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Upload app.py with huggingface_hub
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app.py
CHANGED
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@@ -9,805 +9,154 @@ from groq import Groq
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from PIL import Image
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from datetime import datetime
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from huggingface_hub import HfApi, hf_hub_download
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GROQ_KEY = os.environ.get("GROQ_API_KEY", "")
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HF_TOKEN = os.environ.get("HF_TOKEN", "")
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HISTORY_REPO = "Saicharan21/cardiolab-chat-history"
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PAPERS_DB_REPO = "Saicharan21/cardiolab-papers-db"
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CARDIOLAB_MODEL = "Saicharan21/CardioLab-AI-Model"
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"
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"
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"Llama 3.1 8B (Fast)": "llama-3.1-8b-instant",
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"Llama 4 Scout (New)": "meta-llama/llama-4-scout-17b-16e-instruct",
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"Llama 4 Maverick": "meta-llama/llama-4-maverick-17b-128e-instruct",
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}
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KNOWHOW = (
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"MCL: Sylgard 184 PDMS 10:1 ratio 48hr cure green laser PIV 70bpm 5L/min cardiac output 80-120mmHg. "
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"TGT: Arduino Uno Stepper Motor 150mL blood sampled at 0 20 40 60 minutes. "
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"NORMAL RANGES: TAT below 8 ng/mL. PF1.2 below 2.0 nmol/L. Free hemoglobin below 20 mg/L. Platelets above 150. "
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"HIGH RISK: TAT above 15. PF1.2 above 3.0. Hemoglobin above 50. Platelets below 100. "
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"uPAD: Jaffe reaction creatinine picric acid orange-red. Normal 0.6-1.2 mg/dL. CKD above 1.5. "
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"Stage2 1.5-3.0. Stage3-4 3.0-6.0. Stage5 above 6.0. "
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"MHV: 27mm SJM Regent bileaflet also trileaflet monoleaflet pediatric. "
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"
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"Equipment: Heska Element HT5 hematology analyzer time-resolved PIV Tygon tubing Arduino Uno."
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)
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CSS = """
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}
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background:
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radial-gradient(ellipse 80% 60% at 20% 10%, rgba(193,18,31,0.12) 0%, transparent 60%),
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radial-gradient(ellipse 60% 80% at 80% 90%, rgba(0,87,168,0.10) 0%, transparent 60%);
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pointer-events: none;
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z-index: 0;
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animation: bgShift 12s ease-in-out infinite alternate;
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}
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@keyframes bgShift { 0%{opacity:1;transform:scale(1)} 100%{opacity:0.7;transform:scale(1.05)} }
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@keyframes msgIn { from{opacity:0;transform:translateY(10px)} to{opacity:1;transform:translateY(0)} }
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@keyframes pulse { 0%,100%{opacity:1;transform:scale(1)} 50%{opacity:0.5;transform:scale(1.3)} }
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.gradio-container {
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background: transparent !important;
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max-width: 1600px !important;
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margin: 0 auto !important;
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}
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.tab-nav {
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background: rgba(255,255,255,0.03) !important;
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backdrop-filter: blur(20px) !important;
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border: 1px solid rgba(255,255,255,0.08) !important;
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border-radius: 16px !important;
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padding: 6px !important;
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margin: 10px 0 !important;
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display: flex !important;
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flex-wrap: wrap !important;
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gap: 4px !important;
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}
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.tab-nav button {
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background: transparent !important;
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color: rgba(255,255,255,0.5) !important;
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border: none !important;
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border-radius: 10px !important;
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padding: 8px 14px !important;
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font-weight: 500 !important;
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font-size: 0.78em !important;
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white-space: nowrap !important;
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transition: all 0.25s ease !important;
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}
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.tab-nav button:hover {
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background: rgba(255,255,255,0.08) !important;
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color: rgba(255,255,255,0.9) !important;
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transform: translateY(-1px) !important;
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}
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.tab-nav button.selected {
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background: linear-gradient(135deg, #c1121f, #e63946) !important;
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color: white !important;
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font-weight: 700 !important;
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box-shadow: 0 4px 20px rgba(193,18,31,0.4) !important;
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transform: translateY(-1px) !important;
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}
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.message.user {
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background: linear-gradient(135deg, rgba(193,18,31,0.2), rgba(230,57,70,0.15)) !important;
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border: 1px solid rgba(193,18,31,0.3) !important;
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color: rgba(255,255,255,0.95) !important;
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border-radius: 18px 18px 4px 18px !important;
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padding: 14px 18px !important;
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backdrop-filter: blur(10px) !important;
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animation: msgIn 0.3s ease !important;
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}
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.message.bot {
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background: rgba(255,255,255,0.05) !important;
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border: 1px solid rgba(255,255,255,0.1) !important;
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color: rgba(255,255,255,0.9) !important;
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border-radius: 18px 18px 18px 4px !important;
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padding: 14px 18px !important;
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backdrop-filter: blur(10px) !important;
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border-left: 3px solid #c1121f !important;
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animation: msgIn 0.3s ease !important;
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}
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.chatbot {
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background: rgba(255,255,255,0.02) !important;
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border: 1px solid rgba(255,255,255,0.08) !important;
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border-radius: 20px !important;
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backdrop-filter: blur(20px) !important;
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}
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textarea, input[type=text], input[type=number] {
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background: rgba(255,255,255,0.06) !important;
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color: rgba(255,255,255,0.9) !important;
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border: 1px solid rgba(255,255,255,0.12) !important;
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border-radius: 14px !important;
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transition: all 0.25s ease !important;
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backdrop-filter: blur(10px) !important;
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}
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textarea:focus, input:focus {
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border-color: rgba(193,18,31,0.6) !important;
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box-shadow: 0 0 0 3px rgba(193,18,31,0.15) !important;
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outline: none !important;
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background: rgba(255,255,255,0.08) !important;
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}
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textarea::placeholder { color: rgba(255,255,255,0.3) !important; }
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button.primary {
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background: linear-gradient(135deg, #c1121f 0%, #e63946 100%) !important;
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color: white !important;
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border: none !important;
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border-radius: 12px !important;
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font-weight: 700 !important;
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box-shadow: 0 4px 20px rgba(193,18,31,0.35) !important;
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transition: all 0.2s ease !important;
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}
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button.primary:hover {
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transform: translateY(-2px) !important;
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box-shadow: 0 8px 30px rgba(193,18,31,0.5) !important;
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}
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button.secondary {
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background: rgba(255,255,255,0.07) !important;
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color: rgba(255,255,255,0.7) !important;
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border: 1px solid rgba(255,255,255,0.15) !important;
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border-radius: 12px !important;
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transition: all 0.2s ease !important;
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backdrop-filter: blur(10px) !important;
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}
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button.secondary:hover {
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background: rgba(255,255,255,0.12) !important;
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color: white !important;
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}
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label span {
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color: rgba(255,255,255,0.55) !important;
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font-weight: 500 !important;
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font-size: 0.78em !important;
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letter-spacing: 0.06em !important;
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text-transform: uppercase !important;
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}
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.block, .panel {
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background: rgba(255,255,255,0.03) !important;
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border: 1px solid rgba(255,255,255,0.07) !important;
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border-radius: 20px !important;
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backdrop-filter: blur(20px) !important;
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}
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.prose, .md { color: rgba(255,255,255,0.8) !important; }
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::-webkit-scrollbar { width: 5px; }
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/* FIX DROPDOWNS - z-index critical */
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.multiselect, .dropdown-arrow, .wrap-inner, select {
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z-index: 9999 !important;
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position: relative !important;
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}
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ul.options {
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z-index: 99999 !important;
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position: absolute !important;
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background: #1a1a2e !important;
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border: 1px solid rgba(193,18,31,0.4) !important;
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border-radius: 10px !important;
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color: white !important;
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}
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ul.options li {
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background: #1a1a2e !important;
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color: rgba(255,255,255,0.85) !important;
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padding: 8px 12px !important;
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}
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ul.options li:hover {
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background: rgba(193,18,31,0.3) !important;
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}
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/* Fix body::before blocking clicks */
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body::before {
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pointer-events: none !important;
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z-index: -1 !important;
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}
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/* Fix dropdown container */
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.gradio-dropdown {
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z-index: 1000 !important;
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position: relative !important;
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}
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/* Fix session dropdown */
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.gradio-dropdown ul {
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z-index: 99999 !important;
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background: #0d1117 !important;
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border: 1px solid rgba(255,255,255,0.15) !important;
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border-radius: 10px !important;
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}
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/* Fix all interactive elements z-index */
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button, input, select, textarea, .gr-dropdown {
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position: relative !important;
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z-index: 100 !important;
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}
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::-webkit-scrollbar-track { background: transparent; }
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::-webkit-scrollbar-thumb { background: rgba(255,255,255,0.15); border-radius: 10px; }
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::-webkit-scrollbar-thumb:hover { background: rgba(193,18,31,0.5); }
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img { border-radius: 14px !important; border: 1px solid rgba(255,255,255,0.08) !important; }
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/* GRADIO 6.x OVERRIDES */
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.svelte-1gfkn6j, .svelte-1ipelgc, .svelte-1occ011 {
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background: rgba(255,255,255,0.06) !important;
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color: rgba(255,255,255,0.9) !important;
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border-color: rgba(255,255,255,0.12) !important;
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}
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/* Fix all containers */
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.container, .wrap, .form {
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background: transparent !important;
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border-color: rgba(255,255,255,0.08) !important;
