def test_3_filter_galaxies(self):
"""Filter galaxies.
Update 3/14/2022 - filter_galaxies is no longer returning grid_shape
and coords_min parameters - instead they are calculated inside the
main body of find_voids() for consistency among the 3 mask_mode
types
"""
# Take a table of galaxy coordinates, the name of the survey, and the
# output directory and returns astropy tables of the Cartesian
# coordinates of the wall and field galaxies as well as the shape
# of the grid on which the galaxies will be placed and the coordinates
# of the lower left corner of the grid.
f_wall, f_field = filter_galaxies(self.galaxies_shuffled,
'test_',
'',
dist_metric='redshift',
)
# Check the wall galaxy coordinates
gal_tree = neighbors.KDTree(self.gal)
distances, indices = gal_tree.query(self.gal, k=4)
dist3 = distances[:,3]
TestVoidFinder.wall = self.gal[dist3 < (np.mean(dist3) + 1.5*np.std(dist3))]
self.assertTrue(np.isclose(f_wall, TestVoidFinder.wall).all())
# Check the field galaxy coordinates
field = self.gal[dist3 >= (np.mean(dist3) + 1.5*np.std(dist3))]
self.assertTrue(np.isclose(f_field, field).all())
def kdd_Neigbors_2(dta, index_ano):
# the input data should be under Pandas dataframe format.
start_anp = index_ano
X = list(map(lambda x: [x, dta.values[x][1]], np.arange(len(dta.values))))
#X = np.reshape(dta.value.values, (-1, 1))
tree = nb.KDTree(X, leaf_size=20)
flag_finding = 0
initial_index = []
while flag_finding == 0:
new_anomaly_point = find_anomaly_point(tree, X, index_ano,
initial_index)
if (len(index_ano) < len(new_anomaly_point)):
initial_index = index_ano
index_ano = np.array(new_anomaly_point, dtype=np.int32)
else:
flag_finding = 1
inverse_neighboor = index_ano
print("Nearest Neighboor of Anomaly point ", len(inverse_neighboor))
plt.figure(1)
plt.subplot(211)
plt.plot(dta.value.values)
plt.plot(np.array(inverse_neighboor, dtype=np.int32),
dta.value.values[np.array(inverse_neighboor,
dtype=np.int32)], 'o')
plt.plot(np.array(start_anp, dtype=np.int32),
dta.value.values[np.array(start_anp, dtype=np.int32)], 'x')
plt.show()
return inverse_neighboor
def build(self, embs, labels):
self.labels = labels
if type(embs) == np.ndarray:
self.embs = embs
else:
self.embs = np.vstack(embs)
self.tree = neighbors.KDTree(self.embs)
def build_kdt(X_norm, **kwargs):
kdt_kwds = dict(leaf_size=40, metric="minkowski")
kdt_kwds.update(kwargs)
kdt = neighbours.KDTree(X_norm, **kdt_kwds)
return kdt
def leiden_clustering(umap_res,
resolution_range=(0, 1),
random_state=2,
kdtree_dist='euclidean'):
tree = neighbors.KDTree(umap_res, metric=kdtree_dist)
vals, i, j = [], [], []
for idx in range(umap_res.shape[0]):
dist, ind = tree.query([umap_res[idx]], k=25)
vals.extend(list(dist.squeeze()))
j.extend(list(ind.squeeze()))
i.extend([idx] * len(ind.squeeze()))
print(len(vals))
ginput = sps.csc_matrix(
(numpy.array(vals), (numpy.array(i), numpy.array(j))),
shape=(umap_res.shape[0], umap_res.shape[0]))
sources, targets = ginput.nonzero()
edgelist = zip(sources.tolist(), targets.tolist())
G = ig.Graph(edges=list(edgelist))
optimiser = leidenalg.Optimiser()
optimiser.set_rng_seed(random_state)
profile = optimiser.resolution_profile(G,
leidenalg.CPMVertexPartition,
resolution_range=resolution_range,
number_iterations=0)
print([len(elt) for elt in profile])
return profile
def test_add_tracker(self, mock_write, mock_color, mock_mkdir):
mock_mkdir.side_effect = fake_os
