computeAbsorption

computeAbsorption#

computeAbsorption(imageData, absorpMin)#

Compute absorption ratio from atom/light(/dark) images.

Converts raw images into an absorption ratio \(a = I_\mathrm{atom}/I_\mathrm{light}\) with optional dark subtraction when a third channel is present. Negative or non-physical intensities are clipped to small positive values to avoid division by zero.

Parameters:

  • imageData (double) – 4-D image stack with shape (\(N_y,N_x,N_\mathrm{run},N_\mathrm{ch}\)), where the last dimension is either [atom, light, dark] (3) or [atom, light] (2)

  • absorpMin (double, optional) – Minimum allowed absorption; values below are not clipped in code (default: 0)

Returns:

Absorption ratio \(a = I_\mathrm{atom}/I_\mathrm{light}\); values are in [0, +inf)

Return type:

double

Notes:

  • For 3-channel input, this computes atom = atom-dark and light = light-dark.

  • Light values \(\le 0\) are replaced by eps to keep \(a\) finite.

  • Atom values \(< 0\) are clipped to 0.

Example:

a = computeAbsorption(cat(4, atomImg, lightImg, darkImg));
OD = absorption2Od(a);