# -*- coding: utf-8 -*- """ Standalone Interpreter for Lightning-trained Fish Classification Models. This module provides a self-contained classifier for loading and using models trained with lightning_train.py. All necessary classes are included in this file to enable standalone deployment without additional module dependencies. Features: - Load PyTorch Lightning checkpoints - Support for both ViT and CNN backbones - Multiple pooling strategies (Attention, GeM, Hybrid) - FAISS-based nearest neighbor search (can be disabled) - Centroid-based class filtering - Automatic input size detection - Robust error handling and validation - Configurable kNN classifier (enable/disable) Usage: config = { 'log_level': 'INFO', 'dataset': {'path': 'path/to/embeddings.pt'}, 'model': { 'checkpoint_path': 'path/to/model.ckpt', 'backbone_model_name': 'maxvit_base_tf_224', 'embedding_dim': 512, 'num_classes': 639, 'arcface_s': 64.0, 'arcface_m': 0.2, 'pooling_type': 'attention', 'input_size': 224, # Optional, auto-detected if not provided 'device': 'cuda' }, # Optional inference parameters 'use_knn': True, # Enable/disable kNN classifier (default: True) 'use_albumentations': False, # Use albumentations transforms (default: False, uses torchvision) 'arcface_min_score': 0.1, 'centroid_fallback_score': 0.1, 'topk_centroid': 5, 'topk_neighbors': 10, 'topk_arcface': 5, 'centroid_threshold': 0.7, 'neighbor_threshold': 0.8 } # Initialize classifier classifier = EmbeddingClassifier(config) # Optional: warmup for stable performance classifier.warmup(num_iterations=5) # Single image inference results = classifier(image_array) # np.ndarray [H, W, 3] # Batch inference results = classifier([img1, img2, img3]) # List[np.ndarray] # Get model information info = classifier.get_model_info() # Context manager usage (recommended) with EmbeddingClassifier(config) as classifier: results = classifier(image_array) # Auto cleanup on exit Security Warning: This module uses torch.load() which relies on pickle and can execute arbitrary code. Only load checkpoints from trusted sources. The module attempts to use weights_only=True first for safety, but falls back to weights_only=False if needed. Always verify checksums and only load files from trusted sources in production environments. Performance Notes: - Memory usage scales with number of classes and database size - Expected inference time: ~10-50ms per image (depending on backbone and device) - FAISS indices are pre-built for faster search but require memory - Large batches are automatically split into chunks (MAX_BATCH_SIZE) to prevent OOM errors - For optimal performance, keep batch sizes <= 32 images """ import logging import time import math from collections import defaultdict from dataclasses import dataclass from pathlib import Path from typing import Dict, List, Tuple, Union, Optional, Literal import faiss import numpy as np import torch import torch.nn as nn import torch.nn.functional as F from PIL import Image from scipy.stats import entropy from sklearn.metrics import pairwise_distances from torchvision import transforms import timm from timm.models.vision_transformer import VisionTransformer # Optional: Albumentations support (install with: pip install albumentations) try: import albumentations as A from albumentations.pytorch import ToTensorV2 ALBUMENTATIONS_AVAILABLE = True except ImportError: ALBUMENTATIONS_AVAILABLE = False A = None ToTensorV2 = None # Constants SUPPORTED_VIT_BACKBONES = ['vit', 'beit', 'deit', 'maxvit', 'maxxvit', 'eva', 'dino', 'swin'] DEFAULT_IMAGE_SIZE = 224 GEM_POOLING_DEFAULT_P = 3.0 ATTENTION_HIDDEN_DIVISOR = 4 ATTENTION_HIDDEN_MIN = 128 NUMERICAL_EPSILON = 1e-6 WEIGHT_NORMALIZATION_EPSILON = 1e-10 MAX_BATCH_SIZE = 32 # Maximum batch size to prevent OOM DEFAULT_WARMUP_ITERATIONS = 5 DEFAULT_ARCFACE_MIN_SCORE = 0.1 DEFAULT_CENTROID_FALLBACK_SCORE = 0.1 DEFAULT_TOPK_CENTROID = 5 DEFAULT_TOPK_NEIGHBORS = 10 DEFAULT_TOPK_ARCFACE = 5 DEFAULT_CENTROID_THRESHOLD = 0.7 DEFAULT_NEIGHBOR_THRESHOLD = 0.8 DEFAULT_USE_KNN = True DEFAULT_RERANK_MODE = 'hybrid' # 'hybrid', 'weighted_fusion', or 'rrf' DEFAULT_ARCFACE_WEIGHT = 0.6 # Weight for ArcFace in weighted fusion DEFAULT_KNN_WEIGHT = 0.4 # Weight for kNN in weighted fusion DEFAULT_RRF_K = 60 # Constant for Reciprocal Rank Fusion DEFAULT_USE_ALBUMENTATIONS = False # Use albumentations for transforms (if available) # Setup Logger logger = logging.getLogger("EmbeddingClassifier") if not logger.handlers: handler = logging.StreamHandler() formatter = logging.Formatter( "[%(asctime)s] [%(levelname)s] - %(message)s", datefmt="%Y-%m-%d %H:%M:%S" ) handler.setFormatter(formatter) logger.addHandler(handler) @dataclass class PredictionResult: """Result of a single prediction.""" name: str species_id: int distance: float accuracy: float # Average similarity score (kept for backward compatibility) image_id: Optional[str] annotation_id: Optional[str] drawn_fish_id: Optional[str] @property def average_similarity(self) -> float: """Alias for accuracy field (which is actually average similarity).""" return self.accuracy # ============================================================================= # Pooling Layers # ============================================================================= class GeMPooling(nn.Module): """ Generalized Mean Pooling (GeM). Popular in image retrieval tasks. Provides a learnable pooling between average pooling (p=1) and max pooling (p→∞). Reference: "Fine-tuning CNN Image Retrieval with No Human Annotation" (Radenović et al.) """ def __init__(self, p: float = GEM_POOLING_DEFAULT_P, eps: float = NUMERICAL_EPSILON, learnable: bool = True): super().__init__() if learnable: self.p = nn.Parameter(torch.ones(1) * p) else: self.register_buffer('p', torch.ones(1) * p) self.eps = eps self.learnable = learnable def forward(self, x: torch.Tensor) -> torch.Tensor: """ Args: x: Feature map [B, C, H, W] Returns: Pooled features [B, C] """ # Clamp both min and max for numerical stability x_clamped = x.clamp(min=self.eps, max=1e4) return F.adaptive_avg_pool2d( x_clamped.pow(self.p), 1 ).pow(1.0 / self.p.clamp(min=1e-2)).squeeze(-1).squeeze(-1) def __repr__(self): return f"GeMPooling(p={self.p.item():.2f}, learnable={self.learnable})" class ViTAttentionPooling(nn.Module): """ Attention Pooling for Vision Transformer output of shape [B, N, D]. Computes a weighted sum of patch embeddings based on learned attention. """ def __init__(self, in_features: int, hidden_features: Optional[int] = None): super().__init__() if hidden_features is None: hidden_features = max(in_features // ATTENTION_HIDDEN_DIVISOR, ATTENTION_HIDDEN_MIN) self.attention_net = nn.Sequential( nn.Linear(in_features, hidden_features), nn.Tanh(), nn.Linear(hidden_features, 1) ) def forward( self, x: torch.Tensor, object_mask: Optional[torch.Tensor] = None, return_attention_map: bool = False ) -> Tuple[torch.Tensor, Optional[torch.Tensor]]: """ Args: x: ViT output [B, N, D] object_mask: Not used for ViT, kept for interface compatibility return_attention_map: Whether to return attention weights Returns: pooled: Pooled features [B, D] weights: Optional attention weights [B, N, 1] """ attention_scores = self.attention_net(x) # [B, N, 1] weights = F.softmax(attention_scores, dim=1) # [B, N, 1] pooled = (x * weights).sum(dim=1) # [B, D] if return_attention_map: return pooled, weights return pooled, None class AttentionPooling(nn.Module): """ Attention-based pooling for CNN feature maps. Weighs spatial features based on learned attention, optionally focusing on regions within a provided object mask. """ def __init__(self, in_channels: int, hidden_channels: Optional[int] = None): super().