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test_pykriging2D.py
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Tue, Apr 30, 10:05

test_pykriging2D.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2017-04-24 11:04:39
# @Email: theo.lemaire@epfl.ch
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2017-05-26 14:30:02
''' Predict a 1D Vmeff profile using the PyKriging module. '''
import os, ntpath
import pickle
import re
import numpy as np
from scipy.interpolate import griddata
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from pyKriging.krige import kriging
from utils import OpenFilesDialog, rescale, rmse
class Variable:
''' dummy class to contain information about the variable '''
name = ''
unit = ''
lookup = ''
factor = 1.
max_error = 0.
def __init__(self, var_name, var_unit, var_lookup, var_factor, var_max_error):
self.name = var_name
self.unit = var_unit
self.factor = var_factor
self.lookup = var_lookup
self.max_error = var_max_error
# Set data variable and Kriging parameters
varinf = Variable('V_{m, eff}', 'mV', 'V_eff', 1., 1e-1)
# varinf = Variable('\\alpha_{m, eff}', 'ms^{-1}', 'alpha_m_eff', 1e-3, 1e1)
# varinf = Variable('\\beta_{m, eff}', 'ms^{-1}', 'beta_m_eff', 1e-3, 5e0)
# varinf = Variable('\\alpha_{h, eff}', 'ms^{-1}', 'alpha_h_eff', 1e-3, 1e1)
# varinf = Variable('\\beta_{h, eff}', 'ms^{-1}', 'beta_h_eff', 1e-3, 1e1)
# Define true function by interpolation from specific profile
def f(x):
return griddata(points, values, x, method='linear', rescale=True)
# Select data files (PKL)
lookup_root = '../Output/lookups 0.35MHz charge extended/'
lookup_absroot = os.path.abspath(lookup_root)
lookup_filepaths = OpenFilesDialog(lookup_absroot, 'pkl')
rgxp = re.compile('lookups_a(\d*.\d*)nm_f(\d*.\d*)kHz_A(\d*.\d*)kPa_dQ(\d*.\d*)nC_cm2.pkl')
pltdir = 'C:/Users/admin/Desktop/PyKriging output/'
# Set data variable and Kriging parameters
varinf = Variable('V_{m, eff}', 'mV', 'V_eff', 1., 1.0)
# varinf = Variable('\\alpha_{m, eff}', 'ms^{-1}', 'alpha_m_eff', 1e-3, 1e4)
# varinf = Variable('\\beta_{m, eff}', 'ms^{-1}', 'beta_m_eff', 1e-3, 5e0)
# varinf = Variable('\\alpha_{h, eff}', 'ms^{-1}', 'alpha_h_eff', 1e-3, 1e1)
# varinf = Variable('\\beta_{h, eff}', 'ms^{-1}', 'beta_h_eff', 1e-3, 1e1)
# Check dialog output
if not lookup_filepaths:
print('error: no lookup table selected')
else:
print('importing lookup tables')
nfiles = len(lookup_filepaths)
amps = np.empty(nfiles)
for i in range(nfiles):
# Load lookup table
lookup_filename = ntpath.basename(lookup_filepaths[i])
mo = rgxp.fullmatch(lookup_filename)
if not mo:
print('Error: lookup file does not match regular expression pattern')
else:
# Retrieve stimulus parameters
Fdrive = float(mo.group(2)) * 1e3
Adrive = float(mo.group(3)) * 1e3
dQ = float(mo.group(4)) * 1e-2
amps[i] = Adrive
if Adrive == 0:
baseline_ind = i
# Retrieve coefficients data
with open(lookup_filepaths[i], 'rb') as fh:
lookup = pickle.load(fh)
if i == 0:
Qm = lookup['Q']
nQ = np.size(Qm)
