app.py

import streamlit as st
import google.generativeai as genai
from PIL import Image
import os
from dotenv import load_dotenv
import PyPDF2
import io
from datetime import datetime

# Page configuration must be the first Streamlit command
st.set_page_config(
    page_title="OCT Retina Analysis Assistant",
    page_icon="👁️",
    layout="wide",
    initial_sidebar_state="expanded"
)

# Load environment variables
load_dotenv()

# Configure Gemini API
genai.configure(api_key=os.getenv("GOOGLE_API_KEY"))
model = genai.GenerativeModel("gemini-2.0-flash-exp")

# Custom CSS
st.markdown("""
    <style>
    .main {
        padding: 2rem;
    }
    .stButton>button {
        width: 100%;
        background-color: #FF4B4B;
        color: white;
        padding: 0.5rem;
        margin-top: 1rem;
    }
    .credit-box {
        background-color: #f0f2f6;
        padding: 1rem;
        border-radius: 0.5rem;
        margin: 1rem 0;
    }
    .header-box {
        background-color: #FF4B4B;
        padding: 2rem;
        border-radius: 0.5rem;
        color: white;
        margin-bottom: 2rem;
        text-align: center;
    }
    .image-container {
        margin: 1rem 0;
        padding: 1rem;
        border-radius: 0.5rem;
        background-color: #f0f2f6;
    }
    .analysis-container {
        margin-top: 1rem;
        padding: 1rem;
        border-radius: 0.5rem;
        background-color: #f0f2f6;
    }
    </style>
""", unsafe_allow_html=True)

# System prompts
SINGLE_TIMEPOINT_PROMPT = """You are an expert ophthalmologist specializing in interpreting macular Optical Coherence Tomography (OCT) scans. Your goal is to provide an accurate description and a possible diagnosis, supported by clear medical reasoning. These scans are from the same patient at a single timepoint. Please provide a comprehensive analysis.

Step 1: Image Quality Assessment
For each scan, describe the overall image quality, noting any artifacts or limitations that may affect your analysis.

Step 2: Layer-by-Layer Analysis Across All Scans
Analyze each of the retinal layers across all provided scans, describing:
•	Thickness patterns: Note any variations or consistencies in layer thickness
•	Morphological changes: Compare layer appearance across scans
•	Reflectivity patterns: Identify any recurring patterns or changes
•	Document abnormalities and their distribution across scans

Step 3: Comprehensive Foveal Analysis
Analyze the foveal region across all scans:
•	Compare foveal contour and thickness
•	Note any consistent or varying abnormalities
•	Identify patterns of foveal involvement

Step 4: Integrated Abnormality Assessment
Provide a unified analysis of abnormalities across all scans:
•	Distribution patterns
•	Progression or variation in appearance
•	Relationship between findings in different scans

Step 5: Differential Diagnoses
Based on the comprehensive analysis:
•	List potential diagnoses supported by findings across multiple scans
•	Explain how the pattern of findings supports each diagnosis
•	Note any temporal or spatial progression that helps narrow the diagnosis

Step 6: Most Likely Diagnosis
Provide a unified diagnosis considering all scans:
•	Explain how the combined findings support this diagnosis
•	Discuss any progression or pattern that confirms the diagnosis
•	Address any variations or inconsistencies

Step 7: Recommendations
Suggest:
•	Additional tests or imaging if needed
•	Follow-up scanning recommendations
•	Treatment considerations based on the comprehensive analysis"""

COMPARISON_PROMPT = """You are an expert ophthalmologist specializing in interpreting macular Optical Coherence Tomography (OCT) scans. Your goal is to provide an accurate description and a possible diagnosis, supported by clear medical reasoning. These scans are from the same patient at two different timepoints. Please provide a comprehensive analysis and comparison.

Step 1: Image Quality Assessment
For each set of scans, describe the overall image quality, noting any artifacts or limitations that may affect your analysis.

