BioStack / server.py
AE-Shree
Deploy BioStack RLHF Medical Demo
f3e4ffb
raw
history blame
19.6 kB
import io
import torch
import torch.nn as nn
import timm
import traceback
import os
from PIL import Image
from fastapi import FastAPI, File, UploadFile
from fastapi.middleware.cors import CORSMiddleware
from torchvision import transforms
from transformers import T5ForConditionalGeneration, T5Tokenizer
from huggingface_hub import hf_hub_download
# ─────────────────────────────────────────────────────────────────────────────
# CONFIGURATION - Matching Colab Notebook Exactly
# ─────────────────────────────────────────────────────────────────────────────
CONFIG = {
'coatnet_model': 'coatnet_1_rw_224',
't5_model': 't5-small',
'img_emb_dim': 768,
'train_last_stages': 2,
'image_size': 224,
'max_length': 100,
'num_beams': 4,
}
# ─────────────────────────────────────────────────────────────────────────────
# DEVICE
# ─────────────────────────────────────────────────────────────────────────────
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
print(f"πŸ–₯️ Using device: {device}")
# ─────────────────────────────────────────────────────────────────────────────
# LOAD TOKENIZER - Matching Colab
# ─────────────────────────────────────────────────────────────────────────────
print("\n" + "="*80)
print("LOADING TOKENIZER")
print("="*80)
tokenizer = T5Tokenizer.from_pretrained(CONFIG['t5_model'])
print(f"βœ“ Loaded tokenizer: {CONFIG['t5_model']}")
# ─────────────────────────────────────────────────────────────────────────────
# IMAGE TRANSFORM - Matching Colab Exactly
# ─────────────────────────────────────────────────────────────────────────────
transform = transforms.Compose([
transforms.Resize((CONFIG['image_size'], CONFIG['image_size'])),
transforms.ToTensor(),
transforms.Normalize(
mean=[0.485, 0.456, 0.406],
std=[0.229, 0.224, 0.225]
)
])
print(f"βœ“ Image transform defined (size: {CONFIG['image_size']}x{CONFIG['image_size']})")
# ─────────────────────────────────────────────────────────────────────────────
# ARCHITECTURE 1: CoAtNetEncoder - Exactly from Colab SECTION 6
# ─────────────────────────────────────────────────────────────────────────────
class CoAtNetEncoder(nn.Module):
def __init__(self, model_name="coatnet_1_rw_224", pretrained=True, train_last_stages=2):
super().__init__()
self.encoder = timm.create_model(
model_name,
pretrained=pretrained,
num_classes=0,
global_pool="avg"
)
# Freeze all parameters
for p in self.encoder.parameters():
p.requires_grad = False
# Unfreeze last stages
if hasattr(self.encoder, "stages") and train_last_stages is not None:
stages = self.encoder.stages
for stage in stages[-train_last_stages:]:
for p in stage.parameters():
p.requires_grad = True
def forward(self, x):
return self.encoder(x)
# ─────────────────────────────────────────────────────────────────────────────
# ARCHITECTURE 2: VisionT5Model - Exactly from Colab SECTION 6
# ─────────────────────────────────────────────────────────────────────────────
class VisionT5Model(nn.Module):
def __init__(self, img_encoder, txt_model_name="t5-small", img_emb_dim=768):
super().__init__()
# Vision encoder (CoAtNet)
self.img_encoder = img_encoder
# Text decoder (T5)
self.t5 = T5ForConditionalGeneration.from_pretrained(txt_model_name)
# Projection layer to match image features with T5 d_model
self.proj = nn.Linear(img_emb_dim, self.t5.config.d_model)
# Freeze shared T5 embeddings for faster and stable training
for p in self.t5.shared.parameters():
p.requires_grad = False
def forward(self, pixel_values, input_ids, attention_mask, labels=None):
# Extract image features
img_feats = self.img_encoder(pixel_values)
# Project image features to T5 embedding space
img_feats = self.proj(img_feats)
# Add sequence dimension
encoder_hidden_states = img_feats.unsqueeze(1)
# Run T5 encoder using image embeddings
encoder_outputs = self.t5.encoder(
inputs_embeds=encoder_hidden_states
)
# Run T5 decoder and compute loss
outputs = self.t5(
encoder_outputs=encoder_outputs,
attention_mask=torch.ones(
encoder_hidden_states.size()[:2], device=device
),
input_ids=input_ids,
labels=labels,
)
return outputs
def generate_reports(self, pixel_values, max_length=100, num_beams=4):
"""
Generate reports - EXACTLY matching Colab SECTION 6
"""
# Extract and project image features
img_feats = self.img_encoder(pixel_values)
img_feats = self.proj(img_feats)
encoder_hidden_states = img_feats.unsqueeze(1)
# Encode image features
encoder_outputs = self.t5.encoder(
inputs_embeds=encoder_hidden_states
)
# Generate report using beam search - EXACT parameters from Colab
generated_ids = self.t5.generate(
encoder_outputs=encoder_outputs,
attention_mask=torch.ones(
encoder_hidden_states.size()[:2], device=device
),
max_length=max_length,
num_beams=num_beams,
early_stopping=True
)
return generated_ids
print("βœ“ Model architecture classes defined")
# ─────────────────────────────────────────────────────────────────────────────
# MODEL LOADING FUNCTION - Exactly from Colab SECTION 8
# ─────────────────────────────────────────────────────────────────────────────
def load_model_from_checkpoint(checkpoint_path: str, model_name: str, config: dict):
"""
Load VisionT5Model from checkpoint - EXACT implementation from Colab
"""
print(f"\nLoading {model_name} model...")
