From 1efeff9b40e9790a0dc7607f14caf1d796634106 Mon Sep 17 00:00:00 2001
From: Gagik Vardanyan <vardanyan@ill.fr>
Date: Thu, 13 Feb 2020 15:50:16 +0100
Subject: [PATCH] Re #27918 more flexible absolute scaling
---
.../WorkflowAlgorithms/SANSILLReduction.py | 73 ++++++---
.../analysis/SANSILLAbsoluteScaleTest.py | 144 ++++++++++++++++++
.../tests/analysis/SANSILLReductionTest.py | 57 -------
.../reference/D11_AbsScaleReference.nxs.md5 | 2 +-
.../reference/ILL_SANS_D11_IQ.nxs.md5 | 2 +-
docs/source/release/v4.3.0/sans.rst | 1 +
6 files changed, 202 insertions(+), 77 deletions(-)
create mode 100644 Testing/SystemTests/tests/analysis/SANSILLAbsoluteScaleTest.py
diff --git a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/SANSILLReduction.py b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/SANSILLReduction.py
index 0f13f70f04a..61ea77d2466 100644
--- a/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/SANSILLReduction.py
+++ b/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/SANSILLReduction.py
@@ -333,15 +333,6 @@ class SANSILLReduction(PythonAlgorithm):
Processes the sample
@param ws: input workspace
"""
- reference_ws = self.getProperty('ReferenceInputWorkspace').value
- coll_ws = None
- if reference_ws:
- if not self._check_processed_flag(reference_ws, 'Sample'):
- self.log().warning('Reference input workspace is not processed as sample.')
- Divide(LHSWorkspace=ws, RHSWorkspace=reference_ws, OutputWorkspace=ws, WarnOnZeroDivide=False)
- Scale(InputWorkspace=ws, Factor=self.getProperty('WaterCrossSection').value, OutputWorkspace=ws)
- self._mask(ws, reference_ws)
- coll_ws = reference_ws
sensitivity_in = self.getProperty('SensitivityInputWorkspace').value
if sensitivity_in:
if not self._check_processed_flag(sensitivity_in, 'Sensitivity'):
@@ -357,15 +348,61 @@ class SANSILLReduction(PythonAlgorithm):
DeleteWorkspace(flux_ws)
else:
Divide(LHSWorkspace=ws, RHSWorkspace=flux_in, OutputWorkspace=ws, WarnOnZeroDivide=False)
- if coll_ws:
- self._check_distances_match(mtd[ws], coll_ws)
- sample_coll = mtd[ws].getRun().getLogData('collimation.actual_position').value
- ref_coll = coll_ws.getRun().getLogData('collimation.actual_position').value
- flux_factor = (sample_coll ** 2) / (ref_coll ** 2)
- self.log().notice('Flux factor is: ' + str(flux_factor))
- Scale(InputWorkspace=ws, Factor=flux_factor, OutputWorkspace=ws)
- ReplaceSpecialValues(InputWorkspace=ws, OutputWorkspace=ws,
- NaNValue=0., NaNError=0., InfinityValue=0., InfinityError=0.)
+ AddSampleLog(Workspace=ws, LogText='True', LogType='String', LogName='NormalisedByFlux')
+ self._do_rescale_flux(ws, flux_in)
+ reference_ws = self.getProperty('ReferenceInputWorkspace').value
+ if reference_ws:
+ if not self._check_processed_flag(reference_ws, 'Sample'):
+ self.log().warning('Reference input workspace is not processed as sample.')
+ Divide(LHSWorkspace=ws, RHSWorkspace=reference_ws, OutputWorkspace=ws, WarnOnZeroDivide=False)
+ Scale(InputWorkspace=ws, Factor=self.getProperty('WaterCrossSection').value, OutputWorkspace=ws)
+ self._mask(ws, reference_ws)
+ self._rescale_flux(ws, reference_ws)
+ ReplaceSpecialValues(InputWorkspace=ws, OutputWorkspace=ws,
+ NaNValue=0., NaNError=0., InfinityValue=0., InfinityError=0.)
