Re #19509 Fixed abs. corrections in focus mixing up units

scripts/Diffraction/isis_powder/gem.py

@@ -33,19 +33,17 @@ class Gem(AbstractInst):
                                      do_absorb_corrections=self._inst_settings.do_absorb_corrections)
 
     def set_sample_details(self, **kwargs):
+        kwarg_name = "sample"
         sample_details_obj = common.dictionary_key_helper(
-            dictionary=kwargs, key="new_sample_details",
+            dictionary=kwargs, key=kwarg_name,
             exception_msg="The argument containing sample details was not found. Please"
-                          " set the following argument: new_sample_details")
-        if not isinstance(sample_details_obj, sample_details.SampleDetails):
-            raise ValueError("The object passed was not a SampleDetails object. Please create a"
-                             " SampleDetails object and set the relevant properties to use on this method")
+                          " set the following argument: " + kwarg_name)
         self._sample_details = sample_details_obj
 
     # Private methods
 
     def _get_run_details(self, run_number_string):
-        run_number_string_key = run_number_string + str(self._inst_settings.file_extension)
+        run_number_string_key = str(run_number_string) + str(self._inst_settings.file_extension)
         if run_number_string_key in self._cached_run_details:
             return self._cached_run_details[run_number_string_key]
 
@@ -70,7 +68,7 @@ class Gem(AbstractInst):
         else:
             return absorb_corrections.run_cylinder_absorb_corrections(
                 ws_to_correct=ws_to_correct, multiple_scattering=self._inst_settings.multiple_scattering,
-                sample_details_obj=sample_details)
+                sample_details_obj=self._sample_details)
 
     def _crop_banks_to_user_tof(self, focused_banks):
         return common.crop_banks_using_crop_list(focused_banks, self._inst_settings.focused_cropping_values)

scripts/Diffraction/isis_powder/pearl.py

@@ -47,7 +47,7 @@ class Pearl(AbstractInst):
                                      do_absorb_corrections=self._inst_settings.absorb_corrections)
 
     def _get_run_details(self, run_number_string):
-        run_number_string_key = run_number_string + str(self._inst_settings.file_extension)
+        run_number_string_key = str(run_number_string) + str(self._inst_settings.file_extension)
         if run_number_string_key in self._cached_run_details:
             return self._cached_run_details[run_number_string_key]
 

scripts/Diffraction/isis_powder/polaris.py

@@ -35,13 +35,11 @@ class Polaris(AbstractInst):
                                      do_absorb_corrections=self._inst_settings.do_absorb_corrections)
 
     def set_sample_details(self, **kwargs):
+        kwarg_name = "sample"
         sample_details_obj = common.dictionary_key_helper(
-            dictionary=kwargs, key="new_sample_details",
+            dictionary=kwargs, key=kwarg_name,
             exception_msg="The argument containing sample details was not found. Please"
-                          " set the following argument: new_sample_details")
-        if not isinstance(sample_details_obj, sample_details.SampleDetails):
-            raise ValueError("The object passed was not a SampleDetails object. Please create a"
-                             " SampleDetails object and set the relevant properties to use on this method")
+                          " set the following argument: " + kwarg_name)
         self._sample_details = sample_details_obj
 
     # Overrides
@@ -52,7 +50,7 @@ class Polaris(AbstractInst):
         else:
             return absorb_corrections.run_cylinder_absorb_corrections(
                 ws_to_correct=ws_to_correct, multiple_scattering=self._inst_settings.multiple_scattering,
-                sample_details_obj=sample_details)
+                sample_details_obj=self._sample_details)
 
     @staticmethod
     def _can_auto_gen_vanadium_cal():
@@ -105,7 +103,7 @@ class Polaris(AbstractInst):
         return self._inst_settings.input_mode
 
     def _get_run_details(self, run_number_string):
-        run_number_string_key = run_number_string + str(self._inst_settings.file_extension)
+        run_number_string_key = str(run_number_string) + str(self._inst_settings.file_extension)
         if run_number_string_key in self._run_details_cached_obj:
             return self._run_details_cached_obj[run_number_string_key]
 

scripts/Diffraction/isis_powder/routines/absorb_corrections.py

@@ -2,7 +2,7 @@ from __future__ import (absolute_import, division, print_function)
 
 import mantid.simpleapi as mantid
 
-from isis_powder.routines import common, sample_details
+from isis_powder.routines import common, common_enums, sample_details
 
 
 def create_vanadium_sample_details_obj(config_dict):
@@ -26,7 +26,7 @@ def create_vanadium_sample_details_obj(config_dict):
     formula = common.dictionary_key_helper(dictionary=config_dict, key=formula_key, exception_msg=e_msg + formula_key)
     number_density = common.dictionary_key_helper(dictionary=config_dict, key=number_density_key, throws=False)
 
