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 accessing the metadata tree structure, e.g.
s.metadata.Signal.signal_type
, the HyperSpy methods
set_item()
,
has_item()
and
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
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 ExSpy-Metadata-SEM/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 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’.