""" LaborView AI - MedSigLIP Edge Export Export trained MedSigLIP model to ONNX/CoreML/TFLite for mobile deployment """ # /// script # dependencies = [ # "torch>=2.0.0", # "transformers>=4.50.0", # "onnx>=1.14.0", # "onnxruntime>=1.16.0", # "onnxruntime-gpu>=1.16.0", # "huggingface_hub>=0.20.0", # "numpy>=1.24.0", # "pillow>=10.0.0", # ] # /// import os import sys import json import argparse from pathlib import Path from dataclasses import dataclass from typing import Dict, List, Optional, Tuple import torch import torch.nn as nn import torch.nn.functional as F import numpy as np from PIL import Image @dataclass class Config: # Model encoder_pretrained: str = "google/medsiglip-448" encoder_hidden_dim: int = 1152 projection_dim: int = 256 num_plane_classes: int = 2 num_seg_classes: int = 3 image_size: int = 448 # Export hub_model_id: str = "samwell/laborview-medsiglip" output_dir: Path = Path("./exports") opset_version: int = 17 class SegmentationDecoder(nn.Module): """Decoder for upsampling vision features to segmentation mask""" def __init__(self, input_dim: int, num_classes: int, decoder_channels=[512, 256, 128, 64]): super().__init__() self.input_proj = nn.Conv2d(input_dim, decoder_channels[0], 1) self.up_blocks = nn.ModuleList() in_ch = decoder_channels[0] for out_ch in decoder_channels[1:]: self.up_blocks.append(nn.Sequential( nn.ConvTranspose2d(in_ch, out_ch, 4, stride=2, padding=1), nn.BatchNorm2d(out_ch), nn.GELU() )) in_ch = out_ch self.final_up = nn.Sequential( nn.ConvTranspose2d(decoder_channels[-1], 32, 4, stride=2, padding=1), nn.BatchNorm2d(32), nn.GELU(), nn.ConvTranspose2d(32, 32, 4, stride=2, padding=1), nn.BatchNorm2d(32), nn.GELU(), ) self.classifier = nn.Conv2d(32, num_classes, 1) def forward(self, x, target_size=None): B = x.shape[0] if x.dim() == 3: num_patches = x.shape[1] H = W = int(num_patches ** 0.5) x = x.transpose(1, 2).reshape(B, -1, H, W) x = self.input_proj(x) for block in self.up_blocks: x = block(x) x = self.final_up(x) x = self.classifier(x) if target_size: x = F.interpolate(x, size=target_size, mode='bilinear', align_corners=False) return x class LaborViewMedSigLIP(nn.Module): """LaborView model with MedSigLIP vision encoder""" def __init__(self, config: Config): super().__init__() self.config = config from transformers import AutoModel print(f"Loading MedSigLIP from {config.encoder_pretrained}...") self.encoder = AutoModel.from_pretrained( config.encoder_pretrained, trust_remote_code=True ) if hasattr(self.encoder, 'vision_model'): self.vision_encoder = self.encoder.vision_model else: self.vision_encoder = self.encoder if hasattr(self.vision_encoder.config, 'hidden_size'): hidden_dim = self.vision_encoder.config.hidden_size else: hidden_dim = config.encoder_hidden_dim self.projector = nn.Sequential( nn.Linear(hidden_dim, config.projection_dim), nn.LayerNorm(config.projection_dim), nn.GELU(), nn.Linear(config.projection_dim, config.projection_dim) ) self.cls_head = nn.Linear(config.projection_dim, config.num_plane_classes) self.seg_decoder = SegmentationDecoder(hidden_dim, config.num_seg_classes) def forward(self, pixel_values): if hasattr(self, 'vision_encoder'): outputs = self.vision_encoder(pixel_values) else: outputs = self.encoder.get_image_features(pixel_values, return_dict=True) if hasattr(outputs, 'last_hidden_state'): hidden = outputs.last_hidden_state elif hasattr(outputs, 'pooler_output'): hidden = outputs.pooler_output else: hidden = outputs if hidden.dim() == 2: pooled = hidden B, D = hidden.shape seq = hidden.unsqueeze(1).expand(B, 32*32, D) elif hidden.dim() == 3: pooled = hidden.mean(dim=1) seq = hidden else: B, D, H, W = hidden.shape pooled = hidden.mean(dim=[2, 3]) seq = hidden.flatten(2).transpose(1, 2) projected = self.projector(pooled) plane_logits = self.cls_head(projected) seg_masks = self.seg_decoder(seq, target_size=pixel_values.shape[-2:]) return plane_logits, seg_masks class LaborViewExportWrapper(nn.Module): """Wrapper for ONNX export - returns dict-like outputs""" def __init__(self, model): super().__init__() self.model = model def forward(self, pixel_values): plane_logits, seg_masks = self.model(pixel_values) # Return segmentation probabilities and class prediction seg_probs = F.softmax(seg_masks, dim=1) plane_pred = plane_logits.argmax(dim=1) return seg_probs, plane_pred def load_trained_model(config: Config): """Load trained model from HuggingFace Hub""" from huggingface_hub import hf_hub_download print(f"Downloading model from {config.hub_model_id}...") # Download checkpoint checkpoint_path = hf_hub_download( repo_id=config.hub_model_id, filename="best.pt" ) print(f"Loading checkpoint from {checkpoint_path}...") checkpoint = torch.load(checkpoint_path, map_location="cpu", weights_only=False) # Create model model = LaborViewMedSigLIP(config) # Load state dict model.load_state_dict(checkpoint["model_state_dict"]) print(f"Model loaded successfully!") if "val_loss" in checkpoint: print(f" Val Loss: {checkpoint['val_loss']:.4f}") if "val_iou" in checkpoint: print(f" Val IoU: {checkpoint['val_iou']:.4f}") return model def export_to_onnx(model, config: Config, quantize: bool = True): """Export model to ONNX format""" import onnx from onnxruntime.quantization import quantize_dynamic, QuantType config.output_dir.mkdir(parents=True, exist_ok=True) model.eval() wrapper = LaborViewExportWrapper(model) wrapper.eval() # Create dummy input dummy_input = torch.randn(1, 3, config.image_size, config.image_size) # Export paths onnx_path = config.output_dir / "laborview_medsiglip.onnx" onnx_quant_path = config.output_dir / "laborview_medsiglip_int8.onnx" print(f"Exporting to ONNX: {onnx_path}") # Export to ONNX torch.onnx.export( wrapper, dummy_input, str(onnx_path), export_params=True, opset_version=config.opset_version, do_constant_folding=True, input_names=['pixel_values'], output_names=['seg_probs', 'plane_pred'], dynamic_axes={ 'pixel_values': {0: 'batch_size'}, 'seg_probs': {0: 'batch_size'}, 'plane_pred': {0: 'batch_size'} } ) # Verify ONNX model onnx_model = onnx.load(str(onnx_path)) onnx.checker.check_model(onnx_model) print(f"ONNX model verified successfully!") # Get model size onnx_size = onnx_path.stat().st_size / (1024 * 1024 * 1024) print(f"ONNX model size: {onnx_size:.2f} GB") # Quantize to INT8 if quantize: print(f"Quantizing to INT8: {onnx_quant_path}") quantize_dynamic( str(onnx_path), str(onnx_quant_path), weight_type=QuantType.QInt8 ) quant_size = onnx_quant_path.stat().st_size / (1024 * 1024 * 1024) print(f"Quantized model size: {quant_size:.2f} GB") print(f"Size reduction: {(1 - quant_size/onnx_size) * 100:.1f}%") return onnx_path, onnx_quant_path if quantize else None def export_to_coreml(model, config: Config): """Export model to CoreML format for iOS""" try: import coremltools as ct except ImportError: print("coremltools not installed. Skipping CoreML export.") print("Install with: pip install coremltools") return None config.output_dir.mkdir(parents=True, exist_ok=True) model.eval() wrapper = LaborViewExportWrapper(model) wrapper.eval() # Trace the model dummy_input = torch.randn(1, 3, config.image_size, config.image_size) traced_model = torch.jit.trace(wrapper, dummy_input) coreml_path = config.output_dir / "laborview_medsiglip.mlpackage" print(f"Exporting to CoreML: {coreml_path}") # Convert to CoreML mlmodel = ct.convert( traced_model, inputs=[ ct.TensorType( name="pixel_values", shape=(1, 3, config.image_size, config.image_size), dtype=np.float32 ) ], outputs=[ ct.TensorType(name="seg_probs"), ct.TensorType(name="plane_pred") ], minimum_deployment_target=ct.target.iOS16, compute_precision=ct.precision.FLOAT16 # Use FP16 for mobile ) # Add metadata mlmodel.author = "LaborView AI" mlmodel.short_description = "Ultrasound segmentation for labor monitoring" mlmodel.version = "1.0" # Save mlmodel.save(str(coreml_path)) print(f"CoreML model saved!") return coreml_path def verify_onnx_model(onnx_path: Path, config: Config): """Verify ONNX model with sample inference""" import onnxruntime as ort print(f"\nVerifying ONNX model: {onnx_path}") # Create session session = ort.InferenceSession(str(onnx_path)) # Get input/output info input_info = session.get_inputs()[0] print(f"Input: {input_info.name}, shape: {input_info.shape}, type: {input_info.type}") for output in session.get_outputs(): print(f"Output: {output.name}, shape: {output.shape}, type: {output.type}") # Run inference dummy_input = np.random.randn(1, 3, config.image_size, config.image_size).astype(np.float32) outputs = session.run(None, {"pixel_values": dummy_input}) seg_probs, plane_pred = outputs print(f"\nTest inference:") print(f" Segmentation output shape: {seg_probs.shape}") print(f" Plane prediction: {plane_pred}") # Measure inference time import time times = [] for _ in range(10): start = time.time() session.run(None, {"pixel_values": dummy_input}) times.append(time.time() - start) avg_time = np.mean(times) * 1000 print(f" Average inference time: {avg_time:.1f} ms") return True def main(): parser = argparse.ArgumentParser(description="Export MedSigLIP for edge deployment") parser.add_argument("--output-dir", type=str, default="./exports", help="Output directory") parser.add_argument("--quantize", action="store_true", default=True, help="Quantize to INT8") parser.add_argument("--coreml", action="store_true", help="Export to CoreML") parser.add_argument("--verify", action="store_true", default=True, help="Verify exported model") args = parser.parse_args() config = Config() config.output_dir = Path(args.output_dir) # Load trained model model = load_trained_model(config) model.eval() # Export to ONNX onnx_path, onnx_quant_path = export_to_onnx(model, config, quantize=args.quantize) # Verify if args.verify and onnx_path: verify_onnx_model(onnx_path, config) if onnx_quant_path: verify_onnx_model(onnx_quant_path, config) # Export to CoreML if args.coreml: export_to_coreml(model, config) print("\n" + "="*50) print("Export Summary:") print("="*50) for f in config.output_dir.glob("*"): size_mb = f.stat().st_size / (1024 * 1024) if size_mb > 1024: print(f" {f.name}: {size_mb/1024:.2f} GB") else: print(f" {f.name}: {size_mb:.1f} MB") print("\nDone!") if __name__ == "__main__": main()