print("\ntest add tracker")
matcher = FakeMatcher()
embs = np.eye(12)
labels = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]
matcher.build(embs, labels)
# total 12 tracker
zero = np.zeros(12)
trackers = {}
for i in range(12):
vec = zero.copy()
vec[i] = 1
tracker = create_tracker([vec] * 40)
trackers[i] = tracker
tracker_history = TrackersHistory()
tracker_history.trackers = trackers
tracker_history.current_id = 13
tracker_history.start_time = 0
tracker_history.labels = labels
tracker_history.embs = [embs[i, :] for i in range(12)]
history_matcher = neighbors.KDTree(
embs, leaf_size=Config.Matcher.INDEX_LEAF_SIZE, metric='euclidean')
tracker_history.history_matcher = history_matcher
mock = MagicMock(side_effect=fake_os)
with patch('os.mkdir', mock):
tracker_history.add_tracker(trackers[0], matcher, Mock())
def __predict_proba(self, X):
""" __predict_proba
Private implementation of the predict_proba method.
Parameters
----------
X: Numpy.ndarray of shape (n_samples, n_features)
Returns
-------
tuple list
One list with the k-nearest neighbor's distances and another
one with their indexes.
Notes
-----
If you wish to use our own KDTree implementation please comment
the third line of this function and uncomment the first and
second lines.
"""
#tree = KDTree(self.window.get_attributes_matrix(), metric='euclidean',
# categorical_list=self.categorical_list, return_distance=True)
tree = sk.KDTree(self.window.get_attributes_matrix(),
self.leaf_size,
metric='euclidean')
dist, ind = tree.query(np.asarray(X), k=self.k)
return dist, ind
def _compute_connectivity(positions, radius, add_self_edges):
"""Get the indices of connected edges with radius connectivity.
Args:
positions: Positions of nodes in the graph. Shape:
[num_nodes_in_graph, num_dims].
radius: Radius of connectivity.
add_self_edges: Whether to include self edges or not.
Returns:
senders indices [num_edges_in_graph]
receiver indices [num_edges_in_graph]
"""
tree = neighbors.KDTree(positions)
receivers_list = tree.query_radius(positions, r=radius)
num_nodes = len(positions)
senders = np.repeat(range(num_nodes), [len(a) for a in receivers_list])
receivers = np.concatenate(receivers_list, axis=0)
if not add_self_edges:
# Remove self edges.
mask = senders != receivers
senders = senders[mask]
receivers = receivers[mask]
return senders, receivers
def comparison_kd_tree_library():
#data
n_attributes = 2
n_data = 100
data = np.column_stack(([9, 4, 5, 7, 8, 2], [6, 7, 4, 2, 1, 3]))
#target
target = np.random.uniform(0, 1, n_attributes)
target = np.array([10, 10])
#kdtrees initialization
kdtree_lucas = KDTree
kdtree_scikit = neighbors.KDTree(data, metric='euclidean')
#kdtrees query
k = data.shape[0]
distances_lucas, indices_lucas = kdtree_lucas.query(target, k)
distances_scikit, indices_scikit = kdtree_scikit.query(target, k=k)
nn_scikit = data[indices_scikit]
nn_lucas = data[indices_lucas]
nn_lucas = data[indices_lucas]
#difference
print('nearest neighbors lucas')
print(nn_lucas)
print('')
print('nearest neighbors scikit')
print(nn_scikit)
print('')
print('difference')
print(nn_lucas - nn_scikit)
def __predict_proba(self, X):
""" __predict_proba
Private implementation of the predict_proba method.
Parameters
----------
X: Numpy.ndarray of shape (n_samples, n_features)
Returns
-------
tuple list
One list with the k-nearest neighbor's distances and another
one with their indexes.
