megadetector 5.0.11__py3-none-any.whl → 5.0.12__py3-none-any.whl

megadetector/classification/csv_to_json.py

@@ -0,0 +1,226 @@
+"""
+
+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()