missing taxonomy python notebook to script

tools/missing_taxonomy.py

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+import argparse
+import tdtax 
+import os
+import scope_phenom # https://github.com/bfhealy/scope-phenomenology
+from scope.utils import read_parquet
+import pandas as pd
+import numpy as np
+
+phenom = scope_phenom.taxonomy
+sitewide = tdtax.taxonomy
+
+# Recursive functions to perform a reverse lookup in taxonomy dictionaries
+
+def trace_path(dct, key):
+    if dct == key: 
+        return [dct] 
+    elif isinstance(dct, dict): 
+        for k, v in dct.items(): 
+            p = trace_path(v, key) 
+            if p: 
+                return [k] + p 
+    elif isinstance(dct, list): 
+        lst = dct 
+        for i in range(len(lst)): 
+            p = trace_path(lst[i], key) 
+            if p: 
+                return [str(i)] + p 
+
+def get_class_path(trail, dct, key):
+    stepdown = dct[trail[0]][int(trail[1])]
+    cls = stepdown['class']
+    if cls == key:
+        return [cls]
+    else:
+        trail = trail[2:]
+        p = get_class_path(trail, stepdown, key)
+        return [cls] + p
+
+def missing_taxonomy(parquet, mapper):
+    # Read in golden dataset (downloaded from Fritz), mapper
+    parquet_path = os.path.join(os.path.dirname(__file__), parquet)
+    mapper_path = os.path.join(os.path.dirname(__file__), mapper)
+    output_path = os.path.join(os.path.dirname(__file__), "golden_missing_labels.csv")
+    gold_new = read_parquet(parquet_path)
+    golden_dataset_mapper = pd.read_json(mapper_path)
+    gold_map = golden_dataset_mapper.copy()
+    none_cols = gold_map.loc['fritz_label'] == 'None'
+    gold_map = gold_map.drop(columns=none_cols.index[none_cols.values])
+
+    # Manipulate golden_dataset_mapper to flip keys and values
+    gold_map = gold_map.transpose()
+    gold_map.index.rename('trainingset_label', inplace=True)
+    gold_map = gold_map.reset_index(drop=False).set_index('fritz_label')
+    gold_dict = gold_map.transpose().to_dict()
+
+    labels_gold = gold_new.set_index('obj_id')[gold_new.columns[1:54]]
+
+    classes = labels_gold.columns.values.tolist()
+
+    missing_df = pd.DataFrame({'obj_id':labels_gold.index, 'missing_descr':np.zeros(len(labels_gold),dtype=str)}).set_index('obj_id')
+
+    values = []
+    missing_items = []
+    cnt = 0
+
+    for index, row in labels_gold.iterrows():
+        nonzero_vals = row[row>0].index.values
+        for value in nonzero_vals:
+            mapped_c = golden_dataset_mapper[value]['fritz_label']
+            try:
+                trail = trace_path(sitewide, mapped_c)
+                class_path = get_class_path(trail, sitewide, mapped_c)
+            except TypeError:
+                trail = trace_path(phenom, mapped_c)
+                class_path = get_class_path(trail, phenom, mapped_c)
+            for item in class_path:
+                if (item != mapped_c) & (item in classes):
+                    mapped_item = gold_dict[item]['trainingset_label']
+                    if labels_gold.loc[index, mapped_item] == 0:
+                        cnt += 1
+                        print(cnt, index, value, 'missing', mapped_item, ';')
+                        values += [value]
+                        missing_items += [mapped_item]
+                        missing_df.loc[index, 'missing_descr'] = missing_df.loc[index, 'missing_descr'] + f"{value} missing {mapped_item};"
+        missing_df.loc[index, 'missing_descr'] = missing_df.loc[index, 'missing_descr'][:-1]
+    missing_df[missing_df['missing_descr']!=''].reset_index().to_csv(output_path,index=False)
+    return None
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-parquet", type=str, help="path to parquet")
+    parser.add_argument("-mapper", type=str, help="path to mapper")
+    parser.add_argument(
+        "-merge_features",
+        type=bool,
+        nargs='?',
+        const=True,
+        default=False,
+        help="merge downloaded results with features from Kowalski",
+    )
+    parser.add_argument(
+        "-features_catalog",
+        type=str,
+        default='ZTF_source_features_DR5',
+        help="catalog of features on Kowalski",
+    )
+
+    args = parser.parse_args()
+
+    missing_taxonomy(args.parquet, args.mapper)