class T5_KMEANS:
def __init__(self, ndims=5, nn=25, k=10000, verbose=False):
self.logger = logging.getLogger("T5Clustering")
logging.basicConfig(format='%(asctime)s %(levelname)s: %(message)s',
level=logging.DEBUG)
self.ndims = ndims
self.nn = nn
self.k = k
self.data = None
self.train_data = None
self.test_data = None
self.data_embedded = None
self.sampling = None
self.reducer = DimReducer(n_components=ndims, n_neighbors=nn)
self.kmeans = KMeans(n_clusters=k, verbose=verbose)
def split(self, fname, sampling=False, train_size=1000000, test_size=None):
self.data = read(fname, scale=True)
self.sampling = sampling
if sampling:
self.train_data, test_data = split(train_size=train_size,
test_size=test_size)
else:
self.train_data = self.data
return self
def reduce(self):
self.logger.info("Dimensionality reduction (UMAP): %s",
self.reducer.umap.get_params)
self.reducer.fit(self.train_data)
del self.train_data
step = min(500000, len(self.data))
result = self.reducer.reduce(self.data[0:step], as_df=False)
for i in range(step, len(self.data), step):
result = np.append(result,
self.reducer.reduce(self.data[i:i + step],
as_df=False),
axis=0)
self.logger.debug("Dim reduce batch : %d", i)
self.data = None
self.data_embedded = result
return self
def cluster(self):
self.logger.info("Clustering ... (KMeans)")
self.kmeans.fit(self.data_embedded)
self.logger.info("Clusters: %d", len(self.kmeans.cluster_centers_))
return self
def kmeans_prop_cuda_batch(fname, sample_rate, slice_w, slice_h, down_sample=0.25, num_clusters=8, batch_size=1):
"""Produce a "most frequent" color visualization video file by iterating
over the frames of the source and using a kmean's clustering algorithm using cuda
"""
from cuml.cluster import KMeans as KMeansCuda
cap = cv2.VideoCapture(fname)
total_frames = int(cap.get(cv2.CAP_PROP_FRAME_COUNT))
num_slices = total_frames // sample_rate
vis_output = np.zeros((slice_h, slice_w * num_slices, 3), dtype='uint8')
cluster_model = KMeansCuda(n_clusters=num_clusters, init='scalable-k-means++', n_init=20)
for i in tqdm(range(total_frames)):
ret = cap.grab()
if (i % sample_rate) == 0:
ret, frame = cap.retrieve()
temp_f = cv2.cvtColor(frame, cv2.COLOR_RGB2BGR)
reduc = cv2.resize(temp_f, None, fx=down_sample, fy=down_sample, interpolation=cv2.INTER_CUBIC).astype('float32')
with warnings.catch_warnings():
warnings.simplefilter('ignore')
cluster_model.fit(reduc.reshape((-1,3)))
colors = np.around(cluster_model.cluster_centers_).astype('uint8')
lbl, counts = np.unique(cluster_model.labels_, return_counts=True)
cut = slice_h / np.sum(counts)
ordering = np.argsort(counts)[::-1]
tind = int(i // sample_rate)
prev_ind = 0
for i, val in enumerate(ordering):
height = int(round(cut * counts[val]))
l_ind = (tind * slice_w)
r_ind = (tind + 1) * slice_w
vis_output[prev_ind:prev_ind+height, l_ind:r_ind] = colors[val]
prev_ind += height
cap.release()
return vis_output
def make_clusters_KMeans(dat_to_cluster , nb_clust, n=15000):
estimator = KMeans(n_clusters=nb_clust)
if n < len(dat_to_cluster):
s=np.asarray(sample(list(dat_to_cluster), k = n), dtype=np.float_)
estimator= estimator.fit(s)
res = []
notinit = True
for i in range(0, len(dat_to_cluster) // n + 1):
d = np.asarray(list(dat_to_cluster)[n * i: n * (i + 1)])
if notinit:
res = list(estimator.predict(d))
notinit = False
else:
a =list(estimator.predict(d))
for j in a:
res.append(j)
else :
res = estimator.fit_predict(dat_to_cluster)
return res, estimator
def fit(self, X, y=None) -> "KBinsDiscretizer":
"""
Fit the estimator.
