def __init__(self, *args, **kwargs):
unittest.TestCase.__init__(self, *args, **kwargs)
num_p = 20
# The Kriging model starts by defining a sampling plan, we use an optimal Latin Hypercube here
# sp = samplingplan(k=2)
self.RMSE_mean = []
self.RMSE_std = []
self.X = sp.samplingplan().rlh(num_p)
# self.X = sp.grid(num_p)
# self.X = sp.MC(num_p)
# self.X = sp.optimallhc(num_p)
minx, maxx, miny, maxy = [-2, 2, -2, 2]
self.X[:, 0] = minx + (maxx - minx) * self.X[:, 0]
self.X[:, 1] = miny + (maxy - miny) * self.X[:, 1]
self.testfun = pyKriging.testfunctions().branin
# self.testfun = pyKriging.testfunctions().rosenbrock
self.y = self.testfun(self.X)
#!/usr/bin/env python
import pyKriging
from pyKriging.krige import kriging
from pyKriging.samplingplan import samplingplan
# The Kriging model starts by defining a sampling plan, we use an optimal Latin Hypercube here
sp = samplingplan(2)
X = sp.optimallhc(20)
# Next, we define the problem we would like to solve
testfun = pyKriging.testfunctions().branin
y = testfun(X)
# Now that we have our initial data, we can create an instance of a Kriging model
k = kriging(X, y, testfunction=testfun, name='simple')
k.train()
# Now, five infill points are added. Note that the model is re-trained after each point is added
numiter = 5
for i in range(numiter):
print 'Infill iteration {0} of {1}....'.format(i + 1, numiter)
newpoints = k.infill(1)
for point in newpoints:
k.addPoint(point, testfun(point)[0])
k.train()
# And plot the results
k.plot()
__author__ = 'cpaulson'
import pyKriging
from pyKriging.krige import kriging
from pyKriging.samplingplan import samplingplan
from pyKriging.CrossValidation import Cross_Validation
from pyKriging.utilities import saveModel
# The Kriging model starts by defining a sampling plan, we use an optimal Latin Hypercube here
sp = samplingplan(2)
X = sp.optimallhc(5)
# Next, we define the problem we would like to solve
testfun = pyKriging.testfunctions().branin
# We generate our observed values based on our sampling plan and the test function
y = testfun(X)
print 'Setting up the Kriging Model'
cvMSE = []
# Now that we have our initial data, we can create an instance of a kriging model
k = kriging(X, y, testfunction=testfun, name='simple', testPoints=300)
k.train(optimizer='ga')
k.snapshot()
# cv = Cross_Validation(k)
# cvMSE.append( cv.leave_n_out(q=5)[0] )
k.plot()
for i in range(15):
print i
newpoints = k.infill(1)
for point in newpoints:
__author__ = 'cpaulson'
import pyKriging
from pyKriging.krige import kriging
from pyKriging.samplingplan import samplingplan
# The Kriging model starts by defining a sampling plan, we use an optimal Latin Hypercube here
sp = samplingplan(2)
X = sp.optimallhc(15)
# Next, we define the problem we would like to solve
testfun = pyKriging.testfunctions().paulson1
y = testfun(X)
# We can choose between a ga and a pso here
optimizer = 'ga'
# Now that we have our initial data, we can create an instance of a kriging model
print 'Setting up the Kriging Model'
k = kriging(X, y, testfunction=testfun, name='simple_ei', testPoints=300)
k.train(optimizer=optimizer)
k.snapshot()
# Add 10 points based on model error reduction
for i in range(5):
newpoints = k.infill(1, method='error')
for point in newpoints:
print 'Adding point {}'.format(point)
k.addPoint(point, testfun(point)[0])
k.train(optimizer=optimizer)
k.snapshot()
__author__ = 'cpaulson'
import pyKriging
from pyKriging.krige import kriging
from pyKriging.samplingplan import samplingplan
