def _output_sample_logs(instrument, run_number, van_run_number, workspace,
rb_num):
def write_to_file():
with open(output_path, "w", newline="") as logfile:
writer = csv.writer(logfile, ["Sample Log", "Avg Value"])
for log in output_dict:
writer.writerow([log, output_dict[log]])
output_dict = {}
sample_run = workspace.getRun()
log_names = sample_run.keys()
# Collect numerical sample logs.
for name in log_names:
try:
output_dict[name] = sample_run.getPropertyAsSingleValue(name)
except ValueError:
logger.information(
f"Could not convert {name} to a numerical value. It will not be included in the "
f"sample logs output file.")
focus_dir = path.join(output_settings.get_output_path(), "Focus")
if not path.exists(focus_dir):
makedirs(focus_dir)
output_path = path.join(focus_dir,
(instrument + "_" + run_number + "_" +
van_run_number + "_sample_logs.csv"))
write_to_file()
if rb_num:
focus_user_dir = path.join(output_settings.get_output_path(),
"User", rb_num, "Focus")
if not path.exists(focus_user_dir):
makedirs(focus_user_dir)
output_path = path.join(focus_user_dir,
(instrument + "_" + run_number + "_" +
van_run_number + "_sample_logs.csv"))
write_to_file()
def _save_output(self,
instrument,
sample_run,
van_run,
bank,
sample_workspace,
rb_num,
unit="TOF"):
"""
Save a focused workspace to the file system. Saves separate copies to a User directory if an rb number has
been set.
:param instrument: The instrument the data is from.
:param sample_run: The sample run number that was focussed
:param bank: The name of the bank being saved.
:param sample_workspace: The name of the workspace to be saved.
:param rb_num: Usually an experiment id, defines the name of the user directory.
"""
self._save_focused_output_files_as_nexus(instrument, sample_run,
van_run, bank,
sample_workspace, rb_num,
unit)
self._save_focused_output_files_as_gss(instrument, sample_run, van_run,
bank, sample_workspace, rb_num,
unit)
self._save_focused_output_files_as_topas_xye(instrument, sample_run,
van_run, bank,
sample_workspace, rb_num,
unit)
output_path = path.join(output_settings.get_output_path(), 'Focus')
logger.notice(f"\n\nFocus files saved to: \"{output_path}\"\n\n")
if rb_num:
output_path = path.join(output_settings.get_output_path(), 'User',
rb_num, 'Focus')
logger.notice(
f"\n\nFocus files also saved to: \"{output_path}\"\n\n")
def _save_focused_output_files_as_gss(self, instrument, sample_run,
van_run, bank, sample_workspace,
rb_num, unit):
gss_output_path = path.join(
output_settings.get_output_path(), "Focus",
self._generate_output_file_name(instrument, sample_run, van_run,
bank, unit, ".gss"))
SaveGSS(InputWorkspace=sample_workspace, Filename=gss_output_path)
if rb_num:
gss_output_path = path.join(
output_settings.get_output_path(), "User", rb_num, "Focus",
self._generate_output_file_name(instrument, sample_run,
van_run, bank, unit, ".gss"))
SaveGSS(InputWorkspace=sample_workspace, Filename=gss_output_path)
def test_last_path_updates_with_no_RB_number(self, addlog, nexus, gss, xye):
mocked_workspace = "mocked-workspace"
output_file = path.join(output_settings.get_output_path(), "Focus",
"ENGINX_123_456_North_TOF.nxs")
self.model._save_output("ENGINX", "123", "456", "North",
mocked_workspace, None)
self.assertEqual(self.model._last_focused_files[0], output_file)
def _save_focused_output_files_as_nexus(self, instrument, sample_run,
van_run, bank, sample_workspace,
rb_num, unit):
file_name = self._generate_output_file_name(instrument, sample_run,
van_run, bank, unit,
".nxs")
nexus_output_path = path.join(output_settings.get_output_path(),
"Focus", file_name)
AddSampleLog(Workspace=sample_workspace,
LogName="Vanadium Run",
LogText=van_run)
SaveNexus(InputWorkspace=sample_workspace, Filename=nexus_output_path)
if rb_num:
nexus_output_path = path.join(output_settings.get_output_path(),
"User", rb_num, "Focus", file_name)
SaveNexus(InputWorkspace=sample_workspace,
Filename=nexus_output_path)
if unit == "TOF":
self._last_focused_files.append(nexus_output_path)
def test_save_output_files_with_no_RB_number(self, addlog, nexus, gss, xye):
mocked_workspace = "mocked-workspace"
output_file = path.join(output_settings.get_output_path(), "Focus",
"ENGINX_123_456_North_TOF.nxs")
self.model._save_output("ENGINX", "123", "456", "North",
mocked_workspace, None)
self.assertEqual(1, nexus.call_count)
self.assertEqual(1, gss.call_count)
self.assertEqual(1, xye.call_count)
nexus.assert_called_with(Filename=output_file, InputWorkspace=mocked_workspace)
def _save_focused_output_files_as_topas_xye(self, instrument, sample_run,
van_run, bank,
sample_workspace, rb_num,
unit):
xye_output_path = path.join(
output_settings.get_output_path(), "Focus",
self._generate_output_file_name(instrument, sample_run, van_run,
bank, unit, ".abc"))
SaveFocusedXYE(InputWorkspace=sample_workspace,
Filename=xye_output_path,
SplitFiles=False,
Format="TOPAS")
if rb_num:
xye_output_path = path.join(
output_settings.get_output_path(), "User", rb_num, "Focus",
self._generate_output_file_name(instrument, sample_run,
van_run, bank, unit, ".abc"))
SaveFocusedXYE(InputWorkspace=sample_workspace,
Filename=xye_output_path,
SplitFiles=False,
Format="TOPAS")
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)