def load_existing_calibration_files(self, file_path):
if not path.exists(file_path):
msg = "Could not open GSAS calibration file: " + file_path
logger.warning(msg)
raise
try:
instrument, ceria_no, params_table = self.get_info_from_file(
file_path)
self.update_calibration_params_table(params_table)
except RuntimeError:
logger.error("Invalid file selected: " + file_path)
raise
try:
bank = EnggUtils.load_relevant_calibration_files(file_path)
except Exception as e:
logger.error(
"Unable to loading calibration files corresponding to " +
file_path + ". Error: " + str(e))
raise
try:
grp_ws_name, roi_text = EnggUtils.load_custom_grouping_workspace(
file_path)
except Exception as e:
logger.error(
"Unable to load grouping workspace corresponding to " +
file_path + ". Error: " + str(e))
raise
return instrument, ceria_no, grp_ws_name, roi_text, bank
def save_calibration(ceria_run, van_run, calibration_directory, calibration_general, name, bank_names, zeros, difcs):
"""
save the calibration data
@param ceria_run :: the run number of the ceria
@param van_run :: the run number of the vanadium
@param calibration_directory :: the user specific calibration directory to save to
@param calibration_general :: the general calibration directory to save to
@param name :: the name of the banks being saved
@param bank_names :: the list of banks to save
@param difcs :: the list of difc values to save
@param zeros :: the list of tzero values to save
"""
gsas_iparm_fname = os.path.join(calibration_directory, "ENGINX_" + van_run + "_" + ceria_run + "_" + name + ".prm")
# work out what template to use
if name == "all_banks":
template_file = None
elif name == "bank_South":
template_file = "template_ENGINX_241391_236516_South_bank.prm"
else:
template_file = "template_ENGINX_241391_236516_North_bank.prm"
# write out the param file to the users directory
Utils.write_ENGINX_GSAS_iparam_file(output_file=gsas_iparm_fname, bank_names=bank_names, difc=difcs, tzero=zeros,
ceria_run=ceria_run, vanadium_run=van_run,
template_file=template_file)
if not calibration_general == calibration_directory:
# copy the param file to the general directory
if not os.path.exists(calibration_general):
os.makedirs(calibration_general)
copy2(gsas_iparm_fname, calibration_general)
def create_new_calibration(calibration,
rb_num,
plot_output,
save_dir=output_settings.get_output_path()):
full_calib = load_full_instrument_calibration()
EnggUtils.create_new_calibration(calibration, rb_num, plot_output,
save_dir, full_calib)
def save_calibration(ceria_run, van_run, calibration_directory, calibration_general, name, bank_names, zeros, difcs,
difas):
"""
save the calibration data
@param ceria_run :: the run number of the ceria
@param van_run :: the run number of the vanadium
@param calibration_directory :: the user specific calibration directory to save to
@param calibration_general :: the general calibration directory to save to
@param name :: the name of the banks being saved
@param bank_names :: the list of banks to save
@param difas :: the list of difa values to save
@param difcs :: the list of difc values to save
@param zeros :: the list of tzero values to save
"""
gsas_iparm_fname = os.path.join(calibration_directory, "ENGINX_" + van_run + "_" + ceria_run + "_" + name + ".prm")
# work out what template to use
if name == "all_banks":
template_file = None
elif name == "bank_South":
template_file = "template_ENGINX_241391_236516_South_bank.prm"
else:
template_file = "template_ENGINX_241391_236516_North_bank.prm"
# write out the param file to the users directory
Utils.write_ENGINX_GSAS_iparam_file(output_file=gsas_iparm_fname, bank_names=bank_names, difa=difas, difc=difcs,
tzero=zeros, ceria_run=ceria_run, vanadium_run=van_run,
template_file=template_file)
if not calibration_general == calibration_directory:
# copy the param file to the general directory
if not os.path.exists(calibration_general):
os.makedirs(calibration_general)
copy2(gsas_iparm_fname, calibration_general)
def _check_region_grouping_ws_exists(grouping_ws_name: str,
inst_ws) -> bool:
"""
Check that the required grouping workspace for this focus exists, and if not present for a North/South bank
focus, retrieve them from the user directories or create them (expected if first focus with loaded calibration)
:param grouping_ws_name: Name of the grouping workspace whose presence in the ADS is being checked
:param inst_ws: Workspace containing the instrument data for use in making a bank grouping workspace
:return: True if the required workspace exists (or has just been loaded/created), False if not
"""
if not Ads.doesExist(grouping_ws_name):
if "North" in grouping_ws_name:
logger.notice(
"NorthBank grouping workspace not present in ADS, loading")
EnggUtils.get_bank_grouping_workspace(1, inst_ws)
return True
elif "South" in grouping_ws_name:
logger.notice(
"SouthBank grouping workspace not present in ADS, loading")
EnggUtils.get_bank_grouping_workspace(2, inst_ws)
return True
else:
logger.warning(
f"Cannot focus as the grouping workspace \"{grouping_ws_name}\" is not present."