# The Kriging model starts by defining a sampling plan, we use an optimal Latin Hypercube here
sp = samplingplan(2)
X = sp.optimallhc(15)
# Next, we define the problem we would like to solve
testfun = pyKriging.testfunctions().paulson1
y = testfun(X)
# We can choose between a ga and a pso here
optimizer = 'ga'
# Now that we have our initial data, we can create an instance of a kriging model
print 'Setting up the Kriging Model'
k = kriging(X, y, testfunction=testfun, name='simple_ei', testPoints=300)
k.train(optimizer=optimizer)
k.snapshot()
# Add 10 points based on model error reduction
for i in range(5):
newpoints = k.infill(1, method='error')
for point in newpoints:
print 'Adding point {}'.format(point)
k.addPoint(point, testfun(point)[0])
k.train(optimizer=optimizer)
k.snapshot()
def interpGrid(self):
ptx = np.array(self.x)
pty = np.array(self.y)
z = np.array(self.z)
print(len(ptx), 'length x')
# remove duplicate x values
dups = self.checkdups(self.x)
ptx = np.delete(ptx, dups)
pty = np.delete(pty, dups)
z = np.delete(z, dups)
print(len(ptx), 'length x')
pts = zip(self.x, self.y)
# gridx, gridy = np.mgrid[uprLeft[0]:lwrRight[0]:50j,uprLeft[1]:lwrRight[1]:50j]
gridx, gridy = np.mgrid[self.ext[0]:self.ext[1]:self.ncol*1j,
self.ext[2]:self.ext[3]:self.nrow*1j]
##### using griddata #####
if self.interptype == 'griddata':
from scipy.interpolate import griddata
self.grid = griddata(pts,self.z,(gridx,gridy), method='cubic',fill_value=-3e30)
#### examples from
##### http://stackoverflow.com/questions/24978052/interpolation-over-regular-grid-in-python
##### using radial basis function ####
if self.interptype == 'rbf':
import scipy.interpolate as interpolate
f = interpolate.Rbf(pty, ptx, z, function='linear')
self.grid = f(gridy, gridx)
##### using kriging ####
if self.interptype == 'gauss':
from sklearn.gaussian_process import GaussianProcess
# print math.sqrt(np.var(z))
# gp = GaussianProcess(theta0=0.1, thetaL=1.1, thetaU=10.1, nugget=0.000001)
if np.min(z) <= 0:
thetaL = 0.1
else:
thetaL = np.min(z)
print(np.min(z), thetaL, np.max(z))
# gp = GaussianProcess(regr='quadratic',corr='cubic',theta0=np.min(z),thetaL=thetaL,thetaU=np.max(z),nugget=0.05)
gp = GaussianProcess(theta0=500,thetaL=100,thetaU=2000)
gp.fit(X=np.column_stack([pty,ptx]),y=z)
rr_cc_as_cols = np.column_stack([gridy.flatten(), gridx.flatten()])
self.grid = gp.predict(rr_cc_as_cols).reshape((self.ncol,self.nrow))
if self.interptype == 'krig':
import pyKriging
from pyKriging.krige import kriging
from pyKriging.samplingplan import samplingplan
# The Kriging model starts by defining a sampling plan, we use an optimal Latin Hypercube here
# sp = samplingplan(2)
# X = sp.optimallhc(20)
# print(X)
X = np.array(zip(self.x, self.y))
print(X.shape)
# Next, we define the problem we would like to solve
testfun = pyKriging.testfunctions().squared
# y = testfun(X)
# print(y)
y = self.z
# Now that we have our initial data, we can create an instance of a Kriging model
k = kriging(X, y)#, testfunction=testfun, name='simple')
# k.train()
# Now, five infill points are added. Note that the model is re-trained after each point is added
# numiter = 5
# for i in range(numiter):
# print 'Infill iteration {0} of {1}....'.format(i + 1, numiter)
# newpoints = k.infill(1)
# for point in newpoints:
# k.addPoint(point, testfun(point)[0])
# k.train()
# And plot the results
k.plot()
sys.exit()
self.grid[self.grid < self.minval] = -2.99999989403e+030 #self.minval
self.grid = np.flipud(self.grid.T)