def dbscan(fig):
global X_iris, geo
ax = fig.add_subplot(geo + 5, projection='3d', title='dbscan')
dbscan = cluster.DBSCAN()
dbscan.fit(X_iris)
res = dbscan.labels_
core = dbscan.core_sample_indices_
print(repr(core))
size = [5 if i not in core else 40 for i in range(len(X_iris))]
print(repr(size))
for n, i in enumerate(X_iris):
ax.scatter(*i[: 3], s=size[n], c='bgrcmyk'[res[n] % 7],
alpha=0.8, marker='o')
ax.set_xlabel('X Label')
ax.set_ylabel('Y Label')
ax.set_zlabel('Z Label')
return res
def findClusters(self, dfFrame):
aVX, aVY = np.asarray(dfFrame["SpeedX"]) * 50, np.asarray(
dfFrame["SpeedY"]) * 50
aX, aY = np.asarray(dfFrame["AvgPosX"]), np.asarray(dfFrame["AvgPosY"])
aId = np.asarray(dfFrame["TrackId"])
nFrame = dfFrame["Frame"].iloc[0]
# @UnusedVariable
# aData = [];
# for i in range(len(aX)):
# aData.append([aX[i], aY[i]]);
aData = np.asarray([aX, aY, aVX, aVY]).transpose()
#,aVX,aVY]).transpose();
# print aData;
# return;
# aData = [[np.asarray([aX]).transpose()], [np.asarray([aY]).transpose()]];
# aData = np.asarray([aX,aY]).transpose();
# aData = StandardScaler().fit_transform(aData);
algorithm = cluster.DBSCAN(eps=200, min_samples=2)
# algorithm = cluster.SpectralClustering(n_clusters=5, eigen_solver='arpack', affinity="rbf")
# algorithm = cluster.MeanShift(bandwidth=40, bin_seeding=True); #print ms.bandwidth;
# algorithm = cluster.MiniBatchKMeans(n_clusters=2)
# algorithm = mixture.GMM(n_components=3, covariance_type='full', n_iter=100)
# aData = aData*0.07-20;
# aX, aY = aData[:,0], aData[:,1]
# algorithm = mixture.DPGMM(n_components=len(aData), covariance_type='diag', alpha=10, n_iter=1)
# colors = np.array([x for x in 'bgrcmybgrcmybgrcmybgrcmyk']);
# colors = np.hstack([colors] * 20);
algorithm.fit(aData)
# try: algorithm.fit(aData);
# except: print nFrame, aData;
if hasattr(algorithm, 'labels_'):
y_pred = algorithm.labels_.astype(np.int)
else:
y_pred = algorithm.predict(aData)
# y_pred = hcluster.fclusterdata(aData, t=50, criterion="distance")
y_pred = self.grpActorsMngr.fixGrpsId(y_pred, aId)
# y_pred2 = self.grpActorsMngr.fixGrpsId([1,-1,0,-1,-1,0,-1,1],['3','6','75','140','19','149','124','125']);#y_pred, aId);
# print y_pred2;
# y_pred2 = self.grpActorsMngr.fixGrpsId([0,-1,1,-1,-1,1,-1,0],['3','6','75','140','19','149','124','125']);#y_pred, aId);
# print y_pred2;
# pl.hold(True);
# # self.plotClusters(algorithm, aData, y_pred, aId, aX, aY, nFrame);
return y_pred
def _call_kmapper(data, col_names, interval, overlap, clustering_alg, clustering_alg_params, filter_function, filter_parameters=None):
print(filter_parameters)
mapper = KeplerMapper()
if len(col_names) == 1:
data_new = np.array(data[col_names[0]]).reshape(-1,1)
else:
data_new = np.array(data[col_names])
lens_dict = {}
if len(filter_function) == 1:
f = filter_function[0]
if f in data.columns:
lens = data[f]
else:
lens = compute_lens(f, data_new, mapper, filter_parameters)
lens_dict[f] = lens
elif len(filter_function) == 2:
lens = []
for f in filter_function:
if f in data.columns:
lens_f = np.array(data[f]).reshape(-1,1)
else:
lens_f = compute_lens(f, data_new, mapper, filter_parameters)
lens.append(lens_f)
lens_dict[f] = lens_f
lens = np.concatenate((lens[0], lens[1]), axis=1)
# clusterer = sklearn.cluster.DBSCAN(eps=eps, min_samples=min_samples, metric='euclidean', n_jobs=8)
print(data_new.shape)
print(np.max(np.max(data_new)))
print(np.mean(np.mean(data_new)))
if clustering_alg == "DBSCAN":
graph = mapper.map_parallel(lens, data_new, clusterer=cluster.DBSCAN(eps=float(clustering_alg_params["eps"]), min_samples=float(clustering_alg_params["min_samples"])), cover=Cover(n_cubes=interval, perc_overlap=overlap))
elif clustering_alg == "Agglomerative Clustering":
