megadetector 5.0.9__py3-none-any.whl → 5.0.11__py3-none-any.whl

classification/csv_to_json.py

@@ -1,226 +0,0 @@
-"""
-
-csv_to_json.py
-
-Converts CSV to JSON format for label specification.
-
-There are 3 possible values for the 'type' column in the CSV:
-
-- "row": this selects a specific rowfrom the master taxonomy CSV
-    content syntax: <dataset_name>|<dataset_label>
-
-- "datasettaxon": this selects all animals in a taxon from a particular dataset
-    content syntax: <dataset_name>|<taxon_level>|<taxon_name>
-
-- <taxon_level>: this selects all animals in a taxon across all datasets
-    content syntax: <taxon_name>
-
-Example CSV input:
-
-"
-  # comment lines starting with '#' are allowed
-  output_label,type,content
-  cervid,row,idfg|deer
-  cervid,row,idfg|elk
-  cervid,row,idfg|prong
-  cervid,row,idfg_swwlf_2019|elk
-  cervid,row,idfg_swwlf_2019|muledeer
-  cervid,row,idfg_swwlf_2019|whitetaileddeer
-  cervid,max_count,50000
-  cervid,family,cervidae
-  cervid,datasettaxon,idfg|family|cervidae
-  cervid,datasettaxon,idfg_swwlf_2019|family|cervidae
-  bird,row,idfg_swwlf_2019|bird
-  bird,class,aves
-  bird,max_count,50000
-  bird,prioritize,"[['idfg_swwlf_2019'], ['idfg']]"
-  !bird,row,idfg_swwlf_2019|turkey
-  !bird,genus,meleagris
-"
-
-Example JSON output:
-
-"    
-  {
-      "cervid": {
-          "dataset_labels": {
-              "idfg": ["deer", "elk", "prong"],
-              "idfg_swwlf_2019": ["elk", "muledeer", "whitetaileddeer"]
-          },
-          "taxa": [
-              {
-                  "level": "family",
-                  "name": "cervidae"
-              },
-              {
-                  "level": "family",
-                  "name": "cervidae"
-                  "datasets": ["idfg"]
-              },
-              {
-                  "level": "family",
-                  "name": "cervidae"
-                  "datasets": ["idfg_swwlf_2019"]
-              }
-          ],
-          "max_count": 50000
-      },
-      "bird": {
-          "dataset_labels": {
-              "idfg_swwlf_2019": ["bird"]
-          },
-          "taxa": [
-              {
-                  "level": "class",
-                  "name": "aves"
-              }
-          ],
-          "exclude": {
-              "dataset_labels": {
-                  "idfg_swwlf_2019": ["turkey"]
-              },
-              "taxa": [
-                  {
-                      "level": "genus",
-                      "name": "meleagris"
-                  }
-              ]
-          },
-          "max_count": "50000",
-          "prioritize": [
-              ["idfg_swwlf_2019"],
-              ["idfg"]
-          ],
-      }
-  }
-"
-
-"""
-
-#%% Imports
-
-from __future__ import annotations
-
-import argparse
-from collections import defaultdict
-import json
-from typing import Any
-
-import pandas as pd
-
-
-#%% Main function
-
-def main():
-    args = _parse_args()
-    js = csv_to_jsondict(args.input_csv_file)
-    for label in js:
-        js[label] = order_spec_dict(js[label])
-    with open(args.output_json_path, 'w') as f:
-        json.dump(js, f, indent=args.json_indent)
-
-
-#%% Support functions
-
-def parse_csv_row(obj: dict[str, Any], rowtype: str, content: str) -> None:
-    """
-    Parses a row in the CSV.
-    """
-    
-    if rowtype == 'row':
-        if 'dataset_labels' not in obj:
-            obj['dataset_labels'] = defaultdict(list)
-
-        assert '|' in content
-        ds, ds_label = content.split('|')
-        obj['dataset_labels'][ds].append(ds_label)
-
-    elif rowtype == 'datasettaxon':
-        if 'taxa' not in obj:
-            obj['taxa'] = []
-
-        assert '|' in content
-        ds, taxon_level, taxon_name = content.split('|')
-        obj['taxa'].append({
-            'level': taxon_level,
-            'name': taxon_name,
-            'datasets': [ds]
-        })
-
-    elif rowtype == 'max_count':
-        obj['max_count'] = int(content)
-
-    elif rowtype == 'prioritize':
-        obj['prioritize'] = eval(content)  # pylint: disable=eval-used
-
-    else:
-        if 'taxa' not in obj:
-            obj['taxa'] = []
-
-        taxon_level = rowtype
-        taxon_name = content
-        obj['taxa'].append({
-            'level': taxon_level,
-            'name': taxon_name
-        })
-
-
-def csv_to_jsondict(csv_path: str) -> dict[str, dict[str, Any]]:
-    """
-    Converts CSV to json-style dictionary.
-    """
-    
-    df = pd.read_csv(csv_path, comment='#', skip_blank_lines=True)
-    assert (df.columns == ['output_label', 'type', 'content']).all()
-
-    js: defaultdict[str, dict[str, Any]] = defaultdict(dict)
-
-    for i in df.index:
-        label, rowtype, content = df.loc[i]
-        if label.startswith('!'):
-            label = label[1:]
-            if 'exclude' not in js[label]:
-                js[label]['exclude'] = {}
-            obj = js[label]['exclude']
-        else:
-            obj = js[label]
-        parse_csv_row(obj, rowtype, content)
-
-    return js
-
-
-def order_spec_dict(spec_dict: dict[str, Any]) -> dict[str, Any]:
-    """
-    Returns spec_dict with keys in a specific order.
-    """
-    
-    if 'exclude' in spec_dict:
-        spec_dict['exclude'] = order_spec_dict(spec_dict['exclude'])
-    ordered_spec_dict: dict[str, Any] = {}
-    for key in ['dataset_labels', 'taxa', 'exclude', 'max_count', 'prioritize']:
-        if key in spec_dict:
-            ordered_spec_dict[key] = spec_dict[key]
-    return ordered_spec_dict
-
-
-#%% Command-line driver
-
-def _parse_args() -> argparse.Namespace:
-    
-    parser = argparse.ArgumentParser(
-        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
-        description='Converts CSV to JSON format for label specification.')
-    parser.add_argument(
-        'input_csv_file',
-        help='path to CSV file containing label specification')
-    parser.add_argument(
-        'output_json_path',
-        help='path to save converted JSON file')
-    parser.add_argument(
-        '--json-indent', type=int,
-        help='number of spaces to use for JSON indent (default no indent)')
-    return parser.parse_args()
-
-
-if __name__ == '__main__':
-    main()