def generate_output_file_name(ceria_path, instrument, bank, ext='.prm'):
"""
Generate an output filename in the form INSTRUMENT_ceriaRunNo_BANKS
:param vanadium_path: Path to vanadium data file
:param ceria_path: Path to ceria data file
:param instrument: The instrument in use.
:param bank: The bank being saved.
:param ext: Extension to be used on the saved file
:return: The filename, the vanadium run number, and ceria run number.
"""
ceria_no = path_handling.get_run_number_from_path(ceria_path, instrument)
filename = instrument + "_" + ceria_no + "_"
if bank == "all":
filename = filename + "all_banks" + ext
elif bank == "north":
filename = filename + "bank_1" + ext
elif bank == "south":
filename = filename + "bank_2" + ext
elif bank == "Cropped":
filename = filename + "Cropped" + ext
elif bank == "Custom":
filename = filename + "Custom" + ext
else:
raise ValueError("Invalid bank name entered")
return filename
def _load_run_and_convert_to_dSpacing(filepath, instrument, full_calib):
runno = path_handling.get_run_number_from_path(filepath, instrument)
ws = mantid.Load(Filename=filepath, OutputWorkspace=str(runno))
if ws.getRun().getProtonCharge() > 0:
ws = mantid.NormaliseByCurrent(InputWorkspace=ws,
OutputWorkspace=ws.name())
else:
logger.warning(f"Run {ws.name()} has invalid proton charge.")
mantid.DeleteWorkspace(ws)
return None
mantid.ApplyDiffCal(InstrumentWorkspace=ws,
CalibrationWorkspace=full_calib)
ws = mantid.ConvertUnits(InputWorkspace=ws,
OutputWorkspace=ws.name(),
Target='dSpacing')
return ws
def fetch_correction_workspaces(vanadium_path: str, instrument: str):
# -> Workspace2D, Workspace2D
"""
Fetch workspaces from the ADS or create new ones.
:param vanadium_path: The path to the requested vanadium run raw data.
:param instrument: The instrument the data came from.
"""
van_run_no = path_handling.get_run_number_from_path(
vanadium_path, instrument)
if not check_workspaces_exist(van_run_no):
van_integration_ws, van_processed_inst_ws = create_vanadium_corrections(
vanadium_path, instrument)
else:
van_integration_ws = Ads.retrieve(
str(van_run_no) + '_' + INTEGRATED_WORKSPACE_NAME)
van_processed_inst_ws = Ads.retrieve(
str(van_run_no) + '_' + PROCESSED_WORKSPACE_NAME)
return van_integration_ws, van_processed_inst_ws
def process_vanadium(vanadium_path, calibration, full_calib):
van_run = path_handling.get_run_number_from_path(
vanadium_path, calibration.get_instrument())
van_foc_name = CURVES_PREFIX + calibration.get_group_suffix()
if ADS.doesExist(van_foc_name):
ws_van_foc = ADS.retrieve(van_foc_name)
else:
if ADS.doesExist(van_run):
ws_van = ADS.retrieve(
van_run) # will exist if have only changed the ROI
else:
ws_van = _load_run_and_convert_to_dSpacing(
vanadium_path, calibration.get_instrument(), full_calib)
if not ws_van:
raise RuntimeError(
f"vanadium run {van_run} has no proton_charge - "
f"please supply a valid vanadium run to focus.")
ws_van_foc = _focus_run_and_apply_roi_calibration(
ws_van, calibration, ws_foc_name=van_foc_name)
ws_van_foc = _smooth_vanadium(ws_van_foc)
return ws_van_foc, van_run
def create_vanadium_corrections(vanadium_path: str,
instrument: str): # -> Workspace, Workspace
"""
Runs the vanadium correction algorithm.
:param vanadium_path: The path to the vanadium data.
:return: The integrated workspace and the processed instrument workspace generated.
"""
try:
run_no = path_handling.get_run_number_from_path(
vanadium_path, instrument)
van_ws = Load(Filename=vanadium_path,
OutputWorkspace=str(run_no) + '_' +
VANADIUM_INPUT_WORKSPACE_NAME)
except Exception as e:
logger.error(
"Error when loading vanadium sample data. "
"Could not run Load algorithm with vanadium run number: " +
str(vanadium_path) + ". Error description: " + str(e))
raise RuntimeError
# get full instrument calibration for instrument processing calculation
if Ads.doesExist("full_inst_calib"):
full_calib_ws = 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_ws = 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
integral_ws = _calculate_vanadium_integral(van_ws, run_no)
processed_ws = _calculate_vanadium_processed_instrument(
van_ws, full_calib_ws, integral_ws, run_no)
return integral_ws, processed_ws
def create_output_files(self, calibration_dir, difa, difc, tzero,
bk2bk_params, ceria_path, instrument, bank,
spectrum_numbers, calfile):
"""
Create output files from the algorithms in the specified directory
:param calibration_dir: The directory to save the files into.
:param difa: DIFA values from calibration algorithm.
:param difc: DIFC values from the calibration algorithm.
:param tzero: TZERO values from the calibration algorithm.
:param bk2bk_params: BackToBackExponential parameters from Parameters.xml file.
:param ceria_path: The path to the ceria data file.
:param instrument: The instrument (ENGINX or IMAT).
:param bank: Optional parameter to crop by bank.
:param spectrum_numbers: Optional parameter to crop using spectrum numbers.
