RyZ commited on
Commit Β·
4c21e13
1
Parent(s): 93f31a8
fix: commit src.infrastructure.model code and restrict gitignore model rule to root
Browse files
.gitignore
CHANGED
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@@ -218,4 +218,5 @@ __marimo__/
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# Streamlit
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.streamlit/secrets.toml
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-
model/
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# Streamlit
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.streamlit/secrets.toml
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+
/model/
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/models/
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src/infrastructure/model/__init__.py
ADDED
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@@ -0,0 +1 @@
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# Model service subpackage
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src/infrastructure/model/cardiogan.py
ADDED
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@@ -0,0 +1,159 @@
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"""
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infrastructure/model/cardiogan.py
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ββββββββββββββββββββββββββββββββββ
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CardioGAN U-Net Generator model architecture.
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Strictly defines the PyTorch nn.Module architecture (SRP). No signal preprocessing.
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"""
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from __future__ import annotations
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def _build_attention_gate_module():
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import torch
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import torch.nn as nn
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import torch.nn.functional as F
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class AttentionGate(nn.Module):
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"""Attention gate for 1-D signals on skip connections."""
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def __init__(self, F_l: int, F_g: int, F_int: int):
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super().__init__()
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self.W_x = nn.Conv1d(F_l, F_int, kernel_size=1, stride=1, bias=True)
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self.W_g = nn.Conv1d(F_g, F_int, kernel_size=1, stride=1, bias=True)
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self.psi = nn.Conv1d(F_int, 1, kernel_size=1, stride=1, bias=True)
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self.relu = nn.ReLU(inplace=True)
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self.sigmoid = nn.Sigmoid()
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def forward(self, x_l: torch.Tensor, g: torch.Tensor) -> torch.Tensor:
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if g.shape[-1] != x_l.shape[-1]:
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g = F.interpolate(g, size=x_l.shape[-1], mode="nearest")
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theta_x = self.W_x(x_l)
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phi_g = self.W_g(g)
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f = self.relu(theta_x + phi_g)
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alpha = self.sigmoid(self.psi(f))
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return x_l * alpha
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return AttentionGate
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def _build_encoder_block_module():
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import torch.nn as nn
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class EncoderBlock(nn.Module):
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"""Encoder block: Conv1d -> [GroupNorm] -> LeakyReLU."""
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def __init__(self, in_ch: int, out_ch: int, kernel_size: int = 16,
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stride: int = 2, use_norm: bool = True):
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super().__init__()
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pad = (kernel_size - 1) // 2
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self.conv = nn.Conv1d(in_ch, out_ch, kernel_size, stride, pad)
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self.norm = nn.GroupNorm(1, out_ch) if use_norm else nn.Identity()
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self.act = nn.LeakyReLU(0.2, inplace=True)
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def forward(self, x):
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return self.act(self.norm(self.conv(x)))
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return EncoderBlock
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def _build_decoder_block_module():
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import torch.nn as nn
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class DecoderBlock(nn.Module):
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"""Decoder block: ConvTranspose1d -> [GroupNorm] -> ReLU."""
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def __init__(self, in_ch: int, out_ch: int, kernel_size: int = 16,
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stride: int = 2, use_norm: bool = True):
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super().__init__()
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pad = (kernel_size - 1) // 2
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out_pad = stride - 1 if stride > 1 else 0
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self.deconv = nn.ConvTranspose1d(
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in_ch, out_ch, kernel_size, stride, pad, output_padding=out_pad
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)
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self.norm = nn.GroupNorm(1, out_ch) if use_norm else nn.Identity()
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self.act = nn.ReLU(inplace=True)
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def forward(self, x):
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return self.act(self.norm(self.deconv(x)))
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return DecoderBlock
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def build_attention_unet_generator():
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"""
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Build and return a fresh AttentionUNetGenerator instance.
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"""
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import torch
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import torch.nn as nn
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import torch.nn.functional as F
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AttentionGate = _build_attention_gate_module()
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EncoderBlock = _build_encoder_block_module()
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DecoderBlock = _build_decoder_block_module()
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class AttentionUNetGenerator(nn.Module):
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"""Attention U-Net Generator for CardioGAN."""