)
return False
return True
def generate_prm_output_file(difa_list, difc_list, tzero_list,
bank_name, kwargs_to_pass):
file_path = calibration_dir + EnggUtils.generate_output_file_name(
ceria_path, instrument, bank=bank_name)
EnggUtils.write_ENGINX_GSAS_iparam_file(file_path, difa_list,
difc_list, tzero_list,
bk2bk_params,
**kwargs_to_pass)
set_setting(output_settings.INTERFACES_SETTINGS_GROUP,
output_settings.ENGINEERING_PREFIX,
"last_calibration_path", file_path)
def save_calibration(ceria_run, calibration_directory, calibration_general, name, bank_names, zeros, difcs,
difas, bk2bk_params):
"""
save the calibration data
@param ceria_run :: the run number of the ceria
@param calibration_directory :: the user specific calibration directory to save to
@param calibration_general :: the general calibration directory to save to
@param name :: the name of the banks being saved
@param bank_names :: the list of banks to save
@param difas :: the list of difa values to save
@param difcs :: the list of difc values to save
@param zeros :: the list of tzero values to save
"""
file_save_prefix = os.path.join(calibration_directory, "ENGINX_" + ceria_run + "_")
gsas_iparm_fname = file_save_prefix + name + ".prm"
pdcals_to_save = dict() # fname: workspace
# work out what template to use, and which PDCalibration files to save
if name == "all_banks":
template_file = None
pdcals_to_save[file_save_prefix + "bank_North.nxs"] = 'engg_calibration_bank_1'
pdcals_to_save[file_save_prefix + "bank_South.nxs"] = 'engg_calibration_bank_2'
elif name == "bank_2":
template_file = "template_ENGINX_241391_South_bank.prm"
pdcals_to_save[file_save_prefix + "bank_South.nxs"] = 'engg_calibration_bank_2'
elif name == "bank_1":
template_file = "template_ENGINX_241391_North_bank.prm"
pdcals_to_save[file_save_prefix + "bank_North.nxs"] = 'engg_calibration_bank_1'
else: # cropped uses North bank template
template_file = "template_ENGINX_241391_North_bank.prm"
pdcals_to_save[file_save_prefix + "cropped.nxs"] = 'engg_calibration_cropped'
# write out the param file to the users directory
Utils.write_ENGINX_GSAS_iparam_file(output_file=gsas_iparm_fname, bank_names=bank_names, difa=difas, difc=difcs,
tzero=zeros, ceria_run=ceria_run,
template_file=template_file, bk2bk_params=bk2bk_params)
for fname, ws in pdcals_to_save.items():
simple.SaveNexus(InputWorkspace=ws, Filename=fname)
if not calibration_general == calibration_directory:
# copy the param file to the general directory
if not os.path.exists(calibration_general):
os.makedirs(calibration_general)
copy2(gsas_iparm_fname, calibration_general)
for fname in pdcals_to_save.keys():
copy2(fname, calibration_general)
def focus_cropped(run_number, van_curves, van_int, full_inst_calib, focus_directory, focus_general, do_pre_process, params, time_period,
crop_on,
use_spectra):
"""
focus a partial run, cropping either on banks or on specific spectra
@param van_curves :: the path to the vanadium curves file
@param van_int :: the path to the integrated vanadium file
@param full_inst_calib :: workspace containing the full instrument calibration
@param run_number :: the run nuumber to focus
@param focus_directory :: the user specific focus directory to save to
@param focus_general :: the general focus directory to save to
@param do_pre_process :: whether or not to pre-process the run before focussing it
@param params :: the rebin parameters for pre-processing
@param time_period :: the time period for pre-processing
@param crop_on :: the bank or spectra to crop on
@param use_spectra :: whether to focus by spectra or banks
"""
van_curves_ws, van_integrated_ws, ws_to_focus = _prepare_focus(run_number, van_curves, van_int, do_pre_process,
params, time_period)
tof_output_name = "engg_focus_output{0}{1}"
sample_ws_clone = simple.CloneWorkspace(ws_to_focus)
curves_ws_clone = simple.CloneWorkspace(van_curves_ws)
