def test_boptim(acqf, result):
Z_sparse = initial_seed()
X_full = gprutils.get_full_grid(Z_sparse)
X_sparse = gprutils.get_sparse_grid(Z_sparse)
expected_result = np.load(result)
boptim = boptimizer(X_sparse,
Z_sparse,
X_full,
trial_func,
acquisition_function=acqf,
exploration_steps=20,
use_gpu=False,
verbose=1)
boptim.run()
assert_allclose(boptim.target_func_vals[-1], expected_result)
def test_skgpr_2d(kernel): # sanity check only, due to comput cost
R = get_dummy_data()
X = gprutils.get_sparse_grid(R)
X_true = gprutils.get_full_grid(R)
mean, sd, _ = skgpr.skreconstructor(X,
R,
X_true,
kernel=kernel,
learning_rate=0.1,
iterations=2,
use_gpu=False,
verbose=False).run()
assert_(mean.shape == sd.shape == R.shape)
assert_(not np.isnan(mean).any())
assert_(not np.isnan(sd).any())
def test_gpr_3d(kernel): # sanity check only due to comput cost
R = np.load(test_data3d)
X = gprutils.get_sparse_grid(R)
X_true = gprutils.get_full_grid(R)
mean, sd, _ = gpr.reconstructor(X,
R,
X_true,
kernel=kernel,
lengthscale=None,
indpoints=50,
learning_rate=0.1,
iterations=2,
use_gpu=False,
verbose=True).run()
assert_(mean.shape == sd.shape == R.flatten().shape)
assert_(not np.isnan(mean).any())
assert_(not np.isnan(sd).any())
def test_gpr_2d(kernel):
R = np.load(test_data2d)
R_ = np.load(test2d_expected_result)
X = gprutils.get_sparse_grid(R)
X_true = gprutils.get_full_grid(R)
mean, _, _ = gpr.reconstructor(X,
R,
X_true,
kernel=kernel,
lengthscale=[[1., 1.], [4., 4.]],
indpoints=250,
learning_rate=0.1,
iterations=200,
use_gpu=False,
verbose=False).run()
assert_(ssim(mean, R_) > 0.95)
assert_(np.linalg.norm(mean - R_) < 3)
def test_skgpr_3d(kernel): # sanity check only, due to comput cost
R = np.load(test_data3d)
X = gprutils.get_sparse_grid(R)
X_true = gprutils.get_full_grid(R)
(mean, sd), _ = skgpr.skreconstructor(X,
R,
X_true,
kernel=kernel,
lengthscale=None,
grid_points_ratio=.25,
learning_rate=0.1,
iterations=2,
num_batches=100,
calculate_sd=True,
use_gpu=False,
verbose=True).run()
assert_(mean.shape == sd.shape == R.flatten().shape)
assert_(not np.isnan(mean).any())
assert_(not np.isnan(sd).any())
def test_skgpr_2d(kernel):
R = np.load(test_data)
R_ = np.load(test_expected_result)
X = gprutils.get_sparse_grid(R)
X_true = gprutils.get_full_grid(R)
mean, _ = skgpr.skreconstructor(X,
R,
X_true,
kernel=kernel,
lengthscale=[[1., 1.], [4., 4.]],
grid_points_ratio=1.,
learning_rate=0.1,
iterations=20,
calculate_sd=False,
num_batches=1,
use_gpu=False,
verbose=False).run()
assert_(ssim(mean, R_) > 0.98)
assert_(np.linalg.norm(mean - R_) < 1)
type=int,
help="1 for using GPU, 0 for running on CPU")
parser.add_argument("--SAVEDIR",
nargs="?",
default="Output",
type=str,
help="directory to save outputs")
args = parser.parse_args()
# Load data (e.g. N x M image or N x M x L spectroscopic grid)
R_true = np.load(args.FILEPATH)
if args.NORMALIZE and np.isnan(R_true).any() is False:
R_true = (R_true - np.amin(R_true)) / np.ptp(R_true)
# Get "ground truth" grid indices
X_true = gprutils.get_full_grid(R_true, dense_x=1.)
# Construct lengthscale constraints for all dimensions
LENGTH_CONSTR = [[
float(args.LENGTH_CONSTR_MIN) for i in range(np.ndim(R_true))
], [float(args.LENGTH_CONSTR_MAX) for i in range(np.ndim(R_true))]]
# Corrupt data (if args.PROB > 0)
X, R = gprutils.corrupt_data_xy(X_true, R_true, args.PROB)
# Directory to save results
if not os.path.exists(args.SAVEDIR):
os.makedirs(args.SAVEDIR)
# Reconstruct the corrupt data. Initalize our "reconstructor" first.
reconstr = gpr.reconstructor(X,
R,
X_true,
args.KERNEL,
LENGTH_CONSTR,
help="Directory to save outputs")
args = parser.parse_args()
# Load "ground truth" data (N x M x L spectroscopic grid)
# (in real experiment we will just get an empty array)
R_true = np.load(args.FILEPATH)
if args.NORMALIZE and np.isnan(R_true).any() is False:
R_true = (R_true - np.amin(R_true)) / np.ptp(R_true)
# Make initial set of measurements for exploration analysis.
# Let's start with "opening" several points along each edge
R = R_true * 0
R[R == 0] = np.nan
R = gprutils.open_edge_points(R, R_true)
# Get sparse and full grid indices
X = gprutils.get_sparse_grid(R)
X_true = gprutils.get_full_grid(R)
dist_edge = [0, 0] # set to non-zero vals when edge points are not "opened"
# Construct lengthscale constraints for all 3 dimensions
LENGTH_CONSTR = [[float(args.LENGTH_CONSTR_MIN) for i in range(3)],
[float(args.LENGTH_CONSTR_MAX) for i in range(3)]]
# Run exploratory analysis
uncert_idx_all, uncert_val_all, mean_all, sd_all, R_all = [], [], [], [], []
if not os.path.exists(args.SAVEDIR): os.makedirs(args.SAVEDIR)
indpts_r = args.INDUCING_POINTS_RATIO
for i in range(args.ESTEPS):
print('Exploration step {}/{}'.format(i, args.ESTEPS))
# Make the number of inducing points dependent on the number of datapoints
indpoints = len(gprutils.prepare_training_data(X, R)[0]) // indpts_r
# clip to make sure it fits into GPU memory
indpoints = 2000 if indpoints > 2000 else indpoints
# Initialize explorer