def _get_temperature(self, ws_name):
"""
Gets the sample temperature for a given workspace.
@param ws_name Name of workspace
@returns Temperature in Kelvin or None if not found
"""
from IndirectCommon import getInstrRun
instr, run_number = getInstrRun(ws_name)
facility = config.getFacility()
pad_num = facility.instrument(instr).zeroPadding(int(run_number))
zero_padding = '0' * (pad_num - len(run_number))
run_name = instr + zero_padding + run_number
log_filename = run_name.upper() + '.log'
run = mtd[ws_name].getRun()
if self._sample_log_name in run:
# Look for temperature in logs in workspace
tmp = run[self._sample_log_name].value
value_action = {
'last_value': lambda x: x[len(x) - 1],
'average': lambda x: x.mean()
}
temp = value_action[self._sample_log_value](tmp)
logger.debug('Temperature %d K found for run: %s' %
(temp, run_name))
return temp
else:
# Logs not in workspace, try loading from file
logger.information(
'Log parameter not found in workspace. Searching for log file.'
)
log_path = FileFinder.getFullPath(log_filename)
if log_path != '':
# Get temperature from log file
LoadLog(Workspace=ws_name, Filename=log_path)
run_logs = mtd[ws_name].getRun()
if self._sample_log_name in run_logs:
tmp = run_logs[self._sample_log_name].value
temp = tmp[len(tmp) - 1]
logger.debug('Temperature %d K found for run: %s' %
(temp, run_name))
return temp
else:
logger.warning('Log entry %s for run %s not found' %
(self._sample_log_name, run_name))
else:
logger.warning('Log file for run %s not found' % run_name)
# Can't find log file
logger.warning('No temperature found for run: %s' % run_name)
return None
def _get_temperature(self, ws_name):
"""
Gets the sample temperature for a given workspace.
@param ws_name Name of workspace
@returns Temperature in Kelvin or None if not found
"""
from IndirectCommon import getInstrRun
instr, run_number = getInstrRun(ws_name)
facility = config.getFacility()
pad_num = facility.instrument(instr).zeroPadding(int(run_number))
zero_padding = '0' * (pad_num - len(run_number))
run_name = instr + zero_padding + run_number
log_filename = run_name.upper() + '.log'
run = mtd[ws_name].getRun()
if self._sample_log_name in run:
# Look for temperature in logs in workspace
tmp = run[self._sample_log_name].value
value_action = {'last_value': lambda x: x[len(x)-1],
'average': lambda x: x.mean()
}
temp = value_action[self._sample_log_value](tmp)
logger.debug('Temperature %d K found for run: %s' % (temp, run_name))
return temp
else:
# Logs not in workspace, try loading from file
logger.information('Log parameter not found in workspace. Searching for log file.')
log_path = FileFinder.getFullPath(log_filename)
if log_path != '':
# Get temperature from log file
LoadLog(Workspace=ws_name, Filename=log_path)
run_logs = mtd[ws_name].getRun()
if self._sample_log_name in run_logs:
tmp = run_logs[self._sample_log_name].value
temp = tmp[len(tmp) - 1]
logger.debug('Temperature %d K found for run: %s' % (temp, run_name))
return temp
else:
logger.warning('Log entry %s for run %s not found' % (self._sample_log_name, run_name))
else:
logger.warning('Log file for run %s not found' % run_name)
# Can't find log file
logger.warning('No temperature found for run: %s' % run_name)
return None
def _get_sample_units(self, workspace):
"""
Gets the sample environment units for a given workspace.
@param workspace The workspace
@returns sample in given units or None if not found
"""
from IndirectCommon import getInstrRun
instr, run_number = getInstrRun(workspace.name())
pad_num = config.getInstrument(instr).zeroPadding(int(run_number))
zero_padding = '0' * (pad_num - len(run_number))
run_name = instr + zero_padding + run_number
log_filename = run_name.upper() + '.log'
run = workspace.getRun()
position_logs = ['position', 'samp_posn']
if self._sample_log_name.lower() in position_logs:
self._sample_log_name = _extract_sensor_name(
self._sample_log_name, run, workspace.getInstrument())
if self._sample_log_name in run:
# Look for sample unit in logs in workspace
if self._sample_log_value == 'last_value':
sample = run[self._sample_log_name].value[-1]
else:
sample = run[self._sample_log_name].value.mean()
unit = run[self._sample_log_name].units
else:
# Logs not in workspace, try loading from file
logger.information(
'Log parameter not found in workspace. Searching for log file.'
)
sample, unit = _extract_temperature_from_log(
workspace, self._sample_log_name, log_filename, run_name)
if sample is not None and unit is not None:
logger.debug('{0} {1} found for run: {2}'.format(
sample, unit, run_name))
else:
logger.warning(
'No sample units found for run: {}'.format(run_name))
if unit is not None and unit.isspace():
unit = ""
return sample, unit
def _get_sample_units(self, workspace):
"""
Gets the sample environment units for a given workspace.
