def __init__(self,
m=4,
n=3,
initial_path='initial_airfoil/naca0012.dat',
config_fname='op_conditions.ini'):
# Airfoil parameters
self.m = m
self.n = n
# NACA 0012 as the initial airfoil
try:
self.airfoil0 = np.loadtxt(initial_path, skiprows=1)
except:
self.airfoil0 = np.loadtxt(initial_path, delimiter=',')
x_min = np.min(self.airfoil0[:, 0])
x_max = np.max(self.airfoil0[:, 0])
z_min = np.min(self.airfoil0[:, 1])
z_max = np.max(self.airfoil0[:, 1])
Px = np.linspace(x_min, x_max, self.m, endpoint=True)
Py = np.linspace(z_min, z_max, self.n, endpoint=True)
x, y = np.meshgrid(Px, Py)
P0 = np.stack((x, y), axis=-1)
self.Px = P0[:, :, 0]
self.alpha0 = P0[:, :, 1].flatten()
self.dim = len(self.alpha0)
self.bounds = np.zeros((self.dim, 2))
perturb = 0.2
self.bounds[:, 0] = self.alpha0 - perturb
self.bounds[:, 1] = self.alpha0 + perturb
self.y = None
self.config_fname = config_fname
def import_ganZ_gen_params(gp_fold, iter_nm):
n00 = np.loadtxt(gp_fold + iter_nm + '_00.csv', delimiter=',')
n00 = n00.reshape(1, n00.shape[0])
n01 = np.loadtxt(gp_fold + iter_nm + '_01.csv', delimiter=',')
n10 = np.loadtxt(gp_fold + iter_nm + '_10.csv', delimiter=',')
n10 = n10.reshape(n10.shape[0], 1)
n11 = np.loadtxt(gp_fold + iter_nm + '_11.csv', delimiter=',')
n11 = n11.reshape(1)
genZ_params = [(n00, n01), (n10, n11)]
return genZ_params
def run(self):
plt.imshow(self.data);
plt.show();
plt.imshow(self.psf);
plt.show();
#set up initial guesses
#create initial parameters
tt0 = np.zeros((self.n_grid,self.n_grid)) + self.wlim[1]; #begin with high uniform mass in each pixel
tt0 = self.xi*np.log(np.exp(tt0/self.xi)-1);
#print(tt0);
tt0_k = fft.fft2(tt0); #take fft
t_ini = self.complex_to_real(tt0_k.flatten()) #flatten to 1d for scipy and embed in 2R
alpha_ini = 3.;
f_ini = self.f_true;
#m_1,mf = self.optimize_m(t_ini,self.xi,f_ini,alpha_ini);
m_1 = np.loadtxt('mock00024.out');
m_1 = self.xi*np.log(np.exp(m_1/self.xi)-1);
m_1 = fft.fft2(m_1);
m_1 = self.complex_to_real(m_1.flatten());
a_1 = self.optimize_alpha(m_1,self.xi,f_ini,alpha_ini);
print(a_1);
mf,m_2 = self.optimize_m(tt0,self.xi,f_ini,a_1);
print('new alpha');
print(a_1);
return m_2;
def __init__(self, csvname):
# grab input
data = np.loadtxt(csvname, delimiter=',')
self.x = data[:, :-1]
self.y = data[:, -1]
self.x.shape = (len(self.x), 1)
self.y.shape = (len(self.y), 1)
def test_structure(self):
nelx, nely = 60, 20
left_wall = list(range(0, 2 * (nely + 1), 2))
right_corner = [2 * (nelx + 1) * (nely + 1) - 1]
fixdofs = np.asarray(left_wall + right_corner)
alldofs = np.arange(2 * (nely + 1) * (nelx + 1))
freedofs = np.array(list(set(alldofs) - set(fixdofs)))
forces = np.zeros(2 * (nely + 1) * (nelx + 1))
forces[1] = -1.0
args = topo_physics.default_args()
args.update({
'nelx': nelx,
'nely': nely,
'freedofs': freedofs,
'fixdofs': fixdofs,
'forces': forces
})
_, x, _ = topo_physics.run_toposim(args=args,
loss_only=False,
verbose=False)
x = abs(x) # remove negative zeros!
