app.py

# Import required libraries
import os
import io
import torch
import tempfile
import numpy as np
import streamlit as st

# Import utility and custom functions
from PIL import Image
from Util.DICOM import DICOM_Utils
from Util.Custom_Model import Build_Custom_Model, reshape_transform

# Import additional MONAI and PyTorch Grad-CAM utilities
from monai.config import print_config
from monai.utils import set_determinism
from monai.networks.nets import SEResNet50
from monai.transforms import (
    Activations,
    EnsureChannelFirst,
    AsDiscrete,
    Compose,
    LoadImage,
    RandFlip,
    RandRotate,
    RandZoom,
    ScaleIntensity,
    AsChannelFirst,
    AddChannel,
    RandSpatialCrop,
    ScaleIntensityRangePercentiles,
    Resize,
)
from pytorch_grad_cam import GradCAM
from pytorch_grad_cam.utils.image import show_cam_on_image
from pytorch_grad_cam.utils.model_targets import ClassifierOutputTarget


# (Int) Random seed
SEED = 0

# (Int) Model parameters
NUM_CLASSES = 1

# (String) CT Model directory
CT_MODEL_DIRECTORY = "models/CLOTS/CT"

# (String) MRI Model directory
MRI_MODEL_DIRECTORY = "models/CLOTS/MRI"

# (Boolean) Use custom model
CUSTOM_MODEL_FLAG = True

# (List[int]) Image size
SPATIAL_SIZE = [224, 224]

# (String) CT Model file name
CT_MODEL_FILE_NAME = "best_metric_model.pth"

# (String) MRI Model file name
MRI_MODEL_FILE_NAME = "best_metric_model.pth"

# (Boolean) List model modules
LIST_MODEL_MODULES = False

# (String) Model name
CT_MODEL_NAME = "swin_base_patch4_window7_224"

# (String) Model name
MRI_MODEL_NAME = "swin_base_patch4_window7_224"

# (Float) Model inference threshold
CT_INFERENCE_THRESHOLD = 0.5

# (Float) Model inference threshold
MRI_INFERENCE_THRESHOLD = 0.5

# (Int) Display CAM Class ID
CAM_CLASS_ID = 0

# (Int) Window Center for image display
DEFAULT_CT_WINDOW_CENTER = 40

# (Int) Window Width for image display
DEFAULT_CT_WINDOW_WIDTH = 100

# (Int) Window Center for image display
DEFAULT_MRI_WINDOW_CENTER = 400

# (Int) Window Width for image display
DEFAULT_MRI_WINDOW_WIDTH = 1000

# (Int) Minimum value for Window Center
WINDOW_CENTER_MIN = -600

# (Int) Maximum value for Window Center
WINDOW_CENTER_MAX = 1000

# (Int) Minimum value for Window Width
WINDOW_WIDTH_MIN = 1

# (Int) Maximum value for Window Width
WINDOW_WIDTH_MAX = 3000

# Evaluation Transforms
eval_transforms = Compose(
    [
        LoadImage(image_only=True), 
        AsChannelFirst(), 
        ScaleIntensityRangePercentiles(lower=20, upper=80, b_min=0.0, b_max=1.0, clip=False, relative=True), 
        Resize(spatial_size=SPATIAL_SIZE)
    ]
)

# CAM Original Transforms
cam_original_transforms = Compose(
    [
        LoadImage(image_only=True), 
        AsChannelFirst(), 
        Resize(spatial_size=SPATIAL_SIZE)
    ]
)

# CAM Original Transforms
original_transforms = Compose(
    [
        LoadImage(image_only=True), 
        AsChannelFirst()
    ]
)

# Function to convert PIL Image to byte stream in PNG format for downloading
def image_to_bytes(image):
    byte_stream = io.BytesIO()
    image.save(byte_stream, format='PNG')
    return byte_stream.getvalue()

set_determinism(seed=SEED)
torch.manual_seed(SEED)