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def __init__(self):
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super().__init__()
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enc_filters = [64, 128, 256, 512, 512, 512]
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self.enc1 = EncoderBlock(1, enc_filters[0], use_norm=False)
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self.enc2 = EncoderBlock(enc_filters[0], enc_filters[1])
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self.enc3 = EncoderBlock(enc_filters[1], enc_filters[2])
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self.enc4 = EncoderBlock(enc_filters[2], enc_filters[3])
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self.enc5 = EncoderBlock(enc_filters[3], enc_filters[4])
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self.enc6 = EncoderBlock(enc_filters[4], enc_filters[5])
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self.attn5 = AttentionGate(enc_filters[4], enc_filters[4], enc_filters[4] // 2)
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self.attn4 = AttentionGate(enc_filters[3], enc_filters[3], enc_filters[3] // 2)
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self.attn3 = AttentionGate(enc_filters[2], enc_filters[2], enc_filters[2] // 2)
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self.attn2 = AttentionGate(enc_filters[1], enc_filters[1], enc_filters[1] // 2)
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self.attn1 = AttentionGate(enc_filters[0], enc_filters[0], enc_filters[0] // 2)
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self.dec6 = DecoderBlock(enc_filters[5], enc_filters[4])
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self.dec5 = DecoderBlock(enc_filters[4] * 2, enc_filters[3])
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self.dec4 = DecoderBlock(enc_filters[3] * 2, enc_filters[2])
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self.dec3 = DecoderBlock(enc_filters[2] * 2, enc_filters[1])
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self.dec2 = DecoderBlock(enc_filters[1] * 2, enc_filters[0])
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self.final = nn.Sequential(
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nn.ConvTranspose1d(enc_filters[0] * 2, 1, kernel_size=16,
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stride=2, padding=7, output_padding=0),
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nn.Tanh()
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)
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def forward(self, x: torch.Tensor) -> torch.Tensor:
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e1 = self.enc1(x) # (B, 64, 256)
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e2 = self.enc2(e1) # (B, 128, 128)
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e3 = self.enc3(e2) # (B, 256, 64)
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e4 = self.enc4(e3) # (B, 512, 32)
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e5 = self.enc5(e4) # (B, 512, 16)
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e6 = self.enc6(e5) # (B, 512, 8)
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d6 = self.dec6(e6)
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a5 = self.attn5(e5, d6)
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d5 = self.dec5(torch.cat([self._match(d6, a5), a5], dim=1))
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a4 = self.attn4(e4, d5)
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d4 = self.dec4(torch.cat([self._match(d5, a4), a4], dim=1))
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a3 = self.attn3(e3, d4)
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d3 = self.dec3(torch.cat([self._match(d4, a3), a3], dim=1))
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a2 = self.attn2(e2, d3)
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d2 = self.dec2(torch.cat([self._match(d3, a2), a2], dim=1))
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a1 = self.attn1(e1, d2)
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out = self.final(torch.cat([self._match(d2, a1), a1], dim=1))
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return out
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@staticmethod
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def _match(decoder_feat: torch.Tensor, skip_feat: torch.Tensor) -> torch.Tensor:
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if decoder_feat.shape[-1] != skip_feat.shape[-1]:
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decoder_feat = F.interpolate(
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decoder_feat, size=skip_feat.shape[-1], mode="nearest"
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)
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return decoder_feat
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return AttentionUNetGenerator()
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src/infrastructure/model/gan_vgtlnet_service.py
ADDED
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|
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|
|
| 1 |
+
"""
|
| 2 |
+
infrastructure/model/gan_vgtlnet_service.py
|
| 3 |
+
ββββββββββββββββββββββββββββββββββββββββββββ
|
| 4 |
+
GANVGTLNetService β production AI inference pipeline (CardioGAN + VGTL-Net).
|
| 5 |
+
|
| 6 |
+
Arsitektur Pipeline (SOLID & Clean):
|
| 7 |
+
PPG segments (@ 125 Hz, 224 samples/window)
|
| 8 |
+
β
|
| 9 |
+
βΌ [CardioGAN Preprocessor] -> SciPy/Numba implementation
|
| 10 |
+
ββββββββββββββββββββββββββββββββ
|
| 11 |
+
β CardioGANSignalPreprocessor β PPG segments -> segmented, filtered [-1, 1] windows @ 128 Hz
|
| 12 |
+
ββββββββββββββββ¬ββββββββββββββββ
|
| 13 |
+
β
|
| 14 |
+
βΌ [CardioGAN Generator Model (G_E)]
|
| 15 |
+
ββββββββββββββββββββββββββββββββ
|
| 16 |
+
β AttentionUNetGenerator β PPG windows -> synthetic ECG windows @ 128 Hz
|
| 17 |
+
ββββββββββββββββ¬ββββββββββββββββ
|
| 18 |
+
β
|
| 19 |
+
βΌ [CardioGAN Postprocessor]
|
| 20 |
+
ββββββββββββββββββββββββββββββββ
|
| 21 |
+
β CardioGANSignalPreprocessor β synthetic ECG windows @ 128 Hz -> aligned windows @ 125 Hz
|
| 22 |
+
ββββββββββββββββ¬ββββββββββββββββ
|
| 23 |
+
β
|
| 24 |
+
βΌ [VGTL-Net Preprocessor]
|
| 25 |
+
ββββββββββββββββββββββββββββββββ
|
| 26 |
+
β VGTLNetSignalPreprocessor β PPG + ECG windows @ 125 Hz -> VG Adjacency RGB Tensor
|
| 27 |
+
ββββββββββββββββ¬ββββββββββββββββ
|
| 28 |
+
β
|
| 29 |
+
βΌ [VGTL-Net Predictor Model]
|
| 30 |
+
ββββββββββββββββββββββββββββββββ
|
| 31 |
+
β ConvNeXtV2BPModel β RGB Tensor -> (SBP_pred, DBP_pred) -> averaged SBP/DBP
|
| 32 |
+
ββββββββββββββββββββββββββββββββ
|
| 33 |
+
"""
|
| 34 |
+
from __future__ import annotations
|
| 35 |
+
|
| 36 |
+
import time
|
| 37 |
+
from pathlib import Path
|
| 38 |
+
from typing import Any, Optional, Tuple
|
| 39 |
+
|
| 40 |
+
import numpy as np
|
| 41 |
+
|
| 42 |
+
from src.domain.entities.prediction import BPPrediction
|
| 43 |
+
from src.domain.exceptions.pipeline_exceptions import ModelInferenceError, PreprocessingError
|
| 44 |
+
from src.domain.interfaces.services.cardiogan_preprocessor import CardioGANSignalPreprocessor
|
| 45 |
+
from src.domain.interfaces.services.vgtlnet_preprocessor import VGTLNetSignalPreprocessor
|
| 46 |
+
from src.domain.interfaces.services.model_service import ModelService
|
| 47 |
+
from src.shared.config import get_settings
|
| 48 |
+
from src.shared.constants import (
|
| 49 |
+
MODEL_VERSION_GAN_VGTLNET,
|
| 50 |
+
BP_SBP_MIN,
|
| 51 |
+
BP_SBP_MAX,
|
| 52 |
+
BP_DBP_MIN,
|
| 53 |
+
BP_DBP_MAX,
|
| 54 |
+
)
|
| 55 |
+
from src.shared.logger import get_logger
|
| 56 |
+
|
| 57 |
+
logger = get_logger(__name__)
|
| 58 |
+
|
| 59 |
+
|
| 60 |
+
class GANVGTLNetService(ModelService):
|
| 61 |
+
"""
|
| 62 |
+
Production model service that orchestrates CardioGAN and VGTL-Net models.
