def test_file_get_positions():
bf = BrillouinFile(data_file_path('Water.h5'))
rep = bf.get_repetition('0')
# Test that the shape is correct
assert rep.payload.positions['x'].shape == (1, 10, 1)
assert rep.payload.positions['y'].shape == (1, 10, 1)
assert rep.payload.positions['z'].shape == (1, 10, 1)
# Test some values
assert rep.payload.positions['x'][0, 0, 0] == -5652.5
assert rep.payload.positions['y'][0, 0, 0] == -1963.0
assert rep.payload.positions['z'][0, 0, 0] == 201.425
def test_file_repetition_has_calibration():
bf = BrillouinFile(data_file_path('Water.h5'))
rep = bf.get_repetition('0')
assert not rep.calibration.is_empty()
bf = BrillouinFile(data_file_path('Water_old.h5'))
rep = bf.get_repetition('0')
assert not rep.calibration.is_empty()
def test_file_calibration_image_keys():
bf = BrillouinFile(data_file_path('Water.h5'))
rep = bf.get_repetition('0')
assert rep.calibration.image_keys() == [str(k+1) for k in range(2)]
bf = BrillouinFile(data_file_path('Water_old.h5'))
rep = bf.get_repetition('0')
assert rep.calibration.image_keys() == [str(k+1) for k in range(2)]
def test_file_payload_image_keys():
bf = BrillouinFile(data_file_path('Water.h5'))
rep = bf.get_repetition('0')
assert rep.payload.image_keys() == [str(k) for k in range(10)]
bf = BrillouinFile(data_file_path('Water_old.h5'))
rep = bf.get_repetition('0')
assert rep.payload.image_keys() == [str(k) for k in range(4)]
def test_file_has_one_repetition():
bf = BrillouinFile(data_file_path('Water.h5'))
num_repetitions = bf.repetition_count()
assert num_repetitions == 1
bf = BrillouinFile(data_file_path('Water_old.h5'))
num_repetitions = bf.repetition_count()
assert num_repetitions == 1
def test_file_payload_get_image():
bf = BrillouinFile(data_file_path('Water.h5'))
image = bf.get_repetition('0').payload.get_image('0')
assert image.shape == (2, 400, 400)
bf = BrillouinFile(data_file_path('Water_old.h5'))
image = bf.get_repetition('0').payload.get_image('0')
assert image.shape == (2, 400, 400)
def set_file(self, file_name):
"""
Set the file to be processed.
Loads the corresponding data from HDF file.
Parameters
----------
file_name : str
The file name.
"""
try:
file = BrillouinFile(file_name)
except Exception as e:
raise e
else:
""" Only load data if the file could be opened """
session = Session.get_instance()
session.file = file
session.extraction_models = {
key: ExtractionModel()
for key in self.file.repetition_keys()
}
session.calibration_models = {
key: CalibrationModel()
for key in self.file.repetition_keys()
}
session.peak_selection_models = {
key: PeakSelectionModel()
for key in self.file.repetition_keys()
}
session.evaluation_models = {
key: EvaluationModel()
for key in self.file.repetition_keys()
}
self.set_image_shape()
try:
self.load(file_name)
except Exception as e:
raise e
else:
Session.get_instance().file = file
def test_file_payload_get_time():
bf = BrillouinFile(data_file_path('Water.h5'))
time = bf.get_repetition('0').payload.get_time('0')
assert time == 39.886
def test_file_has_date():
bf = BrillouinFile(data_file_path('Water.h5'))
assert bf.date == datetime.datetime.fromisoformat(
'2020-11-03T15:20:30.682+01:00')
def test_file_calibration_get_time():
bf = BrillouinFile(data_file_path('Water.h5'))
time = bf.get_repetition('0').calibration.get_time('1')
assert time == 36.802
def test_file_calibration_get_date():
bf = BrillouinFile(data_file_path('Water.h5'))
date = bf.get_repetition('0').calibration.get_date('1')
assert date == datetime.datetime.fromisoformat(
'2020-11-03T15:21:07.484+01:00')
def test_file_get_repetition_date():
bf = BrillouinFile(data_file_path('Water.h5'))
rep = bf.get_repetition('0')
assert rep.date == datetime.datetime.fromisoformat(
'2020-11-03T15:20:52.852+01:00')
def test_file_get_resolution():
bf = BrillouinFile(data_file_path('Water.h5'))
rep = bf.get_repetition('0')
assert rep.payload.resolution == (10, 1, 1)
def test_file_get_repetition_keys():
bf = BrillouinFile(data_file_path('Water.h5'))
assert bf.repetition_keys() == ['0']
bf = BrillouinFile(data_file_path('Water_old.h5'))
assert bf.repetition_keys() == ['0']
def test_open_file_with_no_brillouin_data_raises_exception():
with pytest.raises(BadFileException):
BrillouinFile(data_file_path('empty_file.h5'))
def test_file_payload_get_date():
bf = BrillouinFile(data_file_path('Water.h5'))
date = bf.get_repetition('0').payload.get_date('0')
assert date == datetime.datetime.fromisoformat(
'2020-11-03T15:21:10.568+01:00')
def test_file_has_comment():
bf = BrillouinFile(data_file_path('Water.h5'))
assert bf.comment == 'Brillouin data'
def test_non_existing_file_raises_exception():
with pytest.raises(OSError):
BrillouinFile('non_existing_file.h5')