Re #18108 PEARL attenuate for all and trans modes

scripts/Diffraction/isis_powder/pearl.py

@@ -11,6 +11,7 @@ from isis_powder.pearl_routines import pearl_algs, pearl_output, pearl_advanced_
 class Pearl(AbstractInst):
     def __init__(self, **kwargs):
         basic_config_dict = yaml_parser.open_yaml_file_as_dictionary(kwargs.get("config_file", None))
+
         self._inst_settings = InstrumentSettings.InstrumentSettings(
            attr_mapping=pearl_param_mapping.attr_mapping, adv_conf_dict=pearl_advanced_config.get_all_adv_variables(),
            basic_conf_dict=basic_config_dict, kwargs=kwargs)

scripts/Diffraction/isis_powder/pearl_routines/pearl_advanced_config.py

@@ -40,7 +40,8 @@ long_mode_off_params = {
 long_mode_on_params = {
     "monitor_lambda_crop_range": (5.9, 12.0),
     "monitor_integration_range": (6, 10),
-    # This needs to be greater than the bank TOF cropping values or you will get data that divides to 0/inf
+    # raw_data_tof_cropping needs to be greater than the bank TOF cropping values or
+    # you will get data that divides to 0 or inf
     "raw_data_tof_cropping": (20280, 39995),
     "vanadium_tof_cropping": (20295, 39993),
     "tof_cropping_ranges": [
@@ -83,11 +84,11 @@ variable_help = {
         "monitor_integration_range": "The minimum and maximum values to consider whilst integrating the monitor "
                                      "workspace",
         "raw_data_tof_cropping": "The crop values for to apply when loading raw data. This step is applied before any "
-                                 "processing takes place. This is to crop from 40,000 microseconds windows in the "
-                                 "raw data to 20,000 windows in PEARL",
+                                 "processing takes place. This is to crop from 40,000 microseconds in the "
+                                 "raw data to 20,000 microseconds worth of data",
         "tof_cropping_ranges": "These values are used to determine the TOF range to crop a focused (not Vanadium "
-                               "Cal.) workspace to. These are applied on a bank by bank basis. They must be less than "
-                               "the values specified for raw_data_tof_cropping."
+                               "calibration) workspace to. These are applied on a bank by bank basis. They must be "
+                               "less than the values specified for raw_data_tof_cropping."
     },
 
     "general_params": {

scripts/Diffraction/isis_powder/pearl_routines/pearl_output.py

@@ -11,7 +11,7 @@ def generate_and_save_focus_output(instrument, processed_spectra, run_details, p
     output_file_paths = instrument.generate_out_file_paths(run_details=run_details)
 
     if focus_mode == "all":
-        processed_nexus_files = _focus_mode_all(output_file_paths, processed_spectra)
+        processed_nexus_files = _focus_mode_all(output_file_paths, processed_spectra, perform_attenuation, instrument)
     elif focus_mode == "groups":
         processed_nexus_files = _focus_mode_groups(output_file_paths, processed_spectra)
     elif focus_mode == "trans":
@@ -24,6 +24,14 @@ def generate_and_save_focus_output(instrument, processed_spectra, run_details, p
     return processed_nexus_files
 
 
+def _attenuate_workspace(instrument, output_file_paths, ws_to_attenuate):
+    # Clone a workspace which is not attenuated
+    no_att = output_file_paths["output_name"] + "_noatten"
+    mantid.CloneWorkspace(InputWorkspace=ws_to_attenuate, OutputWorkspace=no_att)
+    ws_to_attenuate = instrument.attenuate_workspace(ws_to_attenuate)
+    return ws_to_attenuate
+
+
 def _focus_mode_mods(output_file_paths, calibrated_spectra):
     index = 1
     append = False
@@ -41,44 +49,36 @@ def _focus_mode_mods(output_file_paths, calibrated_spectra):
     return output_list
 
 
-def _focus_mode_trans(output_file_paths, atten, instrument, calibrated_spectra):
-    summed_ws = mantid.CloneWorkspace(InputWorkspace=calibrated_spectra[0])
-    for i in range(1, 9):  # Add workspaces 2-9 to workspace 1
-        summed_ws = mantid.Plus(LHSWorkspace=summed_ws, RHSWorkspace=calibrated_spectra[i])
-
-    summed_ws = mantid.Scale(InputWorkspace=summed_ws, Factor=0.111111111111111)
-
-    if atten:
-        # Clone a workspace which is not attenuated
-        no_att = output_file_paths["output_name"] + "_noatten"
-        mantid.CloneWorkspace(InputWorkspace=summed_ws, OutputWorkspace=no_att)
+def _focus_mode_all(output_file_paths, processed_spectra, perform_attenuation, instrument):
+    summed_spectra_name = output_file_paths["output_name"] + "_mods1-9"
+    summed_spectra = mantid.MergeRuns(InputWorkspaces=processed_spectra[:9], OutputWorkspace=summed_spectra_name)
 