print(f" Checkpoint: {checkpoint_path}")
try:
# Create image encoder
print(f" Creating CoAtNet encoder: {config['coatnet_model']}")
img_encoder = CoAtNetEncoder(
model_name=config['coatnet_model'],
pretrained=False, # Weights will come from checkpoint
train_last_stages=config['train_last_stages']
)
# Create full model
print(f" Creating VisionT5 model with T5: {config['t5_model']}")
model = VisionT5Model(
img_encoder=img_encoder,
txt_model_name=config['t5_model'],
img_emb_dim=config['img_emb_dim']
)
# Load checkpoint
print(f" Loading checkpoint weights...")
checkpoint = torch.load(checkpoint_path, map_location=device)
# Handle different checkpoint formats
if isinstance(checkpoint, dict):
if 'model_state_dict' in checkpoint:
state_dict = checkpoint['model_state_dict']
print(f" Found 'model_state_dict' in checkpoint")
elif 'state_dict' in checkpoint:
state_dict = checkpoint['state_dict']
print(f" Found 'state_dict' in checkpoint")
elif 'model' in checkpoint:
state_dict = checkpoint['model']
print(f" Found 'model' in checkpoint")
else:
# Assume checkpoint is the state dict
state_dict = checkpoint
print(f" Using checkpoint as state_dict directly")
# Print additional checkpoint info if available
if 'epoch' in checkpoint:
print(f" Checkpoint epoch: {checkpoint['epoch']}")
if 'loss' in checkpoint:
print(f" Checkpoint loss: {checkpoint['loss']:.4f}")
else:
state_dict = checkpoint
print(f" Checkpoint is a state_dict")
# Load state dict
missing_keys, unexpected_keys = model.load_state_dict(state_dict, strict=False)
if missing_keys:
print(f" ⚠️ Missing keys: {len(missing_keys)}")
if len(missing_keys) <= 5:
for key in missing_keys:
print(f" - {key}")
if unexpected_keys:
print(f" ⚠️ Unexpected keys: {len(unexpected_keys)}")
if len(unexpected_keys) <= 5:
for key in unexpected_keys:
print(f" - {key}")
# Move to device and set to eval mode
model = model.to(device)
model.eval()
print(f"βœ“ {model_name} model loaded successfully!")
return model
except Exception as e:
print(f"❌ Error loading {model_name} model: {str(e)}")
import traceback
traceback.print_exc()
raise
# ─────────────────────────────────────────────────────────────────────────────
# INFERENCE FUNCTION - Exactly from Colab SECTION 9
# ─────────────────────────────────────────────────────────────────────────────
def generate_report(
image_path: str,
model: VisionT5Model,
config: dict
) -> str:
"""
Generate medical report from X-ray image - EXACT implementation from Colab
"""
try:
# Preprocess image
image = Image.open(image_path).convert('RGB')
pixel_values = transform(image).unsqueeze(0).to(device)
# Generate report - using EXACT parameters from Colab
with torch.no_grad():
generated_ids = model.generate_reports(
pixel_values,
max_length=config['max_length'],
num_beams=config['num_beams']
)
# Decode
report = tokenizer.decode(generated_ids[0], skip_special_tokens=True)
return report.strip()
except Exception as e:
print(f"Error generating report for {image_path}: {str(e)}")
return ""
# ─────────────────────────────────────────────────────────────────────────────
# LOAD MODELS FROM HUGGINGFACE
# ─────────────────────────────────────────────────────────────────────────────
print("\n" + "="*80)
print("LOADING MODELS FROM HUGGINGFACE")
print("="*80)
# Download model files from Hugging Face
try:
SFT_MODEL_PATH = hf_hub_download(
repo_id="vinaykumarhs2020/RLHF_radiology_model",
filename="best_model.pt"
)
PPO_MODEL_PATH = hf_hub_download(
repo_id="vinaykumarhs2020/RLHF_radiology_model",
filename="rlhf_model.pt"
)
print(f"βœ“ Downloaded SFT model: {SFT_MODEL_PATH}")
print(f"βœ“ Downloaded PPO model: {PPO_MODEL_PATH}")
except Exception as e:
print(f"❌ Error downloading models: {e}")
# Fallback to local paths if downloads fail
SFT_MODEL_PATH = "/content/best_model.pt"
PPO_MODEL_PATH = "/content/rlhf_model.pt"
print(f"⚠️ Using local paths instead")
# Load both models
print("\n" + "="*80)
print("LOADING MODELS")
print("="*80)
sft_model = load_model_from_checkpoint(
SFT_MODEL_PATH,
"SFT",
CONFIG
)
ppo_model = load_model_from_checkpoint(
PPO_MODEL_PATH,
"PPO",
CONFIG
)
print("\nβœ“ Both models loaded successfully!")