@param workspace The workspace
@returns sample in given units or None if not found
"""
from IndirectCommon import getInstrRun
instr, run_number = getInstrRun(workspace.getName())
instrument = config.getFacility().instrument(instr)
pad_num = instrument.zeroPadding(int(run_number))
zero_padding = '0' * (pad_num - len(run_number))
run_name = instr + zero_padding + run_number
log_filename = run_name.upper() + '.log'
run = workspace.getRun()
if self._sample_log_name.lower() == 'position':
self._sample_log_name = _extract_sensor_name(self._sample_log_name, run, workspace.getInstrument())
if self._sample_log_name in run:
# Look for sample unit in logs in workspace
if self._sample_log_value == 'last_value':
sample = run[self._sample_log_name].value[-1]
else:
sample = run[self._sample_log_name].value.mean()
unit = run[self._sample_log_name].units
else:
# Logs not in workspace, try loading from file
logger.information('Log parameter not found in workspace. Searching for log file.')
sample, unit = _extract_temperature_from_log(workspace, self._sample_log_name, log_filename, run_name)
if sample is not None and unit is not None:
logger.debug('{0} {1} found for run: {2}'.format(sample, unit, run_name))
else:
logger.warning('No sample units found for run: {}'.format(run_name))
return sample, unit
def PyExec(self):
from IndirectCommon import getInstrRun
# Do setup
self._setup()
logger.debug('in_ws:' + str(type(self._input_workspaces)))
# Get input workspaces
input_workspace_names = self._input_workspaces.getNames()
# Lists of input and output workspaces
q_workspaces = list()
q2_workspaces = list()
run_numbers = list()
temperatures = list()
# Perform the ElasticWindow algorithms
for input_ws in input_workspace_names:
logger.information('Running ElasticWindow for workspace: %s' %
input_ws)
q_ws = '__' + input_ws + '_q'
q2_ws = '__' + input_ws + '_q2'
if self._background_range_start != Property.EMPTY_DBL and self._background_range_end != Property.EMPTY_DBL:
ElasticWindow(
InputWorkspace=input_ws,
OutputInQ=q_ws,
OutputInQSquared=q2_ws,
IntegrationRangeStart=self._integration_range_start,
IntegrationRangeEnd=self._integration_range_end,
BackgroundRangeStart=self._background_range_start,
BackgroundRangeEnd=self._background_range_end)
else:
ElasticWindow(
InputWorkspace=input_ws,
OutputInQ=q_ws,
OutputInQSquared=q2_ws,
IntegrationRangeStart=self._integration_range_start,
IntegrationRangeEnd=self._integration_range_end)
Logarithm(InputWorkspace=q2_ws, OutputWorkspace=q2_ws)
q_workspaces.append(q_ws)
q2_workspaces.append(q2_ws)
# Get the run number
run_no = getInstrRun(input_ws)[1]
run_numbers.append(run_no)
# Get the sample temperature
temp = self._get_temperature(input_ws)
if temp is not None:
temperatures.append(temp)
else:
# No need to output a tmperature workspace if there are no temperatures
self._elt_workspace = ''
logger.information('Creating Q and Q^2 workspaces')
if len(input_workspace_names) == 1:
# Just rename single workspaces
RenameWorkspace(InputWorkspace=q_workspaces[0],
OutputWorkspace=self._q_workspace)
RenameWorkspace(InputWorkspace=q2_workspaces[0],
OutputWorkspace=self._q2_workspace)
else:
# Append the spectra of the first two workspaces
AppendSpectra(InputWorkspace1=q_workspaces[0],
InputWorkspace2=q_workspaces[1],
OutputWorkspace=self._q_workspace)
AppendSpectra(InputWorkspace1=q2_workspaces[0],
InputWorkspace2=q2_workspaces[1],
OutputWorkspace=self._q2_workspace)
# Append to the spectra of each remaining workspace
for idx in range(2, len(input_workspace_names)):
AppendSpectra(InputWorkspace1=self._q_workspace,
InputWorkspace2=q_workspaces[idx],
OutputWorkspace=self._q_workspace)
AppendSpectra(InputWorkspace1=self._q2_workspace,
InputWorkspace2=q2_workspaces[idx],
OutputWorkspace=self._q2_workspace)
# Delete the output workspaces from the ElasticWindow algorithms
for q_ws in q_workspaces:
DeleteWorkspace(q_ws)
for q2_ws in q2_workspaces:
DeleteWorkspace(q2_ws)
logger.information('Setting vertical axis units and values')
# Set the verical axis units
v_axis_is_temp = len(input_workspace_names) == len(temperatures)
if v_axis_is_temp:
logger.notice('Vertical axis is in temperature')
unit = ('Temperature', 'K')
else:
logger.notice('Vertical axis is in run number')
unit = ('Run No', 'last 3 digits')
# Create a new vertical axis for the Q and Q**2 workspaces
q_ws_axis = NumericAxis.create(len(input_workspace_names))
q_ws_axis.setUnit("Label").setLabel(unit[0], unit[1])
q2_ws_axis = NumericAxis.create(len(input_workspace_names))
q2_ws_axis.setUnit("Label").setLabel(unit[0], unit[1])
# Set the vertical axis values
for idx in range(0, len(input_workspace_names)):
if v_axis_is_temp:
q_ws_axis.setValue(idx, float(temperatures[idx]))
q2_ws_axis.setValue(idx, float(temperatures[idx]))
else:
q_ws_axis.setValue(idx, float(run_numbers[idx][-3:]))
q2_ws_axis.setValue(idx, float(run_numbers[idx][-3:]))
# Add the new vertical axis to each workspace
mtd[self._q_workspace].replaceAxis(1, q_ws_axis)
mtd[self._q2_workspace].replaceAxis(1, q2_ws_axis)
# Process the ELF workspace
if self._elf_workspace != '':
logger.information('Creating ELF workspace')
Transpose(InputWorkspace=self._q_workspace,
OutputWorkspace=self._elf_workspace)
SortXAxis(InputWorkspace=self._elf_workspace,
OutputWorkspace=self._elf_workspace)
self.setProperty('OutputELF', self._elf_workspace)
# Do temperature normalisation
if self._elt_workspace != '':
logger.information('Creating ELT workspace')