# check whether to crop on bank or spectra
if not use_spectra:
# get the bank to crop on, focus and save it out
bank = {"North": "1",
"South": "2"}
bank_no = bank.get(crop_on)
cal_file = NORTH_BANK_CAL if bank_no == 1 else SOUTH_BANK_CAL
region_calib = 'engg_calibration_bank_1' if bank_no == 1 else 'engg_calibration_bank_2'
df_kwarg = {"GroupingFileName": cal_file}
tof_output_name = tof_output_name.format("_bank_", bank_no)
dspacing_output_name = tof_output_name + "_dSpacing"
_run_focus(input_workspace=sample_ws_clone, tof_output_name=tof_output_name, vanadium_integration_ws=van_integrated_ws,
vanadium_curves_ws=curves_ws_clone, df_kwarg=df_kwarg, full_calib=full_inst_calib,
region_calib=region_calib)
_save_out(run_number, focus_directory, focus_general, tof_output_name, "ENGINX_{}_{}{{}}", crop_on)
_save_out(run_number, focus_directory, focus_general, dspacing_output_name, "ENGINX_{}_{}{{}}", crop_on)
else:
# crop on the spectra passed in, focus and save it out
tof_output_name = tof_output_name.format("_", "cropped")
dspacing_output_name = tof_output_name + "_dSpacing"
grp_ws = Utils.create_grouping_workspace_from_spectra_list(crop_on, ws_to_focus)
df_kwarg = {"GroupingWorkspace": grp_ws}
region_calib = 'engg_calibration_cropped'
_run_focus(input_workspace=sample_ws_clone, tof_output_name=tof_output_name, vanadium_integration_ws=van_integrated_ws,
vanadium_curves_ws=curves_ws_clone, df_kwarg=df_kwarg, region_calib=region_calib,
full_calib=full_inst_calib)
_save_out(run_number, focus_directory, focus_general, tof_output_name, "ENGINX_{}_bank_{}{{}}", "cropped")
_save_out(run_number, focus_directory, focus_general, dspacing_output_name, "ENGINX_{}_bank_{}{{}}", "cropped")
simple.DeleteWorkspace(sample_ws_clone)
simple.DeleteWorkspace(curves_ws_clone)
def focus_run(
self,
sample_paths: list,
vanadium_path: str,
plot_output: bool,
rb_num: str,
calibration: CalibrationInfo,
save_dir: Optional[str] = output_settings.get_output_path()
) -> None:
full_calib = load_full_instrument_calibration()
focused_files = EnggUtils.focus_run(sample_paths, vanadium_path,
plot_output, rb_num, calibration,
save_dir, full_calib)
self._last_focused_files.extend(focused_files)
def focus_texture_mode(run_number, van_curves, van_int, full_inst_calib, focus_directory, focus_general, do_pre_process, params,
time_period, dg_file):
"""
perform a texture mode focusing using the grouping csv file
@param run_number :: the run number to focus
@param van_curves :: the path to the vanadium curves file
@param van_int :: the path to the integrated vanadium file
@param full_inst_calib :: workspace containing the full instrument calibration
@param focus_directory :: the user specific focus directory to save to
@param focus_general :: the general focus directory to save to
@param do_pre_process :: whether or not to pre-process the run before focussing it
@param params :: the rebin parameters for pre-processing
@param time_period :: the time period for pre-processing
@param dg_file :: the grouping file to use for texture mode
"""
van_curves_ws, van_integrated_ws, ws_to_focus = _prepare_focus(run_number, van_curves, van_int, do_pre_process,
params, time_period)
banks = {}
# read the csv file to work out the banks
# ensure csv reading works on python 2 or 3
with open(dg_file, 'r', newline='', encoding='utf-8') as grouping_file:
group_reader = csv.reader(_decomment_csv(grouping_file), delimiter=',')
for row in group_reader:
banks.update({row[0]: ','.join(row[1:])})
# loop through the banks described in the csv, focusing and saving them out
for bank in banks:
sample_ws_clone = simple.CloneWorkspace(ws_to_focus)
curves_ws_clone = simple.CloneWorkspace(van_curves_ws)
tof_output_name = "engg_focusing_output_ws_texture_bank_{}"
tof_output_name = tof_output_name.format(bank)
dspacing_output_name = tof_output_name + "_dSpacing"
grp_ws = Utils.create_grouping_workspace_from_spectra_list(banks[bank], ws_to_focus)