graph = mapper.map_parallel(lens, data_new, clusterer=cluster.AgglomerativeClustering(n_clusters=None, linkage=clustering_alg_params["linkage"], distance_threshold=float(clustering_alg_params["dist"])), cover=Cover(n_cubes=interval, perc_overlap=overlap))
# graph = mapper.map_parallel(lens, data_new, clusterer=cluster.AgglomerativeClustering( linkage=clustering_alg_params["linkage"]), cover=Cover(n_cubes=interval, perc_overlap=overlap))
elif clustering_alg == "Mean Shift":
graph = mapper.map_parallel(lens, data_new, clusterer=cluster.MeanShift(bandwidth=float(clustering_alg_params["bandwidth"])), cover=Cover(n_cubes=interval, perc_overlap=overlap))
# graph = mapper.map_parallel(lens, data_new, clusterer=cluster.MeanShift(bandwidth=1), cover=Cover(n_cubes=interval, perc_overlap=overlap))
print(len(graph['nodes'].keys()))
# graph = mapper.map(lens, data_new, clusterer=cluster.DBSCAN(eps=eps, min_samples=min_samples), cover=Cover(n_cubes=interval, perc_overlap=overlap))
return graph, lens_dict
def get_algorithm(self):
if(self.algorithmName == "kmeans"):
cluster_alg = cluster.MiniBatchKMeans(n_clusters=int(self.parms['k']))
elif(self.algorithmName == "mean_shift"):
bandwidth = cluster.estimate_bandwidth(self.X, quantile=float(self.parms['quantile']))
cluster_alg = cluster.MeanShift(bandwidth=bandwidth, bin_seeding=True)
elif(self.algorithmName == "affinity_propagation"):
cluster_alg = cluster.AffinityPropagation(damping=float(self.parms['damping']))
elif(self.algorithmName == "birch"):
cluster_alg = cluster.Birch(n_clusters=int(self.parms['k']))
elif(self.algorithmName == "ward"):
connectivity = kneighbors_graph(self.X, n_neighbors=int(self.parms['n_neighbors']), include_self=False)
connectivity = 0.5 * (connectivity + connectivity.T)
cluster_alg = cluster.AgglomerativeClustering(n_clusters=int(self.parms['k']), linkage='ward', connectivity=connectivity)
elif(self.algorithmName == "spectral"):
cluster_alg = cluster.SpectralClustering(n_clusters=int(self.parms['k']), eigen_solver='arpack', affinity="nearest_neighbors")
elif(self.algorithmName == "dbscan"):
cluster_alg = cluster.DBSCAN(eps=float(self.parms['eps']))
elif(self.algorithmName == "agglomerative"):
connectivity = kneighbors_graph(self.X, n_neighbors=int(self.parms['n_neighbors']), include_self=False)
connectivity = 0.5 * (connectivity + connectivity.T)
cluster_alg = cluster.AgglomerativeClustering(linkage="average", affinity="cityblock", n_clusters=int(self.parms['k']), connectivity=connectivity)
else:
return None
return cluster_alg
def DBSCAN(self):
"""
Uses `sklearn's DBSCAN <http://scikit-learn.org/stable/modules/generated/sklearn.cluster.DBSCAN.html>`_
**Defaults and var_params:** sklearn.cluster.DBSCAN(eps=0.5, min_samples=5, metric='euclidean', algorithm='auto', leaf_size=30, p=None, n_jobs=1)
Other Parameters
----------------
var_params: dict
Pass variable params through constructor as dictionary pairs. Current default parameters are listed above
Returns
-------
labels: list of ints
Solution of clustering labels for each object (updated in object.out)
"""
params = {}
params['distance'] = 'euclidean'
params['eps']=0.5
params['min_samples']=5
params['metric']='precomputed'
params['algorithm']='auto'
params['leaf_size']=30
params['p']=None,
params['n_jobs'] = 1
params = returnParams(self.var_params, params, 'DBSCAN')
if 'distance' in self.var_params:
if self.var_params['distance'] == 'precomputed':
d = self.var_params['M']
else:
d = returnDistanceMatrix(self.data, params['distance'])
else:
d = returnDistanceMatrix(self.data, params['distance'])
solution = skc.DBSCAN(eps=params['eps'], min_samples=params['min_samples'], metric=params['metric'],
algorithm=params['algorithm'], leaf_size=params['leaf_size'],
p=params['p'], n_jobs=params['n_jobs'])
solution.fit(d)
self.out = solution.labels_
self.var_params = params #update dictionary of parameters to match that used.
