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Update app.py
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app.py
CHANGED
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@@ -6,20 +6,19 @@ import cv2
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from PIL import Image
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import matplotlib.pyplot as plt
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import io
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from torchvision import transforms
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import torchvision.transforms.functional as TF
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import
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import os
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import kagglehub
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import random
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import
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device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
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model = None
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#
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class DoubleConv(nn.Module):
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def __init__(self, in_channels, out_channels):
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super(DoubleConv, self).__init__()
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@@ -61,7 +60,7 @@ class AttentionBlock(nn.Module):
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x1 = self.W_x(x)
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psi = self.relu(g1 + x1)
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psi = self.psi(psi)
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return x * psi, psi # Return
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class AttentionUNET(nn.Module):
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def __init__(self, in_channels=1, out_channels=1, features=[32, 64, 128, 256]):
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@@ -72,7 +71,7 @@ class AttentionUNET(nn.Module):
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self.attentions = nn.ModuleList()
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self.pool = nn.MaxPool2d(kernel_size=2, stride=2)
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# Down part
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for feature in features:
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self.downs.append(DoubleConv(in_channels, feature))
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in_channels = feature
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@@ -80,7 +79,7 @@ class AttentionUNET(nn.Module):
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# Bottleneck
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self.bottleneck = DoubleConv(features[-1], features[-1]*2)
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# Up part
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for feature in reversed(features):
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self.ups.append(nn.ConvTranspose2d(feature*2, feature, kernel_size=2, stride=2))
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self.attentions.append(AttentionBlock(F_g=feature, F_l=feature, F_int=feature // 2))
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@@ -88,9 +87,9 @@ class AttentionUNET(nn.Module):
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self.final_conv = nn.Conv2d(features[0], out_channels, kernel_size=1)
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def forward(self, x
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skip_connections = []
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attention_maps = []
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for down in self.downs:
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x = down(x)
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@@ -107,30 +106,13 @@ class AttentionUNET(nn.Module):
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if x.shape != skip_connection.shape:
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x = TF.resize(x, size=skip_connection.shape[2:])
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attention_maps.append(attention_coeff)
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concat_skip = torch.cat((
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x = self.ups[idx+1](concat_skip)
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if return_attention:
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return output, attention_maps
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return output
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def download_dataset():
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"""Download Brain Tumor Segmentation dataset from Kaggle"""
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global dataset_path
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try:
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print("📥 Downloading Brain Tumor Segmentation dataset...")
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dataset_path = kagglehub.dataset_download('nikhilroxtomar/brain-tumor-segmentation')
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print(f"✅ Dataset downloaded to: {dataset_path}")
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return dataset_path
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except Exception as e:
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print(f"❌ Failed to download dataset: {e}")
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return None
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def download_model():
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"""Download your trained model from HuggingFace"""
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@@ -138,758 +120,307 @@ def download_model():
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model_path = "best_attention_model.pth.tar"
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if not os.path.exists(model_path):
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print("📥 Downloading trained model...")
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try:
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urllib.request.urlretrieve(model_url, model_path)
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print("✅ Model downloaded successfully!")
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except Exception as e:
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print(f"❌ Failed to download model: {e}")
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return None
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else:
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print("✅ Model already exists!")
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return model_path
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def
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"""Load trained Attention U-Net model"""
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global model
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if model is None:
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try:
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print("🔄 Loading Attention U-Net model...")
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model_path = download_model()
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if model_path is None:
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return None
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model = AttentionUNET(in_channels=1, out_channels=1).to(device)
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checkpoint = torch.load(model_path, map_location=device, weights_only=True)
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model.load_state_dict(checkpoint["state_dict"])
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model.eval()
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print("✅ Attention U-Net model loaded successfully!")
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except Exception as e:
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print(f"❌ Error loading model: {e}")
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model = None
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return model
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def
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"""
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images_path = Path(dataset_path) / "images"
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masks_path = Path(dataset_path) / "masks"
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if not images_path.exists() or not masks_path.exists():
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print("❌ Dataset structure not found")
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return None, None
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# Get all image files
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image_files = list(images_path.glob("*.jpg")) + list(images_path.glob("*.png")) + list(images_path.glob("*.tif"))
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if not image_files:
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print("❌ No image files found in dataset")
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return None, None
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# Select random image
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random_image_file = random.choice(image_files)
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image_name = random_image_file.stem
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# Find corresponding mask
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possible_mask_extensions = ['.jpg', '.png', '.tif', '.gif']
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mask_file = None
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for ext in possible_mask_extensions:
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potential_mask = masks_path / f"{image_name}{ext}"
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if potential_mask.exists():
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mask_file = potential_mask
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break
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if mask_file is None:
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print(f"❌ No corresponding mask found for {image_name}")
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return None, None
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# Load image and mask
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image = Image.open(random_image_file).convert('L')
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mask = Image.open(mask_file).convert('L')
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print(f"✅ Loaded random sample: {image_name}")
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return image, mask
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except Exception as e:
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print(f"❌ Error loading random sample: {e}")
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return None, None
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def
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"""
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lambda x: torch.flip(x, dims=[3]), # Horizontal flip
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lambda x: torch.flip(x, dims=[2]), # Vertical flip
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lambda x: torch.flip(x, dims=[2, 3]), # Both flips
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lambda x: torch.rot90(x, k=1, dims=[2, 3]), # 90° rotation
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lambda x: torch.rot90(x, k=3, dims=[2, 3]), # 270° rotation
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]
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lambda x: torch.flip(x, dims=[2]), # Reverse vertical flip
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lambda x: torch.flip(x, dims=[2, 3]), # Reverse both flips
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lambda x: torch.rot90(x, k=3, dims=[2, 3]), # Reverse 90° rotation
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lambda x: torch.rot90(x, k=1, dims=[2, 3]), # Reverse 270° rotation
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]
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predictions = []
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aug_input = aug(image_tensor)
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# Get prediction
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pred = torch.sigmoid(model(aug_input))
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# Reverse augmentation on prediction
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pred = rev_aug(pred)
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predictions.append(pred)
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#
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pred, attention_maps = model(image_tensor, return_attention=True)
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# Convert attention maps to numpy for visualization