Parameters
----------
X : numeric array-like, shape (n_samples, n_features)
Data to be discretized.
y : None
Ignored. This parameter exists only for compatibility with
:class:`sklearn.pipeline.Pipeline`.
Returns
-------
self
"""
X = self._validate_data(X, dtype='numeric')
valid_encode = ('onehot', 'onehot-dense', 'ordinal')
if self.encode not in valid_encode:
raise ValueError("Valid options for 'encode' are {}. "
"Got encode={!r} instead.".format(
valid_encode, self.encode))
valid_strategy = ('uniform', 'quantile', 'kmeans')
if self.strategy not in valid_strategy:
raise ValueError("Valid options for 'strategy' are {}. "
"Got strategy={!r} instead.".format(
valid_strategy, self.strategy))
n_features = X.shape[1]
n_bins = self._validate_n_bins(n_features)
n_bins = np.asnumpy(n_bins)
bin_edges = cpu_np.zeros(n_features, dtype=object)
for jj in range(n_features):
column = X[:, jj]
col_min, col_max = column.min(), column.max()
if col_min == col_max:
warnings.warn("Feature %d is constant and will be "
"replaced with 0." % jj)
n_bins[jj] = 1
bin_edges[jj] = np.array([-np.inf, np.inf])
continue
if self.strategy == 'uniform':
bin_edges[jj] = np.linspace(col_min, col_max, n_bins[jj] + 1)
elif self.strategy == 'quantile':
quantiles = np.linspace(0, 100, n_bins[jj] + 1)
bin_edges[jj] = np.asarray(np.percentile(column, quantiles))
# Workaround for https://github.com/cupy/cupy/issues/4451
# This should be removed as soon as a fix is available in cupy
# in order to limit alterations in the included sklearn code
bin_edges[jj][-1] = col_max
elif self.strategy == 'kmeans':
# Deterministic initialization with uniform spacing
uniform_edges = np.linspace(col_min, col_max, n_bins[jj] + 1)
init = (uniform_edges[1:] + uniform_edges[:-1])[:, None] * 0.5
# 1D k-means procedure
km = KMeans(n_clusters=n_bins[jj],
init=init,
n_init=1,
output_type='cupy')
km = km.fit(column[:, None])
with using_output_type('cupy'):
centers = km.cluster_centers_[:, 0]
# Must sort, centers may be unsorted even with sorted init
centers.sort()
bin_edges[jj] = (centers[1:] + centers[:-1]) * 0.5
bin_edges[jj] = np.r_[col_min, bin_edges[jj], col_max]
# Remove bins whose width are too small (i.e., <= 1e-8)
if self.strategy in ('quantile', 'kmeans'):
mask = np.diff(bin_edges[jj], prepend=-np.inf) > 1e-8
bin_edges[jj] = bin_edges[jj][mask]
if len(bin_edges[jj]) - 1 != n_bins[jj]:
warnings.warn('Bins whose width are too small (i.e., <= '
'1e-8) in feature %d are removed. Consider '
'decreasing the number of bins.' % jj)
n_bins[jj] = len(bin_edges[jj]) - 1
self.bin_edges_ = bin_edges
self.n_bins_ = n_bins
if 'onehot' in self.encode:
self._encoder = OneHotEncoder(categories=np.array(
[np.arange(i) for i in self.n_bins_]),
sparse=self.encode == 'onehot',
output_type='cupy')
# Fit the OneHotEncoder with toy datasets
# so that it's ready for use after the KBinsDiscretizer is fitted
self._encoder.fit(np.zeros((1, len(self.n_bins_)), dtype=int))
return self
