Add hack workflow for merge_banks in polaris.create_total_scattering

scripts/Diffraction/isis_powder/polaris.py

@@ -53,9 +53,12 @@ class Polaris(AbstractInst):
         # 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"]
+        run_details = self._get_run_details(run_number_string=self._inst_settings.run_number)
         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)
+                                                  merge_banks=self._inst_settings.merge_banks,
+                                                  q_lims=self._inst_settings.q_lims,
+                                                  grouping_file_path=run_details.grouping_file_path)
         return pdf_output
 
     def set_sample_details(self, **kwargs):

scripts/Diffraction/isis_powder/polaris_routines/polaris_algs.py

@@ -79,11 +79,41 @@ def save_unsplined_vanadium(vanadium_ws, output_path):
     mantid.DeleteWorkspace(converted_group)
 
 
-def generate_ts_pdf(run_number, focus_file_path, merge_banks=False):
+def generate_ts_pdf(run_number, focus_file_path, merge_banks=False, instrument=None, q_lims=None,
+                    grouping_file_path=None):
     focused_ws = _obtain_focused_run(run_number, focus_file_path)
     pdf_output = mantid.ConvertUnits(InputWorkspace=focused_ws.name(), Target="MomentumTransfer")
+
     if merge_banks:
-        raise RuntimeError("Merging banks is currently not supported")
+        placzek_self_scattering = mantid.CalculatePlaczekSelfScattering(InputWorkspace=pdf_output)
+        pdf_output = mantid.Subtract(LHSWorkspace=pdf_output, RHSWorkspace=placzek_self_scattering)
+
+        pdf_output = mantid.DiffractionFocussing(InputWorkspace=pdf_output,
+                                                 GroupingFileName=grouping_file_path)
+        pdf_output = mantid.MatchSpectra(InputWorkspace=pdf_output, ReferenceSpectrum=1)
+        if type(q_lims) == str:
+            q_min = []
+            q_max = []
+            try:
+                with open(q_lims, 'r') as f:
+                    line_list = [line.rstrip('\n') for line in f]
+                    for line in line_list[:-1]:
+                        value_list = line.split()
+                        q_min.append(value_list[2])
+                        q_max.append(value_list[3])
+            except IOError:
+                raise RuntimeError("q_lims is not valid")
+        elif type(q_lims) == list:
+            q_min = q_lims[0, :]
+            q_max = q_lims[1, :]
+        else:
+            raise RuntimeError("q_lims is not valid")
+        pdf_x_array = pdf_output.readX()
+        bin_width = pdf_x_array[1] - pdf_x_array[0]
+        pdf_output = mantid.CropWorkspaceRagged(InputWorkspace=pdf_output, XMin=q_min, XMax=q_max)
+        pdf_output = mantid.Rebin(InputWorkspace=pdf_output, Params=[q_min, bin_width, q_max])
+        pdf_output = mantid.SumSpectra(InputWorkspace=pdf_output, WeightedSum=True)
+
     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],

scripts/Diffraction/isis_powder/routines/calibrate.py

@@ -47,28 +47,33 @@ def create_van(instrument, run_details, absorb):
                                        CalibrationFile=run_details.offset_file_path)
     solid_angle = instrument.get_solid_angle_corrections(run_details.run_number, run_details)
     if solid_angle:
-        aligned_ws = mantid.Divide(LHSWorkspace=aligned_ws,RHSWorkspace=solid_angle)
+        aligned_ws = mantid.Divide(LHSWorkspace=aligned_ws, RHSWorkspace=solid_angle)
         mantid.DeleteWorkspace(solid_angle)
-    focused_vanadium = mantid.DiffractionFocussing(InputWorkspace=aligned_ws,
-                                                   GroupingFileName=run_details.grouping_file_path)
 
-    focused_spectra = common.extract_ws_spectra(focused_vanadium)
-    focused_spectra = instrument._crop_van_to_expected_tof_range(focused_spectra)
+    if instrument._inst_settings.mode != 'PDF':
+        focused_vanadium = mantid.DiffractionFocussing(InputWorkspace=aligned_ws,
+                                                       GroupingFileName=run_details.grouping_file_path)
 
-    d_spacing_group, tof_group = instrument._output_focused_ws(processed_spectra=focused_spectra,
-                                                               run_details=run_details)
+        focused_spectra = common.extract_ws_spectra(focused_vanadium)
+        focused_spectra = instrument._crop_van_to_expected_tof_range(focused_spectra)
 
-    _create_vanadium_splines(focused_spectra, instrument, run_details)
+        d_spacing_group, tof_group = instrument._output_focused_ws(processed_spectra=focused_spectra,
+                                                                   run_details=run_details)
 