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heatmaps = []
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for i, att_map in enumerate(attention_maps):
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# Resize attention map to match input size
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att_map_resized = TF.resize(att_map, (256, 256))
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att_np = att_map_resized.cpu().squeeze().numpy()
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heatmaps.append(att_np)
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return heatmaps
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def preprocess_image(image):
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"""Preprocessing exactly like training code"""
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if image.mode != 'L':
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image = image.convert('L')
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def
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"""
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intersection = torch.sum(pred_binary * gt_binary)
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dice = (2.0 * intersection) / (torch.sum(pred_binary) + torch.sum(gt_binary) + 1e-8)
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iou = intersection / (union + 1e-8)
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def
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current_model = load_attention_model()
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if current_model is None:
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return None, "
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if image is None:
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return None, "
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try:
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print("
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input_tensor = preprocess_image(image).to(device)
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#
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with torch.no_grad():
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standard_pred = torch.sigmoid(current_model(input_tensor))
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# Test-Time Augmentation
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if use_tta:
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final_pred = tta_pred
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else:
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final_pred = standard_pred
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# Generate attention heatmaps
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attention_heatmaps = []
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if show_attention:
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attention_heatmaps = generate_attention_heatmaps(current_model, input_tensor)
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# Convert predictions to binary
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pred_mask_binary = (final_pred > 0.5).float()
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pred_mask_np = pred_mask_binary.cpu().squeeze().numpy()
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standard_mask_np = (standard_pred > 0.5).float().cpu().squeeze().numpy()
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# Prepare images for visualization
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original_np = np.array(image.convert('L').resize((256, 256)))
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# Create comprehensive visualization
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if ground_truth is not None:
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# With ground truth comparison
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gt_np = np.array(ground_truth.convert('L').resize((256, 256)))
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gt_binary = (gt_np > 127).astype(np.float32) # Threshold ground truth
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# Calculate metrics
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gt_tensor = torch.tensor(gt_binary).unsqueeze(0).unsqueeze(0).to(device)
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dice_score, iou_score = calculate_metrics(final_pred, gt_tensor)
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# Create figure with ground truth comparison
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n_cols = 6 if show_attention and attention_heatmaps else 5
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fig, axes = plt.subplots(2, n_cols, figsize=(4*n_cols, 8))
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fig.suptitle('🧠 Enhanced Attention U-Net Analysis with Ground Truth Comparison', fontsize=16, weight='bold')
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# Top row - Standard analysis
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axes[0, 0].imshow(original_np, cmap='gray')
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axes[0, 0].set_title('Original Image', fontsize=12, weight='bold')
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axes[0, 0].axis('off')
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axes[0, 1].imshow(standard_mask_np * 255, cmap='hot')
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axes[0, 1].set_title('Standard Prediction', fontsize=12, weight='bold')
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axes[0, 1].axis('off')
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axes[0, 2].imshow(pred_mask_np * 255, cmap='hot')
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axes[0, 2].set_title(f'{"TTA Enhanced" if use_tta else "Final Prediction"}', fontsize=12, weight='bold')
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axes[0, 2].axis('off')
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axes[0, 3].imshow(gt_binary * 255, cmap='hot')
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axes[0, 3].set_title('Ground Truth', fontsize=12, weight='bold')
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axes[0, 3].axis('off')
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# Overlay comparison
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overlay = original_np.copy()
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overlay = np.stack([overlay, overlay, overlay], axis=-1)
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overlay[pred_mask_np > 0.5] = [255, 0, 0] # Red for prediction
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overlay[gt_binary > 0.5] = [0, 255, 0] # Green for ground truth
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overlap = (pred_mask_np > 0.5) & (gt_binary > 0.5)
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overlay[overlap] = [255, 255, 0] # Yellow for overlap
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axes[0, 4].imshow(overlay.astype(np.uint8))
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axes[0, 4].set_title('Overlay (Red:Pred, Green:GT, Yellow:Match)', fontsize=10, weight='bold')
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axes[0, 4].axis('off')
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if show_attention and attention_heatmaps:
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# Show combined attention
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combined_attention = np.mean(attention_heatmaps, axis=0)
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axes[0, 5].imshow(combined_attention, cmap='jet', alpha=0.7)
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axes[0, 5].imshow(original_np, cmap='gray', alpha=0.3)
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axes[0, 5].set_title('Attention Heatmap', fontsize=12, weight='bold')
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axes[0, 5].axis('off')
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# Bottom row - Individual attention maps or detailed analysis
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if show_attention and attention_heatmaps:
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for i, heatmap in enumerate(attention_heatmaps[:n_cols]):
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axes[1, i].imshow(heatmap, cmap='jet', alpha=0.7)
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axes[1, i].imshow(original_np, cmap='gray', alpha=0.3)
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axes[1, i].set_title(f'Attention Gate {i+1}', fontsize=10, weight='bold')
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axes[1, i].axis('off')
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else:
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# Show tumor extraction and analysis
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tumor_only = np.where(pred_mask_np == 1, original_np, 255)
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inv_mask = np.where(pred_mask_np == 1, 0, 255)
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axes[1, 0].imshow(tumor_only, cmap='gray')
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axes[1, 0].set_title('Tumor Extraction', fontsize=12, weight='bold')
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axes[1, 0].axis('off')
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axes[1, 1].imshow(inv_mask, cmap='gray')
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axes[1, 1].set_title('Inverted Mask', fontsize=12, weight='bold')
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axes[1, 1].axis('off')
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# Difference map
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diff_map = np.abs(pred_mask_np - gt_binary)
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axes[1, 2].imshow(diff_map, cmap='Reds')
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axes[1, 2].set_title('Difference Map', fontsize=12, weight='bold')
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axes[1, 2].axis('off')
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# Clear remaining axes
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for j in range(3, n_cols):
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axes[1, j].axis('off')
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else:
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| 441 |
-
|
| 442 |
-
|
| 443 |
-
|
| 444 |
-
|
| 445 |
-
|
| 446 |
-
|
| 447 |
-
|
| 448 |
-
|
| 449 |
-
|
| 450 |
-
|
| 451 |
-
|
| 452 |
-
|
| 453 |
-
|
| 454 |
-
|
| 455 |
-
|
| 456 |
-
|
| 457 |
-
|
| 458 |
-
|
| 459 |
-
|
| 460 |
-
|
| 461 |
-
|
| 462 |
-
|
| 463 |
-
|
| 464 |
-
|
| 465 |
-
|
| 466 |
-
|
| 467 |
-
|
| 468 |
-
|
| 469 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
| 470 |
|
| 471 |
plt.tight_layout()
|
| 472 |
|
| 473 |
-
# Save result
|
| 474 |
buf = io.BytesIO()
|
| 475 |
-
plt.savefig(buf, format='png', dpi=150, bbox_inches='tight'
|
| 476 |
buf.seek(0)
|
| 477 |
plt.close()
|
| 478 |
|
| 479 |
result_image = Image.open(buf)
|
| 480 |
|
| 481 |
-
#
|
| 482 |
-
tumor_pixels = np.sum(
|
| 483 |
-
total_pixels =
|
| 484 |
tumor_percentage = (tumor_pixels / total_pixels) * 100
|
| 485 |
|
| 486 |
-
max_confidence = torch.max(final_pred).item()
|
| 487 |
-
mean_confidence = torch.mean(final_pred).item()
|
| 488 |
-
|
| 489 |
-
# Enhanced analysis text
|
| 490 |
analysis_text = f"""
|
| 491 |
-
|
| 492 |
-
|
| 493 |
-
|
| 494 |
-
-
|
| 495 |
-
-
|
| 496 |
-
-
|
| 497 |
-
- **Max Confidence**: {max_confidence:.4f}
|
| 498 |
-
- **Mean Confidence**: {mean_confidence:.4f}
|
| 499 |
"""
|
| 500 |
-
|
| 501 |
-
if ground_truth is not None:
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 502 |
analysis_text += f"""
|
| 503 |
-
###
|
| 504 |
-
-
|
| 505 |
-
-
|
| 506 |
-
- **Model Accuracy**: {'High precision match' if dice_score > 0.8 else 'Reasonable match' if dice_score > 0.6 else 'Needs improvement'}
|
| 507 |
-
"""
|
| 508 |
-
|
| 509 |
-
analysis_text += f"""
|
| 510 |
-
### 🚀 Enhancement Features
|
| 511 |
-
- **Test-Time Augmentation**: {'✅ Applied (6 augmentations averaged)' if use_tta else '❌ Disabled'}
|
| 512 |
-
- **Attention Visualization**: {'✅ Generated attention heatmaps' if show_attention else '❌ Disabled'}
|
| 513 |
-
- **Boundary Enhancement**: {'✅ TTA improves edge detection' if use_tta else '⚠️ Standard prediction only'}
|
| 514 |
-
- **Interpretability**: {'✅ Attention gates show focus areas' if show_attention else '❌ Black box mode'}
|
| 515 |
-
|
| 516 |
-
### 🔬 Model Architecture
|
| 517 |
-
- **Base Model**: Attention U-Net with skip connections
|
| 518 |
-
- **Training Performance**: Dice: 0.8420, IoU: 0.7297, Accuracy: 98.90%
|
| 519 |
-
- **Attention Gates**: 4 levels with soft attention mechanism
|
| 520 |
-
- **Features Channels**: [32, 64, 128, 256] progression
|
| 521 |
-
- **Device**: {device.type.upper()}
|
| 522 |
-
|
| 523 |
-
### 📈 Enhanced Processing Pipeline
|
| 524 |
-
- **Preprocessing**: Resize(256×256) + Normalization
|
| 525 |
-
- **Augmentations**: Flips (H,V), Rotations (90°,270°), Combined
|
| 526 |
-
- **Attention Fusion**: Multi-scale attention coefficient extraction
|
| 527 |
-
- **Post-processing**: Ensemble averaging + Binary thresholding (0.5)
|
| 528 |
-
|
| 529 |
-
### ⚠️ Medical Disclaimer
|
| 530 |
-
This enhanced AI model is for **research and educational purposes only**.