# If the ELT workspace was not already created then create it here,
# otherwise just clone it
if self._elf_workspace == '':
Transpose(InputWorkspace=self._q_workspace,
OutputWorkspace=self._elt_workspace)
SortXAxis(InputWorkspace=self._elt_workspace,
OutputWorkspace=self._elt_workspace)
else:
CloneWorkspace(InputWorkspace=self._elf_workspace,
OutputWorkspace=self._elt_workspace)
_normalize_to_lowest_temp(self._elt_workspace)
self.setProperty('OutputELT', self._elt_workspace)
# Set the output workspace
self.setProperty('OutputInQ', self._q_workspace)
self.setProperty('OutputInQSquared', self._q2_workspace)
def PyExec(self):
from IndirectCommon import getInstrRun
# Do setup
self._setup()
# Lists of input and output workspaces
q_workspaces = list()
q2_workspaces = list()
run_numbers = list()
sample_param = list()
progress = Progress(self, 0.0, 0.05, 3)
# Perform the ElasticWindow algorithms
for input_ws in self._input_workspaces:
logger.information('Running ElasticWindow for workspace: {}'.format(input_ws.getName()))
progress.report('ElasticWindow for workspace: {}'.format(input_ws.getName()))
q_workspace, q2_workspace = ElasticWindow(InputWorkspace=input_ws,
IntegrationRangeStart=self._integration_range_start,
IntegrationRangeEnd=self._integration_range_end,
BackgroundRangeStart=self._background_range_start,
BackgroundRangeEnd=self._background_range_end,
OutputInQ="__q", OutputInQSquared="__q2",
StoreInADS=False, EnableLogging=False)
q2_workspace = Logarithm(InputWorkspace=q2_workspace, OutputWorkspace="__q2",
StoreInADS=False, EnableLogging=False)
q_workspaces.append(q_workspace)
q2_workspaces.append(q2_workspace)
# Get the run number
run_no = getInstrRun(input_ws.getName())[1]
run_numbers.append(run_no)
# Get the sample environment unit
sample, unit = self._get_sample_units(input_ws)
if sample is not None:
sample_param.append(sample)
else:
# No need to output a temperature workspace if there are no temperatures
self._elt_ws_name = ''
logger.information('Creating Q and Q^2 workspaces')
progress.report('Creating Q workspaces')
if self._input_size == 1:
q_workspace = q_workspaces[0]
q2_workspace = q2_workspaces[0]
else:
q_workspace = _append_all(q_workspaces)
q2_workspace = _append_all(q2_workspaces)
# Set the vertical axis units
v_axis_is_sample = self._input_size == len(sample_param)
if v_axis_is_sample:
logger.notice('Vertical axis is in units of {}'.format(unit))
unit = (self._sample_log_name, unit)
def axis_value(index):
return float(sample_param[index])
else:
logger.notice('Vertical axis is in run number')
unit = ('Run No', 'last 3 digits')
def axis_value(index):
return float(run_numbers[index][-3:])
# Create and set new vertical axis for the Q and Q**2 workspaces
_set_numeric_y_axis(q_workspace, self._input_size, unit, axis_value)
_set_numeric_y_axis(q2_workspace, self._input_size, unit, axis_value)
progress.report('Creating ELF workspaces')
# Process the ELF workspace
if self._elf_ws_name != '':
logger.information('Creating ELF workspace')
elf_workspace = _sort_x_axis(_transpose(q_workspace))
self.setProperty('OutputELF', elf_workspace)
# Do temperature normalisation
if self._elt_ws_name != '':
logger.information('Creating ELT workspace')
# If the ELF workspace was not created, create the ELT workspace
# from the Q workspace. Else, clone the ELF workspace.
if self._elf_ws_name == '':
elt_workspace = _sort_x_axis(_transpose(q_workspace))
else:
elt_workspace = CloneWorkspace(InputWorkspace=elf_workspace, OutputWorkspace="__cloned",
StoreInADS=False, EnableLogging=False)
_normalize_by_index(elt_workspace, np.argmin(sample_param))
self.setProperty('OutputELT', elt_workspace)
# Set the output workspace
self.setProperty('OutputInQ', q_workspace)
self.setProperty('OutputInQSquared', q2_workspace)
def PyExec(self):
from IndirectCommon import getInstrRun
# Do setup
self._setup()
# Lists of input and output workspaces
q_workspaces = list()
q2_workspaces = list()
run_numbers = list()
sample_param = list()
progress = Progress(self, 0.0, 0.05, 3)
# Perform the ElasticWindow algorithms
for input_ws in self._input_workspaces:
logger.information(
'Running ElasticWindow for workspace: {}'.format(
input_ws.name()))
progress.report('ElasticWindow for workspace: {}'.format(
input_ws.name()))
q_workspace, q2_workspace = ElasticWindow(
InputWorkspace=input_ws,
IntegrationRangeStart=self._integration_range_start,
IntegrationRangeEnd=self._integration_range_end,
BackgroundRangeStart=self._background_range_start,
BackgroundRangeEnd=self._background_range_end,
OutputInQ="__q",
OutputInQSquared="__q2",
StoreInADS=False,
EnableLogging=False)
q2_workspace = Logarithm(InputWorkspace=q2_workspace,
OutputWorkspace="__q2",
StoreInADS=False,
EnableLogging=False)
q_workspaces.append(q_workspace)
q2_workspaces.append(q2_workspace)
# Get the run number
run_no = getInstrRun(input_ws.name())[1]
run_numbers.append(run_no)
# Get the sample environment unit
sample, unit = self._get_sample_units(input_ws)
if sample is not None:
sample_param.append(sample)
else:
# No need to output a temperature workspace if there are no temperatures
self._elt_ws_name = ''
logger.information('Creating Q and Q^2 workspaces')
progress.report('Creating Q workspaces')
if self._input_size == 1:
q_workspace = q_workspaces[0]
q2_workspace = q2_workspaces[0]
else:
if not workspaces_have_same_size(
q_workspaces) or not workspaces_have_same_size(
q2_workspaces):
raise RuntimeError(
'The ElasticWindow algorithm produced differently sized workspaces. Please check '
'the input files are compatible.')
