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Add ability to manually specify invalid detectors #64

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merged 15 commits into from
May 12, 2023
Merged

Add ability to manually specify invalid detectors #64

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ba538d1
add ability to manually specify detectors
MialLewis Apr 26, 2023
d6da6db
add system test to test manual detector specification
MialLewis Apr 27, 2023
c18460a
refactor invalid peaks
MialLewis Apr 27, 2023
4001789
improve doc for InvalidDetectors prop
MialLewis Apr 27, 2023
4fdef0f
refactor invalid detectors into helper class
MialLewis Apr 27, 2023
3e2f94f
temp unfinished commit to rebase
MialLewis Apr 27, 2023
0d05bef
add invalid detector feedback from fit class
MialLewis Apr 28, 2023
b35c65d
fix unit tests and slight refactor invalid detectors
MialLewis Apr 28, 2023
56f3562
update documentation
MialLewis Apr 28, 2023
de9b8e7
remove defunct unit test
MialLewis Apr 28, 2023
70a9e4a
respond to pr review comments
MialLewis May 2, 2023
a5d8f04
update paths to run from calibration root
MialLewis May 2, 2023
cc58cbb
resolve conflict in analysis imports
MialLewis May 3, 2023
aede601
do not identify if preset and blank
MialLewis May 3, 2023
f2ee0d5
repond to pr comments
MialLewis May 11, 2023
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52 changes: 29 additions & 23 deletions unpackaged/vesuvio_calibration/calibration_scripts/calibrate_vesuvio_analysis.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
from mantid.kernel import StringArrayProperty, Direction, StringListValidator, FloatArrayBoundedValidator, StringMandatoryValidator,\
IntBoundedValidator, FloatArrayProperty
from mantid.kernel import StringArrayProperty, Direction, StringListValidator, IntArrayBoundedValidator, IntArrayProperty,\
FloatArrayBoundedValidator, StringMandatoryValidator, IntBoundedValidator,FloatArrayProperty
from mantid.api import FileProperty, FileAction, PythonAlgorithm,AlgorithmManager
from mantid.simpleapi import CreateEmptyTableWorkspace, DeleteWorkspace, ReplaceSpecialValues, GroupWorkspaces, mtd,\
ConvertTableToMatrixWorkspace, ConjoinWorkspaces, Transpose, PlotPeakByLogValue,RenameWorkspace
from calibration_scripts.calibrate_vesuvio_helper_functions import EVSGlobals, EVSMiscFunctions

from calibration_scripts.calibrate_vesuvio_helper_functions import EVSGlobals, EVSMiscFunctions,\
InvalidDetectors

import os
import sys
Expand Down Expand Up @@ -35,15 +35,21 @@ def PyInit(self):
self.declareProperty('Mass', sys.float_info.max,
doc="Mass of the sample in amu to be used when calculating energy. Default is Pb: 207.19")

greaterThanZero = FloatArrayBoundedValidator()
greaterThanZero.setLower(0)
self.declareProperty(FloatArrayProperty('DSpacings', [], greaterThanZero, Direction.Input),
greater_than_zero_float = FloatArrayBoundedValidator()
greater_than_zero_float.setLower(0)
self.declareProperty(FloatArrayProperty('DSpacings', [], greater_than_zero_float, Direction.Input),
doc="List of d-spacings used to estimate the positions of peaks in TOF.")

self.declareProperty(FloatArrayProperty('E1FixedValueAndError', [], greaterThanZero, Direction.Input),
self.declareProperty(FloatArrayProperty('E1FixedValueAndError', [], greater_than_zero_float, Direction.Input),
doc="Value at which to fix E1 and E1 error (form: E1 value, E1 Error). If no input is provided,"
"values will be calculated.")

detector_validator = IntArrayBoundedValidator()
detector_validator.setLower(EVSGlobals.DETECTOR_RANGE[0])
detector_validator.setUpper(EVSGlobals.DETECTOR_RANGE[-1])
self.declareProperty(IntArrayProperty('InvalidDetectors', [], detector_validator, Direction.Input),
doc="List of detectors to be marked as invalid (3-198), to be excluded from analysis calculations.")

self.declareProperty('Iterations', 2, validator=IntBoundedValidator(lower=1),
doc="Number of iterations to perform. Default is 2.")

