Merge pull request #27667 from mantidproject/27607_change_pdf_transform_type_for_polaris

Add option to set PDF type on polaris create_total_scattering_pdf

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():

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

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 keyword 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 weighted 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

scripts/Diffraction/isis_powder/polaris.py

@@ -10,6 +10,7 @@ import os
 from isis_powder.routines import absorb_corrections, common, instrument_settings
 from isis_powder.abstract_inst import AbstractInst
 from isis_powder.polaris_routines import polaris_advanced_config, polaris_algs, polaris_param_mapping
+from mantid.kernel import logger
 
 
 class Polaris(AbstractInst):
@@ -51,6 +52,9 @@ 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)'
+            logger.warning('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 +65,8 @@ 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):

scripts/Diffraction/isis_powder/polaris_routines/polaris_algs.py

@@ -81,7 +81,7 @@ 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')
 
@@ -108,11 +108,11 @@ 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')

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"),