"""
# To use our own KDTree implementation please replace it as follows
# tree = KDTree(self.window.get_attributes_matrix(), metric='euclidean',
# nominal_attributes=self._nominal_attributes, return_distance=True)
tree = sk.KDTree(self.window.get_attributes_matrix(),
self.leaf_size,
metric='euclidean')
dist, ind = tree.query(np.asarray(X), k=self.n_neighbors)
return dist, ind
def k_dist(X, metric, k=3):
data = []
tree = sk.KDTree(X, leaf_size=30)
for n, point in enumerate(X):
dist, ind = tree.query([point], k=k)
data.append(dist[0].tolist()[k - 1])
return data
def quantize(img, representative_points):
quantized_img = np.zeros_like(img)
tree = neighbors.KDTree(representative_points, leaf_size=30)
for x in range(img.shape[0]):
for y in range(img.shape[1]):
_, index = tree.query([img[x][y]], k=1)
quantized_img[x][y] = representative_points[index[0][0]]
return quantized_img
def kdtree(df_reduced, lat_col, long_col, leaf_size, k):
"""
Takes in:
Returns:
"""
position = df_reduced[[lat_col, long_col]]
tree = neighbors.KDTree(position, leaf_size=leaf_size)
dist, ind = tree.query([position][0], k=k)
return tree, dist, ind
def store_best_threshold(self, stored_embeddings, dir):
thresholds = np.arange(0, 1, 0.0025)
embedding_size = 512
size = 0
for i, cls in enumerate(stored_embeddings):
for embs in stored_embeddings[cls].values():
size += len(embs)
plain_embeddings = np.zeros([size, embedding_size])
class_index = []
emb_i = 0
for i, cls in enumerate(stored_embeddings):
for embs in stored_embeddings[cls].values():
for emb in embs:
plain_embeddings[emb_i] = emb
emb_i += 1
class_index.append(cls)
embeddings = (plain_embeddings + 1.) / 2.
kd_tree = neighbors.KDTree(embeddings, metric='euclidean')
dists, recognized = np.zeros([size],
dtype=np.float32), np.zeros([size],
np.bool)
for i, emb in enumerate(embeddings):
dist, idx = kd_tree.query(emb.reshape([1, 512]), k=2)
dist = dist[0][np.argmax(dist)]
idx = idx[0][np.argmax(dist)]
detected_class = class_index[idx]
detected = detected_class == class_index[i]
recognized[i] = detected
dists[i] = dist
# __import__('ipdb').set_trace()
best_threshold = 0
max_detect = 0
if recognized.all():
best_threshold = np.max(dists)
else:
for threshold in thresholds:
detected = len(dists[recognized & (dists < threshold)])
if detected > max_detect:
max_detect = detected
best_threshold = threshold
threshold_file = os.path.join(dir, 'threshold.txt')
# best_threshold = best_threshold * 1.1
print_fun('=' * 50)
print_fun('Found best threshold = %s' % best_threshold)
# print_fun('Written to %s.' % threshold_file)
print_fun('=' * 50)
def getKDTrees(places):
trees = {}
for place_type in places.keys():
coords = [[i['lat'], i['lng']] for i in places[place_type]]
X = np.array(coords)
tree = neighbors.KDTree(X, leaf_size=2)
trees[place_type] = tree
return trees
def which_points_inside_source(source, target):
# point-cloudsをnp.arrayに変更
s_points = np.asarray(source.pcd.points)
t_points = np.asarray(target.pcd.points)
# リガンドを0.5ずつ分割する
cut_surface = [i for i in np.arange(s_points[:,2].max(), s_points[:,2].min(), -0.2)]
# 内外判定
points_inside_idx = []
for l in range(len(cut_surface)-1):
# c = 各層に対応するindex
s_c = list((s_points[:,2] > cut_surface[l+1]) & (s_points[:,2] < cut_surface[l]))
s_c = [i for i, x in enumerate(s_c) if x == True]