q_workspace = _append_all(q_workspaces)
q2_workspace = _append_all(q2_workspaces)
# Set the vertical axis units
v_axis_is_sample = self._input_size == len(sample_param)
if v_axis_is_sample:
logger.notice('Vertical axis is in units of {}'.format(unit))
unit = (self._sample_log_name, unit)
def axis_value(index):
return float(sample_param[index])
else:
logger.notice('Vertical axis is in run number')
unit = ('Run No', 'last 3 digits')
def axis_value(index):
return float(run_numbers[index][-3:])
# Create and set new vertical axis for the Q and Q**2 workspaces
_set_numeric_y_axis(q_workspace, self._input_size, unit, axis_value)
_set_numeric_y_axis(q2_workspace, self._input_size, unit, axis_value)
progress.report('Creating ELF workspaces')
# Process the ELF workspace
if self._elf_ws_name != '':
logger.information('Creating ELF workspace')
elf_workspace = _sort_x_axis(_transpose(q_workspace))
self.setProperty('OutputELF', elf_workspace)
# Do temperature normalisation
if self._elt_ws_name != '':
logger.information('Creating ELT workspace')
# If the ELF workspace was not created, create the ELT workspace
# from the Q workspace. Else, clone the ELF workspace.
if self._elf_ws_name == '':
elt_workspace = _sort_x_axis(_transpose(q_workspace))
else:
elt_workspace = CloneWorkspace(InputWorkspace=elf_workspace,
OutputWorkspace="__cloned",
StoreInADS=False,
EnableLogging=False)
_normalize_by_index(elt_workspace, 0)
self.setProperty('OutputELT', elt_workspace)
# Set the output workspace
self.setProperty('OutputInQ', q_workspace)
self.setProperty('OutputInQSquared', q2_workspace)
def PyExec(self):
from IndirectImport import import_mantidplot
from IndirectCommon import getInstrRun
# Do setup
self._setup()
logger.debug('in_ws:'+str(type(self._input_workspaces)))
# Get input workspaces
input_workspace_names = self._input_workspaces.getNames()
# Lists of input and output workspaces
q_workspaces = list()
q2_workspaces = list()
run_numbers = list()
temperatures = list()
# Perform the ElasticWindow algorithms
for input_ws in input_workspace_names:
logger.information('Running ElasticWindow for workspace: %s' % input_ws)
q_ws = '__' + input_ws + '_q'
q2_ws = '__' + input_ws + '_q2'
if self._background_range_start != Property.EMPTY_DBL and self._background_range_end != Property.EMPTY_DBL:
ElasticWindow(InputWorkspace=input_ws,
OutputInQ=q_ws,
OutputInQSquared=q2_ws,
IntegrationRangeStart=self._integration_range_start,
IntegrationRangeEnd=self._integration_range_end,
BackgroundRangeStart=self._background_range_start,
BackgroundRangeEnd=self._background_range_end)
else:
ElasticWindow(InputWorkspace=input_ws,
OutputInQ=q_ws,
OutputInQSquared=q2_ws,
IntegrationRangeStart=self._integration_range_start,
IntegrationRangeEnd=self._integration_range_end)
Logarithm(InputWorkspace=q2_ws,
OutputWorkspace=q2_ws)
q_workspaces.append(q_ws)
q2_workspaces.append(q2_ws)
# Get the run number
run_no = getInstrRun(input_ws)[1]
run_numbers.append(run_no)
# Get the sample temperature
temp = self._get_temperature(input_ws)
if temp is not None:
temperatures.append(temp)
else:
# No need to output a tmperature workspace if there are no temperatures
self._elt_workspace = ''
logger.information('Creating Q and Q^2 workspaces')
if len(input_workspace_names) == 1:
# Just rename single workspaces
RenameWorkspace(InputWorkspace=q_workspaces[0],
OutputWorkspace=self._q_workspace)
RenameWorkspace(InputWorkspace=q2_workspaces[0],
OutputWorkspace=self._q2_workspace)
else:
# Append the spectra of the first two workspaces
AppendSpectra(InputWorkspace1=q_workspaces[0],
InputWorkspace2=q_workspaces[1],
OutputWorkspace=self._q_workspace)
AppendSpectra(InputWorkspace1=q2_workspaces[0],
InputWorkspace2=q2_workspaces[1],
OutputWorkspace=self._q2_workspace)
# Append to the spectra of each remaining workspace
for idx in range(2, len(input_workspace_names)):
AppendSpectra(InputWorkspace1=self._q_workspace,
InputWorkspace2=q_workspaces[idx],
OutputWorkspace=self._q_workspace)
AppendSpectra(InputWorkspace1=self._q2_workspace,
InputWorkspace2=q2_workspaces[idx],
OutputWorkspace=self._q2_workspace)
# Delete the output workspaces from the ElasticWindow algorithms
for q_ws in q_workspaces:
DeleteWorkspace(q_ws)
for q2_ws in q2_workspaces:
DeleteWorkspace(q2_ws)
logger.information('Setting vertical axis units and values')
# Set the verical axis units
v_axis_is_temp = len(input_workspace_names) == len(temperatures)
if v_axis_is_temp:
logger.notice('Vertical axis is in temperature')
unit = ('Temperature', 'K')
else:
logger.notice('Vertical axis is in run number')
unit = ('Run No', 'last 3 digits')
# Create a new vertical axis for the Q and Q**2 workspaces
q_ws_axis = NumericAxis.create(len(input_workspace_names))
