# Copyright 2021 Mechanics of Microstructures Group
# at The University of Manchester
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import numpy as np
import pathlib
from typing import Type
from defdap.quat import Quat
[docs]class EBSDDataWriter(object):
def __init__(self) -> None:
self.metadata = {
'shape': (0, 0),
'step_size': 0.,
'acquisition_rotation': Quat(1.0, 0.0, 0.0, 0.0),
'phases': []
}
self.data = {
'phase': None,
'quat': None,
'band_contrast': None
}
self.data_format = None
[docs] @staticmethod
def get_writer(datatype: str) -> "Type[EBSDDataLoader]":
if datatype is None:
datatype = "OxfordText"
if datatype == "OxfordText":
return OxfordTextWriter()
else:
raise ValueError(f"No loader for EBSD data of type {datatype}.")
[docs]class OxfordTextWriter(EBSDDataWriter):
[docs] def write(self, file_name: str, file_dir: str = "") -> None:
""" Write an Oxford Instruments .ctf file, which is a HKL single
orientation file.
Parameters
----------
file_name
File name.
file_dir
Path to file.
"""
# check output file
file_name = "{}.ctf".format(file_name)
file_path = pathlib.Path(file_dir) / pathlib.Path(file_name)
if file_path.exists():
raise FileExistsError(f"File already exits {file_path}")
shape = self.metadata['shape']
step_size = self.metadata['step_size']
# convert quats to Euler angles
out_euler_array = np.zeros(shape + (3,))
for idx in np.ndindex(shape):
out_euler_array[idx] = self.data['quat'][idx].eulerAngles()
out_euler_array *= 180 / np.pi
acq_rot = self.metadata['acquisition_rotation'].eulerAngles()
acq_rot *= 180 / np.pi
# create coordinate grids
x_grid, y_grid = np.meshgrid(
np.arange(0, shape[1]) * step_size,
np.arange(0, shape[0]) * step_size,
indexing='xy'
)
with open(str(file_path), 'w') as ctf_file:
# write header
ctf_file.write("Channel Text File\n")
ctf_file.write("Prj\t\n")
ctf_file.write("Author\t\n")
ctf_file.write("JobMode\tGrid\n")
ctf_file.write(f"XCells\t{shape[1]}\n")
ctf_file.write(f"YCells\t{shape[0]}\n")
ctf_file.write(f"XStep\t{step_size :.4f}\n")
ctf_file.write(f"YStep\t{step_size :.4f}\n")
ctf_file.write(f"AcqE1\t{acq_rot[0]:.4f}\n")
ctf_file.write(f"AcqE2\t{acq_rot[1]:.4f}\n")
ctf_file.write(f"AcqE3\t{acq_rot[2]:.4f}\n")
ctf_file.write(
"Euler angles refer to Sample Coordinate system (CS0)!\n")
ctf_file.write(f"Phases\t{len(self.metadata['phases'])}\n")
for phase in self.metadata['phases']:
dims = "{:.3f};{:.3f};{:.3f}".format(*phase.latticeParams[:3])
angles = (f * 180 / np.pi for f in phase.latticeParams[3:])
angles = "{:.3f};{:.3f};{:.3f}".format(*angles)
ctf_file.write(f"{dims}\t{angles}\t{phase.name}"
f"\t{phase.laueGroup}\t0\t\t\t\n")
ctf_file.write("Phase\tX\tY\tBands\tError\tEuler1\tEuler2"
"\tEuler3\tMAD\tBC\tBS\n")
for x, y, phase, eulers, bc in zip(
x_grid.flat, y_grid.flat,
self.data['phase'].flat,
out_euler_array.reshape((shape[0] * shape[1], 3)),
self.data['band_contrast'].flat,
):
error = 3 if phase == 0 else 0
ctf_file.write(
f"{phase}\t{x:.3f}\t{y:.3f}\t10\t{error}\t{eulers[0]:.3f}"
f"\t{eulers[1]:.3f}\t{eulers[2]:.3f}\t0.0000\t{bc}\t0\n"
)