Metadata structure

The BaseSignal class stores metadata in the metadata attribute that has a tree structure. By convention, the nodes labels are capitalized and the leaves are not capitalized.

When a leaf contains a quantity that is not dimensionless, the units can be given in an extra leaf with the same label followed by the “_units” suffix.

The metadata structure is represented in the following tree diagram. The default units are given in parentheses. Details about the leaves can be found in the following sections of this chapter.

├── Acquisition_instrument
│   ├── SEM
│   │   ├── Detector
│   │   │   └── EDS
│   │   │       ├── azimuth_angle (º)
│   │   │       ├── elevation_angle (º)
│   │   │       ├── energy_resolution_MnKa (eV)
│   │   │       ├── live_time (s)
│   │   │       └── real_time (s)
│   │   ├── beam_current (nA)
│   │   ├── beam_energy (keV)
│   │   ├── probe_area (nm²)
│   │   ├── convergence_angle (mrad)
│   │   ├── magnification
│   │   ├── microscope
│   │   ├── Stage
│   │   │   ├── rotation (º)
│   │   │   ├── tilt_alpha (º)
│   │   │   ├── tilt_beta (º)
│   │   │   ├── x (mm)
│   │   │   ├── y (mm)
│   │   │   └── z (mm)
│   │   └── working_distance (mm)
│   └── TEM
│       ├── Detector
│       │   ├── EDS
│       │   │   ├── azimuth_angle (º)
│       │   │   ├── elevation_angle (º)
│       │   │   ├── energy_resolution_MnKa (eV)
│       │   │   ├── live_time (s)
│       │   │   └── real_time (s)
│       │   └── EELS
│       │       ├── aperture (mm)
│       │       ├── collection_angle (mrad)
│       │       ├── dwell_time (s)
│       │       ├── exposure (s)
│       │       ├── frame_number
│       │       └── spectrometer
│       ├── Biprism
│       │   ├── azimuth_angle (º)
│       │   ├── position
│       │   └── voltage (V)
│       ├── acquisition_mode
│       ├── beam_current (nA)
│       ├── beam_energy (keV)
│       ├── probe_area (nm²)
│       ├── camera_length (mm)
│       ├── convergence_angle (mrad)
│       ├── magnification
│       ├── microscope
│       └── Stage
│           ├── rotation (º)
│           ├── tilt_alpha (º)
│           ├── tilt_beta (º)
│           ├── x (mm)
│           ├── y (mm)
│           └── z (mm)
├── General
│   ├── authors
│   ├── date
│   ├── doi
│   ├── original_filename
│   ├── notes
│   ├── time
│   ├── time_zone
│   └── title
├── Sample
│   ├── credits
│   ├── description
│   ├── elements
│   ├── thickness
│   └── xray_lines
└── Signal
    ├── Noise_properties
    │   ├── Variance_linear_model
    │   │   ├── correlation_factor
    │   │   ├── gain_factor
    │   │   ├── gain_offset
    │   │   └── parameters_estimation_method
    │   └── variance
    ├── binned
    ├── quantity
    ├── signal_type
    └── signal_origin

General

title

type: Str

A title for the signal, e.g. “Sample overview”

original_filename

type: Str

If the signal was loaded from a file this key stores the name of the original file.

time_zone

type: Str

The time zone as supported by the python-dateutil library, e.g. “UTC”, “Europe/London”, etc. It can also be a time offset, e.g. “+03:00” or “-05:00”.

time

type: Str

The acquisition or creation time in ISO 8601 time format.

date

type: Str

The acquisition or creation date in ISO 8601 date format

authors

type: Str

The authors of the data, in Latex format: Surname1, Name1 and Surname2, Name2, etc.

doi

type: Str

Digital object identifier of the data, e. g. doi:10.5281/zenodo.58841.

notes

type: Str

Notes about the data.

Acquisition_instrument

TEM

Contain information relevant to transmission electron microscope signals.

microscope

type: Str

The microscope model, e.g. VG 501

acquisition_mode

type: Str

Either ‘TEM’ or ‘STEM’

camera_length

type: Float

The camera length in mm.

convergence_angle

type: Float

The beam convergence semi-angle in mrad.

beam_energy

type: Float

The energy of the electron beam in keV

beam_current

type: Float

The beam current in nA.

probe_area

type: Float

The illumination area of the electron beam in nm².

dwell_time

type: Float

The dwell time in seconds. This is relevant for STEM acquisition

exposure

type: Float

The exposure time in seconds. This is relevant for TEM acquisition.

magnification

type: Float

The magnification.

