def testL1Distance(self):
n1 = numpy.array([[1., 2., 3., 4.], [1., 1., 1., 1.]], dtype=numpy.float32)
n2 = numpy.array([[5., 6., 7., -8.], [1., 1., 1., 1.]], dtype=numpy.float32)
out = self.Run(functions.l1_distance(n1, n2))
testing.assert_allclose(
out[0],
numpy.array(
[distance.cityblock(n1[0], n2[0]), distance.cityblock(n1[1], n2[1])
]),
rtol=TOLERANCE)
def testL1DistanceWithBroadcast(self):
n1 = numpy.array([[[1., 2., 3., 4.], [1., 1., 1., 1.]], [[5., 6., 7., 8.],
[1., 1., 1., 2.]]],
dtype=numpy.float32)
n2 = numpy.array([[5., 6., 7., -8.], [1., 1., 1., 1.]], dtype=numpy.float32)
out = self.Run(functions.l1_distance(n1, n2))
expected = numpy.array(
[[distance.cityblock(n1[0, 0], n2[0]), distance.cityblock(
n1[0, 1], n2[1])], [distance.cityblock(n1[1, 0], n2[0]),
distance.cityblock(n1[1, 1], n2[1])]])
testing.assert_allclose(expected, out[0], atol=TOLERANCE)
def question_6():
a = (0, 0)
b = (100, 40)
pairs = [(55, 5), (59, 10), (56, 15), (50, 18)]
for p in pairs:
print('({}, {}):'.format(p[0], p[1]))
print('L1norm(0, 0): {0}'.format(round(distance.cityblock(p, a), 5)))
print('L1norm(100, 40): {0}'.format(round(distance.cityblock(p, b), 5)))
print('L2norm(0, 0): {0}'.format(round(distance.euclidean(p, a), 5)))
print('L2norm(100, 40): {0}'.format(round(distance.euclidean(p, b), 5)))
print('')
def tmpAssignPoints(self, centroids):
print "WYBRANA METRYKA: "+ str(self.metric)
distCount = lambda a, b: euclidean(a, b)
if self.metric == "chebyshev":
distCount = lambda a, b: chebyshev(a, b)
if self.metric == "cityblock":
distCount = lambda a, b: cityblock(a, b)
# chebyshev = nieskonczonosc
# distCount = lambda x, y: chebyshev(x, y)
#cityblock = l1
# distCount = lambda x, y: cityblock(x, y)
labels_centroids=[]
for i in self.df.index:
disctances=[]
c_dist = []
for c in centroids:
# print "i: "+str(self.df.loc[i].values)+ " c: "+str(c)
x= distCount(self.df.loc[i].values, c)
# print "xx: "+str(x)
#klucz-x, wartosc-c
disctances.append(x)
c_dist.append(c)
m = min(disctances)
# print "distances:"
# print disctances
# print "c_dist"
# print c_dist
dm = disctances.index(m)
tmp_nearest_centr = c_dist[dm]
labels_centroids.append(tmp_nearest_centr)
# print"closest centr: "+str(tmp_nearest_centr )
return (labels_centroids, centroids)
def Distance(i,j,type):
if type == 1:
return distance.euclidean(i,j)
elif type == 2:
return distance.cityblock(i,j)
elif type == 3:
return distance.cosine(i,j)
def Classify (self, sample, verbose = True):
length = len (sample)
features = MFCC.extract (numpy.frombuffer (sample, numpy.int16))
gestures = {}
for gesture in self.params:
d = []
for tsample in self.params[gesture]:
total_distance = 0
smpl_length = len(tsample)
if(numpy.abs(length - smpl_length) <= 0):
continue
for i in range (min (len (features), len (tsample))):
total_distance += dist.cityblock(features[i], tsample[i])
d.append (total_distance/float (i))
score = numpy.min(d)
gestures[gesture] = score
if(verbose):
print "Gesture %s: %f" % (gesture, score)
try:
if (score < minimum):
minimum = score
lowest = gesture
except:
minimum = score
lowest = gesture
if verbose:
print lowest, minimum
if(minimum < THRESHOLD):
return lowest
else:
return None
def getDistLambda(metric):
if (metric == "manhattan"):
return lambda x,y : distance.cityblock(x,y)
elif (metric == "cosine"):
return lambda x,y : distance.cosine(x,y)
else:
return lambda x,y : distance.euclidean(x,y)
def calc_dist(e1,e2,mode=1):
if mode == 1:
return ssd.euclidean(e1,e2)
elif mode == 2:
return ssd.cityblock(e1,e2)
elif mode == 3:
return ssd.cosine(e1,e2)
def k_means(data, k=2, distance='e'):
centers = np.array(random.sample(list(data), k))
centers_steps = [centers.tolist()]
changed = True
while changed:
prev_centers = np.copy(centers)
data_nr = data.shape[0]
clusters = np.empty((data_nr, k))
for i in range(data_nr):
if distance == 'e':
clusters[i] = np.array([euclidean(data[i] - centers[j]) for j in range(k)])
elif distance == 'm':
clusters[i] = np.array([cityblock(data[i], centers[j]) for j in range(k)])
elif distance == 'h':
clusters[i] = np.array([hamming(data[i], centers[j]) for j in range(k)])
else:
raise ValueError('Unrecognized distance')
clusters = np.argmin(clusters, axis=1)
for i in range(k):
centers[i] = np.mean(data[np.where(clusters == i)], axis=0)
changed = not np.intersect1d(prev_centers, centers).size == centers.size
centers_steps.append(centers.tolist())
return centers, centers_steps
def iter_kill_spots(cx, cz):
c = w.getChunk(cx, cz)
bedrock_blocks = (c.Blocks == w.materials.Bedrock.ID)
for bx, bz, y in mcbuddy_util.get_block_pos_from_mask(bedrock_blocks):
if is_kill_spot(c, bx, bz, y):
x = bx + (cx << 4)
z = bz + (cz << 4)
dist = cityblock((100, 100), (x, z))
yield x, z, dist
def __init__(self, rad):
super().__init__(rad)
self.mask_ = np.zeros((2*rad+1, 2*rad+1, 2*rad+1), dtype=np.bool)
for r1 in range(2*self.rad+1):
for r2 in range(2*self.rad+1):
for r3 in range(2*self.rad+1):
if(cityblock((r1, r2, r3),
(self.rad, self.rad, self.rad)) <= self.rad):
self.mask_[r1, r2, r3] = True
def calc_dist(di,dj,i=1):
""" Distance calculation for every
distance functions in use"""
if i == 1:
return ssd.euclidean(di,dj) # built-in Euclidean fn
elif i == 2:
return ssd.cityblock(di,dj) # built-in Manhattan fn
elif i == 3:
return ssd.cosine(di,dj) # built-in Cosine fn
def sliced_wasserstein(PD1, PD2, M=50):
""" Implementation of Sliced Wasserstein distance as described in
Sliced Wasserstein Kernel for Persistence Diagrams by Mathieu Carriere, Marco Cuturi, Steve Oudot (https://arxiv.org/abs/1706.03358)
Parameters
-----------
PD1: np.array size (m,2)
Persistence diagram
PD2: np.array size (n,2)
Persistence diagram
M: int, default is 50
Iterations to run approximation.
