Re #18108 Documented adv. params for both instruments

scripts/Diffraction/isis_powder/pearl.py

@@ -65,10 +65,12 @@ class Pearl(AbstractInst):
         return _generate_file_name(run_number=run_number)
 
     def generate_output_file_name(self, run_number):
-        output_name = "PEARL" + str(run_number)
+
+        output_name = "PRL" + str(run_number)
         # Append each mode of operation
         output_name += "_" + self._inst_settings.tt_mode
-        output_name += "_long" if self._inst_settings.absorb_corrections else ""
+        output_name += "_absorb" if self._inst_settings.absorb_corrections else ""
+        output_name += "_long" if self._inst_settings.long_mode else ""
         return output_name
 
     def attenuate_workspace(self, input_workspace):

scripts/Diffraction/isis_powder/pearl_routines/pearl_advanced_config.py

@@ -14,9 +14,9 @@ long_mode_off_params = {
         "tt35_grouping": "pearl_group_12_1_TT35.cal"
     },
 
-    # This needs to be greater than the bank TOF cropping values or you will get data that divides to 0/inf
     "monitor_lambda_crop_range": (0.03, 6.00),
     "monitor_integration_range": (0.6, 5.0),
+    # 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": (0, 19995),
     "tof_cropping_ranges": [
         (1500, 19900),  # Bank 1
@@ -37,9 +37,9 @@ long_mode_off_params = {
 }
 
 long_mode_on_params = {
-    # This needs to be greater than the bank TOF cropping values or you will get data that divides to 0/inf
     "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": (20295, 39995),
     "tof_cropping_ranges": [
         (20300, 39990),  # Bank 1
@@ -61,20 +61,39 @@ long_mode_on_params = {
 
 
 variable_help = {
-    "file_names": {
-        "vanadium_absorb_file_name": "Takes the name of the calculated vanadium absorption corrections. This file "
-                                     " must be located in the top level of the calibration folder",
+    "long_mode_<on/off>_params": {
+        "file_names": {
+            "vanadium_absorb_file_name": "Takes the name of the calculated vanadium absorption corrections. This file "
+                                         " must be located in the top level of the calibration folder",
 
-        "tt88_grouping_name": "The name of the .cal file that defines the grouping of detectors in banks for TT88. "
-                              "This file must be located in the top level of the calibration folder.",
+            "tt88_grouping_name": "The name of the .cal file that defines the grouping of detectors in banks for TT88. "
+                                  "This file must be located in the top level of the calibration folder.",
 
-        "tt70_grouping_name": "The name of the .cal file that defines the grouping of detectors in banks for TT70. "
-                              "This file must be located in the top level of the calibration folder.",
+            "tt70_grouping_name": "The name of the .cal file that defines the grouping of detectors in banks for TT70. "
+                                  "This file must be located in the top level of the calibration folder.",
 
-        "tt35_grouping_name": "The name of the .cal file that defines the grouping of detectors in banks for TT35. "
-                              "This file must be located in the top level of the calibration folder.",
+            "tt35_grouping_name": "The name of the .cal file that defines the grouping of detectors in banks for TT35. "
+                                  "This file must be located in the top level of the calibration folder.",
+        },
 
+        "monitor_lambda_crop_range": "The range in wavelength to crop a monitor workspace to before calculating "
+                                     "the current normalisation",
+        "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",
+        "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."
+    },
 
+    "general_params": {
+        "monitor_spectrum_number": "The spectrum number the monitor is located at in the workspace",
+        "monitor_spline_coefficient": "The coefficient to use whilst calculating a spline from the monitor."
+                                      "workspace. This is used to normalise the workspace current.",
+        "spline_coefficient": "The coefficient to use whilst calculating a spline for each bank during "
+                              "a vanadium calibration."
     }
 }
 

scripts/Diffraction/isis_powder/pearl_routines/pearl_algs.py

@@ -46,8 +46,8 @@ def get_run_details(run_number_string, inst_settings):
     vanadium_run_numbers = mapping_dict["vanadium_run_numbers"]
 
     splined_vanadium_name = _generate_splined_van_name(absorb_on=inst_settings.absorb_corrections,
-                                                       long_mode=inst_settings.long_mode,
-                                                       vanadium_run_string=vanadium_run_numbers)
+                                                       vanadium_run_string=vanadium_run_numbers,
+                                                       long_mode_on=inst_settings.long_mode)
 
     calibration_dir = inst_settings.calibration_dir
     cycle_calibration_dir = os.path.join(calibration_dir, label)
@@ -101,12 +101,10 @@ def normalise_ws_current(ws_to_correct, monitor_ws, spline_coeff, lambda_values,
     return normalised_ws
 