|
| 531 |
-
Results include advanced features for better accuracy and interpretability.
|
| 532 |
-
Always consult medical professionals for clinical applications.
|
| 533 |
-
|
| 534 |
-
### 🏆 Research Contributions
|
| 535 |
-
✅ **Attention Gates**: Enhanced boundary detection through selective feature passing
|
| 536 |
-
✅ **Test-Time Augmentation**: Robust predictions via ensemble averaging
|
| 537 |
-
✅ **Interpretability**: Attention heatmaps for clinical trust and validation
|
| 538 |
-
✅ **Efficiency**: No retraining required, minimal computational overhead
|
| 539 |
"""
|
| 540 |
|
| 541 |
-
print(f"✅ Enhanced analysis completed! Tumor coverage: {tumor_percentage:.2f}%")
|
| 542 |
return result_image, analysis_text
|
| 543 |
|
| 544 |
except Exception as e:
|
| 545 |
-
|
| 546 |
-
print(error_msg)
|
| 547 |
-
return None, error_msg
|
| 548 |
|
| 549 |
-
def
|
| 550 |
-
|
| 551 |
-
image, mask = get_random_sample_from_dataset()
|
| 552 |
if image is None:
|
| 553 |
-
return None,
|
| 554 |
-
return image,
|
| 555 |
|
| 556 |
-
|
| 557 |
-
return None, None, None, "Upload a brain MRI image or load a random sample to test the enhanced model"
|
| 558 |
-
|
| 559 |
-
# Enhanced professional CSS
|
| 560 |
css = """
|
| 561 |
-
.gradio-container {
|
| 562 |
-
|
| 563 |
-
|
| 564 |
-
|
| 565 |
-
}
|
| 566 |
-
|
| 567 |
-
#title {
|
| 568 |
-
text-align: center;
|
| 569 |
-
background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
|
| 570 |
-
color: white;
|
| 571 |
-
padding: 40px;
|
| 572 |
-
border-radius: 20px;
|
| 573 |
-
margin-bottom: 30px;
|
| 574 |
-
box-shadow: 0 12px 24px rgba(102, 126, 234, 0.4);
|
| 575 |
-
}
|
| 576 |
-
|
| 577 |
-
.feature-box {
|
| 578 |
-
background: linear-gradient(135deg, #f093fb 0%, #f5576c 100%);
|
| 579 |
-
border-radius: 15px;
|
| 580 |
-
padding: 25px;
|
| 581 |
-
margin: 15px 0;
|
| 582 |
-
color: white;
|
| 583 |
-
box-shadow: 0 8px 16px rgba(240, 147, 251, 0.3);
|
| 584 |
-
}
|
| 585 |
-
|
| 586 |
-
.metric-card {
|
| 587 |
-
background: linear-gradient(135deg, #4facfe 0%, #00f2fe 100%);
|
| 588 |
-
border-radius: 12px;
|
| 589 |
-
padding: 20px;
|
| 590 |
-
text-align: center;
|
| 591 |
-
margin: 10px;
|
| 592 |
-
box-shadow: 0 6px 12px rgba(79, 172, 254, 0.3);
|
| 593 |
-
}
|
| 594 |
-
|
| 595 |
-
.enhancement-badge {
|
| 596 |
-
display: inline-block;
|
| 597 |
-
background: linear-gradient(45deg, #fa709a 0%, #fee140 100%);
|
| 598 |
-
color: white;
|
| 599 |
-
padding: 8px 16px;
|
| 600 |
-
border-radius: 25px;
|
| 601 |
-
margin: 5px;
|
| 602 |
-
font-weight: bold;
|
| 603 |
-
box-shadow: 0 4px 8px rgba(250, 112, 154, 0.3);
|
| 604 |
-
}
|
| 605 |
"""
|
| 606 |
|
| 607 |
-
|
| 608 |
-
|
| 609 |
-
|
| 610 |
-
gr.HTML("""
|
| 611 |
-
<div id="title">
|
| 612 |
-
<h1>🧠 Enhanced Attention U-Net Brain Tumor Segmentation</h1>
|
| 613 |
-
<p style="font-size: 20px; margin-top: 20px; font-weight: 300;">
|
| 614 |
-
🚀 Advanced Medical AI with Test-Time Augmentation & Attention Visualization
|
| 615 |
-
</p>
|
| 616 |
-
<p style="font-size: 16px; margin-top: 15px; opacity: 0.9;">
|
| 617 |
-
📊 Performance: Dice 0.8420 • IoU 0.7297 • Accuracy 98.90% |
|
| 618 |
-
🔬 Research-Grade Interpretability & Robustness
|
| 619 |
-
</p>
|
| 620 |
-
</div>
|
| 621 |
-
""")
|
| 622 |
|
| 623 |
with gr.Row():
|
| 624 |
with gr.Column(scale=1):
|
| 625 |
-
gr.Markdown("###
|
| 626 |
-
|
| 627 |
-
with gr.Tab("📸 Upload Image"):
|
| 628 |
-
image_input = gr.Image(
|
| 629 |
-
label="Brain MRI Scan",
|
| 630 |
-
type="pil",
|
| 631 |
-
sources=["upload", "webcam"],
|
| 632 |
-
height=300
|
| 633 |
-
)
|
| 634 |
-
|
| 635 |
-
with gr.Tab("🎲 Random Sample"):
|
| 636 |
-
random_image = gr.Image(
|
| 637 |
-
label="Sample Image",
|
| 638 |
-
type="pil",
|
| 639 |
-
height=300,
|
| 640 |
-
interactive=False
|
| 641 |
-
)
|
| 642 |
-
random_ground_truth = gr.Image(
|
| 643 |
-
label="Ground Truth Mask",
|
| 644 |
-
type="pil",
|
| 645 |
-
height=300,
|
| 646 |
-
interactive=False
|
| 647 |
-
)
|
| 648 |
-
load_sample_btn = gr.Button("🎲 Load Random Sample", variant="secondary", size="lg")
|
| 649 |
-
sample_status = gr.Textbox(label="Sample Status", interactive=False)
|
| 650 |
-
|
| 651 |
-
gr.Markdown("### ⚙️ Enhancement Options")
|
| 652 |
-
|
| 653 |
-
use_tta = gr.Checkbox(
|
| 654 |
-
label="🔄 Test-Time Augmentation",
|
| 655 |
-
value=True,
|
| 656 |
-
info="Apply multiple augmentations for robust predictions"
|
| 657 |
-
)
|
| 658 |
-
|
| 659 |
-
show_attention = gr.Checkbox(
|
| 660 |
-
label="🔥 Attention Visualization",
|
| 661 |
-
value=True,
|
| 662 |
-
info="Generate attention heatmaps for interpretability"
|
| 663 |
-
)
|
| 664 |
|
| 665 |
with gr.Row():
|
| 666 |
-
|
| 667 |
-
|
| 668 |
-
|
| 669 |
-
scale=3,
|
| 670 |
-
size="lg"
|
| 671 |
-
)
|
| 672 |
-
clear_btn = gr.Button("🗑️ Clear All", variant="secondary", scale=1)
|
| 673 |
-
|
| 674 |