-        summed_ws = mantid.ConvertUnits(InputWorkspace=summed_ws, Target="dSpacing")
-        summed_ws = instrument.attenuate_workspace(summed_ws)
-        summed_ws = mantid.ConvertUnits(InputWorkspace=summed_ws, Target="TOF")
+    summed_spectra = mantid.Scale(InputWorkspace=summed_spectra, Factor=0.111111111111111,
+                                  OutputWorkspace=summed_spectra_name)
+    if perform_attenuation:
+        summed_spectra = _attenuate_workspace(instrument, output_file_paths, summed_spectra)
 
-    mantid.SaveGSS(InputWorkspace=summed_ws, Filename=output_file_paths["gss_filename"], Append=False, Bank=1)
-    mantid.SaveFocusedXYE(InputWorkspace=summed_ws, Filename=output_file_paths["tof_xye_filename"],
-                          Append=False, IncludeHeader=False)
+    summed_spectra = mantid.ConvertUnits(InputWorkspace=summed_spectra, Target="TOF",
+                                         OutputWorkspace=summed_spectra_name)
 
-    summed_ws = mantid.ConvertUnits(InputWorkspace=summed_ws, Target="dSpacing")
+    mantid.SaveGSS(InputWorkspace=summed_spectra, Filename=output_file_paths["gss_filename"], Append=False, Bank=1)
 
-    # Rename to user friendly name:
-    summed_ws_name = output_file_paths["output_name"] + "_mods1-9"
-    summed_ws = mantid.RenameWorkspace(InputWorkspace=summed_ws, OutputWorkspace=summed_ws_name)
+    summed_spectra = mantid.ConvertUnits(InputWorkspace=summed_spectra, Target="dSpacing",
+                                         OutputWorkspace=summed_spectra_name)
+    mantid.SaveNexus(Filename=output_file_paths["nxs_filename"], InputWorkspace=summed_spectra, Append=False)
 
-    mantid.SaveFocusedXYE(InputWorkspace=summed_ws, Filename=output_file_paths["dspacing_xye_filename"],
-                          Append=False, IncludeHeader=False)
-    mantid.SaveNexus(InputWorkspace=summed_ws, Filename=output_file_paths["nxs_filename"], Append=False)
+    output_list = [summed_spectra]
+    for i in range(0, 5):
+        spectra_index = (i + 9)  # Compensate for 0 based index
+        ws_to_save = processed_spectra[spectra_index]  # Save out workspaces 10/11/12
+        output_name = output_file_paths["output_name"] + "_mod" + str(spectra_index + 1)
 
-    output_list = [summed_ws]
+        ws_to_save = mantid.ConvertUnits(InputWorkspace=ws_to_save, OutputWorkspace=ws_to_save, Target="TOF")
+        mantid.SaveGSS(InputWorkspace=ws_to_save, Filename=output_file_paths["gss_filename"], Append=True, Bank=i + 2)
+        ws_to_save = mantid.ConvertUnits(InputWorkspace=ws_to_save, OutputWorkspace=output_name, Target="dSpacing")
+        mantid.SaveNexus(Filename=output_file_paths["nxs_filename"], InputWorkspace=ws_to_save, Append=True)
 
-    for i in range(0, 9):
-        workspace_name = output_file_paths["output_name"] + "_mod" + str(i + 1)
-        to_save = mantid.ConvertUnits(InputWorkspace=calibrated_spectra[i], Target="dSpacing",
-                                      OutputWorkspace=workspace_name)
-        output_list.append(to_save)
-        mantid.SaveNexus(Filename=output_file_paths["nxs_filename"], InputWorkspace=to_save, Append=True)
+        output_list.append(ws_to_save)
 
     return output_list
 
@@ -121,33 +121,36 @@ def _focus_mode_groups(output_file_paths, calibrated_spectra):
     return output_list
 
 
-def _focus_mode_all(output_file_paths, processed_spectra):
-    summed_spectra_name = output_file_paths["output_name"] + "_mods1-9"
-    summed_spectra = mantid.MergeRuns(InputWorkspaces=processed_spectra[:9], OutputWorkspace=summed_spectra_name)
+def _focus_mode_trans(output_file_paths, atten, instrument, calibrated_spectra):
+    summed_ws = mantid.MergeRuns(InputWorkspaces=calibrated_spectra[:9])
+    summed_ws = mantid.Scale(InputWorkspace=summed_ws, Factor=0.111111111111111)
 
