initial commit for clade-light

examples/claude-light/claude_alab/__init__.py

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+import os
+from pathlib import Path
+
+# keep this line at the top of the file
+os.putenv("ALABOS_CONFIG_PATH", Path(__file__).parent.absolute() / "config.toml")
+
+from alab_management import add_device, add_task
+
+from .devices.claude import ClaudeLight
+from .tasks.claude import MeasureRGB
+
+# set the config path to the default config file
+
+
+add_device(ClaudeLight(name="rgb"))
+add_task(MeasureRGB)
+

examples/claude-light/claude_alab/config.toml

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+[general]
+name = 'claude_alab'  # Put the name of the lab here, it will be used as the DB name
+working_dir = "."  # the working directory of the lab, where the device and task definitions are stored
+
+[mongodb]  # the MongoDB configuration
+host = 'localhost'
+password = ''
+port = 27017
+username = ''
+
+# all the completed experiments are stored in this database
+# the db name will be the lab name + '_completed'
+[mongodb_completed]
+host = "localhost"
+password = ""
+port = 27017
+username = ""
+
+[rabbitmq]  # the RabbitMQ configuration
+host = "localhost"
+port = 5672
+
+# the user notification configuration, currently only email and slack are supported
+# if you don't want to use them, just leave them empty
+[alarm]
+# the email configuration. All the user notification will be sent to all the email_receivers in the list
+# the email_sender is the email address of the sender, e.g. [email protected]
+email_receivers = []
+email_sender = " "
+email_password = " "
+
+# the slack configuration. All the user notification will be sent to the slack_channel_id
+# the slack_bot_token is the token of the slack bot, you can get it from https://api.slack.com/apps
+slack_bot_token = " "
+slack_channel_id = " "
+
+[large_result_storage]
+# the default storage configuration for tasks that generate large results 
+# (>16 MB, cannot be contained in MongoDB)
+# currently only gridfs is supported
+# storage_type is defined by using LargeResult class located in alab_management/task_view/task.py
+# you can override this default configuration by setting the storage_type in the task definition
+default_storage_type = "gridfs"

examples/claude-light/claude_alab/devices/__init__.py

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+"""You don't have to modify this file. It is used to make Python treat the directory as containing packages."""

examples/claude-light/claude_alab/devices/claude.py

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+import json
+import requests
+from typing import ClassVar
+
+from alab_management.device_view import BaseDevice
+from alab_management.sample_view import SamplePosition
+
+
+class ClaudeLight(BaseDevice):
+    """Claude Light definition"""
+    description: ClassVar[str] = "Claude-Light device"
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.running = None
+
+    def __str__(self):
+        return 'An RGB Claude Light'
+
+    @property
+    def sample_positions(self):
+        """Sample positions define the sample positions related to this device."""
+        return [
+            SamplePosition(
+                name="DefaultSamplePosition",
+                number=1,
+                description="Default sample position",
+            )
+        ]
+
+    def connect(self):
+        self.running = True
+
+    def disconnect(self):
+        self.running = False
+
+    def is_running(self):
+        return self.running
+
+    def measure(self, R=0, G=0, B=0):
+        resp = requests.get('https://claude-light.cheme.cmu.edu/api',
+                            params={'R': R, 'G': G, 'B': B})
+        data = resp.json()
+        return data

examples/claude-light/claude_alab/tasks/__init__.py

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+"""You don't have to modify this file. It is used to make Python treat the directory as containing packages."""

examples/claude-light/claude_alab/tasks/claude.py

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+from bson import ObjectId  # type: ignore
+from pydantic import BaseModel
+
+from alab_management.task_view.task import BaseTask
+from claude_alab.devices.claude import ClaudeLight
+
+
+class MeasureRGB(BaseTask):
+    """Measurement task definition."""
+    def __init__(self, R=0, G=0, B=0, **kwargs):
+        super().__init__(**kwargs)
+        self.R = R
+        self.G = G
+        self.B = B
+
+    def run(self):
+        print('Running a job')
+        with self.lab_view.request_resources({"rgb": {}}) as (devices, _):
+            print(devices)
+            return devices["rgb"].measure(self.R, self.G, self.B)

