Revert "Re #18643 Add optional chemical properties for abs. corrections"

Re #18643 Let Mantid handle chemical properties

This reverts commit 60512423.

scripts/Diffraction/isis_powder/gem_routines/gem_advanced_config.py

@@ -14,6 +14,7 @@ absorption_correction_params = {
 gem_adv_config_params = {
     "raw_tof_cropping_values": (500, 20000),
     "spline_coefficient": 30
+
 }
 
 focused_cropping_values = [(550, 19900),  # Bank 1

scripts/Diffraction/isis_powder/gem_routines/gem_algs.py

@@ -27,7 +27,6 @@ def get_run_details(run_number_string, inst_settings):
     label = common.cal_map_dictionary_key_helper(cycle_map, "label")
     offset_file_name = common.cal_map_dictionary_key_helper(cycle_map, "offset_file_name")
     empty_runs = common.cal_map_dictionary_key_helper(cycle_map, "empty_run_numbers")
-    empty_containers_runs = common.cal_map_dictionary_key_helper(cycle_map, "empty_container_run_numbers")
     vanadium_runs = common.cal_map_dictionary_key_helper(cycle_map, "vanadium_run_numbers")
 
     # For GEM the grouping and offset file are identical
@@ -39,6 +38,8 @@ def get_run_details(run_number_string, inst_settings):
     offset_file_path = os.path.join(label_calibration_folder, offset_file_name)
     splined_file_path = os.path.join(label_calibration_folder, splined_vanadium_name)
 
+    # TODO generate splined vanadium name from common
+
     run_details = RunDetails.RunDetails(run_number=run_number)
     run_details.empty_runs = empty_runs
     run_details.user_input_run_number = run_number_string

scripts/Diffraction/isis_powder/routines/RunDetails.py

@@ -11,7 +11,6 @@ class RunDetails(object):
         self.run_number = run_number
         self.user_input_run_number = None
 
-        self.empty_container_runs = None
         self.empty_runs = None
         self.label = None
 

scripts/Diffraction/isis_powder/routines/absorb_corrections.py

@@ -23,7 +23,6 @@ def run_cylinder_absorb_corrections(ws_to_correct, multiple_scattering, config_d
     radius_key = "cylinder_sample_radius"
     pos_key = "cylinder_position"
     formula_key = "chemical_formula"
-    chemical_key = "chemical_properties"
 
     e_msg = "The following key was not found in the advanced configuration for sample correction:\n"
 
@@ -32,23 +31,16 @@ def run_cylinder_absorb_corrections(ws_to_correct, multiple_scattering, config_d
     pos = common.dictionary_key_helper(dictionary=config_dict, key=pos_key, exception_msg=e_msg + pos_key)
 
     formula = common.dictionary_key_helper(dictionary=config_dict, key=formula_key, exception_msg=e_msg + formula_key)
-    chemical_properties = common.dictionary_key_helper(dictionary=config_dict, key=chemical_key, throws=False)
-
-    position_dict = {
-        "cylinder_height": height,
-        "cylinder_radius": radius,
-        "cylinder_pos": pos
-    }
 
     ws_to_correct = _calculate__cylinder_absorb_corrections(
         ws_to_correct=ws_to_correct, multiple_scattering=multiple_scattering,
-        position_dict=position_dict, chemical_formula=formula, material_properties=chemical_properties)
+        c_height=height, c_radius=radius, c_pos=pos, chemical_formula=formula)
 
     return ws_to_correct
 
 
 def _calculate__cylinder_absorb_corrections(ws_to_correct, multiple_scattering,
-                                            position_dict, chemical_formula, material_properties):
+                                            c_height, c_radius, c_pos, chemical_formula):
     """
     Calculates vanadium absorption corrections for the specified workspace. The workspace
     should have any monitor spectra masked before being passed into this method. Additionally
@@ -62,9 +54,9 @@ def _calculate__cylinder_absorb_corrections(ws_to_correct, multiple_scattering,
     :param chemical_formula: The chemical formula of the container - usually set to 'V' for Vanadium
     :return: The workspace with corrections applied
     """
-    geometry_json = {'Shape': 'Cylinder', 'Height': position_dict["cylinder_height"],
-                     'Radius': position_dict["cylinder_radius"], 'Center': position_dict["cylinder_pos"]}
-    material_json = _get_material_json(chemical_formula=chemical_formula, material_properties=material_properties)
+    geometry_json = {'Shape': 'Cylinder', 'Height': c_height,
+                     'Radius': c_radius, 'Center': c_pos}
+    material_json = {'ChemicalFormula': chemical_formula}
 
     mantid.SetSample(InputWorkspace=ws_to_correct, Geometry=geometry_json, Material=material_json)
 
@@ -74,45 +66,3 @@ def _calculate__cylinder_absorb_corrections(ws_to_correct, multiple_scattering,
     ws_to_correct = mantid.ConvertUnits(InputWorkspace=ws_to_correct, OutputWorkspace=ws_to_correct, Target="dSpacing")
 
     return ws_to_correct
-
-
-def _get_material_json(chemical_formula, material_properties):
-    """
-    Returns a material JSON with either a chemical formula when using elemental chemicals
-    or uses user set chemical properties when required or the user has set them to generate
-    the required input for SetMaterial
-    :param chemical_formula: The formula of the chemical to use
-    :param material_properties: The materials properties dictionary as set by the user
-    :return: The material JSON for setSample with appropriate settings.
-    """
-    material_json = {'ChemicalFormula': chemical_formula}
-
-    is_elemental_vanadium = True if chemical_formula.lower() == 'v' else False
-
-    # Test if we can just use built in Mantid properties
-    if is_elemental_vanadium and not material_properties:
-        return material_json
-
-    # Else we have to parse the chemical formula specified below
-    err_message = "Custom properties was detected for the material but the required key was not set:\n"
-
-    attenuation_key = "attenuation_cross_section"
-    scattering_key = "scattering_cross_section"
-    sample_density_key = "sample_number_density"
-
-    attenuation_x_section = common.dictionary_key_helper(material_properties, attenuation_key,
-                                                         exception_msg=err_message + attenuation_key)
-    scattering_x_section = common.dictionary_key_helper(material_properties, scattering_key,
-                                                        exception_msg=err_message + scattering_key)
-    sample_density = common.dictionary_key_helper(material_properties, sample_density_key,
-                                                  exception_msg=err_message + sample_density_key)
-
-    material_json = {"SampleNumberDensity": sample_density,
-                     "AttenuationXSection": attenuation_x_section,
-                     "ScatteringXSection": scattering_x_section}
-
-    print ("Using custom chemical properties:")
-    for k, v in material_json.viewitems():
-        print (k, v)
-
-    return material_json

scripts/Diffraction/isis_powder/routines/calibrate.py

@@ -21,6 +21,8 @@ def create_van(instrument, run_details, absorb):
 
     aligned_ws = mantid.AlignDetectors(InputWorkspace=corrected_van_ws,
                                        CalibrationFile=run_details.offset_file_path)
+    import pydevd
+    pydevd.settrace('localhost', port=51205, stdoutToServer=True, stderrToServer=True)
     if absorb:
         aligned_ws = _apply_absorb_corrections(instrument=instrument, run_details=run_details,
                                                van_ws=aligned_ws)