+
+ def _rescale_flux(self, ws, ref_ws):
+ """
+ This adjusts the absolute scale after normalising by water
+ If both sample and water runs are normalised by flux, there is nothing to do
+ If one is normalised, the other is not, we log a warning
+ If neither is normalised by flux, we have to rescale by the factor
+ @param ws : the workspace to scale (sample)
+ @param ref_ws : the reference workspace (water)
+ """
+ message = 'Sample and water runs are not consistent in terms of flux normalisation; ' \
+ 'the absolute scale will not be correct. ' \
+ 'Make sure they are either both normalised or both not normalised by flux.' \
+ 'Consider specifying the sample flux also to water reduction.' \
+ 'Even if it would be at different distance, it will be rescaled correctly.'
+ run = mtd[ws].getRun()
+ run_ref = ref_ws.getRun()
+ has_log = run.hasProperty('NormalisedByFlux')
+ has_log_ref = run_ref.hasProperty('NormalisedByFlux')
+ if has_log != has_log_ref:
+ raise RuntimeError(message)
+ if has_log and has_log_ref:
+ log_val = run.getLogData('NormalisedByFlux').value
+ log_val_ref = run_ref.getLogData('NormalisedByFlux').value
+ if log_val != log_val_ref:
+ raise RuntimeError(message)
+ elif log_val == 'False':
+ self._do_rescale_flux(ws, ref_ws)
+ else:
+ self._do_rescale_flux(ws, ref_ws)
+
+ def _do_rescale_flux(self, ws, ref_ws):
+ """
+ Scales ws by the magic flux factor wrt the reference
+ @ws : input workspace to scale (sample)
+ @ref_ws : reference workspace (water)
+ """
+ self._check_distances_match(mtd[ws], ref_ws)
+ sample_l2 = mtd[ws].getRun().getLogData('L2').value
+ ref_l2 = ref_ws.getRun().getLogData('L2').value
+ flux_factor = (sample_l2 ** 2) / (ref_l2 ** 2)
+ self.log().notice('Flux factor is: ' + str(flux_factor))
+ Scale(InputWorkspace=ws, Factor=flux_factor, OutputWorkspace=ws)
def _apply_absorber(self, ws, absorber_ws):
"""
diff --git a/Testing/SystemTests/tests/analysis/SANSILLAbsoluteScaleTest.py b/Testing/SystemTests/tests/analysis/SANSILLAbsoluteScaleTest.py
new file mode 100644
index 00000000000..cf39d92a6b4
--- /dev/null
+++ b/Testing/SystemTests/tests/analysis/SANSILLAbsoluteScaleTest.py
@@ -0,0 +1,144 @@
+# Mantid Repository : https://github.com/mantidproject/mantid
+#
+# Copyright © 2020 ISIS Rutherford Appleton Laboratory UKRI,
+# NScD Oak Ridge National Laboratory, European Spallation Source
+# & Institut Laue - Langevin
+# SPDX - License - Identifier: GPL - 3.0 +
+from __future__ import (absolute_import, division, print_function)
+
+import systemtesting
+from mantid.simpleapi import *
+
+
+class D11_AbsoluteScale_Test(systemtesting.MantidSystemTest):
+
+ def __init__(self):
+ super(D11_AbsoluteScale_Test, self).__init__()
+ self.setUp()
+
+ def setUp(self):
+ config['default.facility'] = 'ILL'
+ config['default.instrument'] = 'D11'
+ config.appendDataSearchSubDir('ILL/D11/')
+
+ def cleanup(self):
+ mtd.clear()
+
+ def validate(self):
+ self.tolerance = 1e-5
+ self.tolerance_is_rel_err = True
+ self.disableChecking = ['Instrument']
+ return ['abs_scale_outputs', 'D11_AbsScaleReference.nxs']
+
+ def runTest(self):
+ # Load the mask
+ LoadNexusProcessed(Filename='D11_mask.nxs', OutputWorkspace='mask')
+
+ # Process the dark current Cd/B4C for water
+ SANSILLReduction(Run='010455', ProcessAs='Absorber', OutputWorkspace='Cdw')
+
+ # Process the empty beam for water
+ SANSILLReduction(Run='010414', ProcessAs='Beam', AbsorberInputWorkspace='Cdw', OutputWorkspace='Dbw',