def find_objpcd_list_by_pos(self,
pcd,
x_range=(200, 800),
y_range=(0, 600),
z_range=(790, 1000),
eps=5,
toggledebug=False,
scan_num=1):
real_pcd = pcdu.trans_pcd(pcd, self.amat)
# pcdu.show_pcd([p for p in real_pcd if p[2] < 900], rgba=(.5, .5, .5, .1))
# base.run()
pcd_result = []
for p in real_pcd:
if x_range[0] < p[0] < x_range[1] and y_range[0] < p[1] < y_range[
1] and z_range[0] < p[2] < z_range[1]:
pcd_result.append(p)
pcd_result = np.array(pcd_result)
db = skc.DBSCAN(eps=eps, min_samples=50 * scan_num).fit(pcd_result)
core_samples_mask = np.zeros_like(db.labels_, dtype=bool)
core_samples_mask[db.core_sample_indices_] = True
labels = db.labels_
n_clusters = len(set(labels)) - (1 if -1 in labels else 0)
print("n_clusters:", n_clusters)
unique_labels = set(labels)
objpcd_list = []
for k in unique_labels:
if k == -1:
continue
else:
class_member_mask = (labels == k)
temppartialpcd = pcd_result[class_member_mask
& core_samples_mask]
if len(temppartialpcd) > 500:
objpcd_list.append(temppartialpcd)
if toggledebug:
# pcdu.show_pcd(real_pcd, rgba=(1, 1, 1, .1))
pcdu.show_pcd(pcd_result, rgba=(1, 1, 0, 1))
for objpcd in objpcd_list:
pcdu.show_pcd_withrbt(objpcd,
rgba=(choice([0, 1]), choice([0,
1]), 1, 1))
base.run()
return objpcd_list
def _set_parameters(self, **kwargs):
'''
Sets parameters used in fitting tracks::
vd: drift velocity [mm/us]
clock_period: clock period for timestamp [us]
dbscan_eps: epsilon used for clustering [mm]
dbscan_min_samples: min samples used for clustering
'''
self._vd = kwargs.get('vd', self._vd)
self._clock_period = kwargs.get('clock_period', self._clock_period)
self._z_scale = self._vd * self._clock_period
self._dbscan_eps = kwargs.get('dbscan_eps', self._dbscan_eps)
self._dbscan_min_samples = kwargs.get('dbscan_min_samples',
self._dbscan_min_samples)
self.dbscan = cluster.DBSCAN(eps=self._dbscan_eps,
min_samples=self._dbscan_min_samples)
def bdscan(multishapes):
db = cluster.DBSCAN(eps=0.3, min_samples=60)
db.fit(multishapes)
core_samples_mask = np.zeros_like(db.labels_, dtype=bool)
core_samples_mask[db.core_sample_indices_] = True
unique_labels = set(db.labels_)
print(unique_labels)
# Number of clusters in labels, ignoring noise if present.
n_clusters_ = len(unique_labels) - (1 if -1 in db.labels_ else 0)
fig = plt.figure(figsize=(8, 6))
colors = [
'#ff0000', '#00ff00', '#0000ff', '#ff00ff', '#00ffff', '#ffff00',
'#f6ff00', '#2f800f', '#a221b5', '#21b5ac', '#b1216c'
]
for k, col in zip(unique_labels, colors):
if k == -1:
