Move sKCSD utility functions to a separate file (#100)

* Move sKCSD utility functions to a separate file

* Remove script for an unnecessary figure

* Remove sKCSD_utils from utility_functions

And correct all executions of its objects

* Move sKCSD utility functions to a separate file

* Remove script for an unnecessary figure

* Remove sKCSD_utils from utility_functions

And correct all executions of its objects

* Delete import loop

* Update docstrings

* Define undefined variable

* Allow for execution of make_fig_2 in any directory

To use sinsyn.mod, which is compiled into neuron, it needs to be
compiled in current working directory hence copy sinsyn.mod to current
working directory. Remove sinsym.mod from figures/sKCSD_paper, because
sinsyn.mod will be copied there anyway.

* Same syntax for sKCSD_utils import in all figure scripts

Author: Joanna Jędrzejewska-Szmek

figures/kCSD_properties/skcsd_and_l_curve.py

@@ -4,7 +4,7 @@
 import matplotlib.pyplot as plt
 import sys
 from kcsd import sKCSD
-import kcsd.utility_functions as utils
+from kcsd import sKCSD_utils as utils
 import kcsd.validation.plotting_functions as pl
 sys.path.insert(1, os.path.join(sys.path[0], '../sKCSD_paper'))
 import sKCSD_utils

figures/kCSD_properties/skcsd_and_l_curve_complex_morphology.py

@@ -5,7 +5,7 @@
 import sys
 import os
 from kcsd import sKCSD, sKCSDcell, KCSD3D
-import kcsd.utility_functions as utils
+from kcsd import sKCSD_utils as utils
 import kcsd.validation.plotting_functions as pl
 import sKCSD_utils
 import run_LFP
@@ -141,7 +141,8 @@
             pass
 
 
-        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)
         skcsd = cell_itself.transform_to_3D(skcsd)
 
         ax[(i+1)//3, (i+1)%3].imshow(morpho,

figures/sKCSD_paper/make_fig_10.py

@@ -4,19 +4,22 @@
 from distutils.spawn import find_executable, spawn
 import shutil
 import subprocess
+from kcsd import sample_data_path
 if find_executable('nrnivmodl') is not None:
     for path in ['x86_64', 'i686', 'powerpc']:
         if os.path.isdir(path):
             shutil.rmtree(path)
     spawn([find_executable('nrnivmodl')])
+    sinsyn_loc = os.path.join(sample_data_path, "sinsyn.mod")
+    subprocess.call(["cp", sinsyn_loc, os.getcwd()])
     subprocess.call(["nrnivmodl", "sinsyn.mod"])
 else:
     print("""nrnivmodl script not found in PATH, thus NEURON .mod files could
     not be compiled, and LFPy.test() functions will fail""")
 import numpy as np
 import matplotlib.pyplot as plt
 from kcsd import sKCSD
-import kcsd.utility_functions as utils
+from kcsd import sKCSD_utils as utils
 import sKCSD_utils
 from kcsd.validation import plotting_functions as pl
 

figures/sKCSD_paper/make_fig_2.py

@@ -4,7 +4,7 @@
 import sys
 import os
 from kcsd import sKCSD
-import kcsd.utility_functions as utils
+from kcsd import sKCSD_utils as utils
 import kcsd.validation.plotting_functions as pl
 import sKCSD_utils
 n_src = 512

figures/sKCSD_paper/make_fig_3.py

@@ -4,7 +4,7 @@
 import sys
 import os
 from kcsd import sKCSD, KCSD3D, sKCSDcell
-import kcsd.utility_functions as utils
+from  kcsd import sKCSD_utils as utils
 import kcsd.validation.plotting_functions as pl
 import sKCSD_utils
 
@@ -151,7 +151,8 @@
         try:
             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_object = sKCSDcell(morphology, ele_pos, n_src)
             est_skcsd = cell_itself[i].transform_to_3D(skcsd)
 
 

figures/sKCSD_paper/make_fig_5.py

@@ -4,7 +4,7 @@
 import sys
 import os
 from kcsd import sKCSD
-import kcsd.utility_functions as utils
+from kcsd import sKCSD_utils as utils
 import kcsd.validation.plotting_functions as pl
 import sKCSD_utils
 n_src = 512

figures/sKCSD_paper/make_fig_6.py

@@ -4,7 +4,7 @@
 import sys
 import os
 from kcsd import sKCSD
-import kcsd.utility_functions as utils
+from kcsd import sKCSD_utils as utils
 import kcsd.validation.plotting_functions as pl
 import sKCSD_utils
 dt = 0.5
@@ -36,7 +36,8 @@
                              electrode_orientation=2,
                              simulate_what='symmetric',
                              dt=dt)
-    data = utils.LoadData(c.return_paths_skCSD_python())
+    new_path = c.return_paths_skCSD_python()
+    data = utils.LoadData(new_path)
     ele_pos = data.ele_pos/scale_factor
     pots = data.LFP/scale_factor_LFP
     morphology = data.morphology

figures/sKCSD_paper/make_fig_7.py

@@ -4,7 +4,7 @@
 import sys
 import os
 from kcsd import sKCSD, sKCSDcell, KCSD3D
-import kcsd.utility_functions as utils
+from kcsd import sKCSD_utils as utils
 import kcsd.validation.plotting_functions as pl
 import sKCSD_utils
 n_src = 1024
@@ -115,7 +115,8 @@
     except NameError:
         pass
 
-    skcsd, pot, cell_obj = utils.load_sim(path)
+    skcsd, pot, morphology, ele_pos, n_src = utils.load_sim(path)
+    cell_object = sKCSDcell(morphology, ele_pos, n_src)
     est_skcsd = cell_itself.transform_to_3D(skcsd)
 
     skcsd_seg = cell_itself.transform_to_segments(skcsd)

figures/sKCSD_paper/make_fig_8.py

@@ -5,7 +5,7 @@
 import sys
 import os
 from kcsd import sKCSD, sKCSDcell
-import kcsd.utility_functions as utils
+from  kcsd import sKCSD_utils as utils
 import kcsd.validation.plotting_functions as pl
 import sKCSD_utils
 import numpy.random
@@ -124,7 +124,8 @@
             pass
 
 
-        est_skcsd, est_pot, cell_obj = utils.load_sim(path)
+        est_skcsd, est_pot, morphology, ele_pos, n_src = utils.load_sim(path)
+        cell_object = sKCSDcell(morphology, ele_pos, n_src)
         est_skcsd = cell.transform_to_3D(est_skcsd)
         L1.append(sKCSD_utils.L1_error(ground_truth_grid, est_skcsd))
         if nl == 0: