#!/usr/bin/env python3 """ MILK10k dataset utilities shared by training scripts. Keep dataframe construction and torch Dataset classes here; training scripts should build transforms/loaders and own model/training logic. """ from __future__ import annotations import os import random from pathlib import Path import numpy as np import pandas as pd import torch from PIL import Image, ImageFile from sklearn.model_selection import train_test_split from torch.utils.data import Dataset ImageFile.LOAD_TRUNCATED_IMAGES = True REQUIRED_DATA_FILES = ( "MILK10k_Training_GroundTruth.csv", "MILK10k_Training_Metadata.csv", "MILK10k_Training_Input", ) LABEL_COLUMNS = [ "AKIEC", "BCC", "BEN_OTH", "BKL", "DF", "INF", "MAL_OTH", "MEL", "NV", "SCCKA", "VASC", ] class Milk10kDataset(Dataset): def __init__(self, df: pd.DataFrame, label_to_idx: dict[str, int], transform=None) -> None: self.paths = df["path"].tolist() self.labels = [label_to_idx[label] for label in df["label"].tolist()] self.transform = transform def __len__(self) -> int: return len(self.paths) def __getitem__(self, idx: int) -> tuple[torch.Tensor, int]: with Image.open(self.paths[idx]) as img: img = img.convert("RGB") if self.transform is not None: img = self.transform(img) return img, self.labels[idx] class PairedMilk10kDataset(Dataset): def __init__(self, df: pd.DataFrame, label_to_idx: dict[str, int], transform=None) -> None: self.clinical_paths = df["clinical_path"].tolist() self.dermoscopic_paths = df["dermoscopic_path"].tolist() self.labels = [label_to_idx[label] for label in df["label"].tolist()] self.transform = transform def __len__(self) -> int: return len(self.labels) def _load_image(self, path: str) -> torch.Tensor: with Image.open(path) as img: img = img.convert("RGB") if self.transform is not None: img = self.transform(img) return img def __getitem__(self, idx: int) -> tuple[torch.Tensor, int]: clinical = self._load_image(self.clinical_paths[idx]) dermoscopic = self._load_image(self.dermoscopic_paths[idx]) return torch.stack([clinical, dermoscopic], dim=0), self.labels[idx] def set_seed(seed: int) -> None: os.environ["PYTHONHASHSEED"] = str(seed) random.seed(seed) np.random.seed(seed) torch.manual_seed(seed) torch.cuda.manual_seed_all(seed) torch.backends.cudnn.benchmark = True def normalize_image_type(image_type: str) -> str: if image_type == "clinical: close-up": return "clinical_close_up" return image_type.replace(" ", "_").replace(":", "").replace("-", "_") def has_milk10k_files(path: Path) -> bool: return all((path / name).exists() for name in REQUIRED_DATA_FILES) def resolve_data_dir(data_dir: Path | None) -> Path: if data_dir is not None: data_dir = data_dir.expanduser().resolve() if not has_milk10k_files(data_dir): expected = ", ".join(REQUIRED_DATA_FILES) raise FileNotFoundError(f"--data-dir={data_dir} does not contain required MILK10k files: {expected}") return data_dir candidates = [Path.cwd()] kaggle_input = Path("/kaggle/input") if kaggle_input.exists(): candidates.extend(path.parent for path in kaggle_input.rglob("MILK10k_Training_GroundTruth.csv")) seen = set() for candidate in candidates: candidate = candidate.resolve() if candidate in seen: continue seen.add(candidate) if has_milk10k_files(candidate): return candidate expected = ", ".join(REQUIRED_DATA_FILES) raise FileNotFoundError( f"Could not auto-detect MILK10k data dir. Pass --data-dir PATH containing: {expected}" ) def load_dataframe(data_dir: Path, image_type: str) -> pd.DataFrame: input_dir = data_dir / "MILK10k_Training_Input" gt = pd.read_csv(data_dir / "MILK10k_Training_GroundTruth.csv") meta = pd.read_csv(data_dir / "MILK10k_Training_Metadata.csv") gt["label"] = gt[LABEL_COLUMNS].idxmax(axis=1) df = meta.merge(gt[["lesion_id", "label"]], on="lesion_id", how="inner") df["image_type_norm"] = df["image_type"].map(normalize_image_type) if image_type != "all": df = df[df["image_type_norm"] == image_type].copy() df["path"] = df.apply(lambda r: input_dir / r["lesion_id"] / f"{r['isic_id']}.jpg", axis=1) df = df[df["path"].map(lambda p: p.exists())].copy() df["path"] = df["path"].map(str) if df.empty: raise ValueError(f"No images found for image_type={image_type!r} under {input_dir}") return df[["path", "label", "lesion_id", "isic_id", "image_type_norm"]] def to_paired_lesion_dataframe(df: pd.DataFrame) -> pd.DataFrame: clinical = ( df[df["image_type_norm"] == "clinical_close_up"][["lesion_id", "path"]] .rename(columns={"path": "clinical_path"}) .drop_duplicates("lesion_id") ) dermoscopic = ( df[df["image_type_norm"] == "dermoscopic"][["lesion_id", "path"]] .rename(columns={"path": "dermoscopic_path"}) .drop_duplicates("lesion_id") ) labels = df[["lesion_id", "label"]].drop_duplicates("lesion_id") paired = labels.merge(clinical, on="lesion_id", how="inner").merge(dermoscopic, on="lesion_id", how="inner") if paired.empty: raise ValueError("No paired clinical/dermoscopic lesions found.") return paired[["lesion_id", "label", "clinical_path", "dermoscopic_path"]] def lesion_level_train_val_split( df: pd.DataFrame, val_size: float, seed: int, ) -> tuple[pd.DataFrame, pd.DataFrame]: lesion_df = df[["lesion_id", "label"]].drop_duplicates("lesion_id") train_lesions, val_lesions = train_test_split( lesion_df, test_size=val_size, stratify=lesion_df["label"], random_state=seed, ) train_df = df[df["lesion_id"].isin(train_lesions["lesion_id"])].copy() val_df = df[df["lesion_id"].isin(val_lesions["lesion_id"])].copy() return train_df, val_df