Upload app.py

app.py

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+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()