-    vanadium_sample_details = sample_details.SampleDetails(height=height, radius=radius, pos=pos)
+    vanadium_sample_details = sample_details.SampleDetails(height=height, radius=radius, center=pos)
     vanadium_sample_details.set_material(chemical_formula=formula, number_density=number_density)
     return vanadium_sample_details
 
@@ -43,6 +43,11 @@ def run_cylinder_absorb_corrections(ws_to_correct, multiple_scattering, sample_d
     :return: The corrected workspace
     """
 
+    if not isinstance(sample_details_obj, sample_details.SampleDetails):
+        raise RuntimeError("A SampleDetails object was not set or a different object type was found. Please create a"
+                           " SampleDetails object and set the relevant properties it. Then set the new sample by "
+                           "calling set_sample_details()")
+
     height = sample_details_obj.height
     radius = sample_details_obj.radius
     pos = sample_details_obj.center
@@ -88,9 +93,17 @@ def _calculate__cylinder_absorb_corrections(ws_to_correct, multiple_scattering,
 
     mantid.SetSample(InputWorkspace=ws_to_correct, Geometry=geometry_json, Material=material_json)
 
-    ws_to_correct = mantid.ConvertUnits(InputWorkspace=ws_to_correct, OutputWorkspace=ws_to_correct, Target="TOF")
+    previous_units = ws_to_correct.getAxis(0).getUnit().unitID()
+    ws_units = common_enums.WORKSPACE_UNITS
+
+    # Mayers Sample correction must be completed in TOF, convert if needed. Then back to original units afterwards
+    if previous_units != ws_units.tof:
+        ws_to_correct = mantid.ConvertUnits(InputWorkspace=ws_to_correct, OutputWorkspace=ws_to_correct,
+                                            Target=ws_units.tof)
     ws_to_correct = mantid.MayersSampleCorrection(InputWorkspace=ws_to_correct, OutputWorkspace=ws_to_correct,
                                                   MultipleScattering=multiple_scattering)
-    ws_to_correct = mantid.ConvertUnits(InputWorkspace=ws_to_correct, OutputWorkspace=ws_to_correct, Target="dSpacing")
+    if previous_units != ws_units.tof:
+        ws_to_correct = mantid.ConvertUnits(InputWorkspace=ws_to_correct, OutputWorkspace=ws_to_correct,
+                                            Target=previous_units)
 
     return ws_to_correct

scripts/Diffraction/isis_powder/routines/focus.py

@@ -14,7 +14,7 @@ def focus(run_number_string, instrument, perform_vanadium_norm, absorb):
         return _individual_run_focusing(instrument=instrument, perform_vanadium_norm=perform_vanadium_norm,
                                         run_number=run_number_string, absorb=absorb)
     elif input_batching == INPUT_BATCHING.Summed:
-        return _batched_run_focusing(instrument, perform_vanadium_norm, run_number_string)
+        return _batched_run_focusing(instrument, perform_vanadium_norm, run_number_string, absorb=absorb)
     else:
         raise ValueError("Input batching not passed through. Please contact development team.")
 
@@ -33,17 +33,18 @@ def _focus_one_ws(ws, run_number, instrument, perform_vanadium_norm, absorb):
                                                       empty_sample_ws_string=run_details.sample_empty,
                                                       scale_factor=instrument._inst_settings.sample_empty_scale)
 
-    # Correct for absorption / multiple scattering if required
-    if absorb:
-        input_workspace = instrument._apply_absorb_corrections(run_details=run_details, ws_to_correct=input_workspace)
-
     # Crop to largest acceptable TOF range
     input_workspace = instrument._crop_raw_to_expected_tof_range(ws_to_crop=input_workspace)
 
-    # Align / Focus
+    # Align
     aligned_ws = mantid.AlignDetectors(InputWorkspace=input_workspace,
                                        CalibrationFile=run_details.offset_file_path)
 
+    # Correct for absorption / multiple scattering if required
+    if absorb:
+        input_workspace = instrument._apply_absorb_corrections(run_details=run_details, ws_to_correct=input_workspace)
+
+    # Focus the spectra into banks
     focused_ws = mantid.DiffractionFocussing(InputWorkspace=aligned_ws,
                                              GroupingFileName=run_details.grouping_file_path)
 

scripts/Diffraction/isis_powder/routines/instrument_settings.py

@@ -26,8 +26,8 @@ class InstrumentSettings(object):
         if kwargs:
             config_file_path = kwargs.get("config_file", None)
             if not config_file_path:
-                warnings.warn("No config file was specified. If one was meant to be used the path to a YAML config file"
-                              " is set with the 'config_file' parameter.")
+                warnings.warn("No config file was specified. If a configuration file  was meant to be used "
+                              "the path to the file is set with the 'config_file' parameter.\n")
             # Always do this so we have a known state of the internal variable
             self._basic_conf_dict = yaml_parser.open_yaml_file_as_dictionary(config_file_path)
 

scripts/Diffraction/isis_powder/routines/sample_details.py

@@ -43,7 +43,7 @@ class SampleDetails(object):
                                " have not been set they can be modified with 'set_material_properties()'. Otherwise"
                                " to change the material call 'reset_sample_material()'")
 
