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app.py

@@ -707,6 +707,96 @@ def tgt_manual(t,p,h,pl,tm):
     risk=sum([float(t)>15,float(p)>2.0,float(h)>50,float(pl)<150])
     return "TAT:"+str(t)+" PF1.2:"+str(p)+chr(10)+"Hemo:"+str(h)+" Plt:"+str(pl)+chr(10)+"RESULT: "+("HIGH RISK" if risk>=3 else "MODERATE" if risk>=2 else "LOW RISK")
 
+
+# ── PHASE D: PROTOCOL GENERATOR + REPORT WRITER + HYPOTHESIS ──────
+
+def generate_protocol(experiment_type, specific_params=""):
+    if not GROQ_KEY: return "Error: Add GROQ_API_KEY to Space Settings."
+    try:
+        client = Groq(api_key=GROQ_KEY)
+        paper_context, _ = search_papers(experiment_type, n=4)
+        lab_context = {
+            "MCL": "Sylgard 184 PDMS 10:1 ratio 48hr cure. Tygon tubing. 70bpm 5L/min 80-120mmHg. Blood analog glycerin water.",
+            "PIV": "Green laser 532nm time-resolved. Seeding particles. Velocity 0.5-2.0 m/s normal. Shear below 5 Pa normal.",
+            "TGT": "Arduino Uno stepper motor 48V. 150mL fresh blood. Sample 0 20 40 60 min. Heska HT5 analyzer.",
+            "uPAD": "Whatman filter paper. Wax printer 120C baking. Picric acid alkaline solution. Jaffe reaction orange-red color.",
+            "FSI": "COMSOL Multiphysics ALE mesh. Blood 1060 kg/m3 0.0035 Pa.s. SJM bileaflet geometry.",
+        }
+        extra = next((v for k,v in lab_context.items() if k.lower() in experiment_type.lower()), "")
+        system = """You are CardioLab AI protocol generator for SJSU Biomedical Engineering.
+Generate a COMPLETE detailed lab protocol. Include these sections:
+1. OBJECTIVE
+2. MATERIALS AND EQUIPMENT (with exact quantities)
+3. SAFETY CONSIDERATIONS
+4. STEP-BY-STEP PROCEDURE (numbered, detailed)
+5. DATA COLLECTION
+6. ANALYSIS METHOD
+7. EXPECTED RESULTS (with normal ranges)
+8. TROUBLESHOOTING
+Use exact SJSU CardioLab values and equipment."""
+        user_msg = f"Generate complete protocol for: {experiment_type}"
+        if specific_params: user_msg += f"
+Parameters: {specific_params}"
+        if extra: user_msg += f"
+CardioLab context: {extra}"
+        if paper_context: user_msg += f"
+From SJSU papers: {paper_context[:600]}"
+        resp = client.chat.completions.create(
+            model="llama-3.3-70b-versatile",
+            messages=[{"role":"system","content":system},{"role":"user","content":user_msg}],
+            max_tokens=1200)
+        return resp.choices[0].message.content
+    except Exception as e: return "Error: "+str(e)
+
+def generate_report(data_description, experiment_type, results=""):
+    if not GROQ_KEY: return "Error: Add GROQ_API_KEY to Space Settings."
+    try:
+        client = Groq(api_key=GROQ_KEY)
+        paper_context, _ = search_papers(experiment_type, n=3)
+        system = """You are CardioLab AI report writer for SJSU Biomedical Engineering.
+Generate a professional research report with these sections:
+1. ABSTRACT (150 words)
+2. INTRODUCTION (background and objectives)
+3. MATERIALS AND METHODS
+4. RESULTS AND DISCUSSION
+5. CONCLUSION
+6. RECOMMENDATIONS
+7. REFERENCES (cite SJSU CardioLab papers)
+Use specific values. Write in professional academic style."""
+        user_msg = f"Write research report for: {experiment_type}"+chr(10)+f"Description: {data_description}"
+        if results: user_msg += chr(10)+f"Results: {results}"
+        if paper_context: user_msg += chr(10)+f"SJSU papers: {paper_context[:600]}"
+        resp = client.chat.completions.create(
+            model="llama-3.3-70b-versatile",
+            messages=[{"role":"system","content":system},{"role":"user","content":user_msg}],
+            max_tokens=1500)
+        return resp.choices[0].message.content
+    except Exception as e: return "Error: "+str(e)
+
+def generate_hypothesis(research_area, current_findings=""):
+    if not GROQ_KEY: return "Error: Add GROQ_API_KEY to Space Settings."
+    try:
+        client = Groq(api_key=GROQ_KEY)
+        paper_context, _ = search_papers(research_area, n=3)
+        system = """You are CardioLab AI research assistant for SJSU Biomedical Engineering.
+Generate 3 specific testable research hypotheses. For each:
+- H0 (null hypothesis)
+- H1 (alternative hypothesis)
+- Scientific rationale
+- Suggested experiment
+- Expected outcome and measurable metrics
+Base on SJSU CardioLab research."""
+        user_msg = f"Generate hypotheses for: {research_area}"
+        if current_findings: user_msg += chr(10)+f"Current findings: {current_findings}"
+        if paper_context: user_msg += chr(10)+f"SJSU papers: {paper_context[:500]}"
+        resp = client.chat.completions.create(
+            model="llama-3.3-70b-versatile",
+            messages=[{"role":"system","content":system},{"role":"user","content":user_msg}],
+            max_tokens=1000)
+        return resp.choices[0].message.content
+    except Exception as e: return "Error: "+str(e)
+
+
 with gr.Blocks(title="CardioLab AI - SJSU", css=CSS) as demo:
     gr.HTML(HEADER)
 
