def fill(self):
r_phi = self.r_phi
b_phi = self.b_phi
g_phi = self.g_phi
if not self.r_phi == 0:
r_phi = pi / self.r_phi
if not self.b_phi == 0:
b_phi = pi / self.b_phi
if not self.g_phi == 0:
g_phi = pi / self.g_phi
for idx in range(self.strip_length):
idx2degree = scale(idx + self.counter, 0, self.max_range, 0, self.strip_length)
r = sin(idx2degree + r_phi)
g = sin(idx2degree + g_phi)
b = sin(idx2degree + b_phi)
r = scale(r, 0, 255, -1, 1)
g = scale(g, 0, 255, -1, 1)
b = scale(b, 0, 255, -1, 1)
r = floor(r)
g = floor(g)
b = floor(b)
self.pixels[idx]['color'] = RGB(r=r, g=g, b=b, a=self.color.a)
self.counter += 1
self.counter %= self.strip_length * 255
def printminmaxavg(entries, details=False):
""" Print start, current, minimum, maximum, and average usage
"""
# list comprehension:
values = [int(e[1]) for e in entries]
min_used = min(values)
max_used = max(values)
max_used_entry = entries[values.index(max_used)]
min_used_entry = entries[values.index(min_used)]
avg_used = mean(values)
if details:
print(' started:', scale('M', entries[0][1]), 'on',
entries[0][0].date())
print(' currently:', scale('M', entries[-1][1]), 'on',
entries[-1][0].date())
print(' min used:', scale('M', min_used), 'on',
min_used_entry[0].date())
print(' max used:', scale('M', max_used), 'on',
max_used_entry[0].date())
print(' avg used:', scale('M', avg_used))
else:
print(' started:', humanize(entries[0][1]), 'on',
entries[0][0].date())
print(' currently:', humanize(entries[-1][1]), 'on',
entries[-1][0].date())
print(' min used:', humanize(min_used), 'on',
min_used_entry[0].date())
print(' max used:', humanize(max_used), 'on',
max_used_entry[0].date())
print(' avg used:', humanize(avg_used))
def image(self):
image = pg.Surface(self.original_image.get_rect().size, pg.SRCALPHA)
# rotating image
img = pg.transform.rotate(self.original_image.copy(), self.rotation)
# updating transparency of the image nearing the end of cooldown
img.set_colorkey((102, 255, 0))
alpha = int(self.cooldown * 255 / 100)
img.set_alpha(alpha)
if self.size[0] == 0 or self.size[0] == 0:
self.size[0], self.size[1] = 0, 0
img.set_alpha(0)
else:
if not alpha % 3:
self.size[0] += 1
self.size[1] += 1
img = u.scale(img, self.size)
self.rect.size = img.get_rect().size
#self.rect.center = self.cfg["position"]
image = pg.Surface(self.rect.size, pg.SRCALPHA)
# drawing created image to returning surface
image.blit(img, (0, 0))
if self.scale > 1:
old_posistion = self.rect.center
old_size = image.get_rect().size
image = u.scale(image, self.scale)
new_size = image.get_rect().size
self.rect.centerx -= (new_size[0] - old_size[0]) / self.scale
self.rect.centery -= (new_size[1] - old_size[1]) / self.scale
return image
def scale(rs, gs, bs):
"""
Scale and convert to int lists of rgb values
"""
# get maxs and mins
r_min = min(rs)
r_max = max(rs)
g_min = min(gs)
g_max = max(gs)
b_min = min(bs)
b_max = max(bs)
# scale
rs = [scale(r, 0, 255, r_min, r_max) for r in rs]
gs = [scale(g, 0, 255, g_min, g_max) for g in gs]
bs = [scale(b, 0, 255, b_min, b_max) for b in bs]
# convert to int
rs = [int(elem) for elem in rs]
gs = [int(elem) for elem in gs]
bs = [int(elem) for elem in bs]
return rs, gs, bs
def alpha32(df):
"""
Alpha#32
(scale(((sum(close, 7) / 7) - close)) +
(20 * scale(correlation(vwap, delay(close, 5), 230))))
"""
temp1 = u.scale(((u.ts_sum(df.close, 7) / 7) - df.close))
temp2 = (20 * u.scale(u.corr(df.vwap, u.delay(df.close, 5), 230)))
return temp1 + temp2
def alpha60(df):
"""
Alpha#60
(0 - (1 * ((2 * scale(rank(((((close - low) - (high - close)) / (high - low)) * volume))))
- scale(rank(ts_argmax(close, 10))))))
"""
temp1 = u.scale(
u.rank(((((df.close - df.low) - (df.high - df.close)) /
(df.high - df.low)) * df.volume)))
return (0 - (1 *
((2 * temp1) - u.scale(u.rank(u.ts_argmax(df.close, 10))))))
def _radar(self, spectrum):
r = [0] * spectrum
for b in self.balls:
angle = utils.angle(self.agent.x, b.x, self.agent.y, b.y)
distance = utils.dist(self.agent.x, b.x, self.agent.y, b.y)
r[utils.sector(angle, spectrum)] += utils.scale(distance)
r[utils.sector(0, spectrum)] += utils.scale(self.width - self.agent.x)
r[utils.sector(90,
spectrum)] += utils.scale(self.height - self.agent.y)
r[utils.sector(180, spectrum)] += utils.scale(self.agent.x)
r[utils.sector(270, spectrum)] += utils.scale(self.agent.y)
return r
def _radar(self, spectrum):
r = [0] * spectrum
for b in self.balls:
angle = utils.angle(self.agent.x, b.x, self.agent.y, b.y)
distance = utils.dist(self.agent.x, b.x, self.agent.y, b.y)
r[utils.sector(angle, spectrum)] += utils.scale(distance)
# передаем на вход сети сигналы от стен, чтобы агент не прилипал к краю
r[utils.sector(0, spectrum)] += utils.scale(self.width - self.agent.x)
r[utils.sector(90,
spectrum)] += utils.scale(self.height - self.agent.y)
r[utils.sector(180, spectrum)] += utils.scale(self.agent.x)
r[utils.sector(270, spectrum)] += utils.scale(self.agent.y)
return r
def pre_process(self):
#tf.keras.K.image_data_format() == 'channels_first'
a = False
if a:
x_train = self.x_train.reshape(self.x_train.shape[0], 1,
self.img_rows, self.img_cols)
x_val = self.x_val.reshape(self.x_val.shape[0], 1, self.img_rows,
self.img_cols)
x_test = self.x_test.reshape(self.x_test.shape[0], 1,
self.img_rows, self.img_cols)
input_shape = (1, self.img_rows, self.img_cols)
else:
x_train = self.x_train.reshape(self.x_train.shape[0],
self.img_rows, self.img_cols, 1)
x_val = self.x_val.reshape(self.x_val.shape[0], self.img_rows,
self.img_cols, 1)
x_test = self.x_test.reshape(self.x_test.shape[0], self.img_rows,
self.img_cols, 1)
input_shape = (self.img_rows, self.img_cols, 1)
x_train = x_train.astype('float32')
x_val = x_val.astype('float32')
x_test = x_test.astype('float32')
x_train, X_min, X_max = scale(x_train, 0, 255)
x_val, _, _ = scale(x_val, 0, 255, X_min=X_min, X_max=X_max)
x_test, _, _ = scale(x_test, 0, 255, X_min=X_min, X_max=X_max)
x_train /= 255
x_val /= 255
x_test /= 255
# convert class vectors to binary class matrices
f = False
if f:
i = 0
for row in x_train:
x_train[i, :] = tf.keras.preprocess_input(row)
i = i + 1
i = 0
for row in x_val:
x_val[i, :] = tf.keras.preprocess_input(row)
i = i + 1
for row in x_test:
x_test[i, :] = tf.keras.preprocess_input(row)
i = i + 1
if self.one_hot:
self.y_train = tf.keras.utils.to_categorical(
self.y_train, self.num_classes)
self.y_val = tf.keras.utils.to_categorical(self.y_val,
self.num_classes)
self.y_test = tf.keras.utils.to_categorical(
self.y_test, self.num_classes)
return #x_train, y_train, x_val, y_val, x_test, y_test, input_shape
def alpha28(df):
"""
Alpha#28
scale(((correlation(adv20, low, 5) + ((high + low) / 2)) - close))
"""
return u.scale(((u.corr(u.adv(df, 20), df.low, 5) +
((df.high + df.low) / 2)) - df.close))
def predict(self, X, threshold=0.8):
"""Predict whether samples in X ar anomalous based on reconstruction
performance of the BiGAN.