path = os.path.join(os.path.dirname(__file__), 'truss_test.csv')
# To regenerate, run the test binary directly, e.g., with
# python ./neural_structural_optimization/topo_physics_test
# after uncommenting this line:
# np.savetxt(path, x, delimiter=",", fmt='%.0f',)
target_struct = np.loadtxt(path, delimiter=',')
npo.testing.assert_array_equal(x.round(0), target_struct)
def shape_fit_1d(m, step_size, u_func, num_flows=8, num_samples=1000):
# Parameters
h = np.tanh
q_0_mu = np.array([0,0])
q_0_sigma = 10
D = q_0_mu.shape[0]
# flows
#lambda_flows = np.array([np.array([1., 1., 1., 1., 0.])])
#lambda_flows = np.array([np.array([1., 1., 0.])]*num_flows)
lambda_flows = np.loadtxt("./data_fit_1d/flow_params.txt")
# 1D samples
samples = np.random.randn(num_samples)[:,np.newaxis]
#samples = np.random.uniform(-1, 1, num_samples)[:,np.newaxis]
start = time.time()
grad_energy_bound = autograd.grad(energy_bound)
# JOINT PROBABILITY IS NEW U_FUNC
#print(energy_bound(lambda_flows, samples, h, u_func))
#target = lambda x: (sp.stats.norm.pdf((x-2)) + sp.stats.norm.pdf((x+2)))/2
#gradient_descent(m, lambda_flows, grad_energy_bound, samples)
flowed_samples = adam_solve(lambda_flows, grad_energy_bound, samples,
u_func, h, m, step_size)
# Plot Transformed samples
ax = setup_plot(u_func)
ax.hist(flowed_samples, bins=100, alpha=0.5, density=True, label="Transformed Samples")
#plt.savefig("./plots/adam_fit_test.png")
ax.legend(loc='best')
plt.savefig("./data_fit_1d/adam_fit.png")
def __init__(self,csvname):
# grab input
data = np.loadtxt(csvname,delimiter = ',')
self.x = data[:-1,:]
self.y = data[-1:,:]
self.colors = ['salmon','cornflowerblue','lime','bisque','mediumaquamarine','b','m','g']
def load(name, suffix=[]):
path = path_to_test_resource("problems", *suffix)
X = anp.loadtxt(os.path.join(path, "%s.x" % name))
try:
F = anp.loadtxt(os.path.join(path, "%s.f" % name))
CV = None
if os.path.exists(os.path.join(path, "%s.cv" % name)):
CV = anp.loadtxt(os.path.join(path, "%s.cv" % name))
except:
return X, None, None
return X, F, CV
def __init__(self,csvname):
# grab input
data = np.loadtxt(csvname,delimiter = ',').T
self.x = data[:,:-1]
self.y = data[:,-1]
self.y.shape = (len(self.y),1)
self.colors = ['salmon','cornflowerblue','lime','bisque','mediumaquamarine','b','m','g']
def load(name, n_obj):
path = os.path.join(os.path.dirname(os.path.realpath(__file__)),
"resources", "WFG", "%sobj" % n_obj)
X = anp.loadtxt(os.path.join(path, "%s.x" % name))
try:
F = anp.loadtxt(os.path.join(path, "%s.f" % name))
CV = None
if os.path.exists(os.path.join(path, "%s.cv" % name)):
CV = anp.loadtxt(os.path.join(path, "%s.cv" % name))
except:
return X, None, None
return X, F, CV
def load_data(tag, fname, w, dim=2):
d = np.loadtxt(fname, ndmin=2)
if (np.shape(d)[0] != np.shape(w)[dim]):
print("Number of rows=%d in file '%s' does not match weight cols=%d" %
(np.shape(d)[0], fname, np.shape(w)[dim]))
sys.exit()
print("Loaded [%s] of %s data from '%s'" %
("x".join(map(str, np.shape(d))), tag, fname))
return d
def readImages(imageDir, nImages):
imA = np.zeros((n_grid, n_grid, nImages))
