app.py

import streamlit as st
import openslide
import os
from streamlit_option_menu import option_menu
import torch
import requests

st.set_page_config(page_title="",layout='wide')
@st.cache(suppress_st_warning=True)
def load_model():
    from predict import Predictor
    predictor = Predictor()
    return predictor

@st.cache(suppress_st_warning=True)
def load_dependencies():
    if torch.cuda.is_available():
        os.system("pip install torch-scatter -f https://pytorch-geometric.com/whl/torch-1.7.1+cu113.html")
        os.system("pip install torch-sparse -f https://pytorch-geometric.com/whl/torch-1.7.1+cu113.html")
        os.system("pip install torch-geometric -f https://pytorch-geometric.com/whl/torch-1.7.1+cu113.html")    
    else:
        os.system("pip install torch-scatter -f https://pytorch-geometric.com/whl/torch-1.7.1+cpu.html")
        os.system("pip install torch-sparse -f https://pytorch-geometric.com/whl/torch-1.7.1+cpu.html")
        os.system("pip install torch-geometric -f https://pytorch-geometric.com/whl/torch-1.7.1+cpu.html")


def main():

        # environment variables for the inference api
        os.environ['DATA_DIR'] = 'queries'
        os.environ['PATCHES_DIR'] =  os.path.join(os.environ['DATA_DIR'], 'patches')
        os.environ['SLIDES_DIR'] = os.path.join(os.environ['DATA_DIR'], 'slides')
        os.environ['GRAPHCAM_DIR'] = os.path.join(os.environ['DATA_DIR'], 'graphcam_plots')
        os.makedirs(os.environ['GRAPHCAM_DIR'], exist_ok=True)


        # manually put the metadata in the metadata folder
        os.environ['CLASS_METADATA'] ='metadata/label_map.pkl'

        # manually put the desired weights in the weights folder
        os.environ['WEIGHTS_PATH'] = WEIGHTS_PATH='weights'
        os.environ['FEATURE_EXTRACTOR_WEIGHT_PATH'] = os.path.join(os.environ['WEIGHTS_PATH'], 'feature_extractor', 'model.pth')
        os.environ['GT_WEIGHT_PATH']  = os.path.join(os.environ['WEIGHTS_PATH'], 'graph_transformer', 'GraphCAM.pth')


        
        from predict import Predictor





        # environment variables for the inference api
        os.environ['DATA_DIR'] = 'queries'
        os.environ['PATCHES_DIR'] =  os.path.join(os.environ['DATA_DIR'], 'patches')
        os.environ['SLIDES_DIR'] = os.path.join(os.environ['DATA_DIR'], 'slides')
        os.environ['GRAPHCAM_DIR'] = os.path.join(os.environ['DATA_DIR'], 'graphcam_plots')
        os.makedirs(os.environ['GRAPHCAM_DIR'], exist_ok=True)


        # manually put the metadata in the metadata folder
        os.environ['CLASS_METADATA'] ='metadata/label_map.pkl'

        # manually put the desired weights in the weights folder
        os.environ['WEIGHTS_PATH'] = WEIGHTS_PATH='weights'
        os.environ['FEATURE_EXTRACTOR_WEIGHT_PATH'] = os.path.join(os.environ['WEIGHTS_PATH'], 'feature_extractor', 'model.pth')
        os.environ['GT_WEIGHT_PATH']  = os.path.join(os.environ['WEIGHTS_PATH'], 'graph_transformer', 'GraphCAM.pth')


        predictor = load_model()#Predictor()





        ABOUT_TEXT = "🤗 LastMinute Medical - Web diagnosis tool."
        CONTACT_TEXT = """
        _Built by Christian Cancedda and LabLab lads with love_ ❤️ 

        [![Follow](https://img.shields.io/github/followers/Chris1nexus?style=social)](https://github.com/Chris1nexus)

        [![Follow](https://img.shields.io/twitter/follow/chris_cancedda?style=social)](https://twitter.com/intent/follow?screen_name=chris_cancedda)

        Star project repository:

        [![GitHub stars](https://img.shields.io/github/stars/Chris1nexus/inference-graph-transformer?style=social)](https://github.com/Chris1nexus/inference-graph-transformer)