 
-def _generate_splined_van_name(absorb_on, long_mode, vanadium_run_string):
+def _generate_splined_van_name(absorb_on, long_mode_on, vanadium_run_string):
     output_string = "SVan_" + str(vanadium_run_string)
-    if absorb_on:
-        output_string += "_absorb"
-    if long_mode:
-        output_string += "_long"
+    output_string += "_absorb" if absorb_on else ""
+    output_string += "_long" if long_mode_on else ""
 
     output_string += ".nxs"
     return output_string

scripts/Diffraction/isis_powder/pearl_routines/pearl_calibration.yaml

 94516-:
-  label : "16_3"
+  label : "16_4"
   vanadium_run_numbers : "95634-95647"
   empty_run_numbers : "95648-95654"
-  calibration_file : "pearl_offset_15_3.cal"  # Should be "pearl_offset_16_3.cal"
+  calibration_file : "pearl_offset_16_4.cal"  # Should be "pearl_offset_16_3.cal"

scripts/Diffraction/isis_powder/polaris.py

@@ -46,19 +46,13 @@ class Polaris(AbstractInst):
     def get_default_group_names(self):
         return self._calibration_grouping_names
 
-    # Abstract implementation
-
     def get_run_details(self, run_number_string):
         input_run_number_list = common.generate_run_numbers(run_number_string=run_number_string)
         first_run = input_run_number_list[0]
         if self._run_details_last_run_number == first_run:
             return self._run_details_cached_obj
 
-        # TODO use _inst_settings instead
-        run_details = polaris_algs.get_run_details(
-            chopper_on=self._inst_settings.chopper_on, sac_on=self._inst_settings.solid_angle_on,
-            run_number=first_run, calibration_dir=self._inst_settings.calibration_dir,
-            mapping_path=self._inst_settings.cal_mapping_file)
+        run_details = polaris_algs.get_run_details(run_number=first_run, inst_settings=self._inst_settings)
 
         # Hold obj in case same run range is requested
         self._run_details_last_run_number = first_run
@@ -118,7 +112,8 @@ class Polaris(AbstractInst):
         return d_spacing_group
 
     def crop_short_long_mode(self, ws_to_crop):
-        cropped_ws = common.crop_in_tof(ws_to_crop=ws_to_crop, x_min=800, x_max=20000)
+        cropped_ws = common.crop_in_tof(ws_to_crop=ws_to_crop, x_min=self._inst_settings.raw_data_crop_values[0],
+                                        x_max=self._inst_settings.raw_data_crop_values[1])
         return cropped_ws
 
     def crop_banks_to_user_tof(self, focused_banks):

scripts/Diffraction/isis_powder/polaris_routines/polaris_advanced_config.py

@@ -4,6 +4,7 @@ file_names = {
 
 script_params = {
     "apply_solid_angle": False,
+    "raw_data_cropping_values": (800, 20000),
     "spline_coefficient": 100
 }
 
@@ -15,14 +16,12 @@ tof_cropping_ranges = [
     (1500, 19900),  # Bank 5
     ]
 
-variables = {
-    "file_names_dict": file_names,
-    "script_params": script_params,
-    "tof_cropping_ranges": tof_cropping_ranges
-}
-
 absorption_correction_params = {
-    # These are read directly by the generate absorb corrections functions instead of being parsed
+    # These are read directly by the generate absorb corrections functions instead of being parsed.
+    # Therefore they cannot be overridden using basic config files or keyword arguments.
+
+    # For documentation on their behaviour please see:
+    # http://docs.mantidproject.org/nightly/algorithms/CylinderAbsorption-v1.html
     "cylinder_sample_height": 4.0,
     "cylinder_sample_radius": 0.4,
 
@@ -35,3 +34,33 @@ absorption_correction_params = {
     "number_of_wavelength_points": 100,
     "exponential_method": "Normal"
 }
+
+variable_help = {
+    "file_names": {
+        "masking_file_name": "Specifies the name of the of the file containing the positions of the  Bragg Peaks to "
+                             "mask out. This must be located at the root of the calibration folder the user has "
+                             "specified."
+    },
+
+    "script_params": {
+        "apply_solid_angle": "Specifies if the script should perform solid angle corrections. This is usually "
+                             "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.",
+        "spline_coefficient": "The coefficient to use when calculating the vanadium splines during the calibration "
+                              "step."
+    },
+
+    "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_cropping_values."
+}
+
+variables = {
+    # Used by the script to find the dictionaries in advanced config.
+    "file_names_dict": file_names,
+    "script_params": script_params,
+    "tof_cropping_ranges": tof_cropping_ranges
+}

scripts/Diffraction/isis_powder/polaris_routines/polaris_algs.py

@@ -34,10 +34,10 @@ def generate_solid_angle_corrections(run_details, instrument):
     return corrections
 