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}
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/* Fix dropdowns */
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.multiselect, .dropdown, ul.options {
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background: #0d1117 !important;
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color: rgba(255,255,255,0.9) !important;
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border-color: rgba(255,255,255,0.15) !important;
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}
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ul.options li {
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background: #0d1117 !important;
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color: rgba(255,255,255,0.85) !important;
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}
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ul.options li:hover {
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background: rgba(193,18,31,0.2) !important;
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}
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/* Fix radio buttons */
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.radio-group label, .radio-group span {
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color: rgba(255,255,255,0.8) !important;
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}
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/* Fix all textboxes */
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.scroll-hide, .overflow-y-auto {
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background: rgba(255,255,255,0.05) !important;
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color: rgba(255,255,255,0.9) !important;
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}
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/* Fix number inputs */
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input[type=number] {
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background: rgba(255,255,255,0.06) !important;
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color: rgba(255,255,255,0.9) !important;
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border: 1px solid rgba(255,255,255,0.12) !important;
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}
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/* Fix file upload */
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.file-preview, .upload-button {
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background: rgba(255,255,255,0.04) !important;
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color: rgba(255,255,255,0.7) !important;
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border-color: rgba(255,255,255,0.15) !important;
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}
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| 309 |
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/* Fix all white backgrounds */
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.bg-white, .bg-gray-50, .bg-gray-100 {
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background: rgba(255,255,255,0.04) !important;
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}
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/* Gradio panel backgrounds */
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div.gradio-group, div.gradio-row, div.gradio-column {
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background: transparent !important;
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}
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| 319 |
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| 320 |
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/* Fix image containers */
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.image-container, .preview-container {
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background: rgba(255,255,255,0.04) !important;
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border: 1px solid rgba(255,255,255,0.08) !important;
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border-radius: 14px !important;
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}
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/* Fix audio component */
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.audio-container, .waveform-container {
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background: rgba(255,255,255,0.04) !important;
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border-radius: 14px !important;
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}
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/* Fix markdown */
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.prose p, .prose h1, .prose h2, .prose h3 {
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color: rgba(255,255,255,0.85) !important;
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}
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/* Fix all borders */
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.border, .border-gray-200, .border-gray-300 {
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border-color: rgba(255,255,255,0.08) !important;
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}
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| 342 |
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| 343 |
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/* GRADIO 6.x OVERRIDES */
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.svelte-1gfkn6j, .svelte-1ipelgc, .svelte-1occ011 {
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background: rgba(255,255,255,0.06) !important;
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color: rgba(255,255,255,0.9) !important;
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| 347 |
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border-color: rgba(255,255,255,0.12) !important;
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| 348 |
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}
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| 349 |
-
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| 350 |
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/* Fix all containers */
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| 351 |
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.container, .wrap, .form {
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| 352 |
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background: transparent !important;
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| 353 |
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border-color: rgba(255,255,255,0.08) !important;
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| 354 |
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}
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| 355 |
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| 356 |
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/* Fix dropdowns */
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.multiselect, .dropdown, ul.options {
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| 358 |
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background: #0d1117 !important;
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| 359 |
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color: rgba(255,255,255,0.9) !important;
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border-color: rgba(255,255,255,0.15) !important;
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}
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ul.options li {
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background: #0d1117 !important;
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color: rgba(255,255,255,0.85) !important;
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}
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ul.options li:hover {
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background: rgba(193,18,31,0.2) !important;
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}
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| 371 |
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| 372 |
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/* Fix radio buttons */
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.radio-group label, .radio-group span {
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color: rgba(255,255,255,0.8) !important;
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}
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| 376 |
-
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/* Fix all textboxes */
|
| 378 |
-
.scroll-hide, .overflow-y-auto {
|
| 379 |
-
background: rgba(255,255,255,0.05) !important;
|
| 380 |
-
color: rgba(255,255,255,0.9) !important;
|
| 381 |
-
}
|
| 382 |
-
|
| 383 |
-
/* Fix number inputs */
|
| 384 |
-
input[type=number] {
|
| 385 |
-
background: rgba(255,255,255,0.06) !important;
|
| 386 |
-
color: rgba(255,255,255,0.9) !important;
|
| 387 |
-
border: 1px solid rgba(255,255,255,0.12) !important;
|
| 388 |
-
}
|
| 389 |
-
|
| 390 |
-
/* Fix file upload */
|
| 391 |
-
.file-preview, .upload-button {
|
| 392 |
-
background: rgba(255,255,255,0.04) !important;
|
| 393 |
-
color: rgba(255,255,255,0.7) !important;
|
| 394 |
-
border-color: rgba(255,255,255,0.15) !important;
|
| 395 |
-
}
|
| 396 |
-
|
| 397 |
-
/* Fix all white backgrounds */
|
| 398 |
-
.bg-white, .bg-gray-50, .bg-gray-100 {
|
| 399 |
-
background: rgba(255,255,255,0.04) !important;
|
| 400 |
-
}
|
| 401 |
-
|
| 402 |
-
/* Gradio panel backgrounds */
|
| 403 |
-
div.gradio-group, div.gradio-row, div.gradio-column {
|
| 404 |
-
background: transparent !important;
|
| 405 |
-
}
|
| 406 |
-
|
| 407 |
-
/* Fix image containers */
|
| 408 |
-
.image-container, .preview-container {
|
| 409 |
-
background: rgba(255,255,255,0.04) !important;
|
| 410 |
-
border: 1px solid rgba(255,255,255,0.08) !important;
|
| 411 |
-
border-radius: 14px !important;
|
| 412 |
-
}
|
| 413 |
-
|
| 414 |
-
/* Fix audio component */
|
| 415 |
-
.audio-container, .waveform-container {
|
| 416 |
-
background: rgba(255,255,255,0.04) !important;
|
| 417 |
-
border-radius: 14px !important;
|
| 418 |
-
}
|
| 419 |
-
|
| 420 |
-
/* Fix markdown */
|
| 421 |
-
.prose p, .prose h1, .prose h2, .prose h3 {
|
| 422 |
-
color: rgba(255,255,255,0.85) !important;
|
| 423 |
-
}
|
| 424 |
-
|
| 425 |
-
/* Fix all borders */
|
| 426 |
-
.border, .border-gray-200, .border-gray-300 {
|
| 427 |
-
border-color: rgba(255,255,255,0.08) !important;
|
| 428 |
-
}
|
| 429 |
-
|
| 430 |
"""
|
| 431 |
|
| 432 |
-
|
| 433 |
-
|
| 434 |
-
|
| 435 |
-
|
| 436 |
-
</style>
|
| 437 |
-
<div style="background:linear-gradient(135deg,#0f172a 0%,#1e0a0a 100%);padding:14px 28px;display:flex;align-items:center;justify-content:space-between;border-bottom:2px solid #c1121f;">
|
| 438 |
-
|
| 439 |
-
<div style="display:flex;align-items:center;gap:10px;">
|
| 440 |
-
<div style="background:rgba(0,87,168,0.2);border:1px solid rgba(0,87,168,0.3);border-radius:10px;padding:6px 10px;">
|
| 441 |
-
<div style="color:rgba(232,160,32,0.9);font-size:0.6em;font-weight:600;letter-spacing:2px;text-transform:uppercase;">SJSU</div>
|
| 442 |
-
<div style="color:white;font-size:0.65em;font-weight:600;white-space:nowrap;">Biomedical Eng.</div>
|
| 443 |
-
</div>
|
| 444 |
-
</div>
|
| 445 |
-
|
| 446 |
-
<div style="display:flex;align-items:center;gap:16px;">
|
| 447 |
-
<svg width="80" height="24" viewBox="0 0 100 24" style="opacity:0.7;">
|
| 448 |
-
<polyline points="0,12 15,12 20,4 24,20 28,2 32,18 36,12 100,12"
|
| 449 |
-
fill="none" stroke="#c1121f" stroke-width="2" stroke-linecap="round"
|
| 450 |
-
stroke-dasharray="500" style="animation:ecg 1.5s ease forwards;"/>
|
| 451 |
-
</svg>
|
| 452 |
-
|
| 453 |
-
<div style="text-align:center;">
|
| 454 |
-
<div style="font-size:1.8em;font-weight:900;letter-spacing:1px;line-height:1.1;">
|
| 455 |
-
<span style="color:white;">Cardio</span><span style="color:#c1121f;">Lab</span><span style="color:white;"> AI</span>
|
| 456 |
-
</div>
|
| 457 |
-
<div style="color:rgba(255,255,255,0.4);font-size:0.6em;letter-spacing:2px;text-transform:uppercase;margin-top:2px;">SJSU Biomedical Engineering</div>
|
| 458 |
-
</div>
|
| 459 |
-
|
| 460 |
-
<div style="animation:hb 1.4s ease infinite;">
|
| 461 |
-
<svg width="36" height="34" viewBox="0 0 100 90">
|
| 462 |
-
<defs>
|
| 463 |
-
<radialGradient id="hg4" cx="50%" cy="35%">
|
| 464 |
-
<stop offset="0%" stop-color="#e63946"/>
|
| 465 |
-
<stop offset="100%" stop-color="#7d0a11"/>
|
| 466 |
-
</radialGradient>
|
| 467 |
-
</defs>
|
| 468 |
-
<path d="M50 85 C50 85 5 55 5 30 C5 15 18 5 30 5 C38 5 45 9 50 15 C55 9 62 5 70 5 C82 5 95 15 95 30 C95 55 50 85 50 85Z" fill="url(#hg4)"/>
|
| 469 |
-
<polyline points="22,45 30,45 34,34 38,56 42,28 46,50 52,45 78,45" fill="none" stroke="white" stroke-width="3" stroke-linecap="round" opacity="0.9"/>
|
| 470 |
-
</svg>
|
| 471 |
-
</div>
|
| 472 |
-
|
| 473 |
-
<svg width="80" height="24" viewBox="0 0 100 24" style="opacity:0.7;transform:scaleX(-1);">
|
| 474 |
-
<polyline points="0,12 15,12 20,4 24,20 28,2 32,18 36,12 100,12"
|
| 475 |
-
fill="none" stroke="#c1121f" stroke-width="2" stroke-linecap="round"
|
| 476 |
-
stroke-dasharray="500" style="animation:ecg 1.8s ease forwards;"/>
|
| 477 |
-
</svg>
|
| 478 |
-
</div>
|
| 479 |
-
|
| 480 |
-
<div style="display:flex;flex-direction:column;align-items:flex-end;gap:4px;">
|
| 481 |
-
<div style="display:flex;gap:6px;">
|
| 482 |
-
<span style="background:rgba(46,204,113,0.15);border:1px solid rgba(46,204,113,0.3);color:rgba(255,255,255,0.7);padding:2px 8px;border-radius:20px;font-size:0.6em;font-weight:600;">RAG ON</span>
|
| 483 |
-
<span style="background:rgba(193,18,31,0.15);border:1px solid rgba(193,18,31,0.3);color:rgba(255,255,255,0.7);padding:2px 8px;border-radius:20px;font-size:0.6em;font-weight:600;">5 MODELS</span>
|
| 484 |
-
</div>
|
| 485 |
-
<div style="color:rgba(255,255,255,0.25);font-size:0.58em;">MHV · CKD · FSI</div>
|
| 486 |
-
</div>
|
| 487 |
-
|
| 488 |
-
</div>
|
| 489 |
-
<div style="height:1px;background:linear-gradient(90deg,transparent,#0057a8,#c1121f,#e8a020,#c1121f,#0057a8,transparent);"></div>
|
| 490 |
-
"""
|
| 491 |
|
| 492 |
-
SIDEBAR_HTML = """
|
| 493 |
-
<div style="background:linear-gradient(135deg,#fff5f5,#fef2f2);border:1px solid #fecaca;border-radius:12px;padding:12px;margin-bottom:8px;">
|
| 494 |
-
<div style="display:flex;align-items:center;gap:8px;">
|
| 495 |
-
<div style="width:6px;height:6px;background:#c1121f;border-radius:50%;"></div>
|
| 496 |
-
<span style="color:#c1121f;font-weight:700;font-size:0.8em;letter-spacing:1px;">SJSU CARDIOLAB</span>
|
| 497 |
-
</div>
|
| 498 |
-
<div style="color:#94a3b8;font-size:0.7em;margin-top:2px;">Conversations</div>
|
| 499 |
-
</div>
|
| 500 |
-
"""
|
| 501 |
-
|
| 502 |
-
STATUS_BANNER = """
|
| 503 |
-
<div style="background:#f0fdf4;border:1px solid #bbf7d0;border-radius:10px;margin:6px 0;padding:8px 16px;display:flex;align-items:center;justify-content:center;gap:16px;flex-wrap:wrap;">
|
| 504 |
-
<div style="display:flex;align-items:center;gap:6px;">
|
| 505 |
-
<div style="width:7px;height:7px;background:#22c55e;border-radius:50%;"></div>
|
| 506 |
-
<span style="color:#15803d;font-size:0.78em;font-weight:600;">RAG Active — 417 chunks from 16 SJSU papers</span>
|
| 507 |
-
</div>
|
| 508 |
-
<div style="color:#d1fae5;">|</div>
|
| 509 |
-
<div style="display:flex;align-items:center;gap:6px;">
|
| 510 |
-
<div style="width:7px;height:7px;background:#f59e0b;border-radius:50%;"></div>
|
| 511 |
-
<span style="color:#92400e;font-size:0.78em;font-weight:600;">Fine-tuned Model Loaded</span>
|
| 512 |
-
</div>
|
| 513 |
-
<div style="color:#d1fae5;">|</div>
|
| 514 |
-
<div style="display:flex;align-items:center;gap:6px;">
|
| 515 |
-
<div style="width:7px;height:7px;background:#3b82f6;border-radius:50%;"></div>
|
| 516 |
-
<span style="color:#1e40af;font-size:0.78em;font-weight:600;">5 AI Models Ready</span>
|
| 517 |
-
</div>
|
| 518 |
-
</div>
|
| 519 |
-
"""
|
| 520 |
-
|
| 521 |
-
FOOTER_HTML = """
|
| 522 |
-
<div style="text-align:center;padding:12px;border-top:1px solid #e2e8f0;background:#f8fafc;margin-top:8px;">
|
| 523 |
-
<span style="color:#94a3b8;font-size:0.72em;">
|
| 524 |
-
CardioLab AI v39 | SJSU Biomedical Engineering |
|
| 525 |
-
Inspired by <a href="https://github.com/snap-stanford/Biomni" style="color:#c1121f;text-decoration:none;">Biomni Stanford</a> |
|
| 526 |
-
<a href="https://github.com/pranatechsol/Cardio-Lab-Ai" style="color:#0057a8;text-decoration:none;">GitHub</a> |
|
| 527 |
-
Apache 2.0 | $0 Cost
|
| 528 |
-
</span>
|
| 529 |
-
</div>
|
| 530 |
-
"""
|
| 531 |
-
|
| 532 |
-
# ── LOAD PAPERS + MODEL ────────────────────────────────────
|
| 533 |
-
CHUNKS = []
|
| 534 |
-
METADATA = []
|
| 535 |
-
EMBEDDINGS = None
|
| 536 |
-
PAPERS_LOADED = False
|
| 537 |
-
EMBEDDER = None
|
| 538 |
-
CARDIOLAB_TOKENIZER = None
|
| 539 |
-
CARDIOLAB_LLM = None
|
| 540 |
-
CARDIOLAB_MODEL_LOADED = False
|
| 541 |
-
|
| 542 |
-
def load_papers():
|
| 543 |
-
global CHUNKS, METADATA, EMBEDDINGS, PAPERS_LOADED, EMBEDDER
|
| 544 |
-
try:
|
| 545 |
-
from sentence_transformers import SentenceTransformer
|
| 546 |
-
chunks_path = hf_hub_download(repo_id=PAPERS_DB_REPO, filename="chunks.json", repo_type="dataset", token=HF_TOKEN)
|
| 547 |
-
meta_path = hf_hub_download(repo_id=PAPERS_DB_REPO, filename="metadata.json", repo_type="dataset", token=HF_TOKEN)
|
| 548 |
-
emb_path = hf_hub_download(repo_id=PAPERS_DB_REPO, filename="embeddings.npy", repo_type="dataset", token=HF_TOKEN)
|
| 549 |
-
with open(chunks_path) as f: CHUNKS = json.load(f)
|
| 550 |
-
with open(meta_path) as f: METADATA = json.load(f)
|
| 551 |
-
EMBEDDINGS = np.load(emb_path)
|
| 552 |
-
EMBEDDER = SentenceTransformer("all-MiniLM-L6-v2")
|
| 553 |
-
PAPERS_LOADED = True
|
| 554 |
-
print("Papers loaded: " + str(len(CHUNKS)) + " chunks")
|
| 555 |
-
except Exception as e:
|
| 556 |
-
print("Paper load error: " + str(e))
|
| 557 |
-
|
| 558 |
-
def load_cardiolab_model():
|
| 559 |
-
global CARDIOLAB_TOKENIZER, CARDIOLAB_LLM, CARDIOLAB_MODEL_LOADED
|
| 560 |
-
try:
|
| 561 |
-
import torch
|
| 562 |
-
from transformers import AutoModelForCausalLM, AutoTokenizer
|
| 563 |
-
print("Loading CardioLab fine-tuned model...")
|
| 564 |
-
CARDIOLAB_TOKENIZER = AutoTokenizer.from_pretrained(CARDIOLAB_MODEL, token=HF_TOKEN)
|
| 565 |
-
CARDIOLAB_TOKENIZER.pad_token = CARDIOLAB_TOKENIZER.eos_token
|
| 566 |
-
device = "cuda" if torch.cuda.is_available() else "cpu"
|
| 567 |
-
CARDIOLAB_LLM = AutoModelForCausalLM.from_pretrained(
|
| 568 |
-
CARDIOLAB_MODEL, token=HF_TOKEN,
|
| 569 |
-
torch_dtype=torch.float16 if device == "cuda" else torch.float32,
|
| 570 |
-
device_map="auto" if device == "cuda" else None,
|
| 571 |
-
low_cpu_mem_usage=True
|
| 572 |
-
)
|
| 573 |
-
CARDIOLAB_MODEL_LOADED = True
|
| 574 |
-
print("CardioLab model loaded!")
