""" 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", # "onnxscript>=0.1.0", # "onnxruntime>=1.16.0", # "huggingface_hub>=0.20.0", # "numpy>=1.24.0", # "pillow>=10.0.0", # "coremltools>=7.0", # ] # /// 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 using TorchScript tracing""" import onnx import os os.environ["TORCH_ONNX_USE_DYNAMO"] = "0" # Force legacy exporter config.output_dir.mkdir(parents=True, exist_ok=True) model.eval() wrapper = LaborViewExportWrapper(model) wrapper.eval() # Create dummy input on CPU dummy_input = torch.randn(1, 3, config.image_size, config.image_size) # Move model to CPU for export wrapper = wrapper.cpu() # 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 directly without tracing (for new PyTorch exporter compatibility) with torch.no_grad(): torch.onnx.export( wrapper, (dummy_input,), str(onnx_path), export_params=True, opset_version=14, do_constant_folding=True, input_names=['pixel_values'], output_names=['seg_probs', 'plane_pred'] ) # 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 (with error handling) onnx_quant_path_result = None if quantize and onnx_size > 0.001: try: from onnxruntime.quantization import quantize_dynamic, QuantType 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}%") onnx_quant_path_result = onnx_quant_path except Exception as e: print(f"Quantization failed: {e}") print("Continuing with FP32 model only") return onnx_path, onnx_quant_path_result def export_to_coreml(model, config: Config): """Export model to CoreML format for iOS with Neural Engine optimization""" try: import coremltools as ct from coremltools.models.neural_network import quantization_utils 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() model = model.cpu() # Move to CPU for export wrapper = LaborViewExportWrapper(model) wrapper.eval() # Trace the model print("Tracing model for CoreML...") dummy_input = torch.randn(1, 3, config.image_size, config.image_size) with torch.no_grad(): traced_model = torch.jit.trace(wrapper, dummy_input) coreml_path = config.output_dir / "laborview_medsiglip.mlpackage" coreml_fp16_path = config.output_dir / "laborview_medsiglip_fp16.mlpackage" print(f"Converting to CoreML: {coreml_path}") try: # Convert to CoreML with FP32 first 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_units=ct.ComputeUnit.ALL # Use Neural Engine + GPU + CPU ) # Add metadata mlmodel.author = "LaborView AI" mlmodel.short_description = "MedSigLIP ultrasound segmentation for labor monitoring" mlmodel.version = "1.0" # Save FP32 version mlmodel.save(str(coreml_path)) print(f"CoreML FP32 model saved: {coreml_path}") # Create FP16 version for smaller size and faster inference print("Creating FP16 quantized version...") mlmodel_fp16 = 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_units=ct.ComputeUnit.ALL, compute_precision=ct.precision.FLOAT16 ) mlmodel_fp16.author = "LaborView AI" mlmodel_fp16.short_description = "MedSigLIP ultrasound segmentation (FP16)" mlmodel_fp16.version = "1.0" mlmodel_fp16.save(str(coreml_fp16_path)) print(f"CoreML FP16 model saved: {coreml_fp16_path}") return coreml_path except Exception as e: print(f"CoreML export failed: {e}") import traceback traceback.print_exc() return None 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", default=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()