Follow Plate Configuration

[QATCH-Technologies]

BUG: With Multi, if set to 1 Channel, and COM PORT PID other than 1, mode hopping and peak freq and overtone wrong

We create a "plate-config.json" file when the multiplex device is connected, allowing the user to specify the wells in a 4x6 matrix to use. If the user specifies a custom plate configuration, we should follow it during software measurement runs. Currently, we just use all wells, per default.

[PaulMacNichol]

When the multiplex device is configured to use 1 Channel and a COM Port PID other than 1:

Incorrect Behavior Observed:

• Mode hopping occurs unexpectedly.
• Peak frequency and overtone measurements are incorrect.

Plate Configuration Bug:

• If a custom plate-config.json file is provided, the software does not correctly follow the specified 4x6 matrix well configuration. Instead, it defaults to using all wells.

Potential Workflow Issues:

• The Calibration.py currently processes multiple ports sequentially but may support parallelization in the future.
• The Last_Used.txt file does not consistently reflect the selected ports specified in plate-config.json.
• When the workflow fails, peak frequencies and overtone data may be assigned to the wrong devices.

Steps to Reproduce

1. Configure a multiplex device to 1 Channel mode with a COM Port PID other than 1.
2. Provide a plate-config.json specifying custom wells.
3. Start a measurement run using the software's UI.

Expected Behavior

• The system adheres to the specified plate-config.json wells.
• The Last_Used.txt reflects the correct port configuration.
• Measurements for peak frequency and overtones align with the correct ports.

Actual Behavior

• Defaults to using all wells.
• Mode hopping observed.
• Incorrect peak frequency and overtone values.

Technical Details

Affected Files:

• mainWindow.py (Key lines: 769, 1248, 1287)
• Calibration.py (Order of port calibration)

• Serial.py (Lines 414-867)

  Methods:

• has_active_multi_port()
• Worker.config(..., port, ...)

• DEV_set_active(i, dev_name)

  Temporary Config File:

• %LOCALAPPDATA%\QATCH\nanovisQ\config\Last_Used.txt
• plate-config.json

Tasks

1. Fix Plate Configuration Handling

• [ ] Update logic at mainWindow.py:1248 to append ports from plate-config.json into the selected_port list.
• [ ] Verify that plate-config.json is correctly applied during the initialization and measurement runs.
• [ ] Ensure that Last_Used.txt reflects the ports from plate-config.json.

2. Investigate Mode Hopping Issue

• [ ] Debug the mode hopping behavior when using 1 Channel and a COM Port PID other than 1.
• [ ] Verify port assignments in the SerialProcess.open(port, ...) method.

3. Validate Peak Frequency and Overtone Measurements

• [ ] Confirm that peak frequency and overtone data are assigned to the correct devices.
• [ ] Add error-handling mechanisms to flag misaligned measurements.

4. Improve Debugging and Logging

• [ ] Add debug logs to key points (e.g., start() in mainWindow.py, open() in SerialProcess) to trace port assignments and plate configurations.

5. Future Parallelization Support

• [ ] Investigate if sequential calibration in Calibration.py is required for the current hardware.
• [ ] Plan for potential future parallelization of port calibration and initialization sweeps.

Acceptance Criteria

• The software adheres to the plate-config.json file during measurement runs.
• The Last_Used.txt file accurately reflects the correct port and device configurations.
• Mode hopping is resolved when using 1 Channel and non-default COM Port PID.
• Peak frequency and overtone data are correctly aligned with the respective devices.
• Debug logs are available for tracing port and configuration issues.