def __init__(self, width, height, recursiondepth):
"""Constructor for the Generator class.
Caps the desired space to a size that will
fit the algorithm.
"""
pg.init()
# STEP 1: Limit the map fit the necessary specs
self.width_px = round_down(width, TILESIZE)
self.height_px = round_down(height, TILESIZE)
if not (self.width_px//TILESIZE) % 2:
self.width_px += TILESIZE
if not (self.height_px//TILESIZE) % 2:
self.height_px += TILESIZE
print(f"Width: {self.width_px} Height: {self.height_px}")
self.rec_depth = recursiondepth
min_space_in_px = min(self.width_px//ROOMFRAC, self.width_px//ROOMFRAC)
# minimum number of tiles that the side of a space can have.
self.min_space = round_down(min_space_in_px//TILESIZE, TILESIZE)
# Setup the screen etc.
self.screen = pg.display.set_mode((self.width_px, self.height_px))
self.width_tiles = self.width_px//TILESIZE
self.height_tiles = self.height_px//TILESIZE
print(f"Width: {self.width_tiles} Height: {self.height_tiles}")
pg.display.set_caption("Dungeon Generator")
self.screen.fill(pg.color.THECOLORS["black"])
self.done = False
def slicing(self, start, distance, padding):
"""Calculate a spot to do a slice along
the given distance. Return number of the tile."""
if random.randint(0, 1):
slicing = start + (distance // 2) - padding
else:
slicing = start + (distance // 2) + padding
return round_down(slicing, 1)
import glob
from utils import round_down
segment_size = 500
fileCutoff = 4500
X = []
X_labels = np.array([])
# Grab all the waveforms
files = glob.glob("/home/nsbruce/RFI/data/waveforms/*")
for file in files[:fileCutoff]:
data = np.fromfile(file)
# Get length that rounds to nearest multiple of segment size
new_len = round_down(len(data), segment_size)
if new_len > 0:
data = data[:new_len]
i = 0
while len(data) - i > 0:
X.append(data[i:i + segment_size])
i += segment_size
X_labels = np.append(X_labels, str(file))
# print("File: {}, len(X): {}, len(X_labels): {}".format(file, len(X), len(X_labels)))
X = np.array(X)
print("Training/testing | X.shape: {}, X_labels.shape: {}".format(
X.shape, X_labels.shape))
np.save('/home/nsbruce/RFI/data/training_testing_waveforms.npy', X)
np.save('/home/nsbruce/RFI/data/training_testing_waveform_labels.npy',
def predict(model, test, test_targets, test_coords, test_shape, input_shape,
vnet, bayesian, batch_size, mc_samples, num_percentiles):
"""Uses given model to predict on test data."""
# Ensures MC samples is divisible by batch size.
if mc_samples < batch_size:
raise ValueError("Not enough MC samples.")
old_mc_samples = mc_samples
mc_samples = round_down(old_mc_samples, batch_size)
if old_mc_samples != mc_samples:
print("MC samples rounded from {} to {}".format(
old_mc_samples, mc_samples))
# Initializes prediction variables.
sigmoid = None
percentiles = None
scale = 100 / (num_percentiles - 1)
percentile_points = [scale * k for k in range(num_percentiles)]
if vnet:
# Initializes V-Net specific prediction variables.
sigmoid = np.zeros(test_shape)
counts = np.zeros(test_shape)
percentiles = [np.zeros(test_shape) for i in range(num_percentiles)]
# Predicts on individual chunks.
print()
for i, (chunk, coords) in enumerate(zip(test, test_coords)):
print("Chunk {}/{}".format(i + 1, test.shape[0]))
chunk_samples = np.empty((mc_samples, ) + input_shape)
chunk = np.expand_dims(chunk, axis=0)
batch = np.repeat(chunk, batch_size, axis=0)
# Performs Monte Carlo sampling.
for j in range(0, mc_samples, batch_size):
chunk_samples[j:j + batch_size] = model.predict_on_batch(batch)
# Discards poor edge predictions.
# I use 5% but this can be changed.
trimmed_shape = input_shape
border1 = ceil(input_shape[0] * 0.05)
border2 = ceil(input_shape[1] * 0.05)
border3 = ceil(input_shape[2] * 0.05)
