Code reference

Refocus 1D/2D fields

fft_propagate(fftfield, d, nm, res[, …])	Propagates a 1D or 2D Fourier transformed field
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

nrefocus._propagate.fft_propagate(fftfield, d, nm, res, method='helmholtz', ret_fft=False)

Propagates a 1D or 2D Fourier transformed field

Parameters

• fftfield (1-dimensional or 2-dimensional ndarray) – Fourier transform of 1D Electric field component

• d (float) – Distance to be propagated in pixels (negative for backwards)

• nm (float) – Refractive index of medium

• res (float) – Wavelength 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)

• ret_fft (bool) – Do not perform an inverse Fourier transform and return the field in Fourier space.

Returns

• Electric field at d. If ret_fft is True, then the

• Fourier transform of the electric field will be returned (faster).

Refocus individual fields

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

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._propagate.refocus_stack(fieldstack, d, nm, res, method='helmholtz', num_cpus=2, copy=True, padding=True)

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 (int) – 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)

Compute average gradient norm of an image

nrefocus.metrics.contrast_rms(data, *kwargs)

Compute RMS contrast norm of an image

nrefocus.metrics.spectral(data, lambd, *kwargs)

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)

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

• ret_d (bool) – Return the autofocusing distance in pixels. Defaults to False.

• ret_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)

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

• same_dist (bool) – Refocus entire sinogram with one distance.

• ret_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.

• ret_grads (bool) – Return the computed gradients as a list.

• num_cpus (int) – Number of CPUs to use

• copy (bool) – If False, overwrites input array.

Returns

Return type

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