q_ws_axis.setUnit("Label").setLabel(unit[0], unit[1])
q2_ws_axis = NumericAxis.create(len(input_workspace_names))
q2_ws_axis.setUnit("Label").setLabel(unit[0], unit[1])
# Set the vertical axis values
for idx in range(0, len(input_workspace_names)):
if v_axis_is_temp:
q_ws_axis.setValue(idx, float(temperatures[idx]))
q2_ws_axis.setValue(idx, float(temperatures[idx]))
else:
q_ws_axis.setValue(idx, float(run_numbers[idx][-3:]))
q2_ws_axis.setValue(idx, float(run_numbers[idx][-3:]))
# Add the new vertical axis to each workspace
mtd[self._q_workspace].replaceAxis(1, q_ws_axis)
mtd[self._q2_workspace].replaceAxis(1, q2_ws_axis)
# Process the ELF workspace
if self._elf_workspace != '':
logger.information('Creating ELF workspace')
Transpose(InputWorkspace=self._q_workspace,
OutputWorkspace=self._elf_workspace)
SortXAxis(InputWorkspace=self._elf_workspace,
OutputWorkspace=self._elf_workspace)
self.setProperty('OutputELF', self._elf_workspace)
# Do temperature normalisation
if self._elt_workspace != '':
logger.information('Creating ELT workspace')
# If the ELT workspace was not already created then create it here,
# otherwise just clone it
if self._elf_workspace == '':
Transpose(InputWorkspace=self._q_workspace,
OutputWorkspace=self._elt_workspace)
SortXAxis(InputWorkspace=self._elt_workspace,
OutputWorkspace=self._elt_workspace)
else:
CloneWorkspace(InputWorkspace=self._elf_workspace,
OutputWorkspace=self._elt_workspace)
_normalize_to_lowest_temp(self._elt_workspace)
self.setProperty('OutputELT', self._elt_workspace)
# Set the output workspace
self.setProperty('OutputInQ', self._q_workspace)
self.setProperty('OutputInQSquared', self._q2_workspace)
# Plot spectra plots
if self._plot:
self._mtd_plot = import_mantidplot()
self._plot_spectra(self._q_workspace)
self._plot_spectra(self._q2_workspace)
if self._elf_workspace != '':
self._plot_spectra(self._elf_workspace)
if self._elt_workspace != '':
self._plot_spectra(self._elt_workspace)
def PyExec(self):
from IndirectCommon import getInstrRun
# Do setup
self._setup()
# Get input workspaces
input_workspace_names = self._input_workspaces.getNames()
# Lists of input and output workspaces
q_workspaces = list()
q2_workspaces = list()
run_numbers = list()
sample_param = list()
progress = Progress(self, 0.0, 0.05, 3)
# Perform the ElasticWindow algorithms
for input_ws in input_workspace_names:
logger.information('Running ElasticWindow for workspace: %s' % input_ws)
progress.report('ElasticWindow for workspace: %s' % input_ws)
q_ws = '__' + input_ws + '_q'
q2_ws = '__' + input_ws + '_q2'
elwin_alg = self.createChildAlgorithm("ElasticWindow", enableLogging=False)
elwin_alg.setProperty("InputWorkspace", input_ws)
elwin_alg.setProperty("IntegrationRangeStart", self._integration_range_start)
elwin_alg.setProperty("IntegrationRangeEnd", self._integration_range_end)
elwin_alg.setProperty("OutputInQ", q_ws)
elwin_alg.setProperty("OutputInQSquared", q2_ws)
if self._background_range_start != Property.EMPTY_DBL and self._background_range_end != Property.EMPTY_DBL:
elwin_alg.setProperty("BackgroundRangeStart", self._background_range_start)
elwin_alg.setProperty("BackgroundRangeEnd", self._background_range_end)
elwin_alg.execute()
log_alg = self.createChildAlgorithm("Logarithm", enableLogging=False)
log_alg.setProperty("InputWorkspace", elwin_alg.getProperty("OutputInQSquared").value)
log_alg.setProperty("OutputWorkspace", q2_ws)
log_alg.execute()
q_workspaces.append(elwin_alg.getProperty("OutputInQ").value)
q2_workspaces.append(log_alg.getProperty("OutputWorkspace").value)
# Get the run number
run_no = getInstrRun(input_ws)[1]
run_numbers.append(run_no)
# Get the sample environment unit
sample, unit = self._get_sample_units(input_ws)
if sample is not None:
sample_param.append(sample)
else:
# No need to output a temperature workspace if there are no temperatures
self._elt_ws_name = ''
logger.information('Creating Q and Q^2 workspaces')
progress.report('Creating Q workspaces')
if len(input_workspace_names) == 1:
# Just rename single workspaces
self._q_workspace = elwin_alg.getProperty("OutputInQ").value
self._q2_workspace = log_alg.getProperty("OutputWorkspace").value
else:
# Append the spectra of the first two workspaces
append_alg = self.createChildAlgorithm("AppendSpectra", enableLogging=False)
append_alg.setProperty("InputWorkspace1", q_workspaces[0])
append_alg.setProperty("InputWorkspace2", q_workspaces[1])
append_alg.setProperty("OutputWorkspace", self._q_workspace)
append_alg.execute()
self._q_workspace = append_alg.getProperty("OutputWorkspace").value
append_alg.setProperty("InputWorkspace1", q2_workspaces[0])
append_alg.setProperty("InputWorkspace2", q2_workspaces[1])
