def _output_sample_logs(instrument, 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(path_handling.get_output_path(), "Focus")
if not path.exists(focus_dir):
makedirs(focus_dir)
output_path = path.join(
focus_dir, (instrument + "_" + run_number + "_sample_logs.csv"))
write_to_file()
if rb_num:
focus_user_dir = path.join(path_handling.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 + "_sample_logs.csv"))
write_to_file()
def _save_focused_output_files_as_gss(self, instrument, sample_path, bank,
sample_workspace, rb_num):
gss_output_path = path.join(
path_handling.get_output_path(), "Focus",
self._generate_output_file_name(instrument, sample_path, bank,
".gss"))
SaveGSS(InputWorkspace=sample_workspace, Filename=gss_output_path)
if rb_num:
gss_output_path = path.join(
path_handling.get_output_path(), "User", rb_num, "Focus",
self._generate_output_file_name(instrument, sample_path, bank,
".gss"))
SaveGSS(InputWorkspace=sample_workspace, Filename=gss_output_path)
def _save_output(self, instrument, sample_path, bank, sample_workspace,
rb_num):
"""
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_path: The path to the data file that was focused.
: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_path, bank,
sample_workspace, rb_num)
self._save_focused_output_files_as_gss(instrument, sample_path, bank,
sample_workspace, rb_num)
self._save_focused_output_files_as_topas_xye(instrument, sample_path,
bank, sample_workspace,
rb_num)
logger.notice(
f"\n\nFocus files saved to: \"{path.join(path_handling.get_output_path(), 'Focus')}\"\n\n"
)
if rb_num:
output_path = path.join(path_handling.get_output_path(), 'User',
rb_num, 'Focus')
logger.notice(f"\n\nFocus files saved to: \"{output_path}\"\n\n")
def _save_focused_output_files_as_xye(self, instrument, sample_path, bank,
sample_workspace, rb_num):
xye_output_path = path.join(
path_handling.get_output_path(), "Focus",
self._generate_output_file_name(instrument, sample_path, bank,
".dat"))
SaveFocusedXYE(InputWorkspace=sample_workspace,
Filename=xye_output_path,
SplitFiles=False)
if rb_num:
xye_output_path = path.join(
path_handling.get_output_path(), "User", rb_num, "Focus",
self._generate_output_file_name(instrument, sample_path, bank,
".dat"))
SaveFocusedXYE(InputWorkspace=sample_workspace,
Filename=xye_output_path,
SplitFiles=False)
def _generate_saved_workspace_file_paths(vanadium_number, rb_num=""):
"""
Generate file paths based on a vanadium run number.
:param vanadium_number: The number of the vanadium run.
:param rb_num: User identifier, usually an experiment number.
:return: The full path to the file.
"""
integrated_filename = vanadium_number + SAVED_FILE_INTEG_SUFFIX
curves_filename = vanadium_number + SAVED_FILE_CURVE_SUFFIX
if rb_num:
vanadium_dir = path.join(path_handling.get_output_path(), "User", rb_num,
VANADIUM_DIRECTORY_NAME)
else:
vanadium_dir = path.join(path_handling.get_output_path(), VANADIUM_DIRECTORY_NAME)
if not path.exists(vanadium_dir):
makedirs(vanadium_dir)
return path.join(vanadium_dir, integrated_filename), path.join(vanadium_dir, curves_filename)
def test_save_output_files_with_no_RB_number(self, nexus, gss, xye):
mocked_workspace = "mocked-workspace"
output_file = path.join(path_handling.get_output_path(), "Focus",
"ENGINX_123_bank_North.nxs")
self.model._save_output("ENGINX", "Path/To/ENGINX000123.whatever",
"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 create_new_calibration(self,
vanadium_path,
sample_path,
plot_output,
instrument,
rb_num=None,
bank=None,
spectrum_numbers=None):
"""
Create a new calibration from a vanadium run and sample run
:param vanadium_path: Path to vanadium data file.
:param sample_path: Path to sample (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 spectrum_numbers: Optional parameter to crop using spectrum numbers.
"""
van_integration, van_curves = vanadium_corrections.fetch_correction_workspaces(
vanadium_path, instrument, rb_num=rb_num)
sample_workspace = path_handling.load_workspace(sample_path)
full_calib_path = get_setting(path_handling.INTERFACES_SETTINGS_GROUP,
path_handling.ENGINEERING_PREFIX, "full_calibration")
if full_calib_path is not None and path.exists(full_calib_path):
full_calib = LoadAscii(full_calib_path, OutputWorkspace="det_pos", Separator="Tab")
output = self.run_calibration(sample_workspace,
van_integration,
van_curves,
bank,
spectrum_numbers,
full_calib_ws=full_calib)
else:
output = self.run_calibration(sample_workspace, van_integration, van_curves, bank,
spectrum_numbers)
if plot_output:
self._plot_vanadium_curves()
for i in range(len(output)):
if spectrum_numbers:
bank_name = "cropped"
elif bank is None:
bank_name = str(i + 1)
else:
bank_name = bank
difa = output[i].DIFA
difc = output[i].DIFC
tzero = output[i].TZERO
self._generate_tof_fit_workspace(difa, difc, tzero, bank_name)
if bank is None and spectrum_numbers is None:
self._plot_tof_fit()
elif spectrum_numbers is None:
self._plot_tof_fit_single_bank_or_custom(bank)
else:
self._plot_tof_fit_single_bank_or_custom("cropped")
difa = [i.DIFC for i in output]
difc = [i.DIFC for i in output]
tzero = [i.TZERO for i in output]
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(path_handling.get_output_path(), "Calibration", "")
self.create_output_files(calib_dir, difa, difc, tzero, sample_path, vanadium_path, instrument,
bank, spectrum_numbers)
if rb_num:
user_calib_dir = path.join(path_handling.get_output_path(), "User", rb_num,
"Calibration", "")
self.create_output_files(user_calib_dir, difa, difc, tzero, sample_path, vanadium_path,
instrument, bank, spectrum_numbers)
