From eb32120675347424bafee0f2c58a33afa2be5d96 Mon Sep 17 00:00:00 2001 From: ralf Date: Thu, 11 Jul 2024 13:24:08 +0300 Subject: [PATCH] cleared up more errors --- .gitignore | 1 + Model.py | 43 +++++++++++++++++------- fitter.py | 95 ++++++++++++++++++++++++++++++------------------------ 3 files changed, 85 insertions(+), 54 deletions(-) create mode 100644 .gitignore diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..faf9c85 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +ltcc_current.h5 diff --git a/Model.py b/Model.py index 627e59c..b076230 100644 --- a/Model.py +++ b/Model.py @@ -1,18 +1,13 @@ -# -*- coding: utf-8 -*- - import numpy as np import matplotlib.pyplot as plt from scipy.integrate import ode -# %% Constants - R = 8.314 # ideal gas constant (J/(mol*K)) F = 96.485 # coulomb_per_millimole, Faraday constant T = 298 # room temperature (K) RT = R * T -# %% model class Model: def __init__(self): @@ -20,48 +15,64 @@ class Model: self.C_mem = 1.0 # uF/cm2 Specific membrane capacitance self.V_myo = 25.84e-6 # uL, Myoplasmic volume self.current2flux = self.A_cap * self.C_mem / 2 / F # + self.period = 1000 # ms, pulse period self.V_mem_rest = -80.0 # mV, resting membrane potential + self.Nai = 11000 # uM, Myoplasmic Na+ concentration self.Nao = 150000 # uM, Extracellular Na+ concentration + self.eta = 0.35 # Controls voltage dependance of Na/Ca2+ exchange + self.km_Na = 87500 # uM, Na+ half-saturation constant for Na+/Ca2+ exchange self.k_sat = ( 0.1 # Na+/Ca2+ exchange saturation factor at very negative potentials ) self.km_Ca = (1380,) # uM, Ca2+ half-saturation constant for Na+/Ca2+ exchange self.k_Na_Ca = 292.8 # pA/pF, Scaling factor of Na2+/Ca2+ exchange + self.I_max_pCa = 1.0 # pA/pF, Maximum Ca2+ pump current + # self.Cai = 0.1 # uM, Cytoplasmic Ca2+ concentration fixed at this point + self.LTRPN_tot = ( 70.0 # uM, Total myoplasmic troponin low-affinity site concentration ) self.HTRPN_tot = ( 140.0 # uM, Total myoplasmic troponin high-affinity site concentration ) + # self.LTRPNCa = 11.2684 # uM, Concentration Ca2+ bound low-affinity troponin-binding sites # self.HTRPNCa = 125.290 # uM, Concentration Ca2+ bound high-affinity troponin-binding sites + self.k_htrpn_positive = ( 0.00237 # uM^(-1)/ms, Ca2+ on rate const. for troponin high-affinity sites ) self.k_htrpn_negative = ( 3.2e-5 # ms, Ca2+ off rate const. for troponin high-affinity sites ) + self.k_ltrpn_positive = ( 0.0327 # uM^(-1)/ms, Ca2+ on rate const. for troponin low-affinity sites ) self.k_ltrpn_negative = ( 0.0196 # ms, Ca2+ off rate const. for troponin low-affinity sites ) + self.CMDN_tot = 50 # uM, Total myoplasmic calmodulin concentration self.Km_CMDN = 0.238 # uM, Ca2 half-saturation constant for calmodulin + self.nu_1 = 4.5 # 1/ms, Maximum RyR channel Ca2+ permeability Ca2+ leak rate constant from the NSR self.nu_2 = 1.74e-5 # ms^(-1), Ca2+ leak rate const. from the NSR self.nu_3 = 0.45 # uM/ms, SR Ca2+ -ATPase maximum pupmp rate + self.Km_up = 0.5 # uM, Half-saturation constant for SR Ca2+ -ATPase pump self.km_p_ca = 0.5 # uM, Ca2+ half-saturation constant for Ca2+ pump current + # self.Ca_NSR = 1299.50 # uM,NSR Ca2+ concentration + self.tau_xfer = 8.0 # ms, Time