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Start preparing manuscript.tex towards submission format and working on code

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nkoch1
2022-11-05 22:37:57 -04:00
parent 3f169ba35e
commit 72a840de23
40 changed files with 548 additions and 322 deletions
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4
Code/Sensitivity_Analysis/SA_Cb_stellate.py
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@@ -10,7 +10,7 @@ from numba import types
from numba.typed import Dict
from joblib import Parallel, delayed
import os
from Code.Functions.Utility import capacitance, stimulus_init, init_dict
from Code.Functions.Utility_fxns import capacitance, stimulus_init, init_dict
from Code.Functions.Cb_stellate_fxns import SA_Cb_stellate
# model parameters
@@ -80,7 +80,7 @@ g["Leak"] = 0.07407 * surf_area
# save folder
folder = '../Sensitivity_Analysis/Cb_stellate'
folder = '../Sensitivity_Analysis/Data/Cb_stellate'
if not os.path.isdir(folder):
os.makedirs(folder)

4
Code/Sensitivity_Analysis/SA_Cb_stellate_Delta_Kv.py
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@@ -10,7 +10,7 @@ from numba import types
from numba.typed import Dict
from joblib import Parallel, delayed
import os
from Code.Functions.Utility import capacitance, stimulus_init, init_dict
from Code.Functions.Utility_fxns import capacitance, stimulus_init, init_dict
from Code.Functions.Cb_stellate_fxns_Kv import SA_Cb_stellate_Kv
# model parameters
@@ -88,7 +88,7 @@ g["T"] = 0.45045 * surf_area
g["Leak"] = 0.07407 * surf_area
# save folder
folder = './Sensitivity_Analysis/Cb_stellate_Delta_Kv'
folder = './Sensitivity_Analysis/Data/Cb_stellate_Delta_Kv'
if not os.path.isdir(folder):
os.makedirs(folder)

29
Code/Sensitivity_Analysis/SA_Cb_stellate_Kv.py
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@@ -10,7 +10,7 @@ from numba import types
from numba.typed import Dict
from joblib import Parallel, delayed
import os
from Code.Functions.Utility import capacitance, stimulus_init, init_dict
from Code.Functions.Utility_fxns import capacitance, stimulus_init, init_dict
from Code.Functions.Cb_stellate_fxns_Kv import SA_Cb_stellate_Kv
# model parameters
@@ -87,7 +87,7 @@ g["Leak"] = 0.07407 * surf_area
# save folder
folder = './Sensitivity_Analysis/Cb_stellate_Kv'
folder = './Sensitivity_Analysis/Data/Cb_stellate_Kv'
if not os.path.isdir(folder):
os.makedirs(folder)
@@ -112,28 +112,3 @@ Parallel(n_jobs=8, verbose=9)(
slope_shift,gating, current, prominence, desired_AUC_width, folder, high, low, number_steps,
initial_period, sec, lin_array, log_array, alt_types, alt_ind, alt)
for alt_ind in range(alt_types.shape[0]) for alt in range(21))
# #%% Get pd Dataframes for certain variables
# import pandas as pd
# AUC = pd.DataFrame(columns=mutations.keys())
# AUC_rel = pd.DataFrame(columns=mutations.keys())
# rheobase = pd.DataFrame(columns=mutations.keys())
# rheobase_fit = pd.DataFrame(columns=mutations.keys())
# rheobase_null_fit = pd.DataFrame(columns=mutations.keys())
# for mut in list(mutations.keys()):
# fname = os.path.join(folder, "{}.hdf5".format(mut))
# f = h5py.File(fname, "r")
# AUC['{}'.format(mut)] = f['analysis']['AUC']
# AUC_rel['{}'.format(mut)] = f['analysis']['AUC_rel']
# rheobase['{}'.format(mut)] = f['analysis']['rheobase']
# rheobase_fit['{}'.format(mut)] = f['analysis']['rheobase_fit']
# rheobase_null_fit['{}'.format(mut)] = f['analysis']['rheobase_null_fit']
# AUC.to_json(os.path.join(folder, 'AUC.json'))
# AUC_rel.to_json(os.path.join(folder, 'AUC_rel.json'))
# rheobase.to_json(os.path.join(folder, 'rheobase.json'))
# rheobase_fit.to_json(os.path.join(folder, 'rheobase_fit.json'))
# rheobase_null_fit.to_json(os.path.join(folder, 'rheobase_null_fit.json'))

4
Code/Sensitivity_Analysis/SA_FS.py
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@@ -12,7 +12,7 @@ from numba import types
from numba.typed import Dict
from joblib import Parallel, delayed
import os
from Code.Functions.Utility import capacitance, stimulus_init, init_dict, NumpyEncoder
from Code.Functions.Utility_fxns import capacitance, stimulus_init, init_dict, NumpyEncoder
from Code.Functions.Pospischil_fxns import SA_Pospischil
@@ -89,7 +89,7 @@ g["Leak"] = 0.038 * surf_area
# folder to save to
folder = '../Sensitivity_Analysis/FS'
folder = '../Sensitivity_Analysis/Data/FS'
if not os.path.isdir(folder):
os.makedirs(folder)