t_c = list((t_points[:,2] > cut_surface[l+1]) & (t_points[:,2] < cut_surface[l]))
t_c = [i for i, x in enumerate(t_c) if x == True]
# 抽出
layer = s_points[s_c][:, 0:2]
points = t_points[t_c][:, 0:2]
# ポリゴンを作成する
# 近傍探索
if len(layer)>2:
tree = neighbors.KDTree(layer)
order = []
q = 0 # query
k = 2 # 最近傍の個数
# 最近傍探索
while len(order) != len(layer):
_, idx = tree.query([layer[q]], k=k)
if idx[0,k-1] not in order:
order.append(idx[0,k-1])
q = idx[0,k-1]
k = 2
else:
k = k + 1
# ポリゴン作成
polygon = Polygon(layer[order])
# ポリゴン内に存在する点のindexを返す
in_or_out = [Point(p).within(polygon) for p in points]
c = [i for i, x in enumerate(in_or_out) if x == True]
for i in c:
points_inside_idx.append(t_c[i])
return points_inside_idx, t_points[points_inside_idx]
def classify_nearest_neighbor_kd_tree_sk(k):
print('k = {}'.format(k))
labels = load_labels()
song_samples = []
indexed_genres = []
for genre, song_genres_ids in labels.groupby('category'):
print('Indexing genre: {}'.format(genre))
num_values = len(song_genres_ids.values)
for i in range(int(num_values / 2)):
val = song_genres_ids.values[i]
song_id = val[0]
song = pd.read_csv('song_data/training/{}'.format(song_id),
header=None)
for val in song.values:
song_samples.append(val)
indexed_genres.append(genre)
kd_tree = nb.KDTree(np.vstack(song_samples))
total_count = 0
match_count = 0
for genre, song_genres_ids in labels.groupby('category'):
print('Expected genre: {}'.format(genre))
num_values = len(song_genres_ids.values)
for i in range(int(num_values / 2), num_values):
val = song_genres_ids.values[i]
song_id = val[0]
song = pd.read_csv('song_data/training/{}'.format(song_id),
header=None)
genre_freqs = {}
# s = np.mean(song)
# split_song = np.array_split(song, 5, axis=0) # Split song into sections
for s in song.values:
# avg_song_val = np.mean(s) # Take average of each section
genre_indices = kd_tree.query([s], k, return_distance=False)
logging.debug('Length of indexed genres: {}'.format(
len(indexed_genres)))
logging.debug('genre_indices: {}'.format(genre_indices))
for index in genre_indices[0]:
g = indexed_genres[index]
genre_freqs[g] = genre_freqs.get(g, 0) + 1
actual_genre = max(genre_freqs, key=genre_freqs.get)
print('Predicted genre: {}'.format(actual_genre))
total_count += 1
if genre == actual_genre:
match_count += 1
print('Matched {} out of {} songs: {}%'.format(
match_count, total_count, (match_count / total_count) * 100))
def main():
parser = argparse.ArgumentParser()
parser.add_argument("events", help="Path to events in CSV format")
args = parser.parse_args()
events_path = args.events
events = pd.read_csv(events_path)
i = 19750
events = events.iloc[i:i + 2000]
events["timestamp"] -= events["timestamp"].min()
coordinates = events[["x", "y"]].values
kdtree = skn.KDTree(coordinates, metric="euclidean")
nn_distance = kdtree.query(coordinates, k=5)[0][:, 4]
events = events.loc[nn_distance <= 3]
nn_distance = nn_distance[nn_distance <= 3]
fig = pp.figure(figsize=(8, 8))
ax = fig.add_subplot(111, projection="3d")
ax.w_xaxis.line.set_visible(False)
ax.w_yaxis.line.set_visible(False)
ax.w_zaxis.line.set_visible(False)
ax.set_xlabel("$x$")
ax.set_ylabel("$t$")
ax.set_zlabel("$y$")
ax.w_xaxis.set_ticklabels([])
ax.w_yaxis.set_ticklabels([])
ax.w_zaxis.set_ticklabels([])
ax.set_ylim(bottom=-1000, top=events["timestamp"].max())
