reorganize project structure and add READMEs

README.md

@@ -1,6 +1,145 @@
 # EBEAM System Dashboard Software
 
-### 1. Development Workflow
+
+![GUI layout diagram](media/GUI_layout.png)
+
+### 1. Core Architecture and Flow
+
+- **High-level Design**: The application is divided into several modules:
+  - **main.py**: Entry point that initializes the COM port configuration and launches the dashboard
+  - **dashboard.py**: Core dashboard class that sets up the main GUI layout and manages subsystems
+  - **instrumentctl/**: Instrument-specific command libraries.
+  - **subsystem/**: Contains classes and methods to manage individual hardware subsystems (e.g., VTRXSubsystem, EnvironmentalSubsystem).
+  - **utils.py**: Utility functions and classes that support the main application (Logging, setup scripts, etc.).
+
+```mermaid
+flowchart TD
+    Start([python main.py]) --> PortConfig[Show Port Configuration Dialog]
+    PortConfig --> SaveConfig[Save Port Configuration]
+
+    %% Main Dashboard Setup
+    SaveConfig --> InitDash[Initialize Dashboard]
+    InitDash --> SetupPane[Create Main Pane Structure]
+    SetupPane --> LoadLayout[Load Saved Layout]
+    LoadLayout --> CreateFrames[Create Frame Structure]
+
+    %% Core Components
+    CreateFrames --> Messages[Messages Frame]
+    CreateFrames --> Controls[Main Controls]
+    CreateFrames --> SubSystems[[Subsystem Initialization]]
+
+    %% Subsystems Detail
+    SubSystems --> Vacuum[Vacuum System]
+    SubSystems --> Environmental[Environmental]
+    SubSystems --> Gas[Gas Control]
+    SubSystems --> Interlocks[Interlocks]
+    SubSystems --> Oil[Oil System]
+    SubSystems --> Cathode[Cathode Heating]
+
+    %% Control Components
+    Controls --> MainTab[Main Control Tab]
+    Controls --> ConfigTab[Configuration Tab]
+
+    %% Monitoring Loop
+    CreateFrames --> Monitor[[Start COM Port Monitor Loop]]
+    Monitor --> CheckChanges{Port Changes?}
+    CheckChanges -->|Yes| UpdateSys[Update Affected Systems]
+    UpdateSys --> CheckChanges
+    CheckChanges -->|No| Continue[Continue Monitoring]
+    Continue --> CheckChanges
+```
+
+### 2. Dashboard (dashboard.py)
+
+- **EBEAMSystemDashboard Class**: The main class that sets up the dashboard interface.
+  - Implements a flexible, configurable layout system using Tkinter's PanedWindow container widget.
+  - Allows users to arrange and resize different control sections at run-time.
+   - Each subsystem occupies its own configurable space
+
+### 3. Subsystems
+
+- **`vtrx/vtrx.py`**:
+  - Manages the VTRX system, including serial communication and error handling.
+  - Displays pressure data and switch states, updating the GUI in real-time.