# Parameters
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
ct_root_dir = tempfile.mkdtemp() if CT_MODEL_DIRECTORY is None else CT_MODEL_DIRECTORY
mri_root_dir = tempfile.mkdtemp() if MRI_MODEL_DIRECTORY is None else MRI_MODEL_DIRECTORY

def load_model(root_dir, model_name, model_file_name, map_location):
    if CUSTOM_MODEL_FLAG:
        model = Build_Custom_Model(model_name, NUM_CLASSES, pretrained=False).to(device)
    else:
        model = SEResNet50(spatial_dims=2, in_channels=1, num_classes=NUM_CLASSES).to(device)
    model.load_state_dict(torch.load(os.path.join(root_dir, model_file_name),  map_location=map_location)))
    model.eval()
    return model

ct_model = load_model(ct_root_dir, CT_MODEL_NAME, CT_MODEL_FILE_NAME, device)
mri_model = load_model(mri_root_dir, MRI_MODEL_NAME, MRI_MODEL_FILE_NAME, device)
if LIST_MODEL_MODULES:
    for ct_name, _ in ct_model.named_modules():
        print(ct_name)

    for mri_name, _ in mri_model.named_modules():
        print(mri_name)

# Initialize Streamlit
st.title("Analyze")

# Use Streamlit's number_input to adjust WINDOW_CENTER and WINDOW_WIDTH
st.sidebar.header("Windowing Parameters for DICOM")
CT_WINDOW_CENTER = st.sidebar.number_input("CT Window Center", min_value=WINDOW_CENTER_MIN, max_value=WINDOW_CENTER_MAX, value=DEFAULT_CT_WINDOW_CENTER, step=1)
CT_WINDOW_WIDTH = st.sidebar.number_input("CT Window Width", min_value=WINDOW_WIDTH_MIN, max_value=WINDOW_WIDTH_MAX, value=DEFAULT_CT_WINDOW_WIDTH, step=1)
MRI_WINDOW_CENTER = st.sidebar.number_input("MRI Window Center", min_value=WINDOW_CENTER_MIN, max_value=WINDOW_CENTER_MAX, value=DEFAULT_MRI_WINDOW_CENTER, step=1)
MRI_WINDOW_WIDTH = st.sidebar.number_input("MRI Window Width", min_value=WINDOW_WIDTH_MIN, max_value=WINDOW_WIDTH_MAX, value=DEFAULT_MRI_WINDOW_WIDTH, step=1)

uploaded_ct_file = st.file_uploader("Upload a candidate CT DICOM", type=["dcm"])
if uploaded_ct_file is not None:
    # Save the uploaded file to a temporary location
    with tempfile.NamedTemporaryFile(delete=False, suffix=".dcm") as temp_file:
        temp_file.write(uploaded_ct_file.getvalue())

        # Apply evaluation transforms to the DICOM image for model prediction
        image_tensor = eval_transforms(temp_file.name).unsqueeze(0).to(device)

        # Predict
        with torch.no_grad():
            outputs = ct_model(image_tensor).sigmoid().to("cpu").numpy()
            prob = outputs[0][0]
            CLOTS_CLASSIFICATION = False
            if(prob >= CT_INFERENCE_THRESHOLD):
                CLOTS_CLASSIFICATION=True

        st.header("CT Classification")
        st.subheader(f"Ischaemic Stroke : {CLOTS_CLASSIFICATION}")
        st.subheader(f"Confidence : {prob * 100:.1f}%")

        # Load the original DICOM image for download
        download_image_tensor = original_transforms(temp_file.name).unsqueeze(0).to(device)
        download_image = download_image_tensor.squeeze()

        # Transform the download image and apply windowing
        transformed_download_image = DICOM_Utils.transform_image_for_display(download_image)
        windowed_download_image = DICOM_Utils.apply_windowing(transformed_download_image, CT_WINDOW_CENTER, CT_WINDOW_WIDTH)

        # Streamlit button to trigger image download
        image_data = image_to_bytes(Image.fromarray(windowed_download_image))
        st.download_button(
            label="Download CT Image",
            data=image_data,
            file_name="downloaded_ct_image.png",
            mime="image/png"
        )

        # Load the original DICOM image for display
        display_image_tensor = cam_original_transforms(temp_file.name).unsqueeze(0).to(device)
        display_image = display_image_tensor.squeeze()

        # Transform the image and apply windowing
        transformed_image = DICOM_Utils.transform_image_for_display(display_image)
        windowed_image = DICOM_Utils.apply_windowing(transformed_image, CT_WINDOW_CENTER, CT_WINDOW_WIDTH)
        st.image(Image.fromarray(windowed_image), caption="Original CT Visualization", use_column_width=True)

