app.py

import torch
import torch.nn as nn
import torch.nn.functional as F
from torchvision import transforms, models
from PIL import Image, ImageOps
import numpy as np
import gradio as gr
import os
import pandas as pd

class DoubleConv(nn.Module):
    def __init__(self, in_channels, out_channels):
        super().__init__()
        self.conv_op = nn.Sequential(
            nn.Conv2d(in_channels, out_channels, kernel_size=3, padding=1),
            nn.BatchNorm2d(out_channels),
            nn.ReLU(inplace=True),
            nn.Conv2d(out_channels, out_channels, kernel_size=3, padding=1),
            nn.BatchNorm2d(out_channels),
            nn.ReLU(inplace=True)
        )
    def forward(self, x):
        return self.conv_op(x)

class Downsample(nn.Module):
    def __init__(self, in_channels, out_channels):
        super().__init__()
        self.conv = DoubleConv(in_channels, out_channels)
        self.pool = nn.MaxPool2d(kernel_size=2, stride=2)
    def forward(self, x):
        down = self.conv(x)
        p = self.pool(down)
        return down, p

class UpSample(nn.Module):
    def __init__(self, in_channels, out_channels):
        super().__init__()
        self.up = nn.ConvTranspose2d(in_channels, in_channels // 2, kernel_size=2, stride=2)
        self.conv = DoubleConv(in_channels, out_channels)
    def forward(self, x1, x2):
        x1 = self.up(x1)
        # handle spatial mismatches
        diffY = x2.size()[2] - x1.size()[2]
        diffX = x2.size()[3] - x1.size()[3]
        x1 = F.pad(x1, [diffX // 2, diffX - diffX // 2,
                        diffY // 2, diffY - diffY // 2])
        x = torch.cat([x2, x1], dim=1)
        return self.conv(x)

class UNet(nn.Module):
    def __init__(self, in_channels=3, num_classes=1):
        super().__init__()
        self.down1 = Downsample(in_channels, 64)
        self.down2 = Downsample(64, 128)
        self.down3 = Downsample(128, 256)
        self.down4 = Downsample(256, 512)
        self.bottleneck = DoubleConv(512, 1024)
        self.up1 = UpSample(1024, 512)
        self.up2 = UpSample(512, 256)
        self.up3 = UpSample(256, 128)
        self.up4 = UpSample(128, 64)
        self.out = nn.Conv2d(64, num_classes, kernel_size=1)
    def forward(self, x):
        d1, p1 = self.down1(x)
        d2, p2 = self.down2(p1)
        d3, p3 = self.down3(p2)
        d4, p4 = self.down4(p3)
        b = self.bottleneck(p4)
        u1 = self.up1(b, d4)
        u2 = self.up2(u1, d3)
        u3 = self.up3(u2, d2)
        u4 = self.up4(u3, d1)
        return self.out(u4)


def build_efficientnet_b3(num_output=2, pretrained=False):
    # torchvision efficientnet_b3; weights=None or pretrained control
    model = models.efficientnet_b3(weights=None if not pretrained else models.EfficientNet_B3_Weights.IMAGENET1K_V1)
    in_features = model.classifier[1].in_features
    model.classifier[1] = nn.Linear(in_features, num_output)
    return model


device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
print("Using device:", device)

UNET_PATH = "models/unet.pth"               
MODEL_BACT_PATH = "models/model_bacterial.pt"
MODEL_VIRAL_PATH = "models/model_viral.pt"


unet = UNet(in_channels=3, num_classes=1).to(device)
unet.load_state_dict(torch.load(UNET_PATH, map_location=device))
unet.eval()


model_bact = build_efficientnet_b3(num_output=2).to(device)
model_viral = build_efficientnet_b3(num_output=2).to(device)

model_bact.load_state_dict(torch.load(MODEL_BACT_PATH, map_location=device))
model_viral.load_state_dict(torch.load(MODEL_VIRAL_PATH, map_location=device))

model_bact.eval()
model_viral.eval()


preprocess_unet = transforms.Compose([
    transforms.Resize((300, 300)),
    transforms.ToTensor(),   
])