Returns
--------
sw: float
Sliced Wasserstein distance between PD1 and PD2
"""
diag_theta = np.array(
[np.cos(0.25 * np.pi), np.sin(0.25 * np.pi)], dtype=np.float32)
l_theta1 = [np.dot(diag_theta, x) for x in PD1]
l_theta2 = [np.dot(diag_theta, x) for x in PD2]
if (len(l_theta1) != PD1.shape[0]) or (len(l_theta2) != PD2.shape[0]):
raise ValueError("The projected points and origin do not match")
PD_delta1 = [[np.sqrt(x**2 / 2.0)] * 2 for x in l_theta1]
PD_delta2 = [[np.sqrt(x**2 / 2.0)] * 2 for x in l_theta2]
# i have the input now to compute the sw
sw = 0
theta = 0.5
step = 1.0 / M
for i in range(M):
l_theta = np.array([np.cos(theta * np.pi),
np.sin(theta * np.pi)],
dtype=np.float32)
V1 = [np.dot(l_theta, x)
for x in PD1] + [np.dot(l_theta, x) for x in PD_delta2]
V2 = [np.dot(l_theta, x)
for x in PD2] + [np.dot(l_theta, x) for x in PD_delta1]
sw += step * cityblock(sorted(V1), sorted(V2))
theta += step
return sw
def run(self, video_path=None):
if video_path is not None:
self.video_path = video_path
assert (self.video_path is not None), "you should must the video path!"
self.shots = []
cap = cv2.VideoCapture(self.video_path)
hists = []
frames = []
while True:
success, frame = cap.read()
if not success:
break
if self.output_dir is not None:
frames.append(frame)
# compute RGB histogram for each frame
color_histgrams = [cv2.calcHist([frame], [c], None, [self.hist_size], [0,256]) \
for c in range(3)]
color_histgrams = np.array([chist/float(sum(chist)) for chist in color_histgrams])
hists.append(color_histgrams.flatten())
# manhattan distance of two consecutive histgrams
scores = [cityblock(*h12) for h12 in zip(hists[:-1], hists[1:])]
print("max diff:", max(scores), "min diff:", min(scores))
# compute automatic threshold
mean_score = np.mean(scores)
std_score = np.std(scores)
threshold = self.absolute_threshold
# decide shot boundaries
prev_i = 0
prev_score = scores[0]
for i, score in enumerate(scores[1:]):
if (score >= threshold) and (abs(score - prev_score) >= threshold/2.0):
self.shots.append((prev_i, i+2))
prev_i = i + 2
prev_score = score
video_length = len(hists)
self.shots.append((prev_i, video_length))
assert video_length>=self.min_duration, "duration error"
self.merge_short_shots()
# save key frames
if self.output_dir is not None:
for shot in self.shots:
cv2.imwrite("%s/frame-%d.jpg" % (self.output_dir,shot[0]), frames[shot[0]])
print("key frames written to %s" % self.output_dir)
def calculate(self, row):
q1 = str(row['question1'])
q2 = str(row['question2'])
q1_keywords = self.calculate_keyword(q1)
q2_keywords = self.calculate_keyword(q2)
if not len(q1_keywords) or not len(q2_keywords):
return [0.0, 0.0, 0.0]
q1_vector = self.calculate_vector(q1_keywords)
q2_vector = self.calculate_vector(q2_keywords)
cos_sim = 1 - cosine(q1_vector, q2_vector)
euclidean_sim = 1 - euclidean(q1_vector, q2_vector)
manhattan_sim = 1 - cityblock(q1_vector, q2_vector)
return [cos_sim, euclidean_sim, manhattan_sim]
def get_distances(X):
nfeatures = len(X[0])
man_dist = [cityblock(features, np.zeros(nfeatures)) for features in X]
cosine_dist = [cosine(features, np.ones(nfeatures)) for features in X]
euclid_dist = [
sqeuclidean(features, np.zeros(nfeatures)) for features in X
]
minkowski_dist = [
minkowski(features, np.zeros(nfeatures), 2) for features in X
]
all_dist = np.column_stack((np.column_stack((np.column_stack(
(man_dist, cosine_dist)), euclid_dist)), minkowski_dist))
return all_dist
def calc_puddle_penalization(self, state: tuple) -> float:
"""
Return a float that represents a penalization, the penalization is the lowest distance between current state
and the nearest border in manhattan distance.
:param state:
:return:
"""
# Min distance found!
min_distance = min(
cityblock(self.current_state, state) for state in self.free_spaces)
# Set penalization per distance
return -min_distance
def get_min_dist(incoming_coord):
dist = {}
for coordinate in coordinates.iterrows():
coord = coordinate[0]
x = coordinate[1][0]
y = coordinate[1][1]
dist[coord] = distance.cityblock(incoming_coord, (x, y))
min_value = min(dist.values())
min_keys = [k for k in dist if dist[k] == min_value]
if len(min_keys) > 1:
return -1 # Location is equally far from two or more coordinates
else:
return min_keys[0]
def feature_construct(city,
model_name,
friends,
walk_len=100,
walk_times=20,
num_features=128):
'''construct the feature matrixu2_checkin
Args:
city: city
model_name: 20_locid
friends: friends list (asymetric) [u1, u2]
walk_len: walk length
walk_times: walk times
num_features: dimension for vector
Returns:
'''
if os.path.exists('dataset/'+city+'/feature/'+city+'_'+model_name+'_'+\
str(int(walk_len))+'_'+str(int(walk_times))+'_'+str(int(num_features))+'.feature'):
os.remove('dataset/'+city+'/feature/'+city+'_'+model_name+'_'+\
str(int(walk_len))+'_'+str(int(walk_times))+'_'+str(int(num_features))+'.feature')
emb = pd.read_csv('dataset/'+city+'/emb/'+city+'_'+model_name+'_'+\
str(int(walk_len))+'_'+str(int(walk_times))+'_'+str(int(num_features))+'.emb',\
header=None, skiprows=1, sep=' ')
emb = emb.rename(columns={0: 'uid'}) # last column is user id
emb = emb.loc[emb.uid > 0] # only take users, no loc_type, not necessary
pair = pair_construct(emb.uid.unique(), friends)
for i in range(len(pair)):
u1 = pair.loc[i, 'u1']
u2 = pair.loc[i, 'u2']
label = pair.loc[i, 'label']
u1_vector = emb.loc[emb.uid == u1, range(1, emb.shape[1])]
u2_vector = emb.loc[emb.uid == u2, range(1, emb.shape[1])]
i_feature = pd.DataFrame([[u1, u2, label,\
cosine(u1_vector, u2_vector),\
euclidean(u1_vector, u2_vector),\
correlation(u1_vector, u2_vector),\
chebyshev(u1_vector, u2_vector),\
braycurtis(u1_vector, u2_vector),\
canberra(u1_vector, u2_vector),\
cityblock(u1_vector, u2_vector),\
sqeuclidean(u1_vector, u2_vector)]])
i_feature.to_csv('dataset/'+city+'/feature/'+city+'_'+model_name+'_'+\
str(int(walk_len))+'_'+str(int(walk_times))+'_'+str(int(num_features))+'.feature',\