+  - Logs messages and errors to the messages frame.
+
+- **`environmental/environmental.py`**:
+  - Monitors and displays temperature data from various thermometers.
+
+- **`interlocks/interlocks.py`**:
+  - Monitors the status of various safety critical interlocks (e.g., Vacuum, Water, Door sensors).
+  - Updates GUI indicators based on interlock status.
+
+- **`oil_system/oil_system.py`**:
+  - Monitors and displays oil temperature and pressure.
+
+- **`cathode_heating/cathode_heating.py`**:
+  - Manages three independent cathode heating channels
+  - Power supply control interface
+  - Real-time temperature plotting with overtemp indication
+
+- **`visualization_gas_control.py`**:
+  - Controls the Argon bleed system via serial communication.
+  - TBD
+
+
+### 4. Utilities (`utils.py`)
+
+- **MessagesFrame Class**:
+  - A custom Tkinter frame for displaying messages and errors.
+  - Supports logging messages with timestamps and trimming old messages to maintain a maximum number of lines.
+
+- **TextRedirector Class**:
+  - Redirects stdout to a Tkinter Text widget.
+  - Ensures that all print statements in the application are displayed in the messages frame.
+
+- **SetupScripts Class**:
+  - Manages the selection and execution of configuration scripts.
+  - Provides a GUI for selecting scripts from a dropdown menu and executing them.
+
+### 5. Directory Structure:
+```
+EBEAM_DASHBOARD/
+├── README.md
+├── __init__.py 
+├── dashboard.py
+├── instrumentctl/
+│   ├── README.md
+│   ├── __init__.py
+│   ├── power_supply/
+│   │   ├── README.md
+│   │   └── power_supply_9014.py
+│   ├── G9_driver/
+│   │   ├── README.md
+│   │   └── G9_driver.py
+│   └── E5CN_modbus/
+│       ├── README.md
+│       └── E5CN_modbus.py
+├── main.py
+├── subsystem/
+│   ├── __init__.py
+│   ├── cathode_heating/
+│   │   ├── README.md
+│   │   └── cathode_heating.py
+│   ├── environmental/
+│   │   ├── README.md
+│   │   └── environmental.py
+│   ├── interlocks/
+│   │   ├── README.md
+│   │   └── interlocks.py
+│   ├── oil_system/
+│   │   ├── README.md
+│   │   └── oil_system.py
+│   ├── visualization_gas_control/
+│   │   ├── README.md
+│   │   └── visualization_gas_control.py
+│   └── vtrx/
+│       ├── README.md
+│       └── vtrx.py
+└── utils.py
+```
+
+### 6. Development Workflow
 ![branching](https://github.com/mslaffin/EBEAM_dashboard/blob/main/media/branching_diagram.png)
 #### Branching strategy
 All code development intended to impact a future release is done on the latest `develop` branch. This applies to new instrument features, bug fixes, etc. The `develop` branch is **not stable**.
@@ -56,102 +195,7 @@ Fill in the PR template with a description of your changes, any related issues,
 
