Configuring Zapit

Starting for the first time

Run the following command to make the settings file:

>> zapit.settings.readSettings;

You will be prompted to choose the location where the settings file is created. Make the choice and press return. Then navigate to the location where you asked for the settings file to be created. This will contain a file called zapitSystemSettings.yml that contains device configuration information and also caches the GUI state.

If you already have a known working settings file, you can simply replace the default zapitSystemSettings.yml with your file and skip the rest of the configuration instructions. If you are using a file given to you by someone else, confirm that the NI device ID setting is correct for your system. You can check the ID of your NI device via the NI MAX application. You should also be familiar with the the Laser Power Calibration instructions, as you might need to do that from time to time.

You will need to edit the YML file in a text editor of your choice. The contents of the file will be something like this:

general: {maxSettingsBackUpFiles: 50.0, openPythonBridgeOnStartup: 0.0}
NI:
  device_ID: Dev1
  samplesPerSecond: 100000.0
  triggerChannel: PFI0
  wrapper: dotnet
scanners: {voltsPerPixel: 0.0022, invertXscanner: 0.0, invertYscanner: 0.0}
laser:
  laserMinMaxControlVolts: [1.5, 3.5]
  laserMinMax_mW: [0.0, 75.0]
  name: obis
  maxValueInGUI: 20.0
camera: {connection_index: 1.0, default_exposure: 10.0, micronsPerPixel: 19.3, 
          flipImageUD: 0.0, flipImageLR: 0.0}
calibrateScanners: {areaThreshold: 500.0, calibration_power_mW: 9.0, 
                    beam_calib_exposure: 2.0, bufferMM: 2.0, pointSpacingInMM: 3.0}
experiment: {defaultDutyCycleHz: 40.0, defaultLaserPowerMW: 5.0, 
            offRampDownDuration_ms: 250.0,  maxStimPointsPerCondition: 2.0, blankingTime_ms: 1.5}
calibrateSample: {refAP: 3.0}
cache:
  ROI: []
  previouslyLoadedFiles: []

Some settings you will need to change. Other settings are either cached GUI values, and can be left alone, or are there only for developers or super-users. Proceed through the next steps in order.