41
Code/Sensitivity_Analysis/SA_FS_Kv.py
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@@ -11,7 +11,7 @@ from numba import types
from numba.typed import Dict
from joblib import Parallel, delayed
import os
from Utility import capacitance, stimulus_init, init_dict, NumpyEncoder
from Code.Functions.Utility_fxns import capacitance, stimulus_init, init_dict, NumpyEncoder
from Code.Functions.Pospischil_fxns import SA_Pospischil
@@ -62,19 +62,6 @@ b_param['s_mut'][:] = np.array([-14.16, -10.15, 1.])
b_param['u_mut'] = np.zeros(4)
b_param['u_mut'][:] = np.array([-31., 5.256, 1., 0.245])
# mut_act_Vhalf_wt = -30.01851851851851
# mut_act_k_wt = -7.7333333333333325
# s_diff_Vhalf = mut_act_Vhalf_wt - b_param['s'][0]
# s_diff_k = mut_act_k_wt - b_param['s'][1]
# b_param['s'][1] = b_param['s'][1] + s_diff_k
# b_param['u'][1] = b_param['u'][1] + s_diff_k
# b_param['s'][0] = b_param['s'][0] + s_diff_Vhalf
# b_param['u'][0] = b_param['u'][0] + s_diff_Vhalf
# b_param['s_mut'][1] = b_param['s_mut'][1] + s_diff_k
# b_param['u_mut'][1] = b_param['u_mut'][1] + s_diff_k
# b_param['s_mut'][0] = b_param['s_mut'][0] + s_diff_Vhalf
# b_param['u_mut'][0] = b_param['u_mut'][0] + s_diff_Vhalf
# reversal potentials
E["Na"] = 50.
E["K"] = -90.
@@ -101,7 +88,7 @@ g["L"] = 0. * surf_area
g["Leak"] = 0.038 * surf_area
# save folder
folder = '../Sensitivity_Analysis/FS_Kv'
folder = '../Sensitivity_Analysis/Data/FS_Kv'
if not os.path.isdir(folder):
os.makedirs(folder)
@@ -127,27 +114,3 @@ Parallel(n_jobs=8, verbose=9)(
scale, b_param, slope_shift, gating, current, prominence, desired_AUC_width, folder, high,
low, number_steps, initial_period, sec, lin_array, log_array, alt_types, alt_ind, alt)
for alt_ind in range(alt_types.shape[0]) for alt in range(21))
# #%% Get pd Dataframes for certain variables
# import pandas as pd
# AUC = pd.DataFrame(columns=mutations.keys())
# AUC_rel = pd.DataFrame(columns=mutations.keys())
# rheobase = pd.DataFrame(columns=mutations.keys())
# rheobase_fit = pd.DataFrame(columns=mutations.keys())
# rheobase_null_fit = pd.DataFrame(columns=mutations.keys())
# for mut in list(mutations.keys()):
# fname = os.path.join(folder, "{}.hdf5".format(mut))
# f = h5py.File(fname, "r")
# AUC['{}'.format(mut)] = f['analysis']['AUC']
# AUC_rel['{}'.format(mut)] = f['analysis']['AUC_rel']
# rheobase['{}'.format(mut)] = f['analysis']['rheobase']
# rheobase_fit['{}'.format(mut)] = f['analysis']['rheobase_fit']
# rheobase_null_fit['{}'.format(mut)] = f['analysis']['rheobase_null_fit']
# AUC.to_json(os.path.join(folder, 'AUC.json'))
# AUC_rel.to_json(os.path.join(folder, 'AUC_rel.json'))
# rheobase.to_json(os.path.join(folder, 'rheobase.json'))
# rheobase_fit.to_json(os.path.join(folder, 'rheobase_fit.json'))
# rheobase_null_fit.to_json(os.path.join(folder, 'rheobase_null_fit.json'))

4
Code/Sensitivity_Analysis/SA_RS_inhib.py
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@@ -10,7 +10,7 @@ from numba import types
from numba.typed import Dict
from joblib import Parallel, delayed
import os
from Code.Functions.Utility import capacitance, stimulus_init, init_dict, NumpyEncoder
from Code.Functions.Utility_fxns import capacitance, stimulus_init, init_dict, NumpyEncoder
from Code.Functions.Pospischil_fxns import SA_Pospischil
# model parameters
@@ -86,7 +86,7 @@ g["L"] = 0.
g["Leak"] = 0.0205 * surf_area
# save folder
folder = '../Sensitivity_Analysis/RS_inhib'
folder = '../Sensitivity_Analysis/Data/RS_inhib'
if not os.path.isdir(folder):
os.makedirs(folder)

