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Support real pump controllers and hybrid execution mode
Update files for real pump controller compatibility and enable hybrid (simulation + hardware) API execution
1 parent 15d5060 commit 2a3d90d

7 files changed

Lines changed: 307 additions & 93 deletions

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‎pi-deployment/requirements-api.txt‎

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@@ -1,9 +1,9 @@
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# API-specific dependencies (pinned)
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# These are additive to the base requirements; install when running the API.
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fastapi==0.95.2
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fastapi>=0.103.0
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uvicorn[standard]==0.21.1
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labthings-fastapi==0.0.6
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pydantic==1.10.14
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labthings-fastapi>=0.0.14
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pydantic>=2.0.0
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typing_extensions>=4.7.0
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PyYAML>=6.0
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‎software/README.md‎

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@@ -125,6 +125,7 @@ The repository includes **3 requirements files** for different deployment scenar
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2. **Run the application in simulation mode**:
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```bash
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# Default port (5000)
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# set RIO_SIMULATION=true (Windows)
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export RIO_SIMULATION=true
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python main.py
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@@ -155,16 +156,25 @@ To run without hardware (for testing on a Mac/PC):
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**Option 1: Quick setup and run**
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```bash
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cd software
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# NOTE: These scripts are written for conda/mamba environments. If you are using virtualenv, you will need to modify the scripts.
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# on Linux/Mac
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./scripts/dev/setup-simulation.sh # First time setup
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./scripts/dev/run-simulation.sh # Run simulation
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# on Windows (Git Bash)
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bash ./scripts/dev/setup-simulation.sh
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bash ./scripts/dev/run-simulation.sh
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```
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Need custom parameters for simulation (frame size, ROI defaults, feature flags)? See `configurations/README.md` for the environment-variable profiles and examples you can export before running.
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**Option 2: Manual setup**
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```bash
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cd software
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# set RIO_SIMULATION=true (Windows)
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export RIO_SIMULATION=true
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python main.py
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```