# Black used for noise.
col = 'k'
my_members = db.labels_ == k
xy = multishapes[my_members & core_samples_mask]
plt.plot(xy[:, 0],
xy[:, 1],
'o',
markerfacecolor=col,
markeredgecolor='k',
markersize=11)
xy = multishapes[my_members & ~core_samples_mask]
plt.plot(xy[:, 0],
xy[:, 1],
'o',
markerfacecolor=col,
markeredgecolor='k',
markersize=6)
plt.title('Número estimado de clusters: %d' % n_clusters_)
plt.show()
def update_data(attrname, old, new):
# Get the drop down values
algorithm = dropdown.value
global X
# Generate the new colors:
if algorithm == 'MiniBatchKMeans':
model = cluster.MiniBatchKMeans(n_clusters=2)
elif algorithm == 'AffinityPropagation':
model = cluster.AffinityPropagation(damping=.9, preference=-200)
elif algorithm == 'MeanShift':
model = cluster.MeanShift(bandwidth=bandwidth, bin_seeding=True)
elif algorithm == 'SpectralClustering':
model = cluster.SpectralClustering(n_clusters=2,
eigen_solver='arpack',
affinity="nearest_neighbors")
elif algorithm == 'Ward':
model = cluster.AgglomerativeClustering(n_clusters=2,
linkage='ward',
connectivity=connectivity)
elif algorithm == 'AgglomerativeClustering':
model = cluster.AgglomerativeClustering(linkage="average",
affinity="cityblock",
n_clusters=2,
connectivity=connectivity)
elif algorithm == 'Birch':
model = cluster.Birch(n_clusters=2)
elif algorithm == 'DBSCAN':
model = cluster.DBSCAN(eps=.2)
else:
print('No Algorithm selected')
model.fit(X)
if hasattr(model, 'labels_'):
y_pred = model.labels_.astype(np.int)
else:
y_pred = model.predict(X)
colors = [Spectral6[i] for i in y_pred]
source.data['colors'] = colors
plot.title = algorithm
def train_model(x):
epsilons = np.linspace(0.3, 1.2, 10)
scores = []
models = []
for epsilon in epsilons:
model = sc.DBSCAN(eps=epsilon, min_samples=5).fit(x)
scores.append(
ms.silhouette_score(x,
model.labels_,
sample_size=len(x),
metric='euclidean'))
models.append(model)
scores = np.array(scores)
best_index = scores.argmax()
best_epsilon = epsilons[best_index]
best_score = scores[best_index]
best_model = models[best_index]
print(best_epsilon, best_score)
return best_model
def cluster_pipelines2(clustercount):
return {
'Ward': Pipeline([
('sca', preprocessing.MaxAbsScaler()),
('clu', cluster.AgglomerativeClustering(n_clusters=clustercount, linkage='ward')),
]),
'K-Means': Pipeline([
('sca', preprocessing.MaxAbsScaler()),
('clu', cluster.KMeans(n_clusters=clustercount, init='k-means++', max_iter=100, n_init=1)),
]),
'GMM': Pipeline([
('sca', preprocessing.MaxAbsScaler()),
('clu', mixture.GaussianMixture(n_components=clustercount)),
]),
'DBScan': Pipeline([
('sca', preprocessing.MaxAbsScaler()),
('clu', cluster.DBSCAN(eps=0.1, min_samples=20)),
]),
}
def cluster_face_features(feature_list,
method=None,
precomputed=True,
eps=0.5):
if feature_list is not None:
face_feature_list = feature_list
if face_feature_list is None:
return None
if precomputed:
metric_type = 'precomputed'
dist_matrix = __compute_pairwise_distance(face_feature_list)
dist_matrix = dist_matrix
else:
metric_type = 'euclidean'
dist_matrix = np.vstack(face_feature_list)
dist_matrix = None
if method == 'AP':
cluster_estimator = cluster.AffinityPropagation(affinity=metric_type,
damping=.55,
preference=-1)
if precomputed:
dist_matrix = -dist_matrix
elif method == 'DBSCAN':
cluster_estimator = cluster.DBSCAN(metric=metric_type,
eps=eps,
min_samples=1)
t0 = time.time()
cluster_estimator.fit(dist_matrix)
t1 = time.time()
t = t1 - t0
print 'Clustering takes: %f seconds' % t
if hasattr(cluster_estimator, 'labels_'):
y_pred = cluster_estimator.labels_.astype(np.int)
else:
y_pred = cluster_estimator.predict(dist_matrix)
return y_pred
def clustering(X, algorithm, n_clusters):
