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Thanks,\n\n## Credits: Eng Adam Al mohammedi, Baidalin, Adilzhan, CigarCat, Mattia Angeli, Khoa, samu2505 \n\n## siglep LB: 65 now: -\n\n## dinov3 Lb: 70 now: +","metadata":{}},{"cell_type":"code","source":"import os\nimport gc\nimport random\nimport warnings\nimport numpy as np\nimport pandas as pd\nimport cv2\nimport torch\nimport timm\nfrom PIL import Image\nfrom tqdm.auto import tqdm\nfrom pathlib import Path\nfrom copy import deepcopy\nfrom dataclasses import dataclass\n\n# Sklearn & Models\nfrom sklearn.preprocessing import StandardScaler\nfrom sklearn.decomposition import PCA\nfrom sklearn.cross_decomposition import PLSRegression\nfrom sklearn.mixture import GaussianMixture\nfrom sklearn.ensemble import GradientBoostingRegressor, HistGradientBoostingRegressor\nfrom sklearn.linear_model import Ridge\nfrom lightgbm import LGBMRegressor\nfrom catboost import CatBoostRegressor\nfrom transformers import AutoModel, AutoImageProcessor, AutoTokenizer\nimport torchvision.transforms as T\nfrom xgboost import XGBRegressor\n\nwarnings.filterwarnings('ignore')\nos.environ[\"TOKENIZERS_PARALLELISM\"] = \"false\"\n\n# =========================================================================================\n# 1. CONFIGURATION\n# =========================================================================================\n@dataclass\nclass Config:\n DATA_PATH: Path = Path(\"/kaggle/input/csiro-biomass/\")\n SPLIT_PATH: Path = Path(\"/kaggle/input/csiro-datasplit/csiro_data_split.csv\")\n \n SIGLIP_PATH: str = \"/kaggle/input/google-siglip-so400m-patch14-384/transformers/default/1\"\n DINO_WEIGHTS_DIR: str = '/kaggle/input/modelv3/pytorch/default/1/models_retrained'\n \n SEED: int = 42\n DEVICE: str = \"cuda\" if torch.cuda.is_available() else \"cpu\"\n \n PATCH_SIZE: int = 520\n OVERLAP: int = 16\n DINO_SIZE: int = 512\n \n TARGET_NAMES = ['Dry_Clover_g', 'Dry_Dead_g', 'Dry_Green_g', 'Dry_Total_g', 'GDM_g']\n TARGET_MAX = {\n \"Dry_Clover_g\": 71.7865, \"Dry_Dead_g\": 83.8407, \"Dry_Green_g\": 157.9836,\n \"Dry_Total_g\": 185.70, \"GDM_g\": 157.9836,\n }\n\ncfg = Config()\n\ndef seeding(SEED):\n np.random.seed(SEED)\n random.seed(SEED)\n os.environ['PYTHONHASHSEED'] = str(SEED)\n torch.manual_seed(SEED)\n if torch.cuda.is_available(): \n torch.cuda.manual_seed(SEED)\n torch.backends.cudnn.deterministic = True\n torch.backends.cudnn.benchmark = False\nseeding(cfg.SEED)\n\n# =========================================================================================\n# 2. DATA LOADING\n# =========================================================================================\ndef pivot_table(df: pd.DataFrame) -> pd.DataFrame:\n if 'target' in df.columns.tolist():\n df_pt = pd.pivot_table(df, values='target', index=['image_path', 'Sampling_Date', 'State', 'Species', 'Pre_GSHH_NDVI', 'Height_Ave_cm'], columns='target_name', aggfunc='mean').reset_index()\n else:\n df['target'] = 0\n df_pt = pd.pivot_table(df, values='target', index='image_path', columns='target_name', aggfunc='mean').reset_index()\n return df_pt\n\ndef melt_table(df: pd.DataFrame) -> pd.DataFrame:\n melted = df.melt(id_vars='image_path', value_vars=cfg.TARGET_NAMES, var_name='target_name', value_name='target')\n melted['sample_id'] = melted['image_path'].apply(lambda x: os.path.basename(x)).str.replace(r'\\.jpg$', '', regex=True).str.replace(r'\\.png$', '', regex=True) + '__' + melted['target_name']\n return melted[['sample_id', 'target']].sort_values(by='sample_id')\n\ndef post_process_biomass(df_preds):\n ordered_cols = [\"Dry_Green_g\", \"Dry_Clover_g\", \"Dry_Dead_g\", \"GDM_g\", \"Dry_Total_g\"]\n for c in ordered_cols:\n if c not in df_preds.columns: df_preds[c] = 0.0\n df_out = df_preds.copy()\n clover_threshold = 1.0 \n df_out['Dry_Clover_g'] = df_out['Dry_Clover_g'].apply(lambda x: x if x > clover_threshold else 0.0)\n df_out['GDM_g'] = df_out['Dry_Green_g'] + df_out['Dry_Clover_g']\n df_out['Dry_Total_g'] = df_out['GDM_g'] + df_out['Dry_Dead_g']\n df_out['Dry_Clover_g'] = df_out['Dry_Clover_g'].clip(lower=0.0)\n df_out['GDM_g'] = df_out['GDM_g'].clip(lower=0.0)\n df_out['Dry_Total_g'] = df_out['Dry_Total_g'].clip(lower=0.0)\n return df_out\n\nprint(\"Loading Data...\")\ntrain_df = pd.read_csv(cfg.SPLIT_PATH)\ncols_to_keep = [c for c in train_df.columns if not c.startswith('emb')]\ntrain_df = train_df[cols_to_keep]\nif not str(train_df['image_path'].iloc[0]).startswith('/'):\n train_df['image_path'] = train_df['image_path'].apply(lambda p: str(cfg.DATA_PATH / 'train' / os.path.basename(p)))\ntest_df_raw = pd.read_csv(cfg.DATA_PATH / 'test.csv')\ntest_df = pivot_table(test_df_raw)\ntest_df['image_path'] = test_df['image_path'].apply(lambda p: str(cfg.DATA_PATH / p))\n\n# =========================================================================================\n# 3. FEATURE EXTRACTION (SIGLIP + TTA)\n# =========================================================================================\ndef split_image(image, patch_size=520, overlap=16):\n h, w, c = image.shape\n stride = patch_size - overlap\n patches = []\n for y in range(0, h, stride):\n for x in range(0, w, stride):\n y2 = min(y + patch_size, h); x2 = min(x + patch_size, w)\n y1 = max(0, y2 - patch_size); x1 = max(0, x2 - patch_size)\n patches.append(image[y1:y2, x1:x2, :])\n return patches\n\ndef compute_siglip(df):\n print(f\"Computing SigLIP (TTA)...\")\n try:\n model = AutoModel.from_pretrained(cfg.SIGLIP_PATH, local_files_only=True).eval().to(cfg.DEVICE)\n processor = AutoImageProcessor.from_pretrained(cfg.SIGLIP_PATH, local_files_only=True)\n except: return np.zeros((len(df), 1152))\n EMBEDDINGS = []\n for _, row in tqdm(df.iterrows(), total=len(df)):\n try:\n img = cv2.imread(row['image_path'])\n img = cv2.cvtColor(img, cv2.COLOR_BGR2RGB)\n img_flip = cv2.flip(img, 1)\n batch_feats = []\n for curr_img in [img, img_flip]:\n patches = split_image(curr_img, patch_size=cfg.PATCH_SIZE, overlap=cfg.OVERLAP)\n images = [Image.fromarray(p) for p in patches]\n inputs = processor(images=images, return_tensors=\"pt\").to(cfg.DEVICE)\n with torch.no_grad():\n features = model.get_image_features(**inputs)\n batch_feats.append(features.mean(dim=0).cpu().numpy())\n EMBEDDINGS.append(np.mean(batch_feats, axis=0))\n except: EMBEDDINGS.append(np.zeros(1152))\n torch.cuda.empty_cache(); gc.collect()\n return np.stack(EMBEDDINGS)\n\ntr_sig = compute_siglip(train_df)\nte_sig = compute_siglip(test_df)\n\n# =========================================================================================\n# 4. FEATURE EXTRACTION (DINOv3 + TTA)\n# =========================================================================================\ndef get_dino_transforms(size):\n return T.Compose([\n T.Resize((size, size), interpolation=T.InterpolationMode.BICUBIC),\n T.ToTensor(),\n T.Normalize(mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225]),\n ])\n\ndef compute_dino_offline(df):\n print(f\"Computing DINO (TTA)...\")\n try:\n model = timm.create_model('vit_huge_plus_patch16_dinov3', pretrained=False, num_classes=0)\n weights_dir = Path(cfg.DINO_WEIGHTS_DIR)\n candidates = list(weights_dir.glob(\"*.bin\")) + list(weights_dir.glob(\"*.pth\"))\n if candidates:\n w_path = max(candidates, key=lambda p: p.stat().st_size)\n state_dict = torch.load(w_path, map_location='cpu')\n if 'model' in state_dict: state_dict = state_dict['model']\n elif 'state_dict' in state_dict: state_dict = state_dict['state_dict']\n model.load_state_dict(state_dict, strict=False)\n else: return np.zeros((len(df), 768))\n except: return np.zeros((len(df), 768))\n \n model.to(cfg.DEVICE).eval()\n transform = get_dino_transforms(cfg.DINO_SIZE)\n EMBEDDINGS = []\n for _, row in tqdm(df.iterrows(), total=len(df)):\n try:\n img = cv2.imread(row['image_path'])\n img = cv2.cvtColor(img, cv2.COLOR_BGR2RGB)\n img_flip = cv2.flip(img, 1)\n batch_feats = []\n for curr_img in [img, img_flip]:\n img_t = transform(Image.fromarray(curr_img)).unsqueeze(0).to(cfg.DEVICE)\n with torch.no_grad():\n feat = model(img_t)\n batch_feats.append(feat.cpu().numpy().flatten())\n EMBEDDINGS.append(np.mean(batch_feats, axis=0))\n except: EMBEDDINGS.append(np.zeros(768))\n torch.cuda.empty_cache(); gc.collect()\n return np.stack(EMBEDDINGS)\n\ntr_dino = compute_dino_offline(train_df)\nte_dino = compute_dino_offline(test_df)\n\n# =========================================================================================\n# 5. SEMANTIC FEATURES\n# =========================================================================================\ndef generate_semantic(image_embeddings_np):\n print(\"Generating Semantic Features...\")\n try:\n model = AutoModel.from_pretrained(cfg.SIGLIP_PATH, local_files_only=True).to(cfg.DEVICE)\n tokenizer = AutoTokenizer.from_pretrained(cfg.SIGLIP_PATH, local_files_only=True)\n except:\n return np.zeros((len(image_embeddings_np), 5))\n\n concept_groups = {\n \"bare\": [\"bare soil\", \"dirt ground\", \"sparse vegetation\", \"exposed earth\"],\n \"sparse\": [\"low density pasture\", \"thin grass\", \"short clipped grass\"],\n \"medium\": [\"average pasture cover\", \"medium height grass\", \"grazed pasture\"],\n \"dense\": [\"dense tall pasture\", \"thick grassy volume\", \"high biomass\", \"overgrown vegetation\"],\n \"green\": [\"lush green vibrant pasture\", \"photosynthesizing leaves\", \"fresh growth\"],\n \"dead\": [\"dry brown dead grass\", \"yellow straw\", \"senesced material\", \"standing hay\"],\n \"clover\": [\"white clover\", \"trifolium repens\", \"broadleaf legume\", \"clover flowers\"],\n \"grass\": [\"ryegrass\", \"blade-like leaves\", \"fescue\", \"grassy sward\"],\n \"mixed_sward\": [\"mixed grass and clover\", \"diverse pasture composition\"],\n \"monoculture\": [\"uniform grass species\", \"single type vegetation\"],\n \"shadows\": [\"shadows on grass\", \"sunlight and shade contrast\"],\n \"wet\": [\"wet grass\", \"dew on leaves\", \"rainy pasture\"],\n \"flowering\": [\"grass with seed heads\", \"flowering plants\"],\n \"flat\": [\"mowed grass\", \"closely cropped pasture\", \"flat lawn\", \"golf course grass\"],\n \"tufted\": [\"tufts of grass\", \"clumpy vegetation\", \"uneven grass height\", \"tussocks\"],\n \"lodged\": [\"lodged grass\", \"fallen grass\", \"grass matted down by wind or rain\"],\n \"standing_dead\": [\"standing dead grass\", \"dry stalks\", \"upright hay\"],\n \"litter_layer\": [\"ground litter\", \"decomposing plant material\", \"thatch layer\"],\n \"sunny\": [\"bright sunlight\", \"harsh lighting\", \"sunny day pasture\"],\n \"overcast\": [\"diffuse lighting\", \"cloudy day\", \"soft light\"],\n \"blur\": [\"blurry image\", \"out of focus grass\", \"motion blur\"],\n \"lucerne\": [\"lucerne\", \"alfalfa\", \"medicago sativa\"],\n \"chicory\": [\"chicory plant\", \"broad leaves\", \"cichorium intybus\"]\n }\n concept_vectors = {}\n with torch.no_grad():\n for name, prompts in concept_groups.items():\n inputs = tokenizer(prompts, padding=\"max_length\", return_tensors=\"pt\").to(cfg.DEVICE)\n emb = model.get_text_features(**inputs)\n emb = emb / emb.norm(p=2, dim=-1, keepdim=True)\n concept_vectors[name] = emb.mean(dim=0, keepdim=True)\n img_tensor = torch.tensor(image_embeddings_np, dtype=torch.float32).to(cfg.DEVICE)\n img_tensor = img_tensor / img_tensor.norm(p=2, dim=-1, keepdim=True)\n scores = {}\n for name, vec in concept_vectors.items():\n scores[name] = torch.matmul(img_tensor, vec.T).cpu().numpy().flatten()\n return pd.DataFrame(scores).values\n\nall_sig = np.vstack([tr_sig, te_sig])\nall_sem = generate_semantic(all_sig)\ntr_sem = all_sem[:len(train_df)]\nte_sem = all_sem[len(train_df):]\n\n# =========================================================================================\n# 6. DUAL-STREAM EMBEDDING ENGINE (双流引擎 - 核心改动)\n# =========================================================================================\nclass DualStreamEmbeddingEngine:\n \"\"\"\n 独立处理 SigLIP 和 DINO 流，分别降维后拼接。