append_alg.setProperty("OutputWorkspace", self._q2_workspace)
append_alg.execute()
self._q2_workspace = append_alg.getProperty("OutputWorkspace").value
# Append to the spectra of each remaining workspace
for idx in range(2, len(input_workspace_names)):
append_alg.setProperty("InputWorkspace1", self._q_workspace)
append_alg.setProperty("InputWorkspace2", q_workspaces[idx])
append_alg.setProperty("OutputWorkspace", self._q_workspace)
append_alg.execute()
self._q_workspace = append_alg.getProperty("OutputWorkspace").value
append_alg.setProperty("InputWorkspace1", self._q2_workspace)
append_alg.setProperty("InputWorkspace2", q2_workspaces[idx])
append_alg.setProperty("OutputWorkspace", self._q2_workspace)
append_alg.execute()
self._q2_workspace = append_alg.getProperty("OutputWorkspace").value
# Set the vertical axis units
v_axis_is_sample = len(input_workspace_names) == len(sample_param)
if v_axis_is_sample:
logger.notice('Vertical axis is in units of %s' % unit)
unit = (self._sample_log_name, unit)
else:
logger.notice('Vertical axis is in run number')
unit = ('Run No', 'last 3 digits')
# Create a new vertical axis for the Q and Q**2 workspaces
q_ws_axis = NumericAxis.create(len(input_workspace_names))
q_ws_axis.setUnit("Label").setLabel(unit[0], unit[1])
q2_ws_axis = NumericAxis.create(len(input_workspace_names))
q2_ws_axis.setUnit("Label").setLabel(unit[0], unit[1])
# Set the vertical axis values
for idx in range(0, len(input_workspace_names)):
if v_axis_is_sample:
q_ws_axis.setValue(idx, float(sample_param[idx]))
q2_ws_axis.setValue(idx, float(sample_param[idx]))
else:
q_ws_axis.setValue(idx, float(run_numbers[idx][-3:]))
q2_ws_axis.setValue(idx, float(run_numbers[idx][-3:]))
# Add the new vertical axis to each workspace
self._q_workspace.replaceAxis(1, q_ws_axis)
self._q2_workspace.replaceAxis(1, q2_ws_axis)
progress.report('Creating ELF workspaces')
transpose_alg = self.createChildAlgorithm("Transpose", enableLogging=False)
sort_alg = self.createChildAlgorithm("SortXAxis", enableLogging=False)
# Process the ELF workspace
if self._elf_ws_name != '':
logger.information('Creating ELF workspace')
transpose_alg.setProperty("InputWorkspace", self._q_workspace)
transpose_alg.setProperty("OutputWorkspace", self._elf_ws_name)
transpose_alg.execute()
sort_alg.setProperty("InputWorkspace", transpose_alg.getProperty("OutputWorkspace").value)
sort_alg.setProperty("OutputWorkspace", self._elf_ws_name)
sort_alg.execute()
self.setProperty('OutputELF', sort_alg.getProperty("OutputWorkspace").value)
# Do temperature normalisation
if self._elt_ws_name != '':
logger.information('Creating ELT workspace')
# If the ELF workspace was not created, create the ELT workspace
# from the Q workspace. Else, clone the ELF workspace.
if self._elf_ws_name == '':
transpose_alg.setProperty("InputWorkspace", self._q_workspace)
transpose_alg.setProperty("OutputWorkspace", self._elt_ws_name)
transpose_alg.execute()
sort_alg.setProperty("InputWorkspace", self._elt_ws_name)
sort_alg.setProperty("OutputWorkspace", self._elt_ws_name)
sort_alg.execute()
elt_workspace = sort_alg.getProperty("OutputWorkspace").value
else:
clone_alg = self.createChildAlgorithm("CloneWorkspace", enableLogging=False)
clone_alg.setProperty("InputWorkspace", self.getProperty("OutputELF").value)
clone_alg.setProperty("OutputWorkspace", self._elt_ws_name)
clone_alg.execute()
elt_workspace = clone_alg.getProperty("OutputWorkspace").value
_normalize_by_index(elt_workspace, np.argmin(sample_param))
self.setProperty('OutputELT', elt_workspace)
# Set the output workspace
self.setProperty('OutputInQ', self._q_workspace)
self.setProperty('OutputInQSquared', self._q2_workspace)
def _get_sample_units(self, ws_name):
"""
Gets the sample environment units for a given workspace.
@param ws_name Name of workspace
@returns sample in given units or None if not found
"""
from IndirectCommon import getInstrRun
instr, run_number = getInstrRun(ws_name)
facility = config.getFacility()
pad_num = facility.instrument(instr).zeroPadding(int(run_number))
zero_padding = '0' * (pad_num - len(run_number))
run_name = instr + zero_padding + run_number
log_filename = run_name.upper() + '.log'
run = mtd[ws_name].getRun()
if self._sample_log_name == 'Position':
# Look for sample changer position in logs in workspace
if self._sample_log_name in run:
tmp = run[self._sample_log_name].value
value_action = {'last_value': lambda x: x[-1],
'average': lambda x: x.mean()}
position = value_action['last_value'](tmp)
if position == 0:
self._sample_log_name = 'Bot_Can_Top'
if position == 1:
self._sample_log_name = 'Middle_Can_Top'
if position == 2:
self._sample_log_name = 'Top_Can_Top'
else:
logger.information('Position not found in workspace.')
