diff --git a/scripts/Diffraction/isis_powder/gem.py b/scripts/Diffraction/isis_powder/gem.py
index 553b1b0e9f4f41ed5754d2e02e0e0f335da49c21..13b7c018e1ea956631e643239b5856096f68f9a2 100644
--- a/scripts/Diffraction/isis_powder/gem.py
+++ b/scripts/Diffraction/isis_powder/gem.py
@@ -2,7 +2,7 @@ from __future__ import (absolute_import, division, print_function)
from isis_powder.abstract_inst import AbstractInst
from isis_powder.gem_routines import gem_advanced_config, gem_algs, gem_param_mapping
-from isis_powder.routines import common, instrument_settings
+from isis_powder.routines import common, instrument_settings, sample_details
class Gem(AbstractInst):
@@ -16,6 +16,9 @@ class Gem(AbstractInst):
output_dir=self._inst_settings.output_dir, inst_prefix="GEM")
self._cached_run_details = {}
+ self._sample_details = None
+
+ # Public API
def focus(self, **kwargs):
self._inst_settings.update_attributes(kwargs=kwargs)
@@ -28,6 +31,18 @@ class Gem(AbstractInst):
return self._create_vanadium(run_number_string=self._inst_settings.run_in_range,
do_absorb_corrections=self._inst_settings.do_absorb_corrections)
+ def set_sample_details(self, **kwargs):
+ sample_details_obj = common.dictionary_key_helper(
+ dictionary=kwargs, key="new_sample_details",
+ 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")
+ 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)
if run_number_string_key in self._cached_run_details:
diff --git a/scripts/Diffraction/isis_powder/polaris.py b/scripts/Diffraction/isis_powder/polaris.py
index 1f841dd02984d7daf47b279d213ab5c9e5ce0ffb..56bb5fab00300d4daf458cc3e1b7b98563ffd7a9 100644
--- a/scripts/Diffraction/isis_powder/polaris.py
+++ b/scripts/Diffraction/isis_powder/polaris.py
@@ -2,7 +2,7 @@ from __future__ import (absolute_import, division, print_function)
import os
-from isis_powder.routines import common, instrument_settings
+from isis_powder.routines import common, instrument_settings, sample_details
from isis_powder.abstract_inst import AbstractInst
from isis_powder.polaris_routines import polaris_advanced_config, polaris_algs, polaris_param_mapping
@@ -19,6 +19,9 @@ class Polaris(AbstractInst):
# Hold the last dictionary later to avoid us having to keep parsing the YAML
self._run_details_cached_obj = {}
+ self._sample_details = None
+
+ # Public API
def focus(self, **kwargs):
self._inst_settings.update_attributes(kwargs=kwargs)
@@ -30,6 +33,16 @@ class Polaris(AbstractInst):
return self._create_vanadium(run_number_string=self._inst_settings.run_in_range,
do_absorb_corrections=self._inst_settings.do_absorb_corrections)
+ def set_sample_details(self, **kwargs):
+ sample_details_obj = common.dictionary_key_helper(
+ dictionary=kwargs, key="new_sample_details",
+ 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")
+ self._sample_details = sample_details_obj
+
# Overrides
def _apply_absorb_corrections(self, run_details, van_ws):
return polaris_algs.calculate_absorb_corrections(ws_to_correct=van_ws,
diff --git a/scripts/Diffraction/isis_powder/routines/absorb_corrections.py b/scripts/Diffraction/isis_powder/routines/absorb_corrections.py
index 9544d17a12c3ed3beaad6560d21d62cfbadbf397..dfef2920da4aa9ecc13250337024bb69cadadcb1 100644
--- a/scripts/Diffraction/isis_powder/routines/absorb_corrections.py
+++ b/scripts/Diffraction/isis_powder/routines/absorb_corrections.py
@@ -2,22 +2,15 @@ from __future__ import (absolute_import, division, print_function)
import mantid.simpleapi as mantid
-from isis_powder.routines import common
+from isis_powder.routines import common, sample_details
-def run_cylinder_absorb_corrections(ws_to_correct, multiple_scattering, config_dict):
+def create_vanadium_sample_details_obj(config_dict):
"""
- Sets a cylindrical sample from the user specified config dictionary and performs Mayers
- sample correction on the workspace. The config dictionary must be for a cylinder and contain
- the keys "cylinder_sample_height", "cylinder_sample_radius", "cylinder_position" and
- "chemical_formula". If any of these keys are not found an exception is raise informing
- the user that the key was not in the advanced configuration file.