\n 防止 DINO 的大方差纹理噪声淹没 SigLIP 的语义信息。\n \"\"\"\n def __init__(self, n_pca_sig=0.95, n_pca_dino=0.90, n_pls=8, n_gmm=6, random_state=42):\n # Stream 1: SigLIP\n self.scaler_sig = StandardScaler()\n self.pca_sig = PCA(n_components=n_pca_sig, random_state=random_state)\n self.pls_sig = PLSRegression(n_components=n_pls, scale=False)\n self.gmm_sig = GaussianMixture(n_components=n_gmm, covariance_type='diag', random_state=random_state)\n \n # Stream 2: DINO (不需要 GMM，只提取纹理)\n self.scaler_dino = StandardScaler()\n self.pca_dino = PCA(n_components=n_pca_dino, random_state=random_state)\n self.pls_dino = PLSRegression(n_components=n_pls, scale=False)\n \n # Semantic\n self.sem_scaler = StandardScaler()\n self.pls_fitted_ = False\n\n def fit(self, X_sig, X_dino, y=None, X_semantic=None):\n # --- Fit SigLIP ---\n X_sig_s = self.scaler_sig.fit_transform(X_sig)\n self.pca_sig.fit(X_sig_s)\n self.gmm_sig.fit(X_sig_s)\n \n # --- Fit DINO ---\n X_dino_s = self.scaler_dino.fit_transform(X_dino)\n self.pca_dino.fit(X_dino_s)\n \n # --- Fit PLS (Supervised) ---\n if y is not None:\n self.pls_sig.fit(X_sig_s, y)\n self.pls_dino.fit(X_dino_s, y)\n self.pls_fitted_ = True\n \n # --- Fit Semantic ---\n if X_semantic is not None:\n self.sem_scaler.fit(X_semantic)\n \n return self\n\n def transform(self, X_sig, X_dino, X_semantic=None):\n # --- Transform SigLIP ---\n X_sig_s = self.scaler_sig.transform(X_sig)\n sig_feats = [\n self.pca_sig.transform(X_sig_s),\n self.gmm_sig.predict_proba(X_sig_s)\n ]\n if self.pls_fitted_:\n sig_feats.append(self.pls_sig.transform(X_sig_s))\n \n # --- Transform DINO ---\n X_dino_s = self.scaler_dino.transform(X_dino)\n dino_feats = [self.pca_dino.transform(X_dino_s)]\n if self.pls_fitted_:\n dino_feats.append(self.pls_dino.transform(X_dino_s))\n \n # --- Transform Semantic ---\n all_feats = sig_feats + dino_feats\n if X_semantic is not None:\n sem_norm = self.sem_scaler.transform(X_semantic)\n all_feats.append(sem_norm)\n \n # --- Late Fusion ---\n return np.hstack(all_feats)\n\n# =========================================================================================\n# 7. TRAINING LOOP WITH STACKING\n# =========================================================================================\n# 注意：这里不再预先 hstack，而是传入双流\nprint(f\"SigLIP Shape: {tr_sig.shape}, DINO Shape: {tr_dino.shape}\")\n\nparams_cat = {'iterations': 1900, 'learning_rate': 0.045, 'depth': 4, 'l2_leaf_reg': 0.56, 'random_strength': 0.045, 'bagging_temperature': 0.98, 'verbose': 0, 'random_state': 42, 'allow_writing_files': False, 'task_type': 'GPU' if torch.cuda.is_available() else 'CPU'}\nparams_gb = {'n_estimators': 1354, 'learning_rate': 0.010, 'max_depth': 3, 'subsample': 0.60, 'random_state': 42}\nparams_xgb = {'n_estimators': 2356, 'learning_rate': 0.012, 'max_depth': 4, 'subsample': 0.78, 'colsample_bytree': 0.541, 'reg_alpha': 0.0104, 'reg_lambda': 0.1755, 'random_state': 42, 'tree_method': 'hist'}\nparams_lgbm = {'n_estimators': 1492, 'learning_rate': 0.0064, 'num_leaves': 77, 'max_depth': 9, 'min_child_samples': 12, 'subsample': 0.779, 'colsample_bytree': 0.590, 'reg_alpha': 0.0604, 'reg_lambda': 0.0551, 'verbose': -1, 'random_state': 42, 'device': 'gpu' if torch.cuda.is_available() else 'cpu'}\nparams_hist = {'max_iter': 300, 'learning_rate': 0.05, 'max_depth': None, 'l2_regularization': 0.44, 'random_state': 42}\n\ndef cross_validate_stacking():\n target_max_arr = np.array([cfg.TARGET_MAX[t] for t in cfg.TARGET_NAMES], dtype=float)\n y_pred_final = np.zeros([len(test_df), len(cfg.TARGET_NAMES)], dtype=float)\n \n n_splits = int(train_df['fold'].nunique())\n if n_splits < 2: n_splits = 5\n \n # 初始化双流引擎\n # SigLIP 保留 95%，DINO 保留 90% (纹理信息冗余度高，可以多压一点)\n engine_base = DualStreamEmbeddingEngine(n_pca_sig=0.95, n_pca_dino=0.90, n_pls=8, n_gmm=6)\n \n for k in range(len(cfg.TARGET_NAMES)):\n target_name = cfg.TARGET_NAMES[k]\n print(f\"\\nTraining Target: {target_name}\")\n \n oof_train = np.zeros((len(train_df), 5)) \n test_preds_accum = np.zeros((len(test_df), 5))\n \n for fold in range(n_splits):\n tr_idx = train_df['fold'] != fold\n val_idx = train_df['fold'] == fold\n \n # 数据切分 (双流)\n sig_tr, sig_val = tr_sig[tr_idx], tr_sig[val_idx]\n dino_tr, dino_val = tr_dino[tr_idx], tr_dino[val_idx]\n sem_tr, sem_val = tr_sem[tr_idx], tr_sem[val_idx]\n \n y_tr_all = train_df.loc[tr_idx, cfg.TARGET_NAMES].values / target_max_arr\n y_tr_k = y_tr_all[:, k]\n \n # --- Engine Fit (双流) ---\n engine = deepcopy(engine_base)\n engine.fit(sig_tr, dino_tr, y=y_tr_all, X_semantic=sem_tr)\n \n # --- Transform ---\n X_tr_eng = engine.transform(sig_tr, dino_tr, sem_tr)\n X_val_eng = engine.transform(sig_val, dino_val, sem_val)\n X_te_eng = engine.transform(te_sig, te_dino, te_sem)\n \n # Stacking Base Models\n m1 = HistGradientBoostingRegressor(**params_hist).fit(X_tr_eng, y_tr_k)\n oof_train[val_idx, 0] = m1.predict(X_val_eng)\n test_preds_accum[:, 0] += m1.predict(X_te_eng)\n \n m2 = GradientBoostingRegressor(**params_gb).fit(X_tr_eng, y_tr_k)\n oof_train[val_idx, 1] = m2.predict(X_val_eng)\n test_preds_accum[:, 1] += m2.predict(X_te_eng)\n \n m3 = XGBRegressor(**params_xgb).fit(X_tr_eng, y_tr_k)\n oof_train[val_idx, 2] = m3.predict(X_val_eng)\n test_preds_accum[:, 2] += m3.predict(X_te_eng)\n \n m4 = CatBoostRegressor(**params_cat).fit(X_tr_eng, y_tr_k)\n oof_train[val_idx, 3] = m4.predict(X_val_eng)\n test_preds_accum[:, 3] += m4.predict(X_te_eng)\n \n m5 = LGBMRegressor(**params_lgbm).fit(X_tr_eng, y_tr_k)\n oof_train[val_idx, 4] = m5.predict(X_val_eng)\n test_preds_accum[:, 4] += m5.predict(X_te_eng)\n \n print(f\" Fold {fold} done. Feat Dim: {X_tr_eng.shape[1]}\")\n\n test_preds_avg = test_preds_accum / n_splits\n \n y_true_all = train_df[target_name].values / target_max_arr[k]\n \n # Ridge Alpha=1 (稍微激进一点，信任强模型)\n meta_model = Ridge(alpha=1.0, positive=True) \n meta_model.fit(oof_train, y_true_all)\n print(f\" Weights: {np.round(meta_model.coef_, 3)}\")\n \n final_k_pred = meta_model.predict(test_preds_avg)\n y_pred_final[:, k] = final_k_pred * target_max_arr[k]\n\n return y_pred_final\n\nfinal_preds = cross_validate_stacking()\n\n# =========================================================================================\n# 8. SUBMISSION\n# =========================================================================================\nprint(\"Generating Submission...\")\ntest_df[cfg.TARGET_NAMES] = final_preds\ntest_processed = post_process_biomass(test_df)\nsub_df = melt_table(test_processed)\n\nsub_df.to_csv(\"submission_siglip.csv\", index=False)\nprint(f\"✓ Submission Ready: {sub_df.shape}\")\nprint(sub_df.head())","metadata":{"trusted":true,"execution":{"iopub.status.busy":"2026-01-26T11:52:57.626402Z","iopub.execute_input":"2026-01-26T11:52:57.627121Z","iopub.status.idle":"2026-01-26T12:24:46.903266Z","shell.execute_reply.started":"2026-01-26T11:52:57.627072Z","shell.execute_reply":"2026-01-26T12:24:46.902389Z"}},"outputs":[],"execution_count":null},{"cell_type":"code","source":"%%writefile csiro_infer.py\nfrom PIL import Image\nimport pandas as pd\nimport numpy as np\nimport matplotlib.pyplot as plt\nfrom sklearn.model_selection import KFold, GroupKFold, StratifiedGroupKFold\nfrom tqdm.auto import tqdm\nimport torch\nimport torch.nn as nn\nimport torch.optim as optim\nfrom torch.optim import AdamW\nfrom transformers import get_cosine_schedule_with_warmup\n\nfrom torch.utils.data import Dataset, DataLoader\nfrom torchvision import transforms as T\n\nimport os\nfrom pathlib import Path\nimport timm\nimport warnings \n\nwarnings.filterwarnings('ignore')\ntqdm.pandas()\n\nclass RegressionDataset(Dataset):\n def __init__(self, data, transform=None):\n self.data = data\n self.transform = transform\n def __len__(self):\n return self.data.shape[0]\n\n def __getitem__(self, idx):\n item = self.data.iloc[idx]\n image = item.image\n targets = [item['Dry_Green_g'], item['Dry_Clover_g'], item['Dry_Dead_g']]\n width, height = image.size\n mid_point = width // 2\n left_image = image.crop((0, 0, mid_point, height))\n right_image = image.crop((mid_point, 0, width, height))\n\n if self.transform is not None:\n left_image = self.transform(left_image)\n right_image = self.transform(right_image)\n\n return left_image, right_image, targets\n\ndef get_test_dataloaders(data, image_size, batch_size):\n res = []\n for trans in [None, T.RandomHorizontalFlip(p=1.0), T.RandomVerticalFlip(p=1.0)]:\n transform = T.Compose([\n T.Resize(image_size),\n T.ToTensor(),\n T.Normalize(mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225])\n ])\n if trans:\n transform = T.Compose([\n T.Resize(image_size),\n trans,\n T.ToTensor(),\n T.Normalize(mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225])\n ])\n dataset = RegressionDataset(data, transform=transform)\n res.append(DataLoader(dataset, batch_size=batch_size, shuffle=False, num_workers=4))\n return res\n\n\nclass FiLM(nn.Module):\n def __init__(self, feat_dim):\n super().__init__()\n self.mlp = nn.Sequential(\n nn.Linear(feat_dim, feat_dim // 2), \n nn.ReLU(inplace=True), \n nn.Linear(feat_dim // 2, feat_dim * 2)\n )\n\n def forward(self, context):\n gamma_beta = self.mlp(context)\n return torch.chunk(gamma_beta, 2, dim=1)\n\nclass CSIROModelRegressor(nn.Module):\n def __init__(self, model_name, pretrained=True, num_classes=3, dropout=0.0, freeze_backbone=False):\n super().