:param calfile: Optional parameter to crop with a custom calfile
"""
kwargs = {
"ceria_run":
path_handling.get_run_number_from_path(ceria_path, instrument)
}
def south_kwargs():
kwargs["template_file"] = SOUTH_BANK_TEMPLATE_FILE
kwargs["bank_names"] = ["South"]
def north_kwargs():
kwargs["template_file"] = NORTH_BANK_TEMPLATE_FILE
kwargs["bank_names"] = ["North"]
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_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)
if not path.exists(calibration_dir):
makedirs(calibration_dir)
if not (bank or spectrum_numbers or calfile):
# both banks
generate_prm_output_file(difa, difc, tzero, "all", kwargs)
north_kwargs()
generate_prm_output_file([difa[0]], [difc[0]], [tzero[0]], "north",
kwargs)
save_pdcal_output_file("bank_1", "north")
south_kwargs()
generate_prm_output_file([difa[1]], [difc[1]], [tzero[1]], "south",
kwargs)
save_pdcal_output_file("bank_2", "south")
elif bank == "1":
north_kwargs()
generate_prm_output_file([difa[0]], [difc[0]], [tzero[0]], "north",
kwargs)
save_pdcal_output_file("bank_1", "north")
elif bank == "2":
south_kwargs()
generate_prm_output_file([difa[0]], [difc[0]], [tzero[0]], "south",
kwargs)
save_pdcal_output_file("bank_2", "south")
elif spectrum_numbers: # Custom crops use the north bank template
north_kwargs()
generate_prm_output_file([difa[0]], [difc[0]], [tzero[0]],
"Cropped", kwargs)
save_pdcal_output_file("Cropped", "Cropped")
else: # custom calfile
north_kwargs()
generate_prm_output_file([difa[0]], [difc[0]], [tzero[0]],
"Custom", kwargs)
save_pdcal_output_file("Custom", "Custom")
logger.notice(
f"\n\nCalibration files saved to: \"{calibration_dir}\"\n\n")
def get_ceria_runno(self):
if self.ceria_path and self.instrument:
return path_handling.get_run_number_from_path(
self.ceria_path, self.instrument)
def update_calibration(self, calibration):
instrument = calibration.get_instrument()
sample_no = path_handling.get_run_number_from_path(
calibration.get_sample(), instrument)
self.statusbar_observable.notify_subscribers(
f"CeO2: {sample_no}, Instrument: {instrument}")
def focus_run(self, sample_paths: list, vanadium_path: str,
plot_output: bool, instrument: str, rb_num: str,
regions_dict: dict) -> None:
"""
Focus some data using the current calibration.
:param sample_paths: The paths to the data to be focused.
:param vanadium_path: Path to the vanadium file from the current calibration
:param plot_output: True if the output should be plotted.
:param instrument: The instrument that the data came from.
:param rb_num: Number to signify the user who is running this focus
:param regions_dict: dict region name -> grp_ws_name, defining region(s) of interest to focus over
"""
full_calib_path = get_setting(
output_settings.INTERFACES_SETTINGS_GROUP,
output_settings.ENGINEERING_PREFIX, "full_calibration")
if not Ads.doesExist("full_inst_calib"):
try:
full_calib_workspace = Load(full_calib_path,
OutputWorkspace="full_inst_calib")
except RuntimeError:
logger.error(
"Error loading Full instrument calibration - this is set in the interface settings."
)
return
else:
full_calib_workspace = Ads.retrieve("full_inst_calib")
van_integration_ws, van_processed_inst_ws = vanadium_corrections.fetch_correction_workspaces(
vanadium_path, instrument)
# check correct region calibration(s) and grouping workspace(s) exists
inst_ws = path_handling.load_workspace(sample_paths[0])
for region in regions_dict:
calib_exists = self._check_region_calib_ws_exists(region)
grouping_exists = self._check_region_grouping_ws_exists(
regions_dict[region], inst_ws)
if not (calib_exists and grouping_exists):
return
# loop over samples provided, focus each over region(s) specified in regions_dict
output_workspaces = [] # List of collated workspaces to plot.
self._last_focused_files = []
van_run_no = path_handling.get_run_number_from_path(
vanadium_path, instrument)
for sample_path in sample_paths:
sample_workspace = path_handling.load_workspace(sample_path)
run_no = path_handling.get_run_number_from_path(
sample_path, instrument)
# perform prefocus operations on whole instrument workspace
prefocus_success = self._whole_inst_prefocus(
sample_workspace, van_integration_ws, full_calib_workspace)
if not prefocus_success:
continue
sample_plots = [
] # if both banks focused, pass list with both so plotted on same figure
for region, grouping_kwarg in regions_dict.items():
tof_output_name = str(
run_no) + "_" + FOCUSED_OUTPUT_WORKSPACE_NAME + region
dspacing_output_name = tof_output_name + "_dSpacing"
region_calib_ws = self._get_region_calib_ws(region)
curves = self._get_van_curves_for_roi(region,
van_processed_inst_ws,
grouping_kwarg)
# perform focus over chosen region of interest
self._run_focus(sample_workspace, tof_output_name, curves,
grouping_kwarg, region_calib_ws)
sample_plots.append(tof_output_name)
self._save_output(instrument, run_no, van_run_no, region,
tof_output_name, rb_num)
self._save_output(instrument,
run_no,
van_run_no,
region,
dspacing_output_name,
rb_num,
unit="dSpacing")
self._output_sample_logs(instrument, run_no, van_run_no,
sample_workspace, rb_num)
output_workspaces.append(sample_plots)
DeleteWorkspace(sample_workspace)
# remove created grouping workspace if present
if Ads.doesExist("grp_ws"):
DeleteWorkspace("grp_ws")
# Plot the output
if plot_output:
for ws_names in output_workspaces:
self._plot_focused_workspaces(ws_names)