index = False, header = None, mode = 'a')
def fit(self,data):
# Will do the normalization, if necessary
if (self.l2norm == True):
transformer = Normalizer().fit(data)
data = transformer.transform(data)
# Initialize the Centroids
self.ctrds = {}
# Set the default centroids as the first k points of the data
for i in range(self.k):
self.ctrds[i] = data[i]
# Set the default running iteration
for i in range(self.max_iter):
self.classes = {}
# Set the default classification for k classes
for i in range(self.k):
self.classes[i] = []
# Count the distances between the data and the centroids. Methods : Euclidean, Cityblock, Cosine
for data_rows in data:
if (self.method == "euclidean"):
dst = [distance.euclidean(data_rows, self.ctrds[ctrd]) for ctrd in self.ctrds]
elif (self.method == "cityblock"):
dst = [distance.cityblock(data_rows, self.ctrds[ctrd]) for ctrd in self.ctrds]
elif (self.method == "cosine"):
dst = [distance.cosine(data_rows, self.ctrds[ctrd]) for ctrd in self.ctrds]
clf = dst.index(min(dst))
self.classes[clf].append(data_rows)
# Enter the centroids to a dictionary
prev_ctrds = dict(self.ctrds)
# Determine the average of the distances to determine a new centroid
for clf in self.classes:
self.ctrds[clf] = np.average(self.classes[clf],axis=0)
optimized = True
# Determine the loop if it has passed the minimum tolerance or not
for c in self.ctrds:
default_ctrd = prev_ctrds[c]
current_ctrd = self.ctrds[c]
if np.sum((current_ctrd - default_ctrd)/default_ctrd * 100.0) > self.tol:
optimized = False
if optimized:
break
def get_features(question1, question2):
"""
Get all the features to input into the XGBoost model.
Pre: Both questions cannot be None.
Args:
question1: The first question to match.
question2: The second question to match.
Returns: A dictionary with all the features for the XGBoost model.
"""
w2v = word2vec_features(question1, question2, W2VModel)
output_dict = {
# length based features
"len_q1": [len(question1)],
"len_q2": [len(question2)],
"diff_len": [len(question1) - len(question2)],
"len_char_q1": [len(question1.replace(" ", ""))],
"len_char_q2": [len(question2.replace(" ", ""))],
"len_word_q1": [len(question1.split())],
"len_word_q2": [len(question2.split())],
"common_words": [
len(
set(question1.lower().split()).intersection(
set(question2.lower().split())))
],
# distance based features
# (fuzzywuzzy library tutorial: https://www.datacamp.com/community/tutorials/fuzzy-string-python)
"fuzz_Qratio": [fuzz.QRatio(question1, question2)],
"fuzz_Wratio": [fuzz.WRatio(question1, question2)],
"fuzz_partial_ratio": [fuzz.partial_ratio(question1, question2)],
"fuzz_partial_token_set_ratio":
[fuzz.partial_token_set_ratio(question1, question2)],
"fuzz_partial_token_sort_ratio":
[fuzz.partial_token_sort_ratio(question1, question2)],
"fuzz_token_set_ratio": [fuzz.token_set_ratio(question1, question2)],
"fuzz_token_sort_ratio": [fuzz.token_sort_ratio(question1, question2)],
# word2vec based features
"cosine_distance": [cosine(w2v[0], w2v[1])],
"cityblock_distance": [cityblock(w2v[0], w2v[1])],
"jaccard_distance": [jaccard(w2v[0], w2v[1])],
"canberra_distance": [canberra(w2v[0], w2v[1])],
"euclidean_distance": [euclidean(w2v[0], w2v[1])],
"minkowski_distance": [minkowski(w2v[0], w2v[1])],
"braycurtis_distance": [braycurtis(w2v[0], w2v[1])],
"wmd": [w2v[2]],
"norm_wmd": [w2v[3]]
}
return output_dict
def find_distance(x,y,option):
if option == "1":
# return math.sqrt(sum([(a - b) ** 2 for a, b in zip(x, y)]))
return np.linalg.norm(x-y)
elif option == "2":
# return sum([(a - b) for a,b in zip(x, y)])
return scp.cityblock(x,y)
elif option == "3":
# numer = sum([a*b for a,b in zip(x,y)])
# denom_1 = math.sqrt(sum([a ** 2 for a in x]))
# denom_2 = math.sqrt(sum([b ** 2 for b in y]))
# return numer/(denom_1*denom_2)
# return sum([sum(a*b)/ (math.sqrt(a**2)*math.sqrt(b**2)) for a, b in zip(x,y)])
return scp.cosine(x,y)
def add_lateral_connections_topology(layer, distance_to_weight):
proj = sim.Projection(layer.population, layer.population,
sim.AllToAllConnector(), sim.StaticSynapse())
weights = np.zeros((layer.size(), layer.size()))
# for all combinations of neurons
for x1, y1, x2, y2 in itertools.product(np.arange(layer.shape[0]),
np.arange(layer.shape[1]),
repeat=2):
w = distance_to_weight(distance.cityblock([x1, y1], [x2, y2]))
weights[layer.get_idx(x1, y1)][layer.get_idx(x2, y2)] = w
proj.set(weight=weights)
def get_longest_shortest_routes(self):
""" Return manhattan distance for all pair of batteries and houses"""
import collections
#import math
manhattan_distance = []
for house_key, house_value in self.houses.items():
house_position = house_value.x, house_value.y
for battery_key, battery_value in self.batteries.items():
battery_position = battery_value.x, battery_value.y
manhattan_distance.append([
house_key, battery_key,
distance.cityblock(battery_position, house_position)
])
# shortest routes
shortest_distance_per_house = []
for house in self.houses:
shortest_distance = math.inf
for i in manhattan_distance:
#if i[0] == house and i == 0:
if i[0] == house:
if i[2] < shortest_distance:
shortest_distance = i[2]
shortest_distance_per_house.append(shortest_distance)
smallest_object_value = 0
for i in shortest_distance_per_house:
smallest_object_value += i
print(smallest_object_value)
# largest routes
largest_distance_per_house = []
for house in self.houses:
largest_distance = 0
for i in manhattan_distance:
#if i[0] == house and i == 0:
if i[0] == house:
if i[2] > largest_distance:
largest_distance = i[2]
largest_distance_per_house.append(largest_distance)
biggest_object_value = 0
for i in largest_distance_per_house:
biggest_object_value += i
print(biggest_object_value)
return manhattan_distance
def similarity(svd1, svd2):
scores = [0, 0, 0]
array_depths = [32, number_svd_vectors, number_svd_vectors]
importance_factors = [
475, 1, 310
] #these are weighting numbers (chosen by trial and error) which resulted in the highest accuracy.