preprocess_classifier = transforms.Compose([
    transforms.Resize((300, 300)),
    transforms.ToTensor(),
    transforms.Normalize([0.485,0.456,0.406],[0.229,0.224,0.225])
])

def infer_mask_and_mask_image(pil_img, threshold=0.5):
    """
    Returns: masked_image_tensor_for_classifier (C,H,W), mask_numpy (H,W), masked_pil (PIL)
    """
    # Ensure RGB
    if pil_img.mode != "RGB":
        pil_img = pil_img.convert("RGB")
    # UNet input: tensor
    inp = preprocess_unet(pil_img).unsqueeze(0).to(device)
    with torch.no_grad():
        logits = unet(inp)               
        mask_prob = torch.sigmoid(logits)[0,0] 
    mask_np = mask_prob.cpu().numpy()
    # binary mask
    bin_mask = (mask_np >= threshold).astype(np.uint8)
    # apply mask to original image (resized to 300x300) for classifier
    img_tensor = preprocess_classifier(pil_img).to(device)  # normalized
    # the mask corresponds to preprocess_unet size (300,300) same as classifier
    mask_tensor = torch.from_numpy(bin_mask).unsqueeze(0).to(device).float()
    masked_img_tensor = img_tensor * mask_tensor
    # convert masked tensor back to PIL for display (unnormalize)
    img_for_display = preprocess_unet(pil_img).cpu().numpy().transpose(1,2,0)
    masked_display = (img_for_display * bin_mask[...,None]) 
    masked_display = np.clip(masked_display*255, 0, 255).astype(np.uint8)
    masked_pil = Image.fromarray(masked_display)
    return masked_img_tensor, mask_np, masked_pil

def classify_masked_tensor(masked_img_tensor, thresh_b=0.5, thresh_v=0.5):
    """
    masked_img_tensor: C,H,W on device, normalized for classifier
    Returns (pb, pv, label)
    pb = probability pneumonia in bacterial model
    pv = probability pneumonia in viral model
    """
    x = masked_img_tensor.unsqueeze(0).to(device)

    with torch.no_grad():
        out_b = model_bact(x)
        out_v = model_viral(x)

        pb = torch.softmax(out_b, dim=1)[0,1].item()  
        pv = torch.softmax(out_v, dim=1)[0,1].item()  

    # ----------- DECISION LOGIC -----------
    # Case 1: Both low → NORMAL
    if pb < thresh_b and pv < thresh_v:
        label = "NORMAL"

    # Case 2: Only bacterial high → BACTERIAL
    elif pb >= thresh_b and pv < thresh_v:
        label = "BACTERIAL PNEUMONIA"

    # Case 3: Only viral high → VIRAL
    elif pv >= thresh_v and pb < thresh_b:
        label = "VIRAL PNEUMONIA"

    # Case 4: Both high → pick the dominant type
    else:
        label = "BACTERIAL PNEUMONIA" if pb > pv else "VIRAL PNEUMONIA"
        label += " (fallback-high-confidence-overlap)"

    return pb, pv, label



def inference_pipeline(img, thresh_b=0.5, thresh_v=0.5, seg_thresh=0.5):
    """
    Returns: label, bacterial_prob, viral_prob, masked_image (PIL), mask_overlay (PIL)
    """

    pil = Image.fromarray(img.astype('uint8'), 'RGB')

    masked_tensor, mask_np, masked_pil = infer_mask_and_mask_image(
        pil, threshold=seg_thresh
    )

    pb, pv, pred_label = classify_masked_tensor(
        masked_tensor, 
        thresh_b=thresh_b, 
        thresh_v=thresh_v
    )

    # Convert mask to PIL
    mask_vis = (mask_np * 255).astype(np.uint8)
    mask_pil = Image.fromarray(mask_vis).convert("L")

