diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..3af4b42 --- /dev/null +++ b/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2025 Jacques Attinger + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/README.md b/README.md index 6be02de..c383fd5 100644 --- a/README.md +++ b/README.md @@ -1,271 +1,257 @@ -# miniMBE GUI - -A comprehensive graphical interface for controlling and monitoring a Molecular Beam Epitaxy (MBE) system, featuring real-time data logging, e-beam source control, and automated alert systems. - -## Features - -### 🌡️ Temperature and Pressure Monitoring -The **Temperature/Pressure** tab provides real-time monitoring and logging capabilities: -- **Live Data Display**: Monitor up to 8 temperature channels and 2 pressure gauges simultaneously -- **Data Logging**: Automatically saves timestamped readings to CSV files for analysis -- **Automated Alerts**: Configure low-pressure alerts via email to prevent system failures -- **Visualization**: Plot and analyze historical temperature and pressure trends -- **Configurable Sampling**: Adjust data collection intervals to match your experimental needs - -### ⚡ E-Beam Source Control -The **E-Beam** tab offers precise control over electron beam evaporation sources: -- **Multi-Source Support**: Control multiple e-beam sources independently -- **Real-Time Flux Monitoring**: Track deposition rates with integrated flux sensor readings -- **Data Logging**: Record flux measurements with timestamps for process documentation -- **Safety Features**: Built-in monitoring to ensure safe operation -- **Calibration Support**: Easy configuration for different evaporant materials - -### 🎯 3-Axis Manipulator Control -The **Main** tab provides comprehensive control over the XYZ manipulator system: -- **Individual Axis Control**: Independent control widgets for X, Y, and Z axes -- **Real-Time Position Tracking**: Live position updates displayed on visual canvas and status panel -- **Manual Positioning**: Move axes to specific coordinates at configurable speeds -- **Emergency Stop**: Immediate halt functionality for each axis -- **Homing Operations**: Automated homing sequences for axis calibration -- **Connection Monitoring**: Real-time Modbus connection status for each stepper motor -- **Workspace Visualization**: 2D canvas showing current manipulator position and loaded patterns - -### 📐 DXF Pattern Execution -Advanced pattern execution system for automated deposition: -- **DXF File Import**: Load complex deposition patterns from CAD-generated DXF files -- **Coordinate Validation**: Automatic workspace bounds checking to prevent out-of-range movements -- **Path Optimization**: Smart filtering to remove duplicate points and unnecessary backtracks -- **Jump Detection**: Warning system for large movements that might indicate design errors -- **Dual Speed Control**: Separate configurable speeds for printing (deposition) vs. travel movements -- **Path Visualization**: Real-time display of loaded patterns on the position canvas -- **Progress Monitoring**: Live progress tracking with time estimates and completion predictions -- **Pause/Resume**: Ability to pause and resume pattern execution -- **Nozzle Compensation**: Configurable nozzle diameter for precise deposition control -- **Stop-and-Go Mode**: Automated hop-dwell motion for ultra-slow deposition speeds -- **Recipe System**: Command-based execution supporting both print and travel movements - -### 📸 Camera Integration -Real-time visual monitoring of the MBE chamber: -- **Live Video Feed**: Continuous camera stream for process observation -- **Exposure Control**: Adjustable exposure settings via slider interface -- **Gain Control**: Real-time gain adjustment for optimal image quality -- **Camera Service**: Background thread handling for non-blocking operation -- **Error Handling**: Automatic error reporting and recovery - -### 🔧 Modbus Debugging & Logging -Advanced debugging tools for system development and troubleshooting: -- **Modbus Traffic Logging**: Capture all Modbus communications for debugging -- **Event Timestamping**: Precise timestamps on all controller events -- **Automatic Logging**: Option to auto-start logging when patterns begin -- **Pattern Metadata**: Logs include DXF filename, vertex count, and bounding box information -- **Multi-Axis Coordination**: Monitors communication across all three stepper motor controllers - -### 🏗️ System Architecture -The application follows a modular design with clear separation of concerns: -- **Controllers**: Low-level hardware communication (SMCD14 stepper motor controllers) -- **Services**: Business logic for cameras, sensors, data logging, and DXF parsing -- **Widgets**: Reusable UI components for each control panel and tab -- **Windows**: Top-level application window coordinating all subsystems -- **Utils**: Shared utilities for DXF parsing, speed calculations, and coordinate transformations - -## Hardware Requirements - -This GUI interfaces with the following hardware components: - -### Required -- **SMCD14 Stepper Motor Controllers** (x3): One for each manipulator axis (X, Y, Z) - - Communication: Modbus TCP (default: `192.168.0.100:502`) - - Slave IDs: X=1, Y=2, Z=3 - - See `SMCD14_manual [EN].pdf` for controller documentation - -### Optional -- **Pfeiffer Vacuum Gauge**: For chamber pressure monitoring - - Communication: RS-232 serial (default: `COM4` at 9600 baud) - - Supports Pfeiffer vacuum protocol -- **Temperature Controller/Reader**: For multi-channel temperature monitoring - - Communication: TCP/IP (default: `192.168.111.222`) - - Supports up to 8 temperature channels -- **Camera** (e.g., Basler or similar): For live chamber monitoring - - Must be compatible with the camera service implementation -- **E-Beam Flux Sensor**: For deposition rate monitoring - - Serial communication for real-time flux readings - -## Development setup - -1. Create and activate a virtual environment: + + + +[![Forks][forks-shield]][forks-url] +[![Stargazers][stars-shield]][stars-url] +[![Issues][issues-shield]][issues-url] +[![License][license-shield]][license-url] + +
+
+ + miniMBE GUI logo + + +

