def PyExec(self):
# Get peaks in dSpacing from file, and check we have what we need, before doing anything
expectedPeaksD = EnggUtils.read_in_expected_peaks(self.getPropertyValue("ExpectedPeaksFromFile"),
self.getProperty('ExpectedPeaks').value)
if len(expectedPeaksD) < 1:
raise ValueError("Cannot run this algorithm without any input expected peaks")
inWS = self.getProperty('Workspace').value
WSIndices = EnggUtils.getWsIndicesFromInProperties(inWS, self.getProperty('Bank').value,
self.getProperty(self.INDICES_PROP_NAME).value)
vanWS = self.getProperty("VanadiumWorkspace").value
vanIntegWS = self.getProperty('VanIntegrationWorkspace').value
vanCurvesWS = self.getProperty('VanCurvesWorkspace').value
# These corrections rely on ToF<->Dspacing conversions, so ideally they'd be done after the
# calibration step, which creates a cycle / chicken-and-egg issue.
EnggUtils.applyVanadiumCorrections(self, inWS, WSIndices, vanWS, vanIntegWS, vanCurvesWS)
rebinnedWS = self._prepareWsForFitting(inWS)
posTbl = self._calculateCalibPositionsTbl(rebinnedWS, WSIndices, expectedPeaksD)
# Produce 2 results: 'output table' and 'apply calibration' + (optional) calibration file
self.setProperty("OutDetPosTable", posTbl)
self._applyCalibrationTable(inWS, posTbl)
self._outputDetPosFile(self.getPropertyValue('OutDetPosFilename'), posTbl)
def PyExec(self):
import EnggUtils
# Get peaks in dSpacing from file
expectedPeaksD = EnggUtils.read_in_expected_peaks(
self.getPropertyValue("ExpectedPeaksFromFile"), self.getProperty("ExpectedPeaks").value
)
prog = Progress(self, start=0, end=1, nreports=2)
prog.report("Focusing the input workspace")
focussed_ws = self._focus_run(
self.getProperty("InputWorkspace").value,
self.getProperty("VanadiumWorkspace").value,
self.getProperty("Bank").value,
self.getProperty(self.INDICES_PROP_NAME).value,
)
if len(expectedPeaksD) < 1:
raise ValueError("Cannot run this algorithm without any input expected peaks")
prog.report("Fitting parameters for the focused run")
difc, zero, fitted_peaks = self._fit_params(focussed_ws, expectedPeaksD)
self.log().information(
"Fitted {0} peaks. Resulting difc: {1}, tzero: {2}".format(fitted_peaks.rowCount(), difc, zero)
)
self.log().information(
"Peaks fitted: {0}, centers in ToF: {1}".format(fitted_peaks.column("dSpacing"), fitted_peaks.column("X0"))
)
self._produce_outputs(difc, zero, fitted_peaks)
def PyExec(self):
import EnggUtils
max_reports = 20
prog = Progress(self, start=0, end=1, nreports=max_reports)
# Get peaks in dSpacing from file
prog.report("Reading peaks")
expected_peaks_dsp = EnggUtils.read_in_expected_peaks(filename=self.getPropertyValue("ExpectedPeaksFromFile"),
expected_peaks=self.getProperty('ExpectedPeaks').value)
if len(expected_peaks_dsp) < 1:
raise ValueError("Cannot run this algorithm without any input expected peaks")
prog.report('Focusing the input workspace')
focused_ws = self._focus_run(self.getProperty('InputWorkspace').value,
self.getProperty("VanadiumWorkspace").value,
self.getProperty('Bank').value,
self.getProperty(self.INDICES_PROP_NAME).value,
prog)
prog.report('Fitting parameters for the focused run')
difa, difc, zero, fitted_peaks = self._fit_params(focused_ws, expected_peaks_dsp, prog)
self.log().information("Fitted {0} peaks. Resulting DIFA: {1}, DIFC: {2}, TZERO: {3}".
format(fitted_peaks.rowCount(), difa, difc, zero))
self.log().information("Peaks fitted: {0}, centers in ToF: {1}".