ax.view_init(10, 60)
ax.scatter3D(events["x"],
np.full(len(events), -1000),
events["y"],
s=10,
depthshade=False)
ax.scatter3D(events["x"],
events["timestamp"],
events["y"],
s=8,
c=events["timestamp"],
cmap="Reds")
fig.savefig("hand.pdf", bbox_inches=mpt.Bbox.from_bounds(1, 1.4, 6.0, 4.7))
def __init__(self, resolution, width, height, landmarks, robot):
m = int(height / resolution)
n = int(width / resolution)
self.belief = np.zeros((m, n)) + (float(1) / (m*n))
self.landmarks = landmarks
self.landmarks_tree = neighbors.KDTree([(l.x,l.y) for l in landmarks])
self.resolution = resolution
self.z_noise = robot.z_noise
self.x_noise = robot.x_noise
self.y_noise = robot.y_noise
self.phit = robot.phit
self.pfalse = robot.pfalse
self.max_sense_dist = robot.max_sense_dist
self.correspondence_hash = self.setup_correspondence_hash(m,n)
def perform_test(x_set, x_test, y_set, y_test, k, dist_met, approach):
#Variables Initialization
#Start Time
start_time = time.time()
#Prediction list to store the prediction for each data point
pred = []
#Brute_Force Approach
if approach == 'Brute_Force':
#Iterate over each test point
for pt_test in x_test:
#Compute the distances between x set train and test points
x_dist_list = []
for d in range(0, len(x_set)):
x_dist = dist_met(x_set[d], pt_test)
x_dist_list.append((x_dist, y_set[d]))
#Sort the x distance list from smallest to largest distance
x_dist_list.sort(key=lambda x: x[0])
#Compute the average for k nearest y values
new_dist_list = x_dist_list[:k]
y_tot = []
#Add in all y values to the y_tot list
for y_dist in new_dist_list:
y_tot.append(y_dist[1])
#Compute the average for the y values
y_avg = sum(y_tot) / len(y_tot)
#Add the average value for y into the prediction list
pred.append(y_avg)
#Compute RMSE value for between the predictions and the testing set
error_test = rmse(pred, y_test)
#k-d Tree Approach
elif approach == 'kd_tree':
kd_t = neighbors.KDTree(x_set)
#Compute the distances and indices of the k nearest neighbours
dist, ind = kd_t.query(x_test, k=k)
#Add the predicted values of y to the list
pred = np.sum(y_set[ind], axis=1) / k
#Compute RMSE value for between the predictions and the testing set
error_test = rmse(pred, y_test)
#Compute total time used to run the approach
run_time = time.time() - start_time
return run_time, error_test
def process(inputs, ctx, **kwargs):
original, is_video = helpers.load_image(inputs, 'input')
image = original.copy()
if kwargs.get('detect') == 'false' or len(ctx.drivers) == 1:
detect_driver = None
reid_driver = ctx.drivers[0]
else:
detect_driver = ctx.drivers[0]
reid_driver = ctx.drivers[1]
# reid_input_shape = list(reid_driver.inputs.values())[0]
input_name = list(reid_driver.inputs.keys())[0]
if detect_driver is not None:
boxes = get_boxes(detect_driver, image, threshold=0.3)
else:
boxes = np.array([[0, 0, image.shape[1], image.shape[0]]])
print(f'boxes={len(boxes)}')
for box in boxes:
box = box.astype(int)
img = crop_by_box(image, box)
img = cv2.resize(img,
tuple(PARAMS['input_shape'][::-1]),
interpolation=cv2.INTER_AREA)
prepared = norm(img, need_transpose=PARAMS['driver_type'] == 'pytorch')
prepared = np.expand_dims(prepared, axis=0)
outputs = reid_driver.predict({input_name: prepared})
global kd_tree
embedding = list(outputs.values())[0]
embedding = (embedding + 1.) / 2.
