Commit 07088d4ec503010cac0269a501574acc48e2b3c8
1 parent
9fd9bc58ff
Exists in
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Just change volia importing lines
Showing 1 changed file with 1 additions and 1 deletions Inline Diff
volia/tsne.py
| 1 | ''' | 1 | ''' |
| 2 | The goal of this script is to display calculate tsne of pvectors. | 2 | The goal of this script is to display calculate tsne of pvectors. |
| 3 | ''' | 3 | ''' |
| 4 | 4 | ||
| 5 | import os | 5 | import os |
| 6 | from os.path import isfile | 6 | from os.path import isfile |
| 7 | import argparse | 7 | import argparse |
| 8 | import numpy as np | 8 | import numpy as np |
| 9 | from sklearn.manifold import TSNE | 9 | from sklearn.manifold import TSNE |
| 10 | 10 | ||
| 11 | from volia.data_io import read_features | 11 | from core.data import read_features |
| 12 | 12 | ||
| 13 | if __name__ == "__main__": | 13 | if __name__ == "__main__": |
| 14 | # Defining argparse | 14 | # Defining argparse |
| 15 | parser = argparse.ArgumentParser(prog='pvector tsne', description='Calculate the tsne representation of pvector in 3 or 2d') | 15 | parser = argparse.ArgumentParser(prog='pvector tsne', description='Calculate the tsne representation of pvector in 3 or 2d') |
| 16 | parser.add_argument('features', type=str, | 16 | parser.add_argument('features', type=str, |
| 17 | help='the path of the file you want to calculate tsne') | 17 | help='the path of the file you want to calculate tsne') |
| 18 | parser.add_argument('-o', '--outfile', type=str, | 18 | parser.add_argument('-o', '--outfile', type=str, |
| 19 | default='.', | 19 | default='.', |
| 20 | help='the path of the output file.') | 20 | help='the path of the output file.') |
| 21 | parser.add_argument('-n', '--n-comp', type=int, choices=[2, 3], | 21 | parser.add_argument('-n', '--n-comp', type=int, choices=[2, 3], |
| 22 | default='2', | 22 | default='2', |
| 23 | help='number of components output of tsne') | 23 | help='number of components output of tsne') |
| 24 | 24 | ||
| 25 | args = parser.parse_args() | 25 | args = parser.parse_args() |
| 26 | 26 | ||
| 27 | assert isfile(args.features) | 27 | assert isfile(args.features) |
| 28 | 28 | ||
| 29 | features_list = read_features(args.features) | 29 | features_list = read_features(args.features) |
| 30 | tuples_key_feat = np.vstack([ (key, feats) for key, feats in features_list.items()]) | 30 | tuples_key_feat = np.vstack([ (key, feats) for key, feats in features_list.items()]) |
| 31 | keys, features = zip(*tuples_key_feat) | 31 | keys, features = zip(*tuples_key_feat) |
| 32 | feat_tsne = TSNE(n_components=args.n_comp).fit_transform(features) | 32 | feat_tsne = TSNE(n_components=args.n_comp).fit_transform(features) |
| 33 | 33 | ||
| 34 | with open(args.outfile, "w") as of: | 34 | with open(args.outfile, "w") as of: |
| 35 | for i in range(len(keys)): | 35 | for i in range(len(keys)): |
| 36 | of.write(keys[i] + " " + " ".join([str(feat) for feat in feat_tsne[i]]) + "\n") | 36 | of.write(keys[i] + " " + " ".join([str(feat) for feat in feat_tsne[i]]) + "\n") |
| 37 | print("TSNE finished. Check if everything has been done well.") | 37 | print("TSNE finished. Check if everything has been done well.") |