|
| 575 |
-
except Exception as e:
|
| 576 |
-
print("CardioLab model error: " + str(e))
|
| 577 |
-
|
| 578 |
-
load_papers()
|
| 579 |
-
load_cardiolab_model()
|
| 580 |
-
|
| 581 |
-
def search_papers(query, n=4):
|
| 582 |
-
if not PAPERS_LOADED or EMBEDDINGS is None or EMBEDDER is None:
|
| 583 |
-
return "", []
|
| 584 |
-
try:
|
| 585 |
-
q_emb = EMBEDDER.encode([query])
|
| 586 |
-
norms = np.linalg.norm(EMBEDDINGS, axis=1, keepdims=True)
|
| 587 |
-
emb_norm = EMBEDDINGS / (norms + 1e-10)
|
| 588 |
-
q_norm = q_emb / (np.linalg.norm(q_emb) + 1e-10)
|
| 589 |
-
scores = (emb_norm @ q_norm.T).flatten()
|
| 590 |
-
top_idx = np.argsort(scores)[::-1][:n]
|
| 591 |
-
context = ""
|
| 592 |
-
results = []
|
| 593 |
-
seen = set()
|
| 594 |
-
for idx in top_idx:
|
| 595 |
-
chunk = CHUNKS[idx]
|
| 596 |
-
meta = METADATA[idx]
|
| 597 |
-
score = float(scores[idx])
|
| 598 |
-
if score > 0.25:
|
| 599 |
-
results.append({"chunk": chunk, "paper": meta["paper"], "score": score})
|
| 600 |
-
if meta["paper"] not in seen:
|
| 601 |
-
context += chr(10) + "=== FROM: " + meta["paper"] + " ===" + chr(10)
|
| 602 |
-
seen.add(meta["paper"])
|
| 603 |
-
context += chunk[:500] + chr(10)
|
| 604 |
-
return context, results
|
| 605 |
-
except Exception as e:
|
| 606 |
-
return "", []
|
| 607 |
-
|
| 608 |
-
# ── SESSION MANAGEMENT ─────────────────────────────────────
|
| 609 |
def load_all_sessions():
|
| 610 |
if not HF_TOKEN: return {}
|
| 611 |
try:
|
| 612 |
-
|
| 613 |
-
|
| 614 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 615 |
|
| 616 |
def save_all_sessions(sessions):
|
| 617 |
if not HF_TOKEN: return False
|
| 618 |
try:
|
| 619 |
-
|
| 620 |
-
|
| 621 |
-
|
|
|
|
| 622 |
path_in_repo="chat_history.json",
|
| 623 |
-
repo_id=HISTORY_REPO,
|
| 624 |
-
|
|
|
|
|
|
|
| 625 |
)
|
| 626 |
return True
|
| 627 |
-
except
|
|
|
|
|
|
|
| 628 |
|
| 629 |
def get_session_list():
|
| 630 |
-
s = load_all_sessions()
|
| 631 |
-
return list(reversed(list(s.keys()))) if s else ["No saved sessions"]
|
| 632 |
-
|
| 633 |
-
def save_session(history, name):
|
| 634 |
-
if not history: return "Nothing to save", gr.update()
|
| 635 |
-
if not name or not name.strip():
|
| 636 |
-
name = "Chat " + datetime.now().strftime("%b %d %H:%M")
|
| 637 |
sessions = load_all_sessions()
|
| 638 |
-
|
| 639 |
-
|
| 640 |
-
|
| 641 |
-
return ("Saved: " + name if ok else "Save failed"), gr.update(choices=choices, value=name)
|
| 642 |
|
| 643 |
-
def load_session(
|
| 644 |
-
if not
|
|
|
|
| 645 |
sessions = load_all_sessions()
|
| 646 |
-
|
| 647 |
-
|
| 648 |
-
|
| 649 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 650 |
sessions = load_all_sessions()
|
| 651 |
-
|
| 652 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 653 |
save_all_sessions(sessions)
|
| 654 |
-
|
| 655 |
-
return "Deleted: " +
|
| 656 |
-
return "
|
| 657 |
-
|
| 658 |
-
def new_chat(): return [], "", "New chat started"
|
| 659 |
|
| 660 |
-
# ──
|
| 661 |
-
def
|
| 662 |
try:
|
| 663 |
-
r = requests.get(
|
| 664 |
-
"
|
| 665 |
-
params={"db":"pubmed","term":query+" AND (heart valve OR hemodynamics OR microfluidic OR thrombogen OR creatinine OR CKD)","retmax":n,"retmode":"json","sort":"date","field":"tiab"},
|
| 666 |
-
timeout=10
|
| 667 |
-
)
|
| 668 |
ids = r.json()["esearchresult"]["idlist"]
|
| 669 |
-
|
|
|
|
| 670 |
except: return ""
|
| 671 |
|
| 672 |
-
def
|
| 673 |
-
if not GROQ_KEY: return query
|
| 674 |
-
try:
|
| 675 |
-
client = Groq(api_key=GROQ_KEY)
|
| 676 |
-
resp = client.chat.completions.create(
|
| 677 |
-
model="llama-3.1-8b-instant",
|
| 678 |
-
messages=[
|
| 679 |
-
{"role":"system","content":"Biomedical PubMed expert. Convert to MeSH terms for heart valves hemodynamics PIV thrombogenicity FSI microfluidics CKD. Return ONLY terms."},
|
| 680 |
-
{"role":"user","content":"Optimize: " + query}
|
| 681 |
-
],
|
| 682 |
-
max_tokens=80
|
| 683 |
-
)
|
| 684 |
-
return resp.choices[0].message.content.strip() or query
|
| 685 |
-
except: return query
|
| 686 |
-
|
| 687 |
-
def quick_search(query, search_model="Llama 3.3 70B (Best)"):
|
| 688 |
if not query.strip(): return "Please enter a topic."
|
| 689 |
-
|
| 690 |
-
results = []
|
| 691 |
-
try:
|
| 692 |
-
forced = expanded + " AND (heart valve OR hemodynamics OR microfluidic OR thrombogen OR creatinine OR PIV OR CKD)"
|
| 693 |
-
r = requests.get("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi",
|
| 694 |
-
params={"db":"pubmed","term":forced,"retmax":8,"retmode":"json","sort":"date","field":"tiab"},timeout=12)
|
| 695 |
-
ids = r.json()["esearchresult"]["idlist"]
|
| 696 |
-
if ids:
|
| 697 |
-
r2 = requests.get("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi",
|
| 698 |
-
params={"db":"pubmed","id":",".join(ids),"retmode":"xml","rettype":"abstract"},timeout=12)
|
| 699 |
-
import xml.etree.ElementTree as ET
|
| 700 |
-
root = ET.fromstring(r2.content)
|
| 701 |
-
for article in root.findall(".//PubmedArticle"):
|
| 702 |
-
try:
|
| 703 |
-
title = article.find(".//ArticleTitle").text or "No title"
|
| 704 |
-
pmid = article.find(".//PMID").text or ""
|
| 705 |
-
year_el = article.find(".//PubDate/Year")
|
| 706 |
-
year = year_el.text if year_el is not None else ""
|
| 707 |
-
results.append({"source":"PubMed","title":str(title),"year":year,"url":"https://pubmed.ncbi.nlm.nih.gov/"+pmid})
|
| 708 |
-
except: continue
|
| 709 |
-
except: pass
|
| 710 |
try:
|
| 711 |
r = requests.get("https://api.semanticscholar.org/graph/v1/paper/search",
|
| 712 |
-
params={"query":
|
| 713 |
-
|
| 714 |
-
|
| 715 |
-
|
| 716 |
-
|
| 717 |
-
except: pass
|
| 718 |
-
out = "QUERY: " + query + chr(10) + "AI EXPANDED: " + expanded + chr(10) + "="*45 + chr(10) + chr(10)
|
| 719 |
-
groups = {"PubMed":[],"Scholar":[]}
|
| 720 |
-
seen = set()
|
| 721 |
-
for r in results:
|
| 722 |
-
key = r["title"][:50].lower()
|
| 723 |
-
if key not in seen and r.get("url"):
|
| 724 |
-
seen.add(key); groups.get(r["source"],[]).append(r)
|
| 725 |
-
for source, papers in groups.items():
|
| 726 |
-
if not papers: continue
|
| 727 |
-
out += "--- " + source + " ---" + chr(10)
|
| 728 |
-
for p in papers[:8]:
|
| 729 |
-
out += p["title"][:85] + " (" + p["year"] + ")" + chr(10)
|
| 730 |
-
out += " " + p.get("url","") + chr(10) + chr(10)
|
| 731 |
-
out += "--- SJSU ScholarWorks ---" + chr(10)
|
| 732 |
-
out += "https://scholarworks.sjsu.edu/do/search/?q=" + requests.utils.quote(query) + "&context=6781027"
|
| 733 |
-
return out
|
| 734 |
-
|
| 735 |
-
# ── CHAT ───────────────────────────────────────────────────
|
| 736 |
-
def answer_with_cardiolab_model(question, paper_context=""):
|
| 737 |
-
if not CARDIOLAB_MODEL_LOADED: return None
|
| 738 |
-
try:
|
| 739 |
-
import torch
|
| 740 |
-
system = "You are CardioLab AI for SJSU Biomedical Engineering."
|
| 741 |
-
if paper_context:
|
| 742 |
-
system += " Use these SJSU research papers: " + paper_context[:400]
|
| 743 |
-
prompt = "<|system|>" + system + "</s><|user|>" + question + "</s><|assistant|>"
|
| 744 |
-
inputs = CARDIOLAB_TOKENIZER(prompt, return_tensors="pt", truncation=True, max_length=512)
|
| 745 |
-
device = next(CARDIOLAB_LLM.parameters()).device
|
| 746 |
-
inputs = {k: v.to(device) for k, v in inputs.items()}
|
| 747 |
-
with torch.no_grad():
|
| 748 |
-
outputs = CARDIOLAB_LLM.generate(
|
| 749 |
-
**inputs, max_new_tokens=200, do_sample=True,
|
| 750 |
-
temperature=0.3, pad_token_id=CARDIOLAB_TOKENIZER.eos_token_id
|
| 751 |
-
)
|
| 752 |
-
response = CARDIOLAB_TOKENIZER.decode(outputs[0], skip_special_tokens=True)
|
| 753 |
-
answer = response.split("<|assistant|>")[-1].strip() if "<|assistant|>" in response else response[-300:].strip()
|
| 754 |
-
return answer if len(answer) > 20 else None
|
| 755 |
-
except Exception as e:
|
| 756 |
-
print("CardioLab model error: " + str(e))
|
| 757 |
-
return None
|
| 758 |
|
| 759 |
-
def research_chat(message, history
|
| 760 |
-
if not message.strip(): return "", history
|
| 761 |
-
paper_context, paper_results = search_papers(message, n=4)
|
| 762 |
-
if chat_model == "CardioLab Fine-tuned (SJSU)" and CARDIOLAB_MODEL_LOADED:
|
| 763 |
-
answer = answer_with_cardiolab_model(message, paper_context)
|
| 764 |
-
if answer:
|
| 765 |
-
if paper_results:
|
| 766 |
-
unique_papers = list(dict.fromkeys([r["paper"] for r in paper_results]))
|
| 767 |
-
answer += chr(10) + chr(10) + "Sources from SJSU CardioLab papers:"
|
| 768 |
-
for p in unique_papers[:3]:
|
| 769 |
-
answer += chr(10) + " - " + p.replace(".pdf","").replace("_"," ")
|
| 770 |
-
pubmed = get_pubmed_chat(message, n=2)
|
| 771 |
-
if pubmed: answer += chr(10) + "PubMed: " + pubmed
|
| 772 |
-
history.append({"role":"user","content":message})
|
| 773 |
-
history.append({"role":"assistant","content":"[CardioLab Fine-tuned] " + answer})
|
| 774 |
-
return "", history
|
| 775 |
if not GROQ_KEY:
|
| 776 |
history.append({"role":"user","content":message})
|
| 777 |
-
history.append({"role":"assistant","content":"Error: Add GROQ_API_KEY to Space Settings."})
|
| 778 |
return "", history
|
| 779 |
try:
|
| 780 |
-
model_id = CHAT_MODELS.get(chat_model, "llama-3.3-70b-versatile")
|
| 781 |
client = Groq(api_key=GROQ_KEY)
|
| 782 |
-
|
| 783 |
-
system_prompt = (
|
| 784 |
-
"You are CardioLab AI for SJSU Biomedical Engineering. "
|
| 785 |
-
"Answer using SJSU CardioLab research papers below. "
|
| 786 |
-
"Always cite the paper name when using specific data." +
|
| 787 |
-
chr(10) + chr(10) + "SJSU CARDIOLAB PAPERS:" + chr(10) + paper_context +
|
| 788 |
-
chr(10) + chr(10) + "ADDITIONAL KNOWLEDGE: " + KNOWHOW
|
| 789 |
-
)
|
| 790 |
-
else:
|
| 791 |
-
system_prompt = "You are CardioLab AI for SJSU Biomedical Engineering. Expert in MHV MCL PIV TGT uPAD CKD FSI. " + KNOWHOW
|
| 792 |
-
msgs = [{"role":"system","content":system_prompt}]
|
| 793 |
for item in history:
|
| 794 |
if isinstance(item, dict): msgs.append({"role":item["role"],"content":item["content"]})
|
| 795 |
msgs.append({"role":"user","content":message})
|
| 796 |
-
resp = client.chat.completions.create(model=
|
| 797 |
answer = resp.choices[0].message.content
|
| 798 |
-
|
| 799 |
-
|
| 800 |
-
answer += chr(10) + chr(10) + "Sources from SJSU CardioLab papers:"
|
| 801 |
-
for p in unique_papers[:3]:
|
| 802 |
-
answer += chr(10) + " - " + p.replace(".pdf","").replace("_"," ")
|
| 803 |
-
pubmed = get_pubmed_chat(message, n=2)
|
| 804 |
-
if pubmed: answer += chr(10) + "PubMed: " + pubmed
|
| 805 |
history.append({"role":"user","content":message})
|
| 806 |
history.append({"role":"assistant","content":answer})
|
| 807 |
return "", history
|
| 808 |
except Exception as e:
|
| 809 |
history.append({"role":"user","content":message})
|
| 810 |
-
history.append({"role":"assistant","content":"Error: "
|
| 811 |
return "", history
|
| 812 |
|
| 813 |
def voice_chat(audio, history):
|
|
@@ -818,384 +167,263 @@ def voice_chat(audio, history):
|
|
| 818 |
client = Groq(api_key=GROQ_KEY)
|
| 819 |
with open(audio, "rb") as f:
|
| 820 |
tx = client.audio.transcriptions.create(file=("audio.wav", f, "audio/wav"), model="whisper-large-v3")
|
| 821 |
-
|
| 822 |
-
system = "You are CardioLab AI. " + KNOWHOW
|
| 823 |
-
if paper_context:
|
| 824 |
-
system = "You are CardioLab AI. Use these SJSU papers:" + chr(10) + paper_context + chr(10) + KNOWHOW
|
| 825 |
-
msgs = [{"role":"system","content":system}]
|
| 826 |
for item in history:
|
| 827 |
if isinstance(item, dict): msgs.append({"role":item["role"],"content":item["content"]})
|
| 828 |
msgs.append({"role":"user","content":tx.text})
|
| 829 |
-
resp = client.chat.completions.create(model="llama-3.3-70b-versatile",
|
| 830 |
-
history.append({"role":"user","content":"Voice
|
| 831 |
history.append({"role":"assistant","content":resp.choices[0].message.content})
|
| 832 |
return history
|
| 833 |
except Exception as e:
|
| 834 |
-
history.append({"role":"assistant","content":"Voice error: "
|
| 835 |
return history
|
| 836 |
|
| 837 |
-
# ──
|
| 838 |
-
def generate_protocol(experiment_type, specific_params):
|
| 839 |
-
if not GROQ_KEY: return "Error: Add GROQ_API_KEY to Space Settings."
|
| 840 |
-
if not experiment_type: return "Please select an experiment type."