Parameters
----------
X : np.array of shape=(n_samples, n_features)
Samples to predict.
threshold : float, default=0.8
Maximum MSE to be concidered normal.
Returns
-------
result : np.array of shape=(n_samples,)
Prediction of -1 (anomalous) or +1 (normal).
"""
# Rescale X to range -1 to 1
X = scale(X, min=-1, max=1)
# Get latent representation of X
z = self.encoder.predict(X)
# Reconstruct output of X
r = self.generator_data.predict(z)
# Compute MSE between original and reconstructed
mse = np.square(X - r).reshape(X.shape[0], -1).mean(axis=1)
# Apply threshold for prediction
predict = 2 * (mse <= threshold) - 1
# Return result
return predict
def closest_point(self, f_x, f_y, s_x, s_y, obs_bearing):
'''
Calculate the closest point on the line to the feature
The feature is the point (probably not on the line)
The line is defined by a point (state x and y) and direction (heading)
This probably won't return a point that is behind the x-y-bearing.
Input:
f_x float (feature's x coordinate)
f_y float (feature's y coordinate)
s_x float (robot state's x)
s_y float (robot state's y)
obs_bearing float (robot state's heading)
'''
origin_to_feature = (
f_x - s_x,
f_y - s_y,
0.0,
)
line_parallel = unit((cos(obs_bearing), sin(obs_bearing), 0.0))
# origin_to_feature dot line_parallel = magnitude of otf along line
magmag = dot_product(origin_to_feature, line_parallel)
if magmag < 0:
return (s_x, s_y)
scaled_line = scale(line_parallel, magmag)
scaled_x = scaled_line[0]
scaled_y = scaled_line[1]
return (float(s_x + scaled_x), float(s_y + scaled_y))
def split_image_to_4(image):
image_1 = image
image_2 = rotate(image, 20, BATCH_SIZE_DEFAULT)
image_3 = scale(image, 20, 4, BATCH_SIZE_DEFAULT)
image_4 = random_erease(image, BATCH_SIZE_DEFAULT)
image_1 = image_1.to('cuda')
image_2 = image_2.to('cuda')
image_3 = image_3.to('cuda')
image_4 = image_4.to('cuda')
# image = image.to('cuda')
# show_mnist(image_1[0], 20, 28)
# show_mnist(image_1[1], 20, 28)
# show_mnist(image_1[2], 20, 28)
# show_mnist(image_1[3], 20, 28)
#
# show_mnist(image_2[0], 20, 28)
# show_mnist(image_2[1], 20, 28)
# show_mnist(image_2[2], 20, 28)
# show_mnist(image_2[3], 20, 28)
#
# input()
# print(image_1.shape)
# print(image_2.shape)
# print(image_3.shape)
# print(image_4.shape)
# input()
return image_1, image_2, image_3, image_4
def sample_images(self, outfile, data=None, width=5, height=5):
"""Generate width x height images and write them to outfile.
Parameters
----------
outfile : string
Path to outfile to write image to.
width : int, default=5
Number of generated images in width of output figure.
height : int, default=5
Number of generated images in height of output figure.
"""
# Generate random images
if data is None:
X_fake = self.generate(amount=(height * width))
else:
X_fake = data
# Rescale images 0 - 1
X_fake = scale(X_fake, 0, 1)
# Create subplot
fig, axs = plt.subplots(height, width)
counter = 0
for x in range(height):
for y in range(width):
axs[x, y].imshow(X_fake[counter], cmap='gray')
axs[x, y].axis('off')
counter += 1
fig.savefig(outfile)
plt.close()
def create_image(self):
img = self.original_image.copy()
if self.cfg["scale"]:
img = u.scale(img, (
int(img.get_rect().width * self.cfg["scale"]),
int(img.get_rect().height * self.cfg["scale"]),
))
if self.cfg["rotation"] > 0:
img = pg.transform.rotate(img, self.cfg["rotation"])
if self.bow:
width = int(self.rect.width)
height = int(self.rect.height)
if self.bow == "left" or self.bow == "right":
width -= 3
if self.bow == "up" or self.bow == "down":
height -= 5
img = pg.transform.scale(img, (width, height))
if self.cfg["box"]:
img = u.drawBorder(img, size=1, color=(255, 0, 0))
return img
def get_harmony_generator():
other_harmonies = get_random_valids()
if random.random() < .7:
# fewer other harmonies
percent_other = scale(random.random(), 0, 1, 0.0, 0.1)
else:
# more other harmonies
percent_other = scale(random.random(), 0, 1, 0.1, 0.6)
while True:
if random.random() < percent_other:
yield random.choice(other_harmonies)
else:
yield context_free_harmony.choose()
def closest_point(self, f_x, f_y, s_x, s_y, obs_bearing):
'''
Calculate the closest point on the line to the feature
The feature is the point (probably not on the line)
The line is defined by a point (state x and y) and direction (heading)
This probably won't return a point that is behind the x-y-bearing.
Input:
f_x float (feature's x coordinate)
f_y float (feature's y coordinate)
s_x float (robot state's x)
s_y float (robot state's y)
obs_bearing float (robot state's heading)
'''
origin_to_feature = (f_x - s_x, f_y - s_y, 0.0,)
line_parallel = unit((cos(obs_bearing), sin(obs_bearing), 0.0))
# origin_to_feature dot line_parallel = magnitude of otf along line
magmag = dot_product(origin_to_feature, line_parallel)
if magmag < 0:
return (s_x, s_y)
scaled_line = scale(line_parallel, magmag)
scaled_x = scaled_line[0]
scaled_y = scaled_line[1]
return (float(s_x + scaled_x), float(s_y + scaled_y))
def get_confidence(self):
if self.confidence_level is None or self.confidence_level > constants.ZERO_CONFIDENCE:
return '0', False
elif self.confidence_level == 0:
return '100', False
elif self.confidence_level < constants.SUCCESS_CONFIDENCE:
scaled_val = utils.scale(self.confidence_level,
constants.SUCCESS_CONFIDENCE_SCALE,
constants.SUCCESS_PERCENT_SCALE)
perc = 100 - scaled_val
return '%.2f' % perc, True
else:
scaled_val = utils.scale(self.confidence_level,
constants.FAIL_CONFIDENCE_SCALE,
constants.FAIL_PERCENT_SCALE)
perc = constants.SUCCESS_PERCENT - scaled_val
return '%.2f' % perc, False
def get_confidence(self):
if self.confidence_level is None or self.confidence_level > constants.ZERO_CONFIDENCE:
return '0', False
elif self.confidence_level == 0:
return '100', False
elif self.confidence_level < constants.SUCCESS_CONFIDENCE:
scaled_val = utils.scale(self.confidence_level,
constants.SUCCESS_CONFIDENCE_SCALE,
constants.SUCCESS_PERCENT_SCALE)
perc = 100 - scaled_val
return '%.2f' % perc, True
else:
scaled_val = utils.scale(self.confidence_level,
constants.FAIL_CONFIDENCE_SCALE,
constants.FAIL_PERCENT_SCALE)
perc = constants.SUCCESS_PERCENT - scaled_val
return '%.2f' % perc, False
def main():
z, x, y = read('data/alaska/clipped_elev.tif')
rgb, _, _ = read('data/alaska/clipped_map.tif')
rgb = np.swapaxes(rgb.T, 0, 1)
fig = mlab.figure()
surf = mlab.mesh(x[::2, ::2], y[::2, ::2], z[::2, ::2])
utils.texture(surf, rgb)
build_sides(x, y, z, -1000)
build_bottom(x, y, z, -1000)
utils.scale(fig, (1, 1, 2.5))
utils.scale(fig, 0.00001)
# shapeways_io.save_vrml(fig, 'models/alaska_textured_sides.zip')
utils.present(fig)
def parse_scale(element, csg_graph):
# Get the current csg object
V, F = csg_graph[element.find('operand').text.strip()]
# Scale parameter (required)
s = element.find('scale').text
s = list(map(float, s[s.find('[') + 1:s.find(']')].split(',')))
# Translate and return the "new" vertices
return scale(V, s), F
def test_across_scale_difference(img: np.ndarray, out_file: str,
finer_scale: int, coarse_scale: int):
pyramid = utils.pyramid_dictionary(img, 8)
difference = utils.across_scale_difference(pyramid, finer_scale,
coarse_scale)
difference = utils.scale(difference)
cv2.imwrite(out_file, difference)
def hessian(self, m_dot, project=False):
""" Evaluates the Hessian action at the most recently evaluated control
value in direction m_dot.
