`ComplexSignal`#

class hyperspy.api.signals.ComplexSignal(*args, **kwargs)#

Bases: BaseSignal

General signal class for complex data.

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.

property amplitude#: Get/set the amplitude of the data.

angle(deg=False)#

Return the angle (also known as phase or argument). If the data is real, the angle is 0 for positive values and \(2\pi\) for negative values.

Parameters:

degbool, default False: Return angle in degrees if True, radians if False.

Returns:

BaseSignal: The counterclockwise angle from the positive real axis on the complex plane, with dtype as numpy.float64.

argand_diagram(size=[256, 256], range=None)#

Calculate and plot Argand diagram of complex signal.

Parameters:

sizelist of int, optional: Size of the Argand plot in pixels. Default is [256, 256].
rangeNone, numpy.ndarray, default None: The position of the edges of the diagram with shape (2, 2) or (2,). All values outside of this range will be considered outliers and not tallied in the histogram. If None use the mininum and maximum values.

Returns:

Signal2D: The Argand diagram

Examples

>>> import holospy as holo  
>>> hologram = holo.data.Fe_needle_hologram() 
>>> ref = holo.data.Fe_needle_reference_hologram() 
>>> w = hologram.reconstruct_phase(ref) 
>>> w.argand_diagram(range=[-3, 3]).plot() 

change_dtype(dtype)#

Change the data type.

Parameters:

dtypestr or numpy.dtype: Typecode or data-type to which the array is cast. For complex signals only other complex dtypes are allowed. If real valued properties are required use real, imag, amplitude and phase instead.

property imag#: Get/set the imaginary part of the data.

property phase#: Get/set the phase of the data.

plot(power_spectrum=False, representation='cartesian', same_axes=True, fft_shift=False, navigator='auto', axes_manager=None, norm='auto', **kwargs)#

Plot the signal at the current coordinates.

For multidimensional datasets an optional figure, the “navigator”, with a cursor to navigate that data is raised. In any case it is possible to navigate the data using the sliders. Currently only signals with signal_dimension equal to 0, 1 and 2 can be plotted.

Parameters:

power_spectrumbool, default False.

If True, plot the power spectrum instead of the actual signal, if False, plot the real and imaginary parts of the complex signal.

representation{'cartesian' | 'polar'}

Determines if the real and imaginary part of the complex data is plotted ('cartesian', default), or if the amplitude and phase should be used ('polar').

same_axesbool, default True

If True (default) plot the real and imaginary parts (or amplitude and phase) in the same figure if the signal is one-dimensional.

fft_shiftbool, default False

If True, shift the zero-frequency component. See numpy.fft.fftshift() for more details.

navigatorstr, None, or BaseSignal (or subclass).

Allowed string values are ``’auto’``, ``’slider’``, and ``’spectrum’``.

If 'auto':
- If navigation_dimension > 0, a navigator is provided to explore the data.
- If navigation_dimension is 1 and the signal is an image the navigator is a sum spectrum obtained by integrating over the signal axes (the image).
- If navigation_dimension is 1 and the signal is a spectrum the navigator is an image obtained by stacking all the spectra in the dataset horizontally.
- If navigation_dimension is > 1, the navigator is a sum image obtained by integrating the data over the signal axes.
- Additionally, if navigation_dimension > 2, a window with one slider per axis is raised to navigate the data.
- For example, if the dataset consists of 3 navigation axes “X”, “Y”, “Z” and one signal axis, “E”, the default navigator will be an image obtained by integrating the data over “E” at the current “Z” index and a window with sliders for the “X”, “Y”, and “Z” axes will be raised. Notice that changing the “Z”-axis index changes the navigator in this case.
- For lazy signals, the navigator will be calculated using the compute_navigator() method.
If 'slider':
- If navigation dimension > 0 a window with one slider per axis is raised to navigate the data.
If 'spectrum':
- If navigation_dimension > 0 the navigator is always a spectrum obtained by integrating the data over all other axes.
- Not supported for lazy signals, the 'auto' option will be used instead.
If None, no navigator will be provided.

Alternatively a BaseSignal (or subclass) instance can be provided. The navigation or signal shape must match the navigation shape of the signal to plot or the navigation_shape + signal_shape must be equal to the navigator_shape of the current object (for a dynamic navigator). If the signal dtype is RGB or RGBA this parameter has no effect and the value is always set to 'slider'.

axes_managerNone or AxesManager

If None, the signal’s axes_manager attribute is used.

plot_markersbool, default True

Plot markers added using s.add_marker(marker, permanent=True). Note, a large number of markers might lead to very slow plotting.

navigator_kwdsdict

Only for image navigator, additional keyword arguments for matplotlib.pyplot.imshow().

**kwargsdict

Only when plotting an image: additional (optional) keyword arguments for matplotlib.pyplot.imshow().

property real#: Get/set the real part of the data.

unwrapped_phase(wrap_around=False, seed=None, show_progressbar=None, num_workers=None)#

Return the unwrapped phase as an appropriate HyperSpy signal.

Parameters:

wrap_aroundbool or iterable of bool, default False: When an element of the sequence is True, the unwrapping process will regard the edges along the corresponding axis of the image to be connected and use this connectivity to guide the phase unwrapping process. If only a single boolean is given, it will apply to all axes. Wrap around is not supported for 1D arrays.
seednumpy.random.Generator, int or None, default None: Pass to the rng argument of the unwrap_phase() function. Unwrapping 2D or 3D images uses random initialization. This sets the seed of the PRNG to achieve deterministic behavior.
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:

BaseSignal (or subclass): The unwrapped phase.

Notes

Uses the unwrap_phase() function from skimage. The algorithm is based on Miguel Arevallilo Herraez, David R. Burton, Michael J. Lalor, and Munther A. Gdeisat, “Fast two-dimensional phase-unwrapping algorithm based on sorting by reliability following a noncontinuous path”, Journal Applied Optics, Vol. 41, No. 35, pp. 7437, 2002

ComplexSignal#

`ComplexSignal`#