|
| 841 |
-
try:
|
| 842 |
-
client = Groq(api_key=GROQ_KEY)
|
| 843 |
-
paper_context, _ = search_papers(experiment_type, n=4)
|
| 844 |
-
lab_ctx = {
|
| 845 |
-
"MCL": "Sylgard 184 PDMS 10:1 ratio 48hr cure. Tygon tubing. 70bpm 5L/min 80-120mmHg.",
|
| 846 |
-
"PIV": "Green laser 532nm time-resolved. Normal velocity 0.5-2.0 m/s. Shear below 5 Pa.",
|
| 847 |
-
"Thrombogenicity": "Arduino Uno stepper motor 48V. 150mL fresh blood. Sample at 0 20 40 60 min. Heska HT5. Measures TAT PF1.2 free hemoglobin platelets. TAT normal below 8 ng/mL. PF1.2 normal below 2.0 nmol/L.",
|
| 848 |
-
"uPAD": "Whatman filter paper. Wax printer 120C. Picric acid alkaline solution. Jaffe reaction.",
|
| 849 |
-
"FSI": "COMSOL Multiphysics ALE mesh. Blood 1060 kg/m3 0.0035 Pa.s. SJM bileaflet geometry.",
|
| 850 |
-
}
|
| 851 |
-
extra = next((v for k, v in lab_ctx.items() if k.lower() in experiment_type.lower()), "")
|
| 852 |
-
system_msg = (
|
| 853 |
-
"You are CardioLab AI protocol generator for SJSU Biomedical Engineering. "
|
| 854 |
-
"Generate a COMPLETE detailed lab protocol with sections: "
|
| 855 |
-
"1. OBJECTIVE 2. MATERIALS AND EQUIPMENT with exact quantities "
|
| 856 |
-
"3. SAFETY CONSIDERATIONS 4. STEP-BY-STEP PROCEDURE numbered "
|
| 857 |
-
"5. DATA COLLECTION 6. ANALYSIS METHOD "
|
| 858 |
-
"7. EXPECTED RESULTS with CardioLab normal ranges 8. TROUBLESHOOTING "
|
| 859 |
-
"Use exact SJSU CardioLab values."
|
| 860 |
-
)
|
| 861 |
-
user_msg = "Generate complete protocol for: " + experiment_type
|
| 862 |
-
if specific_params and specific_params.strip():
|
| 863 |
-
user_msg += chr(10) + "Parameters: " + specific_params
|
| 864 |
-
if extra:
|
| 865 |
-
user_msg += chr(10) + "CardioLab context: " + extra
|
| 866 |
-
if paper_context:
|
| 867 |
-
user_msg += chr(10) + "From SJSU papers: " + paper_context[:600]
|
| 868 |
-
resp = client.chat.completions.create(
|
| 869 |
-
model="llama-3.3-70b-versatile",
|
| 870 |
-
messages=[{"role":"system","content":system_msg},{"role":"user","content":user_msg}],
|
| 871 |
-
max_tokens=1200
|
| 872 |
-
)
|
| 873 |
-
return resp.choices[0].message.content
|
| 874 |
-
except Exception as e:
|
| 875 |
-
return "Error: " + str(e)
|
| 876 |
-
|
| 877 |
-
def generate_report(data_description, experiment_type, results):
|
| 878 |
-
if not GROQ_KEY: return "Error: Add GROQ_API_KEY to Space Settings."
|
| 879 |
-
if not experiment_type: return "Please select a study type."
|
| 880 |
-
try:
|
| 881 |
-
client = Groq(api_key=GROQ_KEY)
|
| 882 |
-
paper_context, _ = search_papers(experiment_type, n=3)
|
| 883 |
-
system_msg = (
|
| 884 |
-
"You are CardioLab AI report writer for SJSU Biomedical Engineering. "
|
| 885 |
-
"Generate a professional research report with sections: "
|
| 886 |
-
"1. ABSTRACT 150 words 2. INTRODUCTION background and objectives "
|
| 887 |
-
"3. MATERIALS AND METHODS 4. RESULTS AND DISCUSSION "
|
| 888 |
-
"5. CONCLUSION 6. RECOMMENDATIONS 7. REFERENCES cite SJSU CardioLab papers. "
|
| 889 |
-
"Use specific values. Write in professional academic style."
|
| 890 |
-
)
|
| 891 |
-
user_msg = "Write research report for: " + experiment_type
|
| 892 |
-
if data_description and data_description.strip():
|
| 893 |
-
user_msg += chr(10) + "Description: " + data_description
|
| 894 |
-
if results and results.strip():
|
| 895 |
-
user_msg += chr(10) + "Results: " + results
|
| 896 |
-
if paper_context:
|
| 897 |
-
user_msg += chr(10) + "SJSU papers: " + paper_context[:600]
|
| 898 |
-
resp = client.chat.completions.create(
|
| 899 |
-
model="llama-3.3-70b-versatile",
|
| 900 |
-
messages=[{"role":"system","content":system_msg},{"role":"user","content":user_msg}],
|
| 901 |
-
max_tokens=1500
|
| 902 |
-
)
|
| 903 |
-
return resp.choices[0].message.content
|
| 904 |
-
except Exception as e:
|
| 905 |
-
return "Error: " + str(e)
|
| 906 |
-
|
| 907 |
-
def generate_hypothesis(research_area, current_findings):
|
| 908 |
-
if not GROQ_KEY: return "Error: Add GROQ_API_KEY to Space Settings."
|
| 909 |
-
if not research_area: return "Please select a research area."
|
| 910 |
-
try:
|
| 911 |
-
client = Groq(api_key=GROQ_KEY)
|
| 912 |
-
paper_context, _ = search_papers(research_area, n=3)
|
| 913 |
-
system_msg = (
|
| 914 |
-
"You are CardioLab AI research assistant for SJSU Biomedical Engineering. "
|
| 915 |
-
"Generate 3 specific testable research hypotheses. For each provide: "
|
| 916 |
-
"H0 null hypothesis, H1 alternative hypothesis, Scientific rationale, "
|
| 917 |
-
"Suggested experiment, Expected outcome and measurable metrics. "
|
| 918 |
-
"Base on SJSU CardioLab research."
|
| 919 |
-
)
|
| 920 |
-
user_msg = "Generate hypotheses for: " + research_area
|
| 921 |
-
if current_findings and current_findings.strip():
|
| 922 |
-
user_msg += chr(10) + "Current findings: " + current_findings
|
| 923 |
-
if paper_context:
|
| 924 |
-
user_msg += chr(10) + "SJSU papers: " + paper_context[:500]
|
| 925 |
-
resp = client.chat.completions.create(
|
| 926 |
-
model="llama-3.3-70b-versatile",
|
| 927 |
-
messages=[{"role":"system","content":system_msg},{"role":"user","content":user_msg}],
|
| 928 |
-
max_tokens=1000
|
| 929 |
-
)
|
| 930 |
-
return resp.choices[0].message.content
|
| 931 |
-
except Exception as e:
|
| 932 |
-
return "Error: " + str(e)
|
| 933 |
-
|
| 934 |
-
# ── ANALYSIS TOOLS ─────────────────────────────────────────
|
| 935 |
def analyze_upad_photo(image):
|
| 936 |
if image is None: return None, "Upload a uPAD photo first."
|
| 937 |
try:
|
| 938 |
img = Image.fromarray(image) if not isinstance(image, Image.Image) else image
|
| 939 |
-
arr = np.array(img)
|
| 940 |
-
|
| 941 |
-
|
| 942 |
-
|
| 943 |
-
G = float(np.mean(zone[:,:,1]))
|
| 944 |
-
B = float(np.mean(zone[:,:,2]))
|
| 945 |
c = max(0, round(0.018*(R-B)-0.3, 2))
|
| 946 |
-
if c
|
| 947 |
-
elif c
|
| 948 |
-
elif c
|
| 949 |
-
elif c
|
| 950 |
-
else: s,
|
| 951 |
-
|
| 952 |
import PIL.ImageDraw as D
|
| 953 |
-
D.Draw(
|
| 954 |
-
|
| 955 |
-
|
| 956 |
-
"
|
| 957 |
-
"
|
| 958 |
-
|
| 959 |
-
|
| 960 |
-
|
| 961 |
-
|
| 962 |
-
def mk_chart(fn, title, bg, fg, gc, ac, pb):
|
| 963 |
-
fig2, ax = plt.subplots(figsize=(8,5))
|
| 964 |
-
fig2.patch.set_facecolor(bg); ax.set_facecolor(pb)
|
| 965 |
-
fn(ax)
|
| 966 |
-
ax.set_title(title, color=fg, fontweight="bold", fontsize=13, pad=8)
|
| 967 |
-
ax.tick_params(colors=ac, labelsize=10)
|
| 968 |
-
ax.grid(True, alpha=0.3, color=gc, linestyle="--")
|
| 969 |
-
for sp in ["top","right"]: ax.spines[sp].set_visible(False)
|
| 970 |
-
for sp in ["bottom","left"]: ax.spines[sp].set_color(gc)
|
| 971 |
-
plt.tight_layout()
|
| 972 |
-
buf = io.BytesIO()
|
| 973 |
-
plt.savefig(buf, format="png", facecolor=bg, bbox_inches="tight", dpi=130)
|
| 974 |
-
buf.seek(0)
|
| 975 |
-
res = Image.open(buf).copy()
|
| 976 |
-
plt.close()
|
| 977 |
-
return res
|
| 978 |
|
| 979 |
def analyze_piv_csv(file, theme="White"):
|
| 980 |
-
if file is None: return None,
|
| 981 |
try:
|
| 982 |
df = pd.read_csv(file.name)
|
| 983 |
-
cols = [c.lower().strip() for c in df.columns]
|
|
|
|
| 984 |
num_cols = df.select_dtypes(include=[np.number]).columns.tolist()
|
| 985 |
-
if not num_cols: return None,
|
| 986 |
-
bg = "#
|
| 987 |
fg = "#1a202c" if theme=="White" else "white"
|
| 988 |
gc = "#e2e8f0" if theme=="White" else "#2d4a8a"
|
| 989 |
ac = "#4a5568" if theme=="White" else "#a8b2d8"
|
| 990 |
pb = "#f7fafc" if theme=="White" else "#132340"
|
| 991 |
x = np.arange(len(df))
|
| 992 |
vc = next((c for c in cols if any(k in c for k in ["vel","speed","v_mag"])), num_cols[0] if num_cols else None)
|
| 993 |
-
|
| 994 |
tc = next((c for c in cols if "time" in c or "frame" in c), None)
|
| 995 |
xv = df[tc] if tc else x
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 996 |
def pv(ax):
|
| 997 |
if vc:
|
| 998 |
-
ax.plot(xv,
|
| 999 |
-
ax.fill_between(xv,
|
| 1000 |
-
ax.axhline(y=2.0,
|
| 1001 |
-
ax.set_ylabel("Velocity (m/s)",
|
| 1002 |
-
ax.
|
|
|
|
| 1003 |
def ps(ax):
|
| 1004 |
-
if
|
| 1005 |
xp = xv.values if tc else x
|
| 1006 |
-
ax.plot(xp,
|
| 1007 |
-
ax.fill_between(xp,
|
| 1008 |
-
ax.axhline(y=5,
|
| 1009 |
-
ax.axhline(y=10,
|
| 1010 |
-
ax.set_ylabel("Shear (Pa)",
|
| 1011 |
-
ax.
|
|
|
|
| 1012 |
def psc(ax):
|
| 1013 |
-
if vc and
|
| 1014 |
-
|
| 1015 |
-
cb
|
| 1016 |
-
|
| 1017 |
-
ax.
|
| 1018 |
-
ax.
|
| 1019 |
-
ax.
|
|
|
|
| 1020 |
def psum(ax):
|
| 1021 |
-
ax.axis("off"); risk
|
| 1022 |
-
st
|
| 1023 |
for col in num_cols[:3]:
|
| 1024 |
-
mn
|
| 1025 |
-
st
|
| 1026 |
-
if "vel" in col and mx
|
| 1027 |
-
if "shear" in col and mx
|
| 1028 |
-
|
| 1029 |
-
|
| 1030 |
-
|
| 1031 |
-
|
| 1032 |
-
|
| 1033 |
-
|
| 1034 |
-
|
| 1035 |
-
|
| 1036 |
-
|
|
|
|
|
|
|
| 1037 |
if GROQ_KEY:
|
| 1038 |
try:
|
| 1039 |
-
client
|
| 1040 |
-
resp
|
| 1041 |
-
|
| 1042 |
-
|
| 1043 |
-
|
| 1044 |
-
max_tokens=250
|
| 1045 |
-
)
|
| 1046 |
-
ai = chr(10) + "AI: " + resp.choices[0].message.content
|
| 1047 |
except: pass
|
| 1048 |
-
return i1,
|
| 1049 |
-
except Exception as e:
|
| 1050 |
-
return None, None, None, None, "Error: " + str(e)
|
| 1051 |
|
| 1052 |
def analyze_tgt_csv(file, theme="White"):
|
| 1053 |
-
if file is None: return None,
|
| 1054 |
try:
|
| 1055 |
df = pd.read_csv(file.name)
|
| 1056 |
-
cols = [c.lower().strip() for c in df.columns]
|
|
|
|
| 1057 |
num_cols = df.select_dtypes(include=[np.number]).columns.tolist()
|
| 1058 |
-
bg
|
| 1059 |
-
fg
|
| 1060 |
-
gc
|
| 1061 |
-
ac
|
| 1062 |
-
pb
|
| 1063 |
-
tc
|
| 1064 |
-
tatc
|
| 1065 |
-
pfc
|
| 1066 |
-
hc
|
| 1067 |
-
plc
|
| 1068 |
-
|
| 1069 |
-
|
| 1070 |
-
|
| 1071 |
-
|
| 1072 |
-
|
| 1073 |
-
|
| 1074 |
-
|
| 1075 |
-
|
| 1076 |
-
|
| 1077 |
-
|
| 1078 |
-
|
| 1079 |
-
|
| 1080 |
-
|
| 1081 |
-
|
| 1082 |
-
|
| 1083 |
-
|
| 1084 |
-
|
| 1085 |
-
|
| 1086 |
-
|
| 1087 |
-
|
| 1088 |
-
|
| 1089 |
-
|
| 1090 |
-
|
| 1091 |
-
|
| 1092 |
-
|
| 1093 |
-
|
| 1094 |
-
|
| 1095 |
-
|
|
|
|
| 1096 |
if GROQ_KEY:
|
| 1097 |
try:
|
| 1098 |
-
client
|
| 1099 |
-
resp
|
| 1100 |
-
|
| 1101 |
-
|
| 1102 |
-
|
| 1103 |
-
max_tokens=250
|
| 1104 |
-
)
|
| 1105 |
-
ai = chr(10) + "AI: " + resp.choices[0].message.content
|
| 1106 |
except: pass
|
| 1107 |
-
return i1,
|
| 1108 |
-
except Exception as e:
|
| 1109 |
-
return None, None, None, None, "Error: " + str(e)
|
| 1110 |
|
| 1111 |
def generate_image(prompt):
|
| 1112 |
-
if not prompt.strip(): return None,
|
| 1113 |
-
if not HF_TOKEN: return None,
|
| 1114 |
try:
|
| 1115 |
-
enhanced,
|
| 1116 |
if GROQ_KEY:
|
| 1117 |
try:
|
| 1118 |
-
client
|
| 1119 |
-
resp
|
| 1120 |
-
model="llama-3.3-70b-versatile",
|
| 1121 |
messages=[{"role":"system","content":"Format: DESCRIPTION: [2 sentences] PROMPT: [detailed image prompt]"},
|
| 1122 |
-
{"role":"user","content":"Biomedical image: "
|
| 1123 |
-
|
| 1124 |
-
)
|
| 1125 |
-
full = resp.choices[0].message.content
|
| 1126 |
if "DESCRIPTION:" in full and "PROMPT:" in full:
|
| 1127 |
-
desc
|
| 1128 |
-
enhanced
|
| 1129 |
except: pass
|
| 1130 |
-
headers
|
| 1131 |
-
for url in [
|
| 1132 |
-
|
| 1133 |
-
"https://router.huggingface.co/hf-inference/models/stabilityai/stable-diffusion-xl-base-1.0"
|
| 1134 |
-
]:
|
| 1135 |
try:
|
| 1136 |
-
r
|
| 1137 |
-
|
| 1138 |
-
if r.status_code == 200:
|
| 1139 |
-
return Image.open(io.BytesIO(r.content)), "Generated!", desc
|
| 1140 |
except: continue
|
| 1141 |
-
return None,
|
| 1142 |
-
except Exception as e:
|
| 1143 |
-
return None, "Error: " + str(e), ""
|
| 1144 |
|
| 1145 |
-
def piv_manual(v,
|
| 1146 |
-
vr
|
| 1147 |
-
sr
|
| 1148 |
-
return "Velocity: "
|
| 1149 |
|
| 1150 |
-
def tgt_manual(t,
|
| 1151 |
-
risk
|
| 1152 |
-
return
|
| 1153 |
-
"Hemo:" + str(h) + " Plt:" + str(pl) + chr(10) +
|
| 1154 |
-
"RESULT: " + ("HIGH RISK" if risk>=3 else "MODERATE" if risk>=2 else "LOW RISK"))
|
| 1155 |
|
| 1156 |
-
# ──
|
| 1157 |
-
with gr.Blocks(title="CardioLab AI
|
| 1158 |
-
gr.HTML(
|
| 1159 |
-
gr.HTML(STATUS_BANNER)
|
| 1160 |
|
| 1161 |
with gr.Tabs():
|
| 1162 |
|
| 1163 |
with gr.Tab("Chat"):
|
|
|
|
| 1164 |
with gr.Row():
|
| 1165 |
-
with gr.Column(scale=
|
| 1166 |
-
gr.
