Manage Cold-atom Experiments Using BecExp

Manage Cold-atom Experiments Using BecExp#

The BecExp class provides a comprehensive framework for conducting Bose-Einstein condensate (BEC) experiments with real-time data acquisition, analysis, and visualization. Built on the Trial foundation, it integrates hardware control, image processing, automated analysis pipelines, and database logging for complete experimental orchestration.

Overview#

BecExp serves as the central coordinator for cold-atom experiments, managing:

  • Real-time acquisition: Camera control and image capture

  • Region of interest (ROI): Flexible image analysis regions

  • Analysis pipeline: Modular, event-driven data processing

  • Hardware integration: Cicero sequence control and device logging

  • Database persistence: Automatic data storage and retrieval

  • Visualization: Real-time figure updates and GUI integration

  • Parameter scanning: 1D and 2D experimental parameter sweeps

The system is designed for hands-free operation during long experimental sequences while providing comprehensive monitoring and analysis capabilities.

BecExp Architecture#

../_images/becexp_architecture.svg

Core BecExp Class#

The BecExp class extends Trial to provide specialized functionality for cold-atom experiments:

Essential Components:

  • Roi: Main region of interest for image analysis

  • SubRoi: Optional sub-regions for multi-area analysis

  • Acquisition: Camera settings and hardware interface

  • Atom: Atomic species properties and constants

  • AnalysisMethod: Ordered list of analysis modules to execute

Data Streams:

  • CiceroData: Sequence parameters from Cicero log files

  • HardwareData: Device measurements and settings

  • ScopeData: Oscilloscope-derived measurements

Basic Construction:

% Create BEC experiment with configuration
becExp = BecExp("MagneticTrap", "BecExpSetting");

% The experiment automatically:
% 1. Loads atomic species data
% 2. Configures camera acquisition settings
% 3. Sets up ROI for image analysis
% 4. Initializes analysis modules
% 5. Creates database entries
% 6. Establishes file monitoring

Configuration Loading:

% Load from different configuration sources
becExp = BecExp("OpticalLattice", "MyCustomConfig");      % Database config
becExp = BecExp("DipolarGas", configTable);               % Table config
becExp = BecExp("SpinorBEC", configStruct);              % Struct config

Acquisition System#

Camera Integration:

The acquisition system provides seamless camera control:

% Access acquisition settings
acq = becExp.Acquisition;

% Key properties automatically configured:
% - ImagePath: Data storage directory
% - ImageSize: Camera sensor dimensions
% - ExposureTime: Integration time
% - ROI: Hardware ROI settings
% - TriggerMode: External/software triggering

Automatic vs. Manual Acquisition:

% Automatic acquisition mode
becExp.IsAutoAcquire = true;
becExp.start();  % Begins automatic image capture

% Manual/external acquisition mode
becExp.IsAutoAcquire = false;
becExp.start();  % Monitors for externally saved images

Image File Management:

% Standard file naming pattern:
% run_1_atom.tif   - Atoms + light image
% run_1_probe.tif  - Probe light only
% run_1_bg.tif     - Background (no light)

% Files automatically detected when complete group arrives
% Triggers NewRunFinished event for analysis

Region of Interest (ROI) System#

Main ROI Configuration:

% Configure primary analysis region
becExp.Roi.Center = [512, 384];      % Pixel coordinates [y, x]
becExp.Roi.Size = [200, 300];        % [height, width] in pixels
becExp.Roi.Angle = 0;                % Rotation angle

% ROI automatically applied to all analysis modules

Sub-ROI Analysis:

% Multiple analysis regions
subRoi1 = Roi("Condensate", center=[500, 400], size=[100, 150]);
subRoi2 = Roi("Thermal", center=[520, 420], size=[150, 200]);

becExp.SubRoi = [subRoi1, subRoi2];

% Analysis automatically performed on all sub-regions

Dynamic ROI Adjustment:

% Automatic centering based on previous measurements
becExp.CloudCenter = [512.3, 384.7];  % From previous fit

% ROI automatically adjusts to follow cloud center

Analysis Pipeline#

Modular Analysis System:

BecExp uses a modular analysis architecture with predefined execution order:

% Configure analysis modules
becExp.AnalysisMethod = ["Od", "Imaging", "Ad", "DensityFit", "AtomNumber"];

% Analysis modules execute in dependency order:
% 1. Od: Optical depth calculation
% 2. Imaging: Image processing and enhancement
% 3. Ad: Absorption imaging analysis
% 4. DensityFit: Gaussian/Thomas-Fermi fitting
% 5. AtomNumber: Atom counting and statistics

Analysis Module Details:

Od (Optical Depth)#

Calculates optical depth from absorption imaging:

\[\text{OD}(x,y) = -\ln\left(\frac{I_{\text{atom}}(x,y) - I_{\text{bg}}(x,y)}{I_{\text{probe}}(x,y) - I_{\text{bg}}(x,y)}\right)\]
% Optical depth automatically calculated from image triplets
% Results stored in becExp.Od.OdData for each run

DensityFit#

Performs automated density profile fitting:

% Configure fitting method
becExp.DensityFit.FitMethod = "GaussianFit1D";        % or "BosonicGaussianFit1D"

% Automatic 1D profile fitting in x and y directions
becExp.DensityFit.buildFit(1:10);  % Fit runs 1-10