- Additionally it checks the value of multiple_scattering to determine whether to take
- into account the effects of multiple scattering.
- :param ws_to_correct: The workspace to perform Mayers sample correction on
- :param multiple_scattering: Boolean of whether to account for the effects of multiple scattering
- :param config_dict: A dictionary containing the required keys to set a cylinder sample
- :return: The corrected workspace
+ Creates a SampleDetails object based on a vanadium sample which is found
+ in the advanced config of an instrument.
+ :param config_dict: The advanced config dictionary of the instrument for the vanadium sample
+ :return: A sample details object which holds properties used in sample corrections
"""
height_key = "cylinder_sample_height"
radius_key = "cylinder_sample_radius"
@@ -30,18 +23,37 @@ def run_cylinder_absorb_corrections(ws_to_correct, multiple_scattering, config_d
height = common.dictionary_key_helper(dictionary=config_dict, key=height_key, exception_msg=e_msg + height_key)
radius = common.dictionary_key_helper(dictionary=config_dict, key=radius_key, exception_msg=e_msg + radius_key)
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)
- if len(formula) > 1:
- # Not a trivial element so we need them to manually specify number density as Mantid
- # struggles to calculate it
- number_density = common.dictionary_key_helper(
- dictionary=config_dict, key=number_density_key,
- exception_msg="The number density is required as the chemical formula (" + str(formula) + ")"
- " is not a single element. The number density was not found. Please add the following key: " +
- number_density_key)
- else:
- number_density = None
+ 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.set_material(chemical_formula=formula, number_density=number_density)
+ return vanadium_sample_details
+
+
+def run_cylinder_absorb_corrections(ws_to_correct, multiple_scattering, sample_details_obj):
+ """
+ Sets a cylindrical sample from the user specified config dictionary and performs Mayers
+ sample correction on the workspace. The SampleDetails object defines the sample, material
+ and associated properties. Additionally it checks the value of multiple_scattering to
+ determine whether to take into account the effects of multiple scattering.
+ :param ws_to_correct: The workspace to perform Mayers sample correction on
+ :param multiple_scattering: Boolean of whether to account for the effects of multiple scattering
+ :param sample_details_obj: The object containing the sample details
+ :return: The corrected workspace
+ """
+
+ height = sample_details_obj.height
+ radius = sample_details_obj.radius
+ pos = sample_details_obj.center
+
+ # Get the underlying material object
+ if not sample_details_obj.is_material_set():
+ raise RuntimeError("The material for this sample has not been set yet. Please call"
+ " set_material on the SampleDetails object to set the material")
+ material_obj = sample_details_obj.material_object
+ formula = material_obj.chemical_formula
+ number_density = material_obj.number_density
ws_to_correct = _calculate__cylinder_absorb_corrections(
ws_to_correct=ws_to_correct, multiple_scattering=multiple_scattering,
diff --git a/scripts/Diffraction/isis_powder/routines/sample_details.py b/scripts/Diffraction/isis_powder/routines/sample_details.py
index 041d4da5a839bff6dd32c3ffa91e8af99dd85381..3247e3e7286bd0fb61d5845e13b4f11b7b9c8d08 100644
--- a/scripts/Diffraction/isis_powder/routines/sample_details.py
+++ b/scripts/Diffraction/isis_powder/routines/sample_details.py
@@ -20,13 +20,16 @@ class SampleDetails(object):
self.radius = float(radius)
self.center = [float(i) for i in center] # List of X, Y, Z position
- self._material_object = None
+ self.material_object = None
+
+ def is_material_set(self):
+ return self.material_object is not None
def print_sample_details(self):
self._print()
def reset_sample_material(self):
- self._material_object = None
+ self.material_object = None
def set_material(self, **kwargs):
chemical_formula = common.dictionary_key_helper(dictionary=kwargs, key="chemical_formula",
@@ -34,13 +37,13 @@ class SampleDetails(object):
" passed: chemical_formula")
number_density = common.dictionary_key_helper(dictionary=kwargs, key="number_density", throws=False)
- if self._material_object is not None:
+ if self.material_object is not None:
self.print_sample_details()
raise RuntimeError("The material has already been set to the above details. If the properties"
" 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, numeric_density=number_density)
def set_material_properties(self, **kwargs):
err_msg = "The following argument is required but was not set or passed: "
@@ -48,12 +51,12 @@ class SampleDetails(object):
exception_msg=err_msg + "absorption_cross_section")
scattering_cross_section = common.dictionary_key_helper(dictionary=kwargs, key="scattering_cross_section",
exception_msg=err_msg + "scattering_cross_section")
- if self._material_object is None:
+ if self.material_object is None:
raise RuntimeError("The material has not been set (or reset). Please set it by calling"
" 'set_material()' to set the material details of the sample.")