#this accounts for not all of the things SVD returns being of equal scale/importance.
for i in range(3):
for j in range(array_depths[i]):
scores[i] += distance.cityblock(svd1[0][j],
svd2[0][j]) #(manhattan distance)
return np.array(scores).dot(np.array(importance_factors))
def calculate_similarity(self,
question_ebd,
relation_ebd,
metric='cosine'):
if metric == 'braycurtis':
return distance.braycurtis(question_ebd, relation_ebd)
elif metric == 'canberra':
return distance.canberra(question_ebd, relation_ebd)
elif metric == 'cityblock':
return distance.cityblock(question_ebd, relation_ebd)
elif metric == 'cosine':
return distance.cosine(question_ebd, relation_ebd)
elif metric == 'euclidean':
return distance.euclidean(question_ebd, relation_ebd)
def manhattan(self, x=None, y=None, w=None):
"""
曼哈顿距离（Manhattan Distance）是由十九世纪的赫尔曼·闵可夫斯基所创词汇，是种使用在几何度量空间的几何学用语，
用以标明两个点在标准坐标系上的绝对轴距总和。曼哈顿距离的命名原因是从规划为方型建筑区块的城市（如曼哈顿）
间，最短的行车路径而来（忽略曼哈顿的单向车道以及只存在于3、14大道的斜向车道）。
任何往东三区块、往北六区块的的路径一定最少要走九区块，没有其他捷径。
x = [1, 2, 0]
y = [0, 1, 0]
"""
x = x or self.x
y = y or self.y
w = w or self.w
return distance.cityblock(x, y, w)
def score_routing(self, routing, usage_matrix):
"""
For the given layout, and the routing, produce the score of the
routing.
The score is composed of its constituent nets' scores, and the
score of each net is based on the number of violations it has,
the number of vias and pins and the ratio of its actual length
and the lower bound on its length.
layout is the 3D matrix produced by the placer.
"""
alpha = 3
beta = 0.1
gamma = 1
net_scores = {}
net_num_violations = {}
# Score each net segment in the entire net
for net_name, d in routing.iteritems():
net_scores[net_name] = []
net_num_violations[net_name] = []
for i, segment in enumerate(d["segments"]):
routed_net = segment["net"]
# Violations
violation_matrix = segment["violation"]
violations = self.compute_net_violations(violation_matrix, usage_matrix)
net_num_violations[net_name].append(violations)
# Number of vias and pins
vias = 0
num_pins = 2
pins_vias = vias - num_pins
# Lower length bound
coord_a = segment["pins"][0]["route_coord"]
coord_b = segment["pins"][1]["route_coord"]
lower_length_bound = max(1, cityblock(coord_a, coord_b))
length_ratio = len(routed_net) / lower_length_bound
score = (alpha * violations) + (beta * pins_vias) + (gamma * length_ratio)
net_scores[net_name].append(score)
# print(routing)
# print(net_scores)
return net_scores, net_num_violations
def __init__(self,
height: int,
width: int,
seed: int = None,
levelname: str = ""):
super().__init__(height, width, seed=seed, levelname=levelname)
# Key variables
room_count = max(1, round(self.size / Voronoi.ROOM_SIZE))
rooms = self.random_points(room_count, margin=1)
areas = collections.defaultdict(list)
# Generating vonoroi
for c1 in range(self.height):
for c2 in range(self.width):
areas[tuple(
min(rooms,
key=lambda room: dist.cityblock(room,
(c1, c2))))].append(
(c1, c2))
# Placing walls
for area in areas:
for row in set(point[1] for point in areas[area]):
points = [point for point in areas[area] if point[1] == row]
minimum = min(points, key=lambda p: p[0])
maximum = max(points, key=lambda p: p[0])
self.map[minimum] = 1
self.map[maximum] = 1
for column in set(point[0] for point in areas[area]):
points = [point for point in areas[area] if point[0] == column]
minimum = min(points, key=lambda p: p[1])
maximum = max(points, key=lambda p: p[1])
self.map[minimum] = 1
self.map[maximum] = 1
# Removing borders
for area in [area for area in areas]:
for point in areas[area][:]:
if self.map[point]:
areas[area].remove(point)
if not areas[area]:
areas.pop(area)
# Parameters
self.areas = areas
def manhattan_distance(series1, series2):
"""
Compute the City Block (Manhattan) distance between two series
Quantifies the absolute magnitude of the difference between time series.
Args:
series1 (numpy.ndarray): First series
series2 (numpy.ndarray): Second series
Returns:
City Block (Manhattan) distance coefficient between the two series
"""
return sc.cityblock(series1, series2)
def KNNsearch(query, k, metric):
result = []
for i in range(len(Collection["names"])):
dist = math.inf
if(metric=="eucledian"):
ndist = distance.euclidean(query, Collection["encodings"][i])
elif(metric=="manhattan"):
ndist = distance.cityblock(query, Collection["encodings"][i])
dist = min(dist,ndist)
if(len(result)<k):
heapq.heappush(result,(-dist,Collection["names"][i]))
elif(heapq.nsmallest(1,result)[0][0]<-dist):
heapq.heapreplace(result,(-dist,Collection["names"][i]))
return [heapq.heappop(result) for i in range(len(result))]
def __init__(self, screen_width, screen_height, state_representation):
self.wn = turtle.Screen()
self.screen_width = screen_width
self.screen_height = screen_height
self.max_distance = distance.cityblock(
np.array([0, 0]), np.array([screen_width, screen_height]))
self.current_food = None
self.snake = None
self.actions = {0: "up", 1: "right", 2: "down", 3: "left"}
self.points = 0
self.n_moves = 0
self.max_moves_without_food = 1000
self.theta = 45
self.state_representation = state_representation(self)
def manhattan_distance(a, b):
"""Compute the manhattan (L1) distance between two numpy arrays.
Parameters
----------
a: numpy array
b: numpy array
Returns
-------
distance: float
"""
dist = distance.cityblock(a, b)
return dist
def compute_distance(X, centroid, type="euclidian", weight=1):
"""Computes the distance using the type passed as parameter. Can compute weighted distance only for minkowski."""
