Spaces:
Running
Running
| 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 | |
| # 1. 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) | |
| # 2. Preprocess images | |
| def preprocess_image(image_path): | |
| ext = os.path.splitext(image_path)[-1].lower() | |
| if ext == '.nii' or ext == '.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 | |
| # 3. Label images | |
| def prepare_dataset(extracted_folder): | |
| image_paths = [] | |
| labels = [] | |
| for disease_folder in ['alzheimers', 'parkinsons', 'ms']: | |
| folder_path = os.path.join(extracted_folder, disease_folder) | |
| label = {'alzheimers': 0, 'parkinsons': 1, 'ms': 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 | |
| # 4. Custom Dataset | |
| 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 | |
| # 5. 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 | |
| st.title("Fine-tune ViT on MRI Scans") | |
| # Input for zip file paths | |
| zip_file_1 = st.text_input("https://huggingface.co/spaces/Tanusree88/ViT-MRI-FineTuning/resolve/main/archive%20(5).zip") | |
| zip_file_2 = st.text_input("https://huggingface.co/spaces/Tanusree88/ViT-MRI-FineTuning/resolve/main/MS.zip") | |
| if st.button("Start Training"): | |
| # Define an extraction directory | |
| extraction_dir = 'https://huggingface.co/spaces/Tanusree88/ViT-MRI-FineTuning/resolve/main/extracttedfiles' | |
| os.makedirs(extraction_dir, exist_ok=True) | |
| # Extract both zip files | |
| extract_zip(zip_file_1, extraction_dir) | |
| extract_zip(zip_file_2, 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}") | |