-
gr.HTML("""
|
| 675 |
-
<div class="feature-box">
|
| 676 |
-
<h4 style="margin-bottom: 15px;">🎯 Research Innovations</h4>
|
| 677 |
-
<div class="enhancement-badge">Attention Gates</div>
|
| 678 |
-
<div class="enhancement-badge">Test-Time Augmentation</div>
|
| 679 |
-
<div class="enhancement-badge">Interpretability</div>
|
| 680 |
-
<div class="enhancement-badge">Ground Truth Comparison</div>
|
| 681 |
-
<p style="margin-top: 15px; font-size: 14px; opacity: 0.9;">
|
| 682 |
-
Advanced medical AI combining accuracy, robustness, and clinical interpretability
|
| 683 |
-
</p>
|
| 684 |
-
</div>
|
| 685 |
-
""")
|
| 686 |
|
| 687 |
with gr.Column(scale=2):
|
| 688 |
-
gr.Markdown("###
|
| 689 |
-
|
| 690 |
-
|
| 691 |
-
label="Comprehensive Analysis Visualization",
|
| 692 |
-
type="pil",
|
| 693 |
-
height=600
|
| 694 |
-
)
|
| 695 |
-
|
| 696 |
-
with gr.Accordion("📈 Detailed Analysis Report", open=True):
|
| 697 |
-
analysis_output = gr.Markdown(
|
| 698 |
-
value="Upload a brain MRI image or load a random sample to test the enhanced Attention U-Net model.",
|
| 699 |
-
elem_id="analysis"
|
| 700 |
-
)
|
| 701 |
-
|
| 702 |
-
# Performance metrics section
|
| 703 |
-
gr.HTML("""
|
| 704 |
-
<div style="margin-top: 40px;">
|
| 705 |
-
<h3 style="text-align: center; color: #4a5568; margin-bottom: 25px;">📊 Model Performance & Research Contributions</h3>
|
| 706 |
-
<div style="display: grid; grid-template-columns: repeat(auto-fit, minmax(300px, 1fr)); gap: 20px; margin-bottom: 30px;">
|
| 707 |
-
|
| 708 |
-
<div class="metric-card">
|
| 709 |
-
<h4 style="color: white; margin-bottom: 10px;">🎯 Segmentation Accuracy</h4>
|
| 710 |
-
<div style="font-size: 24px; font-weight: bold; margin: 10px 0;">98.90%</div>
|
| 711 |
-
<p style="font-size: 14px; opacity: 0.9;">Training accuracy on brain tumor dataset</p>
|
| 712 |
-
</div>
|
| 713 |
-
|
| 714 |
-
<div class="metric-card">
|
| 715 |
-
<h4 style="color: white; margin-bottom: 10px;">📐 Dice Score</h4>
|
| 716 |
-
<div style="font-size: 24px; font-weight: bold; margin: 10px 0;">0.8420</div>
|
| 717 |
-
<p style="font-size: 14px; opacity: 0.9;">Overlap similarity coefficient</p>
|
| 718 |
-
</div>
|
| 719 |
-
|
| 720 |
-
<div class="metric-card">
|
| 721 |
-
<h4 style="color: white; margin-bottom: 10px;">🔲 IoU Score</h4>
|
| 722 |
-
<div style="font-size: 24px; font-weight: bold; margin: 10px 0;">0.7297</div>
|
| 723 |
-
<p style="font-size: 14px; opacity: 0.9;">Intersection over Union metric</p>
|
| 724 |
-
</div>
|
| 725 |
-
|
| 726 |
-
<div class="metric-card">
|
| 727 |
-
<h4 style="color: white; margin-bottom: 10px;">⚡ Enhancement Features</h4>
|
| 728 |
-
<div style="font-size: 20px; font-weight: bold; margin: 10px 0;">TTA + Attention</div>
|
| 729 |
-
<p style="font-size: 14px; opacity: 0.9;">Advanced robustness & interpretability</p>
|
| 730 |
-
</div>
|
| 731 |
-
|
| 732 |
-
</div>
|
| 733 |
-
</div>
|
| 734 |
-
""")
|
| 735 |
-
|
| 736 |
-
# Research contributions section
|
| 737 |
-
gr.HTML("""
|
| 738 |
-
<div style="margin-top: 30px; padding: 30px; background: linear-gradient(135deg, #667eea 0%, #764ba2 100%); border-radius: 20px; color: white;">
|
| 739 |
-
<h3 style="text-align: center; margin-bottom: 25px; color: white;">🚀 Novel Research Contributions</h3>
|
| 740 |
-
|
| 741 |
-
<div style="display: grid; grid-template-columns: 1fr 1fr; gap: 30px; margin-bottom: 20px;">
|
| 742 |
-
|
| 743 |
-
<div>
|
| 744 |
-
<h4 style="margin-bottom: 15px; color: #ffd700;">🔍 1. Enhanced Boundary Detection</h4>
|
| 745 |
-
<ul style="line-height: 1.8; margin-left: 20px;">
|
| 746 |
-
<li><strong>Problem:</strong> Traditional U-Net passes noisy features through skip connections</li>
|
| 747 |
-
<li><strong>Solution:</strong> Attention gates filter irrelevant encoder features</li>
|
| 748 |
-
<li><strong>Impact:</strong> Cleaner boundaries, reduced false positives</li>
|
| 749 |
-
</ul>
|
| 750 |
-
</div>
|
| 751 |
-
|
| 752 |
-
<div>
|
| 753 |
-
<h4 style="margin-bottom: 15px; color: #ffd700;">🔄 2. Test-Time Augmentation</h4>
|
| 754 |
-
<ul style="line-height: 1.8; margin-left: 20px;">
|
| 755 |
-
<li><strong>Problem:</strong> Medical datasets are small, MRI scans vary across centers</li>
|
| 756 |
-
<li><strong>Solution:</strong> Multiple augmentations averaged for robust predictions</li>
|
| 757 |
-
<li><strong>Impact:</strong> Improved robustness without retraining</li>
|
| 758 |
-
</ul>
|
| 759 |
-
</div>
|
| 760 |
-
|
| 761 |
-
<div>
|
| 762 |
-
<h4 style="margin-bottom: 15px; color: #ffd700;">🔥 3. Attention Visualization</h4>
|
| 763 |
-
<ul style="line-height: 1.8; margin-left: 20px;">
|
| 764 |
-
<li><strong>Problem:</strong> Deep networks are "black boxes" for clinicians</li>
|
| 765 |
-
<li><strong>Solution:</strong> Extract attention coefficients as interpretable heatmaps</li>
|
| 766 |
-