Args:
m_dot: The direction in control space in which to compute the
Hessian. Must be of the same type as the Control (e.g. Function,
Constant or lists of latter).
project (Optional[bool]): If True, the returned value will be the L2
Riesz representer, if False it will be the l2 Riesz representative.
The L2 projection requires one additional linear solve. Defaults to
False.
Returns:
The directional second derivative. The returned type is the same as the control
type.
Note: Hessian evaluations never delete the forward state.
"""
# Check if we have the gradient already in the cash.
# If so, return the cached value
if self.cache is not None:
hash = value_hash([x.data() for x in self.controls] + [m_dot])
fnspaces = [p.data().function_space() if isinstance(p.data(),
Function) else None for p in self.controls]
if hash in self._cache["hessian_cache"]:
info_green("Got a Hessian cache hit.")
return cache_load(self._cache["hessian_cache"][hash], fnspaces)
else:
info_red("Got a Hessian cache miss")
# Compute the Hessian action by solving the second order adjoint equations
Hm = self.H(m_dot, project=project)
# Apply the scaling factor
scaled_Hm = utils.scale(Hm, self.scale)
# Call callback
control_data = [p.data() for p in self.controls]
if self.current_func_value is not None:
current_func_value = self.scale * self.current_func_value
else:
current_func_value = None
self.hessian_cb(current_func_value,
delist(control_data, list_type=self.controls),
m_dot, scaled_Hm)
# Cache the result
if self.cache is not None:
self._cache["hessian_cache"][hash] = cache_store(scaled_Hm, self.cache)
return scaled_Hm
def __init__(self, ranges=False):
score = self.score = Score()
self.instruments = self.i = Instruments()
self.parts = Parts(self.i)
# Make Metadata
timestamp = datetime.datetime.utcnow()
metadata = Metadata()
metadata.title = 'Short Stories'
metadata.composer = 'Jonathan Marmor'
metadata.date = timestamp.strftime('%Y/%m/%d')
score.insert(0, metadata)
[score.insert(0, part) for part in self.parts.l]
score.insert(0, StaffGroup(self.parts.l))
if ranges:
# Don't make a piece, just show the instrument ranges
for inst, part in zip(self.instruments.l, self.parts.l):
measure = Measure()
measure.timeSignature = TimeSignature('4/4')
low = Note(inst.lowest_note)
measure.append(low)
high = Note(inst.highest_note)
measure.append(high)
part.append(measure)
return
self.duet_options = None
# 8 to 12 minutes
max_duration = 12
piece_duration_minutes = scale(random.random(), 0, 1, 8, max_duration)
# Make the "songs"
self.songs = []
total_minutes = 0
n = 1
while total_minutes < piece_duration_minutes - .75:
print
print 'Song', n
song = Song(self, n)
self.songs.append(song)
print 'Song Duration:', int(round(song.duration_minutes * 60.0))
print 'Tempo:', song.tempo
print 'Number of Beats:', song.duration_beats
n += 1
total_minutes += song.duration_minutes
_minutes, _seconds = divmod(total_minutes, 1.0)
print
print 'Total Duration: {}:{}'.format(int(_minutes), int(round(_seconds * 60)))
print
self.make_notation()
def choose_movement_durations(self):
"""Choose the durations of the two major sections of the piece.
Choose a split point between the golden mean of the whole piece and
the golden mean of the section between the golden mean of the piece and
the end of the piece."""
minimum = GOLDEN_MEAN
# The golden mean of the section between the golden mean and 1
maximum = scale(minimum, 0, 1, minimum, 1)
# Pick a random float between minimum and maximum
division = scale(random.random(), 0, 1, minimum, maximum)
# Get the durations of each section
one = int(scale(division, 0, 1, 0, self.piece_duration))
two = self.piece_duration - one
return one, two
def goal_force(self, pose, goal):
dx = goal.position.x - pose.position.x
dy = goal.position.y - pose.position.y
weight = 5.0
farce = (dx, dy, 0)
farce = unit(farce)
farce = scale(farce, weight)
return farce
def render(edges,
vertices,
scale=(1, 1),
position=(0, 0),
offset=(0, 0),
color="black"):
wn = turtle.Screen()
t = turtle.Turtle()
t.speed(0)
t.pensize(1)
t.hideturtle()
wn.tracer(0, 0)
t.pencolor(color)
t.penup()
# copy by value
local_vertices = [] + vertices
# find center of object
midpoint = utils.vertices_midpoint(local_vertices)
# adjust scale and position
# move center of object to origin point for ease implulation
local_vertices = utils.translate(local_vertices,
[-midpoint[0], -midpoint[1]])
local_vertices = utils.scale(local_vertices, scale)
min_x = utils.get_min_x(local_vertices)
min_y = utils.get_max_y(local_vertices)
local_vertices = utils.translate(
local_vertices,
(-min_x + offset[0] + position[0], min_y + offset[1] + position[1]))
# drawing
for edge in edges:
t.penup()
from_edge = edge[0] - 1
to_edge = edge[1] - 1
p = local_vertices[from_edge]
x_2d = p[0]
y_2d = p[1]
t.goto(x_2d, y_2d)
p = local_vertices[to_edge]
t.pendown()
x_2d = p[0]
y_2d = p[1]
t.goto(x_2d, y_2d)
wn.update()
def compute_scores(f_ground_truth, f_prediction, parameters):
# Load ground truth
raw_graph = np.loadtxt(f_ground_truth, delimiter=",")
row = raw_graph[:, 0] - 1
col = raw_graph[:, 1] - 1
data = raw_graph[:, 2]
valid_index = data > 0
y_true = coo_matrix((data[valid_index],
(row[valid_index], col[valid_index])),
shape=(1000, 1000))
y_true = y_true.toarray()
if parameters.get("killing", None):
# load name_kill_var
killing_file = os.path.join(WORKING_DIR, "datasets", "hidden-neurons",
"{0}_kill_{1}.txt"
"".format(parameters["network"],
parameters["killing"]))
kill = np.loadtxt(killing_file, dtype=np.int)
# make a mask
alive = np.ones((y_true.shape[0],), dtype=bool)
alive[kill - 1] = False # we need to make -1 since it's matlab indexing
y_true = y_true[alive][:, alive]
# Load predictions
rows = []
cols = []
scores = []
with open(f_prediction) as fhandle:
fhandle.next()
for line in fhandle:
line = line.strip()