format(fitted_peaks.column("dSpacing"),
fitted_peaks.column("X0")))
prog.report("Producing outputs")
self._produce_outputs(difa, difc, zero, fitted_peaks)
prog.report(max_reports, "Calibration complete")
def PyExec(self):
# Get peaks in dSpacing from file, and check we have what we need, before doing anything
expected_peaks_d = EnggUtils.read_in_expected_peaks(self.getPropertyValue("ExpectedPeaksFromFile"),
self.getProperty('ExpectedPeaks').value)
if len(expected_peaks_d) < 1:
raise ValueError("Cannot run this algorithm without any input expected peaks")
in_wks = self.getProperty('Workspace').value
wks_indices = EnggUtils.get_ws_indices_from_input_properties(in_wks, self.getProperty('Bank').value,
self.getProperty(self.INDICES_PROP_NAME).value)
van_wks = self.getProperty("VanadiumWorkspace").value
van_integ_wks = self.getProperty('VanIntegrationWorkspace').value
van_curves_wks = self.getProperty('VanCurvesWorkspace').value
# These corrections rely on ToF<->Dspacing conversions, so ideally they'd be done after the
# calibration step, which creates a cycle / chicken-and-egg issue.
EnggUtils.apply_vanadium_corrections(self, in_wks, wks_indices, van_wks, van_integ_wks, van_curves_wks)
rebinned_ws = self._prepare_ws_for_fitting(in_wks, self.getProperty('RebinBinWidth').value)
pos_tbl, peaks_tbl = self._calculate_calib_positions_tbl(rebinned_ws, wks_indices, expected_peaks_d)
# Produce 2 results: 'output table' and 'apply calibration' + (optional) calibration file
self.setProperty("OutDetPosTable", pos_tbl)
self.setProperty("FittedPeaks", peaks_tbl)
self._apply_calibration_table(in_wks, pos_tbl)
self._output_det_pos_file(self.getPropertyValue('OutDetPosFilename'), pos_tbl)
def PyExec(self):
# Get peaks in dSpacing from file, and check we have what we need, before doing anything
expected_peaks_d = EnggUtils.read_in_expected_peaks(self.getPropertyValue("ExpectedPeaksFromFile"),
self.getProperty('ExpectedPeaks').value)
if len(expected_peaks_d) < 1:
raise ValueError("Cannot run this algorithm without any input expected peaks")
in_wks = self.getProperty('Workspace').value
wks_indices = EnggUtils.get_ws_indices_from_input_properties(in_wks, self.getProperty('Bank').value,
self.getProperty(self.INDICES_PROP_NAME).value)
van_wks = self.getProperty("VanadiumWorkspace").value
van_integ_wks = self.getProperty('VanIntegrationWorkspace').value
van_curves_wks = self.getProperty('VanCurvesWorkspace').value
# These corrections rely on ToF<->Dspacing conversions, so ideally they'd be done after the
# calibration step, which creates a cycle / chicken-and-egg issue.
EnggUtils.apply_vanadium_corrections(self, in_wks, wks_indices, van_wks, van_integ_wks, van_curves_wks)
rebinned_ws = self._prepare_ws_for_fitting(in_wks, self.getProperty('RebinBinWidth').value)
pos_tbl, peaks_tbl = self._calculate_calib_positions_tbl(rebinned_ws, wks_indices, expected_peaks_d)
# Produce 2 results: 'output table' and 'apply calibration' + (optional) calibration file
self.setProperty("OutDetPosTable", pos_tbl)
self.setProperty("FittedPeaks", peaks_tbl)
self._apply_calibration_table(in_wks, pos_tbl)
self._output_det_pos_file(self.getPropertyValue('OutDetPosFilename'), pos_tbl)
def PyExec(self):
import EnggUtils
# Get peaks in dSpacing from file
expected_peaks_dsp = EnggUtils.read_in_expected_peaks(
self.getPropertyValue("ExpectedPeaksFromFile"),
self.getProperty('ExpectedPeaks').value)
if len(expected_peaks_dsp) < 1:
raise ValueError(
"Cannot run this algorithm without any input expected peaks")
prog = Progress(self, start=0, end=1, nreports=2)
prog.report('Focusing the input workspace')
focussed_ws = self._focus_run(
self.getProperty('InputWorkspace').value,
self.getProperty("VanadiumWorkspace").value,
self.getProperty('Bank').value,
self.getProperty(self.INDICES_PROP_NAME).value)
prog.report('Fitting parameters for the focused run')
difa, difc, zero, fitted_peaks = self._fit_params(
focussed_ws, expected_peaks_dsp)
self.log().information(
"Fitted {0} peaks. Resulting DIFA: {1}, DIFC: {2}, TZERO: {3}".