-    summed_spectra = mantid.Scale(InputWorkspace=summed_spectra, Factor=0.111111111111111,
-                                  OutputWorkspace=summed_spectra_name)
-    summed_spectra = mantid.ConvertUnits(InputWorkspace=summed_spectra, Target="TOF",
-                                         OutputWorkspace=summed_spectra_name)
+    if atten:
+        summed_ws = _attenuate_workspace(instrument, output_file_paths, summed_ws)
 
-    mantid.SaveGSS(InputWorkspace=summed_spectra, Filename=output_file_paths["gss_filename"], Append=False, Bank=1)
+    summed_ws = mantid.ConvertUnits(InputWorkspace=summed_ws, Target="TOF")
+    mantid.SaveGSS(InputWorkspace=summed_ws, Filename=output_file_paths["gss_filename"], Append=False, Bank=1)
+    mantid.SaveFocusedXYE(InputWorkspace=summed_ws, Filename=output_file_paths["tof_xye_filename"],
+                          Append=False, IncludeHeader=False)
 
-    summed_spectra = mantid.ConvertUnits(InputWorkspace=summed_spectra, Target="dSpacing",
-                                         OutputWorkspace=summed_spectra_name)
-    mantid.SaveNexus(Filename=output_file_paths["nxs_filename"], InputWorkspace=summed_spectra, Append=False)
+    summed_ws = mantid.ConvertUnits(InputWorkspace=summed_ws, Target="dSpacing")
 
-    output_list = [summed_spectra]
-    for i in range(0, 5):
-        spectra_index = (i + 9)  # Compensate for 0 based index
-        ws_to_save = processed_spectra[spectra_index]  # Save out workspaces 10/11/12
-        output_name = output_file_paths["output_name"] + "_mod" + str(spectra_index + 1)
+    # Rename to user friendly name:
+    summed_ws_name = output_file_paths["output_name"] + "_mods1-9"
+    summed_ws = mantid.RenameWorkspace(InputWorkspace=summed_ws, OutputWorkspace=summed_ws_name)
 
-        ws_to_save = mantid.ConvertUnits(InputWorkspace=ws_to_save, OutputWorkspace=ws_to_save, Target="TOF")
-        mantid.SaveGSS(InputWorkspace=ws_to_save, Filename=output_file_paths["gss_filename"], Append=True, Bank=i + 2)
-        ws_to_save = mantid.ConvertUnits(InputWorkspace=ws_to_save, OutputWorkspace=output_name, Target="dSpacing")
-        mantid.SaveNexus(Filename=output_file_paths["nxs_filename"], InputWorkspace=ws_to_save, Append=True)
+    mantid.SaveFocusedXYE(InputWorkspace=summed_ws, Filename=output_file_paths["dspacing_xye_filename"],
+                          Append=False, IncludeHeader=False)
+    mantid.SaveNexus(InputWorkspace=summed_ws, Filename=output_file_paths["nxs_filename"], Append=False)
 
-        output_list.append(ws_to_save)
+    output_list = [summed_ws]
+
+    for i in range(0, 9):
+        workspace_name = output_file_paths["output_name"] + "_mod" + str(i + 1)
+        to_save = mantid.ConvertUnits(InputWorkspace=calibrated_spectra[i], Target="dSpacing",
+                                      OutputWorkspace=workspace_name)
+        output_list.append(to_save)
+        mantid.SaveNexus(Filename=output_file_paths["nxs_filename"], InputWorkspace=to_save, Append=True)
 
     return output_list
 

scripts/Diffraction/isis_powder/polaris_routines/polaris_advanced_config.py

@@ -48,8 +48,7 @@ variable_help = {
                              "defaulted to off and should be overridden in the basic configuration when necessary to "
                              "avoid them being performed accidentally.",
         "raw_data_cropping_values": "This specifies the valid range in TOF of the raw data. This is applied before any "
-                                    "processing takes place to remove negative counts where at very low TOF the empty "
-                                    "count => sample count.",
+                                    "processing takes place to remove negative counts at very low TOF values",
         "spline_coefficient": "The coefficient to use when calculating the vanadium splines during the calibration "
                               "step."
     },

scripts/Diffraction/isis_powder/routines/focus.py

@@ -18,19 +18,10 @@ def focus(run_number, instrument, input_batching, perform_vanadium_norm=True):
 
 def _focus_one_ws(ws, run_number, instrument, perform_vanadium_norm):
     run_details = instrument.get_run_details(run_number_string=run_number)
+    if perform_vanadium_norm:
+        _test_splined_vanadium_exists(instrument, run_details)
 