constant for transfer from subspace to myoplasm + self.K_pc_max = ( 0.23324 # 1/ms, Maximum time constant for Ca2+-induced inactivation ) @@ -70,29 +81,37 @@ class Model: ) self.Kpcb = 0.0005 # 1/ms, Voltage-insensitive rate constant for inactivation self.km_Ca = 1380 # uM, Ca2+ half-saturation constant for Na+/Ca2+ exchange + self.Gcab = 0.000367 # mS/uF + self.Cao = 1130.0 # uM, Ca2+ outside the cell self.gCaL = ( 0.1729 # mS/uF, Specific maximum conductivity for L-type Ca2+ channel ) self.ECaL = 43.0 # mV, Reversal potential for L-type Ca2⫹ channel, kas arvutame voi jaab const? self.V_ss = 1.485e-9 # uL, Dyadic aka subspace volume + # self.Ca_JSR = 1299.50 # uM, JSR Ca2+ concentration self.F_tot = 25 # uM, total concentration of Fluo-4 self.k_on = 0.1 # 1/uM * 1/ms, Fluo-4 reaction rate constant self.k_off = 0.11 # 1/ms, Fluo-4 reaction rate constant 2 + self.V_NSR = 2.098e-6 # ul, Network SR volume self.tau_tr = 20 # ms, Time const for transfer from NSR to JSR + self.CSQN_tot = 15000.0 # uM, total junctional SR calsequestrin concentration self.Km_CSQN = 800.0 # uM, Ca2 half-saturation constant for calsequestrin + self.k_a_positive = 0.006075 # uM^(-4)/ms, RyR Pc1 - Po1 rate constant self.k_a_negative = 0.07125 # 1/ms, RyR Po1 - Pc1 rate constant self.k_b_positive = 0.00405 # uM^(-3)/ms, RyR Po1 - Po2 rate constant self.k_b_negative = 0.965 # 1/ms, RyR Po2 - Po1 rate constant self.k_c_positive = 0.009 # 1/ms, RyR Po1 - Pc2 rate constant self.k_c_negative = 0.0008 # 1/ms, RyR Pc2 - Po1 rate constant + self.n_ryr = 4 # RyR Ca2+ cooperativity parameter Pc1 - Po1 self.m_ryr = 3 # RyR Ca2+ cooperativity parameter Po1 - Po2 + self.I_CaL_max = 7.0 # pA/pF, normalization constant for L-type Ca2+ current self.V_JSR = 0.12e-6 # ul, Junctional SR volume @@ -180,11 +199,11 @@ class Model: Bi = 1 / ( 1 + (self.CMDN_tot * self.Km_CMDN) / (self.Km_CMDN + Cai) ** 2 - ) # A6 !!!!!!! korras V8 + ) Bss = 1 / ( 1 + (self.CMDN_tot * self.Km_CMDN) / (self.Km_CMDN + Cass) ** 2 - ) # A7 !!!!!!!!! korras V8 + ) J_xfer = (Cass - Cai) / self.tau_xfer @@ -199,7 +218,7 @@ class Model: - self.k_htrpn_negative * HTRPNCa + self.k_ltrpn_positive * Cai - * (self.LTRPN_tot - LTRPNCa) # !!!!!! korras v8 + * (self.LTRPN_tot - LTRPNCa) - self.k_ltrpn_negative * LTRPNCa ) @@ -207,7 +226,7 @@ class Model: J_tr = (Ca_NSR - Ca_JSR) / self.tau_tr - J_leak = self.nu_2 * (Ca_NSR - Cai) # puudu CaNSR diff vorrand + J_leak = self.nu_2 * (Ca_NSR - Cai) dCa_NSRdt = (J_up - J_leak) * (self.V_myo / self.V_NSR) -J_tr * (self.V_JSR / self.V_NSR) @@ -239,7 +258,9 @@ class Model: P_C1 = 1 - (P_C2 + P_O1 + P_O2) - dP_O1dt = self.k_a_positive * (Cass) ** self.n_ryr * P_C1 + dP_O1dt = ( + self.k_a_positive * (Cass) ** self.n_ryr * P_C1 + ) -self.k_a_negative * P_O1 - self.k_a_positive * (Cass) ** self.m_ryr * P_O1 +self.k_b_negative * P_O2 - self.k_c_positive * P_O1 + self.k_c_negative * P_C2 @@ -265,7 +286,7 @@ class Model: - (I_Cab - 2 * I_NaCa + I_pCa) * ((self.A_cap * self.C_mem)/(2 * self.V_myo * F))) """ - # J_rel_caf = self.nu_1 * (self.Ca_JSR - Cass) + # J_rel_caf = self.nu_1 * (self.Ca_JSR - Cass) #lisatud ette ennetavalt JFCa = self.k_on * (self.F_tot - FCa) * Cai - self.k_off * FCa diff --git