__init__()\n self.backbone = timm.create_model(model_name, pretrained=pretrained, num_classes=0, global_pool='avg')\n\n self.film = FiLM(self.backbone.num_features)\n\n self.dropout = nn.Dropout(dropout)\n\n def make_head():\n return nn.Sequential(\n nn.Linear(self.backbone.num_features * 2, 8),\n nn.ReLU(inplace=True),\n nn.Dropout(dropout),\n nn.Linear(8, 1),\n )\n\n self.head_green = make_head()\n self.head_clover = make_head()\n self.head_dead = make_head()\n\n self.softplus = nn.Softplus(beta=1.0)\n\n if freeze_backbone:\n for p in self.backbone.parameters():\n p.requires_grad = False\n\n\n def forward(self, left_img, right_img):\n left_feat = self.backbone(left_img)\n right_feat = self.backbone(right_img)\n\n context = (left_feat + right_feat) / 2\n gamma, beta = self.film(context)\n\n left_feat_modulated = left_feat * (1 + gamma) + beta\n right_feat_modulated = right_feat * (1 + gamma) + beta\n\n combined = torch.cat([left_feat_modulated, right_feat_modulated], dim=1)\n\n green = self.softplus(self.head_green(combined)) \n clover = self.softplus(self.head_clover(combined))\n dead = self.softplus(self.head_dead(combined)) \n\n logits = torch.cat([green, clover, dead], dim=1)\n\n return logits\n\ndef predict(model, dataloader, device):\n model.to(device)\n model.eval()\n\n all_outputs = []\n with torch.no_grad():\n for left_images, right_images, targets in dataloader:\n left_images = left_images.to(device)\n right_images = right_images.to(device)\n\n outputs = model(left_images, right_images)\n all_outputs.append(outputs.detach().cpu())\n\n outputs = torch.cat(all_outputs).numpy()\n return outputs\n\ndef predict_loaders(model, dataloaders, device):\n all_outputs = []\n for dataloader in dataloaders:\n outputs = predict(model, dataloader, device)\n all_outputs.append(outputs)\n avg_outputs = np.mean(all_outputs, axis=0)\n return avg_outputs\n\ndef predict_folds(dataloaders,models_dir):\n device = torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')\n\n all_preds = []\n for model_file in Path(models_dir).glob('*.pth'):\n model = CSIROModelRegressor(CFG.MODEL_NAME, pretrained=False, num_classes=3)\n model.load_state_dict(torch.load(model_file))\n preds = predict_loaders(model, dataloaders, device)\n all_preds.append(preds)\n\n avg_preds = np.mean(all_preds, axis=0)\n return avg_preds\n\n\nclass CFG:\n DATA_PATH=\"/kaggle/input/csiro-biomass/\"\n TEST_DATA_PATH=\"/kaggle/input/csiro-biomass/test.csv\"\n MODEL_NAME=\"vit_large_patch16_dinov3_qkvb\"\n MODELS_DIR ='/kaggle/input/modelv3/pytorch/default/1/models_retrained'\n IMG_SIZE=(512,512)\n\n\ntest_df = pd.read_csv(CFG.TEST_DATA_PATH)\n\ntest_df['target'] = 0.0\ntest_df[['sample_id_prefix', 'sample_id_suffix']] = test_df.sample_id.str.split('__', expand=True)\n\ntest_data_df = test_df.groupby(['sample_id_prefix', 'image_path']).apply(lambda df: df.set_index('target_name').target)\ntest_data_df.reset_index(inplace=True)\ntest_data_df.columns.name = None\n\ntest_data_df['image'] = test_data_df.image_path.progress_apply(lambda path: Image.open(CFG.DATA_PATH + path).convert('RGB'))\n\ntest_loaders = get_test_dataloaders(test_data_df, CFG.IMG_SIZE, 32)\npreds = predict_folds(test_loaders,models_dir=CFG.MODELS_DIR)\n\ntest_data_df[['Dry_Green_g', 'Dry_Clover_g', 'Dry_Dead_g']] = preds\ntest_data_df['Dry_Green_g'] = test_data_df['Dry_Green_g'].apply(lambda x: 0.0 if x < 0.09 else x)\ntest_data_df['Dry_Clover_g'] = test_data_df['Dry_Clover_g'].apply(lambda x: 0.0 if x < 0.09 else x)\ntest_data_df['Dry_Dead_g'] = test_data_df['Dry_Dead_g'].apply(lambda x: 0.0 if x < 0.09 else x)\ntest_data_df['Dry_Total_g'] = test_data_df.GDM_g + test_data_df.Dry_Dead_g\n\nTARGETS = ['Dry_Green_g', 'Dry_Dead_g', 'Dry_Clover_g', 'GDM_g', 'Dry_Total_g']\n\nsubmission_rows = []\nfor idx, row in test_data_df.iterrows():\n image_id = row['image_path'].split('/')[-1].replace('.jpg', '')\n \n for target_name in TARGETS:\n sample_id = f\"{image_id}__{target_name}\"\n prediction = row[target_name]\n \n # Post-processing\n if target_name == \"Dry_Clover_g\":\n prediction = prediction * 0.8\n elif target_name == \"Dry_Dead_g\":\n if prediction > 20:\n prediction *= 1.1\n elif prediction < 10:\n prediction *= 0.9\n \n submission_rows.append({\n 'sample_id': sample_id,\n 'target': prediction\n })\n\nsub_df = pd.DataFrame(submission_rows)\nsub_df.to_csv('submission_dinov2026.csv', index=False)\n\nprint(sub_df)","metadata":{"trusted":true,"execution":{"iopub.status.busy":"2026-01-26T12:26:02.132422Z","iopub.execute_input":"2026-01-26T12:26:02.132773Z","iopub.status.idle":"2026-01-26T12:26:02.141366Z","shell.execute_reply.started":"2026-01-26T12:26:02.132745Z","shell.execute_reply":"2026-01-26T12:26:02.140794Z"}},"outputs":[],"execution_count":null},{"cell_type":"code","source":"!python csiro_infer.py","metadata":{"trusted":true,"execution":{"iopub.status.busy":"2026-01-26T12:26:06.971512Z","iopub.execute_input":"2026-01-26T12:26:06.972108Z","iopub.status.idle":"2026-01-26T12:27:23.504943Z","shell.execute_reply.started":"2026-01-26T12:26:06.972082Z","shell.execute_reply":"2026-01-26T12:27:23.504008Z"}},"outputs":[],"execution_count":null},{"cell_type":"code","source":"import pandas as pd\nimport numpy as np\nimport os\n\n# =============================================================================\n# CONFIGURATION\n# =============================================================================\n# Weights for the ensemble (Must sum to 1.0)\n# Adjust based on which model had better local CV or Public LB score.\n# Example: If Siglip was better, give it 0.6.\nW_SIGLIP = 0.35\nW_DINO = 0.65\n\nFILES = {\n 'siglip': 'submission_siglip.csv',\n 'dino': 'submission_dinov2026.csv'\n}\n\nOUTPUT_FILE = 'submission72.csv'\n\n# Target definitions required for Mass Balance\nALL_TARGETS = ['Dry_Green_g', 'Dry_Clover_g', 'Dry_Dead_g', 'GDM_g', 'Dry_Total_g']\n\n# =============================================================================\n# HELPER FUNCTIONS\n# =============================================================================\n\ndef enforce_mass_balance(df_wide, fixed_clover=None):\n \"\"\"\n Applies Orthogonal Projection to enforce biological constraints:\n 1. Dry_Green_g + Dry_Clover_g = GDM_g\n 2. GDM_g + Dry_Dead_g = Dry_Total_g\n \n If fixed_clover is True, Dry_Clover_g is kept fixed and only other targets are adjusted.\n \n This finds the closest set of values to the predictions that satisfy \n the constraints (minimizing Euclidean distance modification).\n \"\"\"\n # 1. Ensure columns are in the specific order for the matrix math\n # Vector x = [Green, Clover, Dead, GDM, Total]\n ordered_cols = ['Dry_Green_g', 'Dry_Clover_g', 'Dry_Dead_g', 'GDM_g', 'Dry_Total_g']\n \n # Extract values: Shape (5, N_samples)\n Y = df_wide[ordered_cols].values.T\n \n if fixed_clover:\n # Keep Dry_Clover_g fixed, adjust only other targets\n # We have: Green + Clover_fixed = GDM, so GDM = Green + Clover_fixed\n # And: GDM + Dead = Total, so Total = GDM + Dead = Green + Clover_fixed + Dead\n # Extract fixed Clover values\n clover_fixed = Y[1, :].copy() # Dry_Clover_g is index 1\n # Adjust: GDM = Green + Clover_fixed\n Y[3, :] = Y[0, :] + clover_fixed # GDM_g\n # Adjust: Total = GDM + Dead = Green + Clover_fixed + Dead\n Y[4, :] = Y[3, :] + Y[2, :] # Dry_Total_g\n # Keep Green and Dead as is (or apply minimal adjustment if needed)\n # Clover stays fixed (already set)\n Y_reconciled = Y\n else:\n # Original method: adjust all targets\n # 2. Define Constraint Matrix C where Cx = 0\n # Eq 1: 1*Gr + 1*Cl + 0*De - 1*GDM + 0*Tot = 0\n # Eq 2: 0*Gr + 0*Cl + 1*De + 1*GDM - 1*Tot = 0\n C = np.array([\n [1, 1, 0, -1, 0],\n [0, 0, 1, 1, -1]\n ])\n \n # 3. Calculate Projection Matrix P = I - C^T * (C * C^T)^-1 * C\n C_T = C.T\n try:\n inv_CCt = np.linalg.inv(C @ C_T)\n P = np.eye(5) - C_T @ inv_CCt @ C\n except np.linalg.LinAlgError:\n # Fallback if singular (unlikely with this specific matrix)\n print(\"Warning: Singular matrix in projection. Skipping constraint enforcement.\")\n return df_wide\n\n # 4. Apply Projection\n Y_reconciled = P @ Y\n \n # 5. Transpose back to (N_samples, 5) and clip negatives\n Y_reconciled = Y_reconciled.T\n Y_reconciled = np.maximum(0, Y_reconciled) \n \n # 6. Update DataFrame\n df_out = df_wide.copy()\n df_out[ordered_cols] = Y_reconciled\n \n return df_out\n\ndef robust_ensemble(file_paths, weights):\n print(f\"--- Starting Ensemble ---\")\n print(f\"Weights: {weights}\")\n print(\"NOTE: Using DINO-only for Dry_Clover_g (better detection)\")\n \n dfs = []\n for name, path in file_paths.items():\n if not os.path.exists(path):\n raise FileNotFoundError(f\"Missing file: {path}\")\n \n # Read and sort by sample_id to ensure alignment\n df = pd.read_csv(path).sort_values('sample_id').reset_index(drop=True)\n dfs.append(df)\n print(f\"Loaded {name}: {len(df)} rows\")\n\n # 1. Check alignment\n base_ids = dfs[0]['sample_id']\n if not all(df['sample_id'].equals(base_ids) for df in dfs[1:]):\n raise ValueError(\"Sample IDs do not match between submission files!\")\n\n # 2. Split by target_name to handle Dry_Clover_g separately\n # Split sample_id into image_id and target_name\n dfs_split = []\n for df in dfs:\n df_split = df.copy()\n df_split[['image_id', 'target_name']] = df_split['sample_id'].str.rsplit('__', n=1, expand=True)\n dfs_split.append(df_split)\n \n # Get DINO and SigLIP dataframes (identify by order in file_paths)\n dino_idx = list(file_paths.keys()).index('dino')\n siglip_idx = list(file_paths.keys()).index('siglip')\n dino_df = dfs_split[dino_idx]\n siglip_df = dfs_split[siglip_idx]\n \n # 3. Separate targets: Dry_Clover_g uses DINO only, others use ensemble\n ensemble_results = []\n \n for target in ALL_TARGETS:\n # Filter for this target\n dino_target = dino_df[dino_df['target_name'] == target].copy()\n siglip_target = siglip_df[siglip_df['target_name'] == target].copy()\n \n if target == 'Dry_Clover_g':\n # Use DINO only for Clover\n print(f\"Using DINO-only for {target}\")\n ensemble_results.append(dino_target[['sample_id', 'target']])\n else:\n # Ensemble for other targets\n # Merge on sample_id to align\n merged = pd.merge(\n dino_target[['sample_id', 'target']].rename(columns={'target': 'dino_pred'}),\n siglip_target[['sample_id', 'target']].rename(columns={'target': 'siglip_pred'}),\n on='sample_id'\n )\n \n # Weighted average\n w_vec = np.array([weights['dino'], weights['siglip']])\n w_vec = w_vec / w_vec.sum()\n \n merged['target'] = merged['dino_pred'] * w_vec[0] + merged['siglip_pred'] * w_vec[1]\n ensemble_results.append(merged[['sample_id', 'target']])\n \n # 4. Combine all targets\n ensemble_df = pd.concat(ensemble_results, ignore_index=True)\n print(\"Weighted average complete (DINO-only for Clover).\")\n\n # 5. Prepare for Mass Balance (Convert Long -> Wide)\n ensemble_df[['image_id', 'target_name']] = ensemble_df['sample_id'].str.rsplit('__', n=1, expand=True)\n \n # Pivot\n wide_df = ensemble_df.pivot(index='image_id', columns='target_name', values='target').reset_index()\n\n # 6. Apply Robust Constraints (with Dry_Clover_g fixed)\n print(\"Applying Mass Balance Constraints (Dry_Clover_g fixed to DINO values)...\")\n wide_balanced = enforce_mass_balance(wide_df, fixed_clover=True)\n\n # 7. Convert back (Wide -> Long)\n long_balanced = wide_balanced.melt(\n id_vars='image_id', \n value_vars=ALL_TARGETS,\n var_name='target_name',\n value_name='target'\n )\n\n # Reconstruct sample_id\n long_balanced['sample_id'] = long_balanced['image_id'] + '__' + long_balanced['target_name']\n\n # 8. Final Formatting\n final_submission = long_balanced[['sample_id', 'target']].sort_values('sample_id').reset_index(drop=True)\n\n return final_submission\n\n# =============================================================================\n# EXECUTION\n# =============================================================================\nif __name__ == \"__main__\":\n \n # Define weights\n ensemble_weights = {\n 'siglip': W_SIGLIP,\n 'dino': W_DINO\n }\n \n try:\n # Run Ensemble\n submission = robust_ensemble(FILES, ensemble_weights)\n \n # Save\n submission.to_csv(OUTPUT_FILE, index=False)\n print(f\"\\nSuccess! Saved to {OUTPUT_FILE}\")\n print(submission.head())\n \n # Sanity Check Stats\n print(\"\\nStats:\")\n print(submission['target'].describe())\n \n except Exception as e:\n print(f\"\\nError during ensembling: {e}\")","metadata":{"trusted":true,"execution":{"iopub.status.busy":"2026-01-26T12:27:23.566551Z","iopub.execute_input":"2026-01-26T12:27:23.566758Z","iopub.status.idle":"2026-01-26T12:27:23.617003Z","shell.execute_reply.started":"2026-01-26T12:27:23.56674Z","shell.execute_reply":"2026-01-26T12:27:23.61651Z"}},"outputs":[],"execution_count":null},{"cell_type":"code","source":"# now import timm fresh\nimport timm, sys\nprint(\"python:\", sys.version)\nprint(\"timm:\", timm.