+ FluxOutputWorkspace='Flw')
+ # Water container transmission
+ SANSILLReduction(Run='010446', ProcessAs='Transmission', AbsorberInputWorkspace='Cdw',
+ BeamInputWorkspace='Dbw', OutputWorkspace='wc_tr')
+ # Water container
+ SANSILLReduction(Run='010454', ProcessAs='Container', AbsorberInputWorkspace='Cdw',
+ BeamInputWorkspace='Dbw', TransmissionInputWorkspace='wc_tr', OutputWorkspace='wc')
+ # Water transmission
+ SANSILLReduction(Run='010445', ProcessAs='Transmission', AbsorberInputWorkspace='Cdw',
+ BeamInputWorkspace='Dbw', OutputWorkspace='w_tr')
+ # Water as reference
+ SANSILLReduction(Run='010453', ProcessAs='Sample', AbsorberInputWorkspace='Cdw', MaskedInputWorkspace='mask',
+ ContainerInputWorkspace='wc', BeamInputWorkspace='Dbw', TransmissionInputWorkspace='wc_tr',
+ SensitivityOutputWorkspace='sens', OutputWorkspace='reference', FluxInputWorkspace='Flw')
+ # Water as sample with sensitivity and flux
+ SANSILLReduction(Run='010453', ProcessAs='Sample', AbsorberInputWorkspace='Cdw', MaskedInputWorkspace='mask',
+ ContainerInputWorkspace='wc', BeamInputWorkspace='Dbw', TransmissionInputWorkspace='wc_tr',
+ SensitivityInputWorkspace='sens', OutputWorkspace='water_with_sens_flux', FluxInputWorkspace='Flw')
+ # Water with itself as reference and flux
+ SANSILLReduction(Run='010453', ProcessAs='Sample', AbsorberInputWorkspace='Cdw', MaskedInputWorkspace='mask',
+ ContainerInputWorkspace='wc', BeamInputWorkspace='Dbw', TransmissionInputWorkspace='wc_tr',
+ ReferenceInputWorkspace='reference', OutputWorkspace='water_with_reference', FluxInputWorkspace='Flw')
+
+ # Group the worksaces
+ GroupWorkspaces(InputWorkspaces=['sens', 'reference', 'water_with_reference', 'water_with_sens_flux'],
+ OutputWorkspace='abs_scale_outputs')
+
+
+class D11_AbsoluteScaleFlux_Test(systemtesting.MantidSystemTest):
+
+ def __init__(self):
+ super(D11_AbsoluteScaleFlux_Test, self).__init__()
+ self.setUp()
+
+ def setUp(self):
+ config['default.facility'] = 'ILL'
+ config['default.instrument'] = 'D11'
+ config.appendDataSearchSubDir('ILL/D11/')
+
+ def cleanup(self):
+ mtd.clear()
+
+ def runTest(self):
+ # Load the mask
+ LoadNexusProcessed(Filename='D11_mask.nxs', OutputWorkspace='mask')
+
+ # Calculate flux for water
+ SANSILLReduction(Run='010414', ProcessAs='Beam', OutputWorkspace='Dbw', FluxOutputWorkspace='flw')
+
+ # Reduce water with flux normalisation
+ SANSILLReduction(Run='010453', ProcessAs='Sample', MaskedInputWorkspace='mask',
+ OutputWorkspace='water_with_flux', FluxInputWorkspace='flw')
+
+ # Reduce water without flux normalisation
+ SANSILLReduction(Run='010453', ProcessAs='Sample', MaskedInputWorkspace='mask', OutputWorkspace='water_wo_flux')
+
+ # Calculate flux for sample
+ SANSILLReduction(Run='010413', ProcessAs='Beam', OutputWorkspace='Db', FluxOutputWorkspace='fl')
+
+ # Reduce sample with flux normalisation and flux normalised water reference
+ SANSILLReduction(Run='010569', ProcessAs='Sample', MaskedInputWorkspace='mask',
+ OutputWorkspace='sample_with_flux', FluxInputWorkspace='fl', ReferenceInputWorkspace='water_with_flux')
+
+ # Reduce sample without flux normalisation and not flux normalised water reference
+ SANSILLReduction(Run='010569', ProcessAs='Sample', MaskedInputWorkspace='mask',
+ OutputWorkspace='sample_wo_flux', ReferenceInputWorkspace='water_wo_flux')
+
