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check_tcga_match.py

@@ -0,0 +1,111 @@
+import argparse
+import os
+import re
+from collections import defaultdict
+
+def is_dir(p):
+    try:
+        return os.path.isdir(p)
+    except Exception:
+        return False
+
+def is_file(p):
+    try:
+        return os.path.isfile(p)
+    except Exception:
+        return False
+
+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 collect_from_dir(path):
+    items = []
+    for n in os.listdir(path):
+        if n.startswith('.'):
+            continue
+        items.append(n)
+    cases = set()
+    case_to_items = defaultdict(list)
+    for n in items:
+        cid = extract_case_id(n)
+        if cid:
+            cases.add(cid)
+            case_to_items[cid].append(n)
+    return items, cases, case_to_items
+
+def collect_from_file(path):
+    items = []
+    with open(path, 'r', encoding='utf-8', errors='ignore') as f:
+        for line in f:
+            line = line.strip()
+            if not line:
+                continue
+            items.append(line)
+    cases = set()
+    case_to_items = defaultdict(list)
+    for n in items:
+        cid = extract_case_id(n)
+        if cid:
+            cases.add(cid)
+            case_to_items[cid].append(n)
+    return items, cases, case_to_items
+
+def collect(path):
+    if is_dir(path):
+        return collect_from_dir(path)
+    if is_file(path):
+        return collect_from_file(path)
+    raise FileNotFoundError(path)
+
+def main():
+    ap = argparse.ArgumentParser()
+    ap.add_argument('--feature_source', type=str, default='/mnt/datadisk0/TCGA_pt/MESO_UNI')
+    ap.add_argument('--label_source', type=str, default='/mnt/datadisk0/datasets/TCGA-MESO')
+    ap.add_argument('--limit', type=int, default=50)
+    args = ap.parse_args()
+
+    feat_items, feat_cases, feat_map = collect(args.feature_source)
+    lab_items, lab_cases, lab_map = collect(args.label_source)
+
+    common = sorted(feat_cases & lab_cases)
+    miss_labels = sorted(feat_cases - lab_cases)
+    miss_features = sorted(lab_cases - feat_cases)
+
+    print('Feature source:', args.feature_source)
+    print('Total feature items:', len(feat_items))
+    print('Feature cases:', len(feat_cases))
+    print('Label source:', args.label_source)
+    print('Total label items:', len(lab_items))
+    print('Label cases:', len(lab_cases))
+    print('Matched cases:', len(common))
+
+    if miss_labels:
+        print('Cases present in features but missing labels:', len(miss_labels))
+        for cid in miss_labels[:args.limit]:
+            print(cid, 'feature_count=', len(feat_map.get(cid, [])))
+        if len(miss_labels) > args.limit:
+            print('... and', len(miss_labels) - args.limit, 'more')
+    else:
+        print('No cases missing labels')
+
+    if miss_features:
+        print('Cases present in labels but missing features:', len(miss_features))
+        for cid in miss_features[:args.limit]:
+            print(cid)
+        if len(miss_features) > args.limit:
+            print('... and', len(miss_features) - args.limit, 'more')
+    else:
+        print('No cases missing features')
+
+    top_counts = sorted(((cid, len(feat_map[cid])) for cid in common), key=lambda x: (-x[1], x[0]))
+    if top_counts:
+        print('Top matched cases by feature count:')
+        for cid, c in top_counts[:min(args.limit, 20)]:
+            print(cid, 'feature_count=', c)
+
+if __name__ == '__main__':
+    main()
+