        """
        VISUALIZE_TEXT = "Visualize WSI slide by uploading it on the provided window"
        DETECT_TEXT = "Generate a preliminary diagnosis about the presence of  pulmonary disease"



        with st.sidebar:
            choice = option_menu("LastMinute - Diagnosis",
                                 ["About", "Visualize WSI slide", "Cancer Detection", "Contact"],
                                 icons=['house', 'upload', 'activity',  'person lines fill'],
                                 menu_icon="app-indicator", default_index=0,
                                 styles={
                                     # "container": {"padding": "5!important", "background-color": "#fafafa", },
                                     "container": {"border-radius": ".0rem"},
                                     # "icon": {"color": "orange", "font-size": "25px"},
                                     # "nav-link": {"font-size": "16px", "text-align": "left", "margin": "0px",
                                     #              "--hover-color": "#eee"},
                                     # "nav-link-selected": {"background-color": "#02ab21"},
                                 }
                                 )
        st.sidebar.markdown(
            """
        <style>
        .aligncenter {
            text-align: center;
        }
        </style>
        <p style='text-align: center'>
            <a href="https://github.com/Chris1nexus/inference-graph-transformer" target="_blank">Project Repository</a>
        </p>


        <p class="aligncenter">
            <a href="https://github.com/Chris1nexus/inference-graph-transformer" target="_blank"> 
                <img src="https://img.shields.io/github/stars/Chris1nexus/inference-graph-transformer?style=social"/>
            </a>
        </p>

        <p class="aligncenter">
            <a href="https://twitter.com/chris_cancedda" target="_blank"> 
                <img src="https://img.shields.io/twitter/follow/chris_cancedda?style=social"/>
            </a>
        </p>
            """,
            unsafe_allow_html=True,
        )


        if choice == "About":
            st.title(choice)
            README = requests.get("https://raw.githubusercontent.com/Chris1nexus/inference-graph-transformer/master/README.md").text
            README = str(README).replace('width="1200"','width="700"')
            # st.title(choose)
            st.markdown(README, unsafe_allow_html=True)

        if choice == "Visualize WSI slide":
            st.title(choice)
            st.markdown(VISUALIZE_TEXT)

            uploaded_file = st.file_uploader("Choose a WSI slide file to diagnose (.svs)")
            if uploaded_file is not None:
                ori = openslide.OpenSlide(uploaded_file.name)
                width, height = ori.dimensions

                REDUCTION_FACTOR = 20
                w, h = int(width/512), int(height/512)
                w_r, h_r = int(width/20), int(height/20)
                resized_img = ori.get_thumbnail((w_r,h_r))
                resized_img = resized_img.resize((w_r,h_r))
                ratio_w, ratio_h = width/resized_img.width, height/resized_img.height
                #print('ratios ', ratio_w, ratio_h)
                w_s, h_s = float(512/REDUCTION_FACTOR), float(512/REDUCTION_FACTOR)   
                st.image(resized_img, use_column_width='never')   

        if choice == "Cancer Detection":
            state = dict()

            st.title(choice)
            st.markdown(DETECT_TEXT)
            uploaded_file = st.file_uploader("Choose a WSI slide file to diagnose (.svs)")
            st.markdown("Examples can be chosen at the [GDC Data repository](https://portal.gdc.cancer.gov/repository?facetTab=cases&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.primary_site%22%2C%22value%22%3A%5B%22bronchus%20and%20lung%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22TCGA%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%5B%22TCGA-LUAD%22%2C%22TCGA-LUSC%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.experimental_strategy%22%2C%22value%22%3A%5B%22Tissue%20Slide%22%5D%7D%7D%5D%7D)")
            st.markdown("Alternatively, for simplicity few test cases are provided at the [drive link](https://drive.google.com/drive/folders/1u3SQa2dytZBHHh6eXTlMKY-pZGZ-pwkk?usp=share_link)")


            if uploaded_file is not None:
                # To read file as bytes:
                #print(uploaded_file)
                with open(os.path.join(uploaded_file.name),"wb") as f:
                     f.write(uploaded_file.getbuffer())
                with st.spinner(text="Computation is running"):
                    predicted_class, viz_dict = predictor.predict(uploaded_file.name)
                st.info('Computation completed.')
                st.header(f'Predicted to be: {predicted_class}')
                st.text('Heatmap of the areas that show markers correlated with the disease.\nIncreasing red tones represent higher likelihood that the area is affected')
                state['cur'] = predicted_class
                mapper = {'ORI': predicted_class, predicted_class:'ORI'}
                readable_mapper = {'ORI': 'Original',  predicted_class :'Disease heatmap' }        
                #def fn():
                #    st.image(viz_dict[mapper[state['cur']]], use_column_width='never', channels='BGR') 
                #    state['cur'] = mapper[state['cur']]
                #    return 

                #st.button(f'See {readable_mapper[mapper[state["cur"]] ]}', on_click=fn   )
                #st.image(viz_dict[state['cur']], use_column_width='never', channels='BGR') 
                st.image([viz_dict[state['cur']],viz_dict['ORI']], caption=['Original', f'{predicted_class} heatmap'] ,channels='BGR'
                    # use_column_width='never', 
                    ) 
                    

        if choice == "Contact":
            st.title(choice)
            st.markdown(CONTACT_TEXT)

if __name__ == '__main__':
    #''' 
    load_dependencies()
    #'''
    main()