Merge pull request #21303 from mantidproject/21294_base_case_for_total_scattering

Total Scattering :: Add most basic form of total scattering workflow

Testing/SystemTests/tests/analysis/ISIS_PowderPolarisTest.py

@@ -95,6 +95,34 @@ class FocusTest(stresstesting.MantidStressTest):
             mantid.mtd.clear()
 
 
+class TotalScatteringTest(stresstesting.MantidStressTest):
+
+    pdf_output = None
+
+    def runTest(self):
+        # Load Focused ws
+        mantid.LoadNexus(Filename="ISIS_Powder-POLARIS98533_FocusSempty.nxs", OutputWorkspace='98533-Results-TOF-Grp')
+        self.pdf_output = run_total_scattering('98533', False)
+
+    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 51
+        expected_peak_values = [0.0187231,
+                                0.0583586,
+                                0.2241280,
+                                0.2752230,
+                                1.0252800]
+        for index, ws in enumerate(self.pdf_output):
+            self.assertAlmostEqual(ws.dataY(0)[51], expected_peak_values[index], places=3)
+
+
+def run_total_scattering(run_number, merge_banks):
+    pdf_inst_obj = setup_inst_object(mode="PDF")
+    return pdf_inst_obj.create_total_scattering_pdf(run_number=run_number,
+                                                    merge_banks=merge_banks)
+
+
 def _gen_required_files():
     required_run_numbers = ["98531", "98532",  # create_van : PDF mode
                             "98533"]  # File to focus (Si)

docs/source/release/v3.12.0/diffraction.rst

@@ -53,6 +53,11 @@ Single Crystal Diffraction
 - :ref:`FindUBUsingLatticeParameters <algm-FindUBUsingLatticeParameters>` now has option to specify number of iterations to refine UB. 
 
 
+Total Scattering
+----------------
+- A basic analysis for total scattering method ``create_total_scattering_pdf`` has been added to POLARIS. More information can be found on the POLARIS reference page.
+
+
 Imaging
 -------
 

docs/source/techniques/ISISPowder-Polaris-v1.rst

@@ -161,8 +161,44 @@ Example
 
   polaris_example.set_sample(sample=sample_obj)
 
+.. _create_total_scattering_pdf_polaris-isis-powder-ref:
+
+
+create_total_scattering_pdf
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+.. warning:: Total scattering support is not yet fully implemented.
+             Any results obtaining from using the below routine in its current
+             state should not be considered accurate or complete.
+
+The *create_total_scattering_pdf* method allows a user to create a Pair Distribution Function (PDF)
+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.
+
+This function requires the run_number you wish to analyse. The focused file for this run number must
+either be loaded in Mantid with the naming format given by the *focus* method:
+
+*<run number>-Results-<TOF/D>-Grp*
+
+for example:
+
+12345-Results-TOF-Grp
+
+Or the focused file must be in the output directory of the POLARIS instrument.
+
+
+Example
+=======
+
+..  code-block:: python
+
+  polaris_example.create_total_scattering_pdf(run_number='12345',
+                                              merge_banks=False)
+
 .. _calibration_mapping_polaris-isis-powder-ref:
 
+
 Calibration Mapping File
 -------------------------
 The calibration mapping file holds the mapping between

scripts/Diffraction/isis_powder/polaris.py

@@ -42,6 +42,16 @@ class Polaris(AbstractInst):
                                              output_path=run_details.unsplined_vanadium_file_path)
         return vanadium_d
 
+    def create_total_scattering_pdf(self, **kwargs):
+        self._inst_settings.update_attributes(kwargs=kwargs)
+        # Generate pdf
+        run_details = self._get_run_details(self._inst_settings.run_number)
+        focus_file_path = self._generate_out_file_paths(run_details)["nxs_filename"]
+        pdf_output = polaris_algs.generate_ts_pdf(run_number=self._inst_settings.run_number,
+                                                  focus_file_path=focus_file_path,
+                                                  merge_banks=self._inst_settings.merge_banks)
+        return pdf_output
+
     def set_sample_details(self, **kwargs):
         self._switch_mode_specific_inst_settings(kwargs.get("mode"))
         kwarg_name = "sample"

scripts/Diffraction/isis_powder/polaris_routines/polaris_algs.py

@@ -76,6 +76,44 @@ def save_unsplined_vanadium(vanadium_ws, output_path):
     mantid.DeleteWorkspace(converted_group)
 
 
+def generate_ts_pdf(run_number, focus_file_path, merge_banks=False):
+    focused_ws = _obtain_focused_run(run_number, focus_file_path)
+    pdf_output = mantid.ConvertUnits(InputWorkspace=focused_ws.getName(), Target="MomentumTransfer")
+    if merge_banks:
+        raise RuntimeError("Merging banks is currently not supported")
+    pdf_output = mantid.PDFFourierTransform(Inputworkspace=pdf_output, InputSofQType="S(Q)", PDFType="G(r)",
+                                            Filter=True)
+    pdf_output = mantid.RebinToWorkspace(WorkspaceToRebin=pdf_output, WorkspaceToMatch=pdf_output[4],
+                                         PreserveEvents=True)
+    return pdf_output
+
+
+def _obtain_focused_run(run_number, focus_file_path):
+    """
+    Searches for the focused workspace to use (based on user specified run number) in the ADS and then the output
+    directory.
+    If unsuccessful, a ValueError exception is thrown.
+    :param run_number: The run number to search for.
+    :param focus_file_path: The expected file path for the focused file.
+    :return: The focused workspace.
+    """
+    # Try the ADS first to avoid undesired loading
+    if mantid.mtd.doesExist('%s-Results-TOF-Grp' % run_number):
+        focused_ws = mantid.mtd['%s-Results-TOF-Grp' % run_number]
+    elif mantid.mtd.doesExist('%s-Results-D-Grp' % run_number):
+        focused_ws = mantid.mtd['%s-Results-D-Grp' % run_number]
+    else:
+        # Check output directory
+        print('No loaded focused files found. Searching in output directory...')
+        try:
+            focused_ws = mantid.LoadNexus(Filename=focus_file_path, OutputWorkspace='focused_ws').OutputWorkspace
+        except ValueError:
+            raise ValueError("Could not find focused file for run number:%s\n"
+                             "Please ensure a focused file has been produced and is located in the output directory."
+                             % run_number)
+    return focused_ws
+
+
 def _apply_bragg_peaks_masking(workspaces_to_mask, mask_list):
     output_workspaces = list(workspaces_to_mask)
 

scripts/Diffraction/isis_powder/polaris_routines/polaris_param_mapping.py

@@ -18,6 +18,7 @@ attr_mapping = \
      ParamMapEntry(ext_name="focused_bin_widths",          int_name="focused_bin_widths"),
      ParamMapEntry(ext_name="grouping_file_name",          int_name="grouping_file_name"),
      ParamMapEntry(ext_name="input_mode",                  int_name="input_mode", enum_class=INPUT_BATCHING),
+     ParamMapEntry(ext_name="merge_banks",                 int_name="merge_banks"),
      ParamMapEntry(ext_name="mode",                        int_name="mode", enum_class=POLARIS_CHOPPER_MODES),
      ParamMapEntry(ext_name="multiple_scattering",         int_name="multiple_scattering"),
      ParamMapEntry(ext_name="raw_data_cropping_values",    int_name="raw_data_crop_values"),