def test_apply_vanadium(project_file, van_project_file, target_project_file):
"""Test applying vanadium to the raw data in project file
Parameters
----------
project_file : str
raw HiDRA project file to convert to 2theta pattern
van_project_file : str
raw HiDra vanadium file
target_project_file : str
target HiDRA
Returns
-------
"""
# Check files' existence
checkFileExists(project_file, feedback='assert')
checkFileExists(van_project_file, feedback='assert')
# Load data
# extract the powder patterns and add them to the project file
reducer = ReductionApp()
# instrument_file, calibration_file, mask, sub_runs
reducer.load_project_file(project_file)
reducer.reduce_data(sub_runs=None, instrument_file=None, calibration_file=None, mask=None,
van_file=van_project_file, num_bins=950)
reducer.save_diffraction_data(target_project_file)
def test_apply_mantid_mask():
"""Test auto reduction script with Mantid mask file applied
Returns
-------
"""
# Specify NeXus
nexus_file = 'data/HB2B_938.nxs.h5'
# Convert the NeXus to file to a project without mask and convert to 2theta diffraction pattern
no_mask_project_file = 'HB2B_938_no_mask.h5'
if os.path.exists(no_mask_project_file):
os.remove(no_mask_project_file)
# Convert to NeXust
no_mask_hidra_ws = convertNeXusToProject(nexus_file, no_mask_project_file, skippable=False,
mask_file_name=None)
mask_array = no_mask_hidra_ws.get_detector_mask(is_default=True)
assert mask_array is None, 'There shall not be any mask'
# Convert the nexus file to a project file and do the "simple" checks
no_mask_reducer = ReductionApp()
no_mask_reducer.load_project_file(no_mask_project_file)
no_mask_reducer.reduce_data(sub_runs=None, instrument_file=None, calibration_file=None, mask=None,
van_file=None, num_bins=950)
no_mask_reducer.save_diffraction_data(no_mask_project_file)
# Convert the NeXus to file to a project with mask and convert to 2theta diffraction pattern
project_file = 'HB2B_938_mask.h5'
if os.path.exists(project_file):
os.remove(project_file)
# Convert
masked_hidra_ws = convertNeXusToProject(nexus_file, project_file, skippable=False,
mask_file_name='data/HB2B_Mask_12-18-19.xml')
mask_array = masked_hidra_ws.get_detector_mask(True)
# check on Mask: num_masked_pixels = (135602,)
assert np.where(mask_array == 0)[0].shape[0] == 135602, 'Mask shall have 135602 pixels masked but not {}' \
''.format(np.where(mask_array == 0)[0].shape[0])
reducer = ReductionApp()
reducer.load_project_file(project_file)
# convert to diffraction pattern with mask
reducer.reduce_data(sub_runs=None, instrument_file=None, calibration_file=None, mask=mask_array,
van_file=None, num_bins=950)
reducer.save_diffraction_data(project_file)
# Compare range of 2theta
no_mask_data_set = no_mask_reducer.get_diffraction_data(sub_run=1)
masked_data_set = reducer.get_diffraction_data(sub_run=1)
print('[DEBUG...] No mask 2theta range: {}, {}'.format(no_mask_data_set[0].min(), no_mask_data_set[0].max()))
print('[DEBUG...] Masked 2theta range: {}, {}'.format(masked_data_set[0].min(), masked_data_set[0].max()))
# verify the masked reduced data shall have smaller or at least equal range of 2theta
assert no_mask_data_set[0].min() <= masked_data_set[0].min()
assert no_mask_data_set[0].max() >= masked_data_set[0].max()
def addPowderToProject(projectfile, calibration_file=None):
checkFileExists(projectfile, feedback='assert')
# extract the powder patterns and add them to the project file
reducer = ReductionApp()
# TODO should add versions for testing arguments: instrument_file, calibration_file, mask, sub_runs
reducer.load_project_file(projectfile)
reducer.reduce_data(sub_runs=None, instrument_file=None, calibration_file=calibration_file, mask=None)
reducer.save_diffraction_data(projectfile)
# tests for the created file
assert os.path.exists(projectfile)