<li><strong>Impact:</strong> Build clinical trust through transparency</li>
|
| 767 |
-
</ul>
|
| 768 |
-
</div>
|
| 769 |
-
|
| 770 |
-
<div>
|
| 771 |
-
<h4 style="margin-bottom: 15px; color: #ffd700;">⚡ 4. Efficient Implementation</h4>
|
| 772 |
-
<ul style="line-height: 1.8; margin-left: 20px;">
|
| 773 |
-
<li><strong>Problem:</strong> Complex architectures are hard to deploy</li>
|
| 774 |
-
<li><strong>Solution:</strong> Low-overhead enhancements within existing backbone</li>
|
| 775 |
-
<li><strong>Impact:</strong> Practical for real-world medical workflows</li>
|
| 776 |
-
</ul>
|
| 777 |
-
</div>
|
| 778 |
-
|
| 779 |
-
</div>
|
| 780 |
-
|
| 781 |
-
<div style="text-align: center; padding-top: 20px; border-top: 2px solid rgba(255,255,255,0.3);">
|
| 782 |
-
<p style="font-size: 16px; font-weight: 600; margin-bottom: 10px;">
|
| 783 |
-
🎯 Research Gap Addressed: Accuracy + Robustness + Interpretability
|
| 784 |
-
</p>
|
| 785 |
-
<p style="font-size: 14px; opacity: 0.9;">
|
| 786 |
-
This combination tackles three major challenges in medical AI with minimal architectural changes
|
| 787 |
-
</p>
|
| 788 |
-
</div>
|
| 789 |
-
</div>
|
| 790 |
-
""")
|
| 791 |
-
|
| 792 |
-
# Dataset and disclaimer section
|
| 793 |
-
gr.HTML("""
|
| 794 |
-
<div style="margin-top: 30px; padding: 25px; background-color: #f7fafc; border-radius: 15px; border-left: 5px solid #667eea;">
|
| 795 |
-
<div style="display: grid; grid-template-columns: 1fr 1fr; gap: 30px;">
|
| 796 |
-
|
| 797 |
-
<div>
|
| 798 |
-
<h4 style="color: #667eea; margin-bottom: 15px;">📚 Dataset Information</h4>
|
| 799 |
-
<p><strong>Source:</strong> Brain Tumor Segmentation (Kaggle)</p>
|
| 800 |
-
<p><strong>Author:</strong> nikhilroxtomar</p>
|
| 801 |
-
<p><strong>Structure:</strong> Images + Ground Truth Masks</p>
|
| 802 |
-
<p><strong>Format:</strong> Grayscale MRI scans</p>
|
| 803 |
-
<p><strong>Use Case:</strong> Medical image segmentation research</p>
|
| 804 |
-
<p><strong>Ground Truth:</strong> Available for metric calculation</p>
|
| 805 |
-
</div>
|
| 806 |
-
|
| 807 |
-
<div>
|
| 808 |
-
<h4 style="color: #dc2626; margin-bottom: 15px;">⚠️ Medical Disclaimer</h4>
|
| 809 |
-
<p style="color: #dc2626; font-weight: 600; line-height: 1.5;">
|
| 810 |
-
This enhanced AI system is designed for <strong>research and educational purposes only</strong>.<br><br>
|
| 811 |
-
|
| 812 |
-
While the model includes advanced features like attention visualization and test-time augmentation
|
| 813 |
-
for improved accuracy and interpretability, all results must be validated by qualified medical professionals.<br><br>
|
| 814 |
-
|
| 815 |
-
<strong>Not approved for clinical diagnosis or medical decision making.</strong>
|
| 816 |
-
</p>
|
| 817 |
-
</div>
|
| 818 |
-
|
| 819 |
-
</div>
|
| 820 |
-
|
| 821 |
-
<hr style="margin: 25px 0; border: none; border-top: 2px solid #e2e8f0;">
|
| 822 |
-
|
| 823 |
-
<p style="text-align: center; color: #4a5568; margin: 15px 0; font-weight: 600;">
|
| 824 |
-
🔬 Research-Grade Medical AI • Enhanced Interpretability • Robust Predictions • Ground Truth Validation
|
| 825 |
-
</p>
|
| 826 |
-
</div>
|
| 827 |
-
""")
|
| 828 |
|
| 829 |
# Event handlers
|
| 830 |
-
|
| 831 |
-
|
| 832 |
-
|
| 833 |
-
|
| 834 |
-
def analyze_uploaded_image(image, use_tta, show_attention):
|
| 835 |
-
"""Wrapper function for uploaded images without ground truth"""
|
| 836 |
-
return predict_with_enhancements(image, None, use_tta, show_attention)
|
| 837 |
-
|
| 838 |
-
# Button event handlers
|
| 839 |
-
analyze_btn.click(
|
| 840 |
-
fn=lambda img, rand_img, rand_gt, tta, attention: (
|
| 841 |
-
analyze_with_ground_truth(rand_img, rand_gt, tta, attention)
|
| 842 |
-
if rand_img is not None
|
| 843 |
-
else analyze_uploaded_image(img, tta, attention)
|
| 844 |
-
),
|
| 845 |
-
inputs=[image_input, random_image, random_ground_truth, use_tta, show_attention],
|
| 846 |
-
outputs=[output_image, analysis_output],
|
| 847 |
-
show_progress=True
|
| 848 |
)
|
| 849 |
|
| 850 |
-
|
| 851 |
-
fn=
|
| 852 |
inputs=[],
|
| 853 |
-
outputs=[
|
| 854 |
-
show_progress=True
|
| 855 |
)
|
| 856 |
|
| 857 |
-
|
| 858 |
-
fn=
|
| 859 |
inputs=[],
|
| 860 |
-
outputs=
|
| 861 |
)
|
| 862 |
|
| 863 |
-
# Auto-load dataset on startup
|
| 864 |
-
gr.HTML("""
|
| 865 |
-
<script>
|
| 866 |
-
document.addEventListener('DOMContentLoaded', function() {
|
| 867 |
-
console.log('Enhanced Brain Tumor Segmentation App Loaded');
|
| 868 |
-
console.log('Features: TTA + Attention Visualization + Ground Truth Comparison');
|
| 869 |
-
});
|
| 870 |
-
</script>
|
| 871 |
-
""")
|
| 872 |
-
|
| 873 |
if __name__ == "__main__":
|
| 874 |
-
|
| 875 |
-
print("📊 Model Performance: Dice 0.8420, IoU 0.7297, Accuracy 98.90%")
|
| 876 |
-
print("🔬 Research Features: Attention Gates + TTA + Interpretability")
|
| 877 |
-
print("📥 Auto-downloading dataset and model...")
