Ad#

class Ad(becExp)#

Bases: BecAnalysis

Ad compute atomic column density (AD) from OD and imaging config.

Converts optical depth (Od) to atomic column density using a chosen cross section model (AdMethod). Supports uniform and spatially varying saturation corrections via CrossSectionData and Imaging.SaturationParameterPropagation. Provides preview GUI and renders 1D mosaics or 2D density maps, with optional GIF export.

Associated Charts:

Chart(1): “AdMix” - Horizontal mosaic or 2D density plot of atomic density
Chart(2): “AdAnimation” - Animated GIF showing AD evolution

Associated GUIs:

Gui(1): “AtomPreviewer” - Real-time preview of atomic density data

Constructor Summary

Ad(becExp)#

Construct Ad analyzer.

Parameters:: becExp (BecExp) – Owning experiment

Property Summary

AdData double#: Atomic column density \(n_\mathrm{col}\) per run [m^{-2}]

AdMethod string = "StrongLight"#: Cross-section model: “TwoLevelWeakLight”|”RandomPolarization”|”UniformStrongLight”|”StrongLight”|”PhaseContrastImaging”

Blur = 100#: Gaussian blur kernel size [pixels] applied to saturation-dependent cross-section maps

CLim double = [0,8]#: Color axis limits for atomic density plots in units of Unit [m^{-2}]

Colormap = jet#: Colormap function handle for atomic density visualization

CrossSectionData double = []#: Cross-section lookup table with columns [\(s\), \(\sigma(s)/\sigma_0\)] for saturation-dependent scattering

Unit = 1e13#: Display scale factor for atomic density values [m^{-2}]

Method Summary

finalize()#

Generate final atomic density visualizations.

Creates the atomic density mosaic plot and animated GIF showing the evolution of atomic column density across parameter values.

static handlePropEvents(src, evnt)#

Handle property change events for color limits and GUI updates.

Parameters:

src (meta.property) – Property metadata object
evnt (event.EventData) – Event data containing affected object

initialize()#

Initialize data storage and preview GUI interface.

Sets up atomic density data arrays, launches the atomic density previewer application, configures OD preview mode, and establishes property change listeners for color limits.

plotAdAnimation()#

Create animated GIF across runs from AD data.

Saves an animated GIF to Chart(2).Path using current AD color scaling and ROI mid-slice profiles.

plotAdMix(adData)#

Plot AD mosaics (1D scans) or 2D map (2D scans).

Parameters:: adData (double, optional) – Optional AD to plot; defaults to AdData
Returns:: None
Return type:: void

plotAdMix1D(fig, adData)#

1D plotting logic (mosaic across runs)

Parameters:

fig (matlab.ui.Figure) – Figure handle
adData (double, optional) – Optional AD to plot; defaults to AdData

plotAdMix2D(fig, adData)#

2D plotting logic

Parameters:

fig (matlab.ui.Figure) – Figure handle
adData (double, optional) – Optional AD to plot; defaults to AdData

Plot OD Data

refresh()#

Recompute atomic density for all runs and refresh visualization.

Reinitializes data storage, updates the preview GUI, reprocesses all completed runs, and regenerates visualization plots.

save()#

Save AD data and figure to disk.

Writes AdData.mat under BecExp.DataAnalysisPath with AD values and ROI axes. If the primary chart is enabled, also saves the PNG figure at Chart(1).Path.

Returns:: None
Return type:: void

show()#

Display atomic density previewer and chart windows.

Initializes the atomic density previewer GUI, configures OD preview mode, establishes property change listeners, and shows chart figures. Loads saved data for backwards compatibility when available.

update(runIdx)#

Compute atomic column density from optical depth for given run.

Converts optical depth to atomic column density using the selected cross-section model, accounting for saturation effects when applicable.

Parameters:: runIdx (double) – Run index to process