__init__() if hidden_channels is None: hidden_channels = max(in_channels // ATTENTION_HIDDEN_DIVISOR, 32) self.attention_conv = nn.Sequential( nn.Conv2d(in_channels, hidden_channels, kernel_size=1, bias=False), nn.ReLU(inplace=True), nn.Conv2d(hidden_channels, 1, kernel_size=1, bias=False) ) def forward( self, x: torch.Tensor, object_mask: Optional[torch.Tensor] = None, return_attention_map: bool = False ) -> Tuple[torch.Tensor, Optional[torch.Tensor]]: """ Args: x: Feature map [B, C, H, W] object_mask: Optional binary mask [B, 1, H', W'] or [B, H', W'] return_attention_map: Whether to return attention weights Returns: pooled: Pooled features [B, C] weights: Optional attention map [B, 1, H, W] """ x_for_attn = x if object_mask is not None: B, _, H_feat, W_feat = x.shape object_mask_for_x = object_mask.float().to(x.device) if object_mask_for_x.ndim == 3: object_mask_for_x = object_mask_for_x.unsqueeze(1) if object_mask_for_x.shape[2] != H_feat or object_mask_for_x.shape[3] != W_feat: object_mask_for_x_resized = F.interpolate( object_mask_for_x, size=(H_feat, W_feat), mode='nearest' ) else: object_mask_for_x_resized = object_mask_for_x x_for_attn = x * object_mask_for_x_resized attention_scores = self.attention_conv(x_for_attn) weights = torch.sigmoid(attention_scores) final_weights_for_pooling = weights if object_mask is not None: B_w, _, H_attn, W_attn = weights.shape object_mask_for_weights = object_mask.float().to(weights.device) if object_mask_for_weights.ndim == 3: object_mask_for_weights = object_mask_for_weights.unsqueeze(1) mask_downsampled_for_weights = F.interpolate( object_mask_for_weights, size=(H_attn, W_attn), mode='nearest' ) final_weights_for_pooling = weights * mask_downsampled_for_weights weighted_features = x * final_weights_for_pooling sum_weighted_features = weighted_features.sum(dim=(2, 3)) sum_weights = final_weights_for_pooling.sum(dim=(2, 3)).clamp(min=NUMERICAL_EPSILON) pooled = sum_weighted_features / sum_weights if return_attention_map: return pooled, final_weights_for_pooling return pooled, None class HybridPooling(nn.Module): """ Hybrid pooling combining GeM and Attention pooling. Concatenates GeM-pooled features with attention-pooled features. """ def __init__( self, in_channels: int, gem_p: float = GEM_POOLING_DEFAULT_P, attention_hidden: Optional[int] = None, output_mode: Literal['concat', 'add'] = 'concat', ): super().__init__() self.gem = GeMPooling(p=gem_p, learnable=True) self.attention = AttentionPooling(in_channels, attention_hidden) self.output_mode = output_mode if output_mode == 'add': # Learnable weights for combining self.gem_weight = nn.Parameter(torch.tensor(0.5)) self.attn_weight = nn.Parameter(torch.tensor(0.5)) def forward( self, x: torch.Tensor, object_mask: Optional[torch.Tensor] = None, return_attention_map: bool = False ) -> Tuple[torch.Tensor, Optional[torch.Tensor]]: gem_out = self.gem(x) attn_out, attn_map = self.attention(x, object_mask, return_attention_map=True) if self.output_mode == 'concat': pooled = torch.cat([gem_out, attn_out], dim=1) else: w_gem = torch.sigmoid(self.gem_weight) w_attn = torch.sigmoid(self.attn_weight) pooled = w_gem * gem_out + w_attn * attn_out if return_attention_map: return pooled, attn_map return pooled, None @property def output_features(self) -> int: """Returns output feature dimension multiplier.""" return 2 if self.output_mode == 'concat' else 1 # ============================================================================= # ArcFace Head # ============================================================================= class ArcFaceHead(nn.Module): """ ArcFace loss head for metric learning. Implements the additive angular margin penalty. Reference: "ArcFace: Additive Angular Margin Loss for Deep Face Recognition" """ def __init__( self, embedding_dim: int, num_classes: int, s: float = 32.0, m: float = 0.10 ): super().__init__() self.embedding_dim = embedding_dim self.num_classes = num_classes self.s = s self.m = m self.weight = nn.Parameter(torch.FloatTensor(num_classes, embedding_dim)) nn.init.xavier_uniform_(self.weight) # Buffers for constants self.register_buffer('cos_m', torch.tensor(math.cos(m))) self.register_buffer('sin_m', torch.tensor(math.sin(m))) self.register_buffer('th', torch.tensor(math.cos(math.pi - m))) self.register_buffer('mm', torch.tensor(math.sin(math.pi - m) * m)) self.register_buffer('eps', torch.tensor(NUMERICAL_EPSILON)) def set_margin(self, new_m: float): """Dynamically update the margin 'm' and its related constants.""" self.m = new_m self.cos_m.data = torch.tensor(math.cos(new_m), device=self.cos_m.device) self.sin_m.data = torch.tensor(math.sin(new_m), device=self.sin_m.device) self.th.data = torch.tensor(math.cos(math.pi - new_m), device=self.th.device) self.mm.data = torch.tensor(math.sin(math.pi - new_m) * new_m, device=self.mm.device) def forward( self, normalized_emb: torch.Tensor, labels: Optional[torch.Tensor] = None ) -> torch.Tensor: """ Args: normalized_emb: L2-normalized embeddings [B, D] labels: Optional class labels [B] (required during training) Returns: Scaled logits [B, num_classes] """ normalized_w = F.normalize(self.weight, dim=1) cosine = F.linear(normalized_emb, normalized_w) if labels is not None: cosine_sq = cosine ** 2 sine = torch.sqrt((1.0 - cosine_sq).clamp(min=self.eps.item())) phi = cosine * self.cos_m - sine * self.sin_m phi = torch.where(cosine > self.th, phi, cosine - self.mm) output = cosine.clone() idx = labels.to(dtype=torch.long, device=cosine.device).view(-1, 1) src = phi.gather(1, idx).to(dtype=output.dtype) output.scatter_(1, idx, src) output *= self.s else: output = cosine * self.s return output # ============================================================================= # Model Classes # ============================================================================= class StableEmbeddingModelViT(nn.Module): """ Embedding model for Vision Transformer backbones. Supports various ViT architectures from timm including: - BEiT v2, DeiT, ViT - MaxViT, MaxxViT - EVA, DINOv2 - Swin Transformer """ def __init__( self, embedding_dim: int = 128, num_classes: int = 1000, pretrained_backbone: bool = True, freeze_backbone_initially: bool = False, backbone_model_name: str = 'beitv2_base_patch16_224.in1k_ft_in22k_in1k', custom_backbone: Optional[VisionTransformer] = None, attention_hidden_channels: Optional[int] = None, arcface_s: float = 64.0, arcface_m: float = 0.5, add_bn_to_embedding: bool = False, embedding_dropout_rate: float = 0.11, pooling_type: str = 'attention', ): super().__init__() self.embedding_dim = embedding_dim self.num_classes = num_classes self.pooling_type = pooling_type if custom_backbone: self.backbone = custom_backbone logger.info("Using custom ViT backbone.") else: logger.info(f"Loading ViT backbone: {backbone_model_name}") self.backbone: VisionTransformer = timm.create_model( backbone_model_name, pretrained=pretrained_backbone, num_classes=0 ) self.backbone_out_features = self._infer_backbone_embedding_dim() self.backbone_feature_extractor = self.backbone.forward_features if freeze_backbone_initially: self.freeze_backbone() # Pooling layer if pooling_type == 'attention': self.pooling = ViTAttentionPooling( in_features=self.backbone_out_features, hidden_features=attention_hidden_channels ) else: # For ViT, we'll use global average pooling self.pooling = None # Embedding layers embedding_layers = [nn.Linear(self.backbone_out_features, embedding_dim)] if add_bn_to_embedding: embedding_layers.append(nn.BatchNorm1d(embedding_dim)) if embedding_dropout_rate > 0.0: embedding_layers.append(nn.Dropout(embedding_dropout_rate)) self.embedding_fc = nn.Sequential(*embedding_layers) self.arcface_head = ArcFaceHead(embedding_dim, num_classes, s=arcface_s, m=arcface_m) logger.info(f"StableEmbeddingModelViT initialized") logger.info(f" Embedding Dim: {embedding_dim}, Num Classes: {num_classes}") logger.info(f" ArcFace s: {arcface_s}, m: {arcface_m}") logger.info(f" Backbone out features: {self.backbone_out_features}") logger.info(f" Pooling type: {pooling_type}") def _tokens_and_grid_from_features(self, features: torch.Tensor): """Normalize backbone features into token tensor [B, N, D] + optional grid.""" if features.ndim == 4: B, C, H, W = features.shape tokens = features.flatten(2).transpose(1, 2).contiguous() return tokens, (H, W) if features.ndim == 3: tokens = features if hasattr(self.backbone, "cls_token") and