|
| 878 |
-
|
| 879 |
-
# Initialize dataset download
|
| 880 |
-
print("📚 Initializing dataset...")
|
| 881 |
-
try:
|
| 882 |
-
dataset_path = download_dataset()
|
| 883 |
-
if dataset_path:
|
| 884 |
-
print(f"✅ Dataset ready at: {dataset_path}")
|
| 885 |
-
else:
|
| 886 |
-
print("⚠️ Dataset download failed, random samples unavailable")
|
| 887 |
-
except Exception as e:
|
| 888 |
-
print(f"⚠️ Dataset initialization error: {e}")
|
| 889 |
-
|
| 890 |
-
app.launch(
|
| 891 |
-
server_name="0.0.0.0",
|
| 892 |
-
server_port=7860,
|
| 893 |
-
show_error=True,
|
| 894 |
-
share=False
|
| 895 |
-
)
|
|
|
|
| 6 |
from PIL import Image
|
| 7 |
import matplotlib.pyplot as plt
|
| 8 |
import io
|
|
|
|
| 9 |
import torchvision.transforms.functional as TF
|
| 10 |
+
from torchvision import transforms
|
| 11 |
import os
|
|
|
|
| 12 |
import random
|
| 13 |
+
import urllib.request
|
| 14 |
+
import zipfile
|
| 15 |
+
import kagglehub
|
| 16 |
|
| 17 |
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
|
| 18 |
model = None
|
| 19 |
+
DATASET_PATH = "brain_tumor_dataset"
|
| 20 |
|
| 21 |
+
# Your model classes (from previous code)
|
| 22 |
class DoubleConv(nn.Module):
|
| 23 |
def __init__(self, in_channels, out_channels):
|
| 24 |
super(DoubleConv, self).__init__()
|
|
|
|
| 60 |
x1 = self.W_x(x)
|
| 61 |
psi = self.relu(g1 + x1)
|
| 62 |
psi = self.psi(psi)
|
| 63 |
+
return x * psi, psi # Return both attended features and attention map
|
| 64 |
|
| 65 |
class AttentionUNET(nn.Module):
|
| 66 |
def __init__(self, in_channels=1, out_channels=1, features=[32, 64, 128, 256]):
|
|
|
|
| 71 |
self.attentions = nn.ModuleList()
|
| 72 |
self.pool = nn.MaxPool2d(kernel_size=2, stride=2)
|
| 73 |
|
| 74 |
+
# Down part
|
| 75 |
for feature in features:
|
| 76 |
self.downs.append(DoubleConv(in_channels, feature))
|
| 77 |
in_channels = feature
|
|
|
|
| 79 |
# Bottleneck
|
| 80 |
self.bottleneck = DoubleConv(features[-1], features[-1]*2)
|
| 81 |
|
| 82 |
+
# Up part
|
| 83 |
for feature in reversed(features):
|
| 84 |
self.ups.append(nn.ConvTranspose2d(feature*2, feature, kernel_size=2, stride=2))
|
| 85 |
self.attentions.append(AttentionBlock(F_g=feature, F_l=feature, F_int=feature // 2))
|
|
|
|
| 87 |
|
| 88 |
self.final_conv = nn.Conv2d(features[0], out_channels, kernel_size=1)
|
| 89 |
|
| 90 |
+
def forward(self, x):
|
| 91 |
skip_connections = []
|
| 92 |
+
attention_maps = [] # To collect attention maps
|
| 93 |
|
| 94 |
for down in self.downs:
|
| 95 |
x = down(x)
|
|
|
|
| 106 |
if x.shape != skip_connection.shape:
|
| 107 |
x = TF.resize(x, size=skip_connection.shape[2:])
|
| 108 |
|
| 109 |
+
attended, attn_map = self.attentions[idx // 2](x, skip_connection) # Get attention map
|
| 110 |
+
attention_maps.append(attn_map)
|
|
|
|
| 111 |
|
| 112 |
+
concat_skip = torch.cat((attended, x), dim=1)
|
| 113 |
x = self.ups[idx+1](concat_skip)
|
| 114 |
|
| 115 |
+
return self.final_conv(x), attention_maps
|
|
|
|
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|
| 116 |
|
| 117 |
def download_model():
|
| 118 |
"""Download your trained model from HuggingFace"""
|
|
|
|
| 120 |
model_path = "best_attention_model.pth.tar"
|
| 121 |
|
| 122 |
if not os.path.exists(model_path):
|
| 123 |
+
print("📥 Downloading your trained model...")
|
| 124 |
try:
|
| 125 |
urllib.request.urlretrieve(model_url, model_path)
|
| 126 |
print("✅ Model downloaded successfully!")
|
| 127 |
except Exception as e:
|
| 128 |
print(f"❌ Failed to download model: {e}")
|
| 129 |
return None
|
|
|
|
|
|
|
|
|
|
| 130 |
return model_path
|
| 131 |
|
| 132 |
+
def load_model():
|
| 133 |
+
"""Load your trained Attention U-Net model"""
|
| 134 |
global model
|
| 135 |
if model is None:
|
| 136 |
try:
|
| 137 |
+
print("🔄 Loading your trained Attention U-Net model...")
|
| 138 |
|
| 139 |
+
# Download model if needed
|
| 140 |
model_path = download_model()
|
| 141 |
if model_path is None:
|
| 142 |
return None
|
| 143 |
|
| 144 |
+
# Initialize your model architecture
|
| 145 |
model = AttentionUNET(in_channels=1, out_channels=1).to(device)
|
| 146 |
+
|
| 147 |
+
# Load your trained weights
|
| 148 |
checkpoint = torch.load(model_path, map_location=device, weights_only=True)
|
| 149 |
model.load_state_dict(checkpoint["state_dict"])
|
| 150 |
model.eval()
|
| 151 |
|
| 152 |
+
print("✅ Your Attention U-Net model loaded successfully!")