if self._sample_log_name in run:
# Look for sample unit in logs in workspace
tmp = run[self._sample_log_name].value
value_action = {'last_value': lambda x: x[-1],
'average': lambda x: x.mean()}
sample = value_action[self._sample_log_value](tmp)
unit = run[self._sample_log_name].units
logger.information('%d %s found for run: %s' % (sample, unit, run_name))
return sample, unit
else:
# Logs not in workspace, try loading from file
logger.information('Log parameter not found in workspace. Searching for log file.')
log_path = FileFinder.getFullPath(log_filename)
if log_path != '':
# Get temperature from log file
LoadLog(Workspace=ws_name, Filename=log_path)
run_logs = mtd[ws_name].getRun()
if self._sample_log_name in run_logs:
tmp = run_logs[self._sample_log_name].value
sample = tmp[len(tmp) - 1]
unit = run[self._sample_log_name].units
logger.debug('%d %s found for run: %s' % (sample, unit, run_name))
return sample, unit
else:
logger.warning('Log entry %s for run %s not found' % (self._sample_log_name, run_name))
else:
logger.warning('Log file for run %s not found' % run_name)
# Can't find log file
logger.warning('No sample units found for run: %s' % run_name)
return None, None
def _get_sample_units(self, ws_name):
"""
Gets the sample environment units for a given workspace.
@param ws_name Name of workspace
@returns sample in given units or None if not found
"""
from IndirectCommon import getInstrRun
instr, run_number = getInstrRun(ws_name)
facility = config.getFacility()
pad_num = facility.instrument(instr).zeroPadding(int(run_number))
zero_padding = '0' * (pad_num - len(run_number))
run_name = instr + zero_padding + run_number
log_filename = run_name.upper() + '.log'
run = mtd[ws_name].getRun()
if self._sample_log_name == 'Position':
# Look for sample changer position in logs in workspace
if self._sample_log_name in run:
tmp = run[self._sample_log_name].value
value_action = {
'last_value': lambda x: x[-1],
'average': lambda x: x.mean()
}
position = value_action['last_value'](tmp)
if position == 0:
self._sample_log_name = 'Bot_Can_Top'
if position == 1:
self._sample_log_name = 'Middle_Can_Top'
if position == 2:
self._sample_log_name = 'Top_Can_Top'
else:
logger.information('Position not found in workspace.')
if self._sample_log_name in run:
# Look for sample unit in logs in workspace
tmp = run[self._sample_log_name].value
value_action = {
'last_value': lambda x: x[-1],
'average': lambda x: x.mean()
}
sample = value_action[self._sample_log_value](tmp)
unit = run[self._sample_log_name].units
logger.information('%d %s found for run: %s' %
(sample, unit, run_name))
return sample, unit
else:
# Logs not in workspace, try loading from file
logger.information(
'Log parameter not found in workspace. Searching for log file.'
)
log_path = FileFinder.getFullPath(log_filename)
if log_path != '':
# Get temperature from log file
LoadLog(Workspace=ws_name, Filename=log_path)
run_logs = mtd[ws_name].getRun()
if self._sample_log_name in run_logs:
tmp = run_logs[self._sample_log_name].value
sample = tmp[len(tmp) - 1]
unit = run[self._sample_log_name].units
logger.debug('%d %s found for run: %s' %
(sample, unit, run_name))
return sample, unit
else:
logger.warning('Log entry %s for run %s not found' %
(self._sample_log_name, run_name))
else:
logger.warning('Log file for run %s not found' % run_name)
# Can't find log file
logger.warning('No sample units found for run: %s' % run_name)
return None, None
def PyExec(self):
from IndirectCommon import getInstrRun
# Do setup
self._setup()
# Get input workspaces
input_workspace_names = self._input_workspaces.getNames()
# Lists of input and output workspaces
q_workspaces = list()
q2_workspaces = list()
run_numbers = list()
sample_param = list()
progress = Progress(self, 0.0, 0.05, 3)
# Perform the ElasticWindow algorithms
for input_ws in input_workspace_names:
logger.information('Running ElasticWindow for workspace: %s' %
input_ws)
progress.report('ElasticWindow for workspace: %s' % input_ws)
q_ws = '__' + input_ws + '_q'
q2_ws = '__' + input_ws + '_q2'
elwin_alg = self.createChildAlgorithm("ElasticWindow",
enableLogging=False)
elwin_alg.setProperty("InputWorkspace", input_ws)
elwin_alg.setProperty("IntegrationRangeStart",
self._integration_range_start)
elwin_alg.setProperty("IntegrationRangeEnd",
self._integration_range_end)
elwin_alg.setProperty("OutputInQ", q_ws)
elwin_alg.setProperty("OutputInQSquared", q2_ws)
if self._background_range_start != Property.EMPTY_DBL and self._background_range_end != Property.EMPTY_DBL:
elwin_alg.setProperty("BackgroundRangeStart",
self._background_range_start)
elwin_alg.setProperty("BackgroundRangeEnd",
self._background_range_end)
elwin_alg.execute()
log_alg = self.createChildAlgorithm("Logarithm",
enableLogging=False)
log_alg.setProperty(
"InputWorkspace",
elwin_alg.getProperty("OutputInQSquared").value)
log_alg.setProperty("OutputWorkspace", q2_ws)
log_alg.execute()