tokens.shape[1] > 1: tokens = tokens[:, 1:, :] if hasattr(self.backbone, "patch_embed") and hasattr(self.backbone.patch_embed, "grid_size"): gs = self.backbone.patch_embed.grid_size if isinstance(gs, (tuple, list)) and len(gs) == 2 and int(gs[0]) * int(gs[1]) == tokens.shape[1]: return tokens, (int(gs[0]), int(gs[1])) N = tokens.shape[1] s = int(round(math.sqrt(N))) if s * s == N: return tokens, (s, s) return tokens, None raise ValueError(f"Unsupported backbone output shape: {tuple(features.shape)}") def freeze_backbone(self): """Freeze all backbone parameters.""" logger.info("Freezing backbone parameters.") for param in self.backbone.parameters(): param.requires_grad = False def unfreeze_backbone(self, specific_layer_keywords=None, verbose=False): """Unfreeze backbone parameters, optionally filtering by keywords.""" logger.info(f"Unfreezing backbone parameters... (Keywords: {specific_layer_keywords})") unfrozen_count = 0 for name, param in self.backbone.named_parameters(): if specific_layer_keywords is None or any(kw in name for kw in specific_layer_keywords): param.requires_grad = True unfrozen_count += 1 if verbose: logger.info(f" Unfroze: {name}") logger.info(f"Total parameters unfrozen: {unfrozen_count}") def _infer_backbone_embedding_dim(self) -> int: """Infer backbone output dimension.""" for attr in ("num_features", "embed_dim"): v = getattr(self.backbone, attr, None) if isinstance(v, int) and v > 0: return int(v) def _infer_input_hw() -> int: cfg = getattr(self.backbone, "default_cfg", None) or {} inp = cfg.get("input_size", None) if isinstance(inp, (tuple, list)) and len(inp) == 3: return int(inp[1]) name = str(getattr(self.backbone, "name", "") or "") for s in (512, 384, 256, 224): if name.endswith(f"_{s}"): return s return 224 self.backbone.eval() orig_device = next(self.backbone.parameters()).device self.backbone.to("cpu") with torch.no_grad(): hw = _infer_input_hw() dummy = torch.randn(1, 3, hw, hw) features = self.backbone.forward_features(dummy) self.backbone.to(orig_device) if features.ndim == 4: return int(features.shape[1]) if features.ndim == 3: return int(features.shape[-1]) raise ValueError(f"Unsupported output shape: {tuple(features.shape)}") def forward( self, x: torch.Tensor, labels: Optional[torch.Tensor] = None, object_mask: Optional[torch.Tensor] = None, return_softmax: bool = False, return_attention_map: bool = True ): """ Forward pass. Args: x: Input images [B, 3, H, W] labels: Optional class labels [B] object_mask: Optional object mask (ignored for ViT) return_softmax: Return softmax probabilities instead of logits return_attention_map: Return attention visualization map Returns: emb_norm: L2-normalized embeddings [B, D] logits/probs: Class logits or probabilities [B, num_classes] attn_map: Optional attention map for visualization """ features = self.backbone_feature_extractor(x) tokens, grid = self._tokens_and_grid_from_features(features) if self.pooling is not None: pooled, attn_weights = self.pooling(tokens, object_mask=object_mask, return_attention_map=True) else: # Global average pooling pooled = tokens.mean(dim=1) attn_weights = None emb_raw = self.embedding_fc(pooled) emb_norm = F.normalize(emb_raw, p=2, dim=1) logits = self.arcface_head(emb_norm, labels) vis_attn_map = None if return_attention_map and attn_weights is not None and grid is not None: try: B, N, _ = attn_weights.shape H, W = grid if H * W == N: vis_attn_map = attn_weights.permute(0, 2, 1).reshape(B, 1, H, W) except Exception: vis_attn_map = None output_attn = vis_attn_map if return_attention_map else None if return_softmax: probabilities = F.softmax(logits, dim=1) return emb_norm, probabilities, output_attn return emb_norm, logits, output_attn class StableEmbeddingModel(nn.Module): """ Embedding model for CNN backbones (ConvNeXt, EfficientNet, ResNet, etc.). """ def __init__( self, embedding_dim: int = 256, num_classes: int = 1000, pretrained_backbone: bool = True, freeze_backbone_initially: bool = False, backbone_model_name: str = 'convnext_tiny', custom_backbone=None, backbone_out_features: int = 768, attention_hidden_channels: Optional[int] = None, arcface_s: float = 32.0, arcface_m: float = 0.11, add_bn_to_embedding: bool = True, embedding_dropout_rate: float = 0.0, pooling_type: str = 'attention', ): super().__init__() self.embedding_dim = embedding_dim self.num_classes = num_classes self.backbone_out_features = backbone_out_features self.pooling_type = pooling_type if custom_backbone: self.backbone = custom_backbone self.backbone_feature_extractor = self.backbone logger.info("Using custom backbone.") elif 'convnext' in backbone_model_name: logger.info(f"Loading backbone from timm: {backbone_model_name}") self.backbone = timm.create_model( backbone_model_name, pretrained=pretrained_backbone, features_only=True, out_indices=(-1,) ) self.backbone_feature_extractor = lambda x: self.backbone(x)[-1] dummy_input = torch.randn(1, 3, 224, 224) with torch.no_grad(): out = self.backbone_feature_extractor(dummy_input) self.backbone_out_features = out.shape[1] logger.info(f" Detected backbone output channels: {self.backbone_out_features}") else: try: logger.info(f"Attempting to load generic backbone from timm: {backbone_model_name}") self.backbone = timm.create_model( backbone_model_name, pretrained=pretrained_backbone, num_classes=0, global_pool='' ) self.backbone_feature_extractor = self.backbone.forward_features dummy_input = torch.randn(1, 3, 224, 224) with torch.no_grad(): out = self.backbone_feature_extractor(dummy_input) self.backbone_out_features = out.shape[1] logger.info(f" Detected backbone output channels: {self.backbone_out_features}") except Exception as e: raise ValueError(f"Unsupported backbone: {backbone_model_name}. Error: {e}") if freeze_backbone_initially: self.freeze_backbone() # Pooling layer if pooling_type == 'attention': self.pooling = AttentionPooling( in_channels=self.backbone_out_features, hidden_channels=attention_hidden_channels ) pooling_out_features = self.backbone_out_features elif pooling_type == 'gem': self.pooling = GeMPooling(p=3.0, learnable=True) pooling_out_features = self.backbone_out_features elif pooling_type == 'hybrid': self.pooling = HybridPooling( in_channels=self.backbone_out_features, attention_hidden=attention_hidden_channels, output_mode='concat' ) pooling_out_features = self.backbone_out_features * 2 else: # 'avg' self.pooling = nn.AdaptiveAvgPool2d(1) pooling_out_features = self.backbone_out_features # Embedding layers embedding_layers = [nn.Linear(pooling_out_features, embedding_dim)] if add_bn_to_embedding: embedding_layers.append(nn.BatchNorm1d(embedding_dim)) if embedding_dropout_rate > 0.0: embedding_layers.append(nn.Dropout(embedding_dropout_rate)) self.embedding_fc = nn.Sequential(*embedding_layers) self.arcface_head = ArcFaceHead(embedding_dim, num_classes, s=arcface_s, m=arcface_m) logger.info(f"StableEmbeddingModel initialized") logger.info(f" Embedding Dim: {embedding_dim}, Num Classes: {num_classes}") logger.info(f" ArcFace s: {arcface_s}, m: {arcface_m}") logger.info(f" Backbone out features: {self.backbone_out_features}") logger.info(f" Pooling type: {pooling_type}") def freeze_backbone(self): """Freeze all backbone parameters.""" logger.info("Freezing backbone parameters.") for param in self.backbone.parameters(): param.requires_grad = False def unfreeze_backbone(self, specific_layer_keywords=None, verbose=False): """Unfreeze backbone parameters.""" logger.info(f"Unfreezing backbone parameters... (Keywords: {specific_layer_keywords})") unfrozen_count = 0 for name, param in self.backbone.named_parameters(): if specific_layer_keywords is None or any(kw in name for kw in specific_layer_keywords): param.requires_grad = True unfrozen_count += 1 if verbose: logger.info(f" Unfroze: {name}") logger.info(f"Total parameters unfrozen: {unfrozen_count}") def forward( self, x: torch.Tensor, labels: Optional[torch.Tensor] = None, object_mask: Optional[torch.Tensor] = None, return_softmax: bool = False, return_attention_map: bool = True ): """ Forward pass. Args: x: Input images [B, 3, H, W] labels: Optional class labels [B] object_mask: Optional object mask for attention guidance return_softmax: Return softmax probabilities instead of logits return_attention_map: Return attention visualization map Returns: emb_norm: L2-normalized embeddings [B, D] logits/probs: Class logits or probabilities [B, num_classes] attn_map: Optional attention map for visualization """ features = self.backbone_feature_extractor(x) attn_map = None if self.pooling_type == 'attention': pooled, attn_map = self.pooling(features, object_mask=object_mask, return_attention_map=return_attention_map) elif self.pooling_type == 'hybrid': pooled, attn_map = self.pooling(features, object_mask=object_mask, return_attention_map=return_attention_map) elif self.pooling_type == 'gem': pooled = self.pooling(features) else: # avg pooled = self.pooling(features).squeeze(-1).squeeze(-1) emb_raw = self.embedding_fc(pooled) emb_norm = F.normalize(emb_raw, p=2, dim=1) logits = self.arcface_head(emb_norm, labels) output_attn = attn_map if return_attention_map else None if return_softmax: probabilities = F.softmax(logits, dim=1) return emb_norm, probabilities, output_attn return emb_norm, logits, output_attn # ============================================================================= # Embedding Classifier # ============================================================================= class EmbeddingClassifier: """ Main classifier for inference using embedding-based approach. This classifier loads a trained model and uses FAISS for fast nearest neighbor search combined with centroid-based filtering for efficient classification. Configuration example: config = { 'log_level': 'INFO', 'dataset': {'path': 'embeddings.pt'}, 'model': { 'checkpoint_path': 'model.ckpt', 'backbone_model_name': 'maxvit_base_tf_224', 'embedding_dim': 512, 'num_classes': 639, 'arcface_s': 64.0, 'arcface_m': 0.2, 'pooling_type': 'attention', 'device': 'cuda' }, 'use_knn': True # Enable/disable kNN classifier (default: True) } """ def __init__(self, config: Dict): # Validate configuration self._validate_config(config) logger.setLevel(getattr(logging, config.get('log_level', 'INFO').upper())) # Load dataset self._load_data(config["dataset"]["path"]) self.dim = self.db_embeddings.shape[1] self._prepare_centroids() logger.info("Initializing EmbeddingClassifier...") # Setup device self.device = config["model"].get("device", "cpu") # Load inference configuration self.use_knn = config.get('use_knn', DEFAULT_USE_KNN) self.arcface_min_score = config.get('arcface_min_score', DEFAULT_ARCFACE_MIN_SCORE) self.centroid_fallback_score = config.get('centroid_fallback_score', DEFAULT_CENTROID_FALLBACK_SCORE) self.default_topk_centroid = config.get('topk_centroid', DEFAULT_TOPK_CENTROID) self.default_topk_neighbors = config.get('topk_neighbors', DEFAULT_TOPK_NEIGHBORS) self.default_centroid_threshold = config.get('centroid_threshold', DEFAULT_CENTROID_THRESHOLD) self.default_neighbor_threshold = config.get('neighbor_threshold', DEFAULT_NEIGHBOR_THRESHOLD) self.default_topk_arcface = config.get('topk_arcface', DEFAULT_TOPK_ARCFACE) # Reranking configuration self.rerank_mode = config.get('rerank_mode', DEFAULT_RERANK_MODE) self.arcface_weight = config.get('arcface_weight', DEFAULT_ARCFACE_WEIGHT) self.knn_weight = config.get('knn_weight', DEFAULT_KNN_WEIGHT) self.rrf_k = config.get('rrf_k', DEFAULT_RRF_K) # Transform configuration self.use_albumentations = config.get('use_albumentations', DEFAULT_USE_ALBUMENTATIONS) logger.info(f"Inference config: use_knn={self.use_knn}, " f"arcface_min={self.arcface_min_score}, " f"centroid_fallback={self.centroid_fallback_score}, " f"topk_centroid={self.default_topk_centroid}, " f"topk_neighbors={self.default_topk_neighbors}, " f"topk_arcface={self.default_topk_arcface}") logger.info(f"Reranking config: mode={self.rerank_mode}, " f"arcface_weight={self.arcface_weight}, " f"knn_weight={self.knn_weight}, " f"rrf_k={self.rrf_k}") # Load model self._load_model(config["model"]) # Validate embedding dimensions match model_embedding_dim = config["model"]["embedding_dim"] if self.dim != model_embedding_dim: raise ValueError( f"Embedding dimension mismatch: dataset has {self.dim}, " f"but model expects {model_embedding_dim}" ) # Infer input size from model or use config/default self.input_size = self._get_input_size(config["model"]) # Setup transforms based on configuration self.transform = self._create_transforms() logger.info(f"Using {'Albumentations' if self.use_albumentations else 'torchvision'} transforms") # Create ID to label mapping self.id_to_label = {internal_id: self.keys[internal_id]['label'] for internal_id in self.keys} # Pre-build FAISS indices for better performance (only if kNN is enabled) if self.use_knn: self._prepare_faiss_indices() else: logger.info("kNN classifier is disabled - skipping FAISS index creation") logger.info("EmbeddingClassifier initialized successfully.") def _create_transforms(self): """Create image transforms based on configuration. Returns: Transform pipeline (Albumentations or torchvision) """ if self.use_albumentations: if not ALBUMENTATIONS_AVAILABLE: logger.warning("Albumentations requested but not installed. Falling back to torchvision.") logger.warning("Install with: pip install albumentations") self.use_albumentations = False else: logger.info("Creating Albumentations transform pipeline") return A.Compose([ A.Resize(self.input_size, self.input_size), A.Normalize(mean=(0.485, 0.456, 0.406), std=(0.229, 0.224, 0.225)), ToTensorV2(), ]) # Default: torchvision transforms logger.info("Creating torchvision transform pipeline") return transforms.Compose([ transforms.Resize((self.input_size, self.input_size), Image.Resampling.BILINEAR), transforms.ToTensor(), transforms.Normalize(mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225]), ]) @staticmethod def _safe_int_to_str(value) -> str: """Safely convert value to string, handling tensors, numpy arrays, UUIDs, etc. Args: value: Any value (tensor, numpy array, int, float, string/UUID, etc.) Returns: String representation of the value """ # Handle torch tensors if hasattr(value, 'item'): value = value.item() # Handle numpy arrays elif hasattr(value, 'tolist'): value = value.tolist() # If already a string, return as is if isinstance(value, str): return value # Try to convert to int, fallback to str if it fails (e.g., UUIDs) try: return str(int(value)) except (ValueError, TypeError): return str(value) def _validate_config(self, config: Dict) -> None: """Validate configuration structure and required fields.""" if not isinstance(config, dict): raise TypeError(f"Config must be a dictionary, got {type(config)}") # Check required keys if "dataset" not in config: raise ValueError("Config must contain 'dataset' key") if "path" not in config["dataset"]: raise ValueError("Config['dataset'] must contain 'path' key") if "model" not in config: raise ValueError("Config must contain 'model' key") required_model_keys = ["checkpoint_path", "backbone_model_name", "embedding_dim", "num_classes"] for key in required_model_keys: if key not in config["model"]: raise ValueError(f"Config['model'] must contain '{key}' key") # Validate numeric parameters if config["model"]["embedding_dim"] <= 0: raise ValueError(f"embedding_dim must be positive, got {config['model']['embedding_dim']}") if config["model"]["num_classes"] <= 0: raise ValueError(f"num_classes must be positive, got {config['model']['num_classes']}") # Validate optional thresholds if present for param in ["arcface_min_score", "centroid_fallback_score", "centroid_threshold", "neighbor_threshold"]: if param in config and (config[param] < 0 or config[param] > 1): raise ValueError(f"{param} must be between 0 and 1, got {config[param]}") logger.info("Configuration validated successfully") def _get_input_size(self, model_config: Dict) -> int: """Infer input size from model config or backbone.""" # Check if explicitly provided in config if "input_size" in model_config: return model_config["input_size"] # Try to infer from backbone name backbone_name = model_config.get("backbone_model_name", "") # Check for common size patterns in backbone name for size in [512, 384, 256, 224]: if f"_{size}" in backbone_name or f"{size}" in backbone_name: logger.info(f"Inferred input size {size} from backbone name") return size # Try to get from model's default config if hasattr(self.model, 'backbone') and hasattr(self.model.backbone, 'default_cfg'): cfg = self.model.backbone.default_cfg if 'input_size' in cfg: input_size = cfg['input_size'] if isinstance(input_size, (tuple, list)) and len(input_size) == 3: size = input_size[1] # Get height logger.info(f"Using input size {size} from model config") return size # Default fallback logger.info(f"Using default input size {DEFAULT_IMAGE_SIZE}") return DEFAULT_IMAGE_SIZE def _load_model(self, model_config: Dict): """Load model from Lightning checkpoint or regular PyTorch checkpoint.""" checkpoint_path = model_config["checkpoint_path"] # Validate checkpoint exists if not Path(checkpoint_path).exists(): raise FileNotFoundError(f"Checkpoint not found: {checkpoint_path}") backbone_name = model_config.get("backbone_model_name", "maxvit_base_tf_224") embedding_dim = model_config.get("embedding_dim", 512) num_classes = model_config.get("num_classes", 639) arcface_s = model_config.get("arcface_s", 64.0) arcface_m = model_config.get("arcface_m", 0.2) pooling_type = model_config.get("pooling_type", "attention") # Determine model class based on backbone is_vit = any(x in backbone_name.lower() for x in SUPPORTED_VIT_BACKBONES) model_cls = StableEmbeddingModelViT if is_vit else StableEmbeddingModel # Create model if is_vit: self.model = model_cls( embedding_dim=embedding_dim, num_classes=num_classes, backbone_model_name=backbone_name, arcface_s=arcface_s, arcface_m=arcface_m, pooling_type=pooling_type, pretrained_backbone=False, # We'll load from checkpoint ) else: self.model = model_cls( embedding_dim=embedding_dim, num_classes=num_classes, backbone_model_name=backbone_name, arcface_s=arcface_s, arcface_m=arcface_m, pooling_type=pooling_type, pretrained_backbone=False, # We'll load from checkpoint ) # Load checkpoint # WARNING: torch.load uses pickle which can execute arbitrary code. # Only load checkpoints from trusted sources! # TODO: Add checksum verification for production use logger.warning(f"Loading checkpoint with weights_only=False (security risk). " f"Only load from trusted sources: {checkpoint_path}") try: checkpoint = torch.load(checkpoint_path, map_location=torch.device('cpu'), weights_only=True) except Exception as e: logger.warning(f"Failed to load with weights_only=True: {e}. Falling back to weights_only=False") checkpoint = torch.load(checkpoint_path, map_location=torch.device('cpu'), weights_only=False) # Handle Lightning checkpoint format if 'state_dict' in checkpoint: state_dict = checkpoint['state_dict'] # Remove 'model.' prefix if present (from Lightning) new_state_dict = {} for k, v in state_dict.items(): if k.startswith('model.'): new_state_dict[k[6:]] = v else: new_state_dict[k] = v state_dict = new_state_dict else: state_dict = checkpoint # Load state dict with error handling try: self.model.load_state_dict(state_dict, strict=True) logger.info(f"Model loaded successfully from {checkpoint_path}") except RuntimeError as e: logger.warning(f"Strict loading failed: {str(e)[:200]}") result = self.model.load_state_dict(state_dict, strict=False) if result.missing_keys: logger.warning(f"Missing keys in checkpoint: {result.missing_keys[:5]}") if result.unexpected_keys: logger.warning(f"Unexpected keys in checkpoint: {result.unexpected_keys[:5]}") logger.info(f"Model loaded with strict=False from {checkpoint_path}") self.model.to(self.device) self.model.eval() # Log model info total_params = sum(p.numel() for p in self.model.parameters()) trainable_params = sum(p.numel() for p in self.model.parameters() if p.requires_grad) logger.info(f"Model loaded and moved to {self.device}") logger.info(f"Total parameters: {total_params:,}, Trainable: {trainable_params:,}") return self.model def _load_data(self, dataset_path: str) -> None: """Load embeddings database.""" # Validate dataset file exists if not Path(dataset_path).exists(): raise FileNotFoundError(f"Dataset file not found: {dataset_path}") try: logger.info(f"Loading dataset from {dataset_path}") try: data = torch.load(dataset_path, weights_only=True) except Exception as e: logger.warning(f"Failed to load dataset with weights_only=True: {e}. Using weights_only=False") data = torch.load(dataset_path, weights_only=False) except Exception as e: raise RuntimeError(f"Failed to load dataset from {dataset_path}: {e}") # Validate required keys required_keys = ['embeddings', 'labels', 'image_ids', 'annotation_ids', 'drawn_fish_ids', 'labels_keys'] for key in required_keys: if key not in data: raise ValueError(f"Dataset missing required key: '{key}'") # Optimize: direct conversion to float32 numpy array self.db_embeddings = np.asarray(data['embeddings'], dtype=np.float32) self.db_labels = np.array(data['labels']) self.image_ids = data['image_ids'] self.annotation_ids = data['annotation_ids'] self.drawn_fish_ids = data['drawn_fish_ids'] self.keys = data['labels_keys'] # Validate array lengths match n_embeddings = len(self.db_embeddings) if not (len(self.db_labels) == len(self.image_ids) == len(self.annotation_ids) == len(self.drawn_fish_ids) == n_embeddings): raise ValueError( f"Array length mismatch: embeddings={n_embeddings}, labels={len(self.db_labels)}, " f"image_ids={len(self.image_ids)}, annotation_ids={len(self.annotation_ids)}, " f"drawn_fish_ids={len(self.drawn_fish_ids)}" ) self.label_to_species_id = { v['label']: v['species_id'] for v in self.keys.values() } # Calculate memory usage embeddings_size_mb = self.db_embeddings.nbytes / (1024 * 1024) logger.info(f"Dataset loaded from {dataset_path}") logger.info(f" Embeddings shape: {self.db_embeddings.shape}") logger.info(f" Embeddings memory: {embeddings_size_mb:.2f} MB") logger.info(f" Unique labels: {len(np.unique(self.db_labels))}") def __call__(self, img: Union[np.ndarray, List[np.ndarray]]): """ Perform inference on image(s). Args: img: Single image as np.ndarray or list of images Returns: List of prediction results for each image """ if isinstance(img, np.ndarray): return self.inference_numpy(img) elif isinstance(img, list) and all(isinstance(i, np.ndarray) for i in img): return self.inference_numpy_batch(img) else: raise TypeError("Input must be np.ndarray or List[np.ndarray].") def _preprocess_image(self, img: np.ndarray, img_index: int = 0) -> np.ndarray: """Preprocess a single image to RGB uint8 format. Args: img: Input image array img_index: Index of image in batch (for error messages) Returns: Preprocessed RGB image as uint8 array """ # Validate input if img.ndim not in [2, 3]: raise ValueError(f"Image {img_index} must be 2D or 3D array, got shape {img.shape}") if img.ndim == 3 and img.shape[2] not in [1, 3, 4]: raise ValueError(f"Image {img_index} must have 1, 3, or 4 channels, got {img.shape[2]}") # Check for empty/invalid images if img.size == 0 or min(img.shape[:2]) == 0: raise ValueError(f"Image {img_index} has invalid dimensions: {img.shape}") # Convert grayscale to RGB if needed if img.ndim == 2 or (img.ndim == 3 and img.shape[2] == 1): img = np.stack([img.squeeze()] * 3, axis=-1) elif img.shape[2] == 4: # RGBA img = img[:, :, :3] # Ensure correct dtype and range if img.dtype != np.uint8: max_val = img.max() if max_val == 0: logger.warning(f"Image {img_index} is completely black (all zeros)") img = np.zeros(img.shape, dtype=np.uint8) elif max_val <= 1.0: img = (img * 255).astype(np.uint8) else: img = img.astype(np.uint8) return img def inference_numpy(self, img: np.ndarray): """Inference on a single numpy image.""" try: img = self._preprocess_image(img, img_index=0) # Apply transforms based on type if self.use_albumentations and ALBUMENTATIONS_AVAILABLE: # Albumentations expects numpy array in HWC format transformed = self.transform(image=img) tensor = transformed['image'].unsqueeze(0).to(self.device) else: # torchvision expects PIL Image pil_img = Image.fromarray(img) tensor = self.transform(pil_img).unsqueeze(0).to(self.device) return self._inference_batch_tensor(tensor)[0] except Exception as e: logger.error(f"Failed to process image: {e}", exc_info=True) raise RuntimeError(f"Image processing failed: {e}") def inference_numpy_batch(self, imgs: List[np.ndarray]): """Inference on a batch of numpy images.""" if not imgs: raise ValueError("Empty image list provided") if len(imgs) > MAX_BATCH_SIZE: logger.info(f"Large batch detected ({len(imgs)} images). " f"Will be processed in chunks of {MAX_BATCH_SIZE}.") try: processed_tensors = [] for i, img in enumerate(imgs): img = self._preprocess_image(img, img_index=i) # Apply transforms based on type if self.use_albumentations and ALBUMENTATIONS_AVAILABLE: # Albumentations expects numpy array transformed = self.transform(image=img) processed_tensors.append(transformed['image']) else: # torchvision expects PIL Image pil_img = Image.fromarray(img) processed_tensors.append(self.transform(pil_img)) tensors = torch.stack(processed_tensors).to(self.device) return self._inference_batch_tensor(tensors) except Exception as e: logger.error(f"Failed to process image batch: {e}", exc_info=True) raise RuntimeError(f"Batch image processing failed: {e}") def _inference_batch_tensor(self, tensors: torch.Tensor): """Internal inference on tensor batch.""" batch_size = tensors.shape[0] # Validate batch size to prevent OOM if batch_size > MAX_BATCH_SIZE: logger.warning(f"Batch size {batch_size} exceeds MAX_BATCH_SIZE={MAX_BATCH_SIZE}. " f"Processing in chunks to prevent OOM.") # Process in chunks all_results = [] for i in range(0, batch_size, MAX_BATCH_SIZE): chunk = tensors[i:i + MAX_BATCH_SIZE] chunk_results = self._inference_batch_tensor(chunk) all_results.extend(chunk_results) return all_results with torch.no_grad(): embeddings, archead_logits, _ = self.model(tensors, return_softmax=False) # Get top-5 ArcFace predictions k_arcface = min(5, archead_logits.shape[1]) top_probabilities, top_indices = torch.topk(archead_logits, k_arcface) # Store top-5 ArcFace predictions with their scores topk_arcface = [] for i in range(len(top_indices)): batch_top5 = [] for rank in range(k_arcface): pred_id = top_indices[i][rank].item() pred_score = top_probabilities[i][rank].item() batch_top5.append((pred_id, pred_score, rank)) topk_arcface.append(batch_top5) # Use kNN search if enabled if self.use_knn: knn_output = self.get_top_neighbors_from_embeddings(embeddings) # Log summary instead of full output (only if debug enabled) if logger.isEnabledFor(logging.DEBUG): logger.debug(f"Inference: {len(knn_output)} predictions generated (kNN enabled)") else: # kNN disabled - use empty results knn_output = [{} for _ in range(len(top_indices))] if logger.isEnabledFor(logging.DEBUG): logger.debug(f"Inference: kNN disabled, using only ArcFace predictions") return self._postprocess_hybrid(knn_output, topk_arcface) def _rerank_predictions( self, arcface_predictions: List[Tuple[int, float, int]], knn_predictions: Dict, mode: str = 'weighted_fusion' ) -> List[Tuple[int, float, str]]: """ Rerank predictions using different fusion strategies. Args: arcface_predictions: List of (label_id, score, rank) from ArcFace knn_predictions: Dict of {label_id: data} from kNN mode: Reranking mode ('weighted_fusion', 'rrf', 'hybrid') Returns: List of (label_id, final_score, source) tuples, sorted by final_score """ combined_scores = {} if mode == 'weighted_fusion': # Weighted Fusion: combine normalized scores with weights # ArcFace scores are already softmax probabilities [0, 1] for label_id, prob, rank in arcface_predictions: combined_scores[label_id] = { 'arcface_score': prob, 'arcface_rank': rank, 'knn_score': 0.0, 'knn_rank': None } # Add kNN scores (already normalized similarities [0, 1]) for idx, (label_id, data) in enumerate( sorted(knn_predictions.items(), key=lambda x: x[1]['similarity'] / x[1]['times'], reverse=True) ): knn_score = data['similarity'] / data['times'] knn_score = max(0.0, min(1.0, knn_score)) # Clamp to [0, 1] if isinstance(label_id, (int, np.integer)): label_id_int = int(label_id) else: # Find corresponding ID for string label label_id_int = None for k, v in self.id_to_label.items(): if v == str(label_id): label_id_int = k break if label_id_int is None: continue if label_id_int not in combined_scores: combined_scores[label_id_int] = { 'arcface_score': 0.0, 'arcface_rank': None, 'knn_score': knn_score, 'knn_rank': idx } else: combined_scores[label_id_int]['knn_score'] = knn_score combined_scores[label_id_int]['knn_rank'] = idx # Calculate weighted final scores final_scores = [] for label_id, scores in combined_scores.items(): final_score = ( self.arcface_weight * scores['arcface_score'] + self.knn_weight * scores['knn_score'] ) # Determine source if scores['arcface_rank'] is not None and scores['knn_rank'] is not None: source = 'both' elif scores['arcface_rank'] is not None: source = 'arcface' else: source = 'knn' final_scores.append((label_id, final_score, source)) elif mode == 'rrf': # Reciprocal Rank Fusion for label_id, prob, rank in arcface_predictions: rrf_score = 1.0 / (self.rrf_k + rank) combined_scores[label_id] = { 'rrf_score': rrf_score, 'arcface_rank': rank } # Add kNN RRF scores for idx, (label_id, data) in enumerate( sorted(knn_predictions.items(), key=lambda x: x[1]['similarity'] / x[1]['times'], reverse=True) ): if isinstance(label_id, (int, np.integer)): label_id_int = int(label_id) else: label_id_int = None for k, v in self.id_to_label.items(): if v == str(label_id): label_id_int = k break if label_id_int is None: continue knn_rrf = 1.0 / (self.rrf_k + idx) if label_id_int not in combined_scores: combined_scores[label_id_int] = { 'rrf_score': knn_rrf, 'knn_rank': idx } else: combined_scores[label_id_int]['rrf_score'] += knn_rrf final_scores = [ (label_id, scores['rrf_score'], 'both' if 'arcface_rank' in scores and 'knn_rank' in scores else 'arcface' if 'arcface_rank' in scores else 'knn') for label_id, scores in combined_scores.items() ] else: # 'hybrid' - original behavior # Top-5 ArcFace first, then top-5 unique kNN return None # Will be handled separately # Sort by final score (descending) final_scores.sort(key=lambda x: x[1], reverse=True) return final_scores def _postprocess_hybrid(self, knn_results, topk_arcface) -> List[PredictionResult]: """Combine top-5 ArcFace and top-5 unique kNN predictions. Args: knn_results: kNN prediction results (list of dicts) topk_arcface: List of lists with (label_id, score, rank) tuples for top-5 ArcFace Returns: List of PredictionResult objects: - Positions 1-5: Top-5 ArcFace predictions (with softmax probabilities) - Positions 6-10: Top-5 unique kNN predictions (not in ArcFace top-5) """ results = [] for batch_idx in range(len(knn_results)): arcface_top5 = topk_arcface[batch_idx] knn_dict = knn_results[batch_idx] # Step 1: Apply softmax to ArcFace logits to get probabilities arcface_scores = torch.tensor([score for _, score, _ in arcface_top5]) arcface_probs = F.softmax(arcface_scores, dim=0).cpu().numpy() # Update arcface_top5 with probabilities arcface_top5_with_probs = [ (label_id, float(arcface_probs[idx]), rank) for idx, (label_id, score, rank) in enumerate(arcface_top5) ] # Step 2: Rerank predictions based on mode if self.rerank_mode in ['weighted_fusion', 'rrf']: reranked = self._rerank_predictions( arcface_top5_with_probs, knn_dict, mode=self.rerank_mode ) # Convert reranked results to PredictionResult objects final_predictions = [] for label_id, final_score, source in reranked[:10]: # Top-10 label = self.id_to_label.get(label_id, str(label_id)) species_id = self.label_to_species_id.get(label, -1) # Get additional info from kNN if available image_id = None annotation_id = None drawn_fish_id = None if label_id in [int(k) if isinstance(k, (int, np.integer)) else None for k in knn_dict.keys()]: for k, data in knn_dict.items(): k_int = int(k) if