    # Resize original for overlay
    display_orig = pil.resize((300, 300))

    # Create red mask overlay
    red_mask = np.zeros((300, 300, 3), dtype=np.uint8)
    red_mask = np.stack([mask_vis, np.zeros_like(mask_vis), np.zeros_like(mask_vis)], axis=2)
    red_mask = Image.fromarray(red_mask).convert("RGBA")

    alpha = (mask_np * 120).astype(np.uint8)
    red_mask.putalpha(Image.fromarray(alpha))

    blended = Image.alpha_composite(display_orig.convert("RGBA"), red_mask)


    return (
        pred_label,      
        float(pb),      
        float(pv),        
        masked_pil,        
        blended            
    )

title = "Chest X-ray: UNet segmentation + 2 binary classifiers"
desc = "Pipeline: UNet -> mask lungs -> two binary classifiers (Normal vs Bacterial, Normal vs Viral). " \
       "If both classifiers fire, the stronger probability is chosen (fallback). Thresholds adjustable."

with gr.Blocks(title=title) as demo:
    
    gr.Markdown(f"## {title}\n{desc}")

    with gr.Row():
        with gr.Column():
            img_in = gr.Image(type="numpy", label="Upload chest X-ray")
            thresh_b = gr.Slider(0.1, 0.9, 0.5, step=0.01, label="Bacterial threshold")
            thresh_v = gr.Slider(0.1, 0.9, 0.5, step=0.01, label="Viral threshold")
            seg_thresh = gr.Slider(0.1, 0.9, 0.5, step=0.01, label="Segmentation mask threshold")
        
            submit_btn = gr.Button("Submit", variant="primary")   
            clear_btn = gr.Button("Clear", variant="secondary") 

            

        with gr.Column():
            pred_out = gr.Label(num_top_classes=1, label="Prediction")
            pb_out = gr.Number(label="Bacterial Probability")
            pv_out = gr.Number(label="Viral Probability")
            masked_img_out = gr.Image(type="pil", label="Masked Image")
            overlay_out = gr.Image(type="pil", label="Segmentation Overlay")

            submit_btn.click(
                inference_pipeline,
                inputs=[img_in, thresh_b, thresh_v, seg_thresh],
                outputs=[pred_out, pb_out, pv_out, masked_img_out, overlay_out]
            )
            
            clear_btn.click(
                lambda: (None, None, None, None, None, None),
                outputs=[img_in, pred_out, pb_out, pv_out, masked_img_out, overlay_out]
            )

    img_in.change(
        inference_pipeline,
        inputs=[img_in, thresh_b, thresh_v, seg_thresh],
        outputs=[pred_out, pb_out, pv_out, masked_img_out, overlay_out]
    )

    gr.Markdown("## Test Samples")

    # with gr.Row():

    #     # NORMAL
    #     with gr.Column(scale=1):
    #         gr.Markdown("### NORMAL")
    #         gr.Image("images/NORMAL.jpeg", show_label=False, height=220)
    
    #     # VIRAL
    #     with gr.Column(scale=1):
    #         gr.Markdown("### VIRAL")
    #         gr.Image("images/VIRAL.jpeg", show_label=False, height=220)
    
    #     # BACTERIAL
    #     with gr.Column(scale=1):
    #         gr.Markdown("### BACTERIAL")
    #         gr.Image("images/BACT.jpeg", show_label=False, height=220)
    with gr.Row():

        with gr.Column(scale=1):
            gr.Markdown("### NORMAL")
            normal_sample = gr.Image("images/NORMAL.jpeg", show_label=False, height=220, interactive=True)
    
        with gr.Column(scale=1):
            gr.Markdown("### VIRAL")
            viral_sample = gr.Image("images/VIRAL.jpeg", show_label=False, height=220, interactive=True)
    
        with gr.Column(scale=1):
            gr.Markdown("### BACTERIAL")
            bact_sample = gr.Image("images/BACT.jpeg", show_label=False, height=220, interactive=True)

    normal_sample.select(
        inference_pipeline,
        inputs=[normal_sample, thresh_b, thresh_v, seg_thresh],
        outputs=[pred_out, pb_out, pv_out, masked_img_out, overlay_out]
    )
    
    viral_sample.select(
        inference_pipeline,
        inputs=[viral_sample, thresh_b, thresh_v, seg_thresh],
        outputs=[pred_out, pb_out, pv_out, masked_img_out, overlay_out]
    )
    
    bact_sample.select(
        inference_pipeline,
        inputs=[bact_sample, thresh_b, thresh_v, seg_thresh],
        outputs=[pred_out, pb_out, pv_out, masked_img_out, overlay_out]
    )

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