app.py

import streamlit as st
import matplotlib.pyplot as plt
import matplotlib.patches as patches
from torchvision import transforms
from PIL import Image
import torch
from torchvision.models.detection import fasterrcnn_resnet50_fpn
from torchvision.models.detection.faster_rcnn import FastRCNNPredictor
import cv2
import numpy as np
from matplotlib.colors import LinearSegmentedColormap
import pytorch_lightning as pl
from tqdm import tqdm
from torchvision import models

# Function Definitions

label_names = [
    "Aortic_enlargement", "Atelectasis", "Calcification", "Cardiomegaly",
    "Consolidation", "ILD", "Infiltration", "Lung_Opacity", "Nodule/Mass",
    "Other_lesion", "Pleural_effusion", "Pleural_thickening", "Pneumothorax",
    "Pulmonary_fibrosis"
    ]

class VinDetector(pl.LightningModule):
    def __init__(self, **kwargs):
        super().__init__()

        self.model = models.detection.fasterrcnn_resnet50_fpn(pretrained=True)
        num_classes = 15
        in_features = self.model.roi_heads.box_predictor.cls_score.in_features
        self.model.roi_heads.box_predictor = FastRCNNPredictor(in_features, num_classes)
        
        self.learning_rate = 1e-3
        self.batch_size = 4

    def forward(self, x):
        return self.model(x)

    def prepare_data(self):
        
        df = pd.read_csv('../input/vinbigdata-chest-xray-abnormalities-detection/train.csv')
        df = df[df['class_id'] != 14].reset_index(drop=True)
        self.train_dataset = VBDDataset(df, '../input/vinbigdata-chest-xray-original-png/train', get_train_transform())

    def train_dataloader(self):
        
        return DataLoader(self.train_dataset, batch_size=self.batch_size, shuffle=True, pin_memory=True, num_workers=4, collate_fn=collate_fn)

    def training_step(self, batch, batch_idx):
        images, targets = batch
        targets = [{k: v for k, v in t.items()} for t in targets]
        
        loss_dict = self.model(images, targets)
        loss = sum(loss for loss in loss_dict.values())
        self.log('Loss', loss, on_step=True, on_epoch=True, prog_bar=True)
        return {"loss": loss}

    def configure_optimizers(self):
        optimizer = torch.optim.SGD(self.model.parameters(), lr=self.learning_rate, momentum=0.95, weight_decay=1e-5, nesterov=True)
        scheduler = torch.optim.lr_scheduler.CosineAnnealingLR(optimizer, T_max=6, eta_min=0, verbose=True)
        return [optimizer], [scheduler]
    

def get_train_transform():
    return A.Compose([
        A.Flip(0.5),  
        ToTensorV2(p=1.0)  
    ], bbox_params={'format': 'pascal_voc', 'label_fields': ['labels']})

def get_valid_transform():
    return A.Compose([
        ToTensorV2(p=1.0)  
    ])


def collate_fn(batch):
    return tuple(zip(*batch))
    
    

def format_prediction_string(labels, boxes, scores):
    pred_strings = []
    for j in zip(labels, scores, boxes):
        pred_strings.append("{0} {1:.4f} {2} {3} {4} {5}".format(
            j[0], j[1], j[2][0], j[2][1], j[2][2], j[2][3]))
    return " ".join(pred_strings)
    
def generate_diagnostic_report(predictions, labels, threshold=0.5):
    # Initialize an empty report string
    report = "Diagnostic Report:\n\n"
    findings_present = False
    
    # Loop through each detection
    for element in range(len(predictions['boxes'])):
        score = predictions['scores'][element].cpu().numpy()
        if score > threshold:
            label_index = predictions['labels'][element].cpu().numpy() - 1
            label_name = labels[label_index]
            report += f"- {label_name} detected with probability {score:.2f}\n"
            findings_present = True

    # If no findings above the threshold, report no significant abnormalities
    if not findings_present:
        report += "No significant abnormalities detected."

    return report

def draw_boxes_cv2(image, boxes, labels, scores, threshold=0.5, font_scale=1.0, thickness=3):
    # Define your labels and their corresponding colors
    label_names = [
        "Aortic_enlargement", "Atelectasis", "Calcification", "Cardiomegaly",
    "Consolidation", "ILD", "Infiltration", "Lung_Opacity", "Nodule/Mass",
    "Other_lesion", "Pleural_effusion", "Pleural_thickening", "Pneumothorax",
    "Pulmonary_fibrosis"
    ]
    
    label2color = [
        [59, 238, 119], [222, 21, 229], [94, 49, 164], [206, 221, 133], [117, 75, 3],
        [210, 224, 119], [211, 176, 166], [63, 7, 197], [102, 65, 77], [194, 134, 175],
        [209, 219, 50], [255, 44, 47], [89, 125, 149], [110, 27, 100]
    ]

    for i, box in enumerate(boxes):
        if scores[i] > threshold:
            # Subtract 1 from label_index to match the zero-indexed Python list
            label_index = labels[i] - 1
            label_name = label_names[label_index] if label_index < len(label_names) else "Unknown"
            color = label2color[label_index] if label_index < len(label2color) else (255, 255, 255)  # Default to white for unknown labels

            label_text = f'{label_name}: {scores[i]:.2f}'
            cv2.rectangle(image, (int(box[0]), int(box[1])), (int(box[2]), int(box[3])), color, thickness)
            cv2.putText(image, label_text, (int(box[0]), int(box[1] - 10)), cv2.FONT_HERSHEY_SIMPLEX, font_scale, color, thickness)

    return image

    # Heatmap Generation Function
def plot_image_with_colored_mask_overlay_and_original(image, predictions):
    # Assuming predictions are in the same format as Faster R-CNN outputs
    boxes = predictions['boxes'].cpu().numpy()
    scores = predictions['scores'].cpu().numpy()

