def run_focus(absorb_corrections):
run_number = 83605
sample_empty = 83608 # Use the vanadium empty again to make it obvious
sample_empty_scale = 0.5 # Set it to 50% scale
# Copy the required splined file into place first (instead of relying on generated one)
splined_file_name = "GEM83608_splined.nxs"
original_splined_path = os.path.join(input_dir, splined_file_name)
shutil.copy(original_splined_path, spline_path)
inst_object = setup_inst_object(mode="PDF")
if absorb_corrections:
sample = SampleDetails(height=5.0,
radius=0.3,
center=[0, 0, 0],
shape='cylinder')
sample.set_material(chemical_formula='(Li7)14 Mg1.05 Si2 S12.05',
number_density=0.001641)
inst_object.set_sample_details(sample=sample, mode="Rietveld")
return inst_object.focus(run_number=run_number,
input_mode="Individual",
vanadium_normalisation=True,
do_absorb_corrections=absorb_corrections,
multiple_scattering=False,
sample_empty=sample_empty,
sample_empty_scale=sample_empty_scale)
def run_focus(do_solid_angle_corrections):
[sample_empty, _, run_number] = gen_required_run_numbers()
sample_empty_scale = 1
# Copy the required spline file into place first (instead of relying on the generated one)
splined_file_name = "HRPD66031_splined.nxs"
original_splined_path = os.path.join(input_dir, splined_file_name)
shutil.copy(original_splined_path, spline_path)
inst_object = setup_inst_object()
sample = SampleDetails(shape="cylinder",
center=[1, 5, 1],
height=1,
radius=1)
sample.set_material(chemical_formula="Si")
inst_object.set_sample_details(sample=sample)
return inst_object.focus(
run_number=run_number,
window=WINDOW,
sample_empty=sample_empty,
sample_empty_scale=sample_empty_scale,
vanadium_normalisation=True,
do_solid_angle_corrections=do_solid_angle_corrections,
do_absorb_corrections=True,
multiple_scattering=False)
def setup_inst_object(mode):
user_name = "Test"
inst_obj = Polaris(user_name=user_name, calibration_mapping_file=calibration_map_path,
calibration_directory=calibration_dir, output_directory=output_dir, mode=mode)
sample_details = SampleDetails(height=4.0, radius=0.2985, center=[0, 0, 0], shape='cylinder')
sample_details.set_material(chemical_formula='Si')
inst_obj.set_sample_details(sample=sample_details)
return inst_obj
def setup_inst_object(mode):
user_name = "Test"
if mode:
inst_obj = Polaris(user_name=user_name, calibration_mapping_file=calibration_map_path,
calibration_directory=calibration_dir, output_directory=output_dir, mode=mode)
else:
inst_obj = Polaris(user_name=user_name, calibration_mapping_file=calibration_map_path,
calibration_directory=calibration_dir, output_directory=output_dir)
sample_details = SampleDetails(height=4.0, radius=0.2985, center=[0, 0, 0], shape='cylinder')
sample_details.set_material(chemical_formula='Si')
inst_obj.set_sample_details(sample=sample_details)
return inst_obj
def main(input_file, output_dir):
validate(input_file, output_dir)
params = web_var.standard_vars
correction_params = web_var.advanced_vars
mapping_file = r"/archive/NDXPOLARIS/user/scripts/autoreduction/Calibration/polaris_cycle_mapping.yaml"
calib_dir = r"/archive/NDXPOLARIS/user/scripts/autoreduction/Calibration"
user = "******"
# If performing absorption corrections add a workspace suffix of _abs
output_suffix = '_abs' if params['do_absorb_corrections'] else ''
instrument_args = {
'user_name': user,
'calibration_directory': calib_dir,
'output_directory': output_dir,
'calibration_mapping_file': mapping_file,
'do_absorb_corrections': params['do_absorb_corrections'],
'do_van_normalisation': params['do_van_normalisation'],
'input_mode': params['input_mode'],