# Initialize the weight to all ones if not specified for weighted minkowski.
if type is "wminkowski" and weight is 1:
weight = np.ones(len(X))
# Computation of the distance using one of the implemented formulas
distance = {
"euclidian": (sp.euclidean(X, centroid)),
"manhattan": (sp.cityblock(X, centroid)),
"wminkowski": (sp.wminkowski(X, centroid, 2, weight))
}[type]
return distance
def chamfer_with_normalize(test, target):
distances = []
for i in range(0, len(test)):
point_dst = []
for j in range(0, len(target)):
point_dst.append(distance.cityblock(test[i], target[j]))
distances.append(min(point_dst))
distances = np.array(distances)
distances = (distances - np.min(distances)) / np.ptp(distances)
return distances
def __call__(self):
'''
returns vector features. They are:
1. cosine similarity
2. L2 normed distance
3. L1 normed distance
4. Bray-Curtis distance
5. Correlation distance
6. absolute distance vector between q1 and q2 (ndim features)
'''
from scipy.spatial import distance
self.q1s = np.array_split(self.q1.values, self.n_batches)
self.q2s = np.array_split(self.q2.values, self.n_batches)
indices = np.array_split(self.feat.index, self.n_batches)
dfs = []
for index, (q1, q2) in zip(indices, zip(self.q1s, self.q2s)):
df = pd.DataFrame(index=index.values)
pre = self.prefix
vec = self.vectorizer
df[pre + 'cos_dist'] = [
distance.cosine(vec(x), vec(y)) for x, y in zip(q1, q2)
]
df[pre + 'euc_dist'] = [
distance.euclidean(vec(x), vec(y)) for x, y in zip(q1, q2)
]
df[pre + 'manhattan_dist'] = [
distance.cityblock(vec(x), vec(y)) for x, y in zip(q1, q2)
]
df[pre + 'braycurt_dist'] = [
distance.braycurtis(vec(x), vec(y)) for x, y in zip(q1, q2)
]
df[pre + 'correlation_dist'] = [
distance.correlation(vec(x), vec(y)) for x, y in zip(q1, q2)
]
for i in range(self.size):
if self.transformer is not None:
df[pre + 'vec_{}'.format(i)] = abs(
self.transformer.transform(
np.array([vec(x) for x in q1]))[:, i] -
self.transformer.transform(
np.array([vec(x) for x in q2]))[:, i])
else:
df[pre + 'vec_{}'.format(i)] = abs(
(np.array([vec(x) for x in q1])) -
(np.array([vec(x) for x in q2])))[:, i]
dfs += [df]
df = pd.concat(dfs)
return self.feat.join(df)
def cross_channel_distance_features(image):
"""calculates the cross channel distance features
Calculates the distances across channels
Parameters
----------
image : 3D array, shape (M, N, C)
The input image with multiple channels.
Returns
-------
features : dict
dictionary including different distances across channels
"""
features = dict()
for ch1 in range(image.shape[2]):
for ch2 in range(ch1 + 1, image.shape[2]):
# rehaping the channels to 1D
channel1 = image[:, :, ch1].ravel()
channel2 = image[:, :, ch2].ravel()
# creating the suffix name for better readability
suffix = "_Ch" + str(ch1 + 1) + "_Ch" + str(ch2 + 1)
# storing the distance values
features["braycurtis_distance" + suffix] = dist.braycurtis(
channel1, channel2)
features["canberra_distance" + suffix] = dist.canberra(
channel1, channel2)
features["chebyshev_distance" + suffix] = dist.chebyshev(
channel1, channel2)
features["cityblock_distance" + suffix] = dist.cityblock(
channel1, channel2)
features["correlation_distance" + suffix] = dist.correlation(
channel1, channel2)
features["cosine_distance" + suffix] = dist.cosine(
channel1, channel2)
features["euclidean_distance" + suffix] = dist.euclidean(
channel1, channel2)
features["jensenshannon_distance" + suffix] = dist.jensenshannon(
channel1, channel2)
features["minkowski_distance" + suffix] = dist.minkowski(
channel1, channel2)
features["sqeuclidean_distance" + suffix] = dist.sqeuclidean(
channel1, channel2)
return features
def trainingAccuracy(K, type):
minVal = []
minVal1 = []
true = 0
false = 0
correct = 0
wrong = 0
for i in range(0, len(trainMatrix)):
initial = np.array(trainMatrix[i])
a = initial[1:len(initial) - 1]
b = np.delete(trainMatrix, (i), axis=0)
for j in range(0, len(b)):
c = np.array(b[j][1:len(b[j]) - 1])
Edist = distance.euclidean(a, c)
Mdist = distance.cityblock(a, c)
result3.append([Edist, b[j][len(b[j]) - 1]])
result4.append([Mdist, b[j][len(b[j]) - 1]])
# print result3
# print result4
result3.sort(key=lambda row: row[0:])
result4.sort(key=lambda row: row[0:])
# print result3
# print result4
for k in range(0, K):
minVal.append(result3[k][1])
minVal1.append(result4[k][1])
# print "top k elements" , minVal
count = Counter(minVal)
count1 = Counter(minVal1)
# print " test ans =" , count.most_common()[0]
# print 'type = ' , count.most_common()
# print 'type1 = ', count1.most_common()
# print " test ans =", count.most_common()[0][0]
# print "real ans = " , testrow[len(testrow)-1]
if (count.most_common()[0][0] == initial[len(initial) - 1]):
true += 1.0
else:
false += 1.0
if (count1.most_common()[0][0] == initial[len(initial) - 1]):
correct += 1.0
else:
wrong += 1.0
minVal = []
minVal1 = []
if (type == 2):
print 'accuracy for K = ', K, "=", (true / (true + false)) * 100, "%"
else:
print 'accuracy for K = ', K, "=", (correct /
(correct + wrong)) * 100, "%"
def testingAccuracy(K):
minVal = []
minVal1 = []
i = 0
j = 0
true = 0
false = 0
correct = 0
wrong = 0
for testrow in testMatrix:
# for testrow in testMatrix1:
j += 1
i = 0
for trainrow in trainMatrix:
a = np.array(trainrow[1:len(trainrow) - 1])
b = np.array(testrow[1:len(testrow) - 1])
# dist = distance.euclidean(a, b)
dist1 = distance.cityblock(a, b)
dist = np.linalg.norm(a - b)
# print "distance for " , i , "= " ,dist
result.append([dist, trainrow[len(trainrow) - 1]])
result1.append([dist1, trainrow[len(trainrow) - 1]])
i += 1
result.sort(key=lambda row: row[0:])
result1.sort(key=lambda row: row[0:])
# print "after sorting = " , result
for k in range(0, K):
minVal.append(result[k][1])
minVal1.append(result[k][1])
# print "top k elements" , minVal
count = Counter(minVal)
count1 = Counter(minVal1)
# print " test ans =" , count.most_common()[0]
# print 'type = ' , count.most_common()
# print " test ans =", count.most_common()[0][0]
# print "real ans = " , testrow[len(testrow)-1]
if (count.most_common()[0][0] == testrow[len(testrow) - 1]):
true += 1.0
else:
false += 1.0
if (count1.most_common()[0][0] == testrow[len(testrow) - 1]):
correct += 1.0
else:
wrong += 1.0
minVal = []
minVal1 = []
# print 'correct = ' , true
# print 'wrong = ' , false
print 'accuracy for K = ', K, "=", (true / (true + false)) * 100, "%"
def determine_longest_at_turn_n(board_state: GameState):
"""
Determine which snake is longest in current state. Tie break using 'closest head to a fruit'
:return:
"""
longest_snake_idx = None
for snake_i, snake in enumerate(board_state.snakes):
if snake.alive:
if longest_snake_idx is None or snake.length > board_state.snakes[
longest_snake_idx].length:
longest_snake_idx = snake_i
continue
if snake.length == board_state.snakes[
longest_snake_idx].length:
# Tie Break
snake_manhattan_dists = sorted([
cityblock(snake.head, trophy_i)
for trophy_i in board_state.fruits_locations
])
longest_manhattan_dists = sorted([
cityblock(board_state.snakes[longest_snake_idx].head,
trophy_i)
for trophy_i in board_state.fruits_locations
])
for d1, d2 in zip(snake_manhattan_dists,
longest_manhattan_dists):
if d1 < d2:
longest_snake_idx = snake_i
break
elif d1 > d2:
break
else:
