.. _metadata_structure: Metadata structure ****************** The :class:`~.signal.BaseSignal` class stores metadata in the :attr:`~.signal.BaseSignal.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 ├── FFT │ └── shifted ├── 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, e.g. '13:29:10'. date type: Str The acquisition or creation date in ISO 8601 date format, e.g. '2018-01-28'. 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 nm\ :sup:`2`. 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 nm\ :sup:`2`. 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:: 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). FFT --- shifted type: bool. Specify if the FFT has the zero-frequency component shifted to the center of the signal. 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 :class:`~.signal.BaseSignal` instance if the noise is heteroscedastic, in which case it must have the same dimensions as :attr:`~.signal.BaseSignal.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 :attr:`~.signal.BaseSignal.metadata` attribute. For example, an "energy" leaf should be accompanied by an "energy_units" leaf. Stacking_history ---------------- Generated when using :py:meth:`~.utils.stack`. Used by :py:meth:`~.signal.BaseSignal.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.