miniMBE GUI

+ +

+ A desktop app to run a Mini-MBE (molecular beam epitaxy) system from one window. +
+ Move the sample stage, draw patterns from DXF files, and watch pressure, temperature, flux and camera feeds. +
+
+ Report a Bug or Request a Feature +

+
+ +
+ Table of Contents +
    +
  1. + About The Project + +
    2. +
  2. + Getting Started + +
    3. +
  3. Usage
    4. +
  4. Project Structure
    5. +
  5. Contributing
    6. +
  6. License
    7. +
  7. Acknowledgments
    8. +
+
+ +## About The Project + +![miniMBE GUI, Main tab][screenshot-main] + +The miniMBE GUI controls the Mini-MBE system of the Yang Research Group at the University of Chicago. +It replaces the vendor's LabVIEW interface with one Python app. +The app also adds logging, alerts and pattern drawing that the vendor tool does not have. +The screenshots show the app with no hardware connected. + +Main features: + +* **Manipulator control.** + Move the X, Y and Z axes, home them, stop them, and see the position on a live 2D canvas. + The axes use three [SMCD14](SMCD14_manual%20[EN].pdf) stepper controllers over Modbus TCP. +* **DXF pattern execution.** + Load a CAD drawing, check it in a coordinate checker (bounds, large jumps, speeds), then run it. + You can set separate print and travel speeds, pause and resume, and see progress and time left. + A stop-and-go mode supports very slow deposition speeds. +* **Temperature and pressure.** + Read up to 8 temperature channels and 2 pressure gauges, log them to CSV, and plot them. + The app can send an email when the pressure goes above a limit. +* **E-beam source.** + Set high voltage, emission current and filament current. + Watch the flux and log it to CSV. +* **Camera.** + Live video of the chamber with exposure and gain sliders. +* **Modbus log.** + Record every Modbus message with timestamps to help debug the hardware. + +![miniMBE GUI, E-Beam tab][screenshot-ebeam] + +

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+ +### Built With + +* [![Python][Python-badge]][Python-url] +* [![Qt][Qt-badge]][Qt-url] +* [![NumPy][NumPy-badge]][NumPy-url] +* [![Matplotlib][Matplotlib-badge]][Matplotlib-url] +* [ezdxf](https://github.com/mozman/ezdxf) for DXF files +* [Shapely](https://github.com/shapely/shapely) for geometry +* [pymodbus](https://github.com/pymodbus-dev/pymodbus) for the motor controllers +* [pyserial](https://github.com/pyserial/pyserial) for the vacuum gauge and e-beam supply +* [VmbPy](https://github.com/alliedvision/VmbPy) for Allied Vision cameras + +

