Utilities (pylorenzmie.utilities)

pylorenzmie.utilities.example_hologram.example_hologram(name='crop.png')

Return a normalized example hologram.

Loads an image from the package’s tutorials directory and returns it as a Hologram.

Parameters:

name (str, optional) – Filename of the image in docs/tutorials/. Default: 'crop.png'.

Return type:

Hologram

Returns:

hologram (Hologram) – Hologram intensity divided by the background level (100 counts), shape (height, width), dtype float64.

class pylorenzmie.utilities.normalizer.Normalizer(method='median', size=51, reference=None)

Bases: object

Normalize a hologram image by its estimated background illumination.

Parameters:

• method (str) – Normalization method:

  'median' (default)

  Divide by the scalar median of the image. Assumes spatially uniform illumination.

  'filter'

  Estimate the background with a large-kernel median filter. Suppresses the rapidly-oscillating fringe pattern while preserving slow illumination variation. Requires no reference.

  'reference'

  Divide by a prerecorded reference image or a scalar value. Gives the highest quality result when a background image is available.

• size (int) – Kernel size (pixels) for the 'filter' method. Should exceed the largest fringe spacing expected in the holograms. Default: 51.

• reference (ndarray or float, optional) – Background for the 'reference' method: either an image array with the same shape as the input or a scalar intensity value.

methods = ('filter', 'median', 'reference')

Efficient approximation to a running median filter.

class pylorenzmie.utilities.vmedian.VMedian(order=0, shape=None)

Bases: object

Running median of a video stream.

Computes an approximate running median using a hierarchical tree of 3-element median buffers. Each level reduces the update rate by a factor of 3, so a tree of depth order accumulates 3**(order + 1) frames before producing its first output.

Parameters:

• order (int) – Depth of the median tree. Default: 0 (single 3-frame buffer).

• shape (tuple of int, optional) – Shape (height, width) of the input images.

filter(data)

Add data and return the current median estimate.

Return type:

ndarray

get(reshape=True)

Return the current median image.

Parameters:

reshape (bool) – If True (default), return array with the original image shape. If False, return the flattened internal buffer.

Return type:

ndarray

Returns:

median (ndarray)

add(data)

Include a new image in the median calculation.

Parameters:

data (ndarray) – New image frame.

Return type:

None

reset()

Reset the filter state.

Return type:

None

property initialized: bool

True once enough frames have been accumulated.

property cycled: bool

True if the buffer completed a cycle on the last add().

property shape: tuple | None

property order: int

pylorenzmie.utilities.vmedian.vmedian

alias of VMedian

Physical properties of water

pylorenzmie.utilities.water.density(temperature=24.0)

Returns the density of water

Accounts for dependence of density on temperature

Source: CRC Handbook of Chemistry and Physics: Thermophysical properties of water and steam.

Parameters:

temperature (float) – Temperature [celsius]. Default: 24.

Return type:

float

Returns:

density (float) – Density of water [kg/m^3].

pylorenzmie.utilities.water.refractiveindex(wavelength=0.589, temperature=24)

Returns the refractive index of water

Accounts for dispersion and temperature dependence

Source: The International Association for the Properties of Water and Steam (IAPWS), Release on the Refractive Index of Ordinary Water Substance as a Function of Wavelength, Temperature and Pressure (1997) http://www.iapws.org/relguide/rindex.pdf

Parameters:

• wavelength (float or ndarray) – Wavelength of light [μm]. Default: 0.589 (sodium D line).

• temperature (float) – Temperature of water [celsius]. Default: 24.

Return type:

float | GenericAlias[float]

Returns:

n (float or ndarray) – Refractive index of water at the specified wavelength and temperature.