# Checks edge cases on edge discarding.
# For example, we don't want to throw away an edge
# if it is the very edge of the volume, because that
# edge may only get predicted on once.
if coords[0] != 0 and coords[0] != test_shape[0] - input_shape[0]:
chunk_samples = chunk_samples[:, border1:-border1, :, :, :]
coords = [coords[0] + border1, coords[1], coords[2]]
trimmed_shape = [
trimmed_shape[0] - (2 * border1), trimmed_shape[1],
trimmed_shape[2], 1
]
elif coords[0] != 0:
chunk_samples = chunk_samples[:, border1:, :, :, :]
coords = [coords[0] + border1, coords[1], coords[2]]
trimmed_shape = [
trimmed_shape[0] - border1, trimmed_shape[1],
trimmed_shape[2], 1
]
elif coords[0] != test_shape[0] - input_shape[0]:
chunk_samples = chunk_samples[:, :-border1, :, :, :]
trimmed_shape = [
trimmed_shape[0] - border1, trimmed_shape[1],
trimmed_shape[2], 1
]
if coords[1] != 0 and coords[1] != test_shape[1] - input_shape[1]:
chunk_samples = chunk_samples[:, :, border2:-border2, :, :]
coords = [coords[0], coords[1] + border2, coords[2]]
trimmed_shape = [
trimmed_shape[0], trimmed_shape[1] - (2 * border2),
trimmed_shape[2], 1
]
elif coords[1] != 0:
chunk_samples = chunk_samples[:, :, border2:, :, :]
coords = [coords[0], coords[1] + border2, coords[2]]
trimmed_shape = [
trimmed_shape[0], trimmed_shape[1] - border2,
trimmed_shape[2], 1
]
elif coords[1] != test_shape[1] - input_shape[1]:
chunk_samples = chunk_samples[:, :, :-border2, :, :]
trimmed_shape = [
trimmed_shape[0], trimmed_shape[1] - border2,
trimmed_shape[2], 1
]
if coords[2] != 0 and coords[2] != test_shape[2] - input_shape[2]:
chunk_samples = chunk_samples[:, :, :, border3:-border3, :]
coords = [coords[0], coords[1], coords[2] + border3]
trimmed_shape = [
trimmed_shape[0], trimmed_shape[1],
trimmed_shape[2] - (2 * border3), 1
]
elif coords[2] != 0:
chunk_samples = chunk_samples[:, :, :, border3:, :]
coords = [coords[0], coords[1], coords[2] + border3]
trimmed_shape = [
trimmed_shape[0], trimmed_shape[1],
trimmed_shape[2] - border3, 1
]
elif coords[2] != test_shape[2] - input_shape[2]:
chunk_samples = chunk_samples[:, :, :, :-border3, :]
trimmed_shape = [
trimmed_shape[0], trimmed_shape[1],
trimmed_shape[2] - border3, 1
]
# Increments each voxel in the counts array.
counts = add_chunk_to_arr(counts, np.ones(trimmed_shape), coords,
trimmed_shape)
# Updates the sigmoid volume with the voxel means.
chunk_mean = np.mean(chunk_samples, axis=0)
sigmoid = add_chunk_to_arr(sigmoid, chunk_mean, coords,
trimmed_shape)
# Updates the percentile volumes.
percentile_samples = np.percentile(chunk_samples,
percentile_points,
axis=0)
percentiles = [
add_chunk_to_arr(p, s, coords, trimmed_shape)
for p, s in zip(percentiles, percentile_samples)
]
# Divides each voxel by the number of times it was predicted.
sigmoid = sigmoid / counts
# Note that division automatically broadcasts across axis 0.
percentiles = percentiles / counts
else:
# Predicts on entire slices.
print()
samples = np.zeros((mc_samples, ) + test_shape)
# Performs Monte Carlo sampling.
for i in range(mc_samples):
samples[i] = model.predict(test, batch_size=batch_size)
sigmoid = np.mean(samples, axis=0)
percentiles = np.percentile(samples, percentile_points, axis=0)
# Calculates prediction and uncertainty.
pred = sigmoid.copy()
pred[pred > 0.5] = 1.
pred[pred <= 0.5] = 0.
twenty = percentiles[num_percentiles // 5]
eighty = percentiles[num_percentiles - ((num_percentiles // 5) + 1)]
unc = eighty - twenty
# If data was chunked, turn it back into the original size.
if vnet and test_coords is not None and test_shape is not None:
test = reconstruct(test, test_coords, test_shape)
test_targets = reconstruct(test_targets, test_coords, test_shape)
# Saves predictions.
save_predictions(sigmoid, pred, percentiles, unc, test, test_targets)
def calc_padding(self, distance):
"""Calculates an offset from a slice-point.
Return the offset as number of tiles."""
percent = random.randint(0, MAX_SLICE_OFFSET)/100
padding = int(distance*percent)
return round_down(padding, 1)
query = SimpleStatement(
'SELECT attribute,value FROM resource_attributes WHERE context = %s AND resource = %s'
)
print("Resources on %s:%s :" % (foreign_source, foreign_id))
for resource in resources:
resource.attributes = []
for row in session.execute(query, (CONTEXT, resource.key)):
resource.attributes.append((row.attribute, row.value))
print("%s: %s" % (resource.key, resource.attributes))
# Convert the times to timestamps expressed in seconds
start_ts = time.mktime(start.timetuple())
end_ts = time.mktime(end.timetuple())
# Compute the partition keys
first_partition = int(round_down(start_ts, SHARD))
last_partition = int(round_down(end_ts, SHARD)) + SHARD
partitions = []
for partition in range(first_partition, last_partition, SHARD):
print("Partition: %d includes data from: %s, to %s" %
(partition, df(partition), df(partition + SHARD)))
partitions.append(partition)
# Gather the samples for every resource in every partition
query = SimpleStatement(
'SELECT * from samples WHERE context = %s AND partition = %s and resource = %s'
)
for resource in resources:
# Execute the query for each partition
for partition in partitions:
tempX = build_dataset('./waveforms/', indexes, featureFile,
args.segment_size)
X = np.append(X, tempX)
print("Length of X so far: {}".format(X.shape))
# Restructure the dataset
X = FloatTensor(X)
X = X.view(-1, segment_size)
# Normalize the data in amplitude
X = (X - X.mean(dim=-1).unsqueeze(1)) / X.std(dim=-1).unsqueeze(1)
# Split training and validation sets from the same dataste
splitSize = round_down(int(len(X) * 0.8), segment_size)
print("Shape of X: {}".format(X.shape))
X_train = X[:splitSize]
X_test = X[splitSize:]
print("X_train length: {}".format(len(X_train)))
print("X_test length: {}".format(len(X_test)))
# number of epochs and training set batch size
num_epochs = args.num_epochs
batch_size = args.batch_size
########## Define the model ##########
model = convautoencoder()
if has_cuda:
model = model.cuda()
model.train()