df_kwarg = {"GroupingWorkspace": grp_ws}
_run_focus(input_workspace=sample_ws_clone, tof_output_name=tof_output_name, region_calib=full_inst_calib,
vanadium_curves_ws=curves_ws_clone, full_calib=full_inst_calib, df_kwarg=df_kwarg,
vanadium_integration_ws=van_integrated_ws)
_save_out(run_number, focus_directory, focus_general, tof_output_name, "ENGINX_{}_texture_{}{{}}", bank)
_save_out(run_number, focus_directory, focus_general, dspacing_output_name, "ENGINX_{}_texture_{}{{}}", bank)
simple.DeleteWorkspace(sample_ws_clone)
simple.DeleteWorkspace(curves_ws_clone)
def run(ceria_run, do_cal, do_van, full_inst_calib, van_run, calibration_directory, calibration_general, cropped,
crop_name, crop_on, focus_directory, focus_general, do_pre_process, params, time_period, focus_run,
grouping_file):
"""
calls methods needed based off of inputs
@param ceria_run :: the run number of the ceria to use
@param do_cal :: whether or not to force running calibration
@param do_van :: whether or not to force calculating the vanadium
@param full_inst_calib :: workspace containing the full instrument calibration
@param van_run :: run number to use for the vanadium
@param calibration_directory :: the users calibration directory
@param calibration_general :: the non-user specific calibration directory
@param crop_on :: where to crop using the cropping method
@param crop_name :: how to name cropped banks
@param cropped :: the cropping method to use
@param focus_directory :: the users focus directory
@param focus_general :: the non-user specific focus directory
@param do_pre_process:: whether or not to pre-process before focussing
@param params :: list of parameters to use for rebinning
@param time_period :: time period to old binning
@param focus_run :: run number to focus
@param grouping_file :: grouping file to use with texture mode
"""
# check whether creating a vanadium is required or requested
if (not os.path.isfile(_get_van_names(van_run, calibration_directory)[0])) or do_van:
create_vanadium_integration(van_run, calibration_directory)
# find the file names of calibration files that would be created by this run
cal_endings = {"banks": ["all_banks", f"bank_{crop_on}"],
"spectra": ["all_banks", f"bank_{crop_name}"],
None: ["all_banks", "bank_North", "bank_South"]}
expected_cals = [f"ENGINX_{van_run}_{ceria_run}_{ending}.prm" for ending in cal_endings.get(cropped)]
expected_cals_present = [os.path.isfile(os.path.join(calibration_directory, cal_file)) for cal_file in
expected_cals]
pdcal_table_endings = {"banks": [f"bank_{crop_on}"],
"spectra": ["cropped"],
None: ["bank_North", "bank_South"]}
expected_pdcal_tables = [f"ENGINX_{van_run}_{ceria_run}_{ending}.nxs" for ending in
pdcal_table_endings.get(cropped)]
expected_tables_present = [os.path.isfile(os.path.join(calibration_directory, cal_file)) for cal_file in
expected_pdcal_tables]
# if the calibration files that this run would create are not present, or the user has requested it, create the
# calibration files
if not all(expected_cals_present) or not all(expected_tables_present) or do_cal:
create_calibration(ceria_run, van_run, full_inst_calib, calibration_directory, calibration_general, cropped,
crop_name, crop_on)
else:
ending_to_load = {"banks": f"bank_{crop_on}",
"spectra": crop_name,
None: "all_banks"}
file_name = os.path.join(calibration_directory,
f"ENGINX_{van_run}_{ceria_run}_{ending_to_load.get(cropped)}.prm")
Utils.load_relevant_calibration_files(file_name, "engg")
# if a focus is requested, run the focus
if focus_run is not None:
focus(focus_run, van_run, full_inst_calib, calibration_directory, focus_directory, focus_general,
do_pre_process, params, time_period, grouping_file, cropped, crop_on)
def load_existing_calibration_files(calibration):
load_full_instrument_calibration()
EnggUtils.load_existing_calibration_files(calibration)
