`holospy.signals`#

`HologramImage`(args, *kwargs)	Signal class for holograms acquired via off-axis electron holography.
`LazyHologramImage`(args, *kwargs)	Lazy signal class for holograms acquired via off-axis electron holography.

Modules containing the HoloSpy signals and their lazy counterparts.

HologramImage: For holography data
LazyHologramImage: For holography data processed lazily

class holospy.signals.HologramImage(*args, **kwargs)#

Bases: Signal2D

Signal class for holograms acquired via off-axis electron holography.

Create a signal instance.

Parameters:

datanumpy.ndarray: The signal data. It can be an array of any dimensions.
axes[dict/axes], optional: List of either dictionaries or axes objects to define the axes (see the documentation of the AxesManager class for more details).
attributesdict, optional: A dictionary whose items are stored as attributes.
metadatadict, optional: A dictionary containing a set of parameters that will to stores in the metadata attribute. Some parameters might be mandatory in some cases.
original_metadatadict, optional: A dictionary containing a set of parameters that will to stores in the original_metadata attribute. It typically contains all the parameters that has been imported from the original data file.
raggedbool or None, optional: Define whether the signal is ragged or not. Overwrite the ragged value in the attributes dictionary. If None, it does nothing. Default is None.

estimate_sideband_position(ap_cb_radius=None, sb='lower', high_cf=True, show_progressbar=False, num_workers=None)#

Estimates the position of the sideband and returns its position.

Parameters:

ap_cb_radiusfloat, None: The aperture radius used to mask out the centerband.
sbstr, optional: Chooses which sideband is taken. 'lower' or 'upper'
high_cfbool, optional: If False, the highest carrier frequency allowed for the sideband location is equal to half of the Nyquist frequency (Default: True).
show_progressbarNone or bool: If True, display a progress bar. If None, the default from the preferences settings is used.
num_workersNone or int: Number of worker used by dask. If None, default to dask default value.

Returns:

hyperspy.api.signals.Signal1D: Sideband positions (y, x), referred to the unshifted FFT.

Raises:

NotImplementedError: If the signal axes are non-uniform axes.

Examples

>>> import holospy as holo
>>> s = holo.data.Fe_needle_hologram()
>>> sb_position = s.estimate_sideband_position()
>>> sb_position.data

array([124, 452])

estimate_sideband_size(sb_position, show_progressbar=False, num_workers=None)#

Estimates the size of the sideband and returns its size.

Parameters:

sb_positionhyperspy.api.signals.BaseSignal: The sideband position (y, x), referred to the non-shifted FFT.
show_progressbarNone or bool: If True, display a progress bar. If None, the default from the preferences settings is used.
num_workersNone or int: Number of worker used by dask. If None, default to dask default value.

Returns:

hyperspy.api.signals.Signal1D: Sideband size referred to the unshifted FFT.

Raises:

NotImplementedError: If the signal axes are non-uniform axes.

Examples

>>> import holospy as holo
>>> s = holo.data.Fe_needle_hologram()
>>> sb_position = s.estimate_sideband_position()
>>> sb_size = s.estimate_sideband_size(sb_position)
>>> sb_size.data
array([ 68.87670143])

reconstruct_phase(reference=None, sb_size=None, sb_smoothness=None, sb_unit=None, sb='lower', sb_position=None, high_cf=True, output_shape=None, plotting=False, store_parameters=True, show_progressbar=False, num_workers=None)#

Reconstruct electron holograms. Operates on multidimensional hyperspy signals. There are several usage schemes:

Reconstruct 1d or Nd hologram without reference
Reconstruct 1d or Nd hologram using single reference hologram
Reconstruct Nd hologram using Nd reference hologram (applies each reference to each hologram in Nd stack)

The reconstruction parameters (sb_position, sb_size, sb_smoothness) have to be 1d or to have same dimensionality as the hologram.

Parameters:

referencendarray, hyperspy.api.signals.Signal2D, None: Vacuum reference hologram.
sb_sizefloat, ndarray, hyperspy.api.signals.BaseSignal, None: Sideband radius of the aperture in corresponding unit (see ‘sb_unit’). If None, the radius of the aperture is set to 1/3 of the distance between sideband and center band.
sb_smoothnessfloat, ndarray, hyperspy.api.signals.BaseSignal, None: Smoothness of the aperture in the same unit as sb_size.
sb_unitstr, None: Unit of the two sideband parameters ‘sb_size’ and ‘sb_smoothness’. Default: None - Sideband size given in pixels ‘nm’: Size and smoothness of the aperture are given in 1/nm. ‘mrad’: Size and smoothness of the aperture are given in mrad.
sbstr, None: Select which sideband is selected. ‘upper’ or ‘lower’.
sb_positiontuple, hyperspy.api.signals.Signal1D, None: The sideband position (y, x), referred to the non-shifted FFT. If None, sideband is determined automatically from FFT.
high_cfbool, optional: If False, the highest carrier frequency allowed for the sideband location is equal to half of the Nyquist frequency (Default: True).
output_shape: tuple, None: Choose a new output shape. Default is the shape of the input hologram. The output shape should not be larger than the input shape.
plottingbool: Shows details of the reconstruction (i.e. SB selection).
store_parametersbool: Store reconstruction parameters in metadata
show_progressbarNone or bool: If True, display a progress bar. If None, the default from the preferences settings is used.
num_workersNone or int: Number of worker used by dask. If None, default to dask default value.