|
| 1167 |
-
new_chat_btn = gr.Button("New Chat", variant="secondary")
|
| 1168 |
-
session_dropdown = gr.Dropdown(choices=get_session_list(), label="Saved Sessions", interactive=True, allow_custom_value=True)
|
| 1169 |
-
load_btn = gr.Button("Load Session", variant="primary")
|
| 1170 |
-
session_name_box = gr.Textbox(placeholder="Session name...", label="", lines=1, container=False)
|
| 1171 |
-
with gr.Row():
|
| 1172 |
-
save_btn = gr.Button("Save", variant="primary", scale=2)
|
| 1173 |
-
delete_btn = gr.Button("Del", variant="secondary", scale=1)
|
| 1174 |
-
session_status = gr.Textbox(label="", lines=1, interactive=False, container=False)
|
| 1175 |
-
with gr.Column(scale=4):
|
| 1176 |
-
chatbot = gr.Chatbot(label="", height=460, show_label=False, container=False)
|
| 1177 |
with gr.Row():
|
| 1178 |
-
msg_box = gr.Textbox(
|
| 1179 |
-
|
| 1180 |
-
label="", lines=2, scale=4, container=False
|
| 1181 |
-
)
|
| 1182 |
-
with gr.Column(scale=1, min_width=160):
|
| 1183 |
-
chat_model_dd = gr.Radio(
|
| 1184 |
-
choices=list(CHAT_MODELS.keys()),
|
| 1185 |
-
value="Llama 3.3 70B (Best)", label="AI Model"
|
| 1186 |
-
)
|
| 1187 |
send_btn = gr.Button("Send", variant="primary")
|
| 1188 |
clear_btn = gr.Button("Clear", variant="secondary")
|
| 1189 |
-
|
| 1190 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1191 |
clear_btn.click(lambda: ([], ""), outputs=[chatbot, msg_box])
|
| 1192 |
-
new_chat_btn.click(new_chat, outputs=[chatbot, msg_box, session_status])
|
| 1193 |
save_btn.click(save_session, inputs=[chatbot, session_name_box], outputs=[session_status, session_dropdown])
|
| 1194 |
load_btn.click(load_session, inputs=session_dropdown, outputs=[chatbot, session_status])
|
| 1195 |
delete_btn.click(delete_session, inputs=session_dropdown, outputs=[session_status, session_dropdown])
|
| 1196 |
|
| 1197 |
with gr.Tab("Voice"):
|
| 1198 |
-
voice_chatbot = gr.Chatbot(label="", height=
|
| 1199 |
audio_input = gr.Audio(sources=["microphone"], type="filepath", label="Record Question")
|
| 1200 |
with gr.Row():
|
| 1201 |
voice_btn = gr.Button("Ask by Voice", variant="primary")
|
|
@@ -1204,177 +432,93 @@ with gr.Blocks(title="CardioLab AI v39 - SJSU", css=CSS) as demo:
|
|
| 1204 |
voice_clear.click(lambda: [], outputs=voice_chatbot)
|
| 1205 |
|
| 1206 |
with gr.Tab("Papers"):
|
| 1207 |
-
gr.Markdown("### Search PubMed + Semantic Scholar + SJSU ScholarWorks")
|
| 1208 |
with gr.Row():
|
| 1209 |
-
search_input = gr.Textbox(
|
| 1210 |
-
placeholder="e.g. bileaflet mechanical heart valve thrombogenicity hemodynamics",
|
| 1211 |
-
label="Research Topic", scale=3
|
| 1212 |
-
)
|
| 1213 |
-
search_model_dd = gr.Dropdown(
|
| 1214 |
-
choices=list(CHAT_MODELS.keys()),
|
| 1215 |
-
value="Llama 3.3 70B (Best)", label="AI Model", scale=1
|
| 1216 |
-
)
|
| 1217 |
search_btn = gr.Button("Search", variant="primary", scale=1)
|
| 1218 |
-
search_output = gr.Textbox(label="Results", lines=
|
| 1219 |
-
search_btn.click(quick_search, inputs=
|
| 1220 |
-
search_input.submit(quick_search, inputs=
|
| 1221 |
|
| 1222 |
with gr.Tab("PIV CSV"):
|
|
|
|
| 1223 |
with gr.Row():
|
| 1224 |
-
piv_file = gr.File(label="
|
| 1225 |
piv_theme = gr.Radio(["White","Dark"], value="White", label="Theme", scale=1)
|
| 1226 |
piv_btn = gr.Button("Analyze PIV Data", variant="primary")
|
| 1227 |
-
piv_result = gr.Textbox(label="AI Analysis", lines=
|
| 1228 |
with gr.Row():
|
| 1229 |
-
piv_c1 = gr.Image(label="Velocity", type="pil")
|
| 1230 |
piv_c2 = gr.Image(label="Shear Stress", type="pil")
|
| 1231 |
with gr.Row():
|
| 1232 |
-
piv_c3 = gr.Image(label="
|
| 1233 |
piv_c4 = gr.Image(label="Clinical Summary", type="pil")
|
| 1234 |
-
piv_btn.click(analyze_piv_csv, inputs=[piv_file,
|
| 1235 |
|
| 1236 |
with gr.Tab("TGT CSV"):
|
|
|
|
| 1237 |
with gr.Row():
|
| 1238 |
-
tgt_file = gr.File(label="
|
| 1239 |
tgt_theme = gr.Radio(["White","Dark"], value="White", label="Theme", scale=1)
|
| 1240 |
tgt_btn = gr.Button("Analyze TGT Data", variant="primary")
|
| 1241 |
-
tgt_result = gr.Textbox(label="AI Assessment", lines=
|
| 1242 |
with gr.Row():
|
| 1243 |
-
tgt_c1 = gr.Image(label="TAT", type="pil")
|
| 1244 |
-
tgt_c2 = gr.Image(label="PF1.2", type="pil")
|
| 1245 |
with gr.Row():
|
| 1246 |
-
tgt_c3 = gr.Image(label="Hemoglobin", type="pil")
|
| 1247 |
-
tgt_c4 = gr.Image(label="
|
| 1248 |
-
tgt_btn.click(analyze_tgt_csv, inputs=[tgt_file,
|
| 1249 |
|
| 1250 |
-
with gr.Tab("uPAD"):
|
|
|
|
| 1251 |
with gr.Row():
|
| 1252 |
with gr.Column():
|
| 1253 |
-
photo_input = gr.Image(label="Upload uPAD Photo", type="numpy", height=
|
| 1254 |
analyze_btn = gr.Button("Analyze uPAD", variant="primary")
|
| 1255 |
with gr.Column():
|
| 1256 |
-
photo_img = gr.Image(label="Detection Zone", type="pil", height=
|
| 1257 |
-
photo_text = gr.Textbox(label="CKD Result", lines=
|
| 1258 |
analyze_btn.click(analyze_upad_photo, inputs=photo_input, outputs=[photo_img, photo_text])
|
| 1259 |
-
with gr.Row():
|
| 1260 |
-
r = gr.Number(label="R", value=210)
|
| 1261 |
-
g = gr.Number(label="G", value=140)
|
| 1262 |
-
b = gr.Number(label="B", value=80)
|
| 1263 |
-
out3 = gr.Textbox(label="Manual Result", lines=3)
|
| 1264 |
-
gr.Button("Analyze RGB", variant="secondary").click(
|
| 1265 |
-
lambda r, g, b: (
|
| 1266 |
-
"Creatinine: " + str(max(0, round(0.02*(r-b)-0.5, 2))) + " mg/dL" + chr(10) +
|
| 1267 |
-
("Normal" if max(0, round(0.02*(r-b)-0.5, 2)) < 1.2
|
| 1268 |
-
else "Borderline" if max(0, round(0.02*(r-b)-0.5, 2)) < 1.5
|
| 1269 |
-
else "CKD")
|
| 1270 |
-
),
|
| 1271 |
-
inputs=[r, g, b], outputs=out3
|
| 1272 |
-
)
|
| 1273 |
|
| 1274 |
with gr.Tab("AI Image"):
|
| 1275 |
with gr.Row():
|
| 1276 |
-
img_prompt = gr.Textbox(
|
| 1277 |
-
placeholder="e.g. 27mm bileaflet mechanical heart valve cross section",
|
| 1278 |
-
label="Describe image", lines=2, scale=4
|
| 1279 |
-
)
|
| 1280 |
with gr.Column(scale=1):
|
| 1281 |
img_btn = gr.Button("Generate", variant="primary")
|
| 1282 |
img_status = gr.Textbox(label="Status", lines=1)
|
| 1283 |
img_desc = gr.Textbox(label="AI Description", lines=2, interactive=False)
|
| 1284 |
-
img_output = gr.Image(label="Generated Image", type="pil", height=
|
| 1285 |
-
img_btn.click(generate_image, inputs=img_prompt, outputs=[img_output,
|
| 1286 |
|
| 1287 |
with gr.Tab("PIV Manual"):
|
| 1288 |
with gr.Row():
|
| 1289 |
with gr.Column():
|
| 1290 |
-
v
|
| 1291 |
-
s
|
| 1292 |
-
h
|
| 1293 |
-
piv_out
|
| 1294 |
-
gr.Button("Analyze PIV",
|
| 1295 |
|
| 1296 |
with gr.Tab("TGT Manual"):
|
| 1297 |
with gr.Row():
|
| 1298 |
with gr.Column():
|
| 1299 |
-
t1
|
| 1300 |
-
t2
|
| 1301 |
-
t3
|
| 1302 |
-
t4
|
| 1303 |
-
t5
|
| 1304 |
-
out2
|
| 1305 |
-
gr.Button("Analyze TGT",
|
| 1306 |
-
|
| 1307 |
-
with gr.Tab("
|
| 1308 |
-
gr.Markdown("### Generate complete lab protocols from SJSU CardioLab knowledge")
|
| 1309 |
-
with gr.Row():
|
| 1310 |
-
with gr.Column(scale=1):
|
| 1311 |
-
proto_type = gr.Dropdown(
|
| 1312 |
-
choices=[
|
| 1313 |
-
"MCL Setup", "PIV Experiment",
|
| 1314 |
-
"Thrombogenicity Tester Blood Clotting Test",
|
| 1315 |
-
"uPAD Fabrication", "uPAD Creatinine Test",
|
| 1316 |
-
"FSI COMSOL Simulation", "Valve Testing"
|
| 1317 |
-
],
|
| 1318 |
-
value="Thrombogenicity Tester Blood Clotting Test",
|
| 1319 |
-
label="Experiment Type"
|
| 1320 |
-
)
|
| 1321 |
-
proto_params = gr.Textbox(
|
| 1322 |
-
placeholder="e.g. 27mm SJM valve 70bpm porcine blood",
|
| 1323 |
-
label="Specific Parameters", lines=2
|
| 1324 |
-
)
|
| 1325 |
-
proto_btn = gr.Button("Generate Protocol", variant="primary")
|
| 1326 |
-
with gr.Column(scale=2):
|
| 1327 |
-
proto_output = gr.Textbox(label="Generated Protocol", lines=28)
|
| 1328 |
-
proto_btn.click(generate_protocol, inputs=[proto_type, proto_params], outputs=proto_output)
|
| 1329 |
-
|
| 1330 |
-
with gr.Tab("Report Writer"):
|
| 1331 |
-
gr.Markdown("### Generate professional research reports from your data")
|
| 1332 |
with gr.Row():
|
| 1333 |
-
with gr.Column(
|
| 1334 |
-
|
| 1335 |
-
|
| 1336 |
-
|
| 1337 |
-
|
| 1338 |
-
|
| 1339 |
-
|
| 1340 |
-
|
| 1341 |
-
)
|
| 1342 |
-
report_desc = gr.Textbox(
|
| 1343 |
-
placeholder="e.g. TGT with 27mm SJM bileaflet at 70bpm 150mL porcine blood",
|
| 1344 |
-
label="Experiment Description", lines=3
|
| 1345 |
-
)
|
| 1346 |
-
report_results = gr.Textbox(
|
| 1347 |
-
placeholder="e.g. TAT=12.3 ng/mL PF1.2=2.8 Hemo=45 Plt=142",
|
| 1348 |
-
label="Your Results", lines=2
|
| 1349 |
-
)
|
| 1350 |
-
report_btn = gr.Button("Generate Report", variant="primary")
|
| 1351 |
-
with gr.Column(scale=2):
|
| 1352 |
-
report_output = gr.Textbox(label="Generated Report", lines=28)
|
| 1353 |
-
report_btn.click(generate_report, inputs=[report_desc, report_exp, report_results], outputs=report_output)
|
| 1354 |
-
|
| 1355 |
-
with gr.Tab("Hypothesis Generator"):
|
| 1356 |
-
gr.Markdown("### Generate testable research hypotheses for CardioLab projects")
|
| 1357 |
-
with gr.Row():
|
| 1358 |
-
with gr.Column(scale=1):
|
| 1359 |
-
hyp_area = gr.Dropdown(
|
| 1360 |
-
choices=[
|
| 1361 |
-
"Bileaflet MHV Thrombogenicity",
|
| 1362 |
-
"uPAD CKD Detection Accuracy",
|
| 1363 |
-
"PIV Flow Characterization",
|
| 1364 |
-
"FSI Simulation Validation",
|
| 1365 |
-
"Valve Design Comparison"
|
| 1366 |
-
],
|
| 1367 |
-
value="Bileaflet MHV Thrombogenicity", label="Research Area"
|
| 1368 |
-
)
|
| 1369 |
-
hyp_findings = gr.Textbox(
|
| 1370 |
-
placeholder="Current observations from your experiments",
|
| 1371 |
-
label="Current Findings", lines=3
|
| 1372 |
-
)
|
| 1373 |
-
hyp_btn = gr.Button("Generate Hypotheses", variant="primary")
|
| 1374 |
-
with gr.Column(scale=2):
|
| 1375 |
-
hyp_output = gr.Textbox(label="Research Hypotheses", lines=25)
|
| 1376 |
-
hyp_btn.click(generate_hypothesis, inputs=[hyp_area, hyp_findings], outputs=hyp_output)
|
| 1377 |
-
|
| 1378 |
-
gr.HTML(FOOTER_HTML)
|
| 1379 |
|
| 1380 |
demo.launch()
|
|
|
|
| 9 |
from PIL import Image
|
| 10 |
from datetime import datetime
|
| 11 |
from huggingface_hub import HfApi, hf_hub_download
|
| 12 |
+
from huggingface_hub.utils import EntryNotFoundError
|
| 13 |
|
| 14 |
GROQ_KEY = os.environ.get("GROQ_API_KEY", "")
|
| 15 |
HF_TOKEN = os.environ.get("HF_TOKEN", "")
|
| 16 |
HISTORY_REPO = "Saicharan21/cardiolab-chat-history"
|
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|
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|
|
| 17 |
|
| 18 |
+
KNOWHOW = ("MCL: Sylgard 184 PDMS 10:1 ratio 48hr cure green laser PIV 70bpm 5L/min. "
|
| 19 |
+
"TGT: Arduino Uno Stepper Motor 150mL blood sampled at 0 20 40 60min measures TAT PF1.2 hemolysis platelets. "
|
| 20 |
+
"uPAD: Jaffe reaction creatinine plus picric acid gives orange-red color normal 0.6-1.2 mg/dL CKD above 1.5. "
|
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|
| 21 |
"MHV: 27mm SJM Regent bileaflet also trileaflet monoleaflet pediatric. "
|
| 22 |
+
"Equipment: Heska HT5 hematology analyzer time-resolved PIV Tygon tubing Arduino Uno.")
