app.py

# Import required libraries
import os
import io
import torch
import pydicom
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,
    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(
    [
        AsChannelFirst(), 
        ScaleIntensityRangePercentiles(lower=20, upper=80, b_min=0.0, b_max=1.0, clip=False, relative=True), 
        Resize(spatial_size=SPATIAL_SIZE)
    ]
)

# CAM Transforms
cam_transforms = Compose(
    [
        AsChannelFirst(), 
        Resize(spatial_size=SPATIAL_SIZE)
    ]
)

# Original Transforms
original_transforms = Compose(
    [
        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()

# Convert the file size from bytes to megabytes
def bytes_to_megabytes(file_size_bytes):
    # Convert bytes to MB (1 MB = 1024 * 1024 bytes)
    file_size_megabytes = round(file_size_bytes / (1024 * 1024), 2)
    return str(file_size_megabytes) + " MB"  # Rounding to 2 decimal places for readability

def meta_tensor_to_numpy(meta_tensor):
    """
    Convert a PyTorch MetaTensor to a NumPy array
    """
    # Ensure the MetaTensor is on the CPU
    meta_tensor = meta_tensor.cpu()

    # Convert the MetaTensor to a PyTorch tensor
    torch_tensor = meta_tensor.to(dtype=torch.float32)

    # Convert the PyTorch tensor to a NumPy array
    numpy_array = torch_tensor.detach().numpy()

    return numpy_array

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

# Parameters
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
USE_CUDA = False
if device == torch.device("cuda"):
    USE_CUDA = True

def load_model(root_dir, model_name, model_file_name):
    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=device))
    model.eval()
    return model

ct_model = load_model(CT_MODEL_DIRECTORY, CT_MODEL_NAME, CT_MODEL_FILE_NAME)
mri_model = load_model(MRI_MODEL_DIRECTORY, MRI_MODEL_NAME, MRI_MODEL_FILE_NAME)
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")
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)
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)

uploaded_mri_file = st.file_uploader("Upload a candidate MRI DICOM", type=["dcm"])
if uploaded_mri_file is not None:
    # Read DICOM file into NumPy array
    dicom_data = pydicom.dcmread(uploaded_mri_file)
    dicom_array = dicom_data.pixel_array

    # Convert the data type to float32
    dicom_array = dicom_array.astype(np.float32)

    # Then add a channel dimension
    dicom_array = dicom_array[:, :, np.newaxis]

    # To check file details
    file_details = {"File_Name": uploaded_mri_file.name, "File_Type": uploaded_mri_file.type, "File_Size": bytes_to_megabytes(uploaded_mri_file.size), "File_Dimension": str((dicom_array.shape[0],dicom_array.shape[1]))}
    st.write(file_details)

    transformed_array = eval_transforms(dicom_array)

    # Convert to PyTorch tensor and move to device
    image_tensor = transformed_array.clone().detach().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(dicom_array).unsqueeze(0).to(device)
    download_image_tensor = download_image_tensor.squeeze()

    # Transform the download image and apply windowing
    download_image_numpy = meta_tensor_to_numpy(download_image_tensor)
    windowed_download_image = DICOM_Utils.apply_windowing(download_image_numpy, 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_transforms(dicom_array).unsqueeze(0).to(device)
    display_image_tensor = display_image_tensor.squeeze()

    # Transform the image and apply windowing
    display_image_numpy = meta_tensor_to_numpy(display_image_tensor)
    windowed_image = DICOM_Utils.apply_windowing(display_image_numpy, 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=USE_CUDA)
    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)

uploaded_ct_file = st.file_uploader("Upload a candidate CT DICOM", type=["dcm"])
if uploaded_ct_file is not None:
    # Read DICOM file into NumPy array
    dicom_data = pydicom.dcmread(uploaded_ct_file)
    dicom_array = dicom_data.pixel_array

    # Convert the data type to float32
    dicom_array = dicom_array.astype(np.float32)

    # Then add a channel dimension
    dicom_array = dicom_array[:, :, np.newaxis]

    # To check file details
    file_details = {"File_Name": uploaded_ct_file.name, "File_Type": uploaded_ct_file.type, "File_Size": bytes_to_megabytes(uploaded_ct_file.size), "File_Dimension": str((dicom_array.shape[0],dicom_array.shape[1]))}
    st.write(file_details)

    transformed_array = eval_transforms(dicom_array)

    # Convert to PyTorch tensor and move to device
    image_tensor = transformed_array.clone().detach().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(dicom_array).unsqueeze(0).to(device)
    download_image_tensor = download_image_tensor.squeeze()

    # Transform the download image and apply windowing
    download_image_numpy = meta_tensor_to_numpy(download_image_tensor)
    windowed_download_image = DICOM_Utils.apply_windowing(download_image_numpy, 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_transforms(dicom_array).unsqueeze(0).to(device)
    display_image_tensor = display_image_tensor.squeeze()

    # Transform the image and apply windowing
    display_image_numpy = meta_tensor_to_numpy(display_image_tensor)
    windowed_image = DICOM_Utils.apply_windowing(display_image_numpy, 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=USE_CUDA)
    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)