def save_pdcal_output_file(ws_name_suffix, bank_name):
file_path = calibration_dir + EnggUtils.generate_output_file_name(
ceria_path, instrument, bank=bank_name, ext=".nxs")
ws_name = "engggui_calibration_" + ws_name_suffix
SaveNexus(InputWorkspace=ws_name, Filename=file_path)
def create_calibration_files(ceria_run, van_run, full_inst_calib, int_van, van_curves_file, calibration_directory,
calibration_general, use_spectrum_number, crop_name, spec_nos):
"""
create and save a calibration
@param ceria_run :: run number for the ceria used
@param van_run :: the run number of the vanadium to use
@param int_van :: name of the integrated vanadium workspace
@param full_inst_calib :: workspace containing the full instrument calibration
@param van_curves_file :: path to save vanadium curves to
@param calibration_directory :: the user specific calibration directory to save to
@param calibration_general :: the general calibration directory
@param use_spectrum_number :: whether or not to crop using spectrum numbers or banks
@param crop_name :: name of the output workspace
@param spec_nos :: the value to crop on, either a spectra number, or a bank
"""
van_integrated_ws = load_van_integration_file(int_van)
ceria_ws = simple.Load(Filename="ENGINX" + ceria_run, OutputWorkspace="engg_calib")
van_file = _gen_filename(van_run)
van_ws = simple.Load(Filename=van_file)
bank_names = ["North", "South"]
# check which cropping method to use
if use_spectrum_number:
spectrum_numbers = spec_nos
bank = None
else:
if spec_nos.lower() == "north" or spec_nos == '1':
spectrum_numbers = None
bank = '1'
elif spec_nos.lower() == "south" or spec_nos == '2':
spectrum_numbers = None
bank = '2'
else:
spectrum_numbers = None
bank = None
output, ceria_raw, curves = run_calibration(sample_ws=ceria_ws,
vanadium_workspace=van_ws,
van_integration=van_integrated_ws,
bank=bank,
spectrum_numbers=spectrum_numbers,
full_inst_calib=full_inst_calib)
handle_van_curves(curves, van_curves_file)
bk2bk_params = extract_b2b_params(ceria_raw)
if len(output) == 1:
# get the values needed for saving out the .prm files
difa = [output[0]['difa']]
difc = [output[0]['difc']]
tzero = [output[0]['tzero']]
if bank is None and spectrum_numbers is None:
save_calibration(ceria_run, calibration_directory, calibration_general, "all_banks", [crop_name],
tzero, difc, difa, bk2bk_params)
if spectrum_numbers is not None:
save_calibration(ceria_run, calibration_directory, calibration_general,
"bank_cropped", [crop_name], tzero, difc, difa, bk2bk_params)
else:
save_calibration(ceria_run, calibration_directory, calibration_general,
"bank_{}".format(spec_nos), [crop_name], tzero, difc, difa, bk2bk_params)
# create the table workspace containing the parameters
param_tbl_name = crop_name if crop_name is not None else "Cropped"
create_params_table(difc, tzero, difa)
plot_dict = Utils.generate_tof_fit_dictionary(param_tbl_name)
Utils.plot_tof_fit([plot_dict], [param_tbl_name])
else:
difas = [row['difa'] for row in output]
difcs = [row['difc'] for row in output]
tzeros = [row['tzero'] for row in output]
plot_dicts = list()
for i in range(1, 3):
save_calibration(ceria_run, calibration_directory, calibration_general,
f"bank_{i}", [bank_names[i - 1]],
[tzeros[i - 1]], [difcs[i - 1]], [difas[i - 1]], bk2bk_params)
plot_dicts.append(Utils.generate_tof_fit_dictionary(f"bank_{i}"))
save_calibration(ceria_run, calibration_directory, calibration_general, "all_banks", bank_names,
tzeros, difcs, difas, bk2bk_params)
# create the table workspace containing the parameters
create_params_table(difcs, tzeros, difas)
Utils.plot_tof_fit(plot_dicts, ["bank_1", "bank_2"])
def create_new_calibration(self,
ceria_path,
plot_output,
instrument,
rb_num=None,
bank=None,
calfile=None,
spectrum_numbers=None):
"""
Create a new calibration from a ceria run
:param ceria_path: Path to ceria (CeO2) data file
:param plot_output: Whether the output should be plotted.