var = np.empty((nfiles, nQ))
var[i, :] = lookup[varinf.lookup]
else:
if np.array_equal(Qm, lookup['Q']):
var[i, :] = lookup[varinf.lookup]
else:
print('Error: charge vector not consistent')
# Compute data metrics
namps = amps.size
Amin = np.amin(amps)
Amax = np.amax(amps)
Qmin = np.amin(Qm)
Qmax = np.amax(Qm)
varmin = np.amin(var)
varmax = np.amax(var)
print('Initial data:', nQ, 'charges,', namps, 'amplitudes')
# Define points for interpolation function
Q_mesh, A_mesh = np.meshgrid(Qm, amps)
points = np.column_stack([A_mesh.flatten(), Q_mesh.flatten()])
values = var.flatten()
# Define algorithmic parameters
n_iter_min = 10
n_iter_max = 30
MAE_pred = []
MAE_true = []
RMSE_true = []
# Define estimation matrix
nAest = 20
nQest = 100
print('Initial estimation matrix:', nQest, 'charges,', nAest, 'amplitudes')
Aest = np.linspace(Amin, Amax, nAest)
Qest = np.linspace(Qmin, Qmax, nQest)
Qest_mesh, Aest_mesh = np.meshgrid(Qest, Aest)
x = np.column_stack([Aest_mesh.flatten(), Qest_mesh.flatten()])
ytrue = f(x).ravel().reshape((nAest, nQest))
# Define initial observation matrix
nAobs = 5
nQobs = 20
print('Initial estimation matrix:', nQobs, 'charges,', nAobs, 'amplitudes')
Aobs = np.linspace(Amin, Amax, nAobs)
Qobs = np.linspace(Qmin, Qmax, nQobs)
Qobs_mesh, Aobs_mesh = np.meshgrid(Qobs, Aobs)
X0 = np.column_stack([Aobs_mesh.flatten(), Qobs_mesh.flatten()])
Y0 = f(X0).ravel()
print('creating Kriging model')
k = kriging(X0, Y0)
print('initial training')
k.train()
print('predicting')
y0 = np.array([k.predict(xx) for xx in x])
y0 = y0.reshape((nAest, nQest))
X = X0
Y = Y0
n_iter = 10
for i in range(n_iter):
print('Infill iteration {0} of {1}....'.format(i + 1, n_iter))
newpoints = k.infill(2, method='error')
for point in newpoints:
newX = k.inversenormX(point)
newY = f(newX)[0]
print('adding point (({:.3f}, {:.3f}), {:.3f})'.format(
newX[0] * 1e-3, newX[1] * 1e5, newY * varinf.factor))
X = np.append(X, [newX], axis=0)
Y = np.append(Y, newY)
k.addPoint(newX, newY, norm=True)
k.train()
y = np.array([k.predict(xx) for xx in x])
y = y.reshape((nAest, nQest))
# Plotting
mymap = cm.get_cmap('viridis')
sm_amp = plt.cm.ScalarMappable(cmap=mymap, norm=plt.Normalize(Amin * 1e-3, Amax * 1e-3))
sm_amp._A = []
var_levels = np.linspace(varmin, varmax, 20) * varinf.factor
sm_var = plt.cm.ScalarMappable(cmap=mymap, norm=plt.Normalize(varmin * varinf.factor, varmax * varinf.factor))
sm_var._A = []
# True function profiles
fig, ax = plt.subplots(figsize=(10, 6))
ax.set_xlabel('$Q_m \ (nC/cm^2)$', fontsize=20)
ax.set_ylabel('$' + varinf.name + '\ (' + varinf.unit + ')$', fontsize=20)
ax.set_title('True function profiles', fontsize=20)
for i in range(nAest):
ax.plot(Qest * 1e5, ytrue[i, :] * varinf.factor, c=mymap(rescale(Aest[i], Amin, Amax)))
fig.subplots_adjust(right=0.85)
cbar_ax = fig.add_axes([0.87, 0.1, 0.02, 0.8])
fig.add_axes()
fig.colorbar(sm_amp, cax=cbar_ax)
cbar_ax.set_ylabel('$A_{drive} \ (kPa)$', fontsize=20)
fig.savefig(pltdir + 'fig1.png', format='png')