examples/claude-light/example.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "07e6b35b-6fde-4bb8-961e-2f2cd7faee16",
+   "metadata": {},
+   "source": [
+    "# Setting up\n",
+    "\n",
+    "Run these commands in this directory. This will install the lab and setup your database .\n",
+    "\n",
+    "\n",
+    "    pip install -e .\n",
+    "\n",
+    "To start the server, run these commands.\n",
+    "\n",
+    "\n",
+    "    export  ALABOS_CONFIG_PATH=`pwd`/claude_alab/config.toml\n",
+    "    export SIM_MODE_FLAG=FALSE\n",
+    "    alabos setup\n",
+    "    alabos launch &\n",
+    "    alabos launch_worker &"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0fa7bd38-8367-41b7-a372-53165592f32e",
+   "metadata": {},
+   "source": [
+    "# setup and submit an experiment"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "63d09232-7f62-4182-8483-d7cd62729aa8",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "ObjectId('6705d63f9fa06af11c9361bc')"
+      ]
+     },
+     "execution_count": 1,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from alab_management.builders import ExperimentBuilder\n",
+    "from claude_alab.tasks.claude import MeasureRGB\n",
+    "\n",
+    "# you need a name for the experiment\n",
+    "# you can also provide tags for better organization\n",
+    "# You can also provide arbitrary kwargs to the builder\n",
+    "# it will be stored as metadata (e.g., description)\n",
+    "exp = ExperimentBuilder(name=\"MyExperiment\",\n",
+    "                        tags=[\"tag1\", \"tag2\"],\n",
+    "                        description=\"My first experiment\")\n",
+    "\n",
+    "sample = exp.add_sample(name=\"my_sample_1\",\n",
+    "                        tags=[\"project\"],\n",
+    "                        description=\"My first sample\")\n",
+    "\n",
+    "\n",
+    "task1 = MeasureRGB(R=0, G=0, B=0)\n",
+    "task2 = MeasureRGB(R=0, G=1, B=0)\n",
+    "# you can also do task.add_to([sample1, sample2, ...]) to add multiple samples to the task\n",
+    "task1.add_to(sample)\n",
+    "task2.add_to(sample)\n",
+    "exp_id = exp.submit(address=\"http://localhost:8895\")\n",
+    "exp_id"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "549ffdc6-7141-4a3c-9b5b-2009a5cce382",
+   "metadata": {},
+   "source": [
+    "# get the experiment status"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "1f9d8e48-af24-4282-9bd0-8ec7375b50ef",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'id': '6705d63f9fa06af11c9361bc',\n",
+       " 'name': 'MyExperiment',\n",
+       " 'progress': 1.0,\n",
+       " 'samples': [{'id': '6705d63f9fa06af11c9361bd',\n",
+       "   'name': 'my_sample_1',\n",
+       "   'position': None}],\n",
+       " 'status': 'COMPLETED',\n",
+       " 'submitted_at': 'Tue, 08 Oct 2024 21:02:55 GMT',\n",
+       " 'tasks': [{'id': '6705d63f9fa06af11c9361be',\n",
+       "   'message': '',\n",
+       "   'status': 'COMPLETED',\n",
+       "   'type': 'MeasureRGB'},\n",
+       "  {'id': '6705d63f9fa06af11c9361bf',\n",
+       "   'message': '',\n",
+       "   'status': 'COMPLETED',\n",
+       "   'type': 'MeasureRGB'}]}"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from alab_management import get_experiment_status, get_experiment_result\n",
+    "\n",
+    "get_experiment_status(exp_id)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "de0259e5-8b27-4be9-a1e4-dcff28aa2e3e",
+   "metadata": {},
+   "source": [
+    "# Get the results"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "60d4cced-f55b-4c30-93e1-4b3c49e9bba3",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'completed_at': '2024-10-08T21:03:00.003000',\n",
+       " 'id': '6705d63f9fa06af11c9361bc',\n",
+       " 'metadata': {'description': 'My first experiment'},\n",
+       " 'name': 'MyExperiment',\n",
+       " 'progress': 1.0,\n",
+       " 'samples': [{'id': '6705d63f9fa06af11c9361bd',\n",
+       "   'metadata': {'description': 'My first sample'},\n",
+       "   'name': 'my_sample_1',\n",
+       "   'tags': ['project']}],\n",
+       " 'status': 'COMPLETED',\n",
+       " 'submitted_at': '2024-10-08T21:02:55.943000',\n",
+       " 'tags': ['tag1', 'tag2'],\n",
+       " 'tasks': [{'completed_at': '2024-10-08T21:02:57.863000',\n",
+       "   'id': '6705d63f9fa06af11c9361be',\n",
+       "   'message': '',\n",
+       "   'parameters': {'B': 0, 'G': 0, 'R': 0},\n",
+       "   'result': {'in': [0.0, 0.0, 0.0],\n",
+       "    'out': {'415nm': 0,\n",
+       "     '445nm': 0,\n",
+       "     '480nm': 0,\n",
+       "     '515nm': 2,\n",
+       "     '555nm': 5,\n",
+       "     '590nm': 2,\n",
+       "     '630nm': 5,\n",
+       "     '680nm': 0,\n",
+       "     'clear': 18,\n",
+       "     'nir': 0}},\n",
+       "   'samples': ['my_sample_1'],\n",
+       "   'started_at': '2024-10-08T21:02:56.118000',\n",
+       "   'status': 'COMPLETED',\n",
+       "   'type': 'MeasureRGB'},\n",
+       "  {'completed_at': '2024-10-08T21:02:59.847000',\n",
+       "   'id': '6705d63f9fa06af11c9361bf',\n",
+       "   'message': '',\n",
+       "   'parameters': {'B': 0, 'G': 1, 'R': 0},\n",
+       "   'result': {'in': [0.0, 1.0, 0.0],\n",
+       "    'out': {'415nm': 923,\n",
+       "     '445nm': 329,\n",
+       "     '480nm': 11541,\n",
+       "     '515nm': 62894,\n",
+       "     '555nm': 9972,\n",
+       "     '590nm': 1298,\n",
+       "     '630nm': 1305,\n",
+       "     '680nm': 1243,\n",
+       "     'clear': 50552,\n",
+       "     'nir': 1294}},\n",
+       "   'samples': ['my_sample_1'],\n",
+       "   'started_at': '2024-10-08T21:02:58.103000',\n",
+       "   'status': 'COMPLETED',\n",
+       "   'type': 'MeasureRGB'}]}"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "results = get_experiment_result(exp_id)\n",
+    "results"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "9be8cdd2-81dc-4363-9f18-1ee498f90112",
+   "metadata": {},
+   "source": [
+    "Here we subtract the background from the measurement. Maybe there is a better way to do this?"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "a39fda51-2ea7-4ada-8589-7ebd379a273c",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "62892"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "r0 = results['tasks'][0]['result']['out']['515nm']\n",
+    "r1 = results['tasks'][1]['result']['out']['515nm']\n",
+    "r1 - r0"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}