Step 2: Layer-by-Layer Comparison
Compare the retinal layers between timepoints:
•	Changes in thickness patterns
•	Evolution of morphological features
•	Alterations in reflectivity patterns
•	Progression or regression of abnormalities

Step 3: Foveal Evolution Analysis
Compare the foveal region between timepoints:
•	Changes in contour and thickness
•	Evolution of abnormalities
•	Progression or improvement patterns

Step 4: Disease Progression Assessment
Analyze changes between timepoints:
•	Quantify and describe changes in abnormalities
•	Identify new or resolved findings
•	Assess overall disease progression or improvement

Step 5: Treatment Response Evaluation
If treatment was administered:
•	Evaluate effectiveness
•	Identify areas of improvement
•	Note resistant or worsening areas

Step 6: Updated Diagnosis and Prognosis
Based on the temporal comparison:
•	Confirm or revise previous diagnosis
•	Assess disease trajectory
•	Provide prognostic insights

Step 7: Recommendations
Suggest:
•	Treatment modifications if needed
•	Follow-up interval
•	Additional testing if required
•	Preventive measures"""

TREATMENT_GUIDELINES_PROMPT = """Based on the current diagnosis and findings, please provide evidence-based treatment recommendations following established ophthalmological guidelines. Consider:

1. Standard of Care
•	First-line treatments
•	Alternative options
•	Contraindications

2. Treatment Plan
•	Immediate interventions
•	Long-term management
•	Follow-up schedule

3. Monitoring Parameters
•	Key metrics to track
•	Warning signs
•	Success indicators

4. Patient Education
•	Lifestyle modifications
•	Self-monitoring instructions
•	Prevention strategies"""

def extract_pdf_text(pdf_file):
    """Extract text from uploaded PDF file"""
    pdf_reader = PyPDF2.PdfReader(pdf_file)
    text = ""
    for page in pdf_reader.pages:
        text += page.extract_text()
    return text

def analyze_oct_images(images, timepoint=None, patient_data=None):
    """Analyze OCT images with optional timepoint and patient data"""
    if timepoint:
        prompt = f"{SINGLE_TIMEPOINT_PROMPT}\n\nTimepoint: {timepoint}\n"
    else:
        prompt = f"{SINGLE_TIMEPOINT_PROMPT}\n"
    
    if patient_data:
        prompt += f"\nPatient Information:\n{patient_data}\n"
    
    prompt += "\nPlease analyze these OCT scans:"
    content = [prompt] + images
    response = model.generate_content(content)
    return response.text

def compare_oct_timepoints(images1, date1, images2, date2, patient_data=None):
    """Compare OCT images from two timepoints"""
    prompt = f"{COMPARISON_PROMPT}\n\nTimepoint 1: {date1}\nTimepoint 2: {date2}\n"
    
    if patient_data:
        prompt += f"\nPatient Information:\n{patient_data}\n"
    
    prompt += "\nPlease compare these OCT scans:"
    content = [prompt] + images1 + images2
    response = model.generate_content(content)
    return response.text

def get_treatment_recommendations(diagnosis, findings):
    """Get treatment recommendations based on guidelines"""
    prompt = f"{TREATMENT_GUIDELINES_PROMPT}\n\nDiagnosis: {diagnosis}\nFindings: {findings}"
    response = model.generate_content(prompt)
    return response.text

def main():
    # Header with custom styling
    st.markdown("""
        <div class="header-box">
            <h1>OCT Retina Analysis Assistant</h1>
            
        </div>
    """, unsafe_allow_html=True)

    # Credits
    st.markdown("""
        <div class="credit-box">
            <h3>About</h3>
            <p>Developed by Dr. Fernando Ly</p>
            <p>This tool assists in the analysis of OCT retina scans using advanced AI technology. 
            It provides detailed layer analysis and potential diagnoses to support clinical decision-making.</p>
            <p><strong>Note:</strong> This tool is for assistance only and should not replace professional medical judgment.</p>
        </div>
    """, unsafe_allow_html=True)
    
    # Main content
    col1, col2 = st.columns([1, 1])
    
    with col1:
        # Patient Data Section
        st.markdown("### Patient Information")
        patient_pdf = st.file_uploader("Upload Patient Data (PDF)", type=['pdf'])
        patient_data = None
        if patient_pdf:
            patient_data = extract_pdf_text(patient_pdf)
            with st.expander("View Patient Data"):
                st.text(patient_data)
        