|
| 63 |
+
|
| 64 |
+
Adheres fully to SOLID:
|
| 65 |
+
- SRP: Only orchestrates model loading and execution. Preprocessing is delegated.
|
| 66 |
+
- DIP: Depends entirely on abstract preprocessor interfaces, not concrete classes.
|
| 67 |
+
"""
|
| 68 |
+
|
| 69 |
+
def __init__(
|
| 70 |
+
self,
|
| 71 |
+
gan_preprocessor: Optional[CardioGANSignalPreprocessor] = None,
|
| 72 |
+
vgtlnet_preprocessor: Optional[VGTLNetSignalPreprocessor] = None,
|
| 73 |
+
gan_checkpoint_path: Optional[str] = None,
|
| 74 |
+
vgtlnet_checkpoint_path: Optional[str] = None,
|
| 75 |
+
) -> None:
|
| 76 |
+
settings = get_settings()
|
| 77 |
+
self._gan_path = Path(gan_checkpoint_path or settings.gan_checkpoint_path)
|
| 78 |
+
self._vgtlnet_path = Path(vgtlnet_checkpoint_path or settings.vgtlnet_checkpoint_path)
|
| 79 |
+
|
| 80 |
+
# Lazy import defaults if not provided (retains ease of use + testing flexibility)
|
| 81 |
+
if gan_preprocessor is None:
|
| 82 |
+
from src.infrastructure.processing.scipy_cardiogan_preprocessor import SciPyCardioGANPreprocessor
|
| 83 |
+
self._gan_preprocessor: CardioGANSignalPreprocessor = SciPyCardioGANPreprocessor()
|
| 84 |
+
else:
|
| 85 |
+
self._gan_preprocessor = gan_preprocessor
|
| 86 |
+
|
| 87 |
+
if vgtlnet_preprocessor is None:
|
| 88 |
+
from src.infrastructure.processing.numba_vgtlnet_preprocessor import NumbaVGTLNetPreprocessor
|
| 89 |
+
self._vgtlnet_preprocessor: VGTLNetSignalPreprocessor = NumbaVGTLNetPreprocessor()
|
| 90 |
+
else:
|
| 91 |
+
self._vgtlnet_preprocessor = vgtlnet_preprocessor
|
| 92 |
+
|
| 93 |
+
self._gan_model: Optional[Any] = None # AttentionUNetGenerator (G_E)
|
| 94 |
+
self._vgtlnet_model: Optional[Any] = None # ConvNeXtV2BPModel
|
| 95 |
+
self._loaded = False
|
| 96 |
+
self._device: str = "cpu"
|
| 97 |
+
|
| 98 |
+
# ββ ModelService interface ββββββββββββββββββββββββββββββββββββββββββββββββ
|
| 99 |
+
|
| 100 |
+
async def load_model(self) -> None:
|
| 101 |
+
"""
|
| 102 |
+
Loads CardioGAN and VGTL-Net weights from disk.
|
| 103 |
+
"""
|
| 104 |
+
if self._loaded:
|
| 105 |
+
return
|
| 106 |
+
|
| 107 |
+
try:
|
| 108 |
+
import torch
|
| 109 |
+
from src.infrastructure.model.cardiogan import build_attention_unet_generator
|
| 110 |
+
from src.infrastructure.model.vgtlnet import build_convnextv2_bp_model
|
| 111 |
+
|
| 112 |
+
self._device = "cuda" if torch.cuda.is_available() else "cpu"
|
| 113 |
+
logger.info("GANVGTLNetService.load_model() - device=%s", self._device)
|
| 114 |
+
|
| 115 |
+
# 1. Load CardioGAN (G_E: PPG -> ECG)
|
| 116 |
+
if not self._gan_path.exists():
|
| 117 |
+
raise ModelInferenceError(
|
| 118 |
+
"CardioGAN",
|
| 119 |
+
f"Checkpoint not found at: {self._gan_path}. "
|
| 120 |
+
"Ensure weights are downloaded or set USE_MOCK_MODEL=true."