4
Code/Sensitivity_Analysis/SA_RS_inhib_Kv.py
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@@ -10,7 +10,7 @@ from numba import types
from numba.typed import Dict
from joblib import Parallel, delayed
import os
from Code.Functions.Utility import capacitance, stimulus_init, init_dict, NumpyEncoder
from Code.Functions.Utility_fxns import capacitance, stimulus_init, init_dict, NumpyEncoder
from Code.Functions.Pospischil_fxns import SA_Pospischil
@@ -87,7 +87,7 @@ g["L"] = 0. * surf_area
g["Leak"] = 0.0205 * surf_area
# save folder
folder = '../Sensitivity_Analysis/RS_inhib_Kv'
folder = '../Sensitivity_Analysis/Data/RS_inhib_Kv'
if not os.path.isdir(folder):
os.makedirs(folder)

4
Code/Sensitivity_Analysis/SA_RS_pyramidal.py
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@@ -8,7 +8,7 @@ Created on Fri Jun 4 08:24:33 2021
import numpy as np
from joblib import Parallel, delayed
import os
from Code.Functions.Utility import capacitance, stimulus_init, init_dict, NumpyEncoder
from Code.Functions.Utility_fxns import capacitance, stimulus_init, init_dict, NumpyEncoder
from Code.Functions.Pospischil_fxns import SA_Pospischil
@@ -71,7 +71,7 @@ g["Kv_mut"] = 0.
g["L"] = 0.
g["Leak"] = 0.0205 * surf_area
folder = '../Sensitivity_Analysis/RS_pyramidal'
folder = '../Sensitivity_Analysis/Data/RS_pyramidal'
if not os.path.isdir(folder):
os.makedirs(folder)

4
Code/Sensitivity_Analysis/SA_RS_pyramidal_Kv.py
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@@ -10,7 +10,7 @@ from numba import types
from numba.typed import Dict
from joblib import Parallel, delayed
import os
from Code.Functions.Utility import capacitance, stimulus_init, init_dict, NumpyEncoder
from Code.Functions.Utility_fxns import capacitance, stimulus_init, init_dict, NumpyEncoder
from Code.Functions.Pospischil_fxns import SA_Pospischil
@@ -86,7 +86,7 @@ g["L"] = 0. * surf_area
g["Leak"] = 0.0205 * surf_area
# save folder
folder = '../Sensitivity_Analysis/RS_pyramidal_Kv'
folder = '../Sensitivity_Analysis/Data/RS_pyramidal_Kv'
if not os.path.isdir(folder):
os.makedirs(folder)

4
Code/Sensitivity_Analysis/SA_STN.py
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@@ -13,7 +13,7 @@ from numba import types
from numba.typed import Dict
from joblib import Parallel, delayed
import os
from Code.Functions.Utility import capacitance, stimulus_init, init_dict
from Code.Functions.Utility_fxns import capacitance, stimulus_init, init_dict
from Code.Functions.STN_fxns import SA_STN
# model parameters
@@ -90,7 +90,7 @@ g["Ca_K"] = 1 * surf_area
g["Leak"] = 0.035 * surf_area
# save folder
folder = '../Sensitivity_Analysis/STN'
folder = '../Sensitivity_Analysis/Data/STN'
if not os.path.isdir(folder):
os.makedirs(folder)

4
Code/Sensitivity_Analysis/SA_STN_Delta_Kv.py
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@@ -11,7 +11,7 @@ from numba import types
from numba.typed import Dict
from joblib import Parallel, delayed
import os
from Code.Functions.Utility import capacitance, stimulus_init, init_dict
from Code.Functions.Utility_fxns import capacitance, stimulus_init, init_dict
from Code.Functions.STN_fxns_Kv import SA_Kv_STN
@@ -99,7 +99,7 @@ g["Leak"] = 0.035 * surf_area
V_init = -70
# save folder
folder = '../Sensitivity_Analysis/STN_Delta_Kv'
folder = '../Sensitivity_Analysis/Data/STN_Delta_Kv'
if not os.path.isdir(folder):
os.makedirs(folder)

4
Code/Sensitivity_Analysis/SA_STN_Kv.py
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@@ -11,7 +11,7 @@ from numba import types
from numba.typed import Dict
from joblib import Parallel, delayed
import os
from Code.Functions.Utility import capacitance, stimulus_init, init_dict
from Code.Functions.Utility_fxns import capacitance, stimulus_init, init_dict
from Code.Functions.STN_fxns_Kv import SA_Kv_STN
# model parameters
@@ -96,7 +96,7 @@ g["Ca_K"] = 1 * surf_area
g["Leak"] = 0.035 * surf_area
# save folder
folder = '../Sensitivity_Analysis/STN_Kv'
folder = '../Sensitivity_Analysis/Data/STN_Kv'
if not os.path.isdir(folder):
os.makedirs(folder)