if not kd_tree:
kd_tree = neighbors.KDTree(embedding, metric='euclidean')
else:
dist, idx = kd_tree.query(embedding, k=1)
print(f'distance={dist}')
cv2.rectangle(image, (box[0], box[1]), (box[2], box[3]),
color=(0, 250, 0),
thickness=2,
lineType=cv2.LINE_AA)
if is_video:
output = image
else:
_, buf = cv2.imencode('.jpg', image[:, :, ::-1])
output = buf.tostring()
return {'output': output}
def over_sample_smote(x, n, k):
minority, _ = x.shape
new_x = []
tree = neighbors.KDTree(x)
for i in range(n):
# choose x_i randomly
index = random.choice(range(minority))
# k-neighbor
k_neighbor = tree.query(x[index, 0], k)
x_mean = k_neighbor[1].mean()
# gene a new x xigma* (k-neighbor mean)
new_x_one = x[index, 0] + random.random() * (x_mean - x[index, 0])
new_x.append(new_x_one)
new_x = np.matrix(new_x).T
return new_x
def test_unsupervised_inputs():
"""test the types of valid input into NearestNeighbors"""
X = rng.random_sample((10, 3))
nbrs_fid = neighbors.NearestNeighbors(n_neighbors=1)
nbrs_fid.fit(X)
dist1, ind1 = nbrs_fid.kneighbors(X)
nbrs = neighbors.NearestNeighbors(n_neighbors=1)
for input in (nbrs_fid, neighbors.BallTree(X), neighbors.KDTree(X)):
nbrs.fit(input)
dist2, ind2 = nbrs.kneighbors(X)
assert_array_almost_equal(dist1, dist2)
assert_array_almost_equal(ind1, ind2)
async def calculate_z_value(alpha, limit_size, normal_point, result_dta, Z):
X = list(
map(lambda x: [x, result_dta.values[x][1]],
np.arange(len(result_dta.values))))
# dt=DistanceMetric.get_metric('pyfunc',func=mydist)
tree = nb.KDTree(X, leaf_size=50)
#print(normal_point)
#await asyncio.sleep(1) await loop.run_in_executor(ProcessPoolExecutor(), sleep, delay)
nomaly_neighboor = np.array(cmfunc.find_inverneghboor_of_point(
tree, X, normal_point, limit_size),
dtype=np.int32)
#nomaly_neighboor = np.array(await loop.run_in_executor(ThreadPoolExecutor(), cmfunc.find_inverneghboor_of_point, tree, X, normal_point, limit_size), dtype=np.int32)
for NN_pair in nomaly_neighboor:
Z[NN_pair[1]] = Z[NN_pair[1]] + (1 - result_dta['anomaly_score'][normal_point]) - NN_pair[0] * alpha if (1 - result_dta['anomaly_score'][normal_point]) - \
NN_pair[0] * alpha > 0 else \
Z[NN_pair[1]]
return True
def create_graph(nodes, k):
g = nx.Graph()
tree = neighbors.KDTree(nodes)
for n1 in nodes:
ind = tree.query([n1], k, return_distance=False)[0]
#print(ind)
for j in ind:
n2 = nodes[j]
#print(n2)
#print(j)
if n2 == n1:
continue
#print('n1, n2',n1,n2)
if can_connect(n1, n2):
dist = np.linalg.norm(np.array(n1) - np.array(n2))
g.add_edge(n1, n2, weight=dist)
return g
def fit_predict(self, X):
"""
Performs clustering on data X and returns cluster labels
:param X: array with data
:return: array of cluster labels
"""
print("# Fit predict ( eps = ", self.eps, ", min_samples = ",
self.min_samples, ") ...")
