{
"cells": [
{
"cell_type": "markdown",
"metadata": {
"nbsphinx": "hidden"
},
"source": [
"This notebook is part of the `kikuchipy` documentation https://kikuchipy.org.\n",
"Links to the documentation won't work from the notebook."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Metadata structure\n",
"\n",
"\n",
"\n",
"Warning\n",
"\n",
"The `Acquisition_instrument.SEM.Detector.EBSD` and `Sample.Phases` metadata\n",
"nodes are deprecated and will be removed in v0.6.\n",
"\n",
"There are three main reasons for this change: the first is that only the static\n",
"background array stored in the\n",
"`Acquisition_instrument.SEM.Detector.EBSD.static_background` node is used\n",
"internally, and so the remaining metadata is unnecessary. The background pattern\n",
"will be stored in its own `EBSD.static_background` property instead. The second\n",
"is that keeping track of the unnecessary metadata makes writing and maintaining\n",
"input/ouput plugins challenging. The third is that the\n",
"[EBSD.xmap](../reference.rst#kikuchipy.signals.EBSD.xmap) and\n",
"[EBSD.detector](../reference.rst#kikuchipy.signals.EBSD.detector) properties,\n",
"which keeps track of the\n",
"[CrystalMap](https://orix.readthedocs.io/en/stable/reference.html#orix.crystal_map.CrystalMap)\n",
"and [EBSDDetector](../reference.rst#kikuchipy.detectors.EBSDDetector) for a\n",
"signal, respectively, should be used instead of the more \"static\" metadata.\n",
"\n",
"
\n",
"\n",
"The [EBSD](../reference.rst#kikuchipy.signals.EBSD) class stores metadata in the\n",
"`metadata` attribute provided by HyperSpy"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Exchange inline for notebook or qt5 (from pyqt) for interactive plotting\n",
"%matplotlib inline\n",
"\n",
"import matplotlib.pyplot as plt\n",
"import kikuchipy as kp\n",
"\n",
"\n",
"s = kp.data.nickel_ebsd_small()\n",
"s"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"s.metadata"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"While kikuchipy's EBSD\n",
"([ebsd_metadata()](../reference.rst#kikuchipy.signals.util.ebsd_metadata)) metadata\n",
"structure is based on\n",
"[HyperSpy's metadata structure](http://hyperspy.org/hyperspy-doc/current/user_guide/metadata_structure.html),\n",
"it includes the nodes `Acquisition_instrument.Sample.Phases` to store phase\n",
"information and `Acquisition_instrument.SEM.Detector.EBSD` for acquisition\n",
"information. The information in these nodes are written, along with the\n",
"patterns, to file when saving an EBSD signal in the\n",
"[kikuchipy h5ebsd format](load_save_data.ipynb#h5ebsd)."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"kp.signals.util.ebsd_metadata()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The complete list of metadata looks like this\n",
"\n",
"```\n",
" ├── Acquisition_instrument\n",
" │ └── SEM\n",
" │ ├── Detector\n",
" │ │ └── EBSD\n",
" │ │ ├── azimuth_angle [º]\n",
" │ │ ├── binning\n",
" │ │ ├── detector\n",
" │ │ ├── elevation_angle [º]\n",
" │ │ ├── exposure_time [s]\n",
" │ │ ├── frame_number\n",
" │ │ ├── frame_rate [1/s]\n",
" │ │ ├── gain [dB]\n",
" │ │ ├── grid_type\n",
" │ │ ├── manufacturer\n",
" │ │ ├── sample_tilt [º]\n",
" │ │ ├── scan_time [s]\n",
" │ │ ├── static_background (numpy.ndarray)\n",
" │ │ ├── version\n",
" │ │ ├── xpc\n",
" │ │ ├── ypc\n",
" │ │ └── zpc\n",
" │ ├── beam_energy [kV]\n",
" │ ├── magnification\n",
" │ ├── microscope\n",
" │ └── working_distance [mm]\n",
" └── Sample\n",
" └── Phases\n",
" └── 1\n",
" ├── atom_coordinates\n",
" │ └── 1\n",
" │ ├── atom\n",
" │ ├── coordinates (x0, y0, z0)\n",
" │ ├── debye_waller_factor [nm^2]\n",
" │ └── site_occupation\n",
" ├── formula\n",
" ├── info\n",
" ├── lattice_constants (a, b, c and alfa, beta, gamma) [nm and º]\n",
" ├── laue_group\n",
" ├── material_name\n",
" ├── point_group\n",
" ├── setting\n",
" ├── source\n",
" ├── space_group\n",
" └── symmetry\n",
"```"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The utility function\n",
"[metadata_nodes()](../reference.rst#kikuchipy.signals.util.metadata_nodes) returns\n",
"the node strings for the `SEM` and `EBSD` nodes for convenience.\n",
"\n",
"\n",
"\n",
"Note \n",
"\n",
"If you regularly use information relevant to EBSD data not included in the\n",
"metadata structure, you can request this in our\n",
"[issue tracker](https://github.com/pyxem/kikuchipy/issues).\n",
"\n",
"
"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"sem_node, ebsd_node = kp.signals.util.metadata_nodes()\n",
"print(sem_node, ebsd_node)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"s.metadata.get_item(f\"{ebsd_node}.xpc\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"nbsphinx-thumbnail": {
"tooltip": "Where relevant microscope, detector, and sample parameters are stored with a signal and how to get and set them"
},
"tags": [
"nbsphinx-thumbnail"
]
},
"outputs": [],
"source": [
"plt.imshow(s.metadata.get_item(f\"{ebsd_node}.static_background\"), cmap=\"gray\")\n",
"_ = plt.axis(\"off\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## EBSD\n",
"\n",
"This node contains information relevant for EBSD data. All parameters can be\n",
"set with the method\n",
"[set_experimental_parameters()](../reference.rst#kikuchipy.signals.EBSD.set_experimental_parameters).\n",
"An explanation of each parameter is given in the method's docstring."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"s.set_experimental_parameters(xpc=5.64)\n",
"s.metadata.get_item(f\"{ebsd_node}.xpc\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Phases\n",
"\n",
"This node contains information relevant for EBSD scans or simulated patterns'\n",
"phases. All parameters can be set with the\n",
"[EBSD](../reference.rst#kikuchipy.signals.EBSD) class method\n",
"[set_phase_parameters()](../reference.rst#kikuchipy.signals.EBSD.set_phase_parameters).\n",
"An explanation of each parameter is given in the methods' docstring."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"s.metadata.Sample.Phases"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"s.set_phase_parameters(info=\"Polycrystalline\")\n",
"s.metadata.Sample.Phases"
]
}
],
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