-    common.keep_single_ws_unit(d_spacing_group=d_spacing_group, tof_group=tof_group,
-                               unit_to_keep=instrument._get_unit_to_keep())
+        _create_vanadium_splines(focused_spectra, instrument, run_details)
 
-    common.remove_intermediate_workspace(corrected_van_ws)
-    common.remove_intermediate_workspace(aligned_ws)
-    common.remove_intermediate_workspace(focused_vanadium)
-    common.remove_intermediate_workspace(focused_spectra)
+        common.keep_single_ws_unit(d_spacing_group=d_spacing_group, tof_group=tof_group,
+                                   unit_to_keep=instrument._get_unit_to_keep())
 
-    return d_spacing_group
+        common.remove_intermediate_workspace(corrected_van_ws)
+        common.remove_intermediate_workspace(aligned_ws)
+        common.remove_intermediate_workspace(focused_vanadium)
+        common.remove_intermediate_workspace(focused_spectra)
+
+        return d_spacing_group
+    else:
+        common.remove_intermediate_workspace(corrected_van_ws)
+        return aligned_ws
 
 
 def _create_vanadium_splines(focused_spectra, instrument, run_details):

scripts/Diffraction/isis_powder/routines/focus.py

@@ -65,35 +65,43 @@ def _focus_one_ws(input_workspace, run_number, instrument, perform_vanadium_norm
         mantid.DeleteWorkspace(solid_angle)
 
     # Focus the spectra into banks
-    focused_ws = mantid.DiffractionFocussing(InputWorkspace=aligned_ws,
-                                             GroupingFileName=run_details.grouping_file_path)
+    if instrument._inst_settings.mode != 'PDF':
+        focused_ws = mantid.DiffractionFocussing(InputWorkspace=aligned_ws,
+                                                 GroupingFileName=run_details.grouping_file_path)
 
-    calibrated_spectra = _apply_vanadium_corrections(instrument=instrument,
-                                                     input_workspace=focused_ws,
-                                                     perform_vanadium_norm=perform_vanadium_norm,
-                                                     vanadium_splines=vanadium_path)
+        calibrated_spectra = _apply_vanadium_corrections(instrument=instrument,
+                                                         input_workspace=focused_ws,
+                                                         perform_vanadium_norm=perform_vanadium_norm,
+                                                         vanadium_splines=vanadium_path)
 
-    output_spectra = instrument._crop_banks_to_user_tof(calibrated_spectra)
+        output_spectra = instrument._crop_banks_to_user_tof(calibrated_spectra)
 
-    bin_widths = instrument._get_instrument_bin_widths()
-    if bin_widths:
-        # Reduce the bin width if required on this instrument
-        output_spectra = common.rebin_workspace_list(workspace_list=output_spectra,
-                                                     bin_width_list=bin_widths)
+        bin_widths = instrument._get_instrument_bin_widths()
+        if bin_widths:
+            # Reduce the bin width if required on this instrument
+            output_spectra = common.rebin_workspace_list(workspace_list=output_spectra,
+                                                         bin_width_list=bin_widths)
 
-    # Output
-    d_spacing_group, tof_group = instrument._output_focused_ws(output_spectra, run_details=run_details)
+        # Output
+        d_spacing_group, tof_group = instrument._output_focused_ws(output_spectra, run_details=run_details)
 
-    common.keep_single_ws_unit(d_spacing_group=d_spacing_group, tof_group=tof_group,
-                               unit_to_keep=instrument._get_unit_to_keep())
+        common.keep_single_ws_unit(d_spacing_group=d_spacing_group, tof_group=tof_group,
+                                   unit_to_keep=instrument._get_unit_to_keep())
 
-    # Tidy workspaces from Mantid
-    common.remove_intermediate_workspace(input_workspace)
-    common.remove_intermediate_workspace(aligned_ws)
-    common.remove_intermediate_workspace(focused_ws)
-    common.remove_intermediate_workspace(output_spectra)
+        # Tidy workspaces from Mantid
+        common.remove_intermediate_workspace(input_workspace)
+        common.remove_intermediate_workspace(aligned_ws)
+        common.remove_intermediate_workspace(focused_ws)
+        common.remove_intermediate_workspace(output_spectra)
 
-    return d_spacing_group
+        return d_spacing_group
+    else:
+        calibrated_spectra = _apply_vanadium_corrections(instrument=instrument,
+                                                         input_workspace=aligned_ws,
+                                                         perform_vanadium_norm=perform_vanadium_norm,
+                                                         vanadium_splines=vanadium_path)
+        common.remove_intermediate_workspace(input_workspace)
+        return calibrated_spectra
 
 
 def _apply_vanadium_corrections(instrument, input_workspace, perform_vanadium_norm, vanadium_splines):