format(fitted_peaks.rowCount(), difa, difc, zero))
self.log().information("Peaks fitted: {0}, centers in ToF: {1}".format(
fitted_peaks.column("dSpacing"), fitted_peaks.column("X0")))
self._produce_outputs(difa, difc, zero, fitted_peaks)
def PyExec(self):
import EnggUtils
# Get peaks in dSpacing from file
expected_peaks_dsp = EnggUtils.read_in_expected_peaks(self.getPropertyValue("ExpectedPeaksFromFile"),
self.getProperty('ExpectedPeaks').value)
if len(expected_peaks_dsp) < 1:
raise ValueError("Cannot run this algorithm without any input expected peaks")
# Get expected peaks in TOF for the detector
in_wks = self.getProperty("InputWorkspace").value
dimType = in_wks.getXDimension().getName()
if self.EXPECTED_DIM_TYPE != dimType:
raise ValueError("This algorithm expects a workspace with %s X dimension, but "
"the X dimension of the input workspace is: '%s'" % (self.EXPECTED_DIM_TYPE, dimType))
wks_index = self.getProperty("WorkspaceIndex").value
# FindPeaks will return a list of peaks sorted by the centre found. Sort the peaks as well,
# so we can match them with fitted centres later.
expected_peaks_ToF = sorted(self._expected_peaks_in_ToF(expected_peaks_dsp, in_wks, wks_index))
found_peaks = self._peaks_from_find_peaks(in_wks, expected_peaks_ToF, wks_index)
if found_peaks.rowCount() < len(expected_peaks_ToF):
txt = "Peaks effectively found: " + str(found_peaks)[1:-1]
self.log().warning("Some peaks from the list of expected peaks were not found by the algorithm "
"FindPeaks which this algorithm uses to check that the data has the the "
"expected peaks. " + txt)
peaks_table_name = self.getPropertyValue("OutFittedPeaksTable")
difc, zero, fitted_peaks = self._fit_all_peaks(in_wks, wks_index,
(found_peaks, expected_peaks_dsp), peaks_table_name)
self._produce_outputs(difc, zero, fitted_peaks)
def PyExec(self):
import EnggUtils
# Get peaks in dSpacing from file
expected_peaks = EnggUtils.read_in_expected_peaks(
self.getPropertyValue("ExpectedPeaksFromFile"),
self.getProperty('ExpectedPeaks').value)
if len(expected_peaks) < 1:
raise ValueError(
"Cannot run this algorithm without any input expected peaks")
# Get expected peaks in TOF for the detector
in_wks = self.getProperty("InputWorkspace").value
dim_type = in_wks.getXDimension().name
if self.EXPECTED_DIM_TYPE != dim_type:
raise ValueError(
"This algorithm expects a workspace with %s X dimension, but "
"the X dimension of the input workspace is: '%s'" %
(self.EXPECTED_DIM_TYPE, dim_type))
wks_index = self.getProperty("WorkspaceIndex").value
if self._any_expected_peaks_in_ws_range(in_wks, expected_peaks):
expected_peaks_tof = sorted(expected_peaks)
else:
expected_peaks_tof = sorted(
self._expected_peaks_in_tof(expected_peaks, in_wks, wks_index))
self._expected_peaks_are_in_tof = False
if not self._any_expected_peaks_in_ws_range(
in_wks, expected_peaks_tof):
raise ValueError(
"Expected peak centres lie outside the limits of the workspace x axis"
)
found_peaks = self._peaks_from_find_peaks(in_wks, expected_peaks_tof,
wks_index)
if found_peaks.rowCount() < len(expected_peaks_tof):
txt = "Peaks effectively found: " + str(found_peaks)[1:-1]
self.log().warning(
"Some peaks from the list of expected peaks were not found by the algorithm "
"FindPeaks which this algorithm uses to check that the data has the the "
"expected peaks. " + txt)
peaks_table_name = self.getPropertyValue("OutFittedPeaksTable")
fitted_peaks = self._fit_all_peaks(in_wks, wks_index,
(found_peaks, expected_peaks),
peaks_table_name)
# mandatory output
self.setProperty('FittedPeaks', fitted_peaks)
def PyExec(self):
import EnggUtils
# Get peaks in dSpacing from file
expected_peaks_dsp = EnggUtils.read_in_expected_peaks(
self.getPropertyValue("ExpectedPeaksFromFile"),
self.getProperty('ExpectedPeaks').value)
if len(expected_peaks_dsp) < 1:
raise ValueError(
"Cannot run this algorithm without any input expected peaks")
# Get expected peaks in TOF for the detector
in_wks = self.getProperty("InputWorkspace").value
dimType = in_wks.getXDimension().getName()
if self.EXPECTED_DIM_TYPE != dimType:
raise ValueError(
"This algorithm expects a workspace with %s X dimension, but "
"the X dimension of the input workspace is: '%s'" %
(self.EXPECTED_DIM_TYPE, dimType))