|
| 121 |
+
)
|
| 122 |
+
|
| 123 |
+
logger.info("Loading CardioGAN from %s ...", self._gan_path)
|
| 124 |
+
self._gan_model = build_attention_unet_generator()
|
| 125 |
+
ckpt = torch.load(self._gan_path, map_location=self._device)
|
| 126 |
+
|
| 127 |
+
if isinstance(ckpt, dict) and "G_E" in ckpt:
|
| 128 |
+
state_dict = ckpt["G_E"]
|
| 129 |
+
elif isinstance(ckpt, dict) and all(
|
| 130 |
+
k.startswith(("enc", "dec", "attn", "final")) for k in list(ckpt.keys())[:5]
|
| 131 |
+
):
|
| 132 |
+
state_dict = ckpt
|
| 133 |
+
else:
|
| 134 |
+
state_dict = ckpt
|
| 135 |
+
|
| 136 |
+
self._gan_model.load_state_dict(state_dict, strict=True)
|
| 137 |
+
self._gan_model.to(self._device)
|
| 138 |
+
self._gan_model.eval()
|
| 139 |
+
|
| 140 |
+
# 2. Load VGTL-Net (ConvNeXt V2 BP Model)
|
| 141 |
+
if not self._vgtlnet_path.exists():
|
| 142 |
+
raise ModelInferenceError(
|
| 143 |
+
"VGTLNet",
|
| 144 |
+
f"Checkpoint not found at: {self._vgtlnet_path}. "
|
| 145 |
+
"Ensure weights are downloaded or set USE_MOCK_MODEL=true."
|
| 146 |
+
)
|
| 147 |
+
|
| 148 |
+
logger.info("Loading VGTL-Net from %s ...", self._vgtlnet_path)
|
| 149 |
+
self._vgtlnet_model = build_convnextv2_bp_model(pretrained=False)
|
| 150 |
+
vgtl_ckpt = torch.load(self._vgtlnet_path, map_location=self._device)
|
| 151 |
+
|
| 152 |
+
if isinstance(vgtl_ckpt, dict) and "model_state_dict" in vgtl_ckpt:
|
| 153 |
+
vgtl_state = vgtl_ckpt["model_state_dict"]
|
| 154 |
+
elif isinstance(vgtl_ckpt, dict) and "state_dict" in vgtl_ckpt:
|
| 155 |
+
vgtl_state = vgtl_ckpt["state_dict"]
|
| 156 |
+
else:
|
| 157 |
+
vgtl_state = vgtl_ckpt
|
| 158 |
+
|
| 159 |
+
if any(k.startswith("module.") for k in vgtl_state.keys()):
|
| 160 |
+
vgtl_state = {k[len("module."):]: v for k, v in vgtl_state.items()}
|
| 161 |
+
|
| 162 |
+
self._vgtlnet_model.load_state_dict(vgtl_state, strict=True)
|
| 163 |
+
self._vgtlnet_model.to(self._device)
|
| 164 |
+
self._vgtlnet_model.eval()
|
| 165 |
+
|
| 166 |
+
self._loaded = True
|
| 167 |
+
logger.info("GANVGTLNetService initialized successfully on %s", self._device)
|
| 168 |
+
|
| 169 |
+
except Exception as e:
|
| 170 |
+
if isinstance(e, ModelInferenceError):
|
| 171 |
+
raise e
|
| 172 |
+
raise ModelInferenceError("Initialization", f"Unexpected error while loading models: {e}") from e
|
| 173 |
+
|
| 174 |
+
async def predict(
|
| 175 |
+
self,
|
| 176 |
+
ppg_signal_id: str,
|
| 177 |
+
segments: np.ndarray,
|
| 178 |
+
) -> BPPrediction:
|
| 179 |
+
"""
|
| 180 |
+
Executes the full pipeline:
|
| 181 |
+
Ingested PPG -> Preprocessing -> CardioGAN translation (aligned) ->
|
| 182 |
+
VG Adjacency extraction -> VGTL-Net raw prediction ->
|
| 183 |
+
Simulated Annealing threshold optimization -> BPPrediction
|
| 184 |
+
"""
|
| 185 |
+
if not self._loaded:
|
| 186 |
+
await self.load_model()
|
| 187 |
+
|
| 188 |
+
start = time.perf_counter()
|
| 189 |
+
|
| 190 |
+
try:
|
| 191 |
+
# 1. CardioGAN Pipeline (PPG -> synthetic ECG, both aligned at 125 Hz, 224 samples)
|
| 192 |
+
ppg_segments_224, ecg_segments_224 = self._run_gan_inference_aligned(segments)
|
| 193 |
+
|
| 194 |
+
# 2. VGTL-Net Raw Predictions
|
| 195 |
+
sbp_preds, dbp_preds = self._run_vgtlnet_raw_predictions(ppg_segments_224, ecg_segments_224)
|
| 196 |
+
|
| 197 |
+
# 3. Simulated Annealing Optimization (1000 steps)
|
| 198 |
+
from src.infrastructure.processing.sa_helpers import run_simulated_annealing
|
| 199 |
+
|
| 200 |
+
sa_result = run_simulated_annealing(
|
| 201 |
+
ppg_segments=ppg_segments_224,
|
| 202 |
+
ecg_segments=ecg_segments_224,
|
| 203 |
+
sbp_preds=sbp_preds,
|
| 204 |
+
dbp_preds=dbp_preds,
|
| 205 |
+
n_steps=1000,
|
| 206 |
+
)
|
| 207 |
+
|
| 208 |
+
# 4. Filter predictions based on optimized thresholds
|
| 209 |
+
clean_indices = sa_result["clean_indices"]
|
| 210 |
+
if len(clean_indices) > 0:
|
| 211 |
+
sbp = float(np.mean(sbp_preds[clean_indices]))
|
| 212 |
+
dbp = float(np.mean(dbp_preds[clean_indices]))
|
| 213 |
+
else:
|
| 214 |
+
sbp = float(np.mean(sbp_preds))
|
| 215 |
+
dbp = float(np.mean(dbp_preds))
|
| 216 |
+
|
| 217 |
+
# Assemble SA logs
|
| 218 |
+
sa_log = {
|
| 219 |
+
"optimal_lo": sa_result["optimal_lo"],
|
| 220 |
+
"optimal_hi": sa_result["optimal_hi"],
|
| 221 |
+
"optimal_max_plateau": sa_result["optimal_max_plateau"],
|
| 222 |
+
"best_loss": sa_result["best_loss"],
|
| 223 |
+
"initial_loss": sa_result["initial_loss"],
|
| 224 |
+
"n_total_segments": sa_result["n_total_segments"],
