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January 4, 2019 21:18
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getting some object oriented errors with kmeans_process function not recognized
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class SequenceFeatureEnricher(object): | |
def __init__(self, regression_features=True, std_features=True, kmeans_features=True, masknan: float = None, n_clusters=8): | |
self.regression_features = regression_features | |
self.std_features = std_features | |
self.kmeans_features= kmeans_features | |
self.n_clusters=n_clusters | |
self.masknan = masknan | |
self.sample_sequences = [] | |
self.sequence_features = [] | |
# So we can map sequence features back to minmax values for scaling | |
self.sequence_features_scalar_map = [] | |
if regression_features: | |
for f in range(d.ENRICH_START, d.NUM_INPUTS): | |
self.sequence_features_scalar_map.append(f) | |
self.sequence_features_scalar_map.append(f) | |
if std_features: | |
for f in range(d.ENRICH_START, d.NUM_INPUTS): | |
self.sequence_features_scalar_map.append(f) | |
def kmeans_process(self, nd: np.ndarray): | |
from sklearn.cluster import KMeans | |
kmeans=KMeans(n_clusters=self.n_clusters, n_jobs=-1, verbose=1).fit(nd) | |
return kmeans.labels_, kmeans.cluster_centers_ | |
def process(self, nd: np.ndarray): | |
# Add some features | |
for sequence in range(0, nd.shape[0]): | |
features_to_add = [] | |
if self.regression_features: | |
for f in range(d.ENRICH_START, d.NUM_INPUTS): | |
m = np.nansum(nd[sequence][:, f]) / np.nansum(np.arange(0, nd.shape[1])) | |
b = nd[sequence][:, f][0] | |
features_to_add.extend([m, b]) | |
if self.std_features: | |
for f in range(d.ENRICH_START, d.NUM_INPUTS): | |
features_to_add.append(np.nanstd(nd[sequence][:, f])) | |
self.sample_sequences.append(nd[sequence]) | |
self.sequence_features.append(features_to_add) |
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