app.py

import gradio as gr
from PIL import Image
from pathlib import Path
from vq_gan_3d import load_VQGAN

# Numerical computing
import numpy as np

# PyTorch
import torch
import torch.nn.functional as F

# Utilities to calculate grids from SMILES and visualization
from utils import get_grid_from_smiles, plot_voxel_grid, change_grid_size

ckpt_path   = Path("./vq_gan_3d/weights/3DGrid-VQGAN_43.pt")
folder      = str(ckpt_path.parent)      
ckpt_file   = ckpt_path.name
vqgan = load_VQGAN(folder=folder, ckpt_filename=ckpt_file).eval()


def comparison(SMILES):
    density_grids = get_grid_from_smiles([SMILES])

    # 1) Prepare density grids → list of ready-to-use tensors
    processed_tensors = []
    for item in density_grids:
        rho   = item["rho"]                   # raw NumPy array from cube generation
        smi   = item["smiles"]
        name  = item["name"]
    
        tensor = torch.from_numpy(rho).float() # convert grid to float32 tensor
        tensor = torch.log1p(tensor)           # apply log(ρ + 1) normalization
    
        # enforce consistent 128×128×128 input size for VQGAN
        if tensor.shape != torch.Size([128, 128, 128]):
            tensor = tensor.unsqueeze(0).unsqueeze(0)  # add batch & channel dims
            tensor = F.interpolate(
                tensor,
                size=(128, 128, 128),
                mode="trilinear",
                align_corners=False
            )[0, 0]                                    # remove extra dims after resizing
            print(f"[info] {smi} was interpolated to 128³")
    
        # store metadata alongside the processed tensor
        processed_tensors.append({
            "name":   name,
            "smiles": smi,
            "tensor": tensor
        })
    
        # log shape and min/max to verify normalization and sizing
        print(
            f"{smi}: shape={tuple(tensor.shape)}, "
            f"min={tensor.min():.4f}, max={tensor.max():.4f}"
        )

    # 2) Encode → Decode (inference with VQGAN)
    reconstructions = []
    for item in processed_tensors:
        smi  = item["smiles"]       # original SMILES string
        name = item["name"]         # unique grid name
        vol  = item["tensor"]       # preprocessed [128³] tensor
    
        # add batch & channel dims and move to the selected device
        x = vol.unsqueeze(0).unsqueeze(0)  # shape [1,1,128,128,128]
    
        with torch.no_grad():  # disable gradient computation for faster inference
            indices = vqgan.encode(x)   # map input volume to discrete latent codes
            recon   = vqgan.decode(indices)  # reconstruct volume from latent codes
    
        # convert reconstructed tensor and original tensor to NumPy arrays
        recon_np = recon.cpu().numpy()[0, 0]
        orig_np  = vol.cpu().numpy()
    
        # compute mean squared error between original and reconstruction
        mse = np.mean((orig_np - recon_np) ** 2)
        print(f"{smi} → reconstruction done | MSE={mse:.6f}")
    
        # collect results for later visualization
        reconstructions.append({
            "smiles":       smi,
            "name":         name,
            "original":     orig_np,
            "reconstructed": recon_np
        })

    original_grid_plot = plot_voxel_grid(
        change_grid_size(
            torch.from_numpy(reconstructions[0]["original"]).unsqueeze(0).unsqueeze(0), 
            size=(48, 48, 48)
        ),
        title=f"Original 3D Grid Plot from {SMILES}"
    )
    rec_grid_plot = plot_voxel_grid(
        change_grid_size(
            torch.from_numpy(reconstructions[0]["reconstructed"]).unsqueeze(0).unsqueeze(0), 
            size=(48, 48, 48)
        ),
        title=f"Reconstructed 3D Grid Plot from {SMILES}"
    )

    np.save("original_grid.npy", reconstructions[0]["original"])
    np.save("reconstructed_grid.npy", reconstructions[0]["reconstructed"])

    original_grid_plot.savefig("original_grid_plot.png", format='png')
    rec_grid_plot.savefig("reconstructed_grid_plot.png", format='png')
    original_grid_plot = Image.open("original_grid_plot.png")
    rec_grid_plot = Image.open("reconstructed_grid_plot.png")
    
    return [original_grid_plot, rec_grid_plot], mse, "original_grid.npy", "reconstructed_grid.npy" 


with gr.Blocks() as demo:
    gr.Markdown(
        """
        # 3DGrid-VQGAN SMILES to 3D Grid Reconstruction
        **Single mode:** paste a SMILES string in the left box.  
        **Batch mode:** upload a CSV file where each row has a SMILES in the first column.  
        - **Maximum 1000 SMILES per batch.** Processing time increases with batch size due to Hugging Face environment limits.  
        _This is just a demo environment; for heavy-duty usage, please visit:_  
        https://github.com/IBM/materials/tree/main/models/smi_ted  
        to download the model and run your own experiments.
        - In both cases, an `embeddings.csv` file will be extracted for download, with the first column as SMILES and the embedding values in the following columns.
        """
    )
    gr.Interface(
        fn=comparison, 
        inputs=[
            gr.Dropdown(choices=["CCCO", "CC", "CCO"], label="Provide a SMILES or pre-select one", allow_custom_value=True)
        ], 
        outputs=[
            gr.Gallery(label="3D Grid Reconstruction Comparison", columns=2),
            gr.Number(label="MSE"),
            gr.File(label="Original 3D Grid numpy file"),
            gr.File(label="Reconstructed 3D Grid numpy file")
        ]
    )


if __name__ == "__main__":
    demo.launch(server_name="0.0.0.0")