From c7a4b57d17954cf916fa3490b8cb2e0f0548ca37 Mon Sep 17 00:00:00 2001
From: Harriet Brown <harriet.brown@stfc.ac.uk>
Date: Mon, 6 Jan 2020 13:59:20 +0000
Subject: [PATCH] Add option to set PDF type on polaris
create_total_scattering_pdf
This commit add the option for the user to set the PDF output type on the polaris
create_total_scattering_pdf function. They can use any of the types available through
PDFFourierTransform (G(r), g(r), RDF(r)), if none given it will default to G(r).
Re #27607
---
.../tests/analysis/ISIS_PowderPolarisTest.py | 23 +++++++++++++++++--
docs/source/release/v4.3.0/diffraction.rst | 1 +
.../techniques/ISISPowder-Polaris-v1.rst | 9 ++++----
scripts/Diffraction/isis_powder/polaris.py | 6 ++++-
.../polaris_routines/polaris_algs.py | 6 ++---
.../polaris_routines/polaris_param_mapping.py | 1 +
6 files changed, 36 insertions(+), 10 deletions(-)
diff --git a/Testing/SystemTests/tests/analysis/ISIS_PowderPolarisTest.py b/Testing/SystemTests/tests/analysis/ISIS_PowderPolarisTest.py
index 75ca0e0c026..cd78da964cb 100644
--- a/Testing/SystemTests/tests/analysis/ISIS_PowderPolarisTest.py
+++ b/Testing/SystemTests/tests/analysis/ISIS_PowderPolarisTest.py
@@ -193,11 +193,30 @@ class TotalScatteringMergedTest(systemtesting.MantidSystemTest):
self.assertAlmostEqual(self.pdf_output.dataY(0)[37], 0.7376667, places=3)
-def run_total_scattering(run_number, merge_banks, q_lims=None):
+class TotalScatteringPdfTypeTest(systemtesting.MantidSystemTest):
+
+ pdf_output = None
+
+ def runTest(self):
+ setup_mantid_paths()
+ # Load Focused ws
+ mantid.LoadNexus(Filename=total_scattering_input_file, OutputWorkspace='98533-Results-TOF-Grp')
+ q_lims = np.array([2.5, 3, 4, 6, 7, 3.5, 5, 7, 11, 40]).reshape((2, 5))
+ self.pdf_output = run_total_scattering('98533', True, q_lims=q_lims, pdf_type="g(r)")
+
+ def validate(self):
+ # Whilst total scattering is in development, the validation will avoid using reference files as they will have
+ # to be updated very frequently. In the meantime, the expected peak in the PDF at ~3.9 Angstrom will be checked.
+ # After rebin this is at X index 37
+ self.assertAlmostEqual(self.pdf_output.dataY(0)[37], 1.0152123, places=3)
+
+
+def run_total_scattering(run_number, merge_banks, q_lims=None, pdf_type="G(r)"):
pdf_inst_obj = setup_inst_object(mode="PDF")
return pdf_inst_obj.create_total_scattering_pdf(run_number=run_number,
merge_banks=merge_banks,
- q_lims=q_lims)
+ q_lims=q_lims,
+ pdf_type=pdf_type)
def _gen_required_files():
diff --git a/docs/source/release/v4.3.0/diffraction.rst b/docs/source/release/v4.3.0/diffraction.rst
index 04f25c089a7..7f6623e2a35 100644
--- a/docs/source/release/v4.3.0/diffraction.rst
+++ b/docs/source/release/v4.3.0/diffraction.rst
@@ -18,6 +18,7 @@ Powder Diffraction
- The create_total_scattering_pdf merging banks now matches spectra to the spectrum with the largest x range.
- The create_total_scattering_pdf merging banks no longer matches spectra with scale, it now only matches with offset.
+- The polaris create_total_scattering_pdf function can now accept a `pdf_type` argument to set the pdf_output type.
- :ref:`HRPDSlabCanAbsorption <algm-HRPDSlabCanAbsorption-v1>` now accepts any thickness parameter and not those in a specified list.
Engineering Diffraction
diff --git a/docs/source/techniques/ISISPowder-Polaris-v1.rst b/docs/source/techniques/ISISPowder-Polaris-v1.rst
index 9db04cec5a8..5c530a6fc50 100644
--- a/docs/source/techniques/ISISPowder-Polaris-v1.rst
+++ b/docs/source/techniques/ISISPowder-Polaris-v1.rst
@@ -168,10 +168,11 @@ The *create_total_scattering_pdf* method allows a user to create a Pair Distribu
from focused POLARIS data, with a view performing further total scattering analysis.
With no merging criteria specified, *merge_banks=False* a PDF will be generated for each bank within
-the focused_workspace. If run with *merge_banks=True* a PDF will be generated based on the wighted
-sum of the detector banks performed using supplied Q limits *q_lims=q_limits*, Q_limits can be in the
-form of a numpy array with shape (2, x) where x is the number rof detectors, or a string containing the
-directory of an appropriately formatted `.lim` file.