a/fitter.py b/fitter.py index b771b90..7c82ca3 100644 --- a/fitter.py +++ b/fitter.py @@ -4,18 +4,19 @@ import pylab as plt import pandas as pd import re - from scipy.optimize import least_squares -from scipy.linalg import svd from Model import Model from Data import Data class Fitter: - def __init__(self, model: Model, data: Data, current_fit_range: tuple = (107, 341)) -> None: + def __init__( + self, model: Model, data: Data, current_fit_range: tuple = (107, 341) + ) -> None: """ current_fit_range : tuple (t0, t1), t0 nad t1 are start and stop times in between current is fitted """ + self.model = model self.data = data self.current_fit_range = current_fit_range @@ -60,19 +61,21 @@ class Fitter: model.solve(times=self.time_points) _calc_curr = model.calculated_current() - calculated_current = self.convolve_current(_calc_curr, tau=tau_RC)[self.current_time_indecies] + offset + calculated_current = ( + self.convolve_current(_calc_curr, tau=tau_RC)[self.current_time_indecies] + + offset + ) res = self.measured_current - calculated_current err = np.mean(res**2) # mean squared error self.iteration += 1 print(self.iteration, parameters.tolist(), "err", err) - # measured_fluo = self.data.fluo - # fluo_interplolator = interp1d(self.time_domain, model.calculated_fluo) - # calculated_fluo = fluo_interplolator(self.data.fluo_time) if self.iteration < -0: t = self.time_points[self.current_time_indecies] - plt.plot(t, _calc_curr[self.current_time_indecies], label="calculated current") + plt.plot( + t, _calc_curr[self.current_time_indecies], label="calculated current" + ) plt.plot(t, self.measured_current, label="measured current") plt.plot(t, calculated_current, label="conv calculated current") plt.plot(t, self.measured_current - calculated_current, label="error") @@ -80,9 +83,8 @@ class Fitter: plt.ylabel("current, pA/pF") plt.legend(frameon=False) plt.show() - # exit() - return res, err # , measured_fluo - calculated_fluo) + return res # , measured_fluo - calculated_fluo) def optimize(self, init_parameters=None): t0 = time.time() @@ -95,15 +97,17 @@ class Fitter: offset = 0 d = self.data - init_parameters = np.array([d.gGaL, d.ECal, K_pc_half, tau_xfer, tau_RC, offset]) + init_parameters = np.array( + [d.gGaL, d.ECal, K_pc_half, tau_xfer, tau_RC, offset] + ) print(init_parameters.tolist()) bounds = ( - (0.01, 10, 0.1, 0.1, 0.1, -5, -10), - (10, 100, 100, 1, 100, 10, 10), + (0.01, 10, 0.1, 0.1, -5, -10), + (10, 100, 100, 100, 10, 10), ) - res, err = least_squares(self.cost_func, init_parameters, bounds=bounds, xtol=1e-10) + res = least_squares(self.cost_func, init_parameters, bounds=bounds, xtol=1e-10) print() print(" Parameters: [gGaL, ECal, K_pc_half, tau_xfer, tau_RC, offset]") print(" Initial:", init_parameters.tolist()) @@ -113,14 +117,19 @@ class Fitter: gGaL, ECal, K_pc_half, tau_xfer, tau_RC, offset = res.x - self.fit_results.update({ - 'gGaL': gGaL, - 'ECal': ECal, - 'K_pc_half': K_pc_half, - 'tau_xfer': tau_xfer, - 'tau_RC': tau_RC, - 'offset': offset, - 'mean_squared_error': err}) + err = self.cost_func(res.x) + + self.fit_results.update( + { + "gGaL": gGaL, + "ECal": ECal, + "K_pc_half": K_pc_half, + "tau_xfer": tau_xfer, + "tau_RC": tau_RC, + "offset": offset, + "mean_squared_error": np.mean((err) ** 