:param instrument: The instrument the data relates to.
:param rb_num: The RB number for file creation.
:param bank: Optional parameter to crop by bank
:param calfile: Optional parameter to crop using a custom calfile
:param spectrum_numbers: Optional parameter to crop using spectrum numbers.
"""
ceria_workspace = path_handling.load_workspace(ceria_path)
if Ads.doesExist("full_inst_calib"):
full_calib = Ads.retrieve("full_inst_calib")
else:
full_calib_path = get_setting(
output_settings.INTERFACES_SETTINGS_GROUP,
output_settings.ENGINEERING_PREFIX, "full_calibration")
try:
full_calib = Load(full_calib_path,
OutputWorkspace="full_inst_calib")
except ValueError:
logger.error(
"Error loading Full instrument calibration - this is set in the interface settings."
)
return
cal_params, ceria_raw, grp_ws = self.run_calibration(
ceria_workspace, bank, calfile, spectrum_numbers, full_calib)
if plot_output:
plot_dicts = list()
if len(cal_params) == 1:
if calfile:
bank_name = "Custom"
elif spectrum_numbers:
bank_name = "Cropped"
else:
bank_name = bank
plot_dicts.append(
EnggUtils.generate_tof_fit_dictionary(bank_name))
EnggUtils.plot_tof_fit(plot_dicts, [bank_name])
else:
plot_dicts.append(
EnggUtils.generate_tof_fit_dictionary("bank_1"))
plot_dicts.append(
EnggUtils.generate_tof_fit_dictionary("bank_2"))
EnggUtils.plot_tof_fit(plot_dicts, ["bank_1", "bank_2"])
difa = [row['difa'] for row in cal_params]
difc = [row['difc'] for row in cal_params]
tzero = [row['tzero'] for row in cal_params]
bk2bk_params = self.extract_b2b_params(ceria_raw)
DeleteWorkspace(ceria_raw)
params_table = []
for i in range(len(difc)):
params_table.append([i, difc[i], difa[i], tzero[i]])
self.update_calibration_params_table(params_table)
calib_dir = path.join(output_settings.get_output_path(), "Calibration",
"")
if calfile:
EnggUtils.save_grouping_workspace(grp_ws,
calib_dir,
ceria_path,
instrument,
calfile=calfile)
elif spectrum_numbers:
EnggUtils.save_grouping_workspace(grp_ws,
calib_dir,
ceria_path,
instrument,
spec_nos=spectrum_numbers)
self.create_output_files(calib_dir, difa, difc, tzero, bk2bk_params,
ceria_path, instrument, bank,
spectrum_numbers, calfile)
if rb_num:
user_calib_dir = path.join(output_settings.get_output_path(),
"User", rb_num, "Calibration", "")
self.create_output_files(user_calib_dir, difa, difc, tzero,
bk2bk_params, ceria_path, instrument,
bank, spectrum_numbers, calfile)
def run_calibration(ceria_ws, bank, calfile, spectrum_numbers, full_calib):
"""
Creates Engineering calibration files with PDCalibration
:param ceria_ws: The workspace with the ceria data.
:param bank: The bank to crop to, both if none.
:param calfile: The custom calibration file to crop to, not used if none.
:param spectrum_numbers: The spectrum numbers to crop to, no crop if none.