-    # Check the necessary splined vanadium file has been created
-    if not os.path.isfile(run_details.splined_vanadium_file_path):
-        if instrument.can_auto_gen_vanadium_cal():
-            warnings.warn("\nAttempting to automatically generate vanadium calibration at this path: "
-                          + str(run_details.splined_vanadium_file_path) + " for these settings.\n")
-            instrument.generate_auto_vanadium_calibration(run_details=run_details)
-        else:
-            ValueError("Processed vanadium runs not found at this path: "
-                       + str(run_details.splined_vanadium_file_path) +
-                       " \nHave you created a vanadium calibration with these settings yet?\n")
-
-    # Compensate for empty sample if specified
+    # Subtract and crop to largest acceptable TOF range
     input_workspace = common.subtract_sample_empty(ws_to_correct=ws, instrument=instrument,
                                                    empty_sample_ws_string=run_details.empty_runs)
     input_workspace = instrument.crop_raw_to_expected_tof_range(ws_to_crop=input_workspace)
@@ -52,7 +43,7 @@ def _focus_one_ws(ws, run_number, instrument, perform_vanadium_norm):
     # Output
     processed_nexus_files = instrument.output_focused_ws(calibrated_spectra, run_details=run_details)
 
-    # Tidy
+    # Tidy workspaces from Mantid
     common.remove_intermediate_workspace(input_workspace)
     common.remove_intermediate_workspace(focused_ws)
     common.remove_intermediate_workspace(calibrated_spectra)
@@ -60,16 +51,6 @@ def _focus_one_ws(ws, run_number, instrument, perform_vanadium_norm):
     return processed_nexus_files
 
 
-def _batched_run_focusing(input_batching, instrument, perform_vanadium_norm, run_number):
-    read_ws_list = common.load_current_normalised_ws_list(run_number_string=run_number,
-                                                          input_batching=input_batching, instrument=instrument)
-    output = None
-    for ws in read_ws_list:
-        output = _focus_one_ws(ws=ws, run_number=run_number, instrument=instrument,
-                               perform_vanadium_norm=perform_vanadium_norm)
-    return output
-
-
 def _apply_vanadium_corrections(instrument, run_number, input_workspace, perform_vanadium_norm):
     run_details = instrument.get_run_details(run_number_string=run_number)
     converted_ws = mantid.ConvertUnits(InputWorkspace=input_workspace, OutputWorkspace=input_workspace, Target="TOF")
@@ -84,6 +65,16 @@ def _apply_vanadium_corrections(instrument, run_number, input_workspace, perform
     return processed_spectra
 
 
+def _batched_run_focusing(input_batching, instrument, perform_vanadium_norm, run_number):
+    read_ws_list = common.load_current_normalised_ws_list(run_number_string=run_number,
+                                                          input_batching=input_batching, instrument=instrument)
+    output = None
+    for ws in read_ws_list:
+        output = _focus_one_ws(ws=ws, run_number=run_number, instrument=instrument,
+                               perform_vanadium_norm=perform_vanadium_norm)
+    return output
+
+
 def _divide_by_vanadium_splines(spectra_list, spline_file_path):
     vanadium_ws_list = mantid.LoadNexus(Filename=spline_file_path)
     output_list = []
@@ -104,3 +95,16 @@ def _individual_run_focusing(input_batching, instrument, perform_vanadium_norm,
         output = _focus_one_ws(ws=ws[0], run_number=run, instrument=instrument,
                                perform_vanadium_norm=perform_vanadium_norm)
     return output
+
+
+def _test_splined_vanadium_exists(instrument, run_details):
+    # Check the necessary splined vanadium file has been created
+    if not os.path.isfile(run_details.splined_vanadium_file_path):
+        if instrument.can_auto_gen_vanadium_cal():
+            warnings.warn("\nAttempting to automatically generate vanadium calibration at this path: "
+                          + str(run_details.splined_vanadium_file_path) + " for these settings.\n")
+            instrument.generate_auto_vanadium_calibration(run_details=run_details)
+        else:
+            ValueError("Processed vanadium runs not found at this path: "
+                       + str(run_details.splined_vanadium_file_path) +
+                       " \nHave you created a vanadium calibration with these settings yet?\n")