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oxford_h5ebsd.py
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oxford_h5ebsd.py
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# Copyright 2019-2023 The kikuchipy developers
#
# This file is part of kikuchipy.
#
# kikuchipy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# kikuchipy is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with kikuchipy. If not, see <http://www.gnu.org/licenses/>.
"""Reader of EBSD data from an Oxford Instruments h5ebsd (H5OINA) file.
"""
import logging
from pathlib import Path
from typing import List, Union
import h5py
import numpy as np
from orix.crystal_map import CrystalMap
from kikuchipy.detectors import EBSDDetector
from kikuchipy.io.plugins._h5ebsd import _hdf5group2dict, H5EBSDReader
__all__ = ["file_reader"]
_logger = logging.getLogger(__name__)
# Plugin characteristics
# ----------------------
format_name = "oxford_h5ebsd"
description = (
"Read support for electron backscatter diffraction patterns stored "
"in an HDF5 file formatted in Oxford Instruments' h5ebsd format, "
"named H5OINA. The format is similar to the format described in "
"Jackson et al.: h5ebsd: an archival data format for electron "
"back-scatter diffraction data sets. Integrating Materials and "
"Manufacturing Innovation 2014 3:4, doi: "
"https://dx.doi.org/10.1186/2193-9772-3-4."
)
full_support = False
# Recognised file extension
file_extensions = ["h5oina"]
default_extension = 0
# Writing capabilities (signal dimensions, navigation dimensions)
writes = False
class OxfordH5EBSDReader(H5EBSDReader):
"""Oxford Instruments h5ebsd (H5OINA) file reader.
The file contents are ment to be used for initializing a
:class:`~kikuchipy.signals.EBSD` signal.
Parameters
----------
filename
Full file path of the HDF5 file.
**kwargs
Keyword arguments passed to :class:`h5py.File`.
"""
def __init__(self, filename: str, **kwargs):
super().__init__(filename, **kwargs)
def scan2dict(self, group: h5py.Group, lazy: bool = False) -> dict:
"""Read (possibly lazily) patterns from group.
Parameters
----------
group
Group with patterns.
lazy
Whether to read dataset lazily (default is ``False``).
Returns
-------
scan_dict
Dictionary with keys ``"axes"``, ``"data"``, ``"metadata"``,
``"original_metadata"``, ``"detector"``,
``"static_background"``, and ``"xmap"``. This dictionary can
be passed as keyword arguments to create an
:class:`~kikuchipy.signals.EBSD` signal.
Raises
------
IOError
If patterns are not acquired in a square grid.
"""
hd = _hdf5group2dict(group["EBSD/Header"], recursive=True)
dd = _hdf5group2dict(group["EBSD/Data"], data_dset_names=self.patterns_name)
# Get data shapes
ny, nx = hd["Y Cells"], hd["X Cells"]
sy, sx = hd["Pattern Height"], hd["Pattern Width"]
dy, dx = hd.get("Y Step", 1), hd.get("X Step", 1)
px_size = 1.0
# --- Metadata
fname, title = self.get_metadata_filename_title(group.name)
metadata = {
"Acquisition_instrument": {
"SEM": {
"beam_energy": hd.get("Beam Voltage"),
"magnification": hd.get("Magnification"),
"working_distance": hd.get("Working Distance"),
},
},
"General": {"original_filename": fname, "title": title},
"Signal": {"signal_type": "EBSD", "record_by": "image"},
}
scan_dict = {"metadata": metadata}
# --- Data
data = self.get_data(group, data_shape=(ny, nx, sy, sx), lazy=lazy)
scan_dict["data"] = data
# --- Axes
scan_dict["axes"] = self.get_axes_list((ny, nx, sy, sx), (dy, dx, px_size))
# --- Original metadata
scan_dict["original_metadata"] = {
"manufacturer": self.manufacturer,
"version": self.version,
}
scan_dict["original_metadata"].update(hd)
# --- Crystal map
# TODO: Implement reader of Oxford Instruments h5ebsd crystal
# maps in orix
xmap = CrystalMap.empty(shape=(ny, nx), step_sizes=(dy, dx))
scan_dict["xmap"] = xmap
# --- Static background
scan_dict["static_background"] = hd.get("Processed Static Background")
# --- Detector
pc = np.column_stack(
(
dd.get("Pattern Center X", 0.5),
dd.get("Pattern Center Y", 0.5),
dd.get("Detector Distance", 0.5),
)
)
if pc.size > 3:
pc = pc.reshape((ny, nx, 3))
detector_kw = dict(
shape=(sy, sx),
pc=pc,
sample_tilt=np.rad2deg(hd.get("Tilt Angle", np.deg2rad(70))),
convention="oxford",
)
detector_tilt_euler = hd.get("Detector Orientation Euler")
binning_str = hd.get("Camera Binning Mode")
try:
detector_kw["tilt"] = np.rad2deg(detector_tilt_euler[1]) - 90
except (IndexError, TypeError): # pragma: no cover
_logger.debug("Could not read detector tilt")
try:
detector_kw["binning"] = int(binning_str.split("x")[0])
except IndexError: # pragma: no cover
_logger.debug("Could not read detector binning")
scan_dict["detector"] = EBSDDetector(**detector_kw)
return scan_dict
def file_reader(
filename: Union[str, Path],
scan_group_names: Union[None, str, List[str]] = None,
lazy: bool = False,
**kwargs,
) -> List[dict]:
"""Read electron backscatter diffraction patterns, a crystal map,
and an EBSD detector from an Oxford Instruments h5ebsd (H5OINA) file
:cite:`jackson2014h5ebsd`.
Not meant to be used directly; use :func:`~kikuchipy.load`.
Parameters
----------
filename
Full file path of the HDF5 file.
scan_group_names
Name or a list of names of HDF5 top group(s) containing the
scan(s) to return. If not given (default), the first scan in the
file is returned.
lazy
Open the data lazily without actually reading the data from disk
until required. Allows opening arbitrary sized datasets. Default
is ``False``.
**kwargs
Keyword arguments passed to :class:`h5py.File`.
Returns
-------
scan_dict_list
List of one or more dictionaries with the keys ``"axes"``,
``"data"``, ``"metadata"``, ``"original_metadata"``,
``"detector"``, and ``"xmap"``. This
dictionary can be passed as keyword arguments to create an
:class:`~kikuchipy.signals.EBSD` signal.
"""
reader = OxfordH5EBSDReader(filename, **kwargs)
return reader.read(scan_group_names, lazy)