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Splits_Head.csv +0 -0
make_merged_labels.py +148 -0
splits_MERGED_labels.csv +4687 -0
splits_MERGED_labels_map.csv +15 -0
splits_Medium.csv +0 -0
splits_Tail.csv +158 -0

Splits_Head.csv ADDED Viewed

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make_merged_labels.py ADDED Viewed

	@@ -0,0 +1,148 @@

+import argparse
+import csv
+import json
+import os
+import re
+TCGA_ID_RE = re.compile(r"(TCGA-[A-Z0-9]{2}-[A-Z0-9]+)")
+def extract_case_id(name):
+    m = TCGA_ID_RE.search(name)
+    return m.group(1) if m else None
+def read_cases_from_split(path):
+    cases = set()
+    with open(path, newline='') as f:
+        reader = csv.DictReader(f)
+        for r in reader:
+            for key in ('train', 'val', 'test'):
+                item = (r.get(key) or '').strip()
+                if not item:
+                    continue
+                cid = extract_case_id(item)
+                if cid:
+                    cases.add(cid)
+    return cases
+def list_input_csvs(input_dir, output_path):
+    files = []
+    for n in os.listdir(input_dir):
+        if n.startswith('.'):
+            continue
+        if not n.startswith('splits_') or not n.endswith('.csv'):
+            continue
+        if 'MERGED' in n.upper():
+            continue
+        files.append(os.path.join(input_dir, n))
+    files = sorted(files)
+    if output_path:
+        out_abs = os.path.abspath(output_path)
+        files = [p for p in files if os.path.abspath(p) != out_abs]
+    return files
+def choose_default_inputs(input_dir):
+    return list_input_csvs(input_dir, None)
+def build_case_label_map(inputs):
+    case_to_label = {}
+    conflicts = []
+    for label, path in enumerate(inputs):
+        cases = read_cases_from_split(path)
+        for cid in cases:
+            if cid in case_to_label and case_to_label[cid] != label:
+                conflicts.append((cid, case_to_label[cid], label, path))
+                continue
+            case_to_label[cid] = label
+    return case_to_label, conflicts
+def write_labels_csv(case_to_label, merged_cases, output_path):
+    missing = []
+    rows = []
+    for cid in sorted(merged_cases):
+        if cid not in case_to_label:
+            missing.append(cid)
+            continue
+        rows.append((cid, case_to_label[cid]))
+    with open(output_path, 'w', newline='') as f:
+        writer = csv.writer(f)
+        writer.writerow(['case_id', 'label'])
+        for cid, label in rows:
+            writer.writerow([cid, label])
+    return rows, missing
+def write_mapping(mapping_rows, mapping_output):
+    if not mapping_output:
+        return
+    if mapping_output.lower().endswith('.json'):
+        with open(mapping_output, 'w', encoding='utf-8') as f:
+            json.dump(mapping_rows, f, ensure_ascii=True, indent=2)
+        return
+    with open(mapping_output, 'w', newline='') as f:
+        writer = csv.writer(f)
+        writer.writerow(['label', 'source_name', 'source_csv'])
+        for row in mapping_rows:
+            writer.writerow([row['label'], row['source_name'], row['source_csv']])
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--input_dir', default='/mnt/datadisk0/data_process')
+    parser.add_argument('--inputs', nargs='*', default=None)
+    parser.add_argument('--merged', default='/mnt/datadisk0/data_process/splits_ALL_MERGED.csv')
+    parser.add_argument('--output', default='/mnt/datadisk0/data_process/splits_5MERGED_labels.csv')
+    parser.add_argument('--mapping_output', default=None)
+    args = parser.parse_args()
+    if args.inputs:
+        inputs = args.inputs
+    else:
+        inputs = choose_default_inputs(args.input_dir)
+    mapping_rows = []
+    for label, path in enumerate(inputs):
+        base_name = os.path.basename(path)
+        source_name = os.path.splitext(base_name)[0].replace('splits_', '')
+        mapping_rows.append({'label': label, 'source_name': source_name, 'source_csv': path})
+    if args.mapping_output is None:
+        base_out = os.path.splitext(args.output)[0]
+        args.mapping_output = base_out + '_map.csv'
+    merged_cases = read_cases_from_split(args.merged)
+    case_to_label, conflicts = build_case_label_map(inputs)
+    rows, missing = write_labels_csv(case_to_label, merged_cases, args.output)
+    write_mapping(mapping_rows, args.mapping_output)
+    print('Input CSVs:', len(inputs))
+    print('Merged file:', args.merged)
+    print('Merged cases:', len(merged_cases))
+    print('Labeled cases:', len(rows))
+    print('Output CSV:', args.output)
+    print('Mapping output:', args.mapping_output)
+    print('Label mapping:')
+    for row in mapping_rows:
+        print(f"  {row['label']} -> {row['source_name']} ({row['source_csv']})")
+    if missing:
+        print('Missing labels for cases:', len(missing))
+        for cid in missing[:20]:
+            print('  ', cid)
+        if len(missing) > 20:
+            print('  ... and', len(missing) - 20, 'more')
+    if conflicts:
+        print('Conflicting labels:', len(conflicts))
+        for cid, old_label, new_label, path in conflicts[:20]:
+            print('  ', cid, 'existing=', old_label, 'new=', new_label, 'from', path)
+        if len(conflicts) > 20:
+            print('  ... and', len(conflicts) - 20, 'more')
+if __name__ == '__main__':
+    main()

splits_MERGED_labels.csv ADDED Viewed

	@@ -0,0 +1,4687 @@

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splits_MERGED_labels_map.csv ADDED Viewed

	@@ -0,0 +1,15 @@

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splits_Medium.csv ADDED Viewed

The diff for this file is too large to render. See raw diff

splits_Tail.csv ADDED Viewed

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