# equal distance, tie break with later trophy..
pass
return longest_snake_idx
def calculate_manhattan_score(self):
# calculate the key hold manhattan scores
# key hold genuine score
for i in range(self.kh_test_genuine.shape[0]):
current_score = cityblock(self.kh_test_genuine.iloc[i].values,
self.kh_mean_vector)
self.kh_genuine_score.append(current_score)
# key hold impostor score
for i in range(self.kh_test_impostor.shape[0]):
current_score = cityblock(self.kh_test_impostor.iloc[i].values,
self.kh_mean_vector)
self.kh_impostor_score.append(current_score)
# calculate the key interval manhattan scores
# key interval genuine score
for i in range(self.ki_test_genuine.shape[0]):
current_score = cityblock(self.ki_test_genuine.iloc[i].values,
self.ki_mean_vector)
self.ki_genuine_score.append(current_score)
# key interval impostor score
for i in range(self.ki_test_impostor.shape[0]):
current_score = cityblock(self.ki_test_impostor.iloc[i].values,
self.ki_mean_vector)
self.ki_impostor_score.append(current_score)
def testReplicaHistAdaptation(self):
"""Verify that adaptation leads to linear replica directions."""
chain = self.GetAdaptiveIsingChain(
self.nsteps_per_sweep, self.nswaps_per_sweep, self.burn_roundtrips)
ntemps = len(self.temps)
linear_hist = [(ntemps/(ntemps-1))*(x/10) for x in reversed(range(ntemps))]
# Run chain with linearly spaced temperatures.
self.RunForRoundtrips(chain, self.adaptation_roundtrips)
pre_ntransitions = chain.statistics.transitions
pre_hist = chain.statistics.replica.hist
# Verify that the histogram of replica directions is far from linear.
self.assertGreater(distance.cityblock(linear_hist, pre_hist), 1.0)
# Adapt temperatures.
chain.AdaptTemperatures()
chain.Reset()
# Run chain with new temperatures.
self.RunForRoundtrips(chain, self.adaptation_roundtrips)
post_ntransitions = chain.statistics.transitions
post_hist = chain.statistics.replica.hist
# Verify that the histogram of replica directions is close to linear.
self.assertLess(distance.cityblock(linear_hist, post_hist), 1.0)
# Verify that the number of transitions necessary to reach the
# same number of roundtrips is shorter after adaptation.
self.assertLess(post_ntransitions, pre_ntransitions)
def calculate(self, row):
seq1 = str(row['question1']).split()
seq2 = str(row['question2']).split()
seq1 = [word for word in seq1 if word in self.model]
seq2 = [word for word in seq2 if word in self.model]
if len(seq1) == 0 or len(seq2) == 0:
return [0.0, 0.0, 0.0]
vec_seq1 = [self.model[x] for x in seq1]
vec_seq2 = [self.model[x] for x in seq2]
vec_seq1 = np.array(vec_seq1).mean(axis=0)
vec_seq2 = np.array(vec_seq2).mean(axis=0)
cos_sim = 1 - cosine(vec_seq1, vec_seq2)
euclidean_sim = 1 - euclidean(vec_seq1, vec_seq2)
manhattan_sim = 1 - cityblock(vec_seq1, vec_seq2)
return [cos_sim, euclidean_sim, manhattan_sim]
def ae_to_distance(mat1, mat2, metric='euclidean', method='avg', cov=None):
# Methods: min, max, avg, centroid
# Metrics: Euclidean, Manhattan (Cityblock), Mahalanobis (requires a covariance matrix) ,Add: Maximum
if not method == 'centroid':
vec_dist = cdist(mat1, mat2, metric=metric)
if method == 'min':
calc_dist = np.min(vec_dist)
elif method == 'max':
calc_dist = np.max(vec_dist)
elif method == 'avg':
calc_dist = np.nanmean(vec_dist)
else:
raise ValueError("Wrong name of method")
else:
cent_1 = np.mean(mat1, axis=0).reshape((1, -1))
cent_2 = np.mean(mat2, axis=0).reshape((1, -1))
if metric == 'euclidean':
calc_dist = euclidean(cent_1, cent_2)
elif metric == 'cityblock':
calc_dist = cityblock(cent_1, cent_2)
elif metric == 'hamming':
calc_dist = hamming(cent_1, cent_2)
elif metric == 'correlation':
calc_dist = correlation(cent_1, cent_2)
elif metric == 'cityblock':
calc_dist = cityblock(cent_1, cent_2)
elif metric == 'sqeuclidean':
calc_dist = sqeuclidean(cent_1, cent_2)
elif metric == 'mahalanobis':
if cov is None:
raise ValueError("Insert covariance matrix")
calc_dist = mahalanobis(cent_1, cent_2, VI=np.linalg.inv(cov))
else:
raise ValueError("Wrong name of metric")
return calc_dist
def calculate_shap_distance(alert, counterfactuals):
alert_counterfactuals = pd.concat([alert, counterfactuals], axis=0)
alert_counterfactuals_shap = get_shap(alert_counterfactuals)
dist = []
for i in range(1, len(alert_counterfactuals.index)):
dist.append(cityblock(alert_counterfactuals_shap[0], alert_counterfactuals_shap[i]))
# sum = 0
# for j in range(0, len(alert_counterfactuals_shap[i])):
# sum = sum + alert_counterfactuals_shap[0][j] - alert_counterfactuals_shap[i][j]
#
# dist.append(sum)
return dist
def __init__(self, rad):
"""Constructor
Parameters
----------
rad: radius, in voxels, of the sphere inscribed in the
searchlight cube, not counting the center voxel
"""
super().__init__(rad)
self.mask_ = np.zeros((2*rad+1, 2*rad+1, 2*rad+1), dtype=np.bool)
for r1 in range(2*self.rad+1):
for r2 in range(2*self.rad+1):
for r3 in range(2*self.rad+1):
if(cityblock((r1, r2, r3),
(self.rad, self.rad, self.rad)) <= self.rad):
self.mask_[r1, r2, r3] = True
def __calculateStatistics(self, result):
"""
Create the RefDB and some statistics
:param result:
:return:
"""
"""
Set the center sequence for each cluster
"""
for cluster in result.cluster_set.all():
# store the cluster representative
min = None
sequence = None
statistics = {
'dists-variance' : 0,
'dists-amax' : 0,
'dists-average' : 0,
'size' : cluster.sequences.count(),
'radius' : 0
}
if cluster.sequences:
distances = []
for sequence in cluster.sequences.all():
dist = cityblock(sequence.dna, cluster.centerMean)
if dist > statistics['radius']:
statistics['radius'] = dist
if (dist < min) or (min == None):
min = dist
sequence = sequence
distances.append(dist)
statistics['dists-variance'] = np.var(distances)
statistics['dists-amax'] = np.amax(distances)
statistics['dists-average'] = np.average(distances)
cluster.statistics = statistics
cluster.representative = sequence
cluster.save()
def compare_segments_image(seg1, seg2, slen, cwl): #return 2 #for i in range(slen): # seg1[:,i:60+i] #tmp=seg1[:,5:55] # seg is 50 by 10 #for i in range(slen): #print 'template size',seg2.shape #print 'template',seg2[:,5:55] #print citblock(seg1[:,0:50],seg2[:,5:55]) dist=[] #print seg2.shape #print seg1.shape for i in range(10): #print 'seg 1 shape',a.shape dist.append(cityblock(seg1[:,i:50+i].flatten(),seg2.flatten())) return min(dist)
def compHist(hist1, hist2, method, formula):
"""Compare two histograms with given method and formula.
