app.py

import os
import zipfile
import numpy as np
import torch
from transformers import ViTForImageClassification, AdamW
import nibabel as nib
from PIL import Image
from torch.utils.data import Dataset, DataLoader
import streamlit as st

# Function to extract zip files
def extract_zip(zip_file, extract_to):
    with zipfile.ZipFile(zip_file, 'r') as zip_ref:
        zip_ref.extractall(extract_to)

# Preprocess images
def preprocess_image(image_path):
    ext = os.path.splitext(image_path)[-1].lower()

    if ext in ['.nii', '.nii.gz']:
        nii_image = nib.load(image_path)
        image_data = nii_image.get_fdata()
        image_tensor = torch.tensor(image_data).float()
        if len(image_tensor.shape) == 3:
            image_tensor = image_tensor.unsqueeze(0)

    elif ext in ['.jpg', '.jpeg']:
        img = Image.open(image_path).convert('RGB').resize((224, 224))
        img_np = np.array(img)
        image_tensor = torch.tensor(img_np).permute(2, 0, 1).float()

    else:
        raise ValueError(f"Unsupported format: {ext}")

    image_tensor /= 255.0  # Normalize to [0, 1]
    return image_tensor

# Prepare dataset
def prepare_dataset(extracted_folder):
    # Ensure the path exists
    neuronii_path = os.path.join(extracted_folder, "neuroniiimages")
    
    if not os.path.exists(neuronii_path):
        raise FileNotFoundError(f"The folder neuroniiimages does not exist in the extracted folder: {neuronii_path}")
    
    image_paths = []
    labels = []
    
    for disease_folder in ['alzheimers_dataset', 'parkinsons_dataset', 'MSjpg']:
        folder_path = os.path.join(neuronii_path, disease_folder)
        
        # Check if the subfolder exists
        if not os.path.exists(folder_path):
            raise FileNotFoundError(f"The folder {disease_folder} does not exist at path: {folder_path}")
        
        label = {'alzheimers_dataset': 0, 'parkinsons_dataset': 1, 'MSjpg': 2}[disease_folder]
        
        for img_file in os.listdir(folder_path):
            if img_file.endswith(('.nii', '.jpg', '.jpeg')):
                image_paths.append(os.path.join(folder_path, img_file))
                labels.append(label)
    
    return image_paths, labels

# Custom Dataset class
class CustomImageDataset(Dataset):
    def __init__(self, image_paths, labels):
        self.image_paths = image_paths
        self.labels = labels

    def __len__(self):
        return len(self.image_paths)

    def __getitem__(self, idx):
        image = preprocess_image(self.image_paths[idx])
        label = self.labels[idx]
        return image, label

# Training function
def fine_tune_model(train_loader):
    model = ViTForImageClassification.from_pretrained('google/vit-base-patch16-224-in21k', num_labels=3)
    model.train()
    optimizer = AdamW(model.parameters(), lr=1e-4)
    criterion = torch.nn.CrossEntropyLoss()
    device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
    model.to(device)
    
    for epoch in range(10):
        running_loss = 0.0
        for images, labels in train_loader:
            images, labels = images.to(device), labels.to(device)
            optimizer.zero_grad()
            outputs = model(pixel_values=images).logits
            loss = criterion(outputs, labels)
            loss.backward()
            optimizer.step()
            running_loss += loss.item()
    return running_loss / len(train_loader)

# Streamlit UI for Fine-tuning
st.title("Fine-tune ViT on MRI/CT Scans for MS & Neurodegenerative Diseases")

# Provide the correct zip file URL
zip_file_url = "https://huggingface.co/spaces/Tanusree88/ViT-MRI-FineTuning/resolve/main/neuroniiimages.zip"

if st.button("Start Training"):
    extraction_dir = "extracted_files"
    os.makedirs(extraction_dir, exist_ok=True)

    # Download the zip file (this is a placeholder; use requests or any other method to download the zip file)
    zip_file = "neuroniiimages.zip"  # Assuming you downloaded it with this name

    # Extract zip file
    extract_zip(zip_file, extraction_dir)

    # Prepare dataset
    image_paths, labels = prepare_dataset(extraction_dir)
    dataset = CustomImageDataset(image_paths, labels)
    train_loader = DataLoader(dataset, batch_size=32, shuffle=True)

    # Fine-tune the model
    final_loss = fine_tune_model(train_loader)
    st.write(f"Training Complete with Final Loss: {final_loss}")