+ # Now the sample_with_flux and sample_wo_flux should be approximately at the same scale
+ result1, _ = CompareWorkspaces(Workspace1='sample_with_flux', Workspace2='sample_wo_flux', Tolerance=0.1)
+ self.assertTrue(result1)
+
+ # Then we want to simulate the situation where water has no flux measurement
+ # Reduce water, but normalise it to the sample flux (water will get scaled here)
+ SANSILLReduction(Run='010453', ProcessAs='Sample', MaskedInputWorkspace='mask',
+ OutputWorkspace='water_with_sample_flux', FluxInputWorkspace='fl')
+
+ # Reduce sample with flux normalisation and sample flux normalised water reference
+ # Here there is no additional scaling, since both are already normalised
+ SANSILLReduction(Run='010569', ProcessAs='Sample', MaskedInputWorkspace='mask',
+ OutputWorkspace='sample_with_flux_water_with_sample_flux',
+ FluxInputWorkspace='fl', ReferenceInputWorkspace='water_with_sample_flux')
+
+ # Now this output should still be at the same scale as the two above
+ # (basically it is the same scaling, just happening in different place)
+ result2, _ = CompareWorkspaces(Workspace1='sample_with_flux_water_with_sample_flux',
+ Workspace2='sample_wo_flux', Tolerance=0.1)
+ self.assertTrue(result2)
+
+ result3, _ = CompareWorkspaces(Workspace1='sample_with_flux_water_with_sample_flux',
+ Workspace2='sample_with_flux', Tolerance=0.1)
+ self.assertTrue(result3)
+
+ # Finally we want to make sure that trying to divide flux normalised sample by
+ # non flux normalised water raises an error
+ kwargs = {
+ 'Run' : '010569',
+ 'ProcessAs' : 'Sample',
+ 'MaskedInputWorkspace' : 'mask',
+ 'OutputWorkspace' : 'sample_with_flux_water_wo_flux',
+ 'FluxInputWorkspace' : 'fl',
+ 'ReferenceInputWorkspace' : 'water_wo_flux'
+ }
+ self.assertRaises(RuntimeError, SANSILLReduction, **kwargs)
diff --git a/Testing/SystemTests/tests/analysis/SANSILLReductionTest.py b/Testing/SystemTests/tests/analysis/SANSILLReductionTest.py
index da6b2fac4a6..583a9ad25c3 100644
--- a/Testing/SystemTests/tests/analysis/SANSILLReductionTest.py
+++ b/Testing/SystemTests/tests/analysis/SANSILLReductionTest.py
@@ -299,60 +299,3 @@ class ILL_D33_Test(systemtesting.MantidSystemTest):
# I(Q)
SANSILLIntegration(InputWorkspace='sample_flux', OutputWorkspace='iq')
-
-
-class ILL_D11_AbsoluteScale_Test(systemtesting.MantidSystemTest):
-
- def __init__(self):
- super(ILL_D11_AbsoluteScale_Test, self).__init__()
- self.setUp()
-
- def setUp(self):
- config['default.facility'] = 'ILL'
- config['default.instrument'] = 'D11'
- config.appendDataSearchSubDir('ILL/D11/')
-
- def cleanup(self):
- mtd.clear()
-
- def validate(self):
- self.tolerance = 1e-5
- self.tolerance_is_rel_err = True
- self.disableChecking = ['Instrument']
- return ['abs_scale_outputs', 'D11_AbsScaleReference.nxs']
-
- def runTest(self):
- # Load the mask
- LoadNexusProcessed(Filename='D11_mask.nxs', OutputWorkspace='mask')
-
- # Process the dark current Cd/B4C for water
- SANSILLReduction(Run='010455', ProcessAs='Absorber', OutputWorkspace='Cdw')
-
- # Process the empty beam for water
- SANSILLReduction(Run='010414', ProcessAs='Beam', AbsorberInputWorkspace='Cdw', OutputWorkspace='Dbw',
- FluxOutputWorkspace='Flw')
- # Water container transmission
- SANSILLReduction(Run='010446', ProcessAs='Transmission', AbsorberInputWorkspace='Cdw',
- BeamInputWorkspace='Dbw', OutputWorkspace='wc_tr')
- # Water container
- SANSILLReduction(Run='010454', ProcessAs='Container', AbsorberInputWorkspace='Cdw',
