megadetector 5.0.10__py3-none-any.whl → 5.0.11__py3-none-any.whl

taxonomy_mapping/prepare_lila_taxonomy_release.py

@@ -1,142 +0,0 @@
-"""
-
-prepare_lila_taxonomy_release.py
-
-Given the private intermediate taxonomy mapping (produced by map_new_lila_datasets.py), 
-prepare the public (release) taxonomy mapping file.
-
-"""
-
-#%% Imports and constants
-
-import os
-import json
-import pandas as pd
-
-
-#%% Prevent execution during infrastructural imports
-
-if False:
-    
-    #%% Filenames
-    
-    lila_taxonomy_file = 'c:/git/agentmorrisprivate/lila-taxonomy/lila-taxonomy-mapping.csv'
-    release_taxonomy_file = os.path.expanduser('~/lila/lila-taxonomy-mapping_release.csv')
-    # import clipboard; clipboard.copy(release_taxonomy_file)
-
-    # Created by get_lila_category_list.py... contains counts for each category
-    lila_dataset_to_categories_file = os.path.expanduser('~/lila/lila_categories_list/lila_dataset_to_categories.json')
-
-    assert os.path.isfile(lila_dataset_to_categories_file)
-    assert os.path.isfile(lila_taxonomy_file)
-
-
-    #%% Find out which categories are actually used
-
-    df = pd.read_csv(lila_taxonomy_file)
-
-    with open(lila_dataset_to_categories_file,'r') as f:
-        lila_dataset_to_categories = json.load(f)
-
-    used_category_mappings = []
-
-    # dataset_name = datasets_to_map[0]
-    for dataset_name in lila_dataset_to_categories.keys():
-        
-        ds_categories = lila_dataset_to_categories[dataset_name]
-        for category in ds_categories:
-            category_name = category['name'].lower()
-            assert ':' not in category_name
-            mapping_name = dataset_name + ':' + category_name
-            used_category_mappings.append(mapping_name)
-
-    df['used'] = False
-
-    # i_row = 0; row = df.iloc[i_row]; row
-    for i_row,row in df.iterrows():
-        ds_name = row['dataset_name']
-        query = row['query']
-        mapping_name = ds_name + ':' + query
-        if mapping_name in used_category_mappings:
-            df.loc[i_row,'used'] = True
-        else:
-            print('Dropping unused mapping {}'.format(mapping_name))
-
-    df = df[df.used]
-    df = df.drop('used',axis=1)
-
-
-    #%% Generate the final output file
-
-    assert not os.path.isfile(release_taxonomy_file)
-
-    known_levels = ['stateofmatter', #noqa
-                        'kingdom',
-                        'phylum','subphylum',
-                        'superclass','class','subclass','infraclass',
-                        'superorder','order','parvorder','suborder','infraorder',
-                        'zoosection',
-                        'superfamily','family','subfamily','tribe',
-                        'genus',
-                        'species','subspecies','variety']
-
-    levels_to_include = ['kingdom',
-                        'phylum','subphylum',
-                        'superclass','class','subclass','infraclass',
-                        'superorder','order','suborder','infraorder',
-                        'superfamily','family','subfamily','tribe',
-                        'genus',
-                        'species','subspecies','variety']
-
-    levels_to_exclude = ['stateofmatter','zoosection','parvorder']
-
-    for s in levels_to_exclude:
-        assert s not in levels_to_include
-        
-    levels_used = set()
-
-    # i_row = 0; row = df.iloc[i_row]; row
-    for i_row,row in df.iterrows():
-        
-        if not isinstance(row['scientific_name'],str):
-            assert not isinstance(row['taxonomy_string'],str)
-            continue
-        
-        taxonomic_match = eval(row['taxonomy_string'])
-        
-        # match_at_level = taxonomic_match[0]
-        for match_at_level in taxonomic_match:
-            assert len(match_at_level) == 4
-            levels_used.add(match_at_level[1])
-            
-    levels_used = [s for s in levels_used if isinstance(s,str)]
-
-    for s in levels_used:
-        assert s in levels_to_exclude or s in levels_to_include, 'Unrecognized level {}'.format(s)
-
-    for s in levels_to_include:
-        assert s in levels_used
-        
-    for s in levels_to_include:
-        df[s] = ''
-        
-    # i_row = 0; row = df.iloc[i_row]; row
-    for i_row,row in df.iterrows():
-        
-        if not isinstance(row['scientific_name'],str):
-            assert not isinstance(row['taxonomy_string'],str)
-            continue
-        
-        # E.g.: (43117, 'genus', 'lepus', ['hares and jackrabbits']
-        taxonomic_match = eval(row['taxonomy_string'])
-        
-        for match_at_level in taxonomic_match:
-            level = match_at_level[1]
-            if level in levels_to_include:
-                df.loc[i_row,level] = match_at_level[2]
-
-    df = df.drop('source',axis=1)
-    df.to_csv(release_taxonomy_file,header=True,index=False)
-
-    print('Wrote final output to {}'.format(release_taxonomy_file))
-