__version__)\nprint(\"timm file:\", timm.__file__)\nprint(\"dinov3 matches:\", timm.list_models(\"*dinov3*\")[:50])\n","metadata":{"trusted":true,"execution":{"iopub.status.busy":"2026-01-26T12:28:09.311874Z","iopub.execute_input":"2026-01-26T12:28:09.312185Z","iopub.status.idle":"2026-01-26T12:28:09.31838Z","shell.execute_reply.started":"2026-01-26T12:28:09.312162Z","shell.execute_reply":"2026-01-26T12:28:09.317727Z"}},"outputs":[],"execution_count":null},{"cell_type":"code","source":"\n# Config\nimport os, gc, math, cv2, numpy as np, pandas as pd\nfrom tqdm import tqdm\nimport torch, torch.nn as nn, torch.optim as optim\nfrom torch.optim.lr_scheduler import LambdaLR\nfrom torch.utils.data import Dataset, DataLoader\nimport albumentations as A\nfrom albumentations.pytorch import ToTensorV2\nimport time\nfrom timm.utils import ModelEmaV2\nfrom sklearn.model_selection import KFold, StratifiedGroupKFold\nimport matplotlib.pyplot as plt\nimport seaborn as sns\n\ntorch.backends.cuda.matmul.allow_tf32 = True\ntorch.backends.cudnn.allow_tf32 = True\ntorch.backends.cudnn.benchmark = True\ntorch.set_float32_matmul_precision(\"high\")\n\nclass CFG:\n CREATE_SUBMISSION = True\n USE_TQDM = False\n PRETRAINED_DIR = None\n PRETRAINED = True\n BASE_PATH = '/kaggle/input/csiro-biomass'\n SEED = 82947501\n FOLDS_TO_TRAIN = [0,1,2,3,4]\n TRAIN_CSV = os.path.join(BASE_PATH, 'train.csv')\n TRAIN_IMAGE_DIR = os.path.join(BASE_PATH, 'train')\n TEST_IMAGE_DIR = '/kaggle/input/csiro-biomass/test'\n TEST_CSV = '/kaggle/input/csiro-biomass/test.csv'\n SUBMISSION_DIR = './'\n MODEL_DIR = '/kaggle/input/baseline-dinov3/pytorch/default/1/baseline-dinov3'\n N_FOLDS = 5\n\n MODEL_NAME = 'vit_huge_plus_patch16_dinov3.lvd1689m'\n BACKBONE_PATH = '/kaggle/input/vit-huge-plus-patch16-dinov3-lvd1689m/vit_huge_plus_patch16_dinov3.lvd1689m_backbone.pth'\n DINO_GRAD_CHECKPOINTING = False\n\n IMG_SIZE = 512\n\n VAL_TTA_TIMES = 1\n TTA_STEPS = 1\n \n \n BATCH_SIZE = 1\n GRAD_ACC = 4\n NUM_WORKERS = 4\n EPOCHS = 1\n FREEZE_EPOCHS = 0\n WARMUP_EPOCHS = 3\n LR_REST = 1e-3\n LR_BACKBONE = 5e-4\n WD = 1e-2\n EMA_DECAY = 0.9\n CLIP_GRAD_NORM = 1.0\n PATIENCE = 5\n TARGET_COLS = ['Dry_Total_g', 'GDM_g', 'Dry_Green_g']\n DERIVED_COLS = ['Dry_Clover_g', 'Dry_Dead_g']\n ALL_TARGET_COLS = ['Dry_Green_g','Dry_Dead_g','Dry_Clover_g','GDM_g','Dry_Total_g']\n R2_WEIGHTS = np.array([0.1, 0.1, 0.1, 0.2, 0.5])\n LOSS_WEIGHTS = np.array([0.1, 0.1, 0.1, 0.0, 0.0])\n DEVICE = torch.device('cuda' if torch.cuda.is_available() else 'cpu')\n\nos.makedirs(CFG.MODEL_DIR, exist_ok=True)\nprint(f'Device : {CFG.DEVICE}')\nprint(f'Backbone: {CFG.MODEL_NAME} | Input: {CFG.IMG_SIZE}')\nprint(f'Freeze Epochs: {CFG.FREEZE_EPOCHS} | Warmup: {CFG.WARMUP_EPOCHS}')\nprint(f'EMA Decay: {CFG.EMA_DECAY} | Grad Acc: {CFG.GRAD_ACC}')","metadata":{"execution":{"iopub.status.busy":"2026-01-26T12:28:11.67098Z","iopub.execute_input":"2026-01-26T12:28:11.671718Z","iopub.status.idle":"2026-01-26T12:28:44.400978Z","shell.execute_reply.started":"2026-01-26T12:28:11.671691Z","shell.execute_reply":"2026-01-26T12:28:44.40033Z"},"papermill":{"duration":37.523526,"end_time":"2026-01-05T05:09:15.453763","exception":false,"start_time":"2026-01-05T05:08:37.930237","status":"completed"},"tags":[],"trusted":true},"outputs":[],"execution_count":null},{"cell_type":"code","source":"# Metrics\ndef weighted_r2_score(y_true: np.ndarray, y_pred: np.ndarray):\n weights = CFG.R2_WEIGHTS\n r2_scores = []\n for i in range(y_true.shape[1]):\n yt = y_true[:, i]; yp = y_pred[:, i]\n ss_res = np.sum((yt - yp) ** 2)\n ss_tot = np.sum((yt - np.mean(yt)) ** 2)\n r2 = 1 - ss_res / ss_tot if ss_tot > 0 else 0.0\n r2_scores.append(r2)\n r2_scores = np.array(r2_scores)\n weighted = np.sum(r2_scores * weights) / np.sum(weights)\n return weighted, r2_scores\n\ndef weighted_r2_score_global(y_true: np.ndarray, y_pred: np.ndarray):\n weights = CFG.R2_WEIGHTS\n flat_true = y_true.reshape(-1)\n flat_pred = y_pred.reshape(-1)\n w = np.tile(weights, y_true.shape[0])\n mean_w = np.sum(w * flat_true) / np.sum(w)\n ss_res = np.sum(w * (flat_true - flat_pred) ** 2)\n ss_tot = np.sum(w * (flat_true - mean_w) ** 2)\n global_r2 = 1 - ss_res / ss_tot if ss_tot > 0 else 0.0\n avg_r2, per_r2 = weighted_r2_score(y_true, y_pred)\n return global_r2, avg_r2, per_r2\n\ndef analyze_errors(val_df, y_true, y_pred, targets, top_n=5):\n print(f'\\n--- Top {top_n} High Loss Samples per Target ---')\n y_true = np.array(y_true)\n y_pred = np.array(y_pred)\n \n for i, target in enumerate(targets):\n errors = np.abs(y_true[:, i] - y_pred[:, i])\n top_indices = np.argsort(errors)[::-1][:top_n]\n \n print(f'\\nTarget: {target}')\n print(f'{\"Index\":<6} | {\"Image Path\":<40} | {\"True\":<10} | {\"Pred\":<10} | {\"AbsErr\":<10}')\n print('-' * 90)\n \n for idx in top_indices:\n path = val_df.iloc[idx]['image_path']\n path_disp = os.path.basename(path)\n t_val = y_true[idx, i]\n p_val = y_pred[idx, i]\n err = errors[idx]\n print(f'{idx:<6} | {path_disp:<40} | {t_val:<10.4f} | {p_val:<10.4f} | {err:<10.4f}')\ndef analyze_errors(val_df, y_true, y_pred, targets, top_n=5):\n print(f'\\n--- Top {top_n} High Loss Samples per Target ---')\n y_true = np.array(y_true)\n y_pred = np.array(y_pred)\n \n for i, target in enumerate(targets):\n errors = np.abs(y_true[:, i] - y_pred[:, i])\n top_indices = np.argsort(errors)[::-1][:top_n]\n \n print(f'\\nTarget: {target}')\n header = f'{\"Index\":<6} | {\"Image Path\":<40} | {\"State\":<6} | {\"True\":<10} | {\"Pred\":<10} | {\"AbsErr\":<10}'\n print(header)\n print('-' * len(header))\n \n for idx in top_indices:\n path = val_df.iloc[idx]['image_path']\n path_disp = os.path.basename(path)\n state = val_df.iloc[idx]['State'] if 'State' in val_df.columns else 'NA'\n t_val = y_true[idx, i]\n p_val = y_pred[idx, i]\n err = errors[idx]\n print(f'{idx:<6} | {path_disp:<40} | {str(state):<6} | {t_val:<10.4f} | {p_val:<10.4f} | {err:<10.4f}')\ndef compare_train_val(tr_df, val_df, targets, show_plots=True):\n \"\"\"Quick comparison of target distributions and metadata between train and val splits.\"\"\"\n print(\"\\n--- Train / Val Comparison ---\")\n\n for t in targets:\n tr = tr_df.get(t, pd.Series(dtype=float)).dropna()\n val = val_df.get(t, pd.Series(dtype=float)).dropna()\n print(f\"\\nTarget: {t}\")\n print(f\" Train: n={len(tr)} mean={tr.mean():.3f} std={tr.std():.3f} min={tr.min():.3f} max={tr.max():.3f}\")\n print(f\" Val : n={len(val)} mean={val.mean():.3f} std={val.std():.3f} min={val.min():.3f} max={val.max():.3f}\")\n if show_plots:\n try:\n plt.figure(figsize=(6, 3))\n sns.kdeplot(tr, label='train', fill=True)\n sns.kdeplot(val, label='val', fill=True)\n plt.legend()\n plt.title(f'Distribution: {t}')\n plt.show()\n except Exception as e:\n print(' Could not plot distributions for', t, '-', e)\n\n # Compare Sampling_Date and State if present\n if 'Sampling_Date' in tr_df.columns:\n try:\n tr_dates = pd.to_datetime(tr_df['Sampling_Date'], errors='coerce')\n val_dates = pd.to_datetime(val_df['Sampling_Date'], errors='coerce')\n print(\"\\nSampling_Date range:\")\n print(f\" Train: {tr_dates.min()} -> {tr_dates.max()} (missing {tr_dates.isna().sum()})\")\n print(f\" Val : {val_dates.min()} -> {val_dates.max()} (missing {val_dates.isna().sum()})\")\n except Exception as e:\n print(' Could not parse Sampling_Date:', e)\n if 'State' in tr_df.columns:\n print(\"\\nState distribution (train vs val):\")\n tr_state = tr_df['State'].value_counts(normalize=True)\n val_state = val_df['State'].value_counts(normalize=True)\n state_df = pd.concat([tr_state, val_state], axis=1, keys=['train', 'val']).fillna(0)\n\n print(state_df)\n\n \ndef biomass_loss(outputs, labels, w=None):\n total, gdm, green, clover, dead = outputs\n mse = nn.MSELoss()\n huber = nn.SmoothL1Loss(beta=5.0) # Huber loss for robust regression (beta=5.0 as recommended)\n \n l_green = huber(green.squeeze(), labels[:,0])\n l_dead = huber(dead.squeeze(), labels[:,1]) # Use Huber loss for Dead\n l_clover = huber(clover.squeeze(), labels[:,2])\n l_gdm = huber(gdm.squeeze(), labels[:,3])\n l_total = huber(total.squeeze(), labels[:,4])\n\n # Stack per-target losses in the SAME order as CFG.ALL_TARGET_COLS\n losses = torch.stack([l_green, l_dead, l_clover, l_gdm, l_total])\n # losses = torch.stack([l_green, l_dead, l_clover])\n\n # Use provided weights, or default to CFG.R2_WEIGHTS\n if w is None:\n return losses.mean()\n w = torch.as_tensor(w, device=losses.device, dtype=losses.dtype)\n w = w / w.sum()\n return (losses * w).sum()","metadata":{"execution":{"iopub.status.busy":"2026-01-26T12:29:16.429402Z","iopub.execute_input":"2026-01-26T12:29:16.429709Z","iopub.status.idle":"2026-01-26T12:29:16.448496Z","shell.execute_reply.started":"2026-01-26T12:29:16.429686Z","shell.execute_reply":"2026-01-26T12:29:16.44788Z"},"papermill":{"duration":0.025723,"end_time":"2026-01-05T05:09:15.502256","exception":false,"start_time":"2026-01-05T05:09:15.476533","status":"completed"},"tags":[],"trusted":true},"outputs":[],"execution_count":null},{"cell_type":"code","source":"# Transforms\ndef get_train_transforms():\n return A.Compose([\n A.Resize(CFG.IMG_SIZE, CFG.IMG_SIZE),\n A.HorizontalFlip(p=0.5),\n A.VerticalFlip(p=0.5),\n A.RandomRotate90(p=0.5),\n A.Rotate(limit=(-10, 10), p=0.3, interpolation=cv2.INTER_LINEAR, border_mode=cv2.BORDER_REFLECT_101),\n A.ColorJitter(brightness=0.1, contrast=0.1, saturation=0.1, hue=0.05, p=0.5),\n A.Normalize(mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225]),\n ToTensorV2()\n ], p=1.0)\n\ndef get_val_transforms():\n return A.Compose([\n A.Resize(CFG.IMG_SIZE, CFG.IMG_SIZE),\n A.Normalize(mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225]),\n ToTensorV2()\n ], p=1.0)\n\ndef get_tta_transforms(mode=0):\n # mode 0: original\n # mode 1: hflip\n # mode 2: vflip\n # mode 3: rotate90\n transforms_list = [\n A.Resize(CFG.IMG_SIZE, CFG.IMG_SIZE),\n ]\n \n if mode == 1:\n transforms_list.append(A.HorizontalFlip(p=1.0))\n elif mode == 2:\n transforms_list.append(A.VerticalFlip(p=1.0))\n elif mode == 3:\n transforms_list.append(A.RandomRotate90(p=1.0)) # RandomRotate90 with p=1.0 rotates 90, 180, 270 randomly? \n # Albumentations RandomRotate90 rotates by 90, 180, 270. \n # Reference uses transforms.RandomRotation([90, 90]) which is exactly 90 degrees.\n # To match exactly 90 degrees in Albumentations, we might need Rotate(limit=(90,90), p=1.0)\n # But RandomRotate90 is standard TTA. Let's use Rotate(limit=(90,90)) to be precise if that's what reference does.\n # Reference: transforms.RandomRotation([90, 90]) -> rotates by exactly 90 degrees.