    # Create a blank mask matching image size
    mask = np.zeros(image.shape[:2], dtype=np.float32)

    # Fill mask based on bounding boxes and scores
    for box, score in zip(boxes, scores):
        if score > 0.5:  # Threshold can be adjusted
            x_min, y_min, x_max, y_max = map(int, box)
            mask[y_min:y_max, x_min:x_max] += score  # Increase mask intensity with score

    # Normalize mask
    normed_mask = cv2.normalize(mask, None, alpha=0, beta=1, norm_type=cv2.NORM_MINMAX, dtype=cv2.CV_32F)

    # Create a custom colormap with transparency
    colors = [(0, 0, 0, 0), (0, 0, 1, 1), (0, 1, 0, 1), (1, 1, 0, 1), (1, 0, 0, 1)]
    cmap_name = 'doctoria_heatmap'
    custom_cmap = LinearSegmentedColormap.from_list(cmap_name, colors, N=256)

    # Apply custom colormap
    heatmap = custom_cmap(normed_mask)

    # Convert heatmap to BGR format with uint8 type
    heatmap_bgr = (heatmap[:, :, 2::-1] * 255).astype(np.uint8)

    # Overlay heatmap on original image
    overlayed_image = image.copy()
    overlayed_image[mask > 0] = overlayed_image[mask > 0] * 0.5 + heatmap_bgr[mask > 0] * 0.5

    # Plotting
    fig, axs = plt.subplots(1, 2, figsize=[12, 6])

    # Original image
    axs[0].imshow(cv2.cvtColor(image, cv2.COLOR_BGR2RGB))
    axs[0].set_title('Original Image')
    axs[0].axis('off')

    # Image with heatmap
    axs[1].imshow(cv2.cvtColor(overlayed_image, cv2.COLOR_BGR2RGB))
    axs[1].set_title('Image with Heatmap Overlay')
    axs[1].axis('off')

    # Adding colorbar
    sm = plt.cm.ScalarMappable(cmap=custom_cmap, norm=plt.Normalize(0, 1))
    sm.set_array([])
    fig.colorbar(sm, ax=axs[1], orientation='vertical', fraction=0.046, pad=0.04)

    plt.show()


# Load the model
def create_model(num_classes):
    model = fasterrcnn_resnet50_fpn(pretrained=False)
    in_features = model.roi_heads.box_predictor.cls_score.in_features
    model.roi_heads.box_predictor = FastRCNNPredictor(in_features, num_classes)
    return model


# Streamlit app title
st.title("Doctoria CXR")

# Sidebar for user input
st.sidebar.title("Upload Chest X-ray Image")

# File uploader allows user to add their own image
uploaded_file = st.sidebar.file_uploader("Upload Chest X-ray image", type=["png", "jpg", "jpeg"])

# Load the model (use your model loading function)
# Ensure the model path is correct and accessible

model = create_model(num_classes=15)
model.load_state_dict(torch.load('Doctoria CXR Thoraric Full Model.pth', map_location=torch.device('cpu')))
model.eval()

def process_image(image_path):
    # Load and transform the image
    image = Image.open(image_path).convert('RGB')
    transform = get_transform()
    image = transform(image).unsqueeze(0)

    # Perform inference
    with torch.no_grad():
        prediction = model(image)

    return prediction, image

# When the user uploads a file
if uploaded_file is not None:
    # Display the uploaded image
    st.image(uploaded_file, caption="Uploaded X-ray", use_column_width=True)
    st.write("")

    # Process the uploaded image
    prediction, image_tensor = process_image(uploaded_file)

    # Convert tensor to PIL Image for display
    image_pil = transforms.ToPILImage()(image_tensor.squeeze(0)).convert("RGB")

    # Visualization and report generation
    image_np = np.array(image_pil)
    for element in range(len(prediction[0]['boxes'])):
        box = prediction[0]['boxes'][element].cpu().numpy()
        score = prediction[0]['scores'][element].cpu().numpy()
        label_index = prediction[0]['labels'][element].cpu().numpy()
        if score > 0.5:
            draw_boxes_cv2(image_np, [box], [label_index], [score], font_scale=3)  # Increased font size

    image_pil_processed = Image.fromarray(image_np)

    # Display processed image
    st.image(image_pil_processed, caption="Processed X-ray with Abnormalities Marked", use_column_width=True)

    # Generate the diagnostic report
    report = generate_diagnostic_report(prediction[0], label_names, 0.5)
    st.write(report)

# Instructions
st.sidebar.write("Instructions:")
st.sidebar.write("1. Upload an X-ray image.")
st.sidebar.write("2. View the processed image and diagnostic report.")