 Assign reviewers to your PR. Merge.
 
-### 2. Executable Build Instructions
+### 6. Executable Build Instructions
 ```
 python -m PyInstaller EBEAM_DASHBOARD.spec
 ```
-
-### 3. Architecture
-![GUI layout diagram](https://github.com/uw-loci/EBEAM_dashboard/blob/main/media/GUI_layout.png)
-- **Language & Libraries**: Python, using the [Tkinter](https://docs.python.org/3/library/tkinter.html) interface for the GUI, [matplotlib](https://matplotlib.org/) for plotting, and [Pyserial](https://pythonhosted.org/pyserial/) for communication with external systems through virtual COM ports.
-- **High-level Design**: The application is divided into several modules:
-  - **main.py**: Manages the main application startup and configuration.
-  - **dashboard.py**: Handles the main user interface and dashboard setup.
-  - **instrumentctl/**: Instrument specific command libraries.
-  - **subsystem/**: Contains classes and methods to manage individual subsystems (e.g., VTRXSubsystem, EnvironmentalSubsystem).
-  - **utils.py**: Utility functions and classes that support the main application (Logging, setup scripts, etc.).
-  - Core Structure:
-```
-EBEAM_DASHBOARD/
-├── __init__.py 
-├── dashboard.py
-├── instrumentctl/
-│   ├── __init__.py
-│   ├── apex_mass_flow_controller.py
-│   └── power_supply_9014.py
-├── main.py
-├── subsystem/
-│   ├── __init__.py
-│   ├── cathode_heating.py
-│   ├── environmental.py
-│   ├── interlocks.py
-│   ├── oil_system.py
-│   ├── visualization_gas_control.py
-│   └── vtrx.py
-└── utils.py
-```
-
-### 4. Components
-
-- **Main Application (main.py)**:
-  - **Configuration Loader**: Responsible for initial configurations, setting up COM ports, and starting the main dashboard.
-  - **COM Port Configuration**: Dynamically detects and assigns COM ports for various hardware interfaces. TODO: Write dropdowns for additional subsystems.
-
-- **Instrument Control (instrumentctl.py)**:
-  - **Equipment specific driver libraries**:
-    - 9104 Cathode Heating Power Supplies [(datasheet)](https://bkpmedia.s3.us-west-1.amazonaws.com/downloads/programming_manuals/en-us/9103_9104_programming_manual.pdf) IN PROGRESS
-    - E5CN Cathode Temperature Controller [(datasheet)]() IN PROGRESS
-    - Apex Mass Flow Controller [(datasheet)]() IN PROGRESS
-    - TODO: Agilent 33120A [(datasheet)]()
-    - TODO: Quantum 9530
-    - TODO: G9SP serial option (status door, e-stops, vac, levels, timer)
-    - VTRX system
-    - TODO: Temp monitor
-    - TODO: A655sc
-    - TODO: BOP-100-2ML
-
-### 5. Dashboard (dashboard.py)
-
-- **EBEAMSystemDashboard Class**: The main class that sets up the dashboard interface.
-  - **`setup_main_pane`**: Initializes the main layout pane and its rows.
-  - **`create_frames`**: Creates frames for different systems and controls within the dashboard.
-  - **`create_messages_frame`**: Creates a frame for displaying messages and errors.
-  - **`create_subsystems`**: Initializes subsystems in their designated frames using component settings.
-
-### 5. Subsystems
-
-- **`vtrx.py`**:
-  - Manages the VTRX system, including serial communication and GUI updates.
-  - Handles pressure data and switch states, updating the GUI in real-time.
-  - Logs messages and errors to the messages frame.
-
-- **`environmental.py`**:
-  - Monitors and displays temperature data from various thermometers.
-  - Uses Matplotlib to create bar charts for temperature visualization.
-
-- **`visualization_gas_control.py`**:
-  - Controls the Argon bleed system via serial communication.
-  - Provides GUI buttons for taring flow and absolute pressure.
-
-- **`interlocks.py`**:
-  - Manages the status of various interlocks (e.g., Vacuum, Water, Door).
-  - Updates GUI indicators based on interlock status.
-
-- **`oil_system.py`**:
-  - Monitors and displays oil temperature and pressure.
-  - Uses a vertical temperature gauge and a dial meter for pressure visualization.
-
-### 6. Utilities (`utils.py`)
-
-- **MessagesFrame Class**:
-  - A custom Tkinter frame for displaying messages and errors.
-  - Supports logging messages with timestamps and trimming old messages to maintain a maximum number of lines.
-
-- **TextRedirector Class**:
-  - Redirects stdout to a Tkinter Text widget.
-  - Ensures that all print statements in the application are displayed in the messages frame.
-
-- **SetupScripts Class**:
-  - Manages the selection and execution of configuration scripts.
-  - Provides a GUI for selecting scripts from a dropdown menu and executing them.
-