|
| 153 |
except Exception as e:
|
| 154 |
+
print(f"❌ Error loading your model: {e}")
|
| 155 |
model = None
|
| 156 |
return model
|
| 157 |
|
| 158 |
+
def preprocess_image(image):
|
| 159 |
+
"""Preprocessing like your Colab code"""
|
| 160 |
+
# Convert to grayscale
|
| 161 |
+
if image.mode != 'L':
|
| 162 |
+
image = image.convert('L')
|
| 163 |
|
| 164 |
+
# Use your exact transform
|
| 165 |
+
val_test_transform = transforms.Compose([
|
| 166 |
+
transforms.Resize((256,256)),
|
| 167 |
+
transforms.ToTensor()
|
| 168 |
+
])
|
| 169 |
|
| 170 |
+
return val_test_transform(image).unsqueeze(0) # Add batch dimension
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
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|
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|
|
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|
|
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|
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|
|
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|
|
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|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 171 |
|
| 172 |
+
def post_process_mask(pred_mask_np):
|
| 173 |
+
"""Post-processing with morphological operations (Novelty 1)"""
|
| 174 |
+
# Binarize
|
| 175 |
+
binary_mask = (pred_mask_np > 0.5).astype(np.uint8)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 176 |
|
| 177 |
+
# Morphological opening to remove small noise
|
| 178 |
+
kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (5,5))
|
| 179 |
+
binary_mask = cv2.morphologyEx(binary_mask, cv2.MORPH_OPEN, kernel)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 180 |
|
| 181 |
+
# Morphological closing to fill gaps
|
| 182 |
+
binary_mask = cv2.morphologyEx(binary_mask, cv2.MORPH_CLOSE, kernel)
|
| 183 |
+
|
| 184 |
+
return binary_mask
|
| 185 |
+
|
| 186 |
+
def test_time_augmentation(input_tensor, model):
|
| 187 |
+
"""Test-Time Augmentation (Novelty 2)"""
|
| 188 |
predictions = []
|
| 189 |
|
| 190 |
+
# Original
|
| 191 |
+
pred, _ = model(input_tensor)
|
| 192 |
+
predictions.append(torch.sigmoid(pred))
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 193 |
|
| 194 |
+
# Horizontal flip
|
| 195 |
+
hflip = TF.hflip(input_tensor)
|
| 196 |
+
pred_h, _ = model(hflip)
|
| 197 |
+
pred_h = TF.hflip(pred_h)
|
| 198 |
+
predictions.append(torch.sigmoid(pred_h))
|
| 199 |
|
| 200 |
+
# Vertical flip
|
| 201 |
+
vflip = TF.vflip(input_tensor)
|
| 202 |
+
pred_v, _ = model(vflip)
|
| 203 |
+
pred_v = TF.vflip(pred_v)
|
| 204 |
+
predictions.append(torch.sigmoid(pred_v))
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 205 |
|
| 206 |
+
# Average predictions
|
| 207 |
+
avg_pred = torch.mean(torch.stack(predictions), dim=0)
|
| 208 |
+
return avg_pred.squeeze().cpu().numpy()
|
| 209 |
+
|
| 210 |
+
def generate_attention_heatmap(attention_maps, size=(256,256)):
|
| 211 |
+
"""Generate attention heatmap visualization (Novelty 3)"""
|
| 212 |
+
# Average attention maps from all levels
|
| 213 |
+
avg_attn = torch.mean(torch.cat([TF.resize(m, size) for m in attention_maps]), dim=0)
|
| 214 |
+
attn_np = avg_attn.squeeze().cpu().numpy()
|
| 215 |
|
| 216 |
+
# Normalize and apply colormap
|
| 217 |
+
attn_norm = (attn_np - attn_np.min()) / (attn_np.max() - attn_np.min() + 1e-8)
|
| 218 |
+
heatmap = plt.cm.hot(attn_norm)[:,:,:3] * 255
|
| 219 |
+
return heatmap.astype(np.uint8)
|
| 220 |
|
| 221 |
+
def download_dataset():
|
| 222 |
+
"""Download and extract the dataset if not present"""
|
| 223 |
+
if not os.path.exists(DATASET_PATH):
|
| 224 |
+
print("📥 Downloading brain tumor dataset...")
|
| 225 |
+
try:
|
| 226 |
+
path = kagglehub.dataset_download('nikhilroxtomar/brain-tumor-segmentation')
|
| 227 |
+
print(f"Dataset downloaded to: {path}")
|
| 228 |
+
|
| 229 |
+
# Extract if zipped
|
| 230 |
+
for file in os.listdir(path):
|
| 231 |
+
if file.endswith('.zip'):
|
| 232 |
+
with zipfile.ZipFile(os.path.join(path, file), 'r') as zip_ref:
|
| 233 |
+
zip_ref.extractall(DATASET_PATH)
|
| 234 |
+
print("✅ Dataset extracted!")
|
| 235 |
+
return True
|
| 236 |
+
except Exception as e:
|
| 237 |
+
print(f"❌ Failed to download dataset: {e}")
|
| 238 |
+
return False
|
| 239 |
+
print("✅ Dataset already exists!")
|
| 240 |
+
return True
|
| 241 |
+
|
| 242 |
+
def get_random_sample():
|
| 243 |
+
"""Get random image and mask from dataset"""
|
| 244 |
+
if not os.path.exists(DATASET_PATH):
|
| 245 |
+
if not download_dataset():
|
| 246 |
+
return None, None
|
| 247 |
+
|
| 248 |
+
images_path = os.path.join(DATASET_PATH, "images")
|
| 249 |
+
masks_path = os.path.join(DATASET_PATH, "masks")
|
| 250 |
+
|
| 251 |
+
image_files = [f for f in os.listdir(images_path) if f.endswith(('.png', '.jpg'))]
|
| 252 |
+
|
| 253 |
+
if not image_files:
|
| 254 |
+
return None, None
|
| 255 |
|
| 256 |
+
random_file = random.choice(image_files)
|
|
|
|
|
|
|
| 257 |
|
| 258 |
+
img_path = os.path.join(images_path, random_file)
|
| 259 |
+
mask_path = os.path.join(masks_path, random_file)
|
|
|
|
| 260 |
|
| 261 |
+
if not os.path.exists(mask_path):
|
| 262 |
+
return None, None
|
| 263 |
+
|
| 264 |
+
return Image.open(img_path), Image.open(mask_path)
|
| 265 |
|
| 266 |
+
def predict_tumor(image, use_tta=True, show_attention=True, is_dataset_sample=False, ground_truth=None):
|
| 267 |
+
current_model = load_your_attention_model()
|
|
|
|
| 268 |
|
| 269 |
if current_model is None:
|
| 270 |
+
return None, "Failed to load your trained model."
|
| 271 |
|
| 272 |
if image is None:
|
| 273 |
+
return None, "Please upload an image first."
|
| 274 |
|
| 275 |
try:
|
| 276 |
+
print("Processing image...")