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+ +## Getting Started + +### Prerequisites + +* Python 3.11 (the repo pins 3.11.3 in `.python-version`). +* The hardware you want to use. + The app starts without hardware, but the related panels show "Disconnected". + +| Device | How it connects | Default setting | +| --- | --- | --- | +| 3 × SMCD14 stepper controllers (X, Y, Z) | Modbus TCP | host `169.254.151.255`, port 502, slave IDs 1, 2, 3 (`controllers/manipulator_manager.py`) | +| Temperature reader | TCP/IP | `192.168.111.222` (`services/temperature_controller.py`) | +| Pfeiffer vacuum gauge | Serial (RS-232) | `COM4`, 9600 baud | +| E-beam power supply and flux sensor | Serial | `COM5` (`services/ebeam_controller.py`) | +| Allied Vision camera | VmbPy | needs the [Vimba X SDK](https://www.alliedvision.com/en/products/software/vimba-x-sdk/) | + +Change the defaults in the files named above to match your setup. + +### Installation + +1. Clone the repo. + ```sh + git clone https://github.com/JacquesAttinger/Mini-MBE-Graphical-User-Interface.git + cd Mini-MBE-Graphical-User-Interface ``` +2. Create a virtual environment and install the packages. + ```sh python -m venv .venv && source .venv/bin/activate - ``` -2. Install dependencies: - ``` pip install -r requirements.txt ``` -3. Install development dependencies to run tests: - ``` - pip install -r requirements-dev.txt - ``` -4. Run the application: +3. Create the email credentials file (see [Email alerts](#email-alerts)). + The temperature tab imports it, so the app needs this file to start. + ```sh + cp email_credentials.py.template email_credentials.py ``` +4. Start the app. + ```sh python app.py ``` -## Running tests +To run the tests, install the development packages and run `pytest`: -After installing the development dependencies, run the test suite with: - -``` +```sh +pip install -r requirements-dev.txt pytest ``` -## Email Alert Configuration +### Email alerts -The **Temperature/Pressure** tab can send automated low-pressure alerts via email to help prevent system failures. To enable this feature: +The Temp/Pressure tab can email you when the pressure goes above a limit. +It sends mail through Gmail with an app password. -### Setup Instructions - -1. **Create your credentials file:** - ```bash - cp email_credentials.py.template email_credentials.py - ``` - -2. **Generate a Gmail App Password:** - - Go to [Google Account App Passwords](https://myaccount.google.com/apppasswords) - - Sign in to your Google account - - Select "Mail" as the app and your device type - - Click "Generate" and copy the 16-character password - -3. **Edit `email_credentials.py`:** +1. Create an app password at [Google App Passwords](https://myaccount.google.com/apppasswords). +2. Fill in `email_credentials.py`: ```python + ALERT_SENDER = "your-sender@gmail.com" ALERT_RECEIVER = "your-email@gmail.com" GMAIL_APP_PASSWORD = "your-16-char-app-password" ``` - -4. **Save the file** - it's already in `.gitignore` and won't be committed to version control - -### Security Notes - -- ✅ `email_credentials.py` is excluded from Git via `.gitignore` -- ✅ Never commit actual credentials to the repository -- ✅ Use Gmail App Passwords (not your regular Gmail password) -- ✅ The template file (`email_credentials.py.template`) is safe to share -- ⚠️ If you change computers, you'll need to set up the credentials file again - -### How Alerts Work - -Once configured, the system will automatically send email notifications when: -- Chamber pressure exceeds safe thresholds -- Pressure readings indicate potential vacuum failures -- System requires immediate attention - -You can configure alert thresholds and monitoring intervals directly from the Temperature/Pressure tab in the GUI. - -## Typical Workflow - -Here's how to use the system for a typical deposition experiment: - -### 1. **System Startup** - - Launch the application: `python app.py` - - Verify all three manipulator axes show "Connected" status in the status panel - - Check the **Camera** tab to ensure live feed is working - - Open the **Temp/Pressure** tab to monitor chamber conditions - -### 2. **Pre-Deposition Setup** - - **Temperature Monitoring**: Start logging temperature and pressure data - - **E-Beam Configuration**: Set up source parameters and begin flux monitoring - - **Email Alerts**: Ensure low-pressure alerts are configured (see Email Alert Configuration above) - - **Position Manipulator**: Use the Main tab to manually position the substrate at the starting location - -### 3. **Load Deposition Pattern** - - Click **Load DXF** in the Main tab - - Select your DXF file (generated from CAD software) - - Specify the origin coordinates where the pattern should be placed - - Review the **Coordinate Checker** dialog: - - Verify vertex count and bounding box - - Check for any large jumps (highlighted in orange) - - Inspect velocity calculations - - Set print speed (deposition) and travel speed when prompted - - Accept or cancel based on the review - -### 4. **Execute Pattern** - - Click **Start Pattern** (enabled after successful DXF load) - - Wait while the manipulator moves to the starting position - - Confirm "Ready to begin printing?" dialog - - Monitor progress: - - Progress bar shows completion percentage - - Time remaining updates in real-time - - Position canvas displays current location - - Use **Pause Pattern** if needed (resumes from the same point) - -### 5. **During Deposition** - - **Temperature/Pressure Tab**: Monitor chamber conditions continuously - - **E-Beam Tab**: Track flux measurements and adjust if needed - - **Camera Tab**: Observe the deposition process visually - - **Modbus Panel**: View real-time communication logs (for debugging) - -### 6. **Post-Deposition** - - Pattern completion triggers automatic logging stop - - Review logged data in `logs/` directory: - - Temperature/pressure CSV files - - Flux measurement CSV files - - Modbus communication logs (if enabled) - - Use **Temp/Pressure** tab to plot data for analysis - -### 7. **Emergency Procedures** - - **Individual Axis Stop**: Click axis-specific stop button - - **Pattern Abort**: Close the confirmation dialog or use Emergency Stop - - **Pressure Alert**: System automatically emails if chamber pressure exceeds threshold - - All safety shutdowns are logged for post-incident analysis - -## Command Line Options - -```bash -# Enable detailed motion logging for debugging +3. Never commit this file. + It is in `.gitignore`. + +If you do not want alerts, leave the placeholder values. +The app still runs, and the email step fails quietly. + +