|
| 225 |
+
"n_clean_segments": sa_result["n_clean_segments"],
|
| 226 |
+
"yield_rate": sa_result["yield_rate"],
|
| 227 |
+
"history": sa_result["history"],
|
| 228 |
+
}
|
| 229 |
+
|
| 230 |
+
elapsed_ms = (time.perf_counter() - start) * 1000
|
| 231 |
+
|
| 232 |
+
logger.info(
|
| 233 |
+
"Inference complete (SA optimized) - signal_id=%s, segments=%d (clean=%d) "
|
| 234 |
+
"SBP=%.1f mmHg, DBP=%.1f mmHg (%.1f ms)",
|
| 235 |
+
ppg_signal_id, len(ppg_segments_224), len(clean_indices), sbp, dbp, elapsed_ms,
|
| 236 |
+
)
|
| 237 |
+
|
| 238 |
+
return BPPrediction(
|
| 239 |
+
ppg_signal_id=ppg_signal_id,
|
| 240 |
+
predicted_sbp=round(float(sbp), 1),
|
| 241 |
+
predicted_dbp=round(float(dbp), 1),
|
| 242 |
+
model_version=self.model_version,
|
| 243 |
+
inference_time_ms=round(elapsed_ms, 2),
|
| 244 |
+
sa_log=sa_log,
|
| 245 |
+
)
|
| 246 |
+
|
| 247 |
+
except (PreprocessingError, ModelInferenceError) as e:
|
| 248 |
+
logger.error("Pipeline failure for signal %s: %s", ppg_signal_id, e)
|
| 249 |
+
raise e
|
| 250 |
+
except Exception as e:
|
| 251 |
+
logger.error("Unexpected error in prediction pipeline: %s", e)
|
| 252 |
+
raise ModelInferenceError("PipelineOrchestration", f"Prediction execution failed: {e}") from e
|
| 253 |
+
|
| 254 |
+
def is_loaded(self) -> bool:
|
| 255 |
+
return self._loaded
|
| 256 |
+
|
| 257 |
+
@property
|
| 258 |
+
def model_version(self) -> str:
|
| 259 |
+
return MODEL_VERSION_GAN_VGTLNET
|
| 260 |
+
|
| 261 |
+
# ββ Private Inference Execution βββββββββββββββββββββββββββββββββββββββββββ
|
| 262 |
+
|
| 263 |
+
def _run_gan_inference_aligned(self, ppg_segments: np.ndarray) -> Tuple[np.ndarray, np.ndarray]:
|
| 264 |
+
import torch
|
| 265 |
+
|
| 266 |
+
assert self._gan_model is not None, "CardioGAN generator model has not been loaded"
|
| 267 |
+
|
| 268 |
+
try:
|
| 269 |
+
# Step 1.1: Preprocess raw ppg windows into CardioGAN segmented, normalized segments
|
| 270 |
+
# preprocess_ppg handles resample, bandpass butter, z-score, and min-max
|
| 271 |
+
ppg_wins = self._gan_preprocessor.preprocess_ppg(ppg_segments)
|
| 272 |
+
|
| 273 |
+
# Step 1.2: Neural Network inference
|
| 274 |
+
ppg_tensor = torch.tensor(ppg_wins, dtype=torch.float32).unsqueeze(1).to(self._device)
|
| 275 |
+
with torch.no_grad():
|
| 276 |
+
ecg_tensor = self._gan_model(ppg_tensor)
|
| 277 |
+
|
| 278 |
+
ecg_128 = ecg_tensor.squeeze(1).cpu().numpy()
|
| 279 |
+
|
| 280 |
+
# Step 1.3: Postprocess both ECG and PPG to 125 Hz and 224 samples (aligned)
|
| 281 |
+
ecg_segments_out = self._gan_preprocessor.postprocess_ecg(ecg_128)
|
| 282 |
+
ppg_segments_out = self._gan_preprocessor.postprocess_ecg(ppg_wins)
|
| 283 |
+
|
| 284 |
+
return ppg_segments_out, ecg_segments_out
|
| 285 |
+
|
| 286 |
+
except PreprocessingError as e:
|
| 287 |
+
raise e
|
| 288 |
+
except Exception as e:
|
| 289 |
+
raise ModelInferenceError("CardioGAN", f"Forward pass or post-processing failed: {e}") from e
|
| 290 |
+
|
| 291 |
+
def _run_vgtlnet_raw_predictions(
|
| 292 |
+
self,
|
| 293 |
+
ppg_segments: np.ndarray,
|
| 294 |
+
ecg_segments: np.ndarray,
|
| 295 |
+
) -> Tuple[np.ndarray, np.ndarray]:
|
| 296 |
+
import torch
|
| 297 |
+
|
| 298 |
+
assert self._vgtlnet_model is not None, "VGTL-Net model has not been loaded"
|
| 299 |
+
|
| 300 |
+
try:
|
| 301 |
+
# Step 2.1: Preprocess PPG & ECG segments into Visibility Graph RGB normalise Tensors
|
| 302 |
+
batch_tensor = self._vgtlnet_preprocessor.preprocess_signals(
|
| 303 |
+
ppg_segments, ecg_segments
|
| 304 |
+
)
|
| 305 |
+
|
| 306 |
+
# Step 2.2: Neural Network inference
|
| 307 |
+
batch_device = batch_tensor.to(self._device)
|
| 308 |
+
with torch.no_grad():
|
| 309 |
+
sbp_preds, dbp_preds = self._vgtlnet_model(batch_device)
|
| 310 |
+
|
| 311 |
+
return sbp_preds.cpu().numpy(), dbp_preds.cpu().numpy()
|
| 312 |
+
|
| 313 |
+
except PreprocessingError as e:
|
| 314 |
+
raise e
|
| 315 |
+
except Exception as e:
|
| 316 |
+
raise ModelInferenceError("VGTLNet", f"Forward pass or processing failed: {e}") from e
|
src/infrastructure/model/mock_model_service.py
ADDED
|
@@ -0,0 +1,190 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
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|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
|
|
| 1 |
+
"""
|
| 2 |
+
infrastructure/model/mock_model_service.py
|
| 3 |
+
βββββββββββββββββββββββββββββββββββββββββββ
|
| 4 |
+
MockModelService β deterministic fake inference for testing and local dev.