# True function map
fig, ax = plt.subplots(figsize=(10, 6))
ax.set_ylabel('$A_{drive} \ (kPa)$', fontsize=20)
ax.set_xlabel('$Q_m \ (nC/cm^2)$', fontsize=20)
ax.set_title('True function map', fontsize=20)
ax.contourf(Qest * 1e5, Aest * 1e-3, ytrue * varinf.factor, levels=var_levels,
cmap='viridis')
fig.subplots_adjust(right=0.85)
cbar_ax = fig.add_axes([0.87, 0.1, 0.02, 0.8])
fig.add_axes()
fig.colorbar(sm_var, cax=cbar_ax)
cbar_ax.set_ylabel('$' + varinf.name + '\ (' + varinf.unit + ')$', fontsize=20)
fig.savefig(pltdir + 'fig2.png', format='png')
# Initial estimation profiles
fig, ax = plt.subplots(figsize=(10, 6))
ax.set_xlabel('$Q_m \ (nC/cm^2)$', fontsize=20)
ax.set_ylabel('$' + varinf.name + '\ (' + varinf.unit + ')$', fontsize=20)
ax.set_title('Initial estimation profiles', fontsize=20)
for i in range(nAest):
ax.plot(Qest * 1e5, y0[i, :] * varinf.factor, c=mymap(rescale(Aest[i], Amin, Amax)))
fig.subplots_adjust(right=0.85)
cbar_ax = fig.add_axes([0.87, 0.1, 0.02, 0.8])
fig.add_axes()
fig.colorbar(sm_amp, cax=cbar_ax)
cbar_ax.set_ylabel('$A_{drive} \ (kPa)$', fontsize=20)
fig.savefig(pltdir + 'fig3.png', format='png')
# Initial estimation map
fig, ax = plt.subplots(figsize=(10, 6))
ax.set_ylabel('$A_{drive} \ (kPa)$', fontsize=20)
ax.set_xlabel('$Q_m \ (nC/cm^2)$', fontsize=20)
ax.set_title('Initial estimation map', fontsize=20)
ax.contourf(Qest * 1e5, Aest * 1e-3, y0 * varinf.factor, levels=var_levels,
cmap='viridis')
ax.scatter(X0[:, 1] * 1e5, X0[:, 0] * 1e-3, c='black')
fig.subplots_adjust(right=0.85)
cbar_ax = fig.add_axes([0.87, 0.1, 0.02, 0.8])
fig.add_axes()
fig.colorbar(sm_var, cax=cbar_ax)
cbar_ax.set_ylabel('$' + varinf.name + '\ (' + varinf.unit + ')$', fontsize=20)
fig.savefig(pltdir + 'fig4.png', format='png')
# Final estimation profiles
fig, ax = plt.subplots(figsize=(10, 6))
ax.set_xlabel('$Q_m \ (nC/cm^2)$', fontsize=20)
ax.set_ylabel('$' + varinf.name + '\ (' + varinf.unit + ')$', fontsize=20)
ax.set_title('Final estimation profiles', fontsize=20)
for i in range(nAest):
ax.plot(Qest * 1e5, y[i, :] * varinf.factor, c=mymap(rescale(Aest[i], Amin, Amax)))
fig.subplots_adjust(right=0.85)
cbar_ax = fig.add_axes([0.87, 0.1, 0.02, 0.8])
fig.add_axes()
fig.colorbar(sm_amp, cax=cbar_ax)
cbar_ax.set_ylabel('$A_{drive} \ (kPa)$', fontsize=20)
fig.savefig(pltdir + 'fig7.png', format='png')
# Final estimation map
fig, ax = plt.subplots(figsize=(10, 6))
ax.set_ylabel('$A_{drive} \ (kPa)$', fontsize=20)
ax.set_xlabel('$Q_m \ (nC/cm^2)$', fontsize=20)
ax.set_title('Final estimation map', fontsize=20)
ax.contourf(Qest * 1e5, Aest * 1e-3, y * varinf.factor, levels=var_levels,
cmap='viridis')
ax.scatter(X[:, 1] * 1e5, X[:, 0] * 1e-3, c='black')
fig.subplots_adjust(right=0.85)
cbar_ax = fig.add_axes([0.87, 0.1, 0.02, 0.8])
fig.add_axes()
fig.colorbar(sm_var, cax=cbar_ax)
cbar_ax.set_ylabel('$' + varinf.name + '\ (' + varinf.unit + ')$', fontsize=20)
fig.savefig(pltdir + 'fig8.png', format='png')
plt.show()

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