# normalize dataset for easier parameter selection
X = StandardScaler().fit_transform(X)
# estimate bandwidth for mean shift
bandwidth = cluster.estimate_bandwidth(X, quantile=0.3)
# connectivity matrix for structured Ward
connectivity = kneighbors_graph(X, n_neighbors=10, include_self=False)
# make connectivity symmetric
connectivity = 0.5 * (connectivity + connectivity.T)
# Generate the new colors:
if algorithm=='MiniBatchKMeans':
model = cluster.MiniBatchKMeans(n_clusters=n_clusters)
elif algorithm=='AffinityPropagation':
model = cluster.AffinityPropagation(damping=.9, preference=-200)
elif algorithm=='MeanShift':
model = cluster.MeanShift(bandwidth=bandwidth, bin_seeding=True)
elif algorithm=='SpectralClustering':
model = cluster.SpectralClustering(n_clusters=n_clusters,
eigen_solver='arpack',
affinity="nearest_neighbors")
elif algorithm=='Ward':
model = cluster.AgglomerativeClustering(n_clusters=n_clusters, linkage='ward',
connectivity=connectivity)
elif algorithm=='AgglomerativeClustering':
model = cluster.AgglomerativeClustering(
linkage="average", affinity="cityblock", n_clusters=n_clusters,
connectivity=connectivity)
elif algorithm=='Birch':
model = cluster.Birch(n_clusters=n_clusters)
elif algorithm=='DBSCAN':
model = cluster.DBSCAN(eps=.2)
else:
print('No Algorithm selected. Default is MiniBatchKMeans')
model = cluster.MiniBatchKMeans(n_clusters=n_clusters)
model.fit(X)
if hasattr(model, 'labels_'):
y_pred = model.labels_.astype(np.int)
else:
y_pred = model.predict(X)
return X, y_pred
def main():
data_origin = read_data('balance-scale.data')
data_converted = convert_data(data_origin, 0)
true_labels = data_converted.iloc[:, 0]
data_clean = clean_data(data_converted.iloc[:, 1:])
plot_distribution(data_clean)
dimension = 2
data_pca = pca(dimension, data_clean)
plot_distribution(data_pca)
n_clusters = 3
dimension_show = [1, 2]
kmeans = cluster.KMeans(n_clusters=n_clusters).fit(data_clean)
show_result(data_clean, data_pca, true_labels, kmeans, n_clusters, dimension_show)
dbscan = cluster.DBSCAN(eps=0.38, min_samples=10).fit(data_clean)
show_result(data_clean, data_pca, true_labels, dbscan, n_clusters, dimension_show)
return 0
def delete_redudants(predictions, embed_model):
X = []
logging.info('\n# Redundancy reduction ...\n')
for i, row in predictions.iterrows():
X.append(get_sentence_vector(row['processed_text'], embed_model))
dbscan = cluster.DBSCAN(eps=0.09, metric='cosine', min_samples=2).fit(X)
labels = dbscan.labels_
logging.info('\n# Labels\n')
print(labels)
predictions['label'] = labels
isolated_tweets = predictions[predictions.label == -1]
predictions = predictions[predictions.label != -1].drop_duplicates(
'label', keep='first')
predictions = pd.concat([predictions, isolated_tweets], sort=True)
predictions = predictions.sort_values('score', ascending=False)
predictions.reset_index(inplace=True)
predictions = predictions.drop(columns='processed_text')
logging.info(
f'\n# Redundancy reduction [OK]\n >> Length= {len(predictions)}\n')
return predictions
def dbscan_seeds(goods, bads):
"""Find regions with concentration of good points."""
from scipy.spatial import ConvexHull
import sklearn.cluster as cl
good_ids, good_loc = goods
bad_ids, bad_loc = bads
labels = cl.DBSCAN(eps=150, min_samples=8).fit_predict(good_loc)
gcluster = []
bcluster = []
hulls = []
for cluster in range(len(np.unique(labels)) - 1):
points = good_loc[labels == cluster, :]
hull = sgeo.Polygon(points[ConvexHull(points).vertices])
gcluster.append(list(i.compress(good_ids, labels == cluster)))
bcluster.append([
id_ for id_, loc in zip(bad_ids, bad_loc)
if hull.contains(sgeo.Point(loc))
])
hulls.append(hull)
return hulls, gcluster, bcluster
def do_dbscan(data):
print(" Do dbscan...")
