def test_get_settings_from_file(self):
settings = get_settings_from_file(SETTING_FILE)
answers = [METADATA, ORIGINAL_METADATA, SCAN_SIZE_FILE]
assert len(settings) == len(answers)
for setting_read, answer in zip(settings, answers):
np.testing.assert_equal(setting_read.as_dictionary(), answer)
def file_reader(filename: str, lazy: bool = False) -> List[dict]:
"""Reader electron backscatter patterns from .bmp files stored in a
NORDIF project directory, their filenames listed in a text file.
Parameters
----------
filename
File path to the NORDIF settings text file.
lazy
This parameter is not used in this reader.
Returns
-------
scan : list of dicts
Data, axes, metadata and original metadata.
"""
# Get metadata from setting file
ebsd_node = metadata_nodes("ebsd")
md, omd, _ = get_settings_from_file(filename)
dirname = os.path.dirname(filename)
# Read static background image into metadata
static_bg_file = os.path.join(dirname,
"Background calibration pattern.bmp")
try:
md.set_item(ebsd_node + ".static_background", imread(static_bg_file))
except FileNotFoundError:
warnings.warn(
f"Could not read static background pattern '{static_bg_file}', however it "
"can be added using set_experimental_parameters().")
# Set required and other parameters in metadata
md.set_item("General.original_filename", filename)
md.set_item("General.title", "Calibration patterns")
md.set_item("Signal.signal_type", "EBSD")
md.set_item("Signal.record_by", "image")
scan = {}
scan["metadata"] = md.as_dictionary()
scan["original_metadata"] = omd.as_dictionary()
coordinates = _get_coordinates(filename)
data = _get_patterns(dirname=dirname, coordinates=coordinates)
scan["data"] = data
units = ["um"] * 3
names = ["x", "dy", "dx"]
scales = np.ones(3)
scan["axes"] = [{
"size": data.shape[i],
"index_in_array": i,
"name": names[i],
"scale": scales[i],
"offset": 0,
"units": units[i],
} for i in range(data.ndim)]
return [scan]