- self._material_object.set_material_properties(abs_cross_sect=absorption_cross_section,
- scattering_cross_sect=scattering_cross_section)
+ self.material_object.set_material_properties(abs_cross_sect=absorption_cross_section,
+ scattering_cross_sect=scattering_cross_section)
def _print(self):
print("Sample Details:")
@@ -63,10 +66,10 @@ class SampleDetails(object):
print("Radius: {}".format(self.radius))
print("Center X:{}, Y:{}, Z{}".format(self.center[0], self.center[1], self.center[2]))
print("------------------------")
- if self._material_object is None:
+ if self.material_object is None:
print("Material has not been set (or has been reset).")
else:
- self._material_object.print_material()
+ self.material_object.print_material()
print() # Newline for visual spacing
@staticmethod
@@ -93,7 +96,7 @@ class SampleDetails(object):
class _Material(object):
def __init__(self, chemical_formula, numeric_density=None):
- self._chemical_formula = chemical_formula
+ self.chemical_formula = chemical_formula
# If it is not an element Mantid requires us to provide the numeric density
# which is required for absorption corrections.
@@ -105,11 +108,11 @@ class _Material(object):
# Always check value is sane if user has given one
_check_value_is_physical(property_name="numeric_density", value=numeric_density)
- self._numeric_density = numeric_density
+ self.numeric_density = numeric_density
# Advanced material properties
- self._absorption_cross_section = None
- self._scattering_cross_section = None
+ self.absorption_cross_section = None
+ self.scattering_cross_section = None
# Internal flags so we are only allowed to set the material properties once
self._is_material_props_set = False
@@ -117,18 +120,18 @@ class _Material(object):
def print_material(self):
print("Material properties:")
print("------------------------")
- print("Chemical formula: {}".format(self._chemical_formula))
+ print("Chemical formula: {}".format(self.chemical_formula))
- if self._numeric_density:
- print("Numeric Density: {}".format(self._numeric_density))
+ if self.numeric_density:
+ print("Numeric Density: {}".format(self.numeric_density))
else:
print("Numeric Density: Set from elemental properties by Mantid")
self._print_material_properties()
def _print_material_properties(self):
if self._is_material_props_set:
- print("Absorption cross section: {}".format(self._absorption_cross_section))
- print("Scattering cross section: {}".format(self._scattering_cross_section))
+ print("Absorption cross section: {}".format(self.absorption_cross_section))
+ print("Scattering cross section: {}".format(self.scattering_cross_section))
else:
print("Absorption cross section: Calculated by Mantid based on chemical/elemental formula")
print("Scattering cross section: Calculated by Mantid based on chemical/elemental formula")
@@ -143,8 +146,8 @@ class _Material(object):
_check_value_is_physical("absorption_cross_section", abs_cross_sect)
_check_value_is_physical("scattering_cross_section", scattering_cross_sect)
- self._absorption_cross_section = float(abs_cross_sect)
- self._scattering_cross_section = float(scattering_cross_sect)
+ self.absorption_cross_section = float(abs_cross_sect)
+ self.scattering_cross_section = float(scattering_cross_sect)
self._is_material_props_set = True
diff --git a/scripts/test/ISISPowderSampleDetailsTest.py b/scripts/test/ISISPowderSampleDetailsTest.py
index 20fb2e828bee6f7d3734e1745f5dd4a02a923ba6..c997f14795fe100bb638579c7df960236af95f85 100644
--- a/scripts/test/ISISPowderSampleDetailsTest.py
+++ b/scripts/test/ISISPowderSampleDetailsTest.py
@@ -112,7 +112,7 @@ class ISISPowderSampleDetailsTest(unittest.TestCase):
# Check that we can only set a material once. We will test the underlying class elsewhere
sample_details_obj.set_material(chemical_formula='V')
- self.assertIsNotNone(sample_details_obj._material_object)
+ self.assertIsNotNone(sample_details_obj.material_object)