\n transforms_list.append(A.Rotate(limit=(90, 90), p=1.0, interpolation=cv2.INTER_LINEAR, border_mode=cv2.BORDER_REFLECT_101))\n\n transforms_list.extend([\n A.Normalize(mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225]),\n ToTensorV2()\n ])\n \n return A.Compose(transforms_list, p=1.0)\ndef clean_image(img):\n # 1. Safe Crop (Remove artifacts at the bottom)\n h, w = img.shape[:2]\n # Cut bottom 10% where artifacts often appear\n img = img[0:int(h*0.90), :] \n\n # 2. Inpaint Date Stamp (Remove orange text)\n hsv = cv2.cvtColor(img, cv2.COLOR_RGB2HSV)\n # Define orange color range (adjust as needed)\n lower = np.array([5, 150, 150])\n upper = np.array([25, 255, 255])\n mask = cv2.inRange(hsv, lower, upper)\n\n # Dilate mask to cover text edges and reduce noise\n mask = cv2.dilate(mask, np.ones((3,3), np.uint8), iterations=2)\n\n # Inpaint if mask is not empty\n if np.sum(mask) > 0:\n img = cv2.inpaint(img, mask, 3, cv2.INPAINT_TELEA)\n\n return img\nclass BiomassDataset(Dataset):\n def __init__(self, df, transform, img_dir):\n self.df = df\n self.transform = transform\n self.img_dir = img_dir\n self.paths = df['image_path'].values\n self.labels = df[CFG.ALL_TARGET_COLS].values.astype(np.float32)\n\n def __len__(self):\n return len(self.df)\n\n def __getitem__(self, idx):\n path = os.path.join(self.img_dir, os.path.basename(self.paths[idx]))\n img = cv2.imread(path)\n if img is None:\n img = np.zeros((1000, 2000, 3), dtype=np.uint8)\n img = cv2.cvtColor(img, cv2.COLOR_BGR2RGB)\n img = clean_image(img)\n h, w, _ = img.shape\n mid = w // 2\n left = img[:, :mid]\n right = img[:, mid:]\n left = self.transform(image=left)['image']\n right = self.transform(image=right)['image']\n label = torch.from_numpy(self.labels[idx])\n return left, right, label","metadata":{"execution":{"iopub.status.busy":"2026-01-26T12:29:19.847213Z","iopub.execute_input":"2026-01-26T12:29:19.847518Z","iopub.status.idle":"2026-01-26T12:29:19.860827Z","shell.execute_reply.started":"2026-01-26T12:29:19.847494Z","shell.execute_reply":"2026-01-26T12:29:19.860142Z"},"papermill":{"duration":0.021348,"end_time":"2026-01-05T05:09:15.546114","exception":false,"start_time":"2026-01-05T05:09:15.524766","status":"completed"},"tags":[],"trusted":true},"outputs":[],"execution_count":null},{"cell_type":"code","source":"# Layers\nclass LocalMambaBlock(nn.Module):\n \"\"\"\n Lightweight Mamba-style block (Gated CNN) from the reference notebook.\n Efficiently mixes tokens with linear complexity.\n \"\"\"\n def __init__(self, dim, kernel_size=5, dropout=0.0):\n super().__init__()\n self.norm = nn.LayerNorm(dim)\n # Depthwise conv mixes spatial information locally\n self.dwconv = nn.Conv1d(dim, dim, kernel_size=kernel_size, padding=kernel_size // 2, groups=dim)\n self.gate = nn.Linear(dim, dim)\n self.proj = nn.Linear(dim, dim)\n self.drop = nn.Dropout(dropout)\n\n def forward(self, x):\n # x: (Batch, Tokens, Dim)\n shortcut = x\n x = self.norm(x)\n # Gating mechanism\n g = torch.sigmoid(self.gate(x))\n x = x * g\n # Spatial mixing via 1D Conv (requires transpose)\n x = x.transpose(1, 2) # -> (B, D, N)\n x = self.dwconv(x)\n x = x.transpose(1, 2) # -> (B, N, D)\n # Projection\n x = self.proj(x)\n x = self.drop(x)\n return shortcut + x\n","metadata":{"execution":{"iopub.status.busy":"2026-01-26T12:29:39.507637Z","iopub.execute_input":"2026-01-26T12:29:39.507942Z","iopub.status.idle":"2026-01-26T12:29:39.513941Z","shell.execute_reply.started":"2026-01-26T12:29:39.507918Z","shell.execute_reply":"2026-01-26T12:29:39.513363Z"},"papermill":{"duration":0.026162,"end_time":"2026-01-05T05:09:15.59418","exception":false,"start_time":"2026-01-05T05:09:15.568018","status":"completed"},"tags":[],"trusted":true},"outputs":[],"execution_count":null},{"cell_type":"code","source":"# Model\nclass BiomassModel(nn.Module):\n def __init__(self, model_name, pretrained=True, backbone_path=None):\n super().__init__()\n self.model_name = model_name\n self.backbone_path = backbone_path\n \n # 1. Load Backbone with global_pool='' to keep patch tokens\n # (B, 197, 1024) instead of (B, 1024)\n self.backbone = timm.create_model(self.model_name, pretrained=False, num_classes=0, global_pool='')\n \n # 2. Enable Gradient Checkpointing (Crucial for ViT-Large memory!)\n if hasattr(self.backbone, 'set_grad_checkpointing') and CFG.DINO_GRAD_CHECKPOINTING:\n self.backbone.set_grad_checkpointing(True)\n print(\"✓ Gradient Checkpointing enabled (saves ~50% VRAM)\")\n \n nf = self.backbone.num_features\n \n # 3. Mamba Fusion Neck\n # Mixes the concatenated tokens [Left, Right]\n self.fusion = nn.Sequential(\n LocalMambaBlock(nf, kernel_size=5, dropout=0.1),\n LocalMambaBlock(nf, kernel_size=5, dropout=0.1)\n )\n \n # 4. Pooling & Heads\n self.pool = nn.AdaptiveAvgPool1d(1)\n \n # Heads (using the same logic as before, but on fused features)\n self.head_green_raw = nn.Sequential(\n nn.Linear(nf, nf//2), nn.GELU(), nn.Dropout(0.2), \n nn.Linear(nf//2, 1), nn.Softplus()\n )\n self.head_clover_raw = nn.Sequential(\n nn.Linear(nf, nf//2), nn.GELU(), nn.Dropout(0.2), \n nn.Linear(nf//2, 1), nn.Softplus()\n )\n self.head_dead_raw = nn.Sequential(\n nn.Linear(nf, nf//2), nn.GELU(), nn.Dropout(0.2), \n nn.Linear(nf//2, 1), nn.Softplus()\n )\n \n if pretrained:\n self.load_pretrained()\n \n def load_pretrained(self):\n try:\n # Load weights normally\n if self.backbone_path and os.path.exists(self.backbone_path):\n print(f\"Loading backbone weights from local file: {self.backbone_path}\")\n sd = torch.load(self.backbone_path, map_location='cpu')\n # Handle common checkpoint wrappers (e.g. if saved with 'model' key)\n if 'model' in sd: sd = sd['model']\n elif 'state_dict' in sd: sd = sd['state_dict']\n else:\n # Original behavior: Download from internet\n print(\"Downloading backbone weights...\")\n sd = timm.create_model(self.model_name, pretrained=True, num_classes=0, global_pool='').state_dict()\n \n # Interpolate pos_embed if needed (for 256x256 vs 224x224)\n if 'pos_embed' in sd and hasattr(self.backbone, 'pos_embed'):\n pe_ck = sd['pos_embed']\n pe_m = self.backbone.pos_embed\n if pe_ck.shape != pe_m.shape:\n print(f\"Interpolating pos_embed: {pe_ck.shape} -> {pe_m.shape}\")\n # (Simple interpolation logic here or rely on timm's load if strict=False handles it well enough)\n # For robust interpolation, use the snippet provided in previous turn\n \n self.backbone.load_state_dict(sd, strict=False)\n print('Pretrained weights loaded.')\n except Exception as e:\n print(f'Warning: pretrained load failed: {e}')\n \n def forward(self, left, right):\n # 1. Extract Tokens (B, N, D)\n # Note: ViT usually returns [CLS, Patch1, Patch2...]\n # We remove CLS token for spatial mixing, or keep it. Let's keep it.\n x_l = self.backbone(left)\n x_r = self.backbone(right)\n \n # 2. Concatenate Left and Right tokens along sequence dimension\n # (B, N, D) + (B, N, D) -> (B, 2N, D)\n x_cat = torch.cat([x_l, x_r], dim=1)\n \n # 3. Apply Mamba Fusion\n # This allows tokens from Left image to interact with tokens from Right image\n x_fused = self.fusion(x_cat)\n \n # 4. Global Pooling\n # (B, 2N, D) -> (B, D, 2N) -> (B, D, 1) -> (B, D)\n x_pool = self.pool(x_fused.transpose(1, 2)).flatten(1)\n \n # 5. Prediction Heads\n green = self.head_green_raw(x_pool)\n clover = self.head_clover_raw(x_pool)\n dead = self.head_dead_raw(x_pool)\n \n # Summation logic\n gdm = green + clover\n total = gdm + dead\n \n return total, gdm, green, clover, dead\n \n\n","metadata":{"trusted":true,"execution":{"iopub.status.busy":"2026-01-26T12:29:42.544548Z","iopub.execute_input":"2026-01-26T12:29:42.545249Z","iopub.status.idle":"2026-01-26T12:29:42.556666Z","shell.execute_reply.started":"2026-01-26T12:29:42.545224Z","shell.execute_reply":"2026-01-26T12:29:42.55599Z"}},"outputs":[],"execution_count":null},{"cell_type":"code","source":"# Utility Functions\ndef set_backbone_requires_grad(model: BiomassModel, requires_grad: bool):\n for p in model.backbone.parameters():\n p.requires_grad = requires_grad\n\n\ndef build_optimizer(model: BiomassModel):\n # 1. Get backbone parameter IDs for exclusion\n backbone_ids = {id(p) for p in model.backbone.parameters()}\n \n # 2. Separate params into backbone vs. everything else (heads, fusion, etc.)\n backbone_params = []\n rest_params = []\n \n for p in model.parameters():\n if p.requires_grad:\n if id(p) in backbone_ids:\n backbone_params.append(p)\n else:\n rest_params.append(p)\n \n return optim.AdamW([\n {'params': backbone_params, 'lr': CFG.LR_BACKBONE, 'weight_decay': CFG.WD},\n {'params': rest_params, 'lr': CFG.LR_REST, 'weight_decay': CFG.WD},\n])\n\ndef build_scheduler(optimizer):\n def lr_lambda(epoch):\n e = max(0, epoch - 1)\n if e < CFG.WARMUP_EPOCHS:\n return float(e + 1) / float(max(1, CFG.WARMUP_EPOCHS))\n progress = (e - CFG.WARMUP_EPOCHS) / float(max(1, CFG.EPOCHS - CFG.WARMUP_EPOCHS))\n return 0.5 * (1.0 + math.cos(math.pi * progress))\n return LambdaLR(optimizer, lr_lambda)","metadata":{"trusted":true,"execution":{"iopub.status.busy":"2026-01-26T12:29:50.416683Z","iopub.execute_input":"2026-01-26T12:29:50.417253Z","iopub.status.idle":"2026-01-26T12:29:50.423859Z","shell.execute_reply.started":"2026-01-26T12:29:50.417226Z","shell.execute_reply":"2026-01-26T12:29:50.423111Z"}},"outputs":[],"execution_count":null},{"cell_type":"code","source":"# Training and Validation Loops \n\nfrom contextlib import nullcontext\n\nUSE_BF16 = True\nAMP_DTYPE = torch.bfloat16 if USE_BF16 else torch.float16\n\nscaler = torch.amp.GradScaler(\n 'cuda',\n enabled=(torch.cuda.is_available() and AMP_DTYPE == torch.float16)\n)\n\ndef autocast_ctx():\n if not torch.cuda.is_available():\n return nullcontext()\n return torch.amp.autocast(device_type='cuda', dtype=AMP_DTYPE)\n\ndef _as_col(x: torch.Tensor, bs: int) -> torch.Tensor:\n \"\"\"Force predictions to (B,1) regardless of model head returning (B,) or (B,1).\"\"\"\n if x.ndim == 1:\n return x.view(bs, 1)\n if x.ndim == 2:\n return x\n return x.view(bs, 1)\n\ndef _ensure_2d_lab(lab: torch.Tensor, bs: int) -> torch.Tensor:\n \"\"\"Force labels to (B,T).\"\"\"\n if lab.ndim == 1:\n return lab.view(bs, -1)\n return lab\n\ndef _pred_pack(p_total, p_gdm, p_green, p_clover, p_dead, bs: int) -> torch.Tensor:\n \"\"\"\n Pack predictions in the exact order expected by your metric:\n CFG.ALL_TARGET_COLS = ['Dry_Green_g','Dry_Dead_g','Dry_Clover_g','GDM_g','Dry_Total_g']\n \"\"\"\n pg = _as_col(p_green, bs)\n pd = _as_col(p_dead, bs)\n pc = _as_col(p_clover, bs)\n pgdm = _as_col(p_gdm, bs)\n pt = _as_col(p_total, bs)\n return torch.cat([pg, pd, pc, pgdm, pt], dim=1) # (B,5)\n\n@torch.inference_mode()\ndef valid_epoch(eval_model, loader, device):\n eval_model.eval()\n\n n = len(loader.dataset)\n n_targets = len(CFG.ALL_TARGET_COLS)\n\n preds_cpu = torch.empty((n, n_targets), dtype=torch.float32)\n labels_cpu = torch.empty((n, n_targets), dtype=torch.float32)\n\n total_loss = 0.0\n offset = 0\n\n for l, r, lab in loader:\n bs = l.size(0)\n l = l.to(device, non_blocking=True)\n r = r.to(device, non_blocking=True)\n lab = lab.to(device, non_blocking=True)\n\n with autocast_ctx():\n p_total, p_gdm, p_green, p_clover, p_dead = eval_model(l, r)\n loss = biomass_loss((p_total, p_gdm, p_green, p_clover, p_dead),\n lab, w=CFG.LOSS_WEIGHTS)\n\n total_loss += loss.detach().float().item() * bs\n\n batch_pred = _pred_pack(p_total, p_gdm, p_green, p_clover, p_dead, bs).float().cpu()\n batch_lab = _ensure_2d_lab(lab, bs).float().cpu()\n\n # Safety: ensure dims match (avoids silent 4/5 bugs)\n if batch_pred.shape[1] != n_targets or batch_lab.shape[1] != n_targets:\n raise RuntimeError(\n f\"Target dim mismatch: pred={batch_pred.shape}, lab={batch_lab.shape}, \"\n f\"CFG.ALL_TARGET_COLS={n_targets}\"\n )\n\n preds_cpu[offset:offset+bs] = batch_pred\n labels_cpu[offset:offset+bs] = batch_lab\n offset += bs\n\n pred_all = preds_cpu.numpy()\n true_labels = labels_cpu.numpy()\n global_r2, avg_r2, per_r2 = weighted_r2_score_global(true_labels, pred_all)\n\n return total_loss / n, global_r2, avg_r2, per_r2, pred_all, true_labels\n\n\n@torch.inference_mode()\ndef valid_epoch_tta(eval_model, loaders, device):\n \"\"\"\n Fixed: always accumulate (N,5). Works even if a head outputs (B,1).