7 @@
 import sys
 import os
 from kcsd import sKCSD, sKCSDcell
-from  kcsd import sKCSD_utils as utils
+from kcsd import sKCSD_utils as utils
 import kcsd.validation.plotting_functions as pl
 import sKCSD_utils
 import numpy.random
@@ -87,6 +87,7 @@
     L1 = []
 
     for i, nl in enumerate(noise_levels):
+        new_LFP = data.LFP + noise
         if nl:
             noise = numpy.random.normal(scale=std/nl, size=shape)
             snr = np.round((new_LFP.var()**.5/noise.var()**.5))
@@ -97,7 +98,7 @@
 
         snrs.append(snr)
 
-        new_LFP = data.LFP + noise
+
 
 
 

kcsd/sKCSD_utils.py

@@ -105,7 +105,7 @@ def load_sim(path):
     morphology = np.array(cell_data['morphology'])
     ele_pos = np.array(cell_data['ele_pos'])
     n_src = cell_data['n_src']
-    return est_csd, est_pot, cell_obj, morphology, ele_pos, n_src
+    return est_csd, est_pot, morphology, ele_pos, n_src
 
 
 def load_elpos(path):