for i in range(0, nImages):
imageId = str(i)
impath = imageDir + str(imageId) + '.dat'
imA[:, :, i] = np.loadtxt(impath)
return imA
def load_data(self, csvname):
data = np.loadtxt(csvname, delimiter=',')
self.data = data
x = data[0:2, :]
y = data[-1, :][np.newaxis, :]
special_class = +1
return x, y, special_class
def load_weights(tag, fname, nheads):
w = np.loadtxt(fname, ndmin=2)
if (np.shape(w)[0] % nheads != 0):
print("Number of rows=%d is not divisible by nheads=%d in file '%s'" %
(np.shape(w)[0], nheads, fname))
sys.exit()
w = np.reshape(w, (nheads, np.shape(w)[0] / nheads, np.shape(w)[1]))
print("Loaded [%s] of %s weights from '%s'" %
("x".join(map(str, np.shape(w))), tag, fname))
return w
def __init__(self,csvname):
# grab input
data = np.loadtxt(csvname,delimiter = ',')
self.x = data[:-1,:]
self.y = data[-1:,:]
self.colors = [[1,0.8,0.5],[0,0.7,1]]
# if 1-d regression data make sure points are sorted
if np.shape(self.x)[1] == 1:
ind = np.argsort(self.x.flatten())
self.x = self.x[ind,:]
self.y = self.y[ind,:]
def dump_state(self, xk):
'''
callback to save the state to disk during optimization
'''
filename = 'state.txt'
if not os.path.exists(filename):
past = np.zeros((0, xk.shape[0]))
else:
past = np.loadtxt(filename)
if past.ndim < 2:
past = past.reshape(1, -1)
np.savetxt(filename, np.append(past, xk.reshape(1, -1), axis=0))
def __init__(self, csvname):
# grab input
data = np.loadtxt(csvname, delimiter=',')
self.x = data[:-1, :]
self.y = data[-1:, :]
# if 1-d regression data make sure points are sorted
if np.shape(self.x)[1] == 1:
ind = np.argsort(self.x.flatten())
self.x = self.x[ind, :]
self.y = self.y[ind, :]
cost_evals = [v / float(np.size(self.y)) for v in cost_evals]
def restore_checkpoint(output_folder, shared_file_object=True, optimizer=None):
i_epoch, i_batch = [
int(i)
for i in np.loadtxt(os.path.join(output_folder, 'checkpoint.txt'))
]
if not shared_file_object:
obj = np.load(os.path.join(output_folder, 'obj_checkpoint.npy'))
obj_delta = np.take(obj, 0, axis=-1)
obj_beta = np.take(obj, 1, axis=-1)
optimizer.restore_param_arrays_from_checkpoint()
return i_epoch, i_batch, obj_delta, obj_beta
else:
return i_epoch, i_batch
def load_data(self, csvname):
data = np.loadtxt(csvname, delimiter=',').T
self.x = data[:, :-1:]
self.y = data[:, -1:]
# center input
mean1 = np.mean(self.x[:, 0])
mean2 = np.mean(self.x[:, 1])
std1 = np.std(self.x[:, 0])
std2 = np.std(self.x[:, 1])
self.x[:, 0] -= mean1
self.x[:, 0] /= std1
self.x[:, 1] -= mean2
self.x[:, 1] /= std2
def __init__(self, csvname):
# grab input
data = np.loadtxt(csvname, delimiter=',')
data = data.T
self.x = data[:, :-1]
self.y = data[:, -1:]
self.colors = [
'salmon', 'cornflowerblue', 'lime', 'bisque', 'mediumaquamarine',
'b', 'm', 'g'
]
# if 1-d regression data make sure points are sorted
if np.shape(self.x)[1] == 1:
ind = np.argsort(self.x.flatten())
self.x = self.x[ind, :]
self.y = self.y[ind, :]
def main():
global args , x , y ,logx
args = parser.parse_args()
datapath = 'datasets/'
csvname = datapath + args.csvname
data = np.loadtxt(csvname,delimiter = ',')