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+ +## Usage + +A typical run looks like this: + +1. **Start up.** + Run `python app.py`. + Check that the three axes show as connected on the Main tab. + Open the Camera and Temp/Pressure tabs to check the chamber. +2. **Prepare.** + Start the temperature and pressure log. + Set the e-beam source and start the flux log. + Move the sample to the start position on the Main tab. +3. **Load a pattern.** + Click **Load DXF** and pick a file. + Enter the origin where the pattern goes. + Read the coordinate checker: vertex count, bounding box, and large jumps (shown in orange). + Set the print speed and the travel speed, then accept. +4. **Run it.** + Click **Start Pattern** and confirm the prompt. + Watch the progress, time left and position. + Click **Pause Pattern** to stop and later resume from the same point. +5. **Finish.** + The app stops logging when the pattern ends. + Find the logs in `logs/`: temperature and pressure CSV files, flux CSV files, and Modbus logs if you enabled them. +6. **Emergency.** + Use the **Stop** button on an axis to stop it. + Close the confirm dialog to abort before a pattern starts. + +To log every motion command for debugging, start the app with: + +```sh python app.py --motion-log ``` +

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+ ## Project Structure ``` -miniMBE-GUI/ -├── app.py # Application entry point -├── controllers/ # Hardware communication layer -│ ├── manipulator_manager.py # Coordinates all 3 axes -│ └── smcd14_controller.py # SMCD14 stepper motor driver -├── services/ # Business logic and hardware interfaces -│ ├── camera_service.py # Camera capture and streaming -│ ├── sensor_readers.py # Pressure and temperature sensors -│ ├── ebeam_controller.py # E-beam source control -│ ├── data_logger.py # CSV logging for temp/pressure -│ ├── flux_logger.py # CSV logging for flux data -│ └── dxf_service.py # DXF file parsing -├── widgets/ # UI components -│ ├── temperature_pressure_tab.py -│ ├── ebeam_tab.py -│ ├── camera_tab.py -│ ├── axis_control.py # Individual axis control widget -│ ├── position_canvas.py # 2D visualization canvas -│ └── modbus_panel.py # Debugging panel -├── windows/ -│ └── main_window.py # Main application window -├── utils/ # Shared utilities -│ └── dxf_parser.py # DXF to recipe conversion -└── tests/ # Unit and integration tests +├── app.py # Entry point +├── controllers/ # Hardware control (SMCD14 motors, multi-axis manager) +├── services/ # Camera, sensors, e-beam, data loggers, DXF loading +├── widgets/ # UI panels for each tab +├── windows/ # Main window +├── utils/ # DXF parsing, speed and Modbus helpers +├── SMCD14_LV2020/ # Vendor LabVIEW project for the SMCD14 (reference) +└── tests/ # Tests and hardware test scripts ``` +

