def test_calibration_json():
"""Test reduce data with calibration file (.json)"""
# Get simulated test data
project_file_name = 'tests/data/HB2B_000.h5'
calib_file = 'tests/data/HB2B_CAL_Si333.json'
# Import file
calib_obj = calibration_file_io.read_calibration_json_file(calib_file)
shift, shift_error, wave_length, wl_error, status = calib_obj
# Verify result
assert shift
assert shift_error
assert abs(wave_length - 1.4499332864) < 1E-8
assert wl_error
assert status == 3
# Import project file
project_file = HidraProjectFile(project_file_name, 'r')
# Reduce
test_workspace = workspaces.HidraWorkspace('test calibration')
test_workspace.load_hidra_project(project_file, load_raw_counts=True, load_reduced_diffraction=False)
# Test set and get wave length
test_workspace.set_wavelength(wave_length, True)
wave_length_i = test_workspace.get_wavelength(True, True)
assert wave_length_i == wave_length
def test_rw_raw():
"""Test read a project to workspace and write in the scope of raw data
Returns
-------
"""
raw_project_name = os.path.join(os.getcwd(), 'data/HZB_Raw_Project.h5')
# Read to workspace
source_project = HidraProjectFile(raw_project_name, 'r')
# To the workspace
source_workspace = workspaces.HidraWorkspace('Source HZB')
source_workspace.load_hidra_project(source_project,
load_raw_counts=True,
load_reduced_diffraction=False)
# Export
target_project = HidraProjectFile('HZB_HiDra_Test.h5', 'w')
# Experiment data
source_workspace.save_experimental_data(target_project,
sub_runs=range(1, 41))
# Instrument
detector_setup = source_workspace.get_instrument_setup()
instrument_setup = HidraSetup(detector_setup=detector_setup)
target_project.write_instrument_geometry(instrument_setup)
# Save
target_project.save(True)
return
def init_session(self, session_name, hidra_ws=None):
"""
Initialize a new session of reduction and thus to store data according to session name
:return:
"""
# Check inputs
checkdatatypes.check_string_variable('Reduction session name',
session_name)
if session_name == '':
raise RuntimeError('Session name {} is empty'.format(session_name))
elif session_name in self._session_dict:
print(
'[WARNING] Session {} is previously taken. The HidraWorkspace associated '
'will be replaced if new HidraWorkspace is not None ({})'
''.format(session_name, hidra_ws is None))
if hidra_ws is None:
# session is initialized without HidraWorkspace
self._curr_workspace = workspaces.HidraWorkspace()
else:
# session starts with a HidraWorkspace
checkdatatypes.check_type('HidraWorkspace', hidra_ws,
workspaces.HidraWorkspace)
self._curr_workspace = hidra_ws
self._session_dict[session_name] = self._curr_workspace
def load_vanadium(self, van_project_file):
"""Load vanadium from HiDRA project file
Parameters
----------
van_project_file : str
vanadium HiDRA project file or NeXus file
Returns
-------
~numpy.narray, float
1D array as vanadium counts and duration of vanadium run (second)
"""
checkdatatypes.check_file_name(van_project_file, True, False, False,
'Vanadium project/NeXus file')
if van_project_file.endswith('.nxs.h5'):
# Input is nexus file
# reduce with PyRS/Python
converter = NeXusConvertingApp(van_project_file,
mask_file_name=None)
self._van_ws = converter.convert(use_mantid=False)
else:
# Input is HiDRA project file
self._van_ws = workspaces.HidraWorkspace(name=van_project_file)
# PyRS HDF5
project_h5_file = HidraProjectFile(
van_project_file, mode=HidraProjectFileMode.READONLY)
# Load
self._van_ws.load_hidra_project(project_h5_file,
load_raw_counts=True,
load_reduced_diffraction=False)
# Close project file
project_h5_file.close()
# Process the vanadium counts
sub_runs = self._van_ws.get_sub_runs()
assert len(
sub_runs
) == 1, 'There shall be more than 1 sub run in vanadium project file'
# get vanadium data
van_array = self._van_ws.get_detector_counts(sub_runs[0]).astype(
np.float64)
# get vanadium run duration
van_duration = self._van_ws.get_sample_log_value(
HidraConstants.SUB_RUN_DURATION, sub_runs[0])
return van_array, van_duration
def __init__(self,
nexus_file_name,
mask_file_name=None,
extra_logs=list()):
"""Initialization
Parameters
----------
nexus_file_name : str
Name of NeXus file
mask_file_name : str
Name of masking file
extra_logs : list, tuple
list of string with no default logs to keep in project file
"""
# configure logging for this class
self._log = Logger(__name__)
# validate NeXus file exists
checkdatatypes.check_file_name(nexus_file_name, True, False, False,
'NeXus file')
self._nexus_name = nexus_file_name
# validate mask file exists
if mask_file_name is None:
self._mask_file_name = None
else:
checkdatatypes.check_file_name(mask_file_name, True, False, False,
'Mask file')
self._mask_file_name = mask_file_name
if not mask_file_name.lower().endswith('.xml'):
raise NotImplementedError(
'Only Mantid mask in XML format is supported now. File '
'{} with type {} is not supported yet.'
''.format(mask_file_name,
mask_file_name.split('.')[-1]))
# workspaces
self._event_ws_name = os.path.basename(nexus_file_name).split('.')[0]
logs_to_keep = list(extra_logs)
logs_to_keep.extend(DEFAULT_KEEP_LOGS)
self.__load_logs(logs_to_keep)
# load the mask
self.mask_array = None # TODO to promote direct access
if mask_file_name:
self.__load_mask(mask_file_name)
# create the hidra workspace
self._hidra_workspace = workspaces.HidraWorkspace(self._nexus_name)
# Set a default instrument with this workspace
# set up instrument
# initialize instrument with hard coded values
instrument = DENEXDetectorGeometry(NUM_PIXEL_1D, NUM_PIXEL_1D,
PIXEL_SIZE, PIXEL_SIZE, ARM_LENGTH,
False)
self._hidra_workspace.set_instrument_geometry(instrument)
# project file
self._project_file = None