Returns:

hyperspy.api.signals.ComplexSignal2D: Reconstructed electron wave. By default object wave is divided by reference wave.

Raises:

NotImplementedError: If the signal axes are non-uniform axes.

Examples

>>> import holospy as holo
>>> s = holo.data.Fe_needle_hologram()
>>> sb_position = s.estimate_sideband_position()
>>> sb_size = s.estimate_sideband_size(sb_position)
>>> wave = s.reconstruct_phase(sb_position=sb_position, sb_size=sb_size)

set_microscope_parameters(beam_energy=None, biprism_voltage=None, tilt_stage=None)#

Set the microscope parameters.

If no arguments are given, raises an interactive mode to fill the values.

Parameters:

beam_energyfloat: The energy of the electron beam in keV
biprism_voltagefloat: In volts
tilt_stagefloat: In degrees

Examples

>>> s.set_microscope_parameters(beam_energy=300.)
>>> print('Now set to %s keV' %
>>>       s.metadata.Acquisition_instrument.
>>>       TEM.beam_energy)

Now set to 300.0 keV

statistics(sb_position=None, sb='lower', high_cf=False, fringe_contrast_algorithm='statistical', apodization='hanning', single_values=True, show_progressbar=False, num_workers=None)#

Calculates following statistics for off-axis electron holograms:

1. Fringe contrast using either statistical definition or Fourier space approach (see description of fringe_contrast_algorithm parameter) 2. Fringe sampling (in pixels) 3. Fringe spacing (in calibrated units) 4. Carrier frequency (in calibrated units, radians and 1/px)

Parameters:

sb_positiontuple, hyperspy.api.signals.Signal1D, None

The sideband position (y, x), referred to the non-shifted FFT. It has to be tuple or to have the same dimensionality as the hologram. If None, sideband is determined automatically from FFT.

sbstr, None

Select which sideband is selected. ‘upper’, ‘lower’, ‘left’ or ‘right’.

high_cfbool, optional

If False, the highest carrier frequency allowed for the sideband location is equal to half of the Nyquist frequency (Default: False).

fringe_contrast_algorithmstr

Select fringe contrast algorithm between:

'fourier': fringe contrast is estimated as 2 * <I(k_0)> / <I(0)>, where I(k_0) is intensity of sideband and I(0) is the intensity of central band (FFT origin). This method delivers also reasonable estimation if the interference pattern do not cover full field of view.
'statistical': fringe contrast is estimated by dividing the standard deviation by the mean of the hologram intensity in real space. This algorithm relies on regularly spaced fringes and covering the entire field of view.

(Default: ‘statistical’)

apodizationstr or None, optional

Used with fringe_contrast_algorithm='fourier'. If 'hanning' or 'hamming' apodization window will be applied in real space before FFT for estimation of fringe contrast. Apodization is typically needed to suppress striking due to sharp edges of the image, which often results in underestimation of the fringe contrast. (Default: ‘hanning’)

single_valuesbool, optional

If True calculates statistics only for the first navigation pixels and returns the values as single floats (Default: True)

show_progressbarNone or bool

If True, display a progress bar. If None, the default from the preferences settings is used.

num_workersNone or int

Number of worker used by dask. If None, default to dask default value.

Returns:

dict: Dictionary with the statistics

Raises:

NotImplementedError: If the signal axes are non-uniform axes.

Examples

>>> import holospy as holo
>>> s = holo.data.Fe_needle_reference_hologram()
>>> sb_position = s.estimate_sideband_position(high_cf=True)
>>> s.statistics(sb_position=sb_position)
{'Fringe spacing (nm)': 3.4860442674236256,
'Carrier frequency (1/px)': 0.26383819985575441,
'Carrier frequency (mrad)': 0.56475154609203482,
'Fringe contrast': 0.071298357213623778,
'Fringe sampling (px)': 3.7902017241882331,
'Carrier frequency (1 / nm)': 0.28685808994016415}

class holospy.signals.LazyHologramImage(*args, **kwargs)#

Bases: LazySignal, HologramImage

Lazy signal class for holograms acquired via off-axis electron holography.

The computation is delayed until explicitly requested.

This class is not expected to be instantiated directly, instead use:

>>> data = da.ones((10, 10))
>>> s = holospy.signals.HologramImage(data).as_lazy()

Create a signal instance.

Parameters:

datanumpy.ndarray: The signal data. It can be an array of any dimensions.
axes[dict/axes], optional: List of either dictionaries or axes objects to define the axes (see the documentation of the AxesManager class for more details).
attributesdict, optional: A dictionary whose items are stored as attributes.
metadatadict, optional: A dictionary containing a set of parameters that will to stores in the metadata attribute. Some parameters might be mandatory in some cases.
original_metadatadict, optional: A dictionary containing a set of parameters that will to stores in the original_metadata attribute. It typically contains all the parameters that has been imported from the original data file.
raggedbool or None, optional: Define whether the signal is ragged or not. Overwrite the ragged value in the attributes dictionary. If None, it does nothing. Default is None.

holospy.signals#

`holospy.signals`#