demo.py

'''
Download Merlin and test the model on sample data that is downloaded from huggingface
'''
import os
import warnings
import torch

from merlin.data import download_sample_data
from merlin.data import DataLoader
from merlin import Merlin


warnings.filterwarnings("ignore")
device = "cuda" if torch.cuda.is_available() else "cpu"

model = Merlin()
model.eval()
model.cuda()

data_dir = os.path.join(os.path.dirname(__file__), "abct_data")
cache_dir = data_dir.replace("abct_data", "abct_data_cache")

datalist = [
    {
        "image": download_sample_data(data_dir), # function returns local path to nifti file
        "text": "Lower thorax: A small low-attenuating fluid structure is noted in the right cardiophrenic angle in keeping with a tiny pericardial cyst."
        "Liver and biliary tree: Normal. Gallbladder: Normal. Spleen: Normal. Pancreas: Normal. Adrenal glands: Normal. "
        "Kidneys and ureters: Symmetric enhancement and excretion of the bilateral kidneys, with no striated nephrogram to suggest pyelonephritis. "
        "Urothelial enhancement bilaterally, consistent with urinary tract infection. No renal/ureteral calculi. No hydronephrosis. "
        "Gastrointestinal tract: Normal. Normal gas-filled appendix. Peritoneal cavity: No free fluid. "
        "Bladder: Marked urothelial enhancement consistent with cystitis. Uterus and ovaries: Normal. "
        "Vasculature: Patent. Lymph nodes: Normal. Abdominal wall: Normal. "
        "Musculoskeletal: Degenerative change of the spine.",
    },
]

dataloader = DataLoader(
    datalist=datalist,
    cache_dir=cache_dir,
    batchsize=8,
    shuffle=True,
    num_workers=0,
)

for batch in dataloader:
    outputs = model(
        batch["image"].to(device), 
        batch["text"]
        )
    print(f"\n================== Output Shapes ==================")
    print(f"Contrastive image embeddings shape: {outputs[0].shape}")
    print(f"Phenotype predictions shape: {outputs[1].shape}")
    print(f"Contrastive text embeddings shape: {outputs[2].shape}")
    
## Get the Image Embeddings
model = Merlin(ImageEmbedding=True)
model.eval()
model.cuda()

for batch in dataloader:
    outputs = model(
        batch["image"].to(device), 
        )
    print(f"\n================== Output Shapes ==================")
    print(f"Image embeddings shape (Can be used for downstream tasks): {outputs[0].shape}")