prefix, score = line.rsplit(",", 1)
scores.append(float(score))
row, col = prefix.split("_")[-2:]
rows.append(int(row) - 1)
cols.append(int(col) - 1)
y_scores = scale(coo_matrix((scores, (rows, cols))).toarray())
print(y_true.shape)
print(y_scores.shape)
# Compute scores
measures = dict((name, metric(y_true.ravel(), y_scores.ravel()))
for name, metric in METRICS.items())
return measures
def create_image(self): # pg.surface
surface = pg.Surface(self.cfg["size"], pg.SRCALPHA)
image = self.original_image.copy()
if bool(random.getrandbits(1)):
pg.transform.flip(image, bool(random.getrandbits(1)),
bool(random.getrandbits(1)))
image = u.scale(image, self.cfg["size"])
surface.blit(image, (0, 0))
return surface
def __getitem__(self, item):
image_path = self.images[item]
boxes = self.objects[item]
image = Image.open(image_path)
shape = image.size
image = self.transforms(image)
boxes = torch.tensor(boxes, dtype=torch.float32)
boxes = scale(boxes, shape)
return image, boxes
def compute_scores(f_ground_truth, f_prediction, parameters):
# Load ground truth
raw_graph = np.loadtxt(f_ground_truth, delimiter=",")
row = raw_graph[:, 0] - 1
col = raw_graph[:, 1] - 1
data = raw_graph[:, 2]
valid_index = data > 0
y_true = coo_matrix(
(data[valid_index], (row[valid_index], col[valid_index])),
shape=(1000, 1000))
y_true = y_true.toarray()
if parameters.get("killing", None):
# load name_kill_var
killing_file = os.path.join(
WORKING_DIR, "datasets", "hidden-neurons", "{0}_kill_{1}.txt"
"".format(parameters["network"], parameters["killing"]))
kill = np.loadtxt(killing_file, dtype=np.int)
# make a mask
alive = np.ones((y_true.shape[0], ), dtype=bool)
alive[kill -
1] = False # we need to make -1 since it's matlab indexing
y_true = y_true[alive][:, alive]
# Load predictions
rows = []
cols = []
scores = []
with open(f_prediction) as fhandle:
fhandle.next()
for line in fhandle:
line = line.strip()
prefix, score = line.rsplit(",", 1)
scores.append(float(score))
row, col = prefix.split("_")[-2:]
rows.append(int(row) - 1)
cols.append(int(col) - 1)
y_scores = scale(coo_matrix((scores, (rows, cols))).toarray())
print(y_true.shape)
print(y_scores.shape)
# Compute scores
measures = dict((name, metric(y_true.ravel(), y_scores.ravel()))
for name, metric in METRICS.items())
return measures
def off_axis_error(self, location, goal):
"""
calc error normal to axis defined by the goal position and direction
input: two nav_msgs.msg.Odometry, current best location estimate and
goal
output: double distance along the axis
axis is defined by a vector from the unit circle aligned with the goal
heading
relative position is the vector from the goal x, y to the location x, y
distance is defined by subtracting the parallel vector from the total
relative position vector
example use:
see calc_errors above
"""
relative_position_x = (location.pose.pose.position.x -
goal.pose.pose.position.x)
relative_position_y = (location.pose.pose.position.y -
goal.pose.pose.position.y)
# relative position of the best estimate position and the goal
# vector points from the goal to the location
## relative_position = (relative_position_x, relative_position_y, 0.0)
goal_heading = quaternion_to_heading(goal.pose.pose.orientation)
goal_vector_x = math.cos(goal_heading)
goal_vector_y = math.sin(goal_heading)
# vector in the direction of the goal heading, axis of desired motion
goal_vector = (goal_vector_x, goal_vector_y, 0.0)
along_axis_error = self.along_axis_error(location, goal)
along_axis_vec = scale(unit(goal_vector), along_axis_error)
new_rel_x = relative_position_x - along_axis_vec[0]
new_rel_y = relative_position_y - along_axis_vec[1]
new_rel_vec = (new_rel_x, new_rel_y, 0.0)
error_magnitude = math.sqrt(new_rel_x*new_rel_x +
new_rel_y*new_rel_y)
if error_magnitude < .0001:
return 0.0
if cross_product(goal_vector, new_rel_vec)[2] >= 0.0:
return error_magnitude
else:
return -error_magnitude
def main():
USING_CACHE = True
series_cache_path = './data/series_cache.pkl'
data_series = extractHourlyPower(series_cache_path, USING_CACHE)
training_day = 20 # 18 for period; 20 for encoder-decoder
total_day = 24
train_series, test_series = data_series[:training_day*24], data_series[(training_day-total_day)*24:]
y_true = copy.copy(test_series[-72:].values)
#history_average
#prediction = history_average(data_series)
scaler, train_series, test_series = scale(train_series, test_series)
# fetch vanilla LSTM training data and model
X_train, y_train, X_test, y_test = SeriesToXy_vanilla(train_series, test_series, window=25)
model = fit_lstm(input_shape=(24,1))
# fetch encoder_decoder training data and model
#X_train, y_train, X_test, y_test = SeriesToXy_ed(train_series, test_series, window=25)
#model = fit_encoder_decoder(12, 1, 1)
#fetch period training data and model
#X_train, y_train, X_test, y_test = SeriesToXy_period(train_series, test_series, window = 73)
#model = fit_period_lstm()
early_stopping = EarlyStopping(monitor='loss', patience=5, mode='min')
# Run training
model.compile(optimizer='adam', loss='mean_squared_error')
model.summary()
model.fit(X_train, y_train,
batch_size=1,
epochs=1,
validation_split=0.2,
callbacks = [early_stopping])
prediction = model.predict(X_test)
prediction = scaler.inverse_transform(prediction)
# encoder decoder
#prediction = prediction[:, -1,:]
prediction = prediction.reshape(-1)
rmse = sqrt(smet.mean_squared_error(y_true, prediction))
print('rmse: ', rmse)
save_cache(prediction, './data/pre_vanilla_batch1_lstm128-32_patience5.pkl')
K.clear_session()# tensorflow bug
def get_loss(self, trip_od, scaled_trip_volume, in_flows, out_flows, g, multitask_weights=[0.5, 0.25, 0.25]):
'''
defines the procedure of evaluating loss function
Inputs:
----------------------------------
trip_od: list of origin destination pairs
trip_volume: ground-truth of volume of trip which serves as our target.