Parameters
----------
hist1 : 1D array
The first histogram
hist2 : 1D array
The second histogram
method : str(cv integer)
Options for method ('cv_comp', 'scipy_comp', 'kl_div')
formula: str(cv integer)
Options for formula.
For method == 'cv_comp' (cv.CV_COMP_CORREL, cv.CV_COMP_CHISQR, cv.CV_COMP_INTERSECT, cv.CV_COMP_BHATTACHARYYA)
For method == 'scipy_comp' ("Euclidean", "Manhattan", "Chebysev")
"""
## using opencv
if method == 'cv_comp':
dis = cv2.compareHist(np.float32(hist1), np.float32(hist2), formula)
if formula == cv.CV_COMP_CORREL:
dis = -dis + 1
## using Scipy distance metrics
if method == 'scipy_comp':
if formula == 'Euclidean':
dis = dist.euclidean(hist1, hist2)
if formula == 'Manhattan':
dis = dist.cityblock(hist1, hist2)
if formula == 'Chebysev':
dis = dist.chebyshev(hist1, hist2)
## using KL divergence
hist1 = np.float32(hist1) + 1
hist2 = np.float32(hist2) + 1
if method == 'kl_div':
kbp = np.sum(hist1 * np.log(hist1 / hist2), 0)
kbq = np.sum(hist2 * np.log(hist2 / hist1), 0)
dis = np.double(kbp + kbq)/2
return dis
def determineDistance(point1, point2, set_type=distance_type): ''' This function determines the distance between two points in any number of dimensions. As such, it can also be used to determine the radius of a preference circle (by inputting a point and the status quo). ''' if preference_shape == 'ellipse': point2 = (point2[0], point2[1]) if set_type == 'pyth': # determines distance between two points using Pythagorean theorem distance = dist.euclidean(point1, point2) elif set_type == 'city-block': # determines the city-block or Manhattan distance between two points distance = dist.cityblock(point1, point2) return distance
def find_block_types(world, type_, player='Player', sort=True,
chunks_to_search=9, limit=0):
px, py, pz = world.getPlayerPosition(player=player)
type_id = world.__getattribute__('materials').__getattribute__(type_).ID
blocks = []
try:
for chunk in get_surrounding_chunks(world, num=chunks_to_search):
cx, cz = chunk.chunkPosition
mask = (chunk.Blocks == type_id)
for bx, bz, y in get_block_pos_from_mask(mask):
x = bx + (cx << 4)
z = bz + (cz << 4)
distance = cityblock((px, pz, py), (x, z, y))
blocks.append((x, z, y, int(distance)))
except ChunkNotPresent:
pass
if not blocks:
return []
if sort:
blocks.sort(key=lambda tup: tup[-1])
return blocks[0:min(len(blocks) - 1, limit - 1)]
def get(self):
args = self.parser.parse_args()
node1, node2 = args['node1'], args['node2']
nodeType1, nodeType2 = nodes[node1], nodes[node2]
nodeKey1, nodeKey2 = args[nodeType1 + '1'], args[nodeType2 + '2']
result1 = self.getVector(node1, nodeType1, nodeKey1)
try:
assert len(result1) > 0
except:
raise ValueError("%s does not exist in database" % node1)
result2 = self.getVector(node2, nodeType2, nodeKey2)
try:
assert len(result2) > 0
except:
raise ValueError("%s does not exist in database" % node2)
result1 = np.array(map(float, result1[0][self.getVecName()].split(' ')))
result2 = np.array(map(float, result2[0][self.getVecName()].split(' ')))
diff = ','.join(map(str, result1 - result2))
inner = np.inner(result1, result2)
l1, l2, cos = cityblock(result1, result2), euclidean(result1, result2), cosine(result1, result2)
return json.dumps({'Difference': diff, 'Manhattan Distance': l1, 'Euclidean Distance': l2, 'Cosine Distance': cos, 'Inner Product': inner})
def assignPoints(self, centroids):
# centroids
# l = len(centroids)
# for i in range(0,l):
# centroids[i]+=random.random()
#set to True when there is a change in assigning points to clusters(centroids)
changed = False
assignedCentroids = pd.DataFrame()
for i in self.df.index:
distances = {}
for c in centroids.index:
if self.metric == "euclidean":
x = self.myEuclidean(self.df.loc[c], self.df.loc[i])
if self.metric == "chebyshev":
x = chebyshev(self.df.loc[c], self.df.loc[i])
if self.metric == "cityblock":
x = cityblock(self.df.loc[c], self.df.loc[i])
# print"i: "+str(i)+" c: "+str(c)
# print "self.df.loc[i]: "+ str(self.df.loc[i])
# print "self.df.loc[c]: "+ str(self.df.loc[c])
# print "x: "+str(x)
#dictionary that stores centroid as a key and distance between point and centroid as a value
distances[c] = x
# find the minimum by comparing the second element of each tuple (values)
m=min(distances.items(), key=lambda x: x[1])
#m[0] is a key of a min value in a dictionary, so m[0] is centroid
# point i 'belongs' to centroid m[0]
# if not assignedCentroids.at[i,'centroids']==m[0]: #if centroid is changed
# changed=True
# changed=True
# assignedCentroids.at[i,'centroids']=m[0]
assignedCentroids.at[i]=m[0]
# print "centroidyyyyyyyyyy"
# print assignedCentroids
return (assignedCentroids, changed)
def metrykaManhattan(self, array1, array2):
"""
Computes the Manhattan distance between two n-vectors u and v,
which is defined as
.. math::
\\sum_i {\\left| u_i - v_i \\right|}.