@@ -831,7 +921,63 @@ with gr.Blocks(title="CardioLab AI - SJSU", css=CSS) as demo:
                     t5=gr.Number(label="Time min",value=40); out2=gr.Textbox(label="Result",lines=6)
                     gr.Button("Analyze TGT",variant="primary").click(tgt_manual,inputs=[t1,t2,t3,t4,t5],outputs=out2)
 
+        with gr.Tab("Protocol Generator"):
+            gr.Markdown("### Generate complete lab protocols from SJSU CardioLab knowledge")
+            with gr.Row():
+                with gr.Column(scale=1):
+                    proto_type = gr.Dropdown(
+                        choices=["MCL Setup","PIV Experiment","TGT Blood Testing",
+                                 "uPAD Fabrication","uPAD Creatinine Test",
+                                 "FSI COMSOL Simulation","Valve Testing"],
+                        value="TGT Blood Testing", label="Experiment Type")
+                    proto_params = gr.Textbox(
+                        placeholder="e.g. 27mm SJM valve 70bpm porcine blood",
+                        label="Specific Parameters", lines=2)
+                    proto_btn = gr.Button("Generate Protocol", variant="primary")
+                with gr.Column(scale=2):
+                    proto_output = gr.Textbox(label="Generated Protocol", lines=28, show_copy_button=True)
+            proto_btn.click(generate_protocol, inputs=[proto_type, proto_params], outputs=proto_output)
+
+        with gr.Tab("Report Writer"):
+            gr.Markdown("### Generate professional research reports from your data")
+            with gr.Row():
+                with gr.Column(scale=1):
+                    report_exp = gr.Dropdown(
+                        choices=["MCL PIV Flow Analysis","TGT Thrombogenicity Study",
+                                 "uPAD CKD Detection","FSI Simulation Study",
+                                 "Heart Valve Comparison"],
+                        value="TGT Thrombogenicity Study", label="Study Type")
+                    report_desc = gr.Textbox(
+                        placeholder="Describe your experiment e.g. TGT with 27mm SJM bileaflet at 70bpm 150mL porcine blood",
+                        label="Experiment Description", lines=3)
+                    report_results = gr.Textbox(
+                        placeholder="e.g. TAT=12.3 ng/mL PF1.2=2.8 Hemo=45 Plt=142",
+                        label="Your Results", lines=2)
+                    report_btn = gr.Button("Generate Report", variant="primary")
+                with gr.Column(scale=2):
+                    report_output = gr.Textbox(label="Generated Report", lines=28, show_copy_button=True)
+            report_btn.click(generate_report, inputs=[report_desc, report_exp, report_results], outputs=report_output)
+
+        with gr.Tab("Hypothesis Generator"):
+            gr.Markdown("### Generate testable research hypotheses for CardioLab projects")
+            with gr.Row():
+                with gr.Column(scale=1):
+                    hyp_area = gr.Dropdown(
+                        choices=["Bileaflet MHV Thrombogenicity",
+                                 "uPAD CKD Detection Accuracy",
+                                 "PIV Flow Characterization",
+                                 "FSI Simulation Validation",
+                                 "Valve Design Comparison"],
+                        value="Bileaflet MHV Thrombogenicity", label="Research Area")
+                    hyp_findings = gr.Textbox(
+                        placeholder="Current observations from your experiments",
+                        label="Current Findings", lines=3)
+                    hyp_btn = gr.Button("Generate Hypotheses", variant="primary")
+                with gr.Column(scale=2):
+                    hyp_output = gr.Textbox(label="Research Hypotheses", lines=25, show_copy_button=True)
+            hyp_btn.click(generate_hypothesis, inputs=[hyp_area, hyp_findings], outputs=hyp_output)
+
     gr.HTML("""<div style="text-align:center;padding:10px;border-top:1px solid #e5e7eb;background:#f9fafb;">
-    <span style="color:#9ca3af;font-size:0.75em;">CardioLab AI v37 | SJSU Biomedical Engineering | Fine-tuned on 16 SJSU Papers | RAG + Custom Model | Inspired by <a href="https://github.com/snap-stanford/Biomni" style="color:#c1121f;">Biomni Stanford</a> | <a href="https://github.com/pranatechsol/Cardio-Lab-Ai" style="color:#0057a8;">GitHub</a> | Apache 2.0 | $0 Cost</span></div>""")
+    <span style="color:#9ca3af;font-size:0.75em;">CardioLab AI v38 | SJSU Biomedical Engineering | Fine-tuned on 16 SJSU Papers | RAG + Custom Model | Inspired by <a href="https://github.com/snap-stanford/Biomni" style="color:#c1121f;">Biomni Stanford</a> | <a href="https://github.com/pranatechsol/Cardio-Lab-Ai" style="color:#0057a8;">GitHub</a> | Apache 2.0 | $0 Cost</span></div>""")
 
 demo.launch()