# Récupération des paramètres
eps = args.associer_param('eps', 1)
min_pts = args.associer_param('min_pts', 1)
model = cluster.DBSCAN(eps=eps,
min_samples=min_pts,
metric=args.args.distance)
labels = model.fit_predict(data)
data['cluster'] = labels
print(" ok !")
return data
def clustering(self, image_urls, min_samples=2, eps=0.4, pick_up_num=3):
train = self.get_train(image_urls)
print(train)
if len(train) < min_samples:
return None
distances = self.calculate_distance(train)
if distances is None:
return None
cls = cluster.DBSCAN(metric='precomputed', min_samples=min_samples, eps=eps)
y = cls.fit_predict(distances)
val = pd.Series(y).value_counts()
target_clusters_index = [x for x in list(val.index) if x != -1][:pick_up_num]
order = {key: i for i, key in enumerate(target_clusters_index)}
picked_up = dict([(index, val) for (index, val) in enumerate(y.tolist()) if val in target_clusters_index])
picked_up_ = [(order[x2], image_urls[x1]) for (x1, x2) in sorted(picked_up.items(), key=lambda x: order[x[1]])]
ret = []
for key, subiter in itertools.groupby(picked_up_, operator.itemgetter(0)):
vals = [item[1] for item in subiter]
ret.append({"row_id": int(key), "sumples_num": len(vals), "vals": vals})
return ret
def cluster(self, params={"alg": "KMeans", "num": 10}):
start = time.time()
encodedLog = self.encodedLog.values.tolist()
if params["alg"].lower() == "kmeans":
if not "runs" in params:
params["runs"] = 0
cluster = TTestKMeans2(params["num"], encodedLog)
print("SSE : ", cluster.inertia_)
print("Clustering Time:", time.time() - start)
return cluster.predict(encodedLog), cluster.cluster_centers_
elif params["alg"].lower() == "dbscan":
cluster = skcl.DBSCAN(min_samples=params["minsamples"],
eps=params["eps"]).fit(encodedLog)
y_pred = cluster.labels_
centers = calcCenters(y_pred, encodedLog)
print("Clustering Time:", time.time() - start)
if "assignNoisy" in params and params["assignNoisy"] == True:
y_pred, centers = assignNoisyPoints(y_pred, encodedLog,
centers)
return y_pred, centers
def cluster_pipelines(clustercount, featuredim, decompstr):
decomp = clustervis_pipelines(featuredim)[decompstr]
return {
'Ward': Pipeline([
('decomp', decomp),
('clu', cluster.AgglomerativeClustering(n_clusters=clustercount, linkage='ward')),
]),
'K-Means': Pipeline([
('decomp', decomp),
('clu', cluster.KMeans(n_clusters=clustercount, init='k-means++', max_iter=100, n_init=1)),
]),
'GMM': Pipeline([
('decomp', decomp),
('clu', mixture.GaussianMixture(n_components=clustercount)),
]),
'DBScan': Pipeline([
('decomp', decomp),
('clu', cluster.DBSCAN(eps=0.1, min_samples=20)),
]),
}
def _optimize_eps(X, eps, Param, verbose=3):
if verbose >= 3: print('[clusteval] >Evaluate using silhouette..')
# Setup resolution
eps = np.arange(0.1, 5, 1 / Param['epsres'])
silscores = np.zeros(len(eps)) * np.nan
sillclust = np.zeros(len(eps)) * np.nan
silllabx = []
# Run over all Epsilons
for i in tqdm(range(len(eps))):
# DBSCAN
db = cluster.DBSCAN(eps=eps[i],
metric=Param['metric'],
min_samples=Param['min_samples'],
n_jobs=Param['n_jobs']).fit(X)
# Get labx
labx = db.labels_
# Fill array
sillclust[i] = len(np.unique(labx))
# Store all labx
silllabx.append(labx)
# Compute Silhouette only if more then 1 cluster
if sillclust[i] > 1:
silscores[i] = silhouette_score(X, db.labels_)
# Convert to array
silllabx = np.array(silllabx)
# Store only if agrees to restriction of input clusters number
I1 = np.isnan(silscores) == False
I2 = sillclust >= Param['min_clust']
I3 = sillclust <= Param['max_clust']
Iloc = I1 & I2 & I3
# Get only those of interest
silscores = silscores[Iloc]
sillclust = sillclust[Iloc]
eps = eps[Iloc]
silllabx = silllabx[Iloc, :]
# Return
return (eps, sillclust, silscores, silllabx)
def main():
# Create random data.
n = 1500 # nb circles.