Expand Down Expand Up @@ -111,7 +117,6 @@ def PyExec(self):
# repeatedly fit L1, E1 and Theta parameters
table_group = []
for i in range(self._iterations):

# calibrate theta for all detectors
theta_fit = self._current_workspace + '_theta'
self._run_calibration_fit(Samples=self._samples, Background=self._background, Function=self._theta_peak_function,
Expand All @@ -123,10 +128,13 @@ def PyExec(self):

# calibrate E1 for backscattering detectors and use the backscattering averaged value for all detectors
E1_fit_back = self._current_workspace + '_E1_back'
invalid_detectors = \
self._run_calibration_fit(Samples=self._samples, Function='Voigt', Mode='SingleDifference',
SpectrumRange=EVSGlobals.BACKSCATTERING_RANGE, InstrumentParameterWorkspace=self._param_table,
Mass=self._sample_mass, OutputWorkspace=E1_fit_back, CreateOutput=self._create_output,
PeakType='Recoil', SharedParameterFitType=self._shared_parameter_fit_type)
PeakType='Recoil', SharedParameterFitType=self._shared_parameter_fit_type,
InvalidDetectors=self._invalid_detectors.get_all_invalid_detectors())
self._invalid_detectors.add_invalid_detectors(invalid_detectors)

E1_peak_fits_back = mtd[self._current_workspace + '_E1_back_Peak_Parameters'].getNames()
self._calculate_final_energy(E1_peak_fits_back, EVSGlobals.BACKSCATTERING_RANGE, self._shared_parameter_fit_type != "Individual")
Expand All @@ -136,10 +144,13 @@ def PyExec(self):

# calibrate L1 for frontscattering detectors based on the averaged E1 value and calibrated theta values
E1_fit_front = self._current_workspace + '_E1_front'
invalid_detectors += \
self._run_calibration_fit(Samples=self._samples, Function='Voigt', Mode='SingleDifference',
SpectrumRange=EVSGlobals.FRONTSCATTERING_RANGE, InstrumentParameterWorkspace=self._param_table,
Mass=self._sample_mass, OutputWorkspace=E1_fit_front, CreateOutput=self._create_output,
PeakType='Recoil', SharedParameterFitType=self._shared_parameter_fit_type)
PeakType='Recoil', SharedParameterFitType=self._shared_parameter_fit_type,
InvalidDetectors=self._invalid_detectors.get_all_invalid_detectors())
self._invalid_detectors.add_invalid_detectors(invalid_detectors)

E1_peak_fits_front = mtd[self._current_workspace + '_E1_front_Peak_Parameters'].getNames()
self._calculate_final_flight_path(E1_peak_fits_front[0], EVSGlobals.FRONTSCATTERING_RANGE)
Expand Down Expand Up @@ -178,14 +189,18 @@ def _run_calibration_fit(self, *args, **kwargs):

@param args - positional arguments to the algorithm
@param kwargs - key word arguments to the algorithm
@returns - returns list of invalid detectors so set in overarching alg
"""
from mantid.simpleapi import set_properties
alg = AlgorithmManager.create('EVSCalibrationFit')
alg.initialize()
alg.setRethrows(True)

set_properties(alg, *args, **kwargs)
alg.execute()

return alg.getProperty("InvalidDetectorsOut").value.tolist()

def _calculate_time_delay(self, table_name, spec_list):
"""
Calculate time delay from frontscattering detectors.
Expand Down Expand Up @@ -245,13 +260,7 @@ def _calculate_final_flight_path(self, peak_table, spec_list):
theta = EVSMiscFunctions.read_table_column(self._current_workspace, 'theta', spec_list)
r_theta = EVSMiscFunctions.calculate_r_theta(self._sample_mass, theta)

peak_centres = EVSMiscFunctions.read_fitting_result_table_column(peak_table, 'f1.LorentzPos', spec_list)
peak_centres_errors = EVSMiscFunctions.read_fitting_result_table_column(peak_table, 'f1.LorentzPos_Err', spec_list)
invalid_spectra = EVSMiscFunctions.identify_invalid_spectra(peak_table, peak_centres, peak_centres_errors, spec_list)
peak_centres[invalid_spectra] = np.nan

print(f'Invalid Spectra Index Found and Marked NAN: {invalid_spectra.flatten()} from Spectra Index List:'
f'{[ x -3 for x in spec_list]}')
peak_centres = self._invalid_detectors.filter_peak_centres_for_invalid_detectors(spec_list, peak_table)

delta_t = (peak_centres - t0) / 1e+6
delta_t_error = t0_error / 1e+6
Expand Down Expand Up @@ -328,11 +337,7 @@ def _calculate_final_energy(self, peak_table, spec_list, calculate_global):
theta = EVSMiscFunctions.read_table_column(self._current_workspace, 'theta', spec_list)
r_theta = EVSMiscFunctions.calculate_r_theta(self._sample_mass, theta)

peak_centres = EVSMiscFunctions.read_fitting_result_table_column(peak_table[0], 'f1.LorentzPos', spec_list)
peak_centres_errors = EVSMiscFunctions.read_fitting_result_table_column(peak_table[0], 'f1.LorentzPos_Err', spec_list)

invalid_spectra = EVSMiscFunctions.identify_invalid_spectra(peak_table[0], peak_centres, peak_centres_errors, spec_list)
peak_centres[invalid_spectra] = np.nan
peak_centres = self._invalid_detectors.filter_peak_centres_for_invalid_detectors(spec_list, peak_table[0])