isinstance(k, (int, np.integer)) else None if k_int == label_id and data.get('index') is not None: idx = data['index'] try: if 0 <= idx < len(self.image_ids): # Convert to string, handling tensors/numpy image_id = self._safe_int_to_str(self.image_ids[idx]) annotation_id = self._safe_int_to_str(self.annotation_ids[idx]) drawn_fish_id = self._safe_int_to_str(self.drawn_fish_ids[idx]) except (IndexError, KeyError): pass break final_predictions.append(PredictionResult( name=label, species_id=species_id, distance=final_score, accuracy=final_score, image_id=image_id, annotation_id=annotation_id, drawn_fish_id=drawn_fish_id, )) results.append(final_predictions) continue # Step 3: Hybrid mode - original behavior (top-5 ArcFace + top-5 unique kNN) arcface_predictions = [] arcface_label_ids = set() for idx, (label_id, score, rank) in enumerate(arcface_top5): label = self.id_to_label.get(label_id, str(label_id)) arcface_label_ids.add(label_id) species_id = self.label_to_species_id.get(label) if species_id is None: species_id = -1 probability = float(arcface_probs[idx]) # Softmax probability [0, 1] arcface_predictions.append(PredictionResult( name=label, species_id=species_id, distance=score, # Keep raw logit for reference accuracy=probability, # Use softmax probability image_id=None, annotation_id=None, drawn_fish_id=None, )) # Step 3: Create kNN predictions (exclude those already in ArcFace top-5) knn_predictions = [] for label_id, data in knn_dict.items(): # Handle label conversion if isinstance(label_id, (int, np.integer)): label = self.id_to_label.get(int(label_id), str(label_id)) label_id_int = int(label_id) else: # Already a string label name label = str(label_id) # Try to find corresponding ID label_id_int = None for k, v in self.id_to_label.items(): if v == label: label_id_int = k break # Skip if this label is already in ArcFace top-5 if label_id_int in arcface_label_ids: continue index = data.get("index") # Safely access arrays with bounds checking image_id = None annotation_id = None drawn_fish_id = None if index is not None: try: if 0 <= index < len(self.image_ids): # Convert to string, handling tensors/numpy image_id = self._safe_int_to_str(self.image_ids[index]) annotation_id = self._safe_int_to_str(self.annotation_ids[index]) drawn_fish_id = self._safe_int_to_str(self.drawn_fish_ids[index]) except (IndexError, KeyError) as e: logger.warning(f"Error accessing index {index}: {e}") species_id = self.label_to_species_id.get(label) if species_id is None: species_id = -1 # Calculate average similarity score (already normalized in [0, 1] from cosine similarity) avg_similarity = data['similarity'] / data['times'] # Clamp to [0, 1] for safety avg_similarity = max(0.0, min(1.0, avg_similarity)) knn_predictions.append(PredictionResult( name=label, species_id=species_id, distance=data['similarity'], accuracy=avg_similarity, # Normalized similarity score image_id=image_id, annotation_id=annotation_id, drawn_fish_id=drawn_fish_id, )) # Step 4: Sort kNN predictions by average similarity (descending) and take top-5 knn_predictions.sort(key=lambda x: x.accuracy, reverse=True) top5_knn = knn_predictions[:5] # Step 5: Combine: ArcFace top-5 first, then unique kNN top-5 final_predictions = arcface_predictions + top5_knn results.append(final_predictions) return results def _postprocess(self, class_results, top1_arcface) -> List[PredictionResult]: """Convert raw results to PredictionResult objects with custom sorting. Args: class_results: Raw prediction results top1_arcface: List of (label_id, score) tuples for top-1 ArcFace predictions Returns: List of sorted PredictionResult objects """ results = [] for batch_idx, single_fish in enumerate(class_results): fish_results = [] top1_result = None top1_label_id = top1_arcface[batch_idx][0] for label_id, data in single_fish.items(): # Handle label conversion - label_id can be int or string if isinstance(label_id, (int, np.integer)): label = self.id_to_label.get(int(label_id), str(label_id)) label_id_int = int(label_id) else: # Already a string label name label = str(label_id) # Try to find corresponding ID for comparison label_id_int = None for k, v in self.id_to_label.items(): if v == label: label_id_int = k break index = data["index"] # Safely access arrays with bounds checking image_id = None annotation_id = None drawn_fish_id = None if index is not None: try: if 0 <= index < len(self.image_ids): # Convert to string, handling tensors/numpy image_id = self._safe_int_to_str(self.image_ids[index]) annotation_id = self._safe_int_to_str(self.annotation_ids[index]) drawn_fish_id = self._safe_int_to_str(self.drawn_fish_ids[index]) else: logger.warning(f"Index {index} out of bounds for arrays of length {len(self.image_ids)}") except (IndexError, KeyError) as e: logger.warning(f"Error accessing index {index}: {e}") species_id = self.label_to_species_id.get(label) if species_id is None: logger.warning(f"Unknown label '{label}' not found in label_to_species_id mapping") species_id = -1 # Fallback for backward compatibility # Calculate average similarity score avg_similarity = data['similarity'] / data['times'] result = PredictionResult( name=label, species_id=species_id, distance=data['similarity'], accuracy=avg_similarity, # Average similarity score image_id=image_id, annotation_id=annotation_id, drawn_fish_id=drawn_fish_id, ) # Check if this is the top-1 ArcFace prediction is_arcface_top1 = ( (label_id_int is not None and label_id_int == top1_label_id) or (data.get('source') == 'arcface' and data.get('arcface_rank') == 0) ) if is_arcface_top1: top1_result = result else: fish_results.append(result) # Sort remaining results by average similarity (descending) fish_results.sort(key=lambda x: x.accuracy, reverse=True) # Place top-1 ArcFace prediction first, then kNN results if top1_result is not None: final_results = [top1_result] + fish_results else: final_results = fish_results if logger.isEnabledFor(logging.WARNING): logger.warning(f"Top-1 ArcFace prediction not found in results for batch {batch_idx}") results.append(final_results) return results def _prepare_centroids(self) -> None: """Compute class centroids for efficient filtering.""" unique_labels = np.unique(self.db_labels) self.label_to_centroid = {} skipped_labels = [] for label in unique_labels: class_embs = self.db_embeddings[self.db_labels == label] if len(class_embs) == 0: logger.warning(f"Label {label} has no embeddings, skipping") skipped_labels.append(label) continue centroid = np.mean(class_embs, axis=0) norm = np.linalg.norm(centroid) if norm < NUMERICAL_EPSILON: logger.warning(f"Label {label} has zero-norm centroid, using unnormalized") self.label_to_centroid[label] = centroid else: self.label_to_centroid[label] = centroid / norm self.centroid_matrix = np.stack([self.label_to_centroid[label] for label in self.label_to_centroid]) self.centroid_labels = list(self.label_to_centroid.keys()) if skipped_labels: logger.warning(f"Skipped {len(skipped_labels)} labels with no embeddings") logger.info(f"Prepared {len(self.centroid_labels)} class centroids") def _prepare_faiss_indices(self) -> None: """Pre-build FAISS indices for each class for faster search.""" logger.info("Building FAISS indices for each class...") self.class_indices = {} unique_labels = np.unique(self.db_labels) for label in unique_labels: # Use np.where directly to get indices (more memory efficient) global_indices = np.where(self.db_labels == label)[0] class_embs = self.db_embeddings[global_indices] if len(class_embs) > 0: # Create FAISS index for this class index = faiss.IndexFlatIP(self.dim) index.add(class_embs) self.class_indices[label] = { 'index': index, 'global_indices': global_indices, 'size': len(class_embs) } logger.info(f"Built FAISS indices for {len(self.class_indices)} classes") def get_top_neighbors_from_embeddings( self, query_embeddings: Union[np.ndarray, torch.Tensor], topk_centroid: Optional[int] = None, topk_neighbors: Optional[int] = None, centroid_threshold: Optional[float] = None, neighbor_threshold: Optional[float] = None ) -> List[Dict[str, Dict[str, Union[float, int, None]]]]: """ Find top neighbors using centroid filtering + FAISS search. Args: query_embeddings: Query embeddings [B, D] topk_centroid: Number of top centroids to consider (None = use default) topk_neighbors: Number of neighbors to retrieve (None = use default) centroid_threshold: Minimum similarity to centroid (None = use default) neighbor_threshold: Minimum similarity to neighbor (None = use default) Returns: List of dictionaries mapping labels to similarity scores """ # Use default values if not specified topk_centroid = self.default_topk_centroid if topk_centroid is None else topk_centroid topk_neighbors = self.default_topk_neighbors if topk_neighbors is None else topk_neighbors centroid_threshold = self.default_centroid_threshold if centroid_threshold is None else centroid_threshold neighbor_threshold = self.default_neighbor_threshold if neighbor_threshold is None else neighbor_threshold # Validate parameters if topk_centroid <= 0: raise ValueError(f"topk_centroid must be positive, got {topk_centroid}") if topk_neighbors <= 0: raise ValueError(f"topk_neighbors must be positive, got {topk_neighbors}") if not 0 <= centroid_threshold <= 1: raise ValueError(f"centroid_threshold must be in [0, 1], got {centroid_threshold}") if not 0 <= neighbor_threshold <= 1: raise ValueError(f"neighbor_threshold must be in [0, 1], got {neighbor_threshold}") start_time = time.time() if logger.isEnabledFor(logging.DEBUG): logger.debug(f"Starting search over {len(query_embeddings)} embeddings") if isinstance(query_embeddings, torch.Tensor): query_embeddings = query_embeddings.cpu().numpy().astype("float32") # Timing breakdown timing = {'centroid': 0, 'faiss': 0, 'aggregation': 0} # Step 1: Vectorized centroid similarity computation for all queries t0 = time.time() # Embeddings are already L2-normalized, use matrix multiplication for cosine similarity all_centroid_sims = np.dot(query_embeddings, self.centroid_matrix.T) # [B, num_centroids] timing['centroid'] = time.time() - t0 results = [] for query_idx, query_emb in enumerate(query_embeddings): centroid_sims = all_centroid_sims[query_idx] top_centroid_indices = np.argsort(-centroid_sims)[:topk_centroid] centroid_scores = { self.centroid_labels[idx]: centroid_sims[idx] for idx in top_centroid_indices if centroid_sims[idx] >= centroid_threshold } selected_classes = set(centroid_scores.keys()) if not selected_classes: if logger.isEnabledFor(logging.DEBUG): max_sim = centroid_sims[top_centroid_indices[0]] if len(top_centroid_indices) > 0 else 0 logger.debug(f"Query {query_idx}: No classes passed centroid threshold " f"(max similarity: {max_sim:.3f}, threshold: {centroid_threshold})") results.append({}) continue # Step 2: FAISS search using pre-built indices t0 = time.time() score_map = defaultdict(lambda: {'index': None, 'similarity': 0.0, 'times': 0, 'source': 'knn'}) for label in selected_classes: if label not in self.class_indices: if logger.isEnabledFor(logging.DEBUG): logger.debug(f"Label {label} not found in class_indices, skipping") continue class_data = self.class_indices[label] class_index = class_data['index'] global_indices = class_data['global_indices'] # Search within this class k = min(topk_neighbors, class_data['size']) distances, indices = class_index.search(query_emb.reshape(1, -1), k) # Aggregate results for this class for rank, idx in enumerate(indices[0]): sim = float(distances[0][rank]) if sim >= neighbor_threshold: original_idx = int(global_indices[idx]) score_map[label]['similarity'] += sim score_map[label]['times'] += 1 score_map[label]['source'] = 'knn' if score_map[label]['index'] is None: score_map[label]['index'] = original_idx timing['faiss'] += time.time() - t0 # Step 3: Add centroid-only predictions for classes without neighbors t0 = time.time() for label, sim in centroid_scores.items(): if label not in score_map: # Use actual centroid similarity instead of fixed fallback score centroid_sim = max(float(sim), self.centroid_fallback_score) score_map[label] = { 'index': None, 'similarity': centroid_sim, 'times': 1, 'source': 'knn' } timing['aggregation'] += time.time() - t0 results.append(dict(score_map)) total_time = time.time() - start_time if logger.isEnabledFor(logging.DEBUG): logger.debug(f"Search completed in {total_time:.3f}s " f"(centroid: {timing['centroid']:.3f}s, " f"faiss: {timing['faiss']:.3f}s, " f"aggregation: {timing['aggregation']:.3f}s)") # Log performance metrics for production monitoring (only for larger batches) if len(query_embeddings) > 5: throughput = len(query_embeddings) / total_time if total_time > 0 else 0 logger.info(f"Batch search: {len(query_embeddings)} queries in {total_time:.3f}s " f"({throughput:.1f} queries/s)") return results def get_model_info(self) -> Dict: """Return model configuration and statistics. Returns: Dictionary with model information """ info = { 'embedding_dim': self.dim, 'num_classes': len(self.keys), 'num_embeddings': len(self.db_embeddings), 'device': str(self.device), 'input_size': self.input_size, 'num_centroid_classes': len(self.centroid_labels) if self.use_knn else 0, 'inference_config': { 'use_knn': self.use_knn, 'arcface_min_score': self.arcface_min_score, 'centroid_fallback_score': self.centroid_fallback_score, 'topk_centroid': self.default_topk_centroid, 'topk_neighbors': self.default_topk_neighbors, 'topk_arcface': self.default_topk_arcface, 'centroid_threshold': self.default_centroid_threshold, 'neighbor_threshold': self.default_neighbor_threshold, } } if hasattr(self, 'model') and hasattr(self.model, 'backbone'): info['backbone'] = self.model.backbone.__class__.__name__ return info def warmup(self, num_iterations: int = DEFAULT_WARMUP_ITERATIONS) -> float: """Warmup model with dummy data for stable performance. Args: num_iterations: Number of warmup iterations Returns: Average warmup time per iteration in seconds """ logger.info(f"Warming up model with {num_iterations} iterations...") dummy = torch.randn(1, 3, self.input_size, self.input_size).to(self.device) # Warmup iterations times = [] for i in range(num_iterations): start = time.time() with torch.no_grad(): self.model(dummy, return_softmax=False) times.append(time.time() - start) avg_time = np.mean(times) logger.info(f"Warmup completed: avg={avg_time*1000:.2f}ms, " f"min={min(times)*1000:.2f}ms, max={max(times)*1000:.2f}ms") return avg_time def __enter__(self): """Context manager entry.""" return self def __exit__(self, exc_type, exc_val, exc_tb): """Context manager exit with cleanup.""" self.cleanup() return False # Don't suppress exceptions def cleanup(self) -> None: """Release resources and cleanup.""" logger.info("Cleaning up resources...") # Clear FAISS indices with error handling (only if kNN was enabled) if self.use_knn and hasattr(self, 'class_indices'): for label, data in self.class_indices.items(): try: if 'index' in data and data['index'] is not None: data['index'].reset() except Exception as e: logger.warning(f"Failed to reset FAISS index for label {label}: {e}") try: self.class_indices.clear() except Exception as e: logger.warning(f"Failed to clear class_indices: {e}") # Move model to CPU and clear cache if hasattr(self, 'model'): try: self.model.cpu() except Exception as e: logger.warning(f"Failed to move model to CPU: {e}") try: if torch.cuda.is_available(): torch.cuda.empty_cache() except Exception as e: logger.warning(f"Failed to empty CUDA cache: {e}") logger.info("Cleanup completed") def __del__(self): """Destructor - logs warning if cleanup wasn't called. Note: Do not rely on __del__ for cleanup. Always use context manager or explicitly call cleanup(). """ try: # Check if resources are still allocated (only relevant if kNN was enabled) if hasattr(self, 'use_knn') and self.use_knn: if hasattr(self, 'class_indices') and self.class_indices: logger.warning("EmbeddingClassifier destroyed without cleanup(). " "Use context manager or call cleanup() explicitly.") except Exception: # Silently ignore errors in destructor during interpreter shutdown pass