\n Assumes each loader iterates in identical order (shuffle=False).\n \"\"\"\n eval_model.eval()\n assert len(loaders) > 0\n\n n = len(loaders[0].dataset)\n n_targets = len(CFG.ALL_TARGET_COLS)\n\n labels_cpu = torch.empty((n, n_targets), dtype=torch.float32)\n preds_sum = torch.zeros((n, n_targets), dtype=torch.float32)\n\n total_loss = 0.0\n\n for tta_i, loader in enumerate(loaders):\n offset = 0\n tta_loss = 0.0\n\n for l, r, lab in loader:\n bs = l.size(0)\n l = l.to(device, non_blocking=True)\n r = r.to(device, non_blocking=True)\n lab = lab.to(device, non_blocking=True)\n\n with autocast_ctx():\n p_total, p_gdm, p_green, p_clover, p_dead = eval_model(l, r)\n loss = biomass_loss((p_total, p_gdm, p_green, p_clover, p_dead),\n lab, w=CFG.LOSS_WEIGHTS)\n\n tta_loss += loss.detach().float().item() * bs\n\n batch_pred = _pred_pack(p_total, p_gdm, p_green, p_clover, p_dead, bs).float().cpu()\n preds_sum[offset:offset+bs] += batch_pred\n\n if tta_i == 0:\n batch_lab = _ensure_2d_lab(lab, bs).float().cpu()\n if batch_lab.shape[1] != n_targets:\n raise RuntimeError(f\"Label dim mismatch: {batch_lab.shape} vs {n_targets}\")\n labels_cpu[offset:offset+bs] = batch_lab\n\n offset += bs\n\n total_loss += tta_loss / n\n\n avg_preds = (preds_sum / len(loaders)).numpy()\n true_labels = labels_cpu.numpy()\n global_r2, avg_r2, per_r2 = weighted_r2_score_global(true_labels, avg_preds)\n\n return total_loss / len(loaders), global_r2, avg_r2, per_r2, avg_preds, true_labels\n\n\ndef train_epoch(model, loader, opt, scheduler, device, ema: ModelEmaV2 | None = None):\n model.train()\n running = 0.0\n\n opt.zero_grad(set_to_none=True)\n itera = tqdm(loader, desc='train', leave=False) if CFG.USE_TQDM else loader\n\n for i, (l, r, lab) in enumerate(itera):\n bs = l.size(0)\n l = l.to(device, non_blocking=True)\n r = r.to(device, non_blocking=True)\n lab = lab.to(device, non_blocking=True)\n\n with autocast_ctx():\n p_total, p_gdm, p_green, p_clover, p_dead = model(l, r)\n loss = biomass_loss((p_total, p_gdm, p_green, p_clover, p_dead),\n lab, w=CFG.LOSS_WEIGHTS)\n loss = loss / CFG.GRAD_ACC\n\n\n if not torch.isfinite(loss):\n print(\"Non-finite loss detected; skipping batch\")\n opt.zero_grad(set_to_none=True)\n continue\n\n if scaler.is_enabled():\n scaler.scale(loss).backward()\n else:\n loss.backward()\n\n running += loss.detach().float().item() * bs * CFG.GRAD_ACC\n\n do_step = ((i + 1) % CFG.GRAD_ACC == 0) or ((i + 1) == len(loader))\n if do_step:\n if scaler.is_enabled():\n scaler.unscale_(opt)\n torch.nn.utils.clip_grad_norm_(model.parameters(), 1.0)\n scaler.step(opt)\n scaler.update()\n else:\n torch.nn.utils.clip_grad_norm_(model.parameters(), 1.0)\n opt.step()\n\n if ema is not None:\n ema.update(model.module if hasattr(model, \"module\") else model)\n\n opt.zero_grad(set_to_none=True)\n\n scheduler.step()\n return running / len(loader.dataset)\n","metadata":{"execution":{"iopub.status.busy":"2026-01-26T12:29:52.59575Z","iopub.execute_input":"2026-01-26T12:29:52.596027Z","iopub.status.idle":"2026-01-26T12:29:52.6168Z","shell.execute_reply.started":"2026-01-26T12:29:52.596005Z","shell.execute_reply":"2026-01-26T12:29:52.6161Z"},"papermill":{"duration":0.048482,"end_time":"2026-01-05T05:09:15.664902","exception":false,"start_time":"2026-01-05T05:09:15.61642","status":"completed"},"tags":[],"trusted":true},"outputs":[],"execution_count":null},{"cell_type":"code","source":"# # === MAIN TRAINING LOOP === #\n\n# # Helper for accurate GPU timings\n# def _sync():\n# if torch.cuda.is_available():\n# torch.cuda.synchronize()\n\n# print('Loading data...')\n# df_long = pd.read_csv(CFG.TRAIN_CSV)\n\n# df_wide = (\n# df_long.pivot(index='image_path', columns='target_name', values='target')\n# .reset_index()\n# )\n# assert df_wide['image_path'].is_unique, 'Leakage risk: duplicate image_path rows'\n\n# # Merge metadata (Sampling_Date, State) for stratification\n# if 'Sampling_Date' in df_long.columns and 'State' in df_long.columns:\n# print('Merging metadata for stratification...')\n# meta_df = df_long[['image_path', 'Sampling_Date', 'State']].drop_duplicates()\n# df_wide = df_wide.merge(meta_df, on='image_path', how='left')\n\n# # Keep necessary columns\n# df_wide = df_wide[['image_path', 'Sampling_Date', 'State'] + CFG.ALL_TARGET_COLS]\n# print(f'{len(df_wide)} training images')\n\n# # Use StratifiedGroupKFold\n# sgkf = StratifiedGroupKFold(n_splits=CFG.N_FOLDS, shuffle=True, random_state=CFG.SEED)\n# oof_true, oof_pred, fold_summary = [], [], []\n\n# # Split based on groups (Sampling_Date) and stratification target (State)\n# groups = df_wide['Sampling_Date']\n# y_stratify = df_wide['State']\n\n# # One place for loader kwargs (fast)\n# DL_KW = dict(\n# num_workers=CFG.NUM_WORKERS,\n# pin_memory=True,\n# persistent_workers=(CFG.NUM_WORKERS > 0),\n# prefetch_factor=4 if CFG.NUM_WORKERS > 0 else None,\n# )\n\n# for fold, (tr_idx, val_idx) in enumerate(sgkf.split(df_wide, y_stratify, groups=groups)):\n# if fold not in CFG.FOLDS_TO_TRAIN:\n# print(f'Skipping fold {fold} as per configuration.')\n# continue\n\n# print('\\n' + '='*70)\n# print(f'FOLD {fold+1}/{CFG.N_FOLDS} | {len(tr_idx)} train / {len(val_idx)} val')\n# print('='*70)\n\n# # NOTE: avoid empty_cache/gc inside epoch loop; only between folds if you really want\n# _sync()\n# torch.cuda.empty_cache()\n# gc.collect()\n\n# tr_df = df_wide.iloc[tr_idx].reset_index(drop=True)\n# val_df = df_wide.iloc[val_idx].reset_index(drop=True)\n\n# tr_set = BiomassDataset(tr_df, get_train_transforms(), CFG.TRAIN_IMAGE_DIR)\n\n# # Create TTA loaders (keep TTAs as requested)\n# val_loaders = []\n# for mode in range(CFG.VAL_TTA_TIMES): # 0: orig, 1: hflip, 2: vflip, 3: rot90\n# val_set_tta = BiomassDataset(val_df, get_tta_transforms(mode), CFG.TRAIN_IMAGE_DIR)\n# val_loader_tta = DataLoader(\n# val_set_tta,\n# batch_size=CFG.BATCH_SIZE,\n# shuffle=False,\n# drop_last=False,\n# **{k: v for k, v in DL_KW.items() if v is not None},\n# )\n# val_loaders.append(val_loader_tta)\n\n# tr_loader = DataLoader(\n# tr_set,\n# batch_size=CFG.BATCH_SIZE,\n# shuffle=True,\n# drop_last=True,\n# **{k: v for k, v in DL_KW.items() if v is not None},\n# )\n\n# print('Building model...')\n# backbone_path = getattr(CFG, 'BACKBONE_PATH', None)\n# model = BiomassModel(CFG.MODEL_NAME, pretrained=CFG.PRETRAINED, backbone_path=backbone_path).to(CFG.DEVICE)\n\n# # Load pretrained fold weights if available (for resuming or fine-tuning)\n# if getattr(CFG, 'PRETRAINED_DIR', None) and os.path.isdir(CFG.PRETRAINED_DIR):\n# pretrained_path = os.path.join(CFG.PRETRAINED_DIR, f'best_model_fold{fold}.pth')\n# if os.path.exists(pretrained_path):\n# try:\n# state = torch.load(pretrained_path, map_location='cpu')\n# if isinstance(state, dict) and ('model_state_dict' in state or 'state_dict' in state):\n# key = 'model_state_dict' if 'model_state_dict' in state else 'state_dict'\n# sd = state[key]\n# else:\n# sd = state\n# model.load_state_dict(sd, strict=False)\n# model.to(CFG.DEVICE)\n# print(f' ✓ Loaded pretrained weights for fold {fold} from {pretrained_path}')\n# except Exception as e:\n# print(f' ✗ Failed to load pretrained fold {fold}: {e}')\n# else:\n# print(f' (No pretrained file for fold {fold} at {pretrained_path})')\n# else:\n# print(' (No PRETRAINED_DIR configured or directory missing)')\n\n# # Single GPU: DO NOT wrap in DataParallel\n# # model = nn.DataParallel(model) # <-- removed\n\n# # Freeze/unfreeze backbone\n# set_backbone_requires_grad(model, False)\n\n# optimizer = build_optimizer(model)\n# scheduler = build_scheduler(optimizer)\n\n# # EMA on the real model\n# ema = ModelEmaV2(model, decay=CFG.EMA_DECAY)\n\n# best_global_r2 = -np.inf\n# best_avg_r2 = -np.inf\n# patience = 0\n# best_fold_preds = None\n# best_fold_true = None\n\n# save_path = os.path.join(CFG.MODEL_DIR, f'best_model_fold{fold}.pth')\n\n# for epoch in range(1, CFG.EPOCHS + 1):\n# if epoch == CFG.FREEZE_EPOCHS + 1:\n# patience = 0\n# set_backbone_requires_grad(model, True)\n# print(f'Epoch {epoch}: backbone unfrozen')\n\n# # ---- Train timing ----\n# _sync()\n# t0 = time.perf_counter()\n# tr_loss = train_epoch(model, tr_loader, optimizer, scheduler, CFG.DEVICE, ema)\n# _sync()\n# t1 = time.perf_counter()\n\n# # choose eval model (EMA weights)\n# eval_model = ema.module if ema is not None else model\n\n# # ---- Val timing (TTA) ----\n# _sync()\n# t2 = time.perf_counter()\n# val_loss, global_r2, avg_r2, per_r2, preds_fold, true_fold = valid_epoch_tta(eval_model, val_loaders, CFG.DEVICE)\n# _sync()\n# t3 = time.perf_counter()\n\n# time_tr = t1 - t0\n# time_val = t3 - t2\n# time_ep = t3 - t0\n\n# per_r2_str = ' | '.join([f'{CFG.ALL_TARGET_COLS[i][:5]}: {r2:.3f}' for i, r2 in enumerate(per_r2)])\n# lrs = [pg['lr'] for pg in optimizer.param_groups]\n# lr_str = ' '.join([f'lr{i}={lr:.3e}' for i, lr in enumerate(lrs)])\n\n# print(\n# f'Fold {fold} | Epoch {epoch:02d} | '\n# f'TLoss {tr_loss:.5f} | VLoss {val_loss:.5f} | '\n# f'avgR2 {avg_r2:.4f} | GlobalR² {global_r2:.4f} '\n# f'{\"[BEST]\" if global_r2 > best_global_r2 else \"\"} | '\n# f'{lr_str} | time_tr={time_tr:.1f}s time_val={time_val:.1f}s time_ep={time_ep:.1f}s'\n# )\n# print(f' → {per_r2_str}')\n\n# if global_r2 > best_global_r2:\n# best_global_r2 = global_r2\n# best_avg_r2 = avg_r2\n\n# # Save EMA weights directly (no CPU clone) for speed\n# # NOTE: safest is to save state_dict tensors as-is; this is typically fine on DGX.\n# torch.save(eval_model.state_dict(), save_path)\n# print(f' → SAVED EMA weights to {save_path} (GlobalR²: {best_global_r2:.4f})')\n\n# patience = 0\n# best_fold_preds = preds_fold\n# best_fold_true = true_fold\n# else:\n# patience += 1\n# if patience >= CFG.PATIENCE:\n# print(f' → EARLY STOP (no improvement in {CFG.PATIENCE} epochs)')\n# break\n\n# # keep memory tidy but avoid heavy cache/gc churn\n# del preds_fold, true_fold\n\n# if best_fold_preds is not None:\n# oof_true.append(best_fold_true)\n# oof_pred.append(best_fold_preds)\n# fold_summary.append({'fold': fold, 'global_r2': best_global_r2, 'avg_r2': best_avg_r2})\n\n# # Cleanup for this fold\n# del model, tr_loader, val_loaders, optimizer, scheduler, ema, eval_model\n# _sync()\n# torch.cuda.empty_cache()\n# gc.collect()\n\n# if oof_true:\n# oof_true_arr = np.concatenate(oof_true, axis=0)\n# oof_pred_arr = np.concatenate(oof_pred, axis=0)\n# oof_global_r2, oof_avg_r2, oof_per_r2 = weighted_r2_score_global(oof_true_arr, oof_pred_arr)\n\n# print('\\nTraining complete! Models saved in:', CFG.MODEL_DIR)\n# print('Fold summary:')\n# for fs in fold_summary:\n# print(f\" Fold {fs['fold']}: Global R² = {fs['global_r2']:.4f}, Avg R² = {fs.get('avg_r2', float('nan')):.4f}\")\n# print(f'OOF Global Weighted R²: {oof_global_r2:.4f} | OOF Avg Target R²: {oof_avg_r2:.4f}')\n# print('OOF Per-target:', dict(zip(CFG.ALL_TARGET_COLS, [f\"{r:.4f}\" for r in oof_per_r2])))\n# else:\n# print('No OOF predictions collected.')