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+ ## Contributing -This is a research project developed for the Yang Research Group at the University of Chicago. If you're using or modifying this code for your own MBE system: +Bug reports and ideas are welcome. +Please [open an issue](https://github.com/JacquesAttinger/Mini-MBE-Graphical-User-Interface/issues/new) and describe what you saw or what you need. +This project does not take pull requests at this time. -1. Fork the repository -2. Create a feature branch -3. Run the test suite: `pytest` -4. Submit a pull request with a clear description of changes +

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## License -*[Add license information here]* +Distributed under the MIT License. +See [`LICENSE`](LICENSE) for details. -## Acknowledgments +

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-Developed at the University of Chicago for the Yang Research Group's Mini-MBE system. +## Acknowledgments +* The Yang Research Group at the University of Chicago, for the Mini-MBE system this app controls. +* The SMCD14 LabVIEW project and manual from the controller vendor. +* [Best-README-Template](https://github.com/othneildrew/Best-README-Template) + +

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+ +[forks-shield]: https://img.shields.io/github/forks/JacquesAttinger/Mini-MBE-Graphical-User-Interface.svg?style=for-the-badge +[forks-url]: https://github.com/JacquesAttinger/Mini-MBE-Graphical-User-Interface/network/members +[stars-shield]: https://img.shields.io/github/stars/JacquesAttinger/Mini-MBE-Graphical-User-Interface.svg?style=for-the-badge +[stars-url]: https://github.com/JacquesAttinger/Mini-MBE-Graphical-User-Interface/stargazers +[issues-shield]: https://img.shields.io/github/issues/JacquesAttinger/Mini-MBE-Graphical-User-Interface.svg?style=for-the-badge +[issues-url]: https://github.com/JacquesAttinger/Mini-MBE-Graphical-User-Interface/issues +[license-shield]: https://img.shields.io/github/license/JacquesAttinger/Mini-MBE-Graphical-User-Interface.svg?style=for-the-badge +[license-url]: https://github.com/JacquesAttinger/Mini-MBE-Graphical-User-Interface/blob/main/LICENSE +[screenshot-main]: images/screenshot-main.png +[screenshot-ebeam]: images/screenshot-ebeam.png +[Python-badge]: https://img.shields.io/badge/Python-3776AB?style=for-the-badge&logo=python&logoColor=white +[Python-url]: https://www.python.org/ +[Qt-badge]: https://img.shields.io/badge/Qt%20for%20Python-41CD52?style=for-the-badge&logo=qt&logoColor=white +[Qt-url]: https://doc.qt.io/qtforpython-6/ +[NumPy-badge]: https://img.shields.io/badge/NumPy-013243?style=for-the-badge&logo=numpy&logoColor=white +[NumPy-url]: https://numpy.org/ +[Matplotlib-badge]: https://img.shields.io/badge/Matplotlib-11557c?style=for-the-badge +[Matplotlib-url]: https://matplotlib.org/ diff --git a/images/logo.png b/images/logo.png new file mode 100644 index 0000000..4b4f251 Binary files /dev/null and b/images/logo.png differ diff --git a/images/screenshot-ebeam.png b/images/screenshot-ebeam.png new file mode 100644 index 0000000..544b2b1 Binary files /dev/null and b/images/screenshot-ebeam.png differ diff --git a/images/screenshot-main.png b/images/screenshot-main.png new file mode 100644 index 0000000..c18c05f Binary files /dev/null and b/images/screenshot-main.png differ diff --git a/logs/temperature_pressure/2026-10-03.csv b/logs/temperature_pressure/2026-10-03.csv new file mode 100644 index 0000000..d780bcb --- /dev/null +++ b/logs/temperature_pressure/2026-10-03.csv @@ -0,0 +1 @@ +timestamp,pressure,temperature