for i, x_y in enumerate([
datasets.make_circles(n, factor=.5, noise=.05),
datasets.make_moons(n_samples=n, noise=.05)
]):
x, y = x_y
# Scale data to reduce weights.
# https://openclassrooms.com/fr/courses/4444646-entrainez-un-modele-predictif-lineaire/4507801-reduisez-l-amplitude-des-poids-affectes-a-vos-variables
std_scale = preprocessing.StandardScaler().fit(x)
x_scaled = std_scale.transform(x)
# Perform DBSCAN on scaled data.
range_eps = [0.05, 0.1, 0.2, 0.3]
range_n_min = [5, 10, 20, 30]
nb_plots = len(range_eps) + 1 # +1: add true clusters.
for j, eps_n_min in enumerate(zip(range_eps, range_n_min)):
# Perform DBSCAN on scaled data.
e, n_min = eps_n_min
cls = cluster.DBSCAN(eps=e, min_samples=n_min)
cls.fit(x_scaled)
# Plot DBSCAN.
axis = plt.subplot(2, nb_plots, 1 + j + nb_plots * i)
axis.scatter(x_scaled[:, 0], x_scaled[:, 1], c=cls.labels_, s=50)
axis.set_title('eps %04.2f, n_min %02d' % (e, n_min))
# Plot true clusters.
axis = plt.subplot(2, nb_plots, nb_plots + nb_plots * i)
axis.scatter(x_scaled[:, 0], x_scaled[:, 1], c=y, s=50)
axis.set_title('true clusters')
plt.subplots_adjust(left=0.1,
bottom=0.1,
right=0.9,
top=0.9,
wspace=0.3,
hspace=0.3)
plt.suptitle('DBSCAN')
plt.show()
def cluster_topics():
#model = cluster.Birch(
#branching_factor=2,
#threshold=0.002 # Lower = more clusters, higher = fewer clusters
#)
#model = cluster.KMeans(
#branching_factor=10,
#threshold=0.1 # Lower = more clusters, higher = fewer clusters
#)
model = cluster.DBSCAN(min_samples=2, eps=0.2)
#model = cluster.AffinityPropagation(
#)
vectorizer = text.HashingVectorizer(
analyzer='char_wb', # The feature is made of words not characters
norm='l2', # Normalize the words
lowercase=True, # Converts everything to lowercase
stop_words=stopwords)
num_samples = 10000
offset = 0
while True:
log.debug(u"Loading topics...")
topic_rows = db.session.query(
models.TopicModel.id,
models.TopicModel.topic).filter_by(clustered=False).order_by(
models.TopicModel.id.asc()).limit(num_samples).offset(
offset).all()
if not topic_rows:
break
log.debug(u"Loaded {} topics".format(len(topic_rows)))
offset += len(topic_rows)
go_cluster(vectorizer, model, topic_rows)
def _get_cluster_dict(peak_array, eps=30, min_samples=2):
"""Sort peaks into cluster using sklearn's DBSCAN.
Each cluster is given its own label, with the unclustered
having the label -1.
Parameters
----------
peak_array : 2D numpy array
In the form [[x0, y0], [x1, y1], ...], i.e. shape = 2
eps : scalar
For the DBSCAN clustering algorithm
min_samples : int
Minimum number of peaks in each cluster
Returns
-------
cluster_dict : dict
The peaks are sorted into a dict with the cluster label as the key.