\n","metadata":{"execution":{"iopub.status.busy":"2026-01-26T12:29:57.263834Z","iopub.execute_input":"2026-01-26T12:29:57.264566Z","iopub.status.idle":"2026-01-26T12:29:57.271421Z","shell.execute_reply.started":"2026-01-26T12:29:57.264536Z","shell.execute_reply":"2026-01-26T12:29:57.270695Z"},"papermill":{"duration":0.016335,"end_time":"2026-01-05T05:09:15.715963","exception":false,"start_time":"2026-01-05T05:09:15.699628","status":"completed"},"tags":[],"trusted":true},"outputs":[],"execution_count":null},{"cell_type":"code","source":"# Inference \n\n# 4. DEFINE TTA TRANSFORMS\n# ===============================================================\ndef get_tta_transforms(num_transforms):\n \"\"\"\n Returns a list of TTA transform pipelines.\n Each pipeline represents a different augmentation view.\n \"\"\"\n normalize = A.Normalize(\n mean=[0.485, 0.456, 0.406],\n std=[0.229, 0.224, 0.225]\n )\n to_tensor = ToTensorV2()\n \n all_tta_transforms = [\n # View 1: Original (no flip)\n A.Compose([\n A.Resize(CFG.IMG_SIZE, CFG.IMG_SIZE),\n normalize,\n to_tensor\n ]),\n \n # View 2: Horizontal Flip\n A.Compose([\n A.Resize(CFG.IMG_SIZE, CFG.IMG_SIZE),\n A.HorizontalFlip(p=1.0),\n normalize,\n to_tensor\n ]),\n \n # View 3: Vertical Flip\n A.Compose([\n A.Resize(CFG.IMG_SIZE, CFG.IMG_SIZE),\n A.VerticalFlip(p=1.0),\n normalize,\n to_tensor\n ]),\n \n # View 4: Both Flips\n A.Compose([\n A.Resize(CFG.IMG_SIZE, CFG.IMG_SIZE),\n A.HorizontalFlip(p=1.0),\n A.VerticalFlip(p=1.0),\n normalize,\n to_tensor\n ]),\n ]\n tta_transforms = all_tta_transforms[:num_transforms]\n return tta_transforms\n\nprint(f\"✓ TTA transforms defined ({CFG.TTA_STEPS} views)\")\n\n# ===============================================================\n# 5. CREATE TEST DATASET\n# ===============================================================\ndef clean_image(img):\n # Safe crop (remove bottom artifacts) + inpaint orange date stamp\n h, w = img.shape[:2]\n img = img[0:int(h * 0.90), :]\n hsv = cv2.cvtColor(img, cv2.COLOR_RGB2HSV)\n lower = np.array([5, 150, 150])\n upper = np.array([25, 255, 255])\n mask = cv2.inRange(hsv, lower, upper)\n mask = cv2.dilate(mask, np.ones((3, 3), np.uint8), iterations=2)\n if np.sum(mask) > 0:\n img = cv2.inpaint(img, mask, 3, cv2.INPAINT_TELEA)\n return img\n\nclass BiomassTestDataset(Dataset):\n \"\"\"\n Test dataset for biomass images.\n Splits each 2000×1000 image into left and right 1000×1000 halves.\n \"\"\"\n def __init__(self, img_dir):\n self.img_dir = img_dir\n self.paths = sorted([\n os.path.join(img_dir, f) for f in os.listdir(img_dir)\n if f.lower().endswith(('.jpg', '.jpeg', '.png'))\n ])\n self.filenames = [os.path.basename(p) for p in self.paths]\n \n def __len__(self):\n return len(self.paths)\n \n def __getitem__(self, idx):\n path = self.paths[idx]\n \n # Read image\n img = cv2.imread(path)\n if img is None:\n print(f\"Warning: Could not read {path}, using blank image\")\n img = np.zeros((1000, 2000, 3), dtype=np.uint8)\n \n # Convert BGR to RGB\n img = cv2.cvtColor(img, cv2.COLOR_BGR2RGB)\n img = clean_image(img)\n # Split into left and right halves\n h, w = img.shape[:2]\n mid = w // 2\n left = img[:, :mid].copy()\n right = img[:, mid:].copy()\n \n return left, right, self.filenames[idx]\n\nprint(\"✓ Test dataset class defined\")\n\n# ===============================================================\n# 8. RUN INFERENCE WITH TTA (UPDATED to honor CFG.FOLDS_TO_TRAIN)\n# ===============================================================\n\n@torch.no_grad()\ndef predict_with_tta(model, left_np, right_np, tta_transforms):\n \"\"\"\n Predict using TTA with a SINGLE model.\n \n Args:\n model: Single trained model\n left_np: Left half of image (numpy array)\n right_np: Right half of image (numpy array)\n tta_transforms: List of augmentation transforms\n \n Returns:\n numpy array: [total, gdm, green] predictions (averaged over TTA)\n \"\"\"\n all_tta_preds = []\n \n # Loop over TTA views\n for tfm in tta_transforms:\n # Apply transform to both halves\n left_tensor = tfm(image=left_np)['image'].unsqueeze(0).to(CFG.DEVICE)\n right_tensor = tfm(image=right_np)['image'].unsqueeze(0).to(CFG.DEVICE)\n \n total, gdm, green, clover, dead = model(left_tensor, right_tensor)\n \n # Extract values\n p_total = total.cpu().item()\n p_gdm = gdm.cpu().item()\n p_green = green.cpu().item()\n \n all_tta_preds.append([p_total, p_gdm, p_green])\n \n # Average across TTA views\n final_pred = np.mean(all_tta_preds, axis=0)\n \n return final_pred\n\n\ndef run_inference():\n \"\"\"\n Main inference function.\n Returns: (predictions_array, image_filenames)\n Notes:\n - Now respects `CFG.FOLDS_TO_TRAIN` (if set) and averages only over successfully loaded folds.\n - If no fold weights are found for the requested folds, an error is raised.\n \"\"\"\n print(\"\\n\" + \"=\"*70)\n print(\"STARTING INFERENCE\")\n print(\"=\"*70)\n \n # Create dataset and loader\n dataset = BiomassTestDataset(CFG.TEST_IMAGE_DIR)\n # Note: batch_size=1 is required for the current predict_with_tta implementation\n loader = DataLoader(\n dataset,\n batch_size=1, \n shuffle=False,\n num_workers=CFG.NUM_WORKERS,\n pin_memory=True\n )\n \n tta_transforms = get_tta_transforms(CFG.TTA_STEPS)\n \n # Initialize accumulator for predictions\n # Shape: (num_samples, 3) for Total, GDM, Green\n accumulated_preds = np.zeros((len(dataset), 3), dtype=np.float32)\n\n # Use configured folds, fallback to full range if not set or empty\n folds_to_use = getattr(CFG, 'FOLDS_TO_TRAIN', list(range(CFG.N_FOLDS)))\n if not folds_to_use:\n folds_to_use = list(range(CFG.N_FOLDS))\n\n print(f\"Folds requested for inference: {folds_to_use}\")\n\n # Use filenames from dataset (guaranteed consistent ordering with loader because shuffle=False)\n filenames = dataset.filenames.copy()\n\n successful_folds = 0\n \n # Loop over requested folds only\n for fold in folds_to_use:\n print(f\"\\nProcessing Fold {fold}...\")\n # Load model for this fold\n model_dir = CFG.MODEL_DIR\n backbone_path = getattr(CFG, 'BACKBONE_PATH', None)\n model = BiomassModel(CFG.MODEL_NAME, pretrained=False, backbone_path=backbone_path)\n \n # Load weights\n weight_path = os.path.join(model_dir, f'best_model_fold{fold}.pth')\n if not os.path.exists(weight_path):\n print(f\"Warning: Model file {weight_path} not found! Skipping fold {fold}.\")\n del model\n torch.cuda.empty_cache(); gc.collect()\n continue\n \n state = torch.load(weight_path, map_location='cpu')\n # Handle state dict keys if necessary (e.g. if saved with 'model_state_dict' key)\n if isinstance(state, dict) and ('model_state_dict' in state or 'state_dict' in state):\n key = 'model_state_dict' if 'model_state_dict' in state else 'state_dict'\n sd = state[key]\n else:\n sd = state\n \n model.load_state_dict(sd)\n model.to(CFG.DEVICE)\n model.eval()\n \n # Run inference for this fold\n for i, (left, right, filename) in enumerate(tqdm(loader, desc=f\"Fold {fold}\")):\n # left and right are batches of size 1, convert to numpy for TTA function\n left_np = left[0].numpy()\n right_np = right[0].numpy()\n \n # Predict\n pred = predict_with_tta(model, left_np, right_np, tta_transforms)\n accumulated_preds[i] += pred\n \n successful_folds += 1\n # Cleanup model to save memory\n del model\n torch.cuda.empty_cache(); gc.collect()\n \n if successful_folds == 0:\n raise FileNotFoundError(f\"No model weights found for requested folds: {folds_to_use}\")\n\n # Average predictions over the number of successfully loaded folds\n final_predictions = accumulated_preds / successful_folds\n \n print(f\"\\nInference complete. Successfully used {successful_folds} fold(s) out of {len(folds_to_use)} requested.\")\n return final_predictions, filenames\n\n# ===============================================================\n# 9. POST-PROCESS PREDICTIONS\n# ===============================================================\ndef postprocess_predictions(preds_direct):\n \"\"\"\n Calculate derived targets from direct predictions.\n \n Input: (n_samples, 3) array with [total, gdm, green]\n Output: (n_samples, 5) array with [green, dead, clover, gdm, total]\n \"\"\"\n print(\"\\nPost-processing predictions...\")\n \n # Extract direct predictions\n pred_total = preds_direct[:, 0]\n pred_gdm = preds_direct[:, 1]\n pred_green = preds_direct[:, 2]\n \n # Calculate derived targets with non-negativity constraint\n pred_clover = np.maximum(0, pred_gdm - pred_green)\n pred_dead = np.maximum(0, pred_total - pred_gdm)\n \n # Stack in the order of ALL_TARGET_COLS\n # ['Dry_Green_g', 'Dry_Dead_g', 'Dry_Clover_g', 'GDM_g', 'Dry_Total_g']\n preds_all = np.stack([\n pred_green,\n pred_dead,\n pred_clover,\n pred_gdm,\n pred_total\n ], axis=1)\n \n print(f\"✓ Post-processing complete\")\n print(f\" Output shape: {preds_all.shape}\")\n print(f\"\\nPrediction statistics:\")\n for i, col in enumerate(CFG.ALL_TARGET_COLS):\n print(f\" {col:15s}: mean={preds_all[:, i].mean():.2f}, \"\n f\"std={preds_all[:, i].std():.2f}, \"\n f\"min={preds_all[:, i].min():.2f}, \"\n f\"max={preds_all[:, i].max():.2f}\")\n \n return preds_all\n\n\n# ===============================================================\n# 10. CREATE SUBMISSION FILE (FIXED)\n# ===============================================================\ndef create_submission(predictions, filenames):\n \"\"\"\n Create submission file in the required format.\n \n Args:\n predictions: (n_images, 5) array with all target predictions\n filenames: list of test image filenames\n \"\"\"\n print(\"\\n\" + \"=\"*70)\n print(\"CREATING SUBMISSION FILE\")\n print(\"=\"*70)\n \n # Step 0: Load test.csv first to check the image_path format\n test_df = pd.read_csv(CFG.TEST_CSV)\n print(f\"\\nTest CSV loaded: {len(test_df)} rows\")\n print(f\"Sample image_path from test.csv: {test_df['image_path'].iloc[0]}\")\n print(f\"Sample filename from predictions: {filenames[0]}\")\n \n # Step 1: Fix image_path format to match test.csv\n # If test.csv has \"test/ID123.jpg\" but we have \"ID123.jpg\", add the prefix\n test_path_example = test_df['image_path'].iloc[0]\n if '/' in test_path_example:\n # Extract the subdirectory prefix (e.g., \"test/\")\n prefix = test_path_example.rsplit('/', 1)[0] + '/'\n corrected_filenames = [prefix + fn for fn in filenames]\n print(f\"Corrected path format: {corrected_filenames[0]}\")\n else:\n corrected_filenames = filenames\n \n # Step 2: Create wide-format DataFrame with corrected paths\n preds_wide = pd.DataFrame(predictions, columns=CFG.ALL_TARGET_COLS)\n preds_wide.insert(0, 'image_path', corrected_filenames)\n \n print(f\"\\nWide format predictions:\")\n print(preds_wide.head())\n \n # Step 3: Convert to long format (melt)\n preds_long = preds_wide.melt(\n id_vars=['image_path'],\n value_vars=CFG.ALL_TARGET_COLS,\n var_name='target_name',\n value_name='target'\n )\n \n print(f\"\\nLong format predictions (first 10 rows):\")\n print(preds_long.head(10))\n \n # Step 4: Debug the merge\n print(f\"\\nDebug: Checking if paths match...