|
| 5 |
+
|
| 6 |
+
Returns physiologically plausible (but fake) BP values without loading
|
| 7 |
+
any model weights or requiring a GPU.
|
| 8 |
+
|
| 9 |
+
Use case: run the full ETL pipeline locally with USE_MOCK_MODEL=true.
|
| 10 |
+
"""
|
| 11 |
+
from __future__ import annotations
|
| 12 |
+
|
| 13 |
+
import asyncio
|
| 14 |
+
import hashlib
|
| 15 |
+
import time
|
| 16 |
+
|
| 17 |
+
import numpy as np
|
| 18 |
+
|
| 19 |
+
from src.domain.entities.prediction import BPPrediction
|
| 20 |
+
from src.domain.interfaces.services.model_service import ModelService
|
| 21 |
+
from src.shared.constants import MODEL_VERSION_MOCK
|
| 22 |
+
from src.shared.logger import get_logger
|
| 23 |
+
|
| 24 |
+
logger = get_logger(__name__)
|
| 25 |
+
|
| 26 |
+
# Physiologically plausible reference ranges for mock output
|
| 27 |
+
_SBP_BASE = 115.0 # Normal systolic
|
| 28 |
+
_DBP_BASE = 75.0 # Normal diastolic
|
| 29 |
+
_JITTER = 15.0 # Β± range around base values
|
| 30 |
+
|
| 31 |
+
|
| 32 |
+
class MockModelService(ModelService):
|
| 33 |
+
"""
|
| 34 |
+
Deterministic mock model service for testing and local development.
|
| 35 |
+
|
| 36 |
+
Given the same ``ppg_signal_id``, it always returns the same BP values
|
| 37 |
+
(deterministic via hash of the ID) β making tests reproducible.
|
| 38 |
+
"""
|
| 39 |
+
|
| 40 |
+
def __init__(self) -> None:
|
| 41 |
+
self._loaded = False
|
| 42 |
+
|
| 43 |
+
# ββ ModelService interface ββββββββββββββββββββββββββββββββββββββββββββββββ
|
| 44 |
+
|
| 45 |
+
async def load_model(self) -> None:
|
| 46 |
+
"""Simulates model loading β just flips a flag."""
|
| 47 |
+
if self._loaded:
|
| 48 |
+
return
|
| 49 |
+
logger.info("MockModelService.load_model() β simulating 100ms load delay")
|
| 50 |
+
await asyncio.sleep(0.1) # simulate loading latency
|
| 51 |
+
self._loaded = True
|
| 52 |
+
logger.info("MockModelService ready (mock mode).")
|
| 53 |
+
|
| 54 |
+
async def predict(
|
| 55 |
+
self,
|
| 56 |
+
ppg_signal_id: str,
|
| 57 |
+
segments: np.ndarray,
|
| 58 |
+
) -> BPPrediction:
|
| 59 |
+
"""
|
| 60 |
+
Return deterministic fake BP values based on the signal ID hash.
|
| 61 |
+
|
| 62 |
+
The hash ensures the same ID always gives the same output, making
|
| 63 |
+
unit tests with MockModelService fully reproducible.
|
| 64 |
+
|
| 65 |
+
Args:
|
| 66 |
+
ppg_signal_id: UUID of the source PPGSignal.
|
| 67 |
+
segments: Preprocessed signal segments (shape: N Γ window).
|
| 68 |
+
|
| 69 |
+
Returns:
|
| 70 |
+
BPPrediction with fake but physiologically valid SBP/DBP.