'suffix': output_suffix,
'sample_empty': 113677,
'sample_empty_scale': 1.0,
}
# Only use the mode if specified by the user
if params['mode']:
instrument_args['mode'] = params['mode']
polaris = Polaris(**instrument_args)
# Add the sample object if we are applying absorption corrections
if params['do_absorb_corrections']:
sample_obj = SampleDetails(shape=correction_params['shape'],
center=correction_params['center'],
height=correction_params['height'],
radius=correction_params['radius'])
sample_obj.set_material(
chemical_formula=correction_params['composition'],
number_density=correction_params['number_density'])
polaris.set_sample_details(sample=sample_obj)
# Prior to running this script, you need to have created a vanadium for cycle 17_2 like so:
#polaris.create_vanadium(first_cycle_run_no=83881)
# Focus run
run_num = get_run_number(input_file)
polaris.focus(run_number=run_num, multiple_scattering=False)
def setUp(self):
sample_details = SampleDetails(height=4.0,
radius=0.2985,
center=[0, 0, 0],
shape='cylinder')
sample_details.set_material(chemical_formula='Si')
self.geometry = {
'Shape': 'Cylinder',
'Height': sample_details.height(),
'Radius': sample_details.radius(),
'Center': sample_details.center()
}
material = sample_details.material_object
material_json = {'ChemicalFormula': material.chemical_formula}
if material.number_density:
material_json["SampleNumberDensity"] = material.number_density
if material.absorption_cross_section:
material_json[
"AttenuationXSection"] = material.absorption_cross_section
if material.scattering_cross_section:
material_json[
"ScatteringXSection"] = material.scattering_cross_section
self.material = material_json
self.cal_file_path = "polaris_grouping_file.cal"
def setUp(self):
sample_details = SampleDetails(height=4.0, radius=0.2985, center=[0, 0, 0], shape='cylinder')
sample_details.set_material(chemical_formula='Si')
self.geometry = {'Shape': 'Cylinder',
'Height': sample_details.height(),
'Radius': sample_details.radius(),
'Center': sample_details.center()}
material = sample_details.material_object
material_json = {'ChemicalFormula': material.chemical_formula}
if material.number_density:
material_json["SampleNumberDensity"] = material.number_density
if material.absorption_cross_section:
material_json["AttenuationXSection"] = material.absorption_cross_section
if material.scattering_cross_section:
material_json["ScatteringXSection"] = material.scattering_cross_section
self.material = material_json
self.dirpath = tempfile.mkdtemp()
self.cal_file_path = os.path.join(self.dirpath, "tot_scat.cal")
file = open(self.cal_file_path, 'w')
file.write("%i\t%i\t%f\t%i\t%i\n" % (1, 1, 0.0, 1, 1))
file.write("%i\t%i\t%f\t%i\t%i\n" % (2, 2, 0.0, 1, 1))
file.write("%i\t%i\t%f\t%i\t%i\n" % (3, 3, 0.0, 1, 2))
file.write("%i\t%i\t%f\t%i\t%i\n" % (4, 4, 0.0, 1, 2))
file.close()
def run_focus():
[sample_empty, _, run_number] = gen_required_run_numbers()
sample_empty_scale = 1
# Copy the required spline file into place first (instead of relying on the generated one)
splined_file_name = "HRPD66031_splined.nxs"
original_splined_path = os.path.join(input_dir, splined_file_name)
shutil.copy(original_splined_path, spline_path)
inst_object = setup_inst_object()
sample = SampleDetails(shape="cylinder", center=[1, 5, 1], height=1, radius=1)
sample.set_material(chemical_formula="Si")
inst_object.set_sample_details(sample=sample)
return inst_object.focus(run_number=run_number, window="10-110", sample_empty=sample_empty,
sample_empty_scale=sample_empty_scale, vanadium_normalisation=True,
do_absorb_corrections=True, multiple_scattering=False)