g: DGL graph object
Outputs:
----------------------------------
loss: value of loss function
'''
# calculate the in/out flow of nodes
# scaled back trip volume
trip_volume = utils.scale_back(scaled_trip_volume)
# get in/out nodes of this batch
out_nodes, out_flows_idx = torch.unique(trip_od[:, 0], return_inverse=True)
in_nodes, in_flows_idx = torch.unique(trip_od[:, 1], return_inverse=True)
# scale the in/out flows of the nodes in this batch
scaled_out_flows = utils.scale(out_flows[out_nodes])
scaled_in_flows = utils.scale(in_flows[in_nodes])
# get embeddings of each node from GNN
src_embedding = self.forward(g)
dst_embedding = self.forward2(g)
# get edge prediction
edge_prediction = self.predict_edge(src_embedding, dst_embedding, trip_od)
# get in/out flow prediction
in_flow_prediction = self.predict_inflow(dst_embedding, in_nodes)
out_flow_prediction = self.predict_outflow(src_embedding, out_nodes)
# get edge prediction loss
edge_predict_loss = MSE(edge_prediction, scaled_trip_volume)
# get in/out flow prediction loss
in_predict_loss = MSE(in_flow_prediction, scaled_in_flows)
out_predict_loss = MSE(out_flow_prediction, scaled_out_flows)
# get regularization loss
reg_loss = 0.5 * (self.regularization_loss(src_embedding) + self.regularization_loss(dst_embedding))
# return the overall loss
return multitask_weights[0] * edge_predict_loss + multitask_weights[1] * in_predict_loss + multitask_weights[2] * out_predict_loss + self.reg_param * reg_loss
def alpha31(df):
"""
Alpha#31
((rank(rank(rank(decay_linear((-1 * rank(rank(delta(close, 10)))), 10))))
+ rank((-1 * delta(close, 3)))) + sign(scale(correlation(adv20, low, 12))))
"""
temp1 = u.rank(
u.rank(
u.rank(
u.decay_linear((-1 * u.rank(u.rank(u.delta(df.close, 10)))),
10))))
temp2 = u.rank((-1 * u.delta(df.close, 3))) + np.sign(
u.scale(u.corr(u.adv(df, 20), df.low, 12)))
return temp1 + temp2
def split_image_to_4(image, vae_enc, vae_dec):
# split_at_pixel = 19
# width = image.shape[2]
# height = image.shape[3]
#
# image_1 = image[:, :, 0: split_at_pixel, :]
# image_2 = image[:, :, width - split_at_pixel:, :]
# image_3 = image[:, :, :, 0: split_at_pixel]
# image_4 = image[:, :, :, height - split_at_pixel:]
# # image_1, _ = torch.split(image, split_at_pixel, dim=3)
# # image_3, _ = torch.split(image, split_at_pixel, dim=2)
#
image_1 = image
image_2 = rotate(image, 20, BATCH_SIZE_DEFAULT)
image_3 = scale(image, BATCH_SIZE_DEFAULT)
#image_4 = random_erease(image, BATCH_SIZE_DEFAULT)
vae_in = torch.reshape(image, (BATCH_SIZE_DEFAULT, 784))
sec_mean, sec_std = vae_enc(vae_in)
e = torch.zeros(sec_mean.shape).normal_()
sec_z = sec_std * e + sec_mean
image_4 = vae_dec(sec_z)
image_4 = torch.reshape(image_4, (BATCH_SIZE_DEFAULT, 1, 28, 28))
image_1 = image_1.to('cuda')
image_2 = image_2.to('cuda')
image_3 = image_3.to('cuda')
image_4 = image_4.to('cuda')
#image = image.to('cuda')
# show_mnist(image_1[0], 20, 28)
# show_mnist(image_1[1], 20, 28)
# show_mnist(image_1[2], 20, 28)
# show_mnist(image_1[3], 20, 28)
#
# show_mnist(image_2[0], 20, 28)
# show_mnist(image_2[1], 20, 28)
# show_mnist(image_2[2], 20, 28)
# show_mnist(image_2[3], 20, 28)
#
# input()
# print(image_1.shape)
# print(image_2.shape)
# print(image_3.shape)
# print(image_4.shape)
# input()
return image_1, image_2, image_3, image_4
def derivative(self, forget=True, project=False):
''' Evaluates the derivative of the reduced functional for the most
recently evaluated control value. '''
# Check if we have the gradient already in the cash.
# If so, return the cached value
if self.cache is not None:
hash = value_hash([x.data() for x in self.controls])
fnspaces = [p.data().function_space() if isinstance(p.data(),
Function) else None for p in self.controls]
if hash in self._cache["derivative_cache"]:
info_green("Got a derivative cache hit.")
return cache_load(self._cache["derivative_cache"][hash], fnspaces)
# Call callback
values = [p.data() for p in self.controls]
self.derivative_cb_pre(delist(values, list_type=self.controls))
# Compute the gradient by solving the adjoint equations
dfunc_value = drivers.compute_gradient(self.functional, self.controls, forget=forget, project=project)
dfunc_value = enlist(dfunc_value)
# Reset the checkpointing state in dolfin-adjoint
adjointer.reset_revolve()
# Apply the scaling factor
scaled_dfunc_value = [utils.scale(df, self.scale) for df in list(dfunc_value)]
# Call callback
# We might have forgotten the control values already,
# in which case we can only return Nones
values = []
for c in self.controls:
try:
values.append(p.data())
except libadjoint.exceptions.LibadjointErrorNeedValue:
values.append(None)
if self.current_func_value is not None:
self.derivative_cb_post(self.scale * self.current_func_value,
delist(scaled_dfunc_value, list_type=self.controls),
delist(values, list_type=self.controls))
# Cache the result
if self.cache is not None:
info_red("Got a derivative cache miss")
self._cache["derivative_cache"][hash] = cache_store(scaled_dfunc_value, self.cache)
return scaled_dfunc_value
def alpha29(df):
"""
Alpha#29
(min(product(rank(rank(scale(log(sum(ts_min(rank(rank((-1 * rank(delta((close - 1),
5))))), 2), 1))))), 1), 5) + ts_rank(delay((-1 * returns), 6), 5))
"""
temp1 = u.scale(
np.log(
u.ts_sum(
u.ts_min(
u.rank(u.rank((-1 * u.rank(u.delta((df.close - 1), 5))))),
2), 1)))
temp2 = u.product(u.rank(u.rank(temp1)), 1)
temp3 = u.ts_rank(u.delay((-1 * df.returns), 6), 5)
return (np.where(temp1 < temp2, temp1, temp2) + temp3)
def update_feat_with_RBMs(s_data, greedy_pre_train=1):
data = scale(s_data.get_data())
print(np.min(data))
print(np.max(data))
# Fit and Transform data
for i in range(greedy_pre_train):
# Initialize the RBM
rbm = BernoulliRBM(n_components=90,
n_iter=50,
learning_rate=0.01,
verbose=True)
rbm.fit(data)
s_data.update_features(rbm.transform)
data = s_data.get_data()
def __init__(self, sections, n_ticks):
"""TODO: Put description here.
`sections`:
If `sections` is an int, then equally divide `n_ticks` into
this number of sections
If `sections` is a list of ints or floats, divide `n_ticks`
into len(`sections`) number of sections with relative
durations matching the values in `sections`
`n_ticks`: The total number of the smallest unit of duration in all
sequential sections combined. Eg, Length of audio in samples.