make_acc_splits.py

@@ -0,0 +1,111 @@
+import argparse
+import os
+import re
+import random
+
+TCGA_ID_RE = re.compile(r"(TCGA-[A-Z0-9]{2}-[A-Z0-9]+)")
+DX_TOKEN_RE = re.compile(r"(?:^|-)DX\d*(?=[\-.]|$)")
+TS_TOKEN_RE = re.compile(r"(?:^|-)TS[A-Za-z0-9]*(?=[\-.]|$)")
+
+def extract_case_id(name):
+    m = TCGA_ID_RE.search(name)
+    return m.group(1) if m else None
+
+def is_dx_item(name):
+    if TS_TOKEN_RE.search(name):
+        return False
+    return DX_TOKEN_RE.search(name) is not None
+
+def collect_features(path):
+    case_to_items = {}
+    for n in os.listdir(path):
+        if n.startswith('.'):
+            continue
+        if not n.endswith('.pt'):
+            continue
+        if not is_dx_item(n):
+            continue
+        cid = extract_case_id(n)
+        if not cid:
+            continue
+        case_to_items.setdefault(cid, []).append(n)
+    for k in list(case_to_items.keys()):
+        case_to_items[k].sort()
+    return case_to_items
+
+def collect_label_cases(path):
+    cases = set()
+    for n in os.listdir(path):
+        if n.startswith('.'):
+            continue
+        p = os.path.join(path, n)
+        if not os.path.isdir(p):
+            continue
+        cid = extract_case_id(n)
+        if cid:
+            cases.add(cid)
+    return cases
+
+def write_csv(train_items, val_items, test_items, out_path):
+    max_len = max(len(train_items), len(val_items), len(test_items))
+    with open(out_path, 'w', encoding='utf-8') as f:
+        f.write(',train,val,test\n')
+        for i in range(max_len):
+            t = train_items[i] if i < len(train_items) else ''
+            v = val_items[i] if i < len(val_items) else ''
+            te = test_items[i] if i < len(test_items) else ''
+            t = os.path.splitext(t)[0]
+            v = os.path.splitext(v)[0]
+            te = os.path.splitext(te)[0]
+            f.write(f"{i},{t},{v},{te}\n")
+
+def main():
+    ap = argparse.ArgumentParser()
+    ap.add_argument('--feature_source', type=str, default='/mnt/datadisk0/TCGA_pt/MESO_UNI')
+    ap.add_argument('--label_source', type=str, default='/mnt/datadisk0/datasets/TCGA-MESO')
+    ap.add_argument('--output_csv', type=str, default='/mnt/datadisk0/BiGen/ocr/dataset_csv/splits_MESO.csv')
+    ap.add_argument('--seed', type=int, default=42)
+    args = ap.parse_args()
+
+    features_map = collect_features(args.feature_source)
+    label_cases = collect_label_cases(args.label_source)
+    common_cases = sorted(set(features_map.keys()) & label_cases)
+
+    random.seed(args.seed)
+    random.shuffle(common_cases)
+
+    total = len(common_cases)
+    n_train = int(total * 0.8)
+    n_val = int(total * 0.1)
+    n_test = total - n_train - n_val
+
+    train_cases = common_cases[:n_train]
+    val_cases = common_cases[n_train:n_train + n_val]
+    test_cases = common_cases[n_train + n_val:]
+
+    train_items = []
+    val_items = []
+    test_items = []
+
+    for c in train_cases:
+        train_items.extend(features_map.get(c, []))
+    for c in val_cases:
+        val_items.extend(features_map.get(c, []))
+    for c in test_cases:
+        test_items.extend(features_map.get(c, []))
+
+    write_csv(train_items, val_items, test_items, args.output_csv)
+
+    print('Feature source:', args.feature_source)
+    print('Label source:', args.label_source)
+    print('Common cases:', total)
+    print('Train cases:', len(train_cases))
+    print('Val cases:', len(val_cases))
+    print('Test cases:', len(test_cases))
+    print('Train items:', len(train_items))
+    print('Val items:', len(val_items))
+    print('Test items:', len(test_items))
+    print('Output CSV:', args.output_csv)
+
+if __name__ == '__main__':
+    main()