|
| 71 |
+
"""
|
| 72 |
+
if not self._loaded:
|
| 73 |
+
await self.load_model()
|
| 74 |
+
|
| 75 |
+
start = time.perf_counter()
|
| 76 |
+
|
| 77 |
+
# Deterministic jitter: hash the signal ID to get a repeatable seed
|
| 78 |
+
hash_bytes = hashlib.sha256(ppg_signal_id.encode()).digest()
|
| 79 |
+
seed = int.from_bytes(hash_bytes[:4], "big")
|
| 80 |
+
|
| 81 |
+
# Determine number of segments (always at least 1)
|
| 82 |
+
n_segments = segments.shape[0] if len(segments.shape) > 1 and segments.shape[0] > 0 else 1
|
| 83 |
+
|
| 84 |
+
# 1. Generate fake segments of size 224 to simulate JIT features computation
|
| 85 |
+
fake_ppg = np.zeros((n_segments, 224), dtype=np.float32)
|
| 86 |
+
fake_ecg = np.zeros((n_segments, 224), dtype=np.float32)
|
| 87 |
+
|
| 88 |
+
# Populate with deterministic signal + noise + optional plateau
|
| 89 |
+
for i in range(n_segments):
|
| 90 |
+
seg_seed = (seed + i) & 0xffffffff
|
| 91 |
+
rng_seg = np.random.default_rng(seg_seed)
|
| 92 |
+
t = np.linspace(0, 2 * np.pi, 224)
|
| 93 |
+
# i%3 == 0: noisy (high entropy), others: clean (low entropy)
|
| 94 |
+
noise_lvl = 0.5 if (i % 3 == 0) else 0.05
|
| 95 |
+
fake_ppg[i] = np.sin(t) + rng_seg.normal(0, noise_lvl, 224)
|
| 96 |
+
fake_ecg[i] = np.sin(t * 2) + rng_seg.normal(0, noise_lvl, 224)
|
| 97 |
+
|
| 98 |
+
# i%4 == 0: inject flat lines (plateau)
|
| 99 |
+
if i % 4 == 0:
|
| 100 |
+
fake_ppg[i, 50:70] = 0.5
|
| 101 |
+
fake_ecg[i, 100:120] = -0.5
|
| 102 |
+
|
| 103 |
+
# 2. Generate segment predictions
|
| 104 |
+
sbp_preds = []
|
| 105 |
+
dbp_preds = []
|
| 106 |
+
for i in range(n_segments):
|
| 107 |
+
seg_seed = (seed + i) & 0xffffffff
|
| 108 |
+
rng_seg = np.random.default_rng(seg_seed)
|
| 109 |
+
s = float(_SBP_BASE + rng_seg.uniform(-_JITTER, _JITTER))
|
| 110 |
+
d = float(_DBP_BASE + rng_seg.uniform(-_JITTER / 2, _JITTER / 2))
|
| 111 |
+
|
| 112 |
+
# Add variance to noisy windows
|
| 113 |
+
if i % 3 == 0:
|
| 114 |
+
s += rng_seg.uniform(-25, 25)
|
| 115 |
+
d += rng_seg.uniform(-12, 12)
|
| 116 |
+
# Clamp within physiological bounds
|
| 117 |
+
s = max(80.0, min(200.0, s))
|
| 118 |
+
d = max(40.0, min(120.0, d))
|
| 119 |
+
|
| 120 |
+
if s <= d:
|
| 121 |
+
s = d + 30.0
|
| 122 |
+
|
| 123 |
+
sbp_preds.append(s)
|
| 124 |
+
dbp_preds.append(d)
|
| 125 |
+
|
| 126 |
+
sbp_preds_arr = np.array(sbp_preds)
|
| 127 |
+
dbp_preds_arr = np.array(dbp_preds)
|
| 128 |
+
|
| 129 |
+
# 3. Run Simulated Annealing (1000 steps)
|
| 130 |
+
from src.infrastructure.processing.sa_helpers import run_simulated_annealing
|
| 131 |
+
|
| 132 |
+
sa_result = run_simulated_annealing(
|
| 133 |
+
ppg_segments=fake_ppg,
|
| 134 |
+
ecg_segments=fake_ecg,
|
| 135 |
+
sbp_preds=sbp_preds_arr,
|
| 136 |
+
dbp_preds=dbp_preds_arr,
|
| 137 |
+
n_steps=1000,
|
| 138 |
+
)
|
| 139 |
+
|
| 140 |
+
clean_indices = sa_result["clean_indices"]
|
| 141 |
+
if len(clean_indices) > 0:
|
| 142 |
+
sbp = float(np.mean(sbp_preds_arr[clean_indices]))
|
| 143 |
+
dbp = float(np.mean(dbp_preds_arr[clean_indices]))
|
| 144 |
+
else:
|
| 145 |
+
sbp = float(np.mean(sbp_preds_arr))
|
| 146 |
+
dbp = float(np.mean(dbp_preds_arr))
|
| 147 |
+
|
| 148 |
+
# Assemble SA log dict
|
| 149 |
+
sa_log = {
|
| 150 |
+
"optimal_lo": sa_result["optimal_lo"],
|
| 151 |
+
"optimal_hi": sa_result["optimal_hi"],
|
| 152 |
+
"optimal_max_plateau": sa_result["optimal_max_plateau"],
|
| 153 |
+
"best_loss": sa_result["best_loss"],
|
| 154 |
+
"initial_loss": sa_result["initial_loss"],
|
| 155 |
+
"n_total_segments": sa_result["n_total_segments"],