        # Expand to three channels
        windowed_image = np.expand_dims(windowed_image, axis=2)
        windowed_image = np.tile(windowed_image, [1, 1, 3])

        # Ensure both are of float32 type
        windowed_image = windowed_image.astype(np.float32)

        # Normalize to [0, 1] range
        windowed_image = np.float32(windowed_image) / 255

        # Build the CAM (Class Activation Map)
        target_layers = [ct_model.model.norm]
        cam = GradCAM(model=ct_model, target_layers=target_layers, reshape_transform=reshape_transform, use_cuda=True)
        grayscale_cam = cam(input_tensor=image_tensor, targets=[ClassifierOutputTarget(CAM_CLASS_ID)])
        grayscale_cam = grayscale_cam[0, :]

        # Now you can safely call the show_cam_on_image function
        visualization = show_cam_on_image(windowed_image, grayscale_cam, use_rgb=True)
        st.image(Image.fromarray(visualization), caption="CAM CT Visualization", use_column_width=True)

uploaded_mri_file = st.file_uploader("Upload a candidate MRI DICOM", type=["dcm"])
if uploaded_mri_file is not None:
    # Save the uploaded file to a temporary location
    with tempfile.NamedTemporaryFile(delete=False, suffix=".dcm") as temp_file:
        temp_file.write(uploaded_mri_file.getvalue())

        # Apply evaluation transforms to the DICOM image for model prediction
        image_tensor = eval_transforms(temp_file.name).unsqueeze(0).to(device)

        # Predict
        with torch.no_grad():
            outputs = mri_model(image_tensor).sigmoid().to("cpu").numpy()
            prob = outputs[0][0]
            CLOTS_CLASSIFICATION = False
            if(prob >= MRI_INFERENCE_THRESHOLD):
                CLOTS_CLASSIFICATION=True

        st.header("MRI Classification")
        st.subheader(f"Ischaemic Stroke : {CLOTS_CLASSIFICATION}")
        st.subheader(f"Confidence : {prob * 100:.1f}%")

        # Load the original DICOM image for download
        download_image_tensor = original_transforms(temp_file.name).unsqueeze(0).to(device)
        download_image = download_image_tensor.squeeze()

        # Transform the download image and apply windowing
        transformed_download_image = DICOM_Utils.transform_image_for_display(download_image)
        windowed_download_image = DICOM_Utils.apply_windowing(transformed_download_image, MRI_WINDOW_CENTER, MRI_WINDOW_WIDTH)

        # Streamlit button to trigger image download
        image_data = image_to_bytes(Image.fromarray(windowed_download_image))
        st.download_button(
            label="Download MRI Image",
            data=image_data,
            file_name="downloaded_mri_image.png",
            mime="image/png"
        )

        # Load the original DICOM image for display
        display_image_tensor = cam_original_transforms(temp_file.name).unsqueeze(0).to(device)
        display_image = display_image_tensor.squeeze()

        # Transform the image and apply windowing
        transformed_image = DICOM_Utils.transform_image_for_display(display_image)
        windowed_image = DICOM_Utils.apply_windowing(transformed_image, MRI_WINDOW_CENTER, MRI_WINDOW_WIDTH)
        st.image(Image.fromarray(windowed_image), caption="Original MRI Visualization", use_column_width=True)

        # Expand to three channels
        windowed_image = np.expand_dims(windowed_image, axis=2)
        windowed_image = np.tile(windowed_image, [1, 1, 3])

        # Ensure both are of float32 type
        windowed_image = windowed_image.astype(np.float32)

        # Normalize to [0, 1] range
        windowed_image = np.float32(windowed_image) / 255

        # Build the CAM (Class Activation Map)
        target_layers = [mri_model.model.norm]
        cam = GradCAM(model=mri_model, target_layers=target_layers, reshape_transform=reshape_transform, use_cuda=True)
        grayscale_cam = cam(input_tensor=image_tensor, targets=[ClassifierOutputTarget(CAM_CLASS_ID)])
        grayscale_cam = grayscale_cam[0, :]

        # Now you can safely call the show_cam_on_image function
        visualization = show_cam_on_image(windowed_image, grayscale_cam, use_rgb=True)
        st.image(Image.fromarray(visualization), caption="CAM MRI Visualization", use_column_width=True)