Merge branch 'master' of code:cdsc_reddit into excise_reindex

[cdsc_reddit.git] / clustering / pick_best_clustering.py

diff --git a/clustering/pick_best_clustering.py b/clustering/pick_best_clustering.py
index 91c443e28a7cc47d31787ddad0ac417ff7d98f55..c541d234e212b5c5876280c4e43b65a6e876987a 100644 (file)
--- a/clustering/pick_best_clustering.py
+++ b/clustering/pick_best_clustering.py
@@ -2,15 +2,15 @@ import fire
 import pandas as pd
 from pathlib import Path
 import shutil
-
-selection_data="/gscratch/comdata/output/reddit_clustering/subreddit_comment_authors-tf_10k_LSI/affinity/selection_data.csv"
+selection_data="/gscratch/comdata/output/reddit_clustering/subreddit_comment_authors-tf_10k_LSI/hdbscan/selection_data.csv"
 
 outpath = 'test_best.feather'
+min_clusters=50; max_isolates=5000; min_cluster_size=2
 
 # pick the best clustering according to silhouette score subject to contraints
-def pick_best_clustering(selection_data, output, min_clusters, max_isolates):
+def pick_best_clustering(selection_data, output, min_clusters, max_isolates, min_cluster_size):
     df = pd.read_csv(selection_data,index_col=0)
-    df = df.sort_values("silhouette_score")
+    df = df.sort_values("silhouette_score",ascending=False)
 
     # not sure I fixed the bug underlying this fully or not.
     df['n_isolates_str'] = df.n_isolates.str.strip("[]")
@@ -18,11 +18,10 @@ def pick_best_clustering(selection_data, output, min_clusters, max_isolates):
     df.loc[df.n_isolates_0,'n_isolates'] = 0
     df.loc[~df.n_isolates_0,'n_isolates'] = df.loc[~df.n_isolates_0].n_isolates_str.apply(lambda l: int(l))
     
-    best_cluster = df[(df.n_isolates <= max_isolates)&(df.n_clusters >= min_clusters)].iloc[df.shape[1]]
+    best_cluster = df[(df.n_isolates <= max_isolates)&(df.n_clusters >= min_clusters)&(df.min_cluster_size==min_cluster_size)].iloc[df.shape[1]]
 
     print(best_cluster.to_dict())
     best_path = Path(best_cluster.outpath) / (str(best_cluster['name']) + ".feather")
-    
     shutil.copy(best_path,output)
 
 if __name__ == "__main__":