make_label_splits.py

@@ -0,0 +1,165 @@
+import argparse
+import os
+import random
+import re
+
+TCGA_ID_RE = re.compile(r"(TCGA-[A-Z0-9]{2}-[A-Z0-9]+)")
+DX_TOKEN_RE = re.compile(r"(?:^|-)DX\d*(?=[\-.]|$)")
+TS_TOKEN_RE = re.compile(r"(?:^|-)TS[A-Za-z0-9]*(?=[\-.]|$)")
+DX_NUM_RE = re.compile(r"(?:^|-)DX(\d*)(?=[\-.]|$)")
+
+
+def extract_case_id(name):
+    m = TCGA_ID_RE.search(name)
+    return m.group(1) if m else None
+
+
+def is_dx_item(name):
+    if TS_TOKEN_RE.search(name):
+        return False
+    return DX_TOKEN_RE.search(name) is not None
+
+
+def list_items(path):
+    items = []
+    if os.path.isdir(path):
+        for n in os.listdir(path):
+            if n.startswith('.'):
+                continue
+            items.append(n)
+    else:
+        with open(path, 'r', encoding='utf-8', errors='ignore') as f:
+            for line in f:
+                line = line.strip()
+                if not line:
+                    continue
+                items.append(line)
+    return items
+
+
+def collect_feature_items(path):
+    items = list_items(path)
+    case_to_items = {}
+    for n in items:
+        if os.path.isdir(path):
+            if not n.endswith('.pt'):
+                continue
+        if not is_dx_item(n):
+            continue
+        cid = extract_case_id(n)
+        if not cid:
+            continue
+        case_to_items.setdefault(cid, []).append(n)
+    for k in list(case_to_items.keys()):
+        case_to_items[k].sort()
+    return case_to_items
+
+
+def collect_label_cases(path):
+    items = list_items(path)
+    cases = set()
+    for n in items:
+        if os.path.isdir(path):
+            p = os.path.join(path, n)
+            if not os.path.isdir(p):
+                continue
+        cid = extract_case_id(n)
+        if cid:
+            cases.add(cid)
+    return cases
+
+
+def dx_rank(name):
+    m = DX_NUM_RE.search(name)
+    if not m:
+        return 50
+    num = m.group(1)
+    if num == '1':
+        return 1
+    if num == '2':
+        return 2
+    if num == '':
+        return 10
+    try:
+        return 10 + int(num)
+    except ValueError:
+        return 50
+
+
+def choose_best_item(items):
+    if not items:
+        return None
+    return sorted(items, key=lambda x: (dx_rank(x), x))[0]
+
+
+def write_csv(train_items, val_items, test_items, out_path):
+    max_len = max(len(train_items), len(val_items), len(test_items))
+    with open(out_path, 'w', encoding='utf-8') as f:
+        f.write(',train,val,test\n')
+        for i in range(max_len):
+            t = train_items[i] if i < len(train_items) else ''
+            v = val_items[i] if i < len(val_items) else ''
+            te = test_items[i] if i < len(test_items) else ''
+            t = os.path.splitext(t)[0]
+            v = os.path.splitext(v)[0]
+            te = os.path.splitext(te)[0]
+            f.write(f"{i},{t},{v},{te}\n")
+
+
+def main():
+    ap = argparse.ArgumentParser()
+    ap.add_argument('--feature_source', type=str, default='/mnt/datadisk0/TCGA_pt/STAD_UNI')
+    ap.add_argument('--label_source', type=str, default='/mnt/datadisk0/datasets/TCGA-STAD')
+    ap.add_argument('--output_csv', type=str, default='/mnt/datadisk0/data_process/splits_STAD.csv')
+    ap.add_argument('--seed', type=int, default=42)
+    args = ap.parse_args()
+
+    features_map = collect_feature_items(args.feature_source)
+    label_cases = collect_label_cases(args.label_source)
+    common_cases = sorted(set(features_map.keys()) & label_cases)
+
+    random.seed(args.seed)
+    random.shuffle(common_cases)
+
+    total = len(common_cases)
+    n_train = int(total * 0.8)
+    n_val = int(total * 0.1)
+    n_test = total - n_train - n_val
+
+    train_cases = common_cases[:n_train]
+    val_cases = common_cases[n_train:n_train + n_val]
+    test_cases = common_cases[n_train + n_val:]
+
+    train_items = []
+    val_items = []
+    test_items = []
+
+    for c in train_cases:
+        item = choose_best_item(features_map.get(c, []))
+        if item:
+            train_items.append(item)
+    for c in val_cases:
+        item = choose_best_item(features_map.get(c, []))
+        if item:
+            val_items.append(item)
+    for c in test_cases:
+        item = choose_best_item(features_map.get(c, []))
+        if item:
+            test_items.append(item)
+
+    write_csv(train_items, val_items, test_items, args.output_csv)
+
+    print('Feature source:', args.feature_source)
+    print('Label source:', args.label_source)
+    print('Common cases:', total)
+    print('Train cases:', len(train_cases))
+    print('Val cases:', len(val_cases))
+    print('Test cases:', len(test_cases))
+    print('Train items:', len(train_items))
+    print('Val items:', len(val_items))
+    print('Test items:', len(test_items))
+    print('Output CSV:', args.output_csv)
+
+
+if __name__ == '__main__':
+    main()