% Access fit results
sigmaX = becExp.DensityFit.getSigmaX();  % Gaussian widths in x
sigmaY = becExp.DensityFit.getSigmaY();  % Gaussian widths in y

AtomNumber#

Calculates total atom numbers and statistics:

% Automatic atom number calculation
% Results include:
% - Total atom number
% - Condensate fraction (for bimodal fits)
% - Statistical uncertainties
% - Temperature estimates

Experimental Workflow#

Complete Experimental Sequence:

% 1. Setup experiment
becExp = BecExp("EvaporativeCooling", "StandardBEC");
becExp.Description = "Magnetic trap evaporation to BEC";
becExp.NRun = 50;  % 50 evaporation steps

% 2. Configure parameter scan
becExp.ScannedVariableID = 5;  % Evaporation RF frequency
becExp.AveragingMethod = "StdErr";

% 3. Start experiment
becExp.start();

% 4. Monitor progress (automatic)
% - Images acquired automatically
% - Analysis runs on each new image set
% - Figures update in real-time
% - Database records all results

% 5. Stop and finalize
becExp.stop();
becExp.refresh();  % Final analysis pass

Real-Time Monitoring:

% Display analysis figures
becExp.show();  % Show on primary monitor
becExp.browserShow(2);  % Show browser GUI on monitor 2

% Access real-time data
currentRun = becExp.NCompletedRun;
atomNumbers = becExp.AtomNumber.AtomNumberData(1:currentRun);
temperatures = becExp.Tof.TemperatureData(1:currentRun);

Parameter Scanning:

% 1D magnetic field scan
becExp.ScannedVariableID = 3;  % Magnetic field strength
fieldValues = linspace(0.5, 5.0, 20);  % 0.5 to 5.0 G

% 2D scan example
becExp.ScannedVariableID = 3;   % Magnetic field
becExp.ScannedVariableID2 = 7;  % Hold time
becExp.Is2dScan = true;
becExp.NRun = 100;  % 10×10 parameter grid

Hardware Integration#

Cicero Sequence Control:

% Automatic Cicero log processing
becExp.CiceroLogOrigin = "C:/Cicero/Logs/";

% Log files automatically moved and parsed:
% - Sequence timing parameters
% - RF frequencies and powers
% - Magnetic field settings
% - Laser intensities and detunings

Hardware Device Logging:

% Configure hardware logging
becExp.HardwareList = loadHardwareConfig();

% Automatic logging of:
% - AWG waveform parameters
% - Lock-in amplifier readings
% - Temperature controller values
% - Laser power measurements

Scope Integration:

% Oscilloscope data integration
becExp.ScopeData  % Automatic scope measurement logging

% Common measurements:
% - Photodiode signals
% - RF power monitoring
% - Timing verification
% - Error signals

Advanced Analysis Features#

Multi-Region Analysis:

% Define multiple analysis regions
condensateROI = Roi("Condensate", center=[500, 400], size=[80, 120]);
thermalROI = Roi("Thermal", center=[500, 400], size=[200, 300]);

becExp.SubRoi = [condensateROI, thermalROI];

% Analysis automatically performed on all regions
% Results indexed by ROI: becExp.AtomNumber.AtomNumberData{roiIndex}

Custom Analysis Modules:

% Add custom analysis to the pipeline
becExp.addAnalysis("CustomModule");

% Custom modules must inherit from BecAnalysis
% and implement updateData() and updateFigure()

Data Export and Visualization:

% Export results for external analysis
results = becExp.exportData();

% Generate publication-quality figures
becExp.generateFigures("publication");

% Save analysis state
becExp.saveAnalysis();

Error Handling and Recovery#

Robust Data Acquisition:

% Handle acquisition failures gracefully
try
    becExp.start();
catch ME
    becExp.displayLog("Acquisition failed: " + ME.message, "error");
    becExp.fastStop();  % Emergency stop
end

Hardware Error Recovery:

% Monitor hardware status during experiment
if becExp.checkHardwareStatus()
    becExp.displayLog("All hardware operating normally");
else
    becExp.displayLog("Hardware error detected", "warning");
    % Implement recovery procedures
end

Data Integrity Checking:

% Validate image data quality
if becExp.validateImageData(runIndex)
    becExp.processRun(runIndex);
else
    becExp.displayLog("Bad image data, skipping run " + runIndex, "warning");
end

Best Practices#

Experiment Design: - Plan appropriate NRun values for statistical significance - Configure ROI to capture full atomic cloud with margin - Set reasonable acquisition rates to avoid data bottlenecks

Analysis Configuration: - Enable only necessary analysis modules to improve performance - Use appropriate averaging methods for your signal-to-noise ratio - Configure sub-ROIs for detailed spatial analysis

Hardware Setup: - Ensure all hardware devices are properly configured and connected - Test Cicero sequences before starting long experimental runs - Verify camera triggering and timing synchronization

Data Management: - Monitor disk space during long experimental sequences - Implement regular data backup procedures - Use descriptive trial names and descriptions for future reference

Performance Optimization: - Disable figure updates during acquisition if performance is critical - Use appropriate image formats and compression - Configure database connections for your network environment

Troubleshooting: - Use fastStop() for emergency experiment termination - Check hardware logs for device-specific error messages - Verify Cicero log parsing for sequence parameter accuracy

The BecExp framework provides a complete solution for modern cold-atom experiments, combining robust hardware control with sophisticated real-time analysis capabilities. Its modular design ensures flexibility while maintaining the reliability required for long-duration experimental sequences.