|
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|
| 23 |
|
| 24 |
CSS = """
|
| 25 |
+
body, .gradio-container { background: #f0f4f8 !important; }
|
| 26 |
+
.tab-nav { background: #ffffff !important; border-bottom: 2px solid #e2e8f0 !important; padding: 4px 5px 0 5px !important; display: flex !important; flex-wrap: wrap !important; gap: 3px !important; }
|
| 27 |
+
.tab-nav button { background: #f7fafc !important; color: #2d3748 !important; border: 1px solid #e2e8f0 !important; border-radius: 6px 6px 0 0 !important; padding: 8px 10px !important; font-weight: 600 !important; font-size: 0.8em !important; white-space: nowrap !important; }
|
| 28 |
+
.tab-nav button:hover { background: #ebf4ff !important; color: #1a237e !important; }
|
| 29 |
+
.tab-nav button.selected { background: linear-gradient(135deg, #e63946, #c1121f) !important; color: #ffffff !important; font-weight: 700 !important; }
|
| 30 |
+
button.primary { background: linear-gradient(135deg, #e63946 0%, #c1121f 100%) !important; color: white !important; border: none !important; border-radius: 8px !important; font-weight: 700 !important; }
|
| 31 |
+
button.secondary { background: #edf2f7 !important; color: #4a5568 !important; border: 1px solid #cbd5e0 !important; border-radius: 8px !important; }
|
| 32 |
+
textarea, input[type=number], input[type=text] { background: #f7fafc !important; color: #1a202c !important; border: 1px solid #cbd5e0 !important; border-radius: 8px !important; }
|
| 33 |
+
.message.user { background: linear-gradient(135deg, #e63946, #c1121f) !important; color: white !important; }
|
| 34 |
+
.message.bot { background: #ebf4ff !important; color: #1a202c !important; border: 1px solid #bee3f8 !important; }
|
| 35 |
+
label span { color: #2b6cb0 !important; font-weight: 600 !important; font-size: 0.85em !important; text-transform: uppercase !important; }
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|
| 36 |
"""
|
| 37 |
|
| 38 |
+
# ── PERSISTENT HISTORY FUNCTIONS ──────────────────────────────────
|
| 39 |
+
def get_history_api():
|
| 40 |
+
if not HF_TOKEN: return None
|
| 41 |
+
return HfApi(token=HF_TOKEN)
|
|
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| 42 |
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|
| 43 |
def load_all_sessions():
|
| 44 |
if not HF_TOKEN: return {}
|
| 45 |
try:
|
| 46 |
+
api = get_history_api()
|
| 47 |
+
path = hf_hub_download(
|
| 48 |
+
repo_id=HISTORY_REPO,
|
| 49 |
+
filename="chat_history.json",
|
| 50 |
+
repo_type="dataset",
|
| 51 |
+
token=HF_TOKEN
|
| 52 |
+
)
|
| 53 |
+
with open(path, "r") as f:
|
| 54 |
+
return json.load(f)
|
| 55 |
+
except Exception:
|
| 56 |
+
return {}
|
| 57 |
|
| 58 |
def save_all_sessions(sessions):
|
| 59 |
if not HF_TOKEN: return False
|
| 60 |
try:
|
| 61 |
+
api = get_history_api()
|
| 62 |
+
content = json.dumps(sessions, indent=2)
|
| 63 |
+
api.upload_file(
|
| 64 |
+
path_or_fileobj=content.encode(),
|
| 65 |
path_in_repo="chat_history.json",
|
| 66 |
+
repo_id=HISTORY_REPO,
|
| 67 |
+
repo_type="dataset",
|
| 68 |
+
token=HF_TOKEN,
|
| 69 |
+
commit_message="Update chat history"
|
| 70 |
)
|
| 71 |
return True
|
| 72 |
+
except Exception as e:
|
| 73 |
+
print("Save error:", e)
|
| 74 |
+
return False
|
| 75 |
|
| 76 |
def get_session_list():
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 77 |
sessions = load_all_sessions()
|
| 78 |
+
if not sessions:
|
| 79 |
+
return ["No saved sessions yet"]
|
| 80 |
+
return list(sessions.keys())
|
|
|
|
| 81 |
|
| 82 |
+
def load_session(session_name):
|
| 83 |
+
if not session_name or session_name == "No saved sessions yet":
|
| 84 |
+
return [], "No session loaded"
|
| 85 |
sessions = load_all_sessions()
|
| 86 |
+
if session_name in sessions:
|
| 87 |
+
history = sessions[session_name]["messages"]
|
| 88 |
+
return history, "Loaded: " + session_name + " (" + str(len(history)) + " messages)"
|
| 89 |
+
return [], "Session not found"
|
| 90 |
+
|
| 91 |
+
def save_session(history, session_name):
|
| 92 |
+
if not history:
|
| 93 |
+
return "Nothing to save — chat is empty", gr.update()
|
| 94 |
+
if not session_name.strip():
|
| 95 |
+
session_name = "Session " + datetime.now().strftime("%Y-%m-%d %H:%M")
|
| 96 |
sessions = load_all_sessions()
|
| 97 |
+
sessions[session_name] = {
|
| 98 |
+
"messages": history,
|
| 99 |
+
"saved_at": datetime.now().isoformat(),
|
| 100 |
+
"message_count": len(history)
|
| 101 |
+
}
|
| 102 |
+
success = save_all_sessions(sessions)
|
| 103 |
+
if success:
|
| 104 |
+
return "Saved: " + session_name, gr.update(choices=get_session_list(), value=session_name)
|
| 105 |
+
return "Save failed — check HF_TOKEN in Space secrets", gr.update()
|
| 106 |
+
|
| 107 |
+
def delete_session(session_name):
|
| 108 |
+
if not session_name or session_name == "No saved sessions yet":
|
| 109 |
+
return "No session selected", gr.update()
|
| 110 |
+
sessions = load_all_sessions()
|
| 111 |
+
if session_name in sessions:
|
| 112 |
+
del sessions[session_name]
|
| 113 |
save_all_sessions(sessions)
|
| 114 |
+
new_list = get_session_list()
|
| 115 |
+
return "Deleted: " + session_name, gr.update(choices=new_list, value=new_list[0] if new_list else None)
|
| 116 |
+
return "Session not found", gr.update()
|
|
|
|
|
|
|
| 117 |
|
| 118 |
+
# ── CHAT FUNCTIONS ────────────────────────────────────────────────
|
| 119 |
+
def get_pubmed(query, n=5):
|
| 120 |
try:
|
| 121 |
+
r = requests.get("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi",
|
| 122 |
+
params={"db":"pubmed","term":query+" AND (mechanical heart valve OR microfluidic OR CKD OR thrombogenicity)","retmax":n,"retmode":"json","sort":"date"},timeout=10)
|
|
|
|
|
|
|
|
|
|
| 123 |
ids = r.json()["esearchresult"]["idlist"]
|
| 124 |
+
if not ids: return ""
|
| 125 |
+
return chr(10).join(["https://pubmed.ncbi.nlm.nih.gov/"+i for i in ids])
|
| 126 |
except: return ""
|
| 127 |
|
| 128 |
+
def quick_search(query):
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| 129 |
if not query.strip(): return "Please enter a topic."
|
| 130 |
+
pubmed = get_pubmed(query, n=8)
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| 131 |
try:
|
| 132 |
r = requests.get("https://api.semanticscholar.org/graph/v1/paper/search",
|
| 133 |
+
params={"query":query+" biomedical","limit":5,"fields":"title,year,url"},timeout=10)
|
| 134 |
+
papers = r.json().get("data",[])
|
| 135 |
+
scholar = chr(10).join([p.get("title","")[:80]+" ("+str(p.get("year",""))+")"+chr(10)+" "+p.get("url","") for p in papers if p.get("url","")])
|
| 136 |
+
except: scholar = ""
|
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+
return "PUBMED:"+chr(10)+pubmed+chr(10)+chr(10)+"SCHOLAR:"+chr(10)+scholar
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| 138 |
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| 139 |
+
def research_chat(message, history):
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| 140 |
if not GROQ_KEY:
|
| 141 |
history.append({"role":"user","content":message})
|
| 142 |
+
history.append({"role":"assistant","content":"Error: Add GROQ_API_KEY to Space Settings Secrets."})
|
| 143 |
return "", history
|
| 144 |
try:
|
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|
| 145 |
client = Groq(api_key=GROQ_KEY)
|
| 146 |
+
msgs = [{"role":"system","content":"You are CardioLab AI. Expert in MHV MCL PIV TGT uPAD CKD FSI. Remember full conversation. Never invent URLs. "+KNOWHOW}]
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| 147 |
for item in history:
|
| 148 |
if isinstance(item, dict): msgs.append({"role":item["role"],"content":item["content"]})
|
| 149 |
msgs.append({"role":"user","content":message})
|
| 150 |
+
resp = client.chat.completions.create(model="llama-3.3-70b-versatile",messages=msgs,max_tokens=700)
|
| 151 |
answer = resp.choices[0].message.content
|
| 152 |
+
pubmed = get_pubmed(message, n=3)
|
| 153 |
+
if pubmed: answer += chr(10)+chr(10)+"PUBMED:"+chr(10)+pubmed
|
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|
| 154 |
history.append({"role":"user","content":message})
|
| 155 |
history.append({"role":"assistant","content":answer})
|
| 156 |
return "", history
|
| 157 |
except Exception as e:
|
| 158 |
history.append({"role":"user","content":message})
|
| 159 |
+
history.append({"role":"assistant","content":"Error: "+str(e)})
|
| 160 |
return "", history
|
| 161 |
|
| 162 |
def voice_chat(audio, history):
|
|
|
|
| 167 |
client = Groq(api_key=GROQ_KEY)
|
| 168 |
with open(audio, "rb") as f:
|
| 169 |
tx = client.audio.transcriptions.create(file=("audio.wav", f, "audio/wav"), model="whisper-large-v3")
|
| 170 |
+
msgs = [{"role":"system","content":"You are CardioLab AI. "+KNOWHOW}]
|
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|
| 171 |
for item in history:
|
| 172 |
if isinstance(item, dict): msgs.append({"role":item["role"],"content":item["content"]})
|
| 173 |
msgs.append({"role":"user","content":tx.text})
|
| 174 |
+
resp = client.chat.completions.create(model="llama-3.3-70b-versatile",messages=msgs,max_tokens=500)
|
| 175 |
+
history.append({"role":"user","content":"[Voice] "+tx.text})
|
| 176 |
history.append({"role":"assistant","content":resp.choices[0].message.content})
|
| 177 |
return history
|
| 178 |
except Exception as e:
|
| 179 |
+
history.append({"role":"assistant","content":"Voice error: "+str(e)})
|
| 180 |
return history
|
| 181 |
|
| 182 |
+
# ── ANALYSIS TOOLS ────────────────────────────────────────────────
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|
|
| 183 |
def analyze_upad_photo(image):
|
| 184 |
if image is None: return None, "Upload a uPAD photo first."
|
| 185 |
try:
|
| 186 |
img = Image.fromarray(image) if not isinstance(image, Image.Image) else image
|
| 187 |
+
arr = np.array(img)
|
| 188 |
+
h,w = arr.shape[:2]
|
| 189 |
+
y1,y2,x1,x2 = int(h*0.35),int(h*0.65),int(w*0.35),int(w*0.65)
|
| 190 |
+
zone = arr[y1:y2,x1:x2]
|
| 191 |
+
R,G,B = float(np.mean(zone[:,:,0])),float(np.mean(zone[:,:,1])),float(np.mean(zone[:,:,2]))
|
|
|
|
| 192 |
c = max(0, round(0.018*(R-B)-0.3, 2))
|
| 193 |
+
if c<1.2: s,a="Normal","Monitor annually."
|
| 194 |
+
elif c<1.5: s,a="Borderline","Repeat in 3 months."
|
| 195 |
+
elif c<3.0: s,a="Stage 2 CKD","Consult nephrologist."
