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# -*- 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