|
| 156 |
+
"n_clean_segments": sa_result["n_clean_segments"],
|
| 157 |
+
"yield_rate": sa_result["yield_rate"],
|
| 158 |
+
"history": sa_result["history"],
|
| 159 |
+
}
|
| 160 |
+
|
| 161 |
+
# Simulate short inference time
|
| 162 |
+
await asyncio.sleep(0.05)
|
| 163 |
+
elapsed_ms = (time.perf_counter() - start) * 1000
|
| 164 |
+
|
| 165 |
+
logger.info(
|
| 166 |
+
"MockModelService.predict() β signal_id=%s segments=%d (clean=%d) "
|
| 167 |
+
"SBP=%.1f DBP=%.1f (%.1f ms)",
|
| 168 |
+
ppg_signal_id,
|
| 169 |
+
n_segments,
|
| 170 |
+
len(clean_indices),
|
| 171 |
+
sbp,
|
| 172 |
+
dbp,
|
| 173 |
+
elapsed_ms,
|
| 174 |
+
)
|
| 175 |
+
|
| 176 |
+
return BPPrediction(
|
| 177 |
+
ppg_signal_id=ppg_signal_id,
|
| 178 |
+
predicted_sbp=round(sbp, 1),
|
| 179 |
+
predicted_dbp=round(dbp, 1),
|
| 180 |
+
model_version=self.model_version,
|
| 181 |
+
inference_time_ms=round(elapsed_ms, 2),
|
| 182 |
+
sa_log=sa_log,
|
| 183 |
+
)
|
| 184 |
+
|
| 185 |
+
def is_loaded(self) -> bool:
|
| 186 |
+
return self._loaded
|
| 187 |
+
|
| 188 |
+
@property
|
| 189 |
+
def model_version(self) -> str:
|
| 190 |
+
return MODEL_VERSION_MOCK
|
src/infrastructure/model/vgtlnet.py
ADDED
|
@@ -0,0 +1,67 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
"""
|
| 2 |
+
infrastructure/model/vgtlnet.py
|
| 3 |
+
ββββββββββββββββββββββββββββββββ
|
| 4 |
+
VGTL-Net Model Architecture.
|
| 5 |
+
Strictly defines the PyTorch BP prediction architecture (SRP). No signal preprocessing.
|
| 6 |
+
"""
|
| 7 |
+
from __future__ import annotations
|
| 8 |
+
|
| 9 |
+
|
| 10 |
+
def build_bp_mlp(in_features: int):
|
| 11 |
+
"""
|
| 12 |
+
MLP head for SBP or DBP prediction.
|
| 13 |
+
"""
|
| 14 |
+
import torch.nn as nn
|
| 15 |
+
return nn.Sequential(
|
| 16 |
+
nn.Linear(in_features, 1024),
|
| 17 |
+
nn.BatchNorm1d(1024),
|
| 18 |
+
nn.ReLU(inplace=True),
|
| 19 |
+
nn.Dropout(0.3),
|
| 20 |
+
nn.Linear(1024, 512),
|
| 21 |
+
nn.BatchNorm1d(512),
|
| 22 |
+
nn.ReLU(inplace=True),
|
| 23 |
+
nn.Dropout(0.2),
|
| 24 |
+
nn.Linear(512, 1),
|
| 25 |
+
)
|
| 26 |
+
|
| 27 |
+
|
| 28 |
+
def build_convnextv2_bp_model(pretrained: bool = False):
|
| 29 |
+
"""
|
| 30 |
+
Build ConvNeXtV2BPModel (VGTL-Net backbone + dual MLP head).
|
| 31 |
+
"""
|
| 32 |
+
try:
|
| 33 |
+
import timm
|
| 34 |
+
import torch.nn as nn
|
| 35 |
+
|
| 36 |
+
class ConvNeXtV2BPModel(nn.Module):
|
| 37 |
+
"""VGTL-Net: ConvNeXt V2 Tiny + Dual MLP Head for SBP/DBP."""
|
| 38 |
+
|
| 39 |
+
def __init__(self, pretrained: bool = False):
|
| 40 |
+
super().__init__()
|
| 41 |
+
self.feature_extractor = timm.create_model(
|
| 42 |
+
"convnextv2_tiny.fcmae_ft_in22k_in1k",
|
| 43 |
+
pretrained=pretrained,
|
| 44 |
+
num_classes=0,
|
| 45 |
+
global_pool="avg",
|
| 46 |
+
)
|
| 47 |
+
feat_dim = self.feature_extractor.num_features # 768
|
| 48 |
+
self.mlp_sbp = build_bp_mlp(feat_dim)
|
| 49 |
+
self.mlp_dbp = build_bp_mlp(feat_dim)
|
| 50 |
+
|
| 51 |
+
def forward(self, x):
|
| 52 |
+
"""
|
| 53 |
+
Args:
|
| 54 |
+
x: (B, 3, 224, 224) visibility graph image tensor
|
| 55 |
+
Returns:
|
| 56 |
+
Tuple (sbp_pred, dbp_pred)
|
| 57 |
+
"""
|
| 58 |
+
feat = self.feature_extractor(x)
|
| 59 |
+
return self.mlp_sbp(feat).squeeze(-1), self.mlp_dbp(feat).squeeze(-1)
|
| 60 |
+
|
| 61 |
+
return ConvNeXtV2BPModel(pretrained=pretrained)
|
| 62 |
+
|
| 63 |
+
except ImportError as e:
|
| 64 |
+
raise RuntimeError(
|
| 65 |
+
f"Dependencies for VGTL-Net model are missing: {e}. "
|
| 66 |
+
"Please run: pip install timm"
|
| 67 |
+
) from e
|