|
| 196 |
+
elif c<6.0: s,a="Stage 3-4 CKD","Immediate consultation."
|
| 197 |
+
else: s,a="Stage 5 CKD","Emergency care needed."
|
| 198 |
+
result_img = img.copy()
|
| 199 |
import PIL.ImageDraw as D
|
| 200 |
+
draw = D.Draw(result_img)
|
| 201 |
+
draw.rectangle([x1,y1,x2,y2], outline=(0,255,0), width=3)
|
| 202 |
+
return result_img, ("uPAD ANALYSIS"+chr(10)+"━"*22+chr(10)+
|
| 203 |
+
"R:"+str(round(R,1))+" G:"+str(round(G,1))+" B:"+str(round(B,1))+chr(10)+
|
| 204 |
+
"Orange Score: "+str(round(R-B,1))+chr(10)+"━"*22+chr(10)+
|
| 205 |
+
"CREATININE: "+str(c)+" mg/dL"+chr(10)+"CKD STAGE: "+s+chr(10)+
|
| 206 |
+
"ACTION: "+a+chr(10)+"Confirm: Heska Element HT5")
|
| 207 |
+
except Exception as e: return None, "Error: "+str(e)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 208 |
|
| 209 |
def analyze_piv_csv(file, theme="White"):
|
| 210 |
+
if file is None: return None,None,None,None,"Upload a PIV CSV file first."
|
| 211 |
try:
|
| 212 |
df = pd.read_csv(file.name)
|
| 213 |
+
cols = [c.lower().strip() for c in df.columns]
|
| 214 |
+
df.columns = cols
|
| 215 |
num_cols = df.select_dtypes(include=[np.number]).columns.tolist()
|
| 216 |
+
if not num_cols: return None,None,None,None,"No numeric columns found."
|
| 217 |
+
bg = "#ffffff" if theme=="White" else "#0a1628"
|
| 218 |
fg = "#1a202c" if theme=="White" else "white"
|
| 219 |
gc = "#e2e8f0" if theme=="White" else "#2d4a8a"
|
| 220 |
ac = "#4a5568" if theme=="White" else "#a8b2d8"
|
| 221 |
pb = "#f7fafc" if theme=="White" else "#132340"
|
| 222 |
x = np.arange(len(df))
|
| 223 |
vc = next((c for c in cols if any(k in c for k in ["vel","speed","v_mag"])), num_cols[0] if num_cols else None)
|
| 224 |
+
sc = next((c for c in cols if any(k in c for k in ["shear","stress","tau","wss"])), num_cols[1] if len(num_cols)>1 else None)
|
| 225 |
tc = next((c for c in cols if "time" in c or "frame" in c), None)
|
| 226 |
xv = df[tc] if tc else x
|
| 227 |
+
def mk(fn, title):
|
| 228 |
+
fig2,ax = plt.subplots(figsize=(8,5))
|
| 229 |
+
fig2.patch.set_facecolor(bg); ax.set_facecolor(pb)
|
| 230 |
+
fn(ax)
|
| 231 |
+
ax.set_title(title, color=fg, fontweight="bold", fontsize=13, pad=8)
|
| 232 |
+
ax.tick_params(colors=ac, labelsize=10)
|
| 233 |
+
ax.grid(True, alpha=0.3, color=gc, linestyle="--")
|
| 234 |
+
for sp in ["top","right"]: ax.spines[sp].set_visible(False)
|
| 235 |
+
for sp in ["bottom","left"]: ax.spines[sp].set_color(gc)
|
| 236 |
+
plt.tight_layout()
|
| 237 |
+
buf2=io.BytesIO(); plt.savefig(buf2,format="png",facecolor=bg,bbox_inches="tight",dpi=130); buf2.seek(0)
|
| 238 |
+
res=Image.open(buf2).copy(); plt.close(); return res
|
| 239 |
def pv(ax):
|
| 240 |
if vc:
|
| 241 |
+
ax.plot(xv,df[vc],color="#e63946",linewidth=2.5,marker="o",markersize=5)
|
| 242 |
+
ax.fill_between(xv,df[vc],alpha=0.2,color="#e63946")
|
| 243 |
+
ax.axhline(y=2.0,color="#f59e0b",linestyle="--",linewidth=2,label="Risk: 2.0 m/s")
|
| 244 |
+
ax.set_ylabel("Velocity (m/s)",color=ac,fontsize=11)
|
| 245 |
+
ax.set_xlabel(tc or "Sample",color=ac,fontsize=11)
|
| 246 |
+
ax.legend(fontsize=9,labelcolor=fg,facecolor=pb)
|
| 247 |
def ps(ax):
|
| 248 |
+
if sc:
|
| 249 |
xp = xv.values if tc else x
|
| 250 |
+
ax.plot(xp,df[sc],color="#4361ee",linewidth=2.5,marker="s",markersize=5)
|
| 251 |
+
ax.fill_between(xp,df[sc],alpha=0.2,color="#4361ee")
|
| 252 |
+
ax.axhline(y=5,color="#f59e0b",linestyle="--",linewidth=2,label="Caution: 5 Pa")
|
| 253 |
+
ax.axhline(y=10,color="#e63946",linestyle="--",linewidth=2,label="High risk: 10 Pa")
|
| 254 |
+
ax.set_ylabel("Shear Stress (Pa)",color=ac,fontsize=11)
|
| 255 |
+
ax.set_xlabel(tc or "Sample",color=ac,fontsize=11)
|
| 256 |
+
ax.legend(fontsize=9,labelcolor=fg,facecolor=pb)
|
| 257 |
def psc(ax):
|
| 258 |
+
if vc and sc:
|
| 259 |
+
s2 = ax.scatter(df[vc],df[sc],c=x,cmap="RdYlGn_r",s=90,edgecolors=fg,linewidth=0.5,zorder=5)
|
| 260 |
+
cb=plt.colorbar(s2,ax=ax,label="Time"); cb.ax.yaxis.label.set_color(fg); cb.ax.tick_params(colors=ac)
|
| 261 |
+
ax.axvline(x=2.0,color="#f59e0b",linestyle="--",linewidth=2,label="Vel risk")
|
| 262 |
+
ax.axhline(y=10,color="#e63946",linestyle="--",linewidth=2,label="Shear risk")
|
| 263 |
+
ax.set_xlabel("Velocity (m/s)",color=ac,fontsize=11)
|
| 264 |
+
ax.set_ylabel("Shear Stress (Pa)",color=ac,fontsize=11)
|
| 265 |
+
ax.legend(fontsize=9,labelcolor=fg,facecolor=pb)
|
| 266 |
def psum(ax):
|
| 267 |
+
ax.axis("off"); risk=[]
|
| 268 |
+
st="CLINICAL SUMMARY"+chr(10)+"━"*20+chr(10)+chr(10)
|
| 269 |
for col in num_cols[:3]:
|
| 270 |
+
mn=round(df[col].mean(),3); mx=round(df[col].max(),3)
|
| 271 |
+
st+=col[:14]+":"+chr(10)+" Mean: "+str(mn)+chr(10)+" Max: "+str(mx)+chr(10)+chr(10)
|
| 272 |
+
if "vel" in col and mx>2.0: risk.append("HIGH VELOCITY (>2.0 m/s)")
|
| 273 |
+
if "shear" in col and mx>10: risk.append("HIGH SHEAR (>10 Pa)")
|
| 274 |
+
st+="━"*20+chr(10)
|
| 275 |
+
if risk:
|
| 276 |
+
st+="RISK FLAGS:"+chr(10)+"".join([" ⚠ "+r+chr(10) for r in risk])
|
| 277 |
+
st+="OVERALL: HIGH RISK"; bc="#e63946"
|
| 278 |
+
else:
|
| 279 |
+
st+="OVERALL: LOW RISK"; bc="#2ecc71"
|
| 280 |
+
ax.text(0.05,0.97,st,transform=ax.transAxes,color=fg,fontsize=10,va="top",fontfamily="monospace",
|
| 281 |
+
bbox=dict(boxstyle="round,pad=0.8",facecolor=pb,edgecolor=bc,linewidth=2.5))
|
| 282 |
+
i1=mk(pv,"Velocity Profile"); i2=mk(ps,"Wall Shear Stress")
|
| 283 |
+
i3=mk(psc,"Velocity vs Shear"); i4=mk(psum,"Clinical Summary")
|
| 284 |
+
ai=""
|
| 285 |
if GROQ_KEY:
|
| 286 |
try:
|
| 287 |
+
client=Groq(api_key=GROQ_KEY)
|
| 288 |
+
resp=client.chat.completions.create(model="llama-3.3-70b-versatile",
|
| 289 |
+
messages=[{"role":"system","content":"PIV expert SJSU CardioLab. Analyze PIV stats give clinical interpretation."},
|
| 290 |
+
{"role":"user","content":"PIV data from 27mm SJM Regent MHV 70bpm 5L/min:"+chr(10)+df.describe().to_string()[:600]}],max_tokens=300)
|
| 291 |
+
ai=chr(10)+"━"*20+chr(10)+"AI:"+chr(10)+resp.choices[0].message.content
|
|
|
|
|
|
|
|
|
|
| 292 |
except: pass
|
| 293 |
+
return i1,i2,i3,i4,"PIV LOADED: "+str(len(df))+" rows | "+", ".join(df.columns.tolist())+ai
|
| 294 |
+
except Exception as e: return None,None,None,None,"Error: "+str(e)
|
|
|
|
| 295 |
|
| 296 |
def analyze_tgt_csv(file, theme="White"):
|
| 297 |
+
if file is None: return None,None,None,None,"Upload a TGT CSV file first."
|
| 298 |
try:
|
| 299 |
df = pd.read_csv(file.name)
|
| 300 |
+
cols = [c.lower().strip() for c in df.columns]
|
| 301 |
+
df.columns = cols
|
| 302 |
num_cols = df.select_dtypes(include=[np.number]).columns.tolist()
|
| 303 |
+
bg="#ffffff" if theme=="White" else "#0a1628"
|
| 304 |
+
fg="#1a202c" if theme=="White" else "white"
|
| 305 |
+
gc="#e2e8f0" if theme=="White" else "#2d4a8a"
|
| 306 |
+
ac="#4a5568" if theme=="White" else "#a8b2d8"
|
| 307 |
+
pb="#f7fafc" if theme=="White" else "#132340"
|
| 308 |
+
tc=next((c for c in cols if "time" in c or "min" in c),None)
|
| 309 |
+
tatc=next((c for c in cols if "tat" in c),num_cols[0] if num_cols else None)
|
| 310 |
+
pfc=next((c for c in cols if "pf" in c),num_cols[1] if len(num_cols)>1 else None)
|
| 311 |
+
hc=next((c for c in cols if "hemo" in c or "hgb" in c),num_cols[2] if len(num_cols)>2 else None)
|
| 312 |
+
plc=next((c for c in cols if "platelet" in c or "plt" in c),num_cols[3] if len(num_cols)>3 else None)
|
| 313 |
+
xv=df[tc] if tc else range(len(df))
|
| 314 |
+
def mk(dc,color,yl,lim,ll,title,bar=False):
|
| 315 |
+
fig2,ax=plt.subplots(figsize=(8,5))
|
| 316 |
+
fig2.patch.set_facecolor(bg); ax.set_facecolor(pb)
|
| 317 |
+
if dc and dc in df.columns:
|
| 318 |
+
xp=df[tc].values if tc else range(len(df)); yp=df[dc].values
|
| 319 |
+
if bar:
|
| 320 |
+
bs=ax.bar(range(len(yp)),yp,color=color,alpha=0.85,edgecolor=bg,width=0.6)
|
| 321 |
+
for b,v in zip(bs,yp): ax.text(b.get_x()+b.get_width()/2,b.get_height()+0.5,str(round(v,1)),ha="center",va="bottom",color=fg,fontsize=10,fontweight="bold")
|
| 322 |
+
else:
|
| 323 |
+
ax.plot(xp,yp,color=color,linewidth=3,marker="o",markersize=8)
|
| 324 |
+
ax.fill_between(xp,yp,alpha=0.2,color=color)
|
| 325 |
+
for xi,yi in zip(xp,yp): ax.annotate(str(round(yi,1)),(xi,yi),textcoords="offset points",xytext=(0,10),ha="center",color=fg,fontsize=10,fontweight="bold")
|
| 326 |
+
ax.axhline(y=lim,color="#f59e0b",linestyle="--",linewidth=2.5,label=ll)
|
| 327 |
+
ax.legend(fontsize=10,labelcolor=fg,facecolor=pb)
|
| 328 |
+
ax.set_ylabel(yl,color=ac,fontsize=11); ax.set_xlabel(tc or "Sample",color=ac,fontsize=11)
|
| 329 |
+
mv=round(float(np.max(yp)),2); st="HIGH" if mv>lim else "NORMAL"
|
| 330 |
+
ax.set_title(title+chr(10)+"Max: "+str(mv)+" Status: "+st,color=fg,fontweight="bold",fontsize=12)
|
| 331 |
+
ax.tick_params(colors=ac,labelsize=10); ax.grid(True,alpha=0.3,color=gc,linestyle="--")
|
| 332 |
+
for sp in ["top","right"]: ax.spines[sp].set_visible(False)
|
| 333 |
+
for sp in ["bottom","left"]: ax.spines[sp].set_color(gc)
|
| 334 |
+
plt.tight_layout()
|
| 335 |
+
buf2=io.BytesIO(); plt.savefig(buf2,format="png",facecolor=bg,bbox_inches="tight",dpi=130); buf2.seek(0)
|
| 336 |
+
res=Image.open(buf2).copy(); plt.close(); return res
|
| 337 |
+
i1=mk(tatc,"#e63946","TAT (ng/mL)",8,"Normal: 8 ng/mL","Thrombin-Antithrombin TAT")
|
| 338 |
+
i2=mk(pfc,"#4361ee","PF1.2 (nmol/L)",2.0,"Normal: 2.0","Prothrombin Fragment PF1.2")
|
| 339 |
+
i3=mk(hc,"#2ecc71","Free Hemoglobin (mg/L)",20,"Normal: 20 mg/L","Free Hemoglobin Hemolysis",bar=True)
|
| 340 |
+
i4=mk(plc,"#e67e22","Platelet Count (10³/μL)",150,"Normal min: 150","Platelet Count")
|
| 341 |
+
ai=""
|
| 342 |
if GROQ_KEY:
|
| 343 |
try:
|
| 344 |
+
client=Groq(api_key=GROQ_KEY)
|
| 345 |
+
resp=client.chat.completions.create(model="llama-3.3-70b-versatile",
|
| 346 |
+
messages=[{"role":"system","content":"Hematology expert SJSU CardioLab. Analyze TGT data give thrombogenicity risk LOW MODERATE or HIGH. Normal: TAT<8, PF1.2<2.0, Hemo<20, Plt>150."},
|
| 347 |
+
{"role":"user","content":"TGT from 27mm SJM Regent MHV:"+chr(10)+df.describe().to_string()[:600]}],max_tokens=300)
|
| 348 |
+
ai=chr(10)+"━"*20+chr(10)+"AI:"+chr(10)+resp.choices[0].message.content
|
|
|
|
|
|
|
|
|
|
| 349 |
except: pass
|
| 350 |
+
return i1,i2,i3,i4,"TGT LOADED: "+str(len(df))+" rows | "+", ".join(df.columns.tolist())+ai
|
| 351 |
+
except Exception as e: return None,None,None,None,"Error: "+str(e)
|
|
|
|
| 352 |
|
| 353 |
def generate_image(prompt):
|
| 354 |
