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import streamlit as st |
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import nibabel as nib |
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import os.path |
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import os |
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from nilearn import plotting |
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import torch |
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from monai.transforms import ( |
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EnsureChannelFirst, |
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Compose, |
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Resize, |
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ScaleIntensity, |
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LoadImage, |
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) |
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import torch.nn.functional as F |
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import numpy as np |
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from statistics import mean |
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from constants import CLASSES |
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from model.download_model import load_model |
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from huggingface_hub import hf_hub_download |
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st.set_page_config(page_title = "Alzheimer Classifier", page_icon = ":brain:", layout = "wide") |
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model = load_model() |
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transforms = Compose([ |
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ScaleIntensity(), |
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EnsureChannelFirst(), |
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Resize((96, 96, 96)), |
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]) |
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load_img = LoadImage(image_only=True) |
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class_names = CLASSES |
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st.set_option('deprecation.showPyplotGlobalUse', False) |
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if 'clicked_pp' not in st.session_state: |
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st.session_state.clicked_pp = False |
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if 'clicked_pred' not in st.session_state: |
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st.session_state.clicked_pred = False |
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def click_pp_true(): |
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st.session_state.clicked_pp = True |
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def click_pred_true(): |
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st.session_state.clicked_pred = True |
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def click_false(): |
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st.session_state.clicked_pp = False |
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st.session_state.clicked_pred = False |
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with st.sidebar: |
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st.title("Alzheimer Classifier Demo") |
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img_path = st.selectbox( |
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"Select Image", |
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tuple(class_names), |
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on_change= click_false, |
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) |
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col1, col2 = st.columns((1,1)) |
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with col1: |
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run_preprocess = st.button("Preprocess Image", on_click=click_pp_true) |
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if st.session_state.clicked_pp: |
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with col2: |
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run_pred = st.button("Run Prediction", on_click= click_pred_true) |
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with st.container(): |
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if img_path != "": |
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if st.session_state.clicked_pp: |
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if st.session_state.clicked_pred == False: |
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with st.container(): |
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pred_image = nib.load(hf_hub_download(repo_id= "rootstrap-org/Alzheimer-Classifier-Demo", repo_type="dataset", subfolder="preprocessed", filename = img_path + ".nii.gz")) |
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bounds_pred = plotting.find_cuts._get_auto_mask_bounds(pred_image) |
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st.sidebar.write("#") |
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y_value_pred = st.sidebar.slider('Move the slider to adjust the coronal cut ', bounds_pred[1][0], bounds_pred[1][1], mean([bounds_pred[1][0], bounds_pred[1][1]])) |
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x_value_pred = st.sidebar.slider('Move the slider to adjust the sagittal cut ', bounds_pred[0][0], bounds_pred[0][1], mean([bounds_pred[0][0], bounds_pred[0][1]])) |
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z_value_pred = st.sidebar.slider('Move the slider to adjust the axial cut ', bounds_pred[2][0], bounds_pred[2][1], mean([bounds_pred[2][0], bounds_pred[2][1]])) |
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plotting.plot_img(pred_image, cmap="grey", cut_coords=(x_value_pred,y_value_pred,z_value_pred), black_bg=True) |
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st.pyplot() |
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else: |
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with st.container(): |
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pred_image = nib.load(hf_hub_download(repo_id= "rootstrap-org/Alzheimer-Classifier-Demo", repo_type="dataset", subfolder="preprocessed", filename = img_path + ".nii.gz")) |
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bounds_pred = plotting.find_cuts._get_auto_mask_bounds(pred_image) |
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st.sidebar.write("#") |
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y_value_pred = st.sidebar.slider('Move the slider to adjust the coronal cut ', bounds_pred[1][0], bounds_pred[1][1], mean([bounds_pred[1][0], bounds_pred[1][1]])) |
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x_value_pred = st.sidebar.slider('Move the slider to adjust the sagittal cut ', bounds_pred[0][0], bounds_pred[0][1], mean([bounds_pred[0][0], bounds_pred[0][1]])) |
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z_value_pred = st.sidebar.slider('Move the slider to adjust the axial cut ', bounds_pred[2][0], bounds_pred[2][1], mean([bounds_pred[2][0], bounds_pred[2][1]])) |
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img_array = load_img(hf_hub_download(repo_id= "rootstrap-org/Alzheimer-Classifier-Demo", repo_type="dataset", subfolder="preprocessed", filename = img_path + ".nii.gz")) |
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new_data = transforms(img_array) |
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new_data_tensor = torch.from_numpy(np.array([new_data])) |
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with torch.no_grad(): |
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output = model(new_data_tensor) |
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probabilities = F.softmax(output, dim=1) |
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probabilities_np = probabilities.numpy() |
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probabilities_item = probabilities_np[0] |
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probabilities_percentage = probabilities_item * 100 |
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predicted_class_index = np.argmax(probabilities_np[0]) |
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predicted_class_name = class_names[predicted_class_index] |
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predicted_probability = probabilities_percentage[predicted_class_index] |
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st.sidebar.write("#") |
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if predicted_class_index == 0: |
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color_name = "red" |
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elif predicted_class_index == 1: |
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color_name = "blue" |
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elif predicted_class_index == 2: |
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color_name = "green" |
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if predicted_probability > 80: |
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color_prob = "green" |
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elif predicted_probability > 60: |
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color_prob = "yellow" |
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else: |
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color_prob = "red" |
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class_col, pred_col = st.columns((1,1)) |
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with class_col: |
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st.write(f"### Predicted Class: :{color_name}[{predicted_class_name}]") |
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with pred_col: |
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st.write(f"### Probability: :{color_prob}[{predicted_probability:.2f}%]") |
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plotting.plot_img(pred_image, cmap="grey", cut_coords=(x_value_pred,y_value_pred,z_value_pred), black_bg=True) |
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st.pyplot() |
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else: |
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raw_image = nib.load(hf_hub_download(repo_id= "rootstrap-org/Alzheimer-Classifier-Demo", repo_type="dataset", subfolder="raw", filename = img_path + ".nii")) |
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bounds_raw = plotting.find_cuts._get_auto_mask_bounds(raw_image) |
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st.sidebar.write("#") |
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y_value_raw = st.sidebar.slider('Move the slider to adjust the coronal cut', bounds_raw[1][0], bounds_raw[1][1], mean([bounds_raw[1][0], bounds_raw[1][1]])) |
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x_value_raw = st.sidebar.slider('Move the slider to adjust the sagittal cut', bounds_raw[0][0], bounds_raw[0][1], mean([bounds_raw[0][0], bounds_raw[0][1]])) |
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z_value_raw = st.sidebar.slider('Move the slider to adjust the axial cut', bounds_raw[2][0], bounds_raw[2][1], mean([bounds_raw[2][0], bounds_raw[2][1]])) |
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plotting.plot_img(raw_image, cmap = "grey", cut_coords=(x_value_raw,y_value_raw,z_value_raw), black_bg=True) |
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st.pyplot() |
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