"""
self.n_ticks = n_ticks
if isinstance(sections, int):
self.n_sections = sections
self.starts = [
int(round(start)) for start in np.linspace(
0, self.n_ticks, self.n_sections, endpoint=False)
]
if isinstance(sections, (list, tuple)):
self.n_sections = len(sections)
self.relative_durations = sections
self.sum_relative_durations = sum(sections)
durations = [
scale(duration, 0, self.sum_relative_durations, 0,
self.n_ticks) for duration in sections
]
start = 0
self.starts = []
for duration in durations:
self.starts.append(start)
start += duration
self.starts = [int(round(start)) for start in self.starts]
self.next_starts = self.starts[1:] + [self.n_ticks + 1]
index = 0
for start, next_start in zip(self.starts, self.next_starts):
section = Section(start, next_start, index, self.n_sections, self)
self.append(section)
index += 1
def intersection_with_xz_plane(origin, vector): # matrix to drop y component to_2d = np.array([ [1, 0, 0, 0], [0, 0, 1, 0], [0, 0, 0, 1] ]) # find intersections with xz plane # 0 = (origin + vector * a).y # => a = -origin.y / vector.y # => int = origin + vector * a return to_2d.dot( origin + utils.scale(all=-origin[1] / vector[1]) .dot(vector) )
def load_test_images():
'''
Loads 64 random images from SVNH test data sets
:return: Tuple of (test images, image labels)
'''
utils.download_train_and_test_data()
_, testset = utils.load_data_sets()
idx = np.random.randint(0, testset['X'].shape[3], size=64)
test_images = testset['X'][:, :, :, idx]
test_labels = testset['y'][idx]
test_images = np.rollaxis(test_images, 3)
test_images = utils.scale(test_images)
return test_images, test_labels
def hessian(self, m_dot, project=False):
''' Evaluates the Hessian action in direction m_dot. '''
assert(len(self.controls) == 1)
# Check if we have the gradient already in the cash.
# If so, return the cached value
if self.cache is not None:
hash = value_hash([x.data() for x in self.controls] + [m_dot])
fnspaces = [p.data().function_space() if isinstance(p.data(),
Function) else None for p in self.controls]
if hash in self._cache["hessian_cache"]:
info_green("Got a Hessian cache hit.")
return cache_load(self._cache["hessian_cache"][hash], fnspaces)
else:
info_red("Got a Hessian cache miss")
# Compute the Hessian action by solving the second order adjoint equations
if isinstance(m_dot, list):
assert len(m_dot) == 1
Hm = self.H(m_dot[0], project=project)
else:
Hm = self.H(m_dot, project=project)
# Apply the scaling factor
scaled_Hm = [utils.scale(Hm, self.scale)]
# Call callback
control_data = [p.data() for p in self.controls]
if self.current_func_value is not None:
current_func_value = self.scale * self.current_func_value
else:
current_func_value = None
self.hessian_cb(current_func_value,
delist(control_data, list_type=self.controls),
m_dot, scaled_Hm[0])
# Cache the result
if self.cache is not None:
self._cache["hessian_cache"][hash] = cache_store(scaled_Hm, self.cache)
return scaled_Hm
def make_tuned_inference(X):
print('Making tuned inference...')
t = [0.100, 0.101, 0.102, 0.103, 0.104, 0.105, 0.106, 0.107, 0.108, 0.109,
0.110, 0.111, 0.112, 0.113, 0.114, 0.115, 0.116, 0.117, 0.118, 0.119,
0.120, 0.121, 0.122, 0.123, 0.124, 0.125, 0.126, 0.127, 0.128, 0.129,
0.130, 0.131, 0.132, 0.133, 0.134, 0.135, 0.136, 0.137, 0.138, 0.139,
0.140, 0.141, 0.142, 0.143, 0.144, 0.145, 0.146, 0.147, 0.148, 0.149,
0.150, 0.151, 0.152, 0.154, 0.155, 0.156, 0.157, 0.158, 0.159, 0.160,
0.161, 0.162, 0.163, 0.164, 0.165, 0.166, 0.167, 0.168, 0.169, 0.170,
0.171, 0.172, 0.173, 0.174, 0.175, 0.176, 0.177, 0.178, 0.179, 0.180,
0.181, 0.182, 0.183, 0.184, 0.185, 0.186, 0.187, 0.188, 0.189, 0.190,
0.191, 0.192, 0.193, 0.194, 0.195, 0.196, 0.197, 0.198, 0.199, 0.200,
0.201, 0.202, 0.203, 0.204, 0.205, 0.206, 0.207, 0.208, 0.209, 0.200,
0.201, 0.202, 0.203, 0.204, 0.205, 0.206, 0.207, 0.208, 0.209, 0.210]
weight = 0
n_samples, n_nodes = X.shape
y_pred_agg = np.zeros((n_nodes, n_nodes))
for threshold in t:
for filtering in ["f1", "f2", "f3", "f4"]:
print('Current: %0.3f, %s' % (threshold, filtering))
X_new = tuned_filter(X, LP = filtering, threshold = t, weights = True)
pca = PCA(whiten=True, n_components=int(0.8 * n_nodes)).fit(X_new)
y_pred = - pca.get_precision()
if filtering == 'f1':
y_pred_agg += y_pred
weight += 1
elif filtering == 'f2':
y_pred_agg += y_pred * 0.9
weight += 0.9
elif filtering == 'f3':
y_pred_agg += y_pred * 0.01
weight += 0.01
elif filtering == 'f4':
y_pred_agg += y_pred * 0.7
weight += 0.7
return scale(y_pred_agg / weight)
def make_prediction_directivity(X, threshold=0.12, n_jobs=1):
"""Score neuron connectivity using a precedence measure
Parameters
----------
X : numpy array of shape (n_samples, n_nodes)
Fluorescence signals
threshold : float, (default=0.11)
Threshold value for hard thresholding filter:
x_new[i] = x[i] if x[i] >= threshold else 0.
n_jobs : integer, optional (default=1)
The number of jobs to run the algorithm in parallel.
If -1, then the number of jobs is set to the number of cores.
Returns
-------
score : numpy array of shape (n_nodes, n_nodes)
Pairwise neuron connectivity score.
"""
# Perform filtering
X_new = np.zeros((X.shape))
for i in range(1, X.shape[0] - 1):
for j in range(X.shape[1]):
X_new[i, j] = (X[i, j] + 1 * X[i - 1, j] + 0.8 * X[i - 2, j] +
0.4 * X[i - 3, j])
X_new = np.diff(X_new, axis=0)
thresh1 = X_new < threshold * 1
thresh2 = X_new >= threshold * 1
X_new[thresh1] = 0
X_new[thresh2] = pow(X_new[thresh2], 0.9)
# Score directivity
n_jobs, starts = _partition_X(X, n_jobs)
all_counts = Parallel(n_jobs=n_jobs)(
delayed(_parallel_count)(X_new, starts[i], starts[i + 1])
for i in range(n_jobs))
count = np.vstack(list(chain.from_iterable(all_counts)))
return scale(count - np.transpose(count))
def derivative(self, forget=True, project=False):
''' Evaluates the derivative of the reduced functional for the most
recently evaluated control value. '''
# Check if we have the gradient already in the cash.
# If so, return the cached value
if self.cache is not None:
hash = value_hash([x.data() for x in self.controls])
fnspaces = [p.data().function_space() if isinstance(p.data(),
Function) else None for p in self.controls]
if hash in self._cache["derivative_cache"]:
info_green("Got a derivative cache hit.")