# Check that the material is now immutable
with assertRaisesRegex(self, RuntimeError, "The material has already been set to the above details"):
@@ -120,16 +120,16 @@ class ISISPowderSampleDetailsTest(unittest.TestCase):
# Check resetting it works
sample_details_obj.reset_sample_material()
- self.assertIsNone(sample_details_obj._material_object)
+ self.assertIsNone(sample_details_obj.material_object)
# And ensure setting it for a second time works
sample_details_obj.set_material(chemical_formula='V')
- self.assertIsNotNone(sample_details_obj._material_object)
+ self.assertIsNotNone(sample_details_obj.material_object)
def test_set_material_properties(self):
sample_details_obj = sample_details.SampleDetails(height=1.0, radius=1.0, center=[2, 3, 5])
- self.assertIsNone(sample_details_obj._material_object)
+ self.assertIsNone(sample_details_obj.material_object)
# Check we cannot set a material property without setting the underlying material
with assertRaisesRegex(self, RuntimeError, "The material has not been set"):
@@ -148,24 +148,24 @@ 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.assertEqual(material_obj_one_char.chemical_formula, chemical_formula_one_char_element)
+ self.assertIsNone(material_obj_one_char.numeric_density)
# Also check that the absorption and scattering X sections have not been set
- self.assertIsNone(material_obj_one_char._absorption_cross_section)
- self.assertIsNone(material_obj_one_char._scattering_cross_section)
+ self.assertIsNone(material_obj_one_char.absorption_cross_section)
+ self.assertIsNone(material_obj_one_char.scattering_cross_section)
self.assertFalse(material_obj_one_char._is_material_props_set)
# Check if it accepts two character elements without numeric density
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.assertEqual(material_obj_two_char.chemical_formula, chemical_formula_two_char_element)
+ self.assertIsNone(material_obj_two_char.numeric_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.numeric_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"):
@@ -174,8 +174,8 @@ class ISISPowderSampleDetailsTest(unittest.TestCase):
# Check it constructs if it is given the numeric density too
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.chemical_formula, chemical_formula_complex)
+ self.assertEqual(material_obj_num_complex_formula.numeric_density, numeric_density_sample)
def test_material_set_properties(self):
bad_absorb = '-1'
@@ -196,20 +196,20 @@ class ISISPowderSampleDetailsTest(unittest.TestCase):
material_obj.set_material_properties(abs_cross_sect=good_absorb, scattering_cross_sect=bad_scattering)
# Check nothing has been set yet
- self.assertIsNone(material_obj._absorption_cross_section)
- self.assertIsNone(material_obj._scattering_cross_section)
+ self.assertIsNone(material_obj.absorption_cross_section)
+ self.assertIsNone(material_obj.scattering_cross_section)
# Set the object this time
material_obj.set_material_properties(abs_cross_sect=good_absorb, scattering_cross_sect=good_scattering)
self.assertTrue(material_obj._is_material_props_set)
- self.assertEqual(material_obj._absorption_cross_section, float(good_absorb))
- self.assertEqual(material_obj._scattering_cross_section, float(good_scattering))
+ self.assertEqual(material_obj.absorption_cross_section, float(good_absorb))
+ self.assertEqual(material_obj.scattering_cross_section, float(good_scattering))
# Check we cannot set it twice and fields do not change
with assertRaisesRegex(self, RuntimeError, "The material properties have already been set"):
material_obj.set_material_properties(abs_cross_sect=999, scattering_cross_sect=999)
- self.assertEqual(material_obj._absorption_cross_section, float(good_absorb))
- self.assertEqual(material_obj._scattering_cross_section, float(good_scattering))
+ self.assertEqual(material_obj.absorption_cross_section, float(good_absorb))
+ self.assertEqual(material_obj.scattering_cross_section, float(good_scattering))
def test_print_sample_details(self):
expected_height = 1