Parameters
----------
u : ndarray
An :math:`n`-dimensional vector.
v : ndarray
An :math:`n`-dimensional vector.
Returns
-------
d : double
The City Block distance between vectors ``u`` and ``v``.
"""
# od = abs(xa-xb) + abs(ya-yb)
return cityblock(array1,array2)
def main():
print "# KNN Classifier"
parser = ld.parse_arguments()
# priting args
print '\t-k = ' + str(parser.k)
print '\t-d = ' + parser.distance
stopwords = None
if parser.stopwords_path:
stopwords = ld.load_stopwords(parser.stopwords_path)
voc = load_vocabulary(parser.train_path, stopwords)
answers = load_answers(parser.train_path)
train = transform(voc, parser.train_path)
test = transform(voc, parser.test_path)
# output file
out_path = '../results/' + parser.distance + '_' + str(parser.k)
out_path += '.txt'
out_file = open(out_path, 'w')
for point in test:
neighbors = []
for i in xrange(len(train)):
neigh = train[i]
distance = 0.0
if parser.distance == 'cosine':
distance = spd.cosine(neigh, point)
elif parser.distance == 'jaccard':
distance = spd.jaccard(neigh, point)
elif parser.distance == 'euclidean':
distance = spd.euclidean(neigh, point)
elif parser.distance == 'dice':
distance = spd.dice(neigh, point)
elif parser.distance == 'correlation':
distance = spd.correlation(neigh, point)
elif parser.distance == 'manhattan':
distance = spd.cityblock(neigh, point)
else:
print >> stderr, "ERRO! - Distância informada inválida."
exit()
tup = (distance, i)
heapq.heappush(neighbors, tup)
# return the highest k similar points
top_k = heapq.nsmallest(parser.k, neighbors)
# classifing
classification = np.zeros(2)
for (_, idi) in top_k:
classe = answers[idi]
classification[int(classe)] += 1
# outputing classification
if(classification[0] >= classification[1]):
print >> out_file, '0'
print '0'
else:
print >> out_file, '1'
print '1'
# outputing the results'
print
print "# Resultados salvos no arquivo: " + out_path
out_file.close()
result.result("../data/imdb_test", out_path)
def _build_phase_data(self):
profile = pyscarphase.proto.meta.load_profile(self.args.profile)
thread = profile.threads[self.args.thread]
reader = pyscarphase.proto.data.DataReader(
thread.profile.filename,
uuid=thread.profile.uuid
)
phases = {}
for w in reader:
#
pid = w.phase_info.phase
#
if not pid in phases:
phases[pid] = self.Phase(pid)
phases[pid].centroid = \
np.zeros(len(w.phase_info.signature.fv_values))
#
phases[pid].centroid = \
np.add(
phases[pid].centroid,
w.phase_info.signature.fv_values[:]
)
# Normalize centroid
for p in phases.itervalues():
p.centroid = np.linalg.norm(p.centroid, 1)
# Do second pass
reader.seek(0)
offset = 0
for w in reader:
#
pid = w.phase_info.phase
# Calc distance
d = spd.cityblock(
phases[pid].centroid,
w.phase_info.signature.fv_values[:]
)
#
phases[pid].windows.append((offset, w.size, d))
#
offset += w.size
# Order phases in descending length
phases = sorted(
phases.itervalues(),
key=lambda p: len(p.windows),
reverse=True
)
#
return phases
#print "[+] Matrix in use is: \n", a #print "===================================================================" normA = normalize(a, norm='l1') temp_max = np.zeros(k) temp_min = np.zeros(k) min_array = np.zeros(k) max_array = np.zeros(k) r = np.zeros(k) for i in range(k): temp_min[i] = sys.maxint temp_max[i] = -1 for i in range(k): for j in range(k): if i != j: if (dist.cityblock(normA[i],normA[j]) < temp_min[i]): min_array[i] = dist.cityblock(normA[i],normA[j]) temp_min[i] = min_array[i] if (dist.cityblock(normA[i],normA[j]) > temp_max[i]): max_array[i] = dist.cityblock(normA[i],normA[j]) temp_max[i] = max_array[i] for i in range(k): r[i] = min_array[i]/max_array[i] #print "[+] Min distances are: \n", min_array #print "===================================================================" #print "[+] Max distances are: \n", max_array #print "===================================================================" #print "[+] Ratios are: \n", r print "*******************************************************************"
Qcosines=cosine_similarity(QuestionTVectorArray[0:1],QuestionTVectorArray) Acosines=cosine_similarity(AnswerTVectorArray[0:1],AnswerTVectorArray) Qbray=[dist.braycurtis(QuestionTVectorArray[0].toarray(),u.toarray()) for u in QuestionTVectorArray] Abray=[dist.braycurtis(AnswerTVectorArray[0].toarray(),u.toarray()) for u in AnswerTVectorArray] Qcanberra=[dist.canberra(QuestionTVectorArray[0].toarray(),u.toarray()) for u in QuestionTVectorArray] Acanberra=[dist.canberra(AnswerTVectorArray[0].toarray(),u.toarray()) for u in AnswerTVectorArray] Qhamming=[dist.hamming(QuestionTVectorArray[0].toarray(),u.toarray()) for u in QuestionTVectorArray] Ahamming=[dist.hamming(AnswerTVectorArray[0].toarray(),u.toarray()) for u in AnswerTVectorArray] Qcorrelation=[dist.correlation(QuestionTVectorArray[0].toarray(),u.toarray()) for u in QuestionTVectorArray] Acorrelation=[dist.correlation(AnswerTVectorArray[0].toarray(),u.toarray()) for u in AnswerTVectorArray] Qcityblock=[dist.cityblock(QuestionTVectorArray[0].toarray(),u.toarray()) for u in QuestionTVectorArray] Acityblock=[dist.cityblock(AnswerTVectorArray[0].toarray(),u.toarray()) for u in AnswerTVectorArray] Qdice=[dist.dice(QuestionTVectorArray[0].toarray(),u.toarray()) for u in QuestionTVectorArray] Adice=[dist.dice(AnswerTVectorArray[0].toarray(),u.toarray()) for u in AnswerTVectorArray] Qyule=[dist.yule(QuestionTVectorArray[0].toarray(),u.toarray()) for u in QuestionTVectorArray] Ayule=[dist.yule(AnswerTVectorArray[0].toarray(),u.toarray()) for u in AnswerTVectorArray] #C_Q=np.histogram2d(QuestionTVectorArray[1],QuestionTVectorArray[1])[0] #print "question mutual info-->",mutual_info_score(None,None,contigency=C_Q)#QuestionTVectorArray[0:1],QuestionTVectorArray) #QuestionVectorArray=Qvectorizer.fit_transform(all_questions).toarray() #AnswerVectorArray=Avectorizer.fit_transform(all_answers).toarray() #QUserinputVectorArray=Qvectorizer.transform(userinput).toarray()
def cityblock((x, y)):
return distance.cityblock(x, y)
def wvCity(a): return [distance.cityblock(x[0], x[1]) for x in a]