return cache_load(self._cache["derivative_cache"][hash], fnspaces)
# Compute the gradient by solving the adjoint equations
dfunc_value = drivers.compute_gradient(self.functional, self.controls, forget=forget, project=project)
dfunc_value = enlist(dfunc_value)
# Reset the checkpointing state in dolfin-adjoint
adjointer.reset_revolve()
# Apply the scaling factor
scaled_dfunc_value = [utils.scale(df, self.scale) for df in list(dfunc_value)]
# Call the user-specific callback routine
if self.derivative_cb:
if self.current_func_value is not None:
values = [p.data() for p in self.controls]
self.derivative_cb(self.scale * self.current_func_value,
delist(scaled_dfunc_value, list_type=self.controls),
delist(values, list_type=self.controls))
else:
info_red("Gradient evaluated without functional evaluation, not calling derivative callback function")
# Cache the result
if self.cache is not None:
info_red("Got a derivative cache miss")
self._cache["derivative_cache"][hash] = cache_store(scaled_dfunc_value, self.cache)
return scaled_dfunc_value
import numpy as N
import pylab as P
from scipy.sandbox import pyem
import utils
oldfaithful = utils.get_faithful()
# We want the relationship between d(t) and w(t+1), but get_faithful gives
# d(t), w(t), so we have to shift to get the "usual" faithful data
waiting = oldfaithful[1:, 1:]
duration = oldfaithful[:len(waiting), :1]
dt = N.concatenate((duration, waiting), 1)
# Scale the data so that each component is in [0..1]
dt = utils.scale(dt)
# This function train a mixture model with k components, returns the trained
# model and the BIC
def cluster(data, k, mode = 'full'):
d = data.shape[1]
gm = pyem.GM(d, k, mode)
gmm = pyem.GMM(gm)
em = pyem.EM()
em.train(data, gmm, maxiter = 20)
return gm, gmm.bic(data)
# bc will contain a list of BIC values for each model trained
bc = []
mode = 'full'
P.figure()
channels, crop, scale, color, avail, colorPicker)
from proto import alias, sharpen, group, find, edge, center, distance
from PIL import Image
print "# fast stuff"
img = load('samples/abstract/colors.png')
#b = take()
show(img)
b, g, r = bgr(img)
img = image(b,b,b)
test = like(img)
bound = bounds(b)
channel = channels(b)
coord = (0,0,50,50)
closer = crop(img, coord)
bigger = scale(closer, 2.0)
eyedrop = color(img, 0, 30)
pallet = avail(img)
colorPicker(img,0,30)
print "# slow stuff"
res1 = alias(img, .3)
res2 = sharpen(img, .3)
blob1 = group(img)
mask = Image.new("RGB", (50, 10), "white")
blob3 = find(img,mask,(3,3))
coords1 = edge(img)
coords2 = center(blob1)
dist = distance(0,3)
print "# yay, got to the end!"
def weighted_traverse(self, start, end, current):
traverse_vector = self.traverse_vector(start, end, current)
w = self.traverse_weight(start, end, current)
# rospy.loginfo('wtr: '+str(traverse_vector[0])[0:4]+' , '+str(traverse_vector[1])[0:4]+' , '+str(w)[0:4])
return scale(traverse_vector, w)
def weighted_arrive(self, start, end, current):
arrive_vector = self.arrive_vector(start, end, current)
w = self.arrive_weight(start, end, current)
# rospy.loginfo('war: '+str(arrive_vector[0])[0:4]+' , '+str(arrive_vector[1])[0:4]+' , '+str(w)[0:4])
return scale(arrive_vector, w)
def weighted_depart(self, start, end, current):
depart_vector = self.depart_vector(start, end, current)
w = self.depart_weight(start, end, current)
# rospy.loginfo('wdp: '+str(depart_vector[0])[0:4]+' , '+str(depart_vector[1])[0:4]+' , '+str(w)[0:4])
return scale(depart_vector, w)
def get_file():
global frame_map
global widget_master
file = tkFileDialog.askopenfilename(parent=widget_master,title='Choose a file')
field_file.delete(0,999)
field_file.insert(0,file)
handle= open(file,'r',0)
handle.readline()
start_freq, end_freq, step= ((handle.readline()).strip()).split(',')
start_freq= int(start_freq)
end_freq= int(end_freq)
step= int(step)
height= (end_freq - start_freq) / step
yscalefactor= float(height) / float(WINDOW_HEIGHT)
field_map.config(height= (height / yscalefactor) + (WINDOW_MARGIN * 2))
# draw scale
for freq in range(start_freq,end_freq,step * 45):
field_map.create_text(WINDOW_MARGIN,((height - ((freq - start_freq) / step)) / yscalefactor) + WINDOW_MARGIN + TEXT_OFFSET,fill= 'white', text= freq, anchor=SW)
handle.readline()
# get signal strength range
strength_min= 999999
strength_max= 0
for data in handle.readline().strip():
try:
position, frequency, symbol_rate, polarity, strength= data.split(',')
if int(strength) < strength_min:
strength_min= int(strength)
if int(strength) > strength_max:
strength_max= int(strength)
except:
break
# reset data
handle.seek(0)
for x in range(4):
handle.readline()
# read data one line at a time. one line == one pixel
y_bot= height - 1
y_top= y_bot
current_polarity= '-'
regions= 0
start_frequency= 0
while True:
data= (handle.readline()).strip()
if not data == '':
position, frequency, symbol_rate, polarity, strength= data.split(',')
x= int(position) + X_OFFSET
if start_frequency == 0:
start_frequency= frequency
if not polarity == current_polarity:
#if not current_polarity == '-':
#field_map.create_line(x,(y_bot / yscalefactor) + WINDOW_MARGIN,x,(y_top / yscalefactor) + WINDOW_MARGIN, fill=COLOURS[current_polarity], tag='%s,%s,%s,%s,%s' % (position, start_frequency, end_frequency, symbol_rate, current_polarity))
field_map.create_line(x,(y_bot / yscalefactor) + WINDOW_MARGIN,x,(y_top / yscalefactor) + WINDOW_MARGIN, fill=COLOURS[current_polarity] % utils.scale(int(strength), strength_min, strength_max, 0xff), tag='%s,%s,%s,%s,%s' % (position, start_frequency, end_frequency, symbol_rate, current_polarity))
current_polarity= polarity
y_bot= y_top
regions += 1
start_frequency= frequency
end_frequency= frequency
y_top -= 1
else:
break
print '%d regions' % regions
For now, regularized EM is pretty crude, but is enough for simple cases where
you need to avoid singular covariance matrices."""
import numpy as N
import pylab as P
from scikits.learn.machine.em import EM, GM, GMM
# Experimental RegularizedEM
from scikits.learn.machine.em.gmm_em import RegularizedEM
import utils
x, y = utils.get_pendigits()
# Take only the first point of pendigits for pdf estimation
dt1 = N.concatenate([x[:, N.newaxis], y[:, N.newaxis]], 1)
dt1 = utils.scale(dt1.astype(N.float))
# pcnt is the poportion of samples to use as prior count. Eg if you have 1000
# samples, and pcn is 0.1, then the prior count would be 100, and 1100 samples
# will be considered as overall when regularizing the parameters.
pcnt = 0.05
# You should try different values of pval. If pval is 0.1, then the
# regularization will be strong. If you use something like 0.01, really sharp
# components will appear. If the values are too small, the regularizer may not
# work (singular covariance matrices).
pval = 0.05
# This function train a mixture model with k components, returns the trained
# model and the BIC
def cluster(data, k, mode = 'full'):
d = data.shape[1]
def choose_when_quarter_tones_start(self):
# somewhere between 2 and 4 minutes in
# in quarter notes at 120 beats per minute (ie, half seconds)
self.quarter_tones_start = scale(random.random(), 0, 1, 120 * 2, 120 * 4)
def derivative(self, forget=True, project=False):
""" Evaluates the derivative of the reduced functional at the most
recently evaluated control value.
Args:
forget (Optional[bool]): Delete the forward state while solving the
adjoint equations. If you want to reevaluate derivative at the same
point (or the Hessian) you will need to set this to False or None. Defaults to True.
project (Optional[bool]): If True, the returned value will be the L2
Riesz representer, if False it will be the l2 Riesz representative.
The L2 projection requires one additional linear solve.
Defaults to False.
Returns:
The functional derivative. The returned type is the same as the control
type.