+the focused_workspace. The type of PDF output can be set with the kayword argument `pdf_type`, with the
+option of `G(r)`, `g(r)`, `RDF(r)` (defaults to `G(r)`). If run with *merge_banks=True* a PDF will be
+generated based on the wighted sum of the detector banks performed using supplied Q limits
+*q_lims=q_limits*, Q_limits can be in the form of a numpy array with shape (2, x) where x is the number
+of detectors, or a string containing the directory of an appropriately formatted `.lim` file.
This function applies the placzek self scattering correction from
:ref:CalculatePlaczekSelfScattering <algm-CalculatePlaczekSelfScattering> before calculating the PDF
diff --git a/scripts/Diffraction/isis_powder/polaris.py b/scripts/Diffraction/isis_powder/polaris.py
index 89b7c365a5a..5f1f76451d8 100644
--- a/scripts/Diffraction/isis_powder/polaris.py
+++ b/scripts/Diffraction/isis_powder/polaris.py
@@ -51,6 +51,9 @@ class Polaris(AbstractInst):
def create_total_scattering_pdf(self, **kwargs):
if 'q_lims' not in kwargs:
kwargs['q_lims'] = None
+ if 'pdf_type' not in kwargs or not kwargs['pdf_type'] in ['G(r)', 'g(r)', 'RDF(r)']:
+ kwargs['pdf_type'] = 'G(r)'
+ print('PDF type not specified or is invalid, defaulting to G(r)')
self._inst_settings.update_attributes(kwargs=kwargs)
# Generate pdf
run_details = self._get_run_details(self._inst_settings.run_number)
@@ -61,7 +64,8 @@ class Polaris(AbstractInst):
merge_banks=self._inst_settings.merge_banks,
q_lims=self._inst_settings.q_lims,
cal_file_name=cal_file_name,
- sample_details=self._sample_details)
+ sample_details=self._sample_details,
+ pdf_type=self._inst_settings.pdf_type)
return pdf_output
def set_sample_details(self, **kwargs):
diff --git a/scripts/Diffraction/isis_powder/polaris_routines/polaris_algs.py b/scripts/Diffraction/isis_powder/polaris_routines/polaris_algs.py
index 8cf5287de59..6990ef53e71 100644
--- a/scripts/Diffraction/isis_powder/polaris_routines/polaris_algs.py
+++ b/scripts/Diffraction/isis_powder/polaris_routines/polaris_algs.py
@@ -80,7 +80,7 @@ def save_unsplined_vanadium(vanadium_ws, output_path):
def generate_ts_pdf(run_number, focus_file_path, merge_banks=False, q_lims=None, cal_file_name=None,
- sample_details=None):
+ sample_details=None, pdf_type="G(r)"):
focused_ws = _obtain_focused_run(run_number, focus_file_path)
focused_ws = mantid.ConvertUnits(InputWorkspace=focused_ws, Target="MomentumTransfer", EMode='Elastic')
@@ -107,11 +107,11 @@ def generate_ts_pdf(run_number, focus_file_path, merge_banks=False, q_lims=None,
q_min, q_max = _load_qlims(q_lims)
merged_ws = mantid.MatchAndMergeWorkspaces(InputWorkspaces=focused_ws, XMin=q_min, XMax=q_max,
CalculateScale=False)
- pdf_output = mantid.PDFFourierTransform(Inputworkspace=merged_ws, InputSofQType="S(Q)-1", PDFType="G(r)",
+ pdf_output = mantid.PDFFourierTransform(Inputworkspace=merged_ws, InputSofQType="S(Q)-1", PDFType=pdf_type,
Filter=True)
else:
pdf_output = mantid.PDFFourierTransform(Inputworkspace='focused_ws', InputSofQType="S(Q)-1",
- PDFType="G(r)", Filter=True)
+ PDFType=pdf_type, Filter=True)
pdf_output = mantid.RebinToWorkspace(WorkspaceToRebin=pdf_output, WorkspaceToMatch=pdf_output[4],
PreserveEvents=True)
common.remove_intermediate_workspace('self_scattering_correction')
diff --git a/scripts/Diffraction/isis_powder/polaris_routines/polaris_param_mapping.py b/scripts/Diffraction/isis_powder/polaris_routines/polaris_param_mapping.py
index 911791606e0..7313731c246 100644
--- a/scripts/Diffraction/isis_powder/polaris_routines/polaris_param_mapping.py
+++ b/scripts/Diffraction/isis_powder/polaris_routines/polaris_param_mapping.py
@@ -28,6 +28,7 @@ attr_mapping = [
ParamMapEntry(ext_name="mode", int_name="mode", enum_class=POLARIS_CHOPPER_MODES,
optional=True),
ParamMapEntry(ext_name="multiple_scattering", int_name="multiple_scattering", optional=True),
+ ParamMapEntry(ext_name="pdf_type", int_name="pdf_type"),
ParamMapEntry(ext_name="q_lims", int_name="q_lims"),
ParamMapEntry(ext_name="raw_data_cropping_values", int_name="raw_data_crop_values"),
ParamMapEntry(ext_name="run_number", int_name="run_number"),
--
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