 
-def get_run_details(chopper_on, sac_on, run_number, calibration_dir, mapping_path):
-    yaml_dict = yaml_parser.get_run_dictionary(run_number=run_number, file_path=mapping_path)
+def get_run_details(run_number, inst_settings):
+    yaml_dict = yaml_parser.get_run_dictionary(run_number=run_number, file_path=inst_settings.cal_mapping_file)
 
-    if chopper_on:
+    if inst_settings.chopper_on:
         chopper_config = yaml_dict["chopper_on"]
     else:
         chopper_config = yaml_dict["chopper_off"]
@@ -46,12 +46,13 @@ def get_run_details(chopper_on, sac_on, run_number, calibration_dir, mapping_pat
     empty_runs = chopper_config["empty_run_numbers"]
     vanadium_runs = chopper_config["vanadium_run_numbers"]
 
-    solid_angle_file_name = _generate_solid_angle_file_name(chopper_on=chopper_on,
+    solid_angle_file_name = _generate_solid_angle_file_name(chopper_on=inst_settings.chopper_on,
                                                             vanadium_run_string=vanadium_runs)
-    splined_vanadium_name = _generate_splined_van_name(chopper_on=chopper_on, sac_applied=sac_on,
+    splined_vanadium_name = _generate_splined_van_name(chopper_on=inst_settings.chopper_on,
+                                                       sac_applied=inst_settings.solid_angle_on,
                                                        vanadium_run_string=vanadium_runs)
 
-    in_calib_dir = os.path.join(calibration_dir, label)
+    in_calib_dir = os.path.join(inst_settings.calibration_dir, label)
     calibration_full_path = os.path.join(in_calib_dir, yaml_dict["offset_file_name"])
     grouping_full_path = os.path.join(in_calib_dir, yaml_dict["offset_file_name"])
     solid_angle_file_path = os.path.join(in_calib_dir, solid_angle_file_name)
@@ -97,6 +98,7 @@ def process_vanadium_for_focusing(bank_spectra, mask_path, spline_number):
     masked_workspace_list = _apply_bragg_peaks_masking(bank_spectra, mask_list=bragg_masking_list)
     output = common.spline_vanadium_for_focusing(focused_vanadium_spectra=masked_workspace_list,
                                                  num_splines=spline_number)
+    common.remove_intermediate_workspace(masked_workspace_list)
     return output
 
 

scripts/Diffraction/isis_powder/polaris_routines/polaris_param_mapping.py

@@ -10,6 +10,7 @@ attr_mapping = [("apply_solid_angle",           "solid_angle_on"),
                 ("do_absorb_corrections",       "do_absorb_corrections"),
                 ("generate_absorb_corrections", "gen_absorb_corrections"),
                 ("masking_file_name",           "masking_file_name"),
+                ("raw_data_cropping_values",    "raw_data_crop_values"),
                 ("spline_coefficient",          "spline_coeff"),
                 ("tof_cropping_ranges",         "tof_cropping_values"),
                 ("output_directory",            "output_dir"),

scripts/Diffraction/isis_powder/routines/common.py

@@ -6,8 +6,6 @@ from isis_powder.routines.common_enums import InputBatchingEnum
 
 # A small workaround to ensure when reading workspaces in a loop
 # the previous workspace does not got overridden
-global g_ads_workaround
-g_ads_workaround = {"read_ws": 0}
 
 
 def create_calibration_by_names(calibration_runs, startup_objects, grouping_file_name, group_names):
@@ -166,14 +164,15 @@ def _normalise_workspaces(ws_list, instrument, run_information):
 
 
 def _check_load_range(list_of_runs_to_load):
-    MAXIMUM_RANGE_LEN = 1000  # If more than this number of runs is entered probably wrong
-    if len(list_of_runs_to_load) > MAXIMUM_RANGE_LEN:
-        raise ValueError("More than " + str(MAXIMUM_RANGE_LEN) + " runs were selected."
+    maximum_range_len = 1000  # If more than this number of runs is entered probably wrong
+    if len(list_of_runs_to_load) > maximum_range_len:
+        raise ValueError("More than " + str(maximum_range_len) + " runs were selected."
                          " Found " + str(len(list_of_runs_to_load)) + " Aborting.")
 
 
 def _create_blank_cal_file(calibration_runs, out_grouping_file_name, instrument, group_names):
-    input_ws_list = load_current_normalised_ws_list(calibration_runs, instrument, input_batching=InputBatchingEnum.Summed)
+    input_ws_list = load_current_normalised_ws_list(calibration_runs, instrument,
+                                                    input_batching=InputBatchingEnum.Summed)
     calibration_d_spacing_ws = mantid.ConvertUnits(InputWorkspace=input_ws_list[0], Target="dSpacing")
     mantid.CreateCalFileByNames(InstrumentWorkspace=calibration_d_spacing_ws,
                                 GroupingFileName=out_grouping_file_name, GroupNames=group_names)