#load in data
x = data[:-1,:]
y = data[-1:,:]
logx = np.log(x)
y = np.log(y)
x = np.concatenate((np.ones((1,1498),dtype=float),logx))
weights = np.random.rand(x.shape[0],1) #initial weights
weight_his, cost_his = gd(square_cost, args.lr, args.iteration, weights)
if args.draw:
draw_pic(weight_his,cost_his)
def get_init(init_type, ndof):
if init_type == 'rand':
init = np.random.random(ndof)
elif init_type == 'vac':
init = np.zeros(ndof) + 1e-5 * np.random.random(ndof)
elif init_type == 'one':
init = np.ones(ndof)
else:
tmp = open(init_type, 'r')
initfile = np.loadtxt(tmp)
if len(initfile) == ndof:
init = initfile
elif len(initfile) < ndof:
init = np.zeros(ndof, dtype=float)
init[:len(initfile)] = initfile
return init
def runSB(imageDir, saveDir, psf, psf_k, imageArray):
nImages = np.shape(imageArray)[2]
results = imageArray * 0
for imageIdx in range(0, nImages):
if imageIdx < start:
continue
grndpath = imageDir + str(imageIdx) + '.truth'
grnd = np.loadtxt(grndpath)
no_source = np.shape(grnd)[0]
if len(np.shape(grnd)) < 2:
no_source = 1
img = imageArray[:, :, imageIdx]
sb = SparseBayes(img, psf, psf_k, no_source)
results[:, :, imageIdx] = sb.res
s = saveDir + str(imageIdx) + '.out'
np.savetxt(s, sb.res)
#plt.imshow(results[:,:,imageIdx]);
#plt.show();
return results
def main():
global args, x, y
args = parser.parse_args()
datapath = 'datasets/'
csvname = datapath + args.csvname
data = np.loadtxt(csvname,delimiter = ',')
x = data[:-1,:]
y = data[-1:,:]
x = np.concatenate((np.ones((1,x.shape[1]),dtype=float),x))
weights = np.random.rand(x.shape[0],1)
alpha = [0.1,0.01]
weight_his1, cost_his1, wrong_num1 = gd2(cost_function, args.lr1, args.iteration, weights)
weight_his2, cost_his2, wrong_num2 = gd2(cost_function, args.lr2, args.iteration, weights)
update_weight1 = weight_his1[-1]
update_weight2 = weight_his2[-1]
res1 = np.sign(np.dot(x.T,update_weight1))
res2 = np.sign(np.dot(x.T,update_weight2))
acc1 = accuracy(res1,y)
acc2 = accuracy(res2,y)
print('the accuracy when lr=0.1 after 50 iterations is {:.3f}'.format(acc1))
print('the accuracy when lr=0.01 after 50 iterations is {:.3f}'.format(acc2))
if args.draw:
plt.figure(21,figsize=(8,6))
#draw pic1
plt.subplot(211)
plt.tight_layout(5)
plt.title('cost function history plot')
plt.plot([i for i in range(args.iteration+1)],cost_his1,'b')
plt.plot([i for i in range(args.iteration+1)],cost_his2,'r')
plt.legend(['$lr=0.1$','$lr=0.01$'])
#draw pic2
plt.subplot(212)
plt.title('misclassification history plot')
plt.scatter([i for i in range(args.iteration+1)],wrong_num1)
plt.scatter([i for i in range(args.iteration+1)],wrong_num2)
plt.legend(['$lr=0.1$','$lr=0.01$'])
plt.show()
def read_image(fframe, data_set='BTLS', background_subtract=False):
''' read given image
:param fframe:
file name. Currently assumes that the file can be opened using
PIL.Image
:param background_subtract:
If True, sigmaclipped background subtraction (default: False)
'''
if data_set == 'BTLS':
im = Image.open(fframe)
imarr = np.array(im)
elif dataset == 'mock_alpha':
imarr = np.loadtxt(fframe)
noise_level = 0.
