Code reference

Refocus 1D/2D fields

fft_propagate
refocus(field, d, nm, res[, method, …]) Refocus a 1D or 2D field
refocus_stack(fieldstack, d, nm, res[, …]) Refocus a stack of 1D or 2D fields

Fourier-domain propagation

Refocus individual fields

nrefocus.refocus(field, d, nm, res, method='helmholtz', num_cpus=1, padding=True)[source]

Refocus a 1D or 2D field

Parameters:
  • field (1d or 2d array) – 1D or 2D background corrected electric field (Ex/BEx)
  • d (float) – Distance to be propagated in pixels (negative for backwards)
  • nm (float) – Refractive index of medium
  • res (float) – Wavelenth in pixels
  • method (str) –

    Defines the method of propagation; one of

    • ”helmholtz” : the optical transfer function exp(idkₘ(M-1))
    • ”fresnel” : paraxial approximation exp(idk²/kₘ)
  • num_cpus (int) – Not implemented. Only one CPU is used.
  • padding (bool) –

    perform padding with linear ramp from edge to average to reduce ringing artifacts.

    New in version 0.1.4.
Returns:
Return type:

Electric field at d.

Refocus field stacks

nrefocus.refocus_stack(fieldstack, d, nm, res, method='helmholtz', num_cpus=2, copy=True, padding=True)[source]

Refocus a stack of 1D or 2D fields

Parameters:
  • fieldstack (2d or 3d array) – Stack of 1D or 2D background corrected electric fields (Ex/BEx). The first axis iterates through the individual fields.
  • d (float) – Distance to be propagated in pixels (negative for backwards)
  • nm (float) – Refractive index of medium
  • res (float) – Wavelenth in pixels
  • method (str) –

    Defines the method of propagation; one of

    • ”helmholtz” : the optical transfer function exp(idkₘ(M-1))
    • ”fresnel” : paraxial approximation exp(idk²/kₘ)
  • num_cpus (str) – Defines the number of CPUs to be used for refocusing.
  • copy (bool) – If False, overwrites input stack.
  • padding (bool) –

    Perform padding with linear ramp from edge to average to reduce ringing artifacts.

    New in version 0.1.4.
Returns:
Return type:

Electric field stack at d.

Autofocus 1D/2D fields

autofocus(field, nm, res, ival[, roi, …]) Numerical autofocusing of a field using the Helmholtz equation.
autofocus_stack(fieldstack, nm, res, ival[, …]) Numerical autofocusing of a stack using the Helmholtz equation.

Metrics

nrefocus.metrics.average_gradient(data, *kwargs)[source]

Compute average gradient norm of an image

nrefocus.metrics.contrast_rms(data, *kwargs)[source]

Compute RMS contrast norm of an image

nrefocus.metrics.spectral(data, lambd, *kwargs)[source]

Compute spectral contrast of image

Performs bandpass filtering in Fourier space according to optical limit of detection system, approximated by twice the wavelength.

Parameters:
  • data (2d ndarray) – the image to compute the norm from
  • lambd (float) – wavelength of the light in pixels

Autofocus single fields

nrefocus.autofocus(field, nm, res, ival, roi=None, metric='average gradient', padding=True, ret_d=False, ret_grad=False, num_cpus=1)[source]

Numerical autofocusing of a field using the Helmholtz equation.

Parameters:
  • field (1d or 2d ndarray) – Electric field is BG-Corrected, i.e. field = EX/BEx
  • nm (float) – Refractive index of medium.
  • res (float) – Size of wavelength in pixels.
  • ival (tuple of floats) – Approximate interval to search for optimal focus in px.
  • roi (rectangular region of interest (x1, y1, x2, y2)) – Region of interest of field for which the metric will be minimized. If not given, the entire field will be used.
  • metric (str) –
    • “average gradient” : average gradient metric of amplitude
    • ”rms contrast” : RMS contrast of phase data
    • ”spectrum” : sum of filtered Fourier coefficients
  • padding (bool) –

    Perform padding with linear ramp from edge to average to reduce ringing artifacts.

    Changed in version 0.1.4: improved padding value and padding location

  • red_d (bool) – Return the autofocusing distance in pixels. Defaults to False.
  • red_grad (bool) – Return the computed gradients as a list.
  • num_cpus (int) – Not implemented.
Returns:

  • field, [d, [grad]]
  • The focused field and optionally, the optimal focusing distance and
  • the computed gradients.

Autofocus field stacks

nrefocus.autofocus_stack(fieldstack, nm, res, ival, roi=None, metric='average gradient', padding=True, same_dist=False, ret_ds=False, ret_grads=False, num_cpus=2, copy=True)[source]

Numerical autofocusing of a stack using the Helmholtz equation.

Parameters:
  • fieldstack (2d or 3d ndarray) – Electric field is BG-Corrected, i.e. Field = EX/BEx
  • nm (float) – Refractive index of medium.
  • res (float) – Size of wavelength in pixels.
  • ival (tuple of floats) – Approximate interval to search for optimal focus in px.
  • metric (str) – see autofocus_field.
  • padding (bool) –

    Perform padding with linear ramp from edge to average to reduce ringing artifacts.

    Changed in version 0.1.4: improved padding value and padding location

  • ret_dopt (bool) – Return optimized distance and gradient plotting data.
  • same_dist (bool) – Refocus entire sinogram with one distance.
  • red_ds (bool) – Return the autofocusing distances in pixels. Defaults to False. If sam_dist is True, still returns autofocusing distances of first pass. The used refocusing distance is the average.
  • red_grads (bool) – Return the computed gradients as a list.
  • copy (bool) – If False, overwrites input array.
Returns:
Return type:

The focused field (and the refocussing distance + data if d is None)