:return: dict containing calibrated diffractometer constants, and copy of the raw ceria workspace
"""
def run_pd_calibration(kwargs_to_pass) -> list:
"""
Call PDCalibration using the keyword arguments supplied, and return it's default list of output workspaces
:param kwargs_to_pass: Keyword arguments to supply to the algorithm
:return: List of output workspaces from PDCalibration
"""
return PDCalibration(**kwargs_to_pass)
def calibrate_region_of_interest(ceria_d_ws, roi: str,
grouping_kwarg: dict,
cal_output: dict) -> None:
"""
Focus the processed ceria workspace (dSpacing) over the chosen region of interest, and run the calibration
using this result
:param ceria_d_ws: Workspace containing the processed ceria data converted to dSpacing
:param roi: String describing chosen region of interest
:param grouping_kwarg: Dict containing kwarg to pass to DiffractionFocussing to select the roi
:param cal_output: Dictionary to append with the output of PDCalibration for the chosen roi
"""
# focus ceria
focused_ceria = DiffractionFocussing(InputWorkspace=ceria_d_ws,
**grouping_kwarg)
ApplyDiffCal(InstrumentWorkspace=focused_ceria,
ClearCalibration=True)
ConvertUnits(InputWorkspace=focused_ceria,
OutputWorkspace=focused_ceria,
Target='TOF')
# calibration of focused data over chosen region of interest
kwargs["InputWorkspace"] = focused_ceria
kwargs["OutputCalibrationTable"] = "engggui_calibration_" + roi
kwargs["DiagnosticWorkspaces"] = "diag_" + roi
cal_roi = run_pd_calibration(kwargs)[0]
cal_output[roi] = cal_roi
# need to clone the data as PDCalibration rebins
ceria_raw = CloneWorkspace(InputWorkspace=ceria_ws)
# initial process of ceria ws
NormaliseByCurrent(InputWorkspace=ceria_ws, OutputWorkspace=ceria_ws)
ApplyDiffCal(InstrumentWorkspace=ceria_ws,
CalibrationWorkspace=full_calib)
ConvertUnits(InputWorkspace=ceria_ws,
OutputWorkspace=ceria_ws,
Target='dSpacing')
kwargs = {
"PeakPositions":
EnggUtils.default_ceria_expected_peaks(final=True),
"TofBinning":
[15500, -0.0003,
52000], # using a finer binning now have better stats
"PeakWindow": 0.04,
"MinimumPeakHeight": 0.5,
"PeakFunction": 'BackToBackExponential',
"CalibrationParameters": 'DIFC+TZERO+DIFA',
"UseChiSq": True
}
cal_output = dict()
grp_ws = None
if (spectrum_numbers or calfile) is None:
if bank == '1' or bank is None:
grp_ws = EnggUtils.get_bank_grouping_workspace(1, ceria_raw)
grouping_kwarg = {"GroupingWorkspace": grp_ws}
calibrate_region_of_interest(ceria_ws, "bank_1",
grouping_kwarg, cal_output)
if bank == '2' or bank is None:
grp_ws = EnggUtils.get_bank_grouping_workspace(2, ceria_raw)
grouping_kwarg = {"GroupingWorkspace": grp_ws}
calibrate_region_of_interest(ceria_ws, "bank_2",
grouping_kwarg, cal_output)
elif calfile is None:
grp_ws = EnggUtils.create_grouping_workspace_from_spectra_list(
spectrum_numbers, ceria_raw)
grouping_kwarg = {"GroupingWorkspace": grp_ws}
calibrate_region_of_interest(ceria_ws, "Cropped", grouping_kwarg,
cal_output)
else:
grp_ws = EnggUtils.create_grouping_workspace_from_calfile(
calfile, ceria_raw)
grouping_kwarg = {"GroupingWorkspace": grp_ws}
calibrate_region_of_interest(ceria_ws, "Custom", grouping_kwarg,
cal_output)
cal_params = list()
# in the output calfile, rows are present for all detids, only read one from the region of interest
for bank_cal in cal_output:
mask_ws_name = "engggui_calibration_" + bank_cal + "_mask"
mask_ws = Ads.retrieve(mask_ws_name)
row_no = EnggUtils.get_first_unmasked_specno_from_mask_ws(mask_ws)
row = cal_output[bank_cal].row(row_no)
current_fit_params = {
'difc': row['difc'],
'difa': row['difa'],
'tzero': row['tzero']
}
cal_params.append(current_fit_params)
return cal_params, ceria_raw, grp_ws
def run_calibration(sample_ws,
vanadium_workspace,
van_integration,
bank,
spectrum_numbers,
full_inst_calib):
"""
Creates Engineering calibration files with PDCalibration
:param sample_ws: The workspace with the sample data.
:param vanadium_workspace: The workspace with the vanadium data
:param van_integration: The integration values from the vanadium corrections
:param bank: The bank to crop to, both if none.
:param spectrum_numbers: The spectrum numbers to crop to, no crop if none.