start_time = time.time()
clusters = 0
labels = [0] * len(X)
tree = sknei.KDTree(X)
for i in range(len(X)):
if labels[i] > 0: # point is already marked
continue
# get indexes of X[i] neighbours within the distance eps
if self.metric == 'euclidean':
N = tree.query_radius([X[i]], r=self.eps)[0]
if len(N) < self.min_samples: # mark as a noise
labels[i] = -1
continue
clusters += 1
labels[i] = clusters
index = 0
while index < len(N): # over all neighbours of point X[i]
if labels[N[index]] > 0: # neighbour is already in the cluster
index += 1
continue
labels[N[index]] = clusters
# get indexes of X[N[index]] neighbours within the distance eps
if self.metric == 'euclidean':
Nq = tree.query_radius([X[N[index]]], r=self.eps)[0]
if len(Nq) >= self.min_samples:
for n in Nq:
if n not in N:
N = np.append(N, n)
index += 1
print("#", clusters, " clusters found.")
print("# Fit predict finished in ", (time.time() - start_time),
" sec.")
return np.array(labels)
async def calculate_z_value(alpha, limit_size, normal_point, result_dta, Z):
if normal_point > 50 and normal_point < (len(result_dta.values) - 50):
point_range = np.arange(normal_point - 50, normal_point + 50)
elif normal_point <= 50:
point_range = np.arange(0, 100)
elif normal_point >= (len(result_dta.values) - 50):
point_range = np.arange(len(result_dta.values) - 100, len(result_dta.values) - 1)
X = list(map(lambda x: [x, result_dta.values[x][1]], point_range))
tree = nb.KDTree(X, leaf_size=50)
#print(normal_point)
#await asyncio.sleep(1) await loop.run_in_executor(ProcessPoolExecutor(), sleep, delay)
nomaly_neighboor = np.array(cmfunc.find_inverneghboor_of_point(tree, X, normal_point, limit_size), dtype=np.int32)
#nomaly_neighboor = np.array(await loop.run_in_executor(ThreadPoolExecutor(), cmfunc.find_inverneghboor_of_point, tree, X, normal_point, limit_size), dtype=np.int32)
for NN_pair in nomaly_neighboor:
Z[NN_pair[1]] = Z[NN_pair[1]] + (1 - result_dta['anomaly_score'][normal_point]) - NN_pair[0] * alpha if (1 - result_dta['anomaly_score'][normal_point]) - \
NN_pair[0] * alpha > 0 else \
Z[NN_pair[1]]
return True
def _kd_match(self, treated_group, control_group, observation_count):
tree = sk.KDTree([[x] for x in control_group],
leaf_size=1,
metric='minkowski',
p=2)
matches = self._make_match_array(treated_group, control_group)
# for match in treated_group.index:
# dist, ind = tree.query(treated_group[match], k=1, breadth_first=True)
# matches[match] = control_group.index[ind[0]][0]
queries = treated_group[treated_group.index]
dist, ind = tree.query([[x] for x in queries], k=1, breadth_first=True)
matches[treated_group.index] = control_group.index[[
x for x in ind
]].values.flatten()
return matches
def DBSCAN(D, eps, MinPts):
labels = [0]*len(D)
kdTree = neighbors.KDTree(D)
C = 0
for P in range(0, len(D)):
if not (labels[P] == 0):
continue
NeighborPts = kdTree.query_radius(D[P].reshape(1,-1), r=eps)[0]
if (NeighborPts.shape[0] < MinPts):
labels[P] = -1
else:
C += 1
growCluster(D, kdTree, labels, P, NeighborPts, C, eps, MinPts)
return labels
def build_kdtree(X, relative_scales=None,**kwargs):
"""
Build a KD-tree from the finite values in the given array.
"""
offset = np.mean(X, axis=0)
if relative_scales is None:
# Whiten the data.
relative_scales = np.ptp(X, axis=0)
X_norm = (X - offset)/relative_scales
kdt_kwds = dict(leaf_size=40, metric="minkowski")
kdt_kwds.update(kwargs)
kdt = neighbours.KDTree(X_norm, **kdt_kwds)
return (kdt, relative_scales, offset)