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feat updated ephys link instructions for exe
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‎source/ephys_link/installation_and_use.md‎

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# Ephys Link
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[![PyPI version](https://badge.fury.io/py/ephys-link.svg)](https://badge.fury.io/py/ephys-link)
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[![Build](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/build.yml/badge.svg)](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/build.yml)
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[![CodeQL](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/codeql-analysis.yml/badge.svg)](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/codeql-analysis.yml)
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[![Dependency Review](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/dependency-review.yml/badge.svg)](https://github.com/VirtualBrainLab/ephys-link/actions/workflows/dependency-review.yml)
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[![Hatch project](https://img.shields.io/badge/%F0%9F%A5%9A-Hatch-4051b5.svg)](https://github.com/pypa/hatch)
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**Supported Manipulators:**
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| Manufacturer | Model |
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|--------------|-------------------------------------------------------------------|
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| Sensapex | <ul> <li>uMp-4</li> <li>uMp-3</li> </ul> |
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| New Scale | <ul> <li>Pathfinder MPM Control</li> <li>M3-USB-3:1-EP</li> </ul> |
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| Manufacturer | Model |
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|--------------|---------------------------------------------------------------------------|
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| Sensapex | <ul> <li>uMp-4</li> <li>uMp-3</li> </ul> |
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| New Scale | <ul> <li>Pathfinder MPM Control v2.8.8+</li> <li>M3-USB-3:1-EP</li> </ul> |
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Ephys Link is an open and extensible platform. It is designed to easily support integration with other manipulators.
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### Prerequisites
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1. [Python ≥ 3.8, < 3.13](https://www.python.org/downloads/release/python-3116/)
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1. Python 3.12+ requires the latest version
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of Microsoft Visual C++ (MSVC v143+ x86/64) and the Windows SDK (10/11) to
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be installed. They can be acquired through
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the [Visual Studio Build Tools Installer](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
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2. An **x86 Windows PC is required** to run the server.
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3. For Sensapex devices, the controller unit must be connected via an ethernet
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1. An **x86 Windows PC is required** to run the server.
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2. For Sensapex devices, the controller unit must be connected via an ethernet
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cable and powered. A USB-to-ethernet adapter is acceptable. For New Scale manipulators,
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the controller unit must be connected via USB and be powered by a 6V power
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supply.
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4. To use the emergency stop feature, ensure an Arduino with
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3. To use the emergency stop feature, ensure an Arduino with
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the [StopSignal](https://github.com/VirtualBrainLab/StopSignal) sketch is
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connected to the computer. Follow the instructions on that repo for how to
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set up the Arduino.
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is currently designed to interface with local/desktop instances of Pinpoint. It
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will not work with the web browser versions of Pinpoint at this time.
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<div style="padding: 15px; border: 1px solid transparent; border-color: transparent; margin-bottom: 20px; border-radius: 4px; color: #31708f; background-color: #d9edf7; border-color: #bce8f1;">
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<h3>Using a Python virtual environment is encouraged.</h3>
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<p>Create a virtual environment by running <code>python -m venv ephys_link</code></p>
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<p>Activate the environment by running <code>.\ephys_link\scripts\activate</code></p>
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<p>A virtual environment helps to isolate installed packages from other packages on your computer and ensures a clean installation of Ephys Link</p>
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</div>
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### Install as Standalone Executable
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### Install for use
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1. Download the latest executable from
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the [releases page](https://github.com/VirtualBrainLab/ephys-link/releases/latest).
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2. Double-click the executable file to launch the configuration window.
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1. Take note of the IP address and port. **Copy this information into Pinpoint to connect**.
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3. Select the desired configuration and click "Launch Server".
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Run the following command to install the server:
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The configuration window will close and the server will launch. Your configurations will be saved for future use.
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```bash
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pip install ephys-link
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```
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To connect to the server from Pinpoint, provide the IP address and port. For example, if the server is running on the
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same computer that Pinpoint is, use
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Update the server like any other Python package:
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- Server: `localhost`
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- Port: `8081`
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```bash
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pip install --upgrade ephys-link
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```
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If the server is running on a different (local) computer, use the IP address of that computer as shown in the startup
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window instead of `localhost`.
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### Install for development
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### Install for Development
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1. Clone the repository.
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2. Install [Hatch](https://hatch.pypa.io/latest/install/)
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3. In a terminal, navigate to the repository's root directory and run
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3. Install the latest Microsoft Visual C++ (MSVC v143+ x86/64) and the Windows SDK (10/11)
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via [Visual Studio Build Tools Installer](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
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4. In a terminal, navigate to the repository's root directory and run
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```bash
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hatch shell
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hatch shell
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```
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This will create a virtual environment and install the package in editable mode.
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This will create a virtual environment, install Python 12 (if not found), and install the package in editable mode.
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### Install as a Python package
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## Usage
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```bash
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pip install ephys-link
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```
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Import the modules you need and launch the server.
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Run the following commands in a terminal to start the server for the desired manipulator platform:
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```python
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from ephys_link.server import Server
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| Manipulator Platform | Command |
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|--------------------------------------|--------------------------------------|
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| Sensapex uMp-4 | `ephys-link` |
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| Sensapex uMp-3 | `ephys-link -t ump3` |
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| New Scale | `ephys-link -t new_scale` |
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| New Scale via Pathfinder HTTP server | `ephys-link -t new_scale_pathfinder` |
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server = Server()
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server.launch("sensapex", 8081)
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```
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There are a couple additional aliases for the Ephys Link executable: `ephys_link` and `el`.
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## CLI Usage
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By default, the server will broadcast with its local IP address on port 8081.
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**Copy this information into Pinpoint to connect**.
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Ephys Link can be launched from the command line directly. This is useful for computers or servers without graphical
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user interfaces.
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For example, if the server is running on the same computer that Pinpoint is, use
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Run the following commands in a terminal to start the server for the desired manipulator platform without the startup
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window:
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- Server: `localhost`
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- Port: `8081`
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| Manipulator Platform | Command |
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|--------------------------------------|---------------------------------------------|
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| Sensapex uMp-4 | `ephys-link.exe -b` |
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| Sensapex uMp-3 | `ephys-link.exe -b -t ump3` |
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| New Scale | `ephys-link.exe -b -t new_scale` |
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| New Scale via Pathfinder HTTP server | `ephys-link.exe -b -t new_scale_pathfinder` |
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More options can be viewed by running `ephys-link.exe -h`.
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### "New Scale" vs "New Scale via Pathfinder HTTP server"
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