"""
# Check if we have the gradient already in the cash.
# If so, return the cached value
if self.cache is not None:
hash = value_hash([x.data() for x in self.controls])
fnspaces = [p.data().function_space() if isinstance(p.data(),
Function) else None for p in self.controls]
if hash in self._cache["derivative_cache"]:
info_green("Got a derivative cache hit.")
return cache_load(self._cache["derivative_cache"][hash], fnspaces)
# Call callback
values = [p.data() for p in self.controls]
self.derivative_cb_pre(delist(values, list_type=self.controls))
# Compute the gradient by solving the adjoint equations
dfunc_value = drivers.compute_gradient(self.functional, self.controls, forget=forget, project=project)
dfunc_value = enlist(dfunc_value)
# Reset the checkpointing state in dolfin-adjoint
adjointer.reset_revolve()
# Apply the scaling factor
scaled_dfunc_value = [utils.scale(df, self.scale) for df in list(dfunc_value)]
# Call callback
# We might have forgotten the control values already,
# in which case we can only return Nones
values = []
for c in self.controls:
try:
values.append(p.data())
except libadjoint.exceptions.LibadjointErrorNeedValue:
values.append(None)
if self.current_func_value is not None:
self.derivative_cb_post(self.scale * self.current_func_value,
delist(scaled_dfunc_value, list_type=self.controls),
delist(values, list_type=self.controls))
# Cache the result
if self.cache is not None:
info_red("Got a derivative cache miss")
self._cache["derivative_cache"][hash] = cache_store(scaled_dfunc_value, self.cache)
return scaled_dfunc_value
mixtures, etc..."""
import numpy as N
import pylab as P
import matplotlib as MPL
from scipy.sandbox import svm
import utils
from scikits.learn.datasets import german
data = german.load()
features = N.vstack([data['feat']['feat' + str(i)].astype(N.float) for i in range(1, 25)]).T
label = data['label']
t, s = utils.scale(features)
training = svm.LibSvmClassificationDataSet(label, features)
def train_svm(cost, gamma, fold = 5):
"""Train a SVM for given cost and gamma."""
kernel = svm.RBFKernel(gamma = gamma)
model = svm.LibSvmCClassificationModel(kernel, cost = cost)
cv = model.cross_validate(training, fold)
return cv
c_range = N.exp(N.log(2.) * N.arange(-5, 15))
g_range = N.exp(N.log(2.) * N.arange(-15, 3))
# Train the svm on a log distributed grid
gr = N.meshgrid(c_range, g_range)
def scale_corners(corners):
result = []
for point in corners:
point = scale(point, 1/RESIZE)
result.append(shift(point, (60,70)))
return result
def __init__(self, ranges=False):
score = self.score = Score()
self.instruments = self.i = Instruments()
self.parts = Parts(self.i)
# Make Metadata
timestamp = datetime.datetime.utcnow()
metadata = Metadata()
metadata.title = 'Early Montreal'
metadata.composer = 'Jonathan Marmor'
metadata.date = timestamp.strftime('%Y/%m/%d')
score.insert(0, metadata)
[score.insert(0, part) for part in self.parts.l]
score.insert(0, StaffGroup(self.parts.l))
if ranges:
# Don't make a piece, just show the instrument ranges
for inst, part in zip(self.instruments.l, self.parts.l):
measure = Measure()
measure.timeSignature = TimeSignature('4/4')
low = Note(inst.lowest_note)
measure.append(low)
high = Note(inst.highest_note)
measure.append(high)
part.append(measure)
return
# 18 to 21 minutes
piece_duration_minutes = scale(random.random(), 0, 1, 18, 21)
# Make the "songs"
songs = []
total_minutes = 0
n = 1
while total_minutes < piece_duration_minutes:
print 'Song {}'.format(n)
n += 1
song = Song(self)
songs.append(song)
total_minutes += song.duration_minutes
# Make notation
previous_duration = None
for song in songs:
for bar in song.bars:
for part in bar.parts:
measure = Measure()
if bar.tempo:
measure.insert(0, MetronomeMark(number=bar.tempo, referent=Duration(1)))
measure.leftBarline = 'double'
if bar.duration != previous_duration:
ts = TimeSignature('{}/4'.format(bar.duration))
measure.timeSignature = ts
# Fix Durations
durations = [note['duration'] for note in part['notes']]
components_list = split_at_beats(durations)
components_list = [join_quarters(note_components) for note_components in components_list]
for note, components in zip(part['notes'], components_list):
note['durations'] = components
for note in part['notes']:
if note['pitch'] == 'rest':
n = Rest()
if isinstance(note['pitch'], list):
pitches = []
for pitch_number in note['pitch']:
p = Pitch(pitch_number)
# Force all flats
if p.accidental.name == 'sharp':
p = p.getEnharmonic()
pitches.append(p)
n = Chord(notes=pitches)
# TODO add slurs
# TODO add glissandos
# TODO add -50 cent marks
else:
p = Pitch(note['pitch'])
# Force all flats
if p.accidental.name == 'sharp':
p = p.getEnharmonic()
n = Note(p)
# TODO add slurs
# TODO add glissandos
# TODO add -50 cent marks
d = Duration()
if note['duration'] == 0:
d.quarterLength = .5
d = d.getGraceDuration()
else:
d.fill(note['durations'])
n.duration = d
measure.append(n)
self.parts.d[part['instrument_name']].append(measure)
previous_duration = bar.duration
def make_prediction_PCA(X):
"""Score neuron connectivity using a partial correlation approach
Parameters
----------
X : numpy array of shape (n_samples, n_nodes)
Fluorescence signals
Returns
-------
score : numpy array of shape (n_nodes, n_nodes)
Pairwise neuron connectivity score.
"""
n_samples, n_nodes = X.shape
# Init for a given data set
y_pred_agg = np.zeros((n_nodes, n_nodes))
# Thresholds to evaluate
# Some thresohlds are duplicated or missing.
t = [0.100, 0.101, 0.102, 0.103, 0.104, 0.105, 0.106, 0.107, 0.108, 0.109,
0.110, 0.111, 0.112, 0.113, 0.114, 0.115, 0.116, 0.117, 0.118, 0.119,
0.120, 0.121, 0.122, 0.123, 0.124, 0.125, 0.126, 0.127, 0.128, 0.129,
0.130, 0.131, 0.132, 0.133, 0.134, 0.135, 0.136, 0.137, 0.138, 0.139,
0.140, 0.141, 0.142, 0.143, 0.144, 0.145, 0.146, 0.147, 0.148, 0.149,
0.150, 0.151, 0.152, 0.154, 0.155, 0.156, 0.157, 0.158, 0.159, 0.160,
0.161, 0.162, 0.163, 0.164, 0.165, 0.166, 0.167, 0.168, 0.169, 0.170,
0.171, 0.172, 0.173, 0.174, 0.175, 0.176, 0.177, 0.178, 0.179, 0.180,
0.181, 0.182, 0.183, 0.184, 0.185, 0.186, 0.187, 0.188, 0.189, 0.190,
0.191, 0.192, 0.193, 0.194, 0.195, 0.196, 0.197, 0.198, 0.199, 0.200,
0.201, 0.202, 0.203, 0.204, 0.205, 0.206, 0.207, 0.208, 0.209, 0.200,
0.201, 0.202, 0.203, 0.204, 0.205, 0.206, 0.207, 0.208, 0.209, 0.210]
weight = 0
# Loop over all the tresholds and methods
for threshold in t:
for filtering in ['sym', 'future', 'past', 'alt']:
print(threshold, filtering)
# Preprocess data
X_new = _preprocess(X, filtering=filtering, threshold=threshold)
# Making the prediction
pca = PCA(whiten=True, n_components=int(0.8 * n_nodes)).fit(X_new)
y_pred = - pca.get_precision()
# Adding the (weigthed) prediction to global prediction
if filtering == 'sym':
y_pred_agg += y_pred
weight += 1
elif filtering == 'alt':
y_pred_agg += y_pred * 0.9
weight += 0.9
elif filtering == 'future':
y_pred_agg += y_pred * 0.01
weight += 0.01
elif filtering == 'past':
y_pred_agg += y_pred * 0.7
weight += 0.7
# Normalizing the global prediction
return scale(y_pred_agg / weight)