2), + } + ) model = self.model() @@ -135,27 +144,26 @@ class Fitter: calculated_current = self.convolve_current(_calc_curr, tau=tau_RC) + offset print("Elapsed time:", time.time() - t0) - fig = plt.figure(figsize=(24, 12)) + fig = plt.figure(figsize=(6, 3)) ax1 = fig.add_subplot(121) ax2 = fig.add_subplot(122) - ax1.plot(1000 * self.data.current_t, self.data.current, label="Measured") - ax1.plot(self.time_points, calculated_current, label="Calculated") - ax1.set_xlabel("time, ms") - ax1.set_ylabel("current, pA/pF") + ax1.plot(1000 * self.data.current_t, self.data.current, label="Mõõdetud") + ax1.plot(self.time_points, calculated_current, label="Arvutatud") + ax1.set_xlabel("Aeg [ms]") + ax1.set_ylabel("Vool [pA/pF]") ax1.legend(frameon=False) tp = self.time_points[self.current_time_indecies] - ax2.plot(tp, self.measured_current, label="Measured") - ax2.plot(tp, calculated_current[self.current_time_indecies], label="Calculated") - ax2.set_xlabel("time, ms") - ax2.set_ylabel("current, pA/pF") + ax2.plot(tp, self.measured_current, label="Mõõdetud") + ax2.plot(tp, calculated_current[self.current_time_indecies], label="Arvutatud") + ax2.set_xlabel("Aeg [ms]") + ax2.set_ylabel("Vool [pA/pF]") ax2.legend(frameon=False) - return res, fig def covcor_from_lsq(res): - _, s, VT = svd(res.jac, full_matrices=False) + _, s, VT = np.linalg.svd(res.jac, full_matrices=False) threshold = np.finfo(float).eps * max(res.jac.shape) * s[0] s = s[s > threshold] VT = VT[: s.size] @@ -168,18 +176,18 @@ class Fitter: return cov, cor def plot_correlation_matrix(cor): - plt.imshow(cor, cmap='viridis', interpolation='nearest') - plt.colorbar(label='Correlation') - plt.title('Correlation Matrix') - plt.xlabel('Variables') - plt.ylabel('Variables') + plt.imshow(cor, cmap="viridis", interpolation="nearest") + plt.colorbar(label="Correlation") + plt.title("Correlation Matrix") + plt.xlabel("Variables") + plt.ylabel("Variables") plt.show() if __name__ == "__main__": filename = "ltcc_current.h5" - eid = "0033635a51b096dc449eb9964e70443a67fc16b9587ae3ff6564eea1fa0e3437_2018.06.18 14:48:40" + eid = "1c5ca4b12ae2ddffc3960c1fe39a3cce35967ce23dbac57c010f450e796d01fd_2017.11.27 14:07:04" data = Data(filename, eid) @@ -187,14 +195,16 @@ if __name__ == "__main__": res, fig = fit.optimize() - fit_hist = pd.DataFrame.from_dict(fit.fit_results, orient='index').T - fit_hist.index.name = 'Iterations' + fit_hist = pd.DataFrame.from_dict(fit.fit_results, orient="index").T + fit_hist.index.name = "Iterations" res_filename = f"fit_results_{eid}.csv" res_filename = res_filename.replace(" ", "_").replace(":", "-") fit_hist.to_csv(res_filename, index=True) - eid_cleaned = re.sub(r'[^\w.-]', '', eid) # Eemalda kõik eritähed ja jääb alles alphanumbrilised tähed, sidekriipsud ja punktid + eid_cleaned = re.sub( + r"[^\w.-]", "", eid + ) # Eemalda kõik eritähed ja jääb alles alphanumbrilised tähed, sidekriipsud ja punktid fig.savefig(f"plot_{eid_cleaned}.png") fig.savefig(f"plot_{eid_cleaned}.pdf") @@ -202,5 +212,4 @@ if __name__ == "__main__": # fig.savefig(f"{plot_filename}.png") # fig.savefig(f"{plot_filename}.pdf") fig.savefig("naidis_fit.pdf") - plt.show()