Example
-------
>>> import numpy as np
>>> peak_array = np.random.randint(1000, size=(100, 2))
>>> import pyxem.utils.cluster_tools as ct
>>> cluster_dict = ct._get_cluster_dict(peak_array)
>>> cluster0 = cluster_dict[0]
"""
dbscan = cluster.DBSCAN(eps=eps, min_samples=min_samples)
dbscan.fit(peak_array)
label_list = dbscan.labels_
label_unique_list = sorted(list(set(label_list)))
cluster_dict = {}
for label_unique in label_unique_list:
cluster_dict[label_unique] = []
for peak, label in zip(peak_array, label_list):
cluster_dict[label].append(peak.tolist())
return cluster_dict
def dbscan(data, eps=0.3, min_samples=10):
"""DBScan clustering
Parameters
----------
data : float array
features array
Returns
-------
cl : int array
cluster indicies
Notes
-----
This function requires scikits-learn
"""
db = skcluster.DBSCAN(eps=eps, min_samples=min_samples).fit(data)
labels = db.labels_
return labels
def DBSCAN(P, eps=15, minpts=10):
pointlist = []
for y in range(P.shape[1]):
for x in range(P.shape[0]):
if P[x, y] > 0:
pointlist.append([x, y])
pointlist = np.array(pointlist)
db = skc.DBSCAN(eps, minpts).fit(pointlist)
labels = db.labels_
n_clusters_ = len(set(labels)) - (1 if -1 in labels else 0)
cluster_list = []
#找到最大的簇并标在图上
for i in range(n_clusters_):
one_cluster = pointlist[labels == i]
cluster_list.append([len(one_cluster), one_cluster])
cluster_list.sort(key=lambda x: x[0], reverse=True)
P = np.zeros((P.shape[0], P.shape[1]))
for pixel in cluster_list[0][1]:
P[pixel[0], pixel[1]] = 1
return P
def __apply_cluster_algorithms__(self, x):
if self.algorithms == 'k-mean':
kmeans = cluster.KMeans(n_clusters=3)
kmeans.fit(x)
self.labels = kmeans.labels_
for i, label in enumerate(kmeans.labels_):
self.clusterid_docids_map[
label] = self.clusterid_docids_map.get(label, []) + [i]
elif self.algorithms == 'dbscan':
dbscan = cluster.DBSCAN(eps=2, min_samples=3)
dbscan.fit(x)
self.labels = dbscan.labels_
for i, label in enumerate(dbscan.labels_):
self.clusterid_docids_map[
label] = self.clusterid_docids_map.get(label, []) + [i]
else:
sm_cluster = SparseMatrixClustering(
cluster_sim_threshold=0.8, graph_manager=self.graph_manager)
sm_cluster.fit(x)
self.score_mat = sm_cluster.score_mat
self.clusterid_docids_map = sm_cluster.clusterid_docids_mapping
def getDataPandas():
reader = pd.DataFrame()
reader = pd.read_table(r'.\dbscanData.txt', header=None,
sep=' ') #iterator=True,chunksize=1000)
print reader
#hello=reader.iloc[0]
reader = reader.T #转置
print reader
f3 = lambda x: x / x.sum()
reader = reader.apply(f3)
reader = reader.T #转回来
print reader
dbscan = cluster.DBSCAN(eps=0.3,
min_samples=3,
algorithm='brute',
metric='euclidean')
dbscan.fit(reader)
res = dbscan.labels_
print res
def filter_isolated_idxs(idxs=[], maxdist=3.0):
newidxs = idxs.copy()
seq = np.where(idxs==True)[0]
if len(seq):
X = np.array(zip(seq, np.zeros(len(seq))))
cfn = cluster.DBSCAN(eps=3, min_samples=1)
cfn.fit(X)
clusters = {}
for v in np.unique(cfn.labels_):
clusters[v] = len(cfn.labels_[cfn.labels_==v])
maxv = sorted(clusters, key=clusters.get)[-1]
for i in xrange(len(cfn.labels_)):
if cfn.labels_[i] != maxv:
newidxs[seq[i]] = False
return newidxs
def process(img: Image):
img.thumbnail((200, 200))
data = np.array(img.getdata())
least_clusters = None
clusters = None
for i in np.linspace(5, 7, 5):
db = cluster.DBSCAN(eps=i, min_samples=10).fit(data)
ln = len(set(db.labels_))
if least_clusters is None or least_clusters > ln:
least_clusters = ln
clusters = db.labels_
if least_clusters <= 7:
break
result = []
for i in set(clusters):
result.append(
list(
map(int, list(np.round(np.average(data[clusters == i],
axis=0)))))) #govnokod
return result