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Metadata structure

The EBSD class stores metadata in the metadata attribute provided by HyperSpy

# exchange inline for qt5 for interactive plotting from the pyqt package
%matplotlib inline

import matplotlib.pyplot as plt
import kikuchipy as kp


s = kp.data.nickel_ebsd_small()
s

WARNING:hyperspy.api:The ipywidgets GUI elements are not available, probably because the hyperspy_gui_ipywidgets package is not installed.
WARNING:hyperspy.api:The traitsui GUI elements are not available, probably because the hyperspy_gui_traitsui package is not installed.

<EBSD, title: patterns My awes0m4 ..., dimensions: (3, 3|60, 60)>

s.metadata

Acquisition_instrument
SEM
Detector
EBSD
• azimuth_angle = 0.0
• binning = 8
• detector = NORDIF UF1100
• elevation_angle = 0.0
• exposure_time = 0.0035
• frame_number = 1
• frame_rate = 202
• gain = 0.0
• grid_type = square
• manufacturer = kikuchipy
• sample_tilt = 70.0
• scan_time = 148
• static_background = array([[84, 87, 90, ..., 27, 29, 30], [87, 90, 93, ..., 27, 28, 30], ... 80, 82, ..., 28, 26, 26], [76, 78, 80, ..., 26, 26, 25]], dtype=uint8)
• version = 0.1
• xpc = -5.64
• ypc = 17.28
• zpc = 2087
• beam_energy = 20.0
• magnification = 200
• microscope = Hitachi SU-6600
• working_distance = 24.7

General
• title = patterns My awes0m4 ...

Sample
Phases
1
atom_coordinates
1
• atom = Ni
• coordinates = array([0, 0, 0])
• debye_waller_factor = 0.0035
• site_occupation = 1
• formula = Ni
• info =
• lattice_constants = array([ 0.35236, 0.35236, 0.35236, 90. , 90. , 90. ])
• laue_group =
• material_name = Ni
• point_group =
• setting = 0
• space_group = 225
• symmetry = 0

Signal
• binned = False
• signal_type = EBSD

While kikuchipy’s EBSD (ebsd_metadata()) metadata structure is based on HyperSpy’s metadata structure, it includes the nodes Acquisition_instrument.Sample.Phases to store phase information and Acquisition_instrument.SEM.Detector.EBSD for acquisition information. The information in these nodes are written, along with the patterns, to file when saving an EBSD signal in the kikuchipy h5ebsd format.

kp.signals.util.ebsd_metadata()

Acquisition_instrument
SEM
Detector
EBSD
• azimuth_angle = -1.0
• binning = 1
• detector =
• elevation_angle = -1.0
• exposure_time = -1
• frame_number = -1
• frame_rate = -1
• gain = -1.0
• grid_type =
• sample_tilt = -1.0
• scan_time = -1.0
• static_background = -1
• xpc = -1.0
• ypc = -1.0
• zpc = -1.0
• beam_energy = -1.0
• magnification = -1
• microscope =
• working_distance = -1.0

The complete list of metadata looks like this

├── Acquisition_instrument
│   └── SEM
│       ├── Detector
│       │   └── EBSD
│       │       ├── azimuth_angle [º]
│       │       ├── binning
│       │       ├── detector
│       │       ├── elevation_angle [º]
│       │       ├── exposure_time [s]
│       │       ├── frame_number
│       │       ├── frame_rate [1/s]
│       │       ├── gain [dB]
│       │       ├── grid_type
│       │       ├── manufacturer
│       │       ├── sample_tilt [º]
│       │       ├── scan_time [s]
│       │       ├── static_background (numpy.ndarray)
│       │       ├── version
│       │       ├── xpc
│       │       ├── ypc
│       │       └── zpc
│       ├── beam_energy [kV]
│       ├── magnification
│       ├── microscope
│       └── working_distance [mm]
└── Sample
    └── Phases
        └── 1
            ├── atom_coordinates
            │   └── 1
            │       ├── atom
            │       ├── coordinates (x0, y0, z0)
            │       ├── debye_waller_factor [nm^2]
            │       └── site_occupation
            ├── formula
            ├── info
            ├── lattice_constants (a, b, c and alfa, beta, gamma) [nm and º]
            ├── laue_group
            ├── material_name
            ├── point_group
            ├── setting
            ├── source
            ├── space_group
            └── symmetry

The utility function metadata_nodes() returns the node strings for the SEM and EBSD nodes for convenience.

Note

If you regularly use information relevant to EBSD data not included in the metadata structure, you can request this in our issue tracker.

sem_node, ebsd_node = kp.signals.util.metadata_nodes()
print(sem_node, ebsd_node)

Acquisition_instrument.SEM Acquisition_instrument.SEM.Detector.EBSD

s.metadata.get_item(f"{ebsd_node}.xpc")

-5.64

plt.imshow(s.metadata.get_item(f"{ebsd_node}.static_background"), cmap="gray")
_ = plt.axis("off")

EBSD

This node contains information relevant for EBSD data. All parameters can be set with the method set_experimental_parameters(). An explanation of each parameter is given in the method’s docstring.

s.set_experimental_parameters(xpc=5.64)
s.metadata.get_item(f"{ebsd_node}.xpc")

5.64

Phases

This node contains information relevant for EBSD scans or simulated patterns’ phases. All parameters can be set with the EBSD class method set_phase_parameters(). An explanation of each parameter is given in the methods’ docstring.

s.metadata.Sample.Phases

1
atom_coordinates
1
• atom = Ni
• coordinates = array([0, 0, 0])
• debye_waller_factor = 0.0035
• site_occupation = 1
• formula = Ni
• info =
• lattice_constants = array([ 0.35236, 0.35236, 0.35236, 90. , 90. , 90. ])
• laue_group =
• material_name = Ni
• point_group =
• setting = 0
• space_group = 225
• symmetry = 0

s.set_phase_parameters(info="Polycrystalline")
s.metadata.Sample.Phases

1
atom_coordinates
1
• atom = Ni
• coordinates = array([0, 0, 0])
• debye_waller_factor = 0.0035
• site_occupation = 1
• formula = Ni
• info = Polycrystalline
• lattice_constants = array([ 0.35236, 0.35236, 0.35236, 90. , 90. , 90. ])
• laue_group =
• material_name = Ni
• point_group =
• setting = 0
• space_group = 225
• symmetry = 0