wks_index = self.getProperty("WorkspaceIndex").value
# FindPeaks will return a list of peaks sorted by the centre found. Sort the peaks as well,
# so we can match them with fitted centres later.
expected_peaks_ToF = sorted(
self._expected_peaks_in_ToF(expected_peaks_dsp, in_wks, wks_index))
found_peaks = self._peaks_from_find_peaks(in_wks, expected_peaks_ToF,
wks_index)
if found_peaks.rowCount() < len(expected_peaks_ToF):
txt = "Peaks effectively found: " + str(found_peaks)[1:-1]
self.log().warning(
"Some peaks from the list of expected peaks were not found by the algorithm "
"FindPeaks which this algorithm uses to check that the data has the the "
"expected peaks. " + txt)
peaks_table_name = self.getPropertyValue("OutFittedPeaksTable")
fitted_peaks = self._fit_all_peaks(in_wks, wks_index,
(found_peaks, expected_peaks_dsp),
peaks_table_name)
# mandatory output
self.setProperty('FittedPeaks', fitted_peaks)
def PyExec(self):
import EnggUtils
# Get peaks in dSpacing from file
expected_peaks = EnggUtils.read_in_expected_peaks(self.getPropertyValue("ExpectedPeaksFromFile"),
self.getProperty('ExpectedPeaks').value)
if len(expected_peaks) < 1:
raise ValueError("Cannot run this algorithm without any input expected peaks")
# Get expected peaks in TOF for the detector
in_wks = self.getProperty("InputWorkspace").value
dim_type = in_wks.getXDimension().name
if self.EXPECTED_DIM_TYPE != dim_type:
raise ValueError("This algorithm expects a workspace with %s X dimension, but "
"the X dimension of the input workspace is: '%s'" % (self.EXPECTED_DIM_TYPE, dim_type))
wks_index = self.getProperty("WorkspaceIndex").value
if self._any_expected_peaks_in_ws_range(in_wks, expected_peaks):
expected_peaks_tof = sorted(expected_peaks)
else:
expected_peaks_tof = sorted(self._expected_peaks_in_tof(expected_peaks, in_wks, wks_index))
self._expected_peaks_are_in_tof = False
if not self._any_expected_peaks_in_ws_range(in_wks, expected_peaks_tof):
raise ValueError("Expected peak centres lie outside the limits of the workspace x axis")
found_peaks = self._peaks_from_find_peaks(in_wks, expected_peaks_tof, wks_index)
if found_peaks.rowCount() < len(expected_peaks_tof):
txt = "Peaks effectively found: " + str(found_peaks)[1:-1]
self.log().warning("Some peaks from the list of expected peaks were not found by the algorithm "
"FindPeaks which this algorithm uses to check that the data has the the "
"expected peaks. " + txt)
peaks_table_name = self.getPropertyValue("OutFittedPeaksTable")
fitted_peaks = self._fit_all_peaks(in_wks, wks_index,
(found_peaks, expected_peaks), peaks_table_name)
# mandatory output
self.setProperty('FittedPeaks', fitted_peaks)
def PyExec(self):
mantid.logger.warning(
"EnggCalibrate is deprecated as of May 2021. Please use PDCalibration instead."
)
import EnggUtils
max_reports = 20
prog = Progress(self, start=0, end=1, nreports=max_reports)
# Get peaks in dSpacing from file
prog.report("Reading peaks")
expected_peaks_dsp = EnggUtils.read_in_expected_peaks(
filename=self.getPropertyValue("ExpectedPeaksFromFile"),
expected_peaks=self.getProperty('ExpectedPeaks').value)
if len(expected_peaks_dsp) < 1:
raise ValueError(
"Cannot run this algorithm without any input expected peaks")
prog.report('Focusing the input workspace')
focused_ws = self._focus_run(
self.getProperty('InputWorkspace').value,
self.getProperty("VanadiumWorkspace").value,
self.getProperty('Bank').value,
self.getProperty(self.INDICES_PROP_NAME).value, prog)
prog.report('Fitting parameters for the focused run')
difa, difc, zero, fitted_peaks = self._fit_params(
focused_ws, expected_peaks_dsp, prog)
self.log().information(
"Fitted {0} peaks. Resulting DIFA: {1}, DIFC: {2}, TZERO: {3}".
format(fitted_peaks.rowCount(), difa, difc, zero))
self.log().information("Peaks fitted: {0}, centers in ToF: {1}".format(
fitted_peaks.column("dSpacing"), fitted_peaks.column("X0")))
prog.report("Producing outputs")
self._produce_outputs(difa, difc, zero, fitted_peaks)
prog.report(max_reports, "Calibration complete")