-        self.material_object = _Material(chemical_formula=chemical_formula, numeric_density=number_density)
+        self.material_object = _Material(chemical_formula=chemical_formula, number_density=number_density)
 
     def set_material_properties(self, **kwargs):
         err_msg = "The following argument is required but was not set or passed: "
@@ -95,20 +95,20 @@ class SampleDetails(object):
 
 
 class _Material(object):
-    def __init__(self, chemical_formula, numeric_density=None):
+    def __init__(self, chemical_formula, number_density=None):
         self.chemical_formula = chemical_formula
 
-        # If it is not an element Mantid requires us to provide the numeric density
+        # If it is not an element Mantid requires us to provide the number density
         # which is required for absorption corrections.
-        if len(chemical_formula) > 2 and numeric_density is None:
-                raise ValueError("A numeric density formula must be set on a chemical formula which is not elemental."
-                                 " An element can only be a maximum of 2 characters (e.g. 'Si' or 'V'). The numeric"
-                                 " density can be set using the following key: numeric_density")
-        if numeric_density:
+        if len(chemical_formula) > 2 and number_density is None:
+                raise ValueError("A number density formula must be set on a chemical formula which is not elemental."
+                                 " An element can only be a maximum of 2 characters (e.g. 'Si' or 'V'). The number"
+                                 " density can be set using the following key: number_density")
+        if number_density:
             # Always check value is sane if user has given one
-            _check_value_is_physical(property_name="numeric_density", value=numeric_density)
+            _check_value_is_physical(property_name="number_density", value=number_density)
 
-        self.numeric_density = numeric_density
+        self.number_density = number_density
 
         # Advanced material properties
         self.absorption_cross_section = None
@@ -122,10 +122,10 @@ class _Material(object):
         print("------------------------")
         print("Chemical formula: {}".format(self.chemical_formula))
 
-        if self.numeric_density:
-            print("Numeric Density: {}".format(self.numeric_density))
+        if self.number_density:
+            print("Number Density: {}".format(self.number_density))
         else:
-            print("Numeric Density: Set from elemental properties by Mantid")
+            print("Number Density: Set from elemental properties by Mantid")
         self._print_material_properties()
 
     def _print_material_properties(self):

scripts/test/ISISPowderSampleDetailsTest.py

@@ -149,7 +149,7 @@ class ISISPowderSampleDetailsTest(unittest.TestCase):
         material_obj_one_char = sample_details._Material(chemical_formula=chemical_formula_one_char_element)
         self.assertIsNotNone(material_obj_one_char)
         self.assertEqual(material_obj_one_char.chemical_formula, chemical_formula_one_char_element)
-        self.assertIsNone(material_obj_one_char.numeric_density)
+        self.assertIsNone(material_obj_one_char.number_density)
 
         # Also check that the absorption and scattering X sections have not been set
         self.assertIsNone(material_obj_one_char.absorption_cross_section)
@@ -160,12 +160,12 @@ class ISISPowderSampleDetailsTest(unittest.TestCase):
         material_obj_two_char = sample_details._Material(chemical_formula=chemical_formula_two_char_element)
         self.assertIsNotNone(material_obj_two_char)
         self.assertEqual(material_obj_two_char.chemical_formula, chemical_formula_two_char_element)
-        self.assertIsNone(material_obj_two_char.numeric_density)
+        self.assertIsNone(material_obj_two_char.number_density)
 
         # Check it stores numeric density if passed
         material_obj_numeric_density = sample_details._Material(chemical_formula=chemical_formula_two_char_element,
                                                                 numeric_density=numeric_density_sample)
-        self.assertEqual(material_obj_numeric_density.numeric_density, numeric_density_sample)
+        self.assertEqual(material_obj_numeric_density.number_density, numeric_density_sample)
 
         # Check that it raises an error if we have a non-elemental formula without numeric density
         with assertRaisesRegex(self, ValueError, "A numeric density formula must be set on a chemical formula"):
@@ -175,7 +175,7 @@ class ISISPowderSampleDetailsTest(unittest.TestCase):
         material_obj_num_complex_formula = sample_details._Material(chemical_formula=chemical_formula_complex,
                                                                     numeric_density=numeric_density_sample)
         self.assertEqual(material_obj_num_complex_formula.chemical_formula, chemical_formula_complex)
-        self.assertEqual(material_obj_num_complex_formula.numeric_density, numeric_density_sample)
+        self.assertEqual(material_obj_num_complex_formula.number_density, numeric_density_sample)
 
     def test_material_set_properties(self):
         bad_absorb = '-1'