- BeamInputWorkspace='Dbw', TransmissionInputWorkspace='wc_tr', OutputWorkspace='wc')
- # Water transmission
- SANSILLReduction(Run='010445', ProcessAs='Transmission', AbsorberInputWorkspace='Cdw',
- BeamInputWorkspace='Dbw', OutputWorkspace='w_tr')
- # Water as reference
- SANSILLReduction(Run='010453', ProcessAs='Sample', AbsorberInputWorkspace='Cdw', MaskedInputWorkspace='mask',
- ContainerInputWorkspace='wc', BeamInputWorkspace='Dbw', TransmissionInputWorkspace='wc_tr',
- SensitivityOutputWorkspace='sens', OutputWorkspace='reference', FluxInputWorkspace='Flw')
- # Water as sample with sensitivity and flux
- SANSILLReduction(Run='010453', ProcessAs='Sample', AbsorberInputWorkspace='Cdw', MaskedInputWorkspace='mask',
- ContainerInputWorkspace='wc', BeamInputWorkspace='Dbw', TransmissionInputWorkspace='wc_tr',
- SensitivityInputWorkspace='sens', OutputWorkspace='water_with_sens_flux', FluxInputWorkspace='Flw')
- # Water with itself as reference and flux
- SANSILLReduction(Run='010453', ProcessAs='Sample', AbsorberInputWorkspace='Cdw', MaskedInputWorkspace='mask',
- ContainerInputWorkspace='wc', BeamInputWorkspace='Dbw', TransmissionInputWorkspace='wc_tr',
- ReferenceInputWorkspace='reference', OutputWorkspace='water_with_reference', FluxInputWorkspace='Flw')
-
- # Group the worksaces
- GroupWorkspaces(InputWorkspaces=['sens', 'reference', 'water_with_reference', 'water_with_sens_flux'],
- OutputWorkspace='abs_scale_outputs')
diff --git a/Testing/SystemTests/tests/analysis/reference/D11_AbsScaleReference.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/D11_AbsScaleReference.nxs.md5
index 258b1b7bb25..f54a61cae43 100644
--- a/Testing/SystemTests/tests/analysis/reference/D11_AbsScaleReference.nxs.md5
+++ b/Testing/SystemTests/tests/analysis/reference/D11_AbsScaleReference.nxs.md5
@@ -1 +1 @@
-37ca323c47478b6c49b26676a89423a8
+8d9ed6b7ed46d696b8f81b754d7c7ae7
diff --git a/Testing/SystemTests/tests/analysis/reference/ILL_SANS_D11_IQ.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/ILL_SANS_D11_IQ.nxs.md5
index 1f96700f486..93a9a998fed 100644
--- a/Testing/SystemTests/tests/analysis/reference/ILL_SANS_D11_IQ.nxs.md5
+++ b/Testing/SystemTests/tests/analysis/reference/ILL_SANS_D11_IQ.nxs.md5
@@ -1 +1 @@
-cd7c39ac8e064f4a639155f3e747c832
+036c8504fc9d7f68be0f8f42c8a64e8e
diff --git a/docs/source/release/v4.3.0/sans.rst b/docs/source/release/v4.3.0/sans.rst
index 075f832984e..6a4185defd9 100644
--- a/docs/source/release/v4.3.0/sans.rst
+++ b/docs/source/release/v4.3.0/sans.rst
@@ -15,6 +15,7 @@ Improved
- :ref:`MaskBTP <algm-MaskBTP>` now handles both old and new instrument definitions for BIOSANS and GPSANS
- :ref:`SANSILLReduction <algm-SANSILLReduction>` and :ref:`SANSILLAutoProcess <algm-SANSILLAutoProcess>` are improved to better handle the absolute scale normalisation.
- :ref:`SANSILLIntegration <algm-SANSILLIntegration>` will now offer to produce I(Q) for separate detector components separately, which is useful for D33.
+- :ref:`SANSILLReduction <algm-SANSILLReduction>` will now allow for correct absolute scale normalisation even in circumstances when, for example, there is no flux measurement for the water run configuration.
- Data with invalid proton charge logs will now be fixed before performing
slicing. A warning is emitted when this happens.
- ISIS SANS history for top level algorithms now works correctly. A user
--
GitLab