if background_subtract:
# if true, simple sigmaclipped background subtraction
noise_level = np.median(stats.sigmaclip(imarr.flatten(), high=3.)[0])
return imarr - noise_level
def load_data(self,csvname):
data = np.loadtxt(csvname,delimiter = ',')
self.data = data
x = data[0:2,:]
y = data[-1,:][np.newaxis,:]
# remove points from one class for illustrative purposes
ind0 = np.argwhere(y == -1)
ind0 = [v[1] for v in ind0]
ind1 = np.argwhere(y == +1)
ind1 = [v[1] for v in ind1]
ind0 = ind0[-5:]
inds = ind0 + ind1
x = x[:,inds]
y = y[:,inds]
special_class = -1
return x,y,special_class
def _load_boston():
"""
Attribute Information:
1. CRIM: per capita crime rate by town
2. ZN: proportion of residential land zoned for lots over 25,000 sq.ft.
3. INDUS: proportion of non-retail business acres per town
4. CHAS: Charles River dummy variable (= 1 if tract bounds river; 0 otherwise)
5. NOX: nitric oxides concentration (parts per 10 million)
6. RM: average number of rooms per dwelling
7. AGE: proportion of owner-occupied units built prior to 1940
8. DIS: weighted distances to five Boston employment centres
9. RAD: index of accessibility to radial highways
10. TAX: full-value property-tax rate per $10,000
11. PTRATIO: pupil-teacher ratio by town
12. B: 1000(Bk - 0.63)^2 where Bk is the proportion of blacks by town
13. LSTAT: % lower status of the population
14. MEDV: Median value of owner-occupied homes in $1000's
"""
data = np.loadtxt(
os.path.join(data_dir, 'boston-housing/boston_housing.txt'))
X = data[:, :-1]
y = data[:, -1]
return X, y
# vector of time windows
T_vec = np.arange(Ts, T_bar, Ts)
# number of trials
M = 100
# vector of data
rate_data = np.zeros((len(T_vec), M))
# input matrix
B = I
# output matrix
C = I
for pp in range(M):
# upload C. elegans connectivity matrix (insert full file path)
A = np.loadtxt("insert_full_path/A_C_elegans.txt", usecols=range(n))
for tt in range(279):
for qq in range(279):
if tt > qq:
if random() < 0.5:
A_tmp = A[tt, qq]
A[tt, qq] = A[qq, tt]
A[qq, tt] = A_tmp
w, v = np.linalg.eig(A)
A = A - (max(np.real(w)) + 0.1) * I
# vector of transmission rates
rate_vec = np.zeros(len(T_vec))
with bl.Model() as m:
X = bl.Placeholder('X', dimensions=agnp.array([100, 784]))
encoder = bl.ml.neural_network.DenseNeuralNetwork(
'Encoder',
X,
layer_dims=[784, 50, 20],
nonlinearity=bl.math.utils.sigmoid)
decoder = bl.ml.neural_network.DenseNeuralNetwork(
'Decoder',
encoder,
layer_dims=[20, 50, 784],
nonlinearity=bl.math.utils.sigmoid,
last_layer_nonlinearity=bl.math.utils.sigmoid)
y = bl.rvs.Bernoulli('obs', decoder, observed=X)
fit_params = agnp.loadtxt("pos.txt", delimiter=',')
m.set_param(fit_params)
out = m.evaluate(decoder, feed_dict={X: train_images})
for i in range(out.shape[1]):
out[0, i, :] = out[0, i, :] > 0.5
fig, ax = plt.subplots(10, 10)
for i in range(10):
for j in range(10):
ax[i, j].imshow(out[0, i * 10 + j, :].reshape(28, 28))
ax[i, j].axis('off')
plt.show()
def __init__(self, csvname):
# grab input
data = np.loadtxt(csvname, delimiter=',')
data = data.T
self.x = data[:, :-1]
self.y = data[:, -1]