SEM

Contain information relevant to scanning electron microscope signals.

microscope

type: Str

The microscope model, e.g. VG 501

convergence_angle

type: Float

The beam convergence semi-angle in mrad.

beam_energy

type: Float

The energy of the electron beam in keV

beam_current

type: Float

The beam current in nA.

probe_area

type: Float

The illumination area of the electron beam in nm².

magnification

type: Float

The magnification.

working_distance

type: Float

The working distance in mm.

Stage

tilt_alpha

type: Float

A tilt of the stage in degree.

tilt_beta

type: Float

Another tilt of the stage in degree.

rotation

type: Float

The rotation of the stage in degree.

x

type: Float

The position of the stage in mm along the x axis.

y

type: Float

The position of the stage in mm along the y axis.

z

type: Float

The position of the stage in mm along the z axis.

Detector

All instruments can contain a “Detector” node with information about the detector used to acquire the signal. EDX and EELS detectors should follow the following structure:

EELS

This node stores parameters relevant to electron energy loss spectroscopy signals.

aperture_size

type: Float

The entrance aperture size of the spectrometer in mm.

collection_angle

type: Float

The collection semi-angle in mrad.

dwell_time

type: Float

The dwell time in seconds. This is relevant for STEM acquisition

exposure

type: Float

The exposure time in seconds. This is relevant for TEM acquisition.

frame_number

type: int

The number of frames/spectra integrated during the acquisition.

spectrometer

type: Str

The spectrometer model, e.g. Gatan Enfinium ER (Model 977).

EDS

This node stores parameters relevant to electron X-ray energy dispersive spectroscopy data.

azimuth_angle

type: Float

The azimuth angle of the detector in degree. If the azimuth is zero, the detector is perpendicular to the tilt axis.

elevation_angle

type: Float

The elevation angle of the detector in degree. The detector is perpendicular to the surface with an angle of 90.

energy_resolution_MnKa

type: Float

The full width at half maximum (FWHM) of the manganese K alpha (Mn Ka) peak in eV. This value is used as a first approximation of the energy resolution of the detector.

real_time

type: Float

The time spent to record the spectrum in second.

live_time

type: Float

The time spent to record the spectrum in second, compensated for the dead time of the detector.

Biprism

This node stores parameters of biprism used in off-axis electron holography

azimuth_angle (º)

type: Float

Rotation angle of the biprism in degree

position

type: Str

Position of the biprism in microscope column, e.g. Selected area aperture plane

voltage

type: Float

Voltage of electrostatic biprism in volts

Sample

credits

type: Str

Acknowledgment of sample supplier, e.g. Prepared by Putin, Vladimir V.

description

type: Str

A brief description of the sample

elements

type: list

A list of the symbols of the elements composing the sample, e.g. [‘B’, ‘N’] for a sample composed of Boron and Nitrogen.

xray_lines

type: list

A list of the symbols of the X-ray lines to be used for processing, e.g. [‘Al_Ka’, ‘Ni_Lb’] for the K alpha line of Aluminum and the L beta line of Nickel.

thickness

type: Float

The thickness of the sample in m.

Signal

signal_type

type: Str

A term that describes the signal type, e.g. EDS, PES… This information can be used by HyperSpy to load the file as a specific signal class and therefore the naming should be standarised. Currently HyperSpy provides special signal class for photoemission spectroscopy, electron energy loss spectroscopy and energy dispersive spectroscopy. The signal_type in these cases should be respectively PES, EELS and EDS_TEM (EDS_SEM).

signal_origin

type: Str

Describes the origin of the signal e.g. ‘simulation’ or ‘experiment’.

record_by

Deprecated since version 1.2.

type: Str

One of ‘spectrum’ or ‘image’. It describes how the data is stored in memory. If ‘spectrum’ the spectral data is stored in the faster index.

quantity

type: Str

The name of the quantity of the “intensity axis” with the units in round brackets if required, for example Temperature (K).

Noise_properties

variance

type: float or BaseSignal instance.

The variance of the data. It can be a float when the noise is Gaussian or a BaseSignal instance if the noise is heteroscedastic, in which case it must have the same dimensions as data.

Variance_linear_model

In some cases the variance can be calculated from the data using a simple linear model: variance = (gain_factor * data + gain_offset) * correlation_factor.

gain_factor

type: Float

gain_offset

type: Float

correlation_factor

type: Float

parameters_estimation_method

type: Str

_Internal_parameters

This node is “private” and therefore is not displayed when printing the metadata attribute. For example, an “energy” leaf should be accompanied by an “energy_units” leaf.

Stacking_history

Generated when using stack(). Used by split(), to retrieve the former list of signal.

step_sizes

type: list of int

Step sizes used that can be used in split.

axis

type: int

The axis index in axes manager on which the dataset were stacked.

Folding

Constains parameters that related to the folding/unfolding of signals.