‎software/api/client/notebooks/.ipynb_checkpoints/tutorial-checkpoint.ipynb‎

Lines changed: 132 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -25,9 +25,22 @@
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"execution_count": 1,
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"metadata": {
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"jupyter": {
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"source_hidden": true
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}
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},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"✅ Rio API client initialized\n",
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" Base URL: http://localhost:8000\n"
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]
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}
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],
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"source": [
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"# Configuration\n",
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"import os\n",
@@ -42,23 +55,23 @@
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"import sys\n",
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"from pathlib import Path\n",
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"\n",
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"# Add software/client to path for client import\n",
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"# This works whether running from repo root or software/client/notebooks/\n",
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"# Add software/api/client to path for client import\n",
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"# This works whether running from repo root or software/api/client/notebooks/\n",
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"repo_root = Path.cwd()\n",
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"if (repo_root / \"software\" / \"client\").exists():\n",
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"if (repo_root / \"software\" / \"api\" / \"client\").exists():\n",
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" # Running from repo root\n",
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" sys.path.insert(0, str(repo_root / \"software\"))\n",
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"elif (repo_root.parent.parent / \"software\" / \"client\").exists():\n",
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" # Running from software/client/notebooks/\n",
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"elif (repo_root.parent.parent / \"software\" / \"api\" / \"client\").exists():\n",
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" # Running from software/api/client/notebooks/\n",
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" sys.path.insert(0, str(repo_root.parent.parent))\n",
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"else:\n",
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" # Fallback: try to find software directory\n",
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" for parent in repo_root.parents:\n",
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" if (parent / \"software\" / \"client\").exists():\n",
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" if (parent / \"software\" / \"api\" / \"client\").exists():\n",
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" sys.path.insert(0, str(parent / \"software\"))\n",
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" break\n",
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"\n",
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"from client import RioClient, RioStreamClient\n",
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"from api.client import RioClient, RioStreamClient\n",
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"import requests\n",
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"import json\n",
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"import time\n",
@@ -72,12 +85,14 @@
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"client = RioClient(base_url=API_BASE_URL)\n",
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"\n",
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"print(\"✅ Rio API client initialized\")\n",
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"print(f\" Base URL: {API_BASE_URL}\")\n"
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"print(f\" Base URL: {API_BASE_URL}\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"metadata": {
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"jp-MarkdownHeadingCollapsed": true
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},
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"source": [
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"## 1. System Health and Capabilities\n",
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"\n",
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 2,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Status: ok\n",
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"Simulation mode: True\n",
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"\n",
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"Available modules:\n",
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" ✅ flow: True\n",
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" ✅ pressure: True\n",
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" ✅ heater: True\n",
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" ❌ strobe: False\n",
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" ❌ camera: False\n",
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" ❌ droplet: False\n",
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" ✅ pump: True\n"
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]
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}
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],
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"source": [
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"# Check health\n",
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"health = client.health()\n",
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"print(\"\\nAvailable modules:\")\n",
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"for module, available in capabilities['modules'].items():\n",
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" status = \"✅\" if available else \"❌\"\n",
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" print(f\" {status} {module}: {available}\")\n"
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" print(f\" {status} {module}: {available}\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"metadata": {
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"jp-MarkdownHeadingCollapsed": true
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},
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"source": [
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"## 2. Channel Configuration\n",
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"\n",
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"metadata": {
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"jp-MarkdownHeadingCollapsed": true
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},
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"source": [
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"## 3. Flow/Pressure Control\n",
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"\n",
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"metadata": {
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"jp-MarkdownHeadingCollapsed": true
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},
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"source": [
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"## 4. Heater Control\n",
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"\n",
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"metadata": {
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"jp-MarkdownHeadingCollapsed": true
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},
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"source": [
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"## 5. Camera Snapshot\n",
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"\n",
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"metadata": {
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"jp-MarkdownHeadingCollapsed": true
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},
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"source": [
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"## 6. WebSocket Telemetry Streaming\n",
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"\n",
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"metadata": {
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"jp-MarkdownHeadingCollapsed": true
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},
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"source": [
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"## 7. Plot Streaming Data\n",
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"\n",
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"metadata": {
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"jp-MarkdownHeadingCollapsed": true
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},
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"source": [
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"## 8. On-Demand Data Capture\n",
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"\n",
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"metadata": {
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"jp-MarkdownHeadingCollapsed": true
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},
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"source": [
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"## 9. Droplet Detection (if available)\n",
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"\n",
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" print(\"❌ Droplet detection not available\")\n"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## 10. Syringe Pump Control (if available)\n",
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"\n",
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"This section uses the lightweight pump client. It supports the WoT pump Thing at `/pump/` and falls back to legacy `/api/control/pump/*` endpoints if present.\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Pump D state: {'pump': 'D', 'flow': 2500.0, 'diameter': 8.17, 'direction': 1, 'state': False, 'unit': 'UL/HR', 'gearbox': '100:1', 'microstep': '1/8', 'threadrod': '1-START', 'enabled': False}\n"
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]
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}
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],
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"source": [
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"from api.client.syringe_pump_api import SyringePumpAPI, PumpAPIError\n",
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"\n",
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"pump_api = SyringePumpAPI(base_url=API_BASE_URL, use_wot=False)\n",
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"\n",
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"try:\n",
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" pump=\"D\"\n",
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" state = pump_api.get_state(pump)\n",
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" print(f\"Pump {pump} state: {state}\")\n",
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" #print(state)\n",
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"\n",
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" # Example commands (uncomment when pump backend is available):\n",
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" # pump_api.set_diameter(pump, 8.17)\n",
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" # pump_api.set_direction(pump, \"infuse\")\n",
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" # pump_api.set_flow(pump, 100.0)\n",
500+
" # pump_api.set_state(pump, \"run\")\n",
501+
"except PumpAPIError as e:\n",
502+
" print(f\"❌ Pump API error: {e}\")\n",
503+
"except Exception as e:\n",
504+
" print(f\"❌ Pump not available: {e}\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"name": "python"
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.4"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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"nbformat_minor": 4
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}

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