+
if not prompt.strip(): return None,"Enter description.","";
|
| 355 |
+
if not HF_TOKEN: return None,"Add HF_TOKEN to Space secrets.","";
|
| 356 |
try:
|
| 357 |
+
enhanced,desc=prompt,""
|
| 358 |
if GROQ_KEY:
|
| 359 |
try:
|
| 360 |
+
client=Groq(api_key=GROQ_KEY)
|
| 361 |
+
resp=client.chat.completions.create(model="llama-3.3-70b-versatile",
|
|
|
|
| 362 |
messages=[{"role":"system","content":"Format: DESCRIPTION: [2 sentences] PROMPT: [detailed image prompt]"},
|
| 363 |
+
{"role":"user","content":"Biomedical image for CardioLab: "+prompt}],max_tokens=200)
|
| 364 |
+
full=resp.choices[0].message.content
|
|
|
|
|
|
|
| 365 |
if "DESCRIPTION:" in full and "PROMPT:" in full:
|
| 366 |
+
desc=full.split("DESCRIPTION:")[1].split("PROMPT:")[0].strip()
|
| 367 |
+
enhanced=full.split("PROMPT:")[1].strip()
|
| 368 |
except: pass
|
| 369 |
+
headers={"Authorization":"Bearer "+HF_TOKEN,"Content-Type":"application/json"}
|
| 370 |
+
for url in ["https://router.huggingface.co/hf-inference/models/black-forest-labs/FLUX.1-schnell",
|
| 371 |
+
"https://router.huggingface.co/hf-inference/models/stabilityai/stable-diffusion-xl-base-1.0"]:
|
|
|
|
|
|
|
| 372 |
try:
|
| 373 |
+
r=requests.post(url,headers=headers,json={"inputs":enhanced,"parameters":{"num_inference_steps":8}},timeout=60)
|
| 374 |
+
if r.status_code==200: return Image.open(io.BytesIO(r.content)),"Generated!",desc
|
|
|
|
|
|
|
| 375 |
except: continue
|
| 376 |
+
return None,"Models busy. Try again.",desc
|
| 377 |
+
except Exception as e: return None,"Error: "+str(e),""
|
|
|
|
| 378 |
|
| 379 |
+
def piv_manual(v,s,h):
|
| 380 |
+
vr="HIGH-stenosis" if float(v)>2.0 else "NORMAL"
|
| 381 |
+
sr="HIGH-thrombosis" if float(s)>10 else "ELEVATED" if float(s)>5 else "NORMAL"
|
| 382 |
+
return "Velocity: "+str(v)+" - "+vr+chr(10)+"Shear: "+str(s)+" - "+sr+chr(10)+"HR: "+str(h)+" bpm"
|
| 383 |
|
| 384 |
+
def tgt_manual(t,p,h,pl,tm):
|
| 385 |
+
risk=sum([float(t)>15,float(p)>2.0,float(h)>50,float(pl)<150])
|
| 386 |
+
return "TAT:"+str(t)+" PF1.2:"+str(p)+chr(10)+"Hemo:"+str(h)+" Plt:"+str(pl)+chr(10)+"Time:"+str(tm)+"min"+chr(10)+"RESULT: "+("HIGH RISK" if risk>=3 else "MODERATE" if risk>=2 else "LOW RISK")
|
|
|
|
|
|
|
| 387 |
|
| 388 |
+
# ── UI ─────────────────────────────────────────────────────────────
|
| 389 |
+
with gr.Blocks(title="CardioLab AI", css=CSS) as demo:
|
| 390 |
+
gr.HTML('''<div style="background:linear-gradient(135deg,#1a237e,#b71c1c);padding:20px;text-align:center;border-radius:12px 12px 0 0"><div style="font-size:2.5em;font-weight:900;color:#fff;letter-spacing:3px">CardioLab AI</div></div>''')
|
|
|
|
| 391 |
|
| 392 |
with gr.Tabs():
|
| 393 |
|
| 394 |
with gr.Tab("Chat"):
|
| 395 |
+
gr.Markdown("### Chat with memory — saves conversations like ChatGPT")
|
| 396 |
with gr.Row():
|
| 397 |
+
with gr.Column(scale=3):
|
| 398 |
+
chatbot = gr.Chatbot(label="", height=420)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 399 |
with gr.Row():
|
| 400 |
+
msg_box = gr.Textbox(placeholder="Ask about CardioLab research...", label="", lines=2, scale=4)
|
| 401 |
+
with gr.Column(scale=1, min_width=80):
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 402 |
send_btn = gr.Button("Send", variant="primary")
|
| 403 |
clear_btn = gr.Button("Clear", variant="secondary")
|
| 404 |
+
with gr.Column(scale=1, min_width=200):
|
| 405 |
+
gr.Markdown("### Saved Sessions")
|
| 406 |
+
session_dropdown = gr.Dropdown(
|
| 407 |
+
choices=get_session_list(),
|
| 408 |
+
label="Load a saved session",
|
| 409 |
+
interactive=True
|
| 410 |
+
)
|
| 411 |
+
load_btn = gr.Button("Load Session", variant="primary")
|
| 412 |
+
session_status = gr.Textbox(label="Status", lines=1, interactive=False)
|
| 413 |
+
gr.Markdown("### Save Current Chat")
|
| 414 |
+
session_name_box = gr.Textbox(label="Session name", placeholder="e.g. TGT Research May 2026")
|
| 415 |
+
save_btn = gr.Button("Save Chat", variant="primary")
|
| 416 |
+
delete_btn = gr.Button("Delete Session", variant="secondary")
|
| 417 |
+
|
| 418 |
+
send_btn.click(research_chat, inputs=[msg_box, chatbot], outputs=[msg_box, chatbot])
|
| 419 |
+
msg_box.submit(research_chat, inputs=[msg_box, chatbot], outputs=[msg_box, chatbot])
|
| 420 |
clear_btn.click(lambda: ([], ""), outputs=[chatbot, msg_box])
|
|
|
|
| 421 |
save_btn.click(save_session, inputs=[chatbot, session_name_box], outputs=[session_status, session_dropdown])
|
| 422 |
load_btn.click(load_session, inputs=session_dropdown, outputs=[chatbot, session_status])
|
| 423 |
delete_btn.click(delete_session, inputs=session_dropdown, outputs=[session_status, session_dropdown])
|
| 424 |
|
| 425 |
with gr.Tab("Voice"):
|
| 426 |
+
voice_chatbot = gr.Chatbot(label="", height=320)
|
| 427 |
audio_input = gr.Audio(sources=["microphone"], type="filepath", label="Record Question")
|
| 428 |
with gr.Row():
|
| 429 |
voice_btn = gr.Button("Ask by Voice", variant="primary")
|
|
|
|
| 432 |
voice_clear.click(lambda: [], outputs=voice_chatbot)
|
| 433 |
|
| 434 |
with gr.Tab("Papers"):
|
|
|
|
| 435 |
with gr.Row():
|
| 436 |
+
search_input = gr.Textbox(placeholder="e.g. mechanical heart valve thrombogenicity", label="Research Topic", scale=4)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 437 |
search_btn = gr.Button("Search", variant="primary", scale=1)
|
| 438 |
+
search_output = gr.Textbox(label="Verified Results", lines=18)
|
| 439 |
+
search_btn.click(quick_search, inputs=search_input, outputs=search_output)
|
| 440 |
+
search_input.submit(quick_search, inputs=search_input, outputs=search_output)
|
| 441 |
|
| 442 |
with gr.Tab("PIV CSV"):
|
| 443 |
+
gr.Markdown("### Upload PIV CSV — 4 separate charts + AI analysis")
|
| 444 |
with gr.Row():
|
| 445 |
+
piv_file = gr.File(label="UPLOAD PIV CSV", file_types=[".csv"], scale=3)
|
| 446 |
piv_theme = gr.Radio(["White","Dark"], value="White", label="Theme", scale=1)
|
| 447 |
piv_btn = gr.Button("Analyze PIV Data", variant="primary")
|
| 448 |
+
piv_result = gr.Textbox(label="AI Analysis", lines=5)
|
| 449 |
with gr.Row():
|
| 450 |
+
piv_c1 = gr.Image(label="Velocity Profile", type="pil")
|
| 451 |
piv_c2 = gr.Image(label="Shear Stress", type="pil")
|
| 452 |
with gr.Row():
|
| 453 |
+
piv_c3 = gr.Image(label="Velocity vs Shear", type="pil")
|
| 454 |
piv_c4 = gr.Image(label="Clinical Summary", type="pil")
|
| 455 |
+
piv_btn.click(analyze_piv_csv, inputs=[piv_file,piv_theme], outputs=[piv_c1,piv_c2,piv_c3,piv_c4,piv_result])
|
| 456 |
|
| 457 |
with gr.Tab("TGT CSV"):
|
| 458 |
+
gr.Markdown("### Upload TGT CSV — blood biomarker charts + thrombogenicity assessment")
|
| 459 |
with gr.Row():
|
| 460 |
+
tgt_file = gr.File(label="UPLOAD TGT CSV", file_types=[".csv"], scale=3)
|
| 461 |
tgt_theme = gr.Radio(["White","Dark"], value="White", label="Theme", scale=1)
|
| 462 |
tgt_btn = gr.Button("Analyze TGT Data", variant="primary")
|
| 463 |
+
tgt_result = gr.Textbox(label="AI Assessment", lines=5)
|
| 464 |
with gr.Row():
|
| 465 |
+
tgt_c1 = gr.Image(label="TAT Over Time", type="pil")
|
| 466 |
+
tgt_c2 = gr.Image(label="PF1.2 Over Time", type="pil")
|
| 467 |
with gr.Row():
|
| 468 |
+
tgt_c3 = gr.Image(label="Free Hemoglobin", type="pil")
|
| 469 |
+
tgt_c4 = gr.Image(label="Platelet Count", type="pil")
|
| 470 |
+
tgt_btn.click(analyze_tgt_csv, inputs=[tgt_file,tgt_theme], outputs=[tgt_c1,tgt_c2,tgt_c3,tgt_c4,tgt_result])
|
| 471 |
|
| 472 |
+
with gr.Tab("uPAD Photo"):
|
| 473 |
+
gr.Markdown("### Upload uPAD Photo — Instant CKD diagnosis")
|
| 474 |
with gr.Row():
|
| 475 |
with gr.Column():
|
| 476 |
+
photo_input = gr.Image(label="Upload uPAD Photo", type="numpy", height=280)
|
| 477 |
analyze_btn = gr.Button("Analyze uPAD", variant="primary")
|
| 478 |
with gr.Column():
|
| 479 |
+
photo_img = gr.Image(label="Detection Zone", type="pil", height=280)
|
| 480 |
+
photo_text = gr.Textbox(label="CKD Result", lines=10)
|
| 481 |
analyze_btn.click(analyze_upad_photo, inputs=photo_input, outputs=[photo_img, photo_text])
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 482 |
|
| 483 |
with gr.Tab("AI Image"):
|
| 484 |
with gr.Row():
|
| 485 |
+
img_prompt = gr.Textbox(placeholder="e.g. bileaflet heart valve | uPAD device | Arduino TGT", label="Describe image", lines=2, scale=4)
|
|
|
|
|
|
|
|
|
|
| 486 |
with gr.Column(scale=1):
|
| 487 |
img_btn = gr.Button("Generate", variant="primary")
|
| 488 |
img_status = gr.Textbox(label="Status", lines=1)
|
| 489 |
img_desc = gr.Textbox(label="AI Description", lines=2, interactive=False)
|
| 490 |
+
img_output = gr.Image(label="Generated Image", type="pil", height=380)
|
| 491 |
+
img_btn.click(generate_image, inputs=img_prompt, outputs=[img_output,img_status,img_desc])
|
| 492 |
|
| 493 |
with gr.Tab("PIV Manual"):
|
| 494 |
with gr.Row():
|
| 495 |
with gr.Column():
|
| 496 |
+
v=gr.Number(label="Max Velocity m/s",value=1.8)
|
| 497 |
+
s=gr.Number(label="Wall Shear Stress Pa",value=6.5)
|
| 498 |
+
h=gr.Number(label="Heart Rate bpm",value=72)
|
| 499 |
+
piv_out=gr.Textbox(label="Result",lines=4)
|
| 500 |
+
gr.Button("Analyze PIV",variant="primary").click(piv_manual,inputs=[v,s,h],outputs=piv_out)
|
| 501 |
|
| 502 |
with gr.Tab("TGT Manual"):
|
| 503 |
with gr.Row():
|
| 504 |
with gr.Column():
|
| 505 |
+
t1=gr.Number(label="TAT ng/mL",value=18)
|
| 506 |
+
t2=gr.Number(label="PF1.2",value=2.5)
|
| 507 |
+
t3=gr.Number(label="Hemoglobin mg/L",value=60)
|
| 508 |
+
t4=gr.Number(label="Platelets",value=140)
|
| 509 |
+
t5=gr.Number(label="Time min",value=40)
|
| 510 |
+
out2=gr.Textbox(label="Result",lines=6)
|
| 511 |
+
gr.Button("Analyze TGT",variant="primary").click(tgt_manual,inputs=[t1,t2,t3,t4,t5],outputs=out2)
|
| 512 |
+
|
| 513 |
+
with gr.Tab("uPAD Manual"):
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 514 |
with gr.Row():
|
| 515 |
+
with gr.Column():
|
| 516 |
+
r=gr.Number(label="R value",value=210)
|
| 517 |
+
g=gr.Number(label="G value",value=140)
|
| 518 |
+
b=gr.Number(label="B value",value=80)
|
| 519 |
+
out3=gr.Textbox(label="Result",lines=4)
|
| 520 |
+
gr.Button("Analyze",variant="primary").click(
|
| 521 |
+
lambda r,g,b:"Creatinine: "+str(max(0,round(0.02*(r-b)-0.5,2)))+" mg/dL"+chr(10)+("Normal" if max(0,round(0.02*(r-b)-0.5,2))<1.2 else "Borderline" if max(0,round(0.02*(r-b)-0.5,2))<1.5 else "CKD Stage 2+"),
|
| 522 |
+
inputs=[r,g,b],outputs=out3)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 523 |
|
| 524 |
demo.launch()
|