merge_splits_all.py

@@ -0,0 +1,79 @@
+import argparse
+import csv
+import fnmatch
+import os
+
+
+def list_input_csvs(input_dir, output_path):
+    files = []
+    for n in os.listdir(input_dir):
+        if n.startswith('.'):
+            continue
+        if not fnmatch.fnmatch(n, 'splits_*.csv'):
+            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 collect_columns(paths):
+    trains, vals, tests = [], [], []
+    for path in paths:
+        if not os.path.exists(path):
+            continue
+        with open(path, newline='') as f:
+            reader = csv.DictReader(f)
+            for r in reader:
+                t = (r.get('train') or '').strip()
+                v = (r.get('val') or '').strip()
+                te = (r.get('test') or '').strip()
+                if t:
+                    trains.append(t)
+                if v:
+                    vals.append(v)
+                if te:
+                    tests.append(te)
+    return trains, vals, tests
+
+
+def write_parallel(trains, vals, tests, output):
+    n = max(len(trains), len(vals), len(tests))
+    with open(output, 'w', newline='') as f:
+        writer = csv.writer(f)
+        writer.writerow(['', 'train', 'val', 'test'])
+        for i in range(n):
+            t = trains[i] if i < len(trains) else ''
+            v = vals[i] if i < len(vals) else ''
+            te = tests[i] if i < len(tests) else ''
+            writer.writerow([i, t, v, te])
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    base = os.path.dirname(os.path.abspath(__file__))
+    default_output = os.path.join(base, 'splits_ALL_MERGED.csv')
+    parser.add_argument('--input_dir', default='/mnt/datadisk0/data_process')
+    parser.add_argument('--inputs', nargs='*', default=None)
+    parser.add_argument('--output', default='/mnt/datadisk0/data_process/splits_ALL_MERGED.csv')
+    args = parser.parse_args()
+
+    if args.inputs:
+        inputs = args.inputs
+    else:
+        inputs = list_input_csvs(args.input_dir, args.output)
+
+    trains, vals, tests = collect_columns(inputs)
+    write_parallel(trains, vals, tests, args.output)
+
+    print('Input CSVs:', len(inputs))
+    print('Train items:', len(trains))
+    print('Val items:', len(vals))
+    print('Test items:', len(tests))
+    print('Output CSV:', args.output)
+
+
+if __name__ == '__main__':
+    main()

splits_ACC.csv

@@ -0,0 +1,45 @@
+,train,val,test
+0,TCGA-OR-A5K0-01Z-00-DX1.D73A3597-A2C4-48C1-88B1-3FCCE90ACB6C,TCGA-OR-A5K4-01Z-00-DX1.57E02BED-3F3E-4CFC-A4D5-8FFD347B9533,TCGA-OR-A5JG-01Z-00-DX1.8798846B-E00D-4BEF-9CE6-F3FDB2DB642C
+1,TCGA-OR-A5JS-01Z-00-DX1.AE76284D-A640-4716-A96A-93CF02DC7D5D,TCGA-OR-A5LO-01Z-00-DX1.05378BBB-AE4E-47D8-A1D3-0CEB0418A124,TCGA-OR-A5JI-01Z-00-DX1.E133042C-62B2-4015-853B-436830988A53
+2,TCGA-PA-A5YG-01Z-00-DX1.4D794DEC-B848-4CF1-AD0D-F7ABDD3B46D9,TCGA-OR-A5J8-01Z-00-DX1.B95FA93F-A0E1-4148-BF52-A96547F5CC2A,TCGA-OR-A5JK-01Z-00-DX1.175C14F3-8CB4-40A0-8E61-A1E77F4CA538
+3,TCGA-OR-A5JD-01Z-00-DX1.83A2D0A6-70F2-49C8-BAAF-795AC206ED04,TCGA-PK-A5H9-01Z-00-DX1.EF93DA44-7E63-4210-81B2-11DB5C0FDB31,TCGA-OR-A5LT-01Z-00-DX1.030142AE-23DC-4082-87B4-D4D6E4CB9335
+4,TCGA-OR-A5JJ-01Z-00-DX1.459B5DFE-47B1-426F-B009-7664C1B6FEEC,TCGA-OR-A5JA-01Z-00-DX1.368A5252-AD03-48EE-B356-FC1BF2E8FE6D,TCGA-OR-A5J2-01Z-00-DX1.02350C2F-1B2D-4195-8105-56E0AD3A3A66
+5,TCGA-OR-A5JP-01Z-00-DX1.15ED1958-011D-4247-91A3-99893466935D,,TCGA-OR-A5J9-01Z-00-DX1.178CB96D-045A-459A-9E41-0580F4E3EF42
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+9,TCGA-OR-A5JM-01Z-00-DX1.94A515FD-5AA8-410C-8F52-170A3BA94AB3,,
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+27,TCGA-OR-A5JV-01Z-00-DX1.3CFCEE78-A603-4FD9-9146-71C1CD44E019,,
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+30,TCGA-OR-A5K1-01Z-00-DX1.F9126763-FCA7-4F1D-8180-08EDE1C965A2,,
+31,TCGA-OR-A5K6-01Z-00-DX1.BA1BA159-1A51-4CB6-992B-5D6BF6D332E7,,
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splits_CHOL.csv

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splits_COAD.csv

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splits_KICH.csv

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splits_KIRC.csv

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