delta_t = (peak_centres - t0) / 1e+6
v1 = (L0 * r_theta + L1) / delta_t
Expand Down Expand Up @@ -381,6 +386,7 @@ def _setup(self):
self._sample_mass = self.getProperty("Mass").value
self._d_spacings = self.getProperty("DSpacings").value.tolist()
self._E1_value_and_error = self.getProperty("E1FixedValueAndError").value.tolist()
self._invalid_detectors = InvalidDetectors(self.getProperty("InvalidDetectors").value.tolist())
self._shared_parameter_fit_type = self.getProperty("SharedParameterFitType").value
self._calc_L0 = self.getProperty("CalculateL0").value
self._make_IP_file = self.getProperty("CreateIPFile").value
Expand Down
25 changes: 18 additions & 7 deletions unpackaged/vesuvio_calibration/calibration_scripts/calibrate_vesuvio_fit.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
ReplaceSpecialValues, FindPeaks, GroupWorkspaces, mtd, Plus, LoadVesuvio, LoadRaw, ConvertToDistribution, FindPeakBackground,\
ExtractSingleSpectrum, SumSpectra, AppendSpectra, CloneWorkspace, Fit, MaskDetectors, ExtractUnmaskedSpectra, CreateWorkspace
from functools import partial
from calibration_scripts.calibrate_vesuvio_helper_functions import EVSGlobals, EVSMiscFunctions
from calibration_scripts.calibrate_vesuvio_helper_functions import EVSGlobals, EVSMiscFunctions, InvalidDetectors

import os
import sys
Expand Down Expand Up @@ -68,6 +68,14 @@ def PyInit(self):
doc='Calculate shared parameters using an individual and/or'
'global fit.', validator=shared_fit_type_validator)

detector_validator = IntArrayBoundedValidator()
detector_validator.setLower(EVSGlobals.DETECTOR_RANGE[0])
detector_validator.setUpper(EVSGlobals.DETECTOR_RANGE[-1])
self.declareProperty(IntArrayProperty('InvalidDetectors', [], detector_validator, Direction.Input),
doc="List of detectors to be marked as invalid (3-198), to be excluded from analysis calculations.")
self.declareProperty(IntArrayProperty('InvalidDetectorsOut', [], detector_validator, Direction.Output),
doc="List of detectors found as invalid to be output.")

self.declareProperty(
ITableWorkspaceProperty("InstrumentParameterWorkspace", "", Direction.Input, PropertyMode.Optional),
doc='Workspace contain instrument parameters.')
Expand All @@ -91,6 +99,9 @@ def PyExec(self):
if self._create_output and not self._fitting_bragg_peaks:
self._generate_fit_workspaces()

# set invalid detectors output param
self.setProperty("InvalidDetectorsOut", self._invalid_detectors.get_all_invalid_detectors())

# clean up workspaces
if self._param_file != "":
DeleteWorkspace(self._param_table)
Expand All @@ -112,6 +123,7 @@ def _setup_class_variables_from_properties(self):
self._sample_mass = self.getProperty("Mass").value
self._create_output = self.getProperty("CreateOutput").value
self._shared_parameter_fit_type = self.getProperty("SharedParameterFitType").value
self._invalid_detectors = InvalidDetectors(self.getProperty("InvalidDetectors").value.tolist())

def _setup_spectra_list(self):
self._spec_list = self.getProperty("SpectrumRange").value.tolist()
Expand Down Expand Up @@ -549,6 +561,7 @@ def _fit_peaks(self):

self._output_parameter_tables = []
self._peak_fit_workspaces = []

for peak_index, estimated_peak_positions in enumerate(estimated_peak_positions_all_peaks):

self._peak_fit_workspaces_by_spec = []
Expand Down Expand Up @@ -585,12 +598,10 @@ def _shared_parameter_fit(self, output_parameter_table_name, output_parameter_ta
initial_params = {'A0': 0.0, 'A1': 0.0, 'LorentzAmp': init_Lorentz_Amp, 'LorentzPos': init_Lorentz_Pos,
'LorentzFWHM': init_Lorentz_FWHM, 'GaussianFWHM': init_Gaussian_FWHM}

peak_centres = EVSMiscFunctions.read_fitting_result_table_column(output_parameter_table_name, 'f1.LorentzPos', self._spec_list)
peak_centres_errors = EVSMiscFunctions.read_fitting_result_table_column(output_parameter_table_name, 'f1.LorentzPos_Err',
self._spec_list)
invalid_spectra = EVSMiscFunctions.identify_invalid_spectra(output_parameter_table_name, peak_centres, peak_centres_errors,
self._spec_list)
self._fit_shared_parameter(invalid_spectra, initial_params, output_parameter_table_headers)
self._invalid_detectors.identify_and_set_invalid_detectors_from_range(self._spec_list, output_parameter_table_name)

self._fit_shared_parameter(self._invalid_detectors.get_invalid_detectors_index(self._spec_list), initial_params,
output_parameter_table_headers)

def _fit_peak(self, peak_index, spec_index, peak_position, output_parameter_table_name,
output_parameter_table_headers):
Expand Down
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