:param full_inst_calib : workspace containing the full instrument calibration
:return: The calibration output files, the vanadium curves workspace(s), and a clone of the sample file
"""
def run_pd_calibration(kwargs_to_pass):
return simple.PDCalibration(**kwargs_to_pass)
def focus_and_make_van_curves(ceria_d, vanadium_d, grouping_kwarg):
# focus ceria
focused_ceria = simple.DiffractionFocussing(InputWorkspace=ceria_d, **grouping_kwarg)
simple.ApplyDiffCal(InstrumentWorkspace=focused_ceria, ClearCalibration=True)
tof_focused = simple.ConvertUnits(InputWorkspace=focused_ceria, Target='TOF')
# focus van data
focused_van = simple.DiffractionFocussing(InputWorkspace=vanadium_d, **grouping_kwarg)
background_van = simple.EnggEstimateFocussedBackground(InputWorkspace=focused_van, NIterations='15',
XWindow=0.03)
simple.DeleteWorkspace(focused_ceria)
simple.DeleteWorkspace(focused_van)
return tof_focused, background_van
def ws_initial_process(ws):
"""Run some processing common to both the sample and vanadium workspaces"""
simple.NormaliseByCurrent(InputWorkspace=ws, OutputWorkspace=ws)
simple.ApplyDiffCal(InstrumentWorkspace=ws, CalibrationWorkspace=full_inst_calib)
simple.ConvertUnits(InputWorkspace=ws, OutputWorkspace=ws, Target='dSpacing')
return ws
def calibrate_region_of_interest(roi, df_kwarg):
focused_roi, curves_roi = focus_and_make_van_curves(ws_d, ws_van_d, df_kwarg)
simple.RenameWorkspace(curves_roi, ("curves_" + roi))
curves_output.append(curves_roi)
# final calibration of focused data
kwargs["InputWorkspace"] = focused_roi
kwargs["OutputCalibrationTable"] = "engg_calibration_" + roi
kwargs["DiagnosticWorkspaces"] = "diag_" + roi
cal_roi = run_pd_calibration(kwargs)[0]
cal_output[roi] = cal_roi
# need to clone the data as PDCalibration rebins
sample_raw = simple.CloneWorkspace(InputWorkspace=sample_ws)
ws_van = simple.CloneWorkspace(vanadium_workspace)
ws_van_d = ws_initial_process(ws_van)
# sensitivity correction
ws_van_d /= van_integration
simple.ReplaceSpecialValues(InputWorkspace=ws_van_d, OutputWorkspace=ws_van_d, NaNValue=0, InfinityValue=0)
ws_d = ws_initial_process(sample_ws)
simple.DeleteWorkspace(van_integration)
kwargs = {
"PeakPositions": Utils.default_ceria_expected_peaks(final=True),
"TofBinning": [15500, -0.0003, 52000], # using a finer binning now have better stats
"PeakWindow": 0.04,
"MinimumPeakHeight": 0.5,
"PeakFunction": 'BackToBackExponential',
"CalibrationParameters": 'DIFC+TZERO+DIFA',
"UseChiSq": True
}
cal_output = dict()
curves_output = list()
if spectrum_numbers is None:
if bank == '1' or bank is None:
df_kwarg = {"GroupingFileName": NORTH_BANK_CAL}
calibrate_region_of_interest("bank_1", df_kwarg)
if bank == '2' or bank is None:
df_kwarg = {"GroupingFileName": SOUTH_BANK_CAL}
calibrate_region_of_interest("bank_2", df_kwarg)
else:
grp_ws = Utils.create_grouping_workspace_from_spectra_list(spectrum_numbers, sample_raw)
df_kwarg = {"GroupingWorkspace": grp_ws}
calibrate_region_of_interest("Cropped", df_kwarg)
simple.DeleteWorkspace(ws_van)
simple.DeleteWorkspace("tof_focused")
cal_params = list()
# in the output calfile, rows are present for all detids, only read one from the region of interest
bank_1_read_row = 0
bank_2_read_row = 1200
for bank_cal in cal_output:
if bank_cal == "bank_1":
read = bank_1_read_row
elif bank_cal == "bank_2":
read = bank_2_read_row
else:
read = int(Utils.create_spectrum_list_from_string(spectrum_numbers)[0]) # this can be int64
row = cal_output[bank_cal].row(read)
current_fit_params = {'difc': row['difc'], 'difa': row['difa'], 'tzero': row['tzero']}
cal_params.append(current_fit_params)
return cal_params, sample_raw, curves_output