Major update to Output control

    Including:
    - Control panel
    - Change status of simulation after devices creation.
    - Arduino serial conflict with multiple channels.
    - Claude instructions.
    - Update to arduino on board code.

1 files changed, 81 insertions, 0 deletions

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+# CLAUDE.md
+
+Guidance for Claude Code (claude.ai/code) working in this repo.
+
+## Running the app
+
+```bash
+python main.py
+```
+
+No build step. Simulation mode default (no hardware needed).
+
+## Dependencies
+
+```bash
+pip install PyQt6 pyqtgraph numpy pyserial
+pip install nidaqmx   # optional — only for real NI hardware
+```
+
+## Architecture
+
+### Data flow
+
+```
+Hardware / Simulation
+        ↓
+  api_layers/          ArduinoLayer, NidaqmxLayer — low-level I/O, background threads
+        ↓
+  devices/             BaseDevice subclasses — wrap api_layers, expose read_channels() / write_channel()
+        ↓
+  core/acquisition.py  AcquisitionEngine — polls devices at 100 ms, fills ChannelBuffers, emits new_data signal
+        ↓
+  core/signal_processor.py  SignalProcessor — filters + derived channels, re-emits processed_data
+        ↓
+  ui/strip_chart.py    StripChartWidget — consumes processed_data, renders via pyqtgraph
+```
+
+Control widgets (left panel) go other direction: UI → `ControlWidget._write()` → `DeviceRegistry.get_instance()` → `device.write_channel()` → api_layer.
+
+### Key design patterns
+
+**Shared serial port** — `api_layers/port_registry.py` holds module-level `port_registry` singleton. When multiple devices share one Arduino (e.g. `AnalogInputDevice` + `DigitalIODevice` on same port), both call `port_registry.get_layer(port, baud)`, get same `ArduinoLayer` instance. Never construct `ArduinoLayer` directly in device code.
+
+**Device auto-discovery** — `DeviceRegistry._discover()` scans `devices/` with `pkgutil`, imports every module, registers any class subclassing `BaseDevice`. New device type = drop file in `devices/`, no registration needed.
+
+**Backend switching at runtime** — `AnalogInputDevice` and `DigitalIODevice` both have `switch_backend(backend, simulate, ...)` — disconnects, reconfigures, reconnects without restart. Called from "Apply & Reconnect" in config dialog.
+
+**Profile persistence** — `core/profile.py` serialises full operator state (controls, plot layout, signal pipelines, derived channels) to `.labdaq` JSON files. `ProfileManager` handles save/load.
+
+### Directory map
+
+| Path | Purpose |
+|------|---------|
+| `api_layers/arduino_layer.py` | Serial protocol + simulation; `ARDUINO_FIRMWARE` string is the uploadable sketch |
+| `api_layers/nidaqmx_layer.py` | NI-DAQmx wrapper with simulation fallback |
+| `api_layers/port_registry.py` | Shared `ArduinoLayer` singleton per (port, baud) |
+| `devices/base_device.py` | `BaseDevice`, `ChannelConfig`, `DeviceInfo`, `DeviceStatus` |
+| `devices/analog_input.py` | Analog input — NI or Arduino backend |
+| `devices/digital_io.py` | Digital I/O — NI or Arduino backend |
+| `devices/serial_device.py` | Generic UART device |
+| `core/acquisition.py` | `AcquisitionEngine` + `ChannelBuffer` |
+| `core/signal_processor.py` | Filter chain + derived/virtual channels |
+| `core/profile.py` | `.labdaq` profile save/load |
+| `ui/main_window.py` | Top-level window, toolbar, demo device init |
+| `ui/control_panel.py` | Left panel output widgets (`OnOffSwitch`, `MotorControl`, etc.) |
+| `ui/strip_chart.py` | Live pyqtgraph chart, config-driven by `LayoutConfig` |
+| `ui/windows/` | Floating tool windows (Devices, Signals, Plot, Settings) |
+| `ui/style_dark.qss` / `style_light.qss` | Full app theme |
+
+### Arduino firmware
+
+Firmware embedded as `ARDUINO_FIRMWARE` in `api_layers/arduino_layer.py`. When editing: set `N_DIG_OUT` to match digital output pins in use (default 0 — leaves pins in INPUT mode, causes inverted write behaviour). Upload via Arduino IDE.
+
+Serial protocol: `A0:3.14,D2:1\n` stream from Arduino; `W:D7:1\n` / `P:D9:128\n` commands from PC.
+
+### Adding a new device type
+
+1. Subclass `BaseDevice` in new file under `devices/`
+2. Implement: `connect()`, `disconnect()`, `read_channels() → Dict[str, float]`, `write_channel(channel_id, value) → bool`, `get_config_widget() → QWidget`
+3. Include `switch_backend()` if device supports runtime reconfiguration
+4. `DeviceRegistry` discovers it automatically on next run
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