# ─────────────────────────────────────────────────────────────────────────────
# FASTAPI APP
# ─────────────────────────────────────────────────────────────────────────────
app = FastAPI(title="Medical Report Generation - Matching Colab")
app.add_middleware(
CORSMiddleware,
allow_origins=["*"],
allow_methods=["*"],
allow_headers=["*"],
)
def preprocess_bytes(file_bytes: bytes) -> torch.Tensor:
"""Preprocess image bytes for inference"""
img = Image.open(io.BytesIO(file_bytes)).convert("RGB")
return transform(img).unsqueeze(0).to(device)
@app.get("/health")
def health():
return {
"status": "ok",
"device": str(device),
"models_loaded": True,
"config": CONFIG
}
@app.post("/sft")
async def sft_inference(file: UploadFile = File(...)):
"""
SFT model inference - EXACTLY matching Colab behavior
"""
try:
# Preprocess image
tensor = preprocess_bytes(await file.read())
# Generate report using EXACT Colab parameters
with torch.no_grad():
generated_ids = sft_model.generate_reports(
tensor,
max_length=CONFIG['max_length'],
num_beams=CONFIG['num_beams']
)
# Decode - EXACTLY as Colab does
report = tokenizer.decode(generated_ids[0], skip_special_tokens=True).strip()
print(f"[SFT] Generated: {report}")
# Return FULL report without truncation
return {"report": report, "model": "SFT", "config_used": CONFIG}
except Exception as e:
traceback.print_exc()
return {"report": f"ERROR: {str(e)}", "model": "SFT"}
@app.post("/ppo")
async def ppo_inference(file: UploadFile = File(...)):
"""
PPO model inference - EXACTLY matching Colab behavior
"""
try:
# Preprocess image
tensor = preprocess_bytes(await file.read())
# Generate report using EXACT Colab parameters
with torch.no_grad():
generated_ids = ppo_model.generate_reports(
tensor,
max_length=CONFIG['max_length'],
num_beams=CONFIG['num_beams']
)
# Decode - EXACTLY as Colab does
report = tokenizer.decode(generated_ids[0], skip_special_tokens=True).strip()
print(f"[PPO] Generated: {report}")
# Return FULL report without truncation
return {"report": report, "model": "PPO", "config_used": CONFIG}
except Exception as e:
traceback.print_exc()
return {"report": f"ERROR: {str(e)}", "model": "PPO"}
@app.post("/compare")
async def compare_models(file: UploadFile = File(...)):
"""
Generate reports from both models for comparison
"""
try:
file_bytes = await file.read()
tensor = preprocess_bytes(file_bytes)
# SFT Generation
with torch.no_grad():
sft_ids = sft_model.generate_reports(
tensor,
max_length=CONFIG['max_length'],
num_beams=CONFIG['num_beams']
)
sft_report = tokenizer.decode(sft_ids[0], skip_special_tokens=True).strip()
# PPO Generation
with torch.no_grad():
ppo_ids = ppo_model.generate_reports(
tensor,
max_length=CONFIG['max_length'],
num_beams=CONFIG['num_beams']
)
ppo_report = tokenizer.decode(ppo_ids[0], skip_special_tokens=True).strip()
print(f"[COMPARE] SFT: {sft_report}")
print(f"[COMPARE] PPO: {ppo_report}")
return {
"sft_report": sft_report,
"ppo_report": ppo_report,
"config_used": CONFIG
}
except Exception as e:
traceback.print_exc()
return {
"sft_report": f"ERROR: {str(e)}",
"ppo_report": f"ERROR: {str(e)}"
}
@app.get("/debug_config")
def debug_config():
"""Debug endpoint to check configuration"""
return {
"config": CONFIG,
"device": str(device),
"tokenizer": CONFIG['t5_model'],
"image_size": CONFIG['image_size'],
"max_length": CONFIG['max_length'],
"num_beams": CONFIG['num_beams'],
"models_loaded": {
"sft": sft_model is not None,
"ppo": ppo_model is not None
}
}
# ─────────────────────────────────────────────────────────────────────────────
# STATIC FILE SERVING
# ─────────────────────────────────────────────────────────────────────────────
from fastapi.staticfiles import StaticFiles
if os.path.exists("build"):
app.mount("/", StaticFiles(directory="build", html=True), name="static")
print("βœ… React app mounted at /")
else:
print("⚠️ Build directory not found, serving API only")
if __name__ == "__main__":
import uvicorn
uvicorn.run(app, host="0.0.0.0", port=7860, reload=False)