diff --git a/scripts/Diffraction/isis_powder/gem_routines/gem_advanced_config.py b/scripts/Diffraction/isis_powder/gem_routines/gem_advanced_config.py
index a37298079e2e85eebc10e99525a80cceea9e8063..0f1d6e7f40ee08f7519216cf6e1a9a2e21718642 100644
--- a/scripts/Diffraction/isis_powder/gem_routines/gem_advanced_config.py
+++ b/scripts/Diffraction/isis_powder/gem_routines/gem_advanced_config.py
@@ -14,7 +14,6 @@ absorption_correction_params = {
gem_adv_config_params = {
"raw_tof_cropping_values": (500, 20000),
"spline_coefficient": 30
-
}
focused_cropping_values = [(550, 19900), # Bank 1
diff --git a/scripts/Diffraction/isis_powder/gem_routines/gem_algs.py b/scripts/Diffraction/isis_powder/gem_routines/gem_algs.py
index 3e4bba06b542c30dd095951e8c2cd5723e549d00..0cca76da2c26d307fbe2c4461982b940ca34530e 100644
--- a/scripts/Diffraction/isis_powder/gem_routines/gem_algs.py
+++ b/scripts/Diffraction/isis_powder/gem_routines/gem_algs.py
@@ -27,6 +27,7 @@ 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
@@ -38,8 +39,6 @@ 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
diff --git a/scripts/Diffraction/isis_powder/routines/RunDetails.py b/scripts/Diffraction/isis_powder/routines/RunDetails.py
index b03e87ba945cb334eba7da417341362b99f84748..3b761192da5f721115999e0230ddc51a33e865f6 100644
--- a/scripts/Diffraction/isis_powder/routines/RunDetails.py
+++ b/scripts/Diffraction/isis_powder/routines/RunDetails.py
@@ -11,6 +11,7 @@ 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
diff --git a/scripts/Diffraction/isis_powder/routines/absorb_corrections.py b/scripts/Diffraction/isis_powder/routines/absorb_corrections.py
index 4a9933e04827a45333acec99920026d0b78fa1f5..7f4dfbd8d4a0f6b44842e2ec1c65f82746d7abf5 100644
--- a/scripts/Diffraction/isis_powder/routines/absorb_corrections.py
+++ b/scripts/Diffraction/isis_powder/routines/absorb_corrections.py
@@ -23,6 +23,7 @@ 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"
@@ -31,16 +32,23 @@ 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,
- c_height=height, c_radius=radius, c_pos=pos, chemical_formula=formula)
+ position_dict=position_dict, chemical_formula=formula, material_properties=chemical_properties)
return ws_to_correct
def _calculate__cylinder_absorb_corrections(ws_to_correct, multiple_scattering,
- c_height, c_radius, c_pos, chemical_formula):
+ position_dict, chemical_formula, material_properties):
"""
Calculates vanadium absorption corrections for the specified workspace. The workspace
should have any monitor spectra masked before being passed into this method. Additionally
@@ -54,9 +62,9 @@ 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': c_height,
- 'Radius': c_radius, 'Center': c_pos}
- material_json = {'ChemicalFormula': chemical_formula}
+ 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)
mantid.SetSample(InputWorkspace=ws_to_correct, Geometry=geometry_json, Material=material_json)
@@ -66,3 +74,45 @@ 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
diff --git a/scripts/Diffraction/isis_powder/routines/calibrate.py b/scripts/Diffraction/isis_powder/routines/calibrate.py
index 77077021941fbfd8b32d1db075265dc3076f1c05..eafce174eee6399dff5fb081372efcf480eaf015 100644
--- a/scripts/Diffraction/isis_powder/routines/calibrate.py
+++ b/scripts/Diffraction/isis_powder/routines/calibrate.py
@@ -21,8 +21,6 @@ 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)