LumiSpy metadata structure

LumiSpy extends the HyperSpy metadata structure with conventions for metadata specific to its signal types. Refer to the HyperSpy metadata documentation for general metadata fields.

The metadata of any signal objects is stored in the metadata attribute, which has a tree structure. By convention, the node labels are capitalized and the ones for 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.

Besides directly accesing the metadata tree structure, e.g. s.metadata.Signal.signal_type, the HyperSpy methods hyperspy.misc.utils.DictionaryTreeBrowser.set_item(), hyperspy.misc.utils.DictionaryTreeBrowser.has_item() and hyperspy.misc.utils.DictionaryTreeBrowser.get_item() can be used to add to, search for and read from items in the metadata tree, respectively.

The luminescence specific 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. Note that not all types of leaves will apply to every type of measurement. For example, while parallel acquisition with a CCD is characterized by the central_wavelength, a serial acquisition with a PMT will require a start_wavelength and a step_size.

metadata
├── General
│   └── # see HyperSpy
├── Sample
│   └── # see HyperSpy
├── Signal
│   ├── signal_type
│   ├── quantity
│   └── # otherwise see HyperSpy
└── Acquisition_instrument
    ├── Laser / SEM / TEM
    │   ├── laser_type
    │   ├── model
    │   ├── wavelength (nm)
    │   ├── power (mW)
    │   ├── objective_magnification
    │   ├── Filter
    │   │   ├── filter_type
    │   │   ├── position
    │   │   ├── optical_density
    │   │   ├── cut_on_wavelength (nm)
    │   │   └── cut_off_wavelength (nm)
    │   └── # for SEM/TEM see HyperSpy
    ├── Spectrometer
    │   ├── model
    │   ├── acquisition_mode
    │   ├── entrance_slit_width (mm)
    │   ├── exit_slit_width (mm)
    │   ├── central_wavelength (nm)
    │   ├── start_wavelength (nm)
    │   ├── step_size (nm)
    │   ├── Grating
    │   │   ├── groove_density (grooves/mm)
    │   │   ├── blazing_angle (º)
    │   │   └── blazing_wavelength (nm)
    │   └── Filter
    │       ├── filter_type
    │       ├── position
    │       ├── optical_density
    │       ├── cut_on_wavelength (nm)
    │       └── cut_off_wavelength (nm)
    ├── Detector
    │   ├── detector_type
    │   ├── model
    │   ├── frames
    │   ├── integration_time (s)
    │   ├── saturation_fraction
    │   ├── binning
    │   ├── processing
    │   ├── sensor_roi
    │   └── pixel_size (µm)
    └── Spectral_image
        ├── mode
        ├── drift_correction_periodicity
        └── drift_correction_units (s)

General

See HyperSpy-Metadata-General.

Sample

See HyperSpy-Metadata-Sample.

Signal

signal_type

type: string

String that describes the type of signal. The LumiSpy specific signal classes are summarized under Signal types.

quantity

type: string

The name of the quantity of the “intensity axis” with the units in round brackets if required, for example ‘Intensity (counts/s)’.

See HyperSpy-Metadata-Signal for additional fields.

Acquisition Instrument

Laser / SEM / TEM

For SEM or TEM see HyperSpy-Metadata-SEM or HyperSpy-Metadata-TEM.

Laser

laser_type

type: string

The type of laser used, e.g. ‘HeCd’.

model

type: string

Model of the laser (branding by manufacturer).

wavelength

type: float

Emission wavelength of the exciting laser in nm.

power

type: float

Measured power of the excitation laser in mW.

magnification

type: int

Magnification of the microscope objective used to focus the beam to the sample.

Filter

Information about additional filters entered into the lightpath before the sample. In case multiple filters are used, they should be numbered Filter_1, etc.

filter_type

type: string

Type of filter (e.g. ‘optical density’, ‘short pass’, ‘long pass’, ‘bandpass’, ‘color’).

position

type: string

Position in the beam (e.g. ‘excitation’ vs. ‘detection’ in case of optical excitation).

optical_density

type: float

Optical density in case of an intensity filter.

cut_on_wavelength

type: float

Cut on wavelength in nm in case of a long-pass or bandpass filter.

cut_off_wavelength

type: float

Cut off wavelength in nm in case of a short-pass or bandpass filter.

Spectrometer

Contains information about the spectrometer, configuration and grating used for the measurement. In case multiple spectrometers are connected in series, they should be numbered Spectrometer_1, etc.

model

type: string

Model of the spectrometer (branding by manufacturer).

acquisition_mode

type: string

Acquisition mode (e.g. ‘Parallel dispersive’, versus ‘Serial dispersive’).

entrance_slit_width

type: float

Width of the entrance slit in mm.

exit_slit_width

type: float

Width of the exit slit (serial acquisition) in mm.

central_wavelength

type: float

Central wavelength during acquisition (parallel acquisition).

start_wavelength

type: float

Start wavelength in nm (serial acquisition).

step_size

type: float

Step size in nm (serial acquisition).

Grating

Information of the dispersion grating employed in the measurement.

groove_density

type: int

Density of lines on the grating in grooves/mm.

blazing_angle

type: int

Angle in degree (º) that the grating is blazed at.

blazing_wavelength

type: int

Wavelength that the grating blaze is optimized for in nm.

Filter

Information about additional filters entered into the lightpath after the sample. In case multiple filters are used, they should be numbered Filter_1, etc. See filter-label above for details on items that may potentially be included.

Detector

Contains information about the detector used to acquire the signal. Contained leaves will differ depending on the type of detector.

detector_type

type: string

The type of detector used to acquire the signal (CCD, PMT, StreakCamera, TCSPD).

model

type: string

The model of the used detector.

frames

type: int

Number of frames that are summed to yield the total integration time.

integration_time (s)

type: float

Time over which the signal is integrated. In case multiple frames are summed, it is the total exposure time. In case of serial acquisition, it is the dwell time per data point.

saturation_fraction

type: float

Fraction of the signal intensity compared with the saturation threshold of the CCD.

binning

type: tuple of int

A tuple that describes the binning of a parallel detector such a CCD on readout in x and y directions.

processing

type: string

Information about automatic processing performed on the data, e.g. ‘dark subtracted’.

sensor_roi

type: tuple of int

Tuple of length 2 or 4 that specifies range of pixels on a detector that are read out: (offset x, offset y, size x, size y) for a 2D array detector and (offset, size) for a 1D line detector.

pixel_size

type: float or tuple of float

Size of a pixel in µm. Tuple of length 2 (width, height), when the pixel is not square.

Spectral_image

Contains information about mapping parameters, such as step size, drift correction, etc.

mode

type: string

Mode of the spectrum image acquisition such as ‘Map’ or ‘Linescan’.

drift_correction_periodicity

type: int/float

Periodicity of the drift correction in specified units (standard s).

drift_correction_units

type: string

Units of the drift correction such as ‘s’, ‘px’, ‘rows’.