q_workspaces.append(elwin_alg.getProperty("OutputInQ").value)
q2_workspaces.append(log_alg.getProperty("OutputWorkspace").value)
# Get the run number
run_no = getInstrRun(input_ws)[1]
run_numbers.append(run_no)
# Get the sample environment unit
sample, unit = self._get_sample_units(input_ws)
if sample is not None:
sample_param.append(sample)
else:
# No need to output a temperature workspace if there are no temperatures
self._elt_ws_name = ''
logger.information('Creating Q and Q^2 workspaces')
progress.report('Creating Q workspaces')
if len(input_workspace_names) == 1:
# Just rename single workspaces
self._q_workspace = elwin_alg.getProperty("OutputInQ").value
self._q2_workspace = log_alg.getProperty("OutputWorkspace").value
else:
# Append the spectra of the first two workspaces
append_alg = self.createChildAlgorithm("AppendSpectra",
enableLogging=False)
append_alg.setProperty("InputWorkspace1", q_workspaces[0])
append_alg.setProperty("InputWorkspace2", q_workspaces[1])
append_alg.setProperty("OutputWorkspace", self._q_workspace)
append_alg.execute()
self._q_workspace = append_alg.getProperty("OutputWorkspace").value
append_alg.setProperty("InputWorkspace1", q2_workspaces[0])
append_alg.setProperty("InputWorkspace2", q2_workspaces[1])
append_alg.setProperty("OutputWorkspace", self._q2_workspace)
append_alg.execute()
self._q2_workspace = append_alg.getProperty(
"OutputWorkspace").value
# Append to the spectra of each remaining workspace
for idx in range(2, len(input_workspace_names)):
append_alg.setProperty("InputWorkspace1", self._q_workspace)
append_alg.setProperty("InputWorkspace2", q_workspaces[idx])
append_alg.setProperty("OutputWorkspace", self._q_workspace)
append_alg.execute()
self._q_workspace = append_alg.getProperty(
"OutputWorkspace").value
append_alg.setProperty("InputWorkspace1", self._q2_workspace)
append_alg.setProperty("InputWorkspace2", q2_workspaces[idx])
append_alg.setProperty("OutputWorkspace", self._q2_workspace)
append_alg.execute()
self._q2_workspace = append_alg.getProperty(
"OutputWorkspace").value
# Set the vertical axis units
v_axis_is_sample = len(input_workspace_names) == len(sample_param)
if v_axis_is_sample:
logger.notice('Vertical axis is in units of %s' % unit)
unit = (self._sample_log_name, unit)
else:
logger.notice('Vertical axis is in run number')
unit = ('Run No', 'last 3 digits')
# Create a new vertical axis for the Q and Q**2 workspaces
q_ws_axis = NumericAxis.create(len(input_workspace_names))
q_ws_axis.setUnit("Label").setLabel(unit[0], unit[1])
q2_ws_axis = NumericAxis.create(len(input_workspace_names))
q2_ws_axis.setUnit("Label").setLabel(unit[0], unit[1])
# Set the vertical axis values
for idx in range(0, len(input_workspace_names)):
if v_axis_is_sample:
q_ws_axis.setValue(idx, float(sample_param[idx]))
q2_ws_axis.setValue(idx, float(sample_param[idx]))
else:
q_ws_axis.setValue(idx, float(run_numbers[idx][-3:]))
q2_ws_axis.setValue(idx, float(run_numbers[idx][-3:]))
# Add the new vertical axis to each workspace
self._q_workspace.replaceAxis(1, q_ws_axis)
self._q2_workspace.replaceAxis(1, q2_ws_axis)
progress.report('Creating ELF workspaces')
transpose_alg = self.createChildAlgorithm("Transpose",
enableLogging=False)
sort_alg = self.createChildAlgorithm("SortXAxis", enableLogging=False)
# Process the ELF workspace
if self._elf_ws_name != '':
logger.information('Creating ELF workspace')
transpose_alg.setProperty("InputWorkspace", self._q_workspace)
transpose_alg.setProperty("OutputWorkspace", self._elf_ws_name)
transpose_alg.execute()
sort_alg.setProperty(
"InputWorkspace",
transpose_alg.getProperty("OutputWorkspace").value)
sort_alg.setProperty("OutputWorkspace", self._elf_ws_name)
sort_alg.execute()
self.setProperty('OutputELF',
sort_alg.getProperty("OutputWorkspace").value)
# Do temperature normalisation
if self._elt_ws_name != '':
logger.information('Creating ELT workspace')
# If the ELF workspace was not created, create the ELT workspace
# from the Q workspace. Else, clone the ELF workspace.
if self._elf_ws_name == '':
transpose_alg.setProperty("InputWorkspace", self._q_workspace)
transpose_alg.setProperty("OutputWorkspace", self._elt_ws_name)
transpose_alg.execute()
sort_alg.setProperty("InputWorkspace", self._elt_ws_name)
sort_alg.setProperty("OutputWorkspace", self._elt_ws_name)
sort_alg.execute()
elt_workspace = sort_alg.getProperty("OutputWorkspace").value
else:
clone_alg = self.createChildAlgorithm("CloneWorkspace",
enableLogging=False)
clone_alg.setProperty("InputWorkspace",
self.getProperty("OutputELF").value)
clone_alg.setProperty("OutputWorkspace", self._elt_ws_name)
clone_alg.execute()
elt_workspace = clone_alg.getProperty("OutputWorkspace").value
_normalize_by_index(elt_workspace, np.argmin(sample_param))
self.setProperty('OutputELT', elt_workspace)
# Set the output workspace
self.setProperty('OutputInQ', self._q_workspace)
self.setProperty('OutputInQSquared', self._q2_workspace)