instrumentctl/E5CN_modbus/README.md

@@ -0,0 +1,112 @@
+# E5CN Temperature Controller Driver Documentation
+
+### Hardware Specifications
+- Manufacturer: Omron
+- Model: E5CN-HV2M-500
+- Datasheet [(link)](https://mm.digikey.com/Volume0/opasdata/d220001/medias/docus/518/E5CN-H.pdf)
+- Communication interface: Modbus RTU over RS485
+- Resolution: 0.01 °C
+- Sampling cycle: 60 ms
+
+### Serial Port Configuration Settings
+| Setting | Value |
+|---------|-------|
+| Baud rate | 9600 |
+| Data bits | 8 |
+| Parity | Even |
+| Stop bits | 2 |
+| Slave Address | 1-3 (supports multiple units) |
+
+### Basic Usage
+
+```python
+>>> from instrumentctl import E5CNModbus
+
+# Initialize controller with default settings
+>>> controller = E5CNModbus(port="COM4")
+
+# Connect to the device
+>>> controller.connect()
+True
+
+# Read temperature from a single unit
+>>> temp = controller.read_temperature(unit=1)
+>>> print(f"Temperature: {temp}°C")
+Temperature: 23.5°C
+
+# Clean up
+>>> controller.disconnect()
+```
+
+### Flowcharts
+```mermaid
+flowchart TD
+    %% Connection Management
+    subgraph Connection_Management[E5CN Modbus Management]
+        Connect[Connect] --> CheckConnection{Is Socket Open?}
+        CheckConnection -- Yes --> AlreadyConnected[Return True]
+        CheckConnection -- No --> AttemptConnect{Attempt Connection}
+        AttemptConnect -- Success --> UpdateConnected[Set Connected State]
+        AttemptConnect -- Failure --> HandleError[Log Error]
+        HandleError --> ReturnFalse[Return False]
+    end
+```
+
+```mermaid
+flowchart TD
+    %% Single Temperature Read
+    subgraph Single_Read[Single Temperature Read]
+        ReadTemperature[read_temperature] --> CheckUnit{Valid Unit?}
+        CheckUnit -- No --> ReturnNone1[Return None]
+        CheckUnit -- Yes --> InitAttempts[Initialize Attempts]
+        InitAttempts --> CheckSocket{Socket Open?}
+        CheckSocket -- No --> ReconnectAttempt[Attempt Reconnect]
+        CheckSocket -- Yes --> ReadRegisters[Read Registers]
+
+        ReconnectAttempt -- Success --> ReadRegisters
+        ReconnectAttempt -- Failure --> DecrementAttempts1[Decrement Attempts]
+
+        ReadRegisters -- Success --> ProcessTemp[Process Temperature]
+        ReadRegisters -- Error --> DecrementAttempts2[Decrement Attempts]
+
+        DecrementAttempts1 --> CheckAttempts1{Attempts<br>left > 0?}
+        DecrementAttempts2 --> CheckAttempts2{Attempts<br>left > 0?}
+
+        CheckAttempts1 -- Yes --> CheckSocket
+        CheckAttempts1 -- No --> ReturnNone2[Return None]
+
+        CheckAttempts2 -- Yes --> CheckSocket
+        CheckAttempts2 -- No --> ReturnNone3[Return None]
+
+        ProcessTemp --> ValidateRange{Temperature in Range?}
+        ValidateRange -- Yes --> ReturnTemp[Return Temperature]
+        ValidateRange -- No --> LogWarning[Log Warning]
+        LogWarning --> ReturnTemp
+    end
+```
+
+```mermaid
+flowchart TD
+    %% Temperature Reading Process
+    subgraph Temperature_Reading[Temperature Reading Process]
+        StartReading[start_reading_temperatures] --> ForEachUnit[For Each Unit in UNIT_NUMBERS]
+        ForEachUnit --> CreateThread[Create Reading Thread]
+        CreateThread --> StartThread[Start Thread]
+        StartThread --> AddToThreadList[Add to Thread List]
+
+        %% Continuous Reading Loop
+        ReadContinuously[_read_temperature_continuously] --> CheckStop{Check stop_event}
+        CheckStop -- Not Set --> ReadTemp[Read Temperature]
+        CheckStop -- Set --> ExitThread[Exit Thread]
+
+        ReadTemp --> ValidateReading{Valid Reading?}
+        ValidateReading -- Yes --> AcquireLock[Acquire Lock]
+        AcquireLock --> UpdateTemp[Update Temperature]
+        UpdateTemp --> ReleaseLock[Release Lock]
+        ValidateReading -- No --> LogError[Log Error]
+
+        ReleaseLock --> Sleep[Sleep 500ms]
+        LogError --> Sleep
+        Sleep --> CheckStop
+    end
+```