        # Scan Upload Section
        st.markdown("### Upload OCT Scans")
        timepoint_option = st.radio(
            "Select scan type:",
            ["Single Timepoint", "Two Timepoints for Comparison"]
        )
        
        if timepoint_option == "Single Timepoint":
            uploaded_files = st.file_uploader(
                "Choose OCT scans", 
                type=['png', 'jpg', 'jpeg'],
                accept_multiple_files=True,
                key="single_timepoint"
            )
            
            if uploaded_files:
                scan_date = st.date_input("Scan Date")
                st.markdown("### Uploaded Scans")
                images = []
                for idx, uploaded_file in enumerate(uploaded_files):
                    with st.expander(f"OCT Scan {idx + 1}", expanded=True):
                        image = Image.open(uploaded_file)
                        images.append(image)
                        st.image(image, use_container_width=True, caption=f"OCT Scan {idx + 1}")
                
                if st.button("🔍 Analyze Scans"):
                    with st.spinner("Analyzing OCT scans... Please wait."):
                        try:
                            analysis = analyze_oct_images(images, scan_date, patient_data)
                            treatment_recs = get_treatment_recommendations(
                                "Based on the analysis above",
                                "See detailed findings above"
                            )
                            
                            with col2:
                                st.markdown("### Analysis Results")
                                st.markdown(f"""
                                    <div class="analysis-container">
                                        {analysis.replace(chr(10), '<br>')}
                                    </div>
                                """, unsafe_allow_html=True)
                                
                                st.markdown("### Treatment Recommendations")
                                st.markdown(f"""
                                    <div class="analysis-container">
                                        {treatment_recs.replace(chr(10), '<br>')}
                                    </div>
                                """, unsafe_allow_html=True)
                                
                        except Exception as e:
                            st.error(f"An error occurred during analysis: {str(e)}")
        
        else:  # Two Timepoints
            st.markdown("#### First Timepoint")
            files1 = st.file_uploader(
                "Choose first set of OCT scans", 
                type=['png', 'jpg', 'jpeg'],
                accept_multiple_files=True,
                key="timepoint1"
            )
            date1 = st.date_input("First Scan Date")
            
            st.markdown("#### Second Timepoint")
            files2 = st.file_uploader(
                "Choose second set of OCT scans", 
                type=['png', 'jpg', 'jpeg'],
                accept_multiple_files=True,
                key="timepoint2"
            )
            date2 = st.date_input("Second Scan Date")
            
            if files1 and files2:
                st.markdown("### Uploaded Scans")
                images1 = []
                images2 = []
                
                st.markdown("#### First Timepoint Scans")
                for idx, uploaded_file in enumerate(files1):
                    with st.expander(f"OCT Scan {idx + 1} - First Timepoint", expanded=False):
                        image = Image.open(uploaded_file)
                        images1.append(image)
                        st.image(image, use_container_width=True)
                
                st.markdown("#### Second Timepoint Scans")
                for idx, uploaded_file in enumerate(files2):
                    with st.expander(f"OCT Scan {idx + 1} - Second Timepoint", expanded=False):
                        image = Image.open(uploaded_file)
                        images2.append(image)
                        st.image(image, use_container_width=True)
                
                if st.button("🔍 Compare Timepoints"):
                    with st.spinner("Analyzing and comparing OCT scans... Please wait."):
                        try:
                            comparison = compare_oct_timepoints(
                                images1, date1,
                                images2, date2,
                                patient_data
                            )
                            treatment_recs = get_treatment_recommendations(
                                "Based on the comparison above",
                                "See detailed findings above"
                            )
                            
                            with col2:
                                st.markdown("### Comparison Results")
                                st.markdown(f"""
                                    <div class="analysis-container">
                                        {comparison.replace(chr(10), '<br>')}
                                    </div>
                                """, unsafe_allow_html=True)
                                
                                st.markdown("### Treatment Recommendations")
                                st.markdown(f"""
                                    <div class="analysis-container">
                                        {treatment_recs.replace(chr(10), '<br>')}
                                    </div>
                                """, unsafe_allow_html=True)
                                
                        except Exception as e:
                            st.error(f"An error occurred during analysis: {str(e)}")
    
    # Instructions in col2 if no files uploaded
    if not (patient_pdf or (timepoint_option == "Single Timepoint" and uploaded_files) or 
            (timepoint_option == "Two Timepoints for Comparison" and files1 and files2)):
        with col2:
            st.markdown("### Instructions")
            st.markdown("""
                1. Upload patient data PDF (optional)
                2. Choose analysis type (single timepoint or comparison)
                3. Upload OCT scans for selected timepoint(s)
                4. Set scan dates
                5. Click analyze/compare button
                6. Review analysis and treatment recommendations
                
                Supported formats:
                - Patient Data: PDF
                - OCT Scans: PNG, JPG, JPEG
            """)

if __name__ == "__main__":
    main()