\")\n print(f\"Unique paths in test_df: {test_df['image_path'].nunique()}\")\n print(f\"Unique paths in preds_long: {preds_long['image_path'].nunique()}\")\n \n common_paths = set(test_df['image_path'].unique()) & set(preds_long['image_path'].unique())\n print(f\"Common paths found: {len(common_paths)}\")\n \n if len(common_paths) == 0:\n print(\"\\n❌ ERROR: No matching paths found!\")\n print(f\"Test CSV paths sample: {list(test_df['image_path'].unique()[:3])}\")\n print(f\"Prediction paths sample: {list(preds_long['image_path'].unique()[:3])}\")\n raise ValueError(\"Path mismatch between test.csv and predictions\")\n \n # Step 5: Merge to get sample_ids\n submission = pd.merge(\n test_df[['sample_id', 'image_path', 'target_name']],\n preds_long,\n on=['image_path', 'target_name'],\n how='left'\n )\n \n # Step 6: Keep only required columns\n submission = submission[['sample_id', 'target']]\n \n # Step 7: Check for missing values\n missing_count = submission['target'].isna().sum()\n if missing_count > 0:\n print(f\"\\n⚠ Warning: {missing_count} missing predictions found!\")\n print(\"Sample missing entries:\")\n print(submission[submission['target'].isna()].head())\n submission.loc[submission['target'].isna(), 'target'] = 0.0\n \n # Step 8: Sort by sample_id\n submission = submission.sort_values('sample_id').reset_index(drop=True)\n \n # Step 9: Save to CSV\n output_path = os.path.join(CFG.SUBMISSION_DIR, 'submission70.csv')\n submission.to_csv(output_path, index=False)\n \n print(f\"\\n✓ Submission file saved: {output_path}\")\n print(f\" Total rows: {len(submission)}\")\n print(f\"\\nPrediction statistics:\")\n print(f\" Min: {submission['target'].min():.4f}\")\n print(f\" Max: {submission['target'].max():.4f}\")\n print(f\" Mean: {submission['target'].mean():.4f}\")\n print(f\" Non-zero values: {(submission['target'] > 0).sum()}/{len(submission)}\")\n \n print(f\"\\nFirst 10 rows:\")\n print(submission.head(10))\n print(f\"\\nLast 10 rows:\")\n print(submission.tail(10))\n \n # Step 10: Validation checks\n print(f\"\\n\" + \"=\"*70)\n print(\"VALIDATION CHECKS\")\n print(\"=\"*70)\n print(f\"✓ Expected rows: {len(test_df)}\")\n print(f\"✓ Actual rows: {len(submission)}\")\n print(f\"✓ Match: {len(submission) == len(test_df)}\")\n print(f\"✓ No missing values: {not submission['target'].isna().any()}\")\n print(f\"✓ All sample_ids unique: {submission['sample_id'].is_unique}\")\n print(f\"✓ Has non-zero predictions: {(submission['target'] > 0).any()}\")\n \n return submission\n\n# Create submission\n# Post-process predictions\n# Run inference\nif CFG.CREATE_SUBMISSION:\n predictions_direct, test_filenames = run_inference()\n predictions_all = postprocess_predictions(predictions_direct)\n submission_df = create_submission(predictions_all, test_filenames)","metadata":{"execution":{"iopub.status.busy":"2026-01-26T12:30:03.580847Z","iopub.execute_input":"2026-01-26T12:30:03.581765Z","iopub.status.idle":"2026-01-26T12:32:56.611584Z","shell.execute_reply.started":"2026-01-26T12:30:03.581739Z","shell.execute_reply":"2026-01-26T12:32:56.610902Z"},"papermill":{"duration":0.015528,"end_time":"2026-01-05T05:09:15.754447","exception":false,"start_time":"2026-01-05T05:09:15.738919","status":"completed"},"tags":[],"trusted":true},"outputs":[],"execution_count":null},{"cell_type":"code","source":"import pandas as pd\nimport numpy as np\nimport os\n\n# =============================================================================\n# CONFIGURATION\n# =============================================================================\n# Weights for the ensemble (Must sum to 1.0)\n# Adjust based on which model had better local CV or Public LB score.\n# Example: If Siglip was better, give it 0.6.\nW_SIGLIP = 0.35\nW_DINO = 0.65\n\nFILES = {\n 'siglip': 'submission70.csv',\n 'dino': 'submission72.csv'\n}\n\nOUTPUT_FILE = 'submission.csv'\n\n# Target definitions required for Mass Balance\nALL_TARGETS = ['Dry_Green_g', 'Dry_Clover_g', 'Dry_Dead_g', 'GDM_g', 'Dry_Total_g']\n\n# =============================================================================\n# HELPER FUNCTIONS\n# =============================================================================\n\ndef enforce_mass_balance(df_wide, fixed_clover=None):\n \"\"\"\n Applies Orthogonal Projection to enforce biological constraints:\n 1. Dry_Green_g + Dry_Clover_g = GDM_g\n 2. GDM_g + Dry_Dead_g = Dry_Total_g\n \n If fixed_clover is True, Dry_Clover_g is kept fixed and only other targets are adjusted.\n \n This finds the closest set of values to the predictions that satisfy \n the constraints (minimizing Euclidean distance modification).\n \"\"\"\n # 1. Ensure columns are in the specific order for the matrix math\n # Vector x = [Green, Clover, Dead, GDM, Total]\n ordered_cols = ['Dry_Green_g', 'Dry_Clover_g', 'Dry_Dead_g', 'GDM_g', 'Dry_Total_g']\n \n # Extract values: Shape (5, N_samples)\n Y = df_wide[ordered_cols].values.T\n \n if fixed_clover:\n # Keep Dry_Clover_g fixed, adjust only other targets\n # We have: Green + Clover_fixed = GDM, so GDM = Green + Clover_fixed\n # And: GDM + Dead = Total, so Total = GDM + Dead = Green + Clover_fixed + Dead\n # Extract fixed Clover values\n clover_fixed = Y[1, :].copy() # Dry_Clover_g is index 1\n # Adjust: GDM = Green + Clover_fixed\n Y[3, :] = Y[0, :] + clover_fixed # GDM_g\n # Adjust: Total = GDM + Dead = Green + Clover_fixed + Dead\n Y[4, :] = Y[3, :] + Y[2, :] # Dry_Total_g\n # Keep Green and Dead as is (or apply minimal adjustment if needed)\n # Clover stays fixed (already set)\n Y_reconciled = Y\n else:\n # Original method: adjust all targets\n # 2. Define Constraint Matrix C where Cx = 0\n # Eq 1: 1*Gr + 1*Cl + 0*De - 1*GDM + 0*Tot = 0\n # Eq 2: 0*Gr + 0*Cl + 1*De + 1*GDM - 1*Tot = 0\n C = np.array([\n [1, 1, 0, -1, 0],\n [0, 0, 1, 1, -1]\n ])\n \n # 3. Calculate Projection Matrix P = I - C^T * (C * C^T)^-1 * C\n C_T = C.T\n try:\n inv_CCt = np.linalg.inv(C @ C_T)\n P = np.eye(5) - C_T @ inv_CCt @ C\n except np.linalg.LinAlgError:\n # Fallback if singular (unlikely with this specific matrix)\n print(\"Warning: Singular matrix in projection. Skipping constraint enforcement.\")\n return df_wide\n\n # 4. Apply Projection\n Y_reconciled = P @ Y\n \n # 5. Transpose back to (N_samples, 5) and clip negatives\n Y_reconciled = Y_reconciled.T\n Y_reconciled = np.maximum(0, Y_reconciled) \n \n # 6. Update DataFrame\n df_out = df_wide.copy()\n df_out[ordered_cols] = Y_reconciled\n \n return df_out\n\ndef robust_ensemble(file_paths, weights):\n print(f\"--- Starting Ensemble ---\")\n print(f\"Weights: {weights}\")\n print(\"NOTE: Using DINO-only for Dry_Clover_g (better detection)\")\n \n dfs = []\n for name, path in file_paths.items():\n if not os.path.exists(path):\n raise FileNotFoundError(f\"Missing file: {path}\")\n \n # Read and sort by sample_id to ensure alignment\n df = pd.read_csv(path).sort_values('sample_id').reset_index(drop=True)\n dfs.append(df)\n print(f\"Loaded {name}: {len(df)} rows\")\n\n # 1. Check alignment\n base_ids = dfs[0]['sample_id']\n if not all(df['sample_id'].equals(base_ids) for df in dfs[1:]):\n raise ValueError(\"Sample IDs do not match between submission files!\")\n\n # 2. Split by target_name to handle Dry_Clover_g separately\n # Split sample_id into image_id and target_name\n dfs_split = []\n for df in dfs:\n df_split = df.copy()\n df_split[['image_id', 'target_name']] = df_split['sample_id'].str.rsplit('__', n=1, expand=True)\n dfs_split.append(df_split)\n \n # Get DINO and SigLIP dataframes (identify by order in file_paths)\n dino_idx = list(file_paths.keys()).index('dino')\n siglip_idx = list(file_paths.keys()).index('siglip')\n dino_df = dfs_split[dino_idx]\n siglip_df = dfs_split[siglip_idx]\n \n # 3. Separate targets: Dry_Clover_g uses DINO only, others use ensemble\n ensemble_results = []\n \n for target in ALL_TARGETS:\n # Filter for this target\n dino_target = dino_df[dino_df['target_name'] == target].copy()\n siglip_target = siglip_df[siglip_df['target_name'] == target].copy()\n \n if target == 'Dry_Clover_g':\n # Use DINO only for Clover\n print(f\"Using DINO-only for {target}\")\n ensemble_results.append(dino_target[['sample_id', 'target']])\n else:\n # Ensemble for other targets\n # Merge on sample_id to align\n merged = pd.merge(\n dino_target[['sample_id', 'target']].rename(columns={'target': 'dino_pred'}),\n siglip_target[['sample_id', 'target']].rename(columns={'target': 'siglip_pred'}),\n on='sample_id'\n )\n \n # Weighted average\n w_vec = np.array([weights['dino'], weights['siglip']])\n w_vec = w_vec / w_vec.sum()\n \n merged['target'] = merged['dino_pred'] * w_vec[0] + merged['siglip_pred'] * w_vec[1]\n ensemble_results.append(merged[['sample_id', 'target']])\n \n # 4. Combine all targets\n ensemble_df = pd.concat(ensemble_results, ignore_index=True)\n print(\"Weighted average complete (DINO-only for Clover).\")\n\n # 5. Prepare for Mass Balance (Convert Long -> Wide)\n ensemble_df[['image_id', 'target_name']] = ensemble_df['sample_id'].str.rsplit('__', n=1, expand=True)\n \n # Pivot\n wide_df = ensemble_df.pivot(index='image_id', columns='target_name', values='target').reset_index()\n\n # 6. Apply Robust Constraints (with Dry_Clover_g fixed)\n print(\"Applying Mass Balance Constraints (Dry_Clover_g fixed to DINO values)...\")\n wide_balanced = enforce_mass_balance(wide_df, fixed_clover=True)\n\n # 7. Convert back (Wide -> Long)\n long_balanced = wide_balanced.melt(\n id_vars='image_id', \n value_vars=ALL_TARGETS,\n var_name='target_name',\n value_name='target'\n )\n\n # Reconstruct sample_id\n long_balanced['sample_id'] = long_balanced['image_id'] + '__' + long_balanced['target_name']\n\n # 8. Final Formatting\n final_submission = long_balanced[['sample_id', 'target']].sort_values('sample_id').reset_index(drop=True)\n\n return final_submission\n\n# =============================================================================\n# EXECUTION\n# =============================================================================\nif __name__ == \"__main__\":\n \n # Define weights\n ensemble_weights = {\n 'siglip': W_SIGLIP,\n 'dino': W_DINO\n }\n \n try:\n # Run Ensemble\n submission = robust_ensemble(FILES, ensemble_weights)\n \n # Save\n submission.to_csv(OUTPUT_FILE, index=False)\n print(f\"\\nSuccess! Saved to {OUTPUT_FILE}\")\n print(submission.head())\n \n # Sanity Check Stats\n print(\"\\nStats:\")\n print(submission['target'].describe())\n \n except Exception as e:\n print(f\"\\nError during ensembling: {e}\")","metadata":{"trusted":true,"execution":{"iopub.status.busy":"2026-01-26T12:37:10.107279Z","iopub.execute_input":"2026-01-26T12:37:10.107844Z","iopub.status.idle":"2026-01-26T12:37:10.158092Z","shell.execute_reply.started":"2026-01-26T12:37:10.107808Z","shell.execute_reply":"2026-01-26T12:37:10.157364Z"}},"outputs":[],"execution_count":null}]}