|
| 277 |
|
| 278 |
input_tensor = preprocess_image(image).to(device)
|
| 279 |
|
| 280 |
+
# Use TTA if enabled
|
|
|
|
|
|
|
|
|
|
|
|
|
| 281 |
if use_tta:
|
| 282 |
+
pred_np = test_time_augmentation(input_tensor, current_model)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
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|
|
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|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 283 |
else:
|
| 284 |
+
pred, attn_maps = current_model(input_tensor)
|
| 285 |
+
pred_np = torch.sigmoid(pred).squeeze().cpu().numpy()
|
| 286 |
+
attn_maps = attn_maps if show_attention else None
|
| 287 |
+
|
| 288 |
+
# Post-processing
|
| 289 |
+
binary_mask = post_process_mask(pred_np)
|
| 290 |
+
|
| 291 |
+
# Generate attention heatmap if enabled
|
| 292 |
+
attention_heatmap = None
|
| 293 |
+
if show_attention and attn_maps:
|
| 294 |
+
attention_heatmap = generate_attention_heatmap(attn_maps)
|
| 295 |
+
|
| 296 |
+
# Create visualization
|
| 297 |
+
fig, axes = plt.subplots(1, 3 + int(show_attention) + int(is_dataset_sample and ground_truth is not None), figsize=(20, 5))
|
| 298 |
+
fig.suptitle('Brain Tumor Segmentation Results', fontsize=16)
|
| 299 |
+
|
| 300 |
+
# Original image
|
| 301 |
+
original_np = np.array(image.resize((256, 256)))
|
| 302 |
+
axes[0].imshow(original_np, cmap='gray')
|
| 303 |
+
axes[0].set_title('Original Image')
|
| 304 |
+
axes[0].axis('off')
|
| 305 |
+
|
| 306 |
+
# Predicted mask
|
| 307 |
+
axes[1].imshow(binary_mask * 255, cmap='gray')
|
| 308 |
+
axes[1].set_title('Predicted Mask')
|
| 309 |
+
axes[1].axis('off')
|
| 310 |
+
|
| 311 |
+
# Overlay
|
| 312 |
+
overlay = cv2.cvtColor(original_np, cv2.COLOR_GRAY2RGB) if len(original_np.shape) == 2 else original_np
|
| 313 |
+
overlay[binary_mask == 1] = [255, 0, 0] # Red for tumor
|
| 314 |
+
overlay = cv2.addWeighted(original_np, 0.7, overlay, 0.3, 0)
|
| 315 |
+
axes[2].imshow(overlay)
|
| 316 |
+
axes[2].set_title('Overlay')
|
| 317 |
+
axes[2].axis('off')
|
| 318 |
+
|
| 319 |
+
col = 3
|
| 320 |
+
if show_attention and attention_heatmap is not None:
|
| 321 |
+
axes[col].imshow(attention_heatmap)
|
| 322 |
+
axes[col].set_title('Attention Heatmap')
|
| 323 |
+
axes[col].axis('off')
|
| 324 |
+
col += 1
|
| 325 |
+
|
| 326 |
+
if is_dataset_sample and ground_truth is not None:
|
| 327 |
+
gt_np = np.array(ground_truth.resize((256, 256)))
|
| 328 |
+
axes[col].imshow(gt_np, cmap='gray')
|
| 329 |
+
axes[col].set_title('Ground Truth')
|
| 330 |
+
axes[col].axis('off')
|
| 331 |
|
| 332 |
plt.tight_layout()
|
| 333 |
|
|
|
|
| 334 |
buf = io.BytesIO()
|
| 335 |
+
plt.savefig(buf, format='png', dpi=150, bbox_inches='tight')
|
| 336 |
buf.seek(0)
|
| 337 |
plt.close()
|
| 338 |
|
| 339 |
result_image = Image.open(buf)
|
| 340 |
|
| 341 |
+
# Statistics
|
| 342 |
+
tumor_pixels = np.sum(binary_mask)
|
| 343 |
+
total_pixels = binary_mask.size
|
| 344 |
tumor_percentage = (tumor_pixels / total_pixels) * 100
|
| 345 |
|
|
|
|
|
|
|
|
|
|
|
|
|
| 346 |
analysis_text = f"""
|
| 347 |
+
### Segmentation Statistics
|
| 348 |
+
- Tumor Area Percentage: {tumor_percentage:.2f}%
|
| 349 |
+
- Tumor Pixels: {tumor_pixels}
|
| 350 |
+
- Total Pixels: {total_pixels}
|
| 351 |
+
- TTA Used: {'Yes' if use_tta else 'No'}
|
| 352 |
+
- Attention Visualization: {'Yes' if show_attention else 'No'}
|
|
|
|
|
|
|
| 353 |
"""
|
| 354 |
+
|
| 355 |
+
if is_dataset_sample and ground_truth is not None:
|
| 356 |
+
gt_np = np.array(ground_truth.resize((256, 256)))
|
| 357 |
+
intersection = np.logical_and(binary_mask, gt_np > 0).sum()
|
| 358 |
+
union = np.logical_or(binary_mask, gt_np > 0).sum()
|
| 359 |
+
iou = intersection / (union + 1e-8)
|
| 360 |
+
dice = (2 * intersection) / (binary_mask.sum() + (gt_np > 0).sum() + 1e-8)
|
| 361 |
+
|
| 362 |
analysis_text += f"""
|
| 363 |
+
### Comparison with Ground Truth
|
| 364 |
+
- IoU Score: {iou:.4f}
|
| 365 |
+
- Dice Score: {dice:.4f}
|
|
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|
| 366 |
"""
|
| 367 |
|
|
|
|
| 368 |
return result_image, analysis_text
|
| 369 |
|
| 370 |
except Exception as e:
|
| 371 |
+
return None, f"Error: {str(e)}"
|
|
|
|
|
|
|
| 372 |
|
| 373 |
+
def test_random_sample():
|
| 374 |
+
image, mask = get_random_sample()
|
|
|
|
| 375 |
if image is None:
|
| 376 |
+
return None, "Failed to load dataset sample. Please download dataset first."
|
| 377 |
+
return predict_tumor(image, use_tta=True, show_attention=True, is_dataset_sample=True, ground_truth=mask)
|
| 378 |
|
| 379 |
+
# Custom CSS for professional, minimalist look
|
|
|
|
|
|
|
|
|
|
| 380 |
css = """
|
| 381 |
+
body, .gradio-container { font-family: 'Arial', sans-serif; color: #333; }
|
| 382 |
+
h1, h2, h3, h4 { color: #2c3e50; font-weight: 500; }
|
| 383 |
+
.button { background-color: #3498db; color: white; border: none; border-radius: 4px; padding: 10px 20px; font-size: 16px; cursor: pointer; }
|
| 384 |
+
.button:hover { background-color: #2980b9; }
|
| 385 |
+
.card { border: 1px solid #e0e0e0; border-radius: 8px; padding: 20px; background: white; box-shadow: 0 2px 4px rgba(0,0,0,0.1); }
|
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|
|
| 386 |
"""
|
| 387 |
|
| 388 |
+
with gr.Blocks(css=css, title="Brain Tumor Segmentation") as app:
|
| 389 |
+
gr.Markdown("# Brain Tumor Segmentation Using Attention U-Net")
|
|
|
|
|
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|
| 390 |
|
| 391 |
with gr.Row():
|
| 392 |
with gr.Column(scale=1):
|
| 393 |
+
gr.Markdown("### Input")
|
| 394 |
+
image_input = gr.Image(label="Upload Image", type="pil")
|
|
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|
|
|
|
|
|
|
| 395 |
|
| 396 |
with gr.Row():
|
| 397 |
+
predict_btn = gr.Button("Predict")
|
| 398 |
+
random_btn = gr.Button("Test Random Sample")
|
| 399 |
+
download_btn = gr.Button("Download Dataset")
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
|
|
|
|
|
|
|
| 400 |
|
| 401 |
with gr.Column(scale=2):
|
| 402 |
+
gr.Markdown("### Output")
|
| 403 |
+
output_image = gr.Image(label="Result")
|
| 404 |
+
analysis_output = gr.Textbox(label="Analysis", lines=10)
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 405 |
|
| 406 |
# Event handlers
|
| 407 |
+
predict_btn.click(
|
| 408 |
+
fn=predict_tumor,
|
| 409 |
+
inputs=[image_input],
|
| 410 |
+
outputs=[output_image, analysis_output]
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
| 411 |
)
|
| 412 |
|
| 413 |
+
random_btn.click(
|
| 414 |
+
fn=test_random_sample,
|
| 415 |
inputs=[],
|
| 416 |
+
outputs=[output_image, analysis_output]
|
|
|
|
| 417 |
)
|
| 418 |
|
| 419 |
+
download_btn.click(
|
| 420 |
+
fn=download_dataset,
|
| 421 |
inputs=[],
|
| 422 |
+
outputs=gr.Textbox(value="Dataset download status...")
|
| 423 |
)
|
| 424 |
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
| 425 |
if __name__ == "__main__":
|
| 426 |
+
app.launch()
|
|
|
|
|
|
|
|
|
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|
|
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