From 9c3206e0451b7922bcbcf977d9b38d544c3e4803 Mon Sep 17 00:00:00 2001
From: Elliot Oram <elliot.oram@stfc.ac.uk>
Date: Mon, 20 Nov 2017 17:19:40 +0000
Subject: [PATCH] propagate material through workflow to mantid layer
Refs #21214
---
.../Diffraction/isis_powder/abstract_inst.py | 4 +--
scripts/Diffraction/isis_powder/polaris.py | 3 ++-
.../routines/absorb_corrections.py | 15 ++---------
.../isis_powder/routines/calibrate.py | 3 +++
.../Diffraction/isis_powder/routines/focus.py | 25 ++++++++++++-------
5 files changed, 25 insertions(+), 25 deletions(-)
diff --git a/scripts/Diffraction/isis_powder/abstract_inst.py b/scripts/Diffraction/isis_powder/abstract_inst.py
index b854c139a1f..3429aafcc7f 100644
--- a/scripts/Diffraction/isis_powder/abstract_inst.py
+++ b/scripts/Diffraction/isis_powder/abstract_inst.py
@@ -49,7 +49,7 @@ class AbstractInst(object):
return calibrate.create_van(instrument=self, run_details=run_details,
absorb=do_absorb_corrections)
- def _focus(self, run_number_string, do_van_normalisation, do_absorb_corrections):
+ def _focus(self, run_number_string, do_van_normalisation, do_absorb_corrections, sample_details=None):
"""
Focuses the user specified run - should be called by the concrete instrument
:param run_number_string: The run number(s) to be processed
@@ -58,7 +58,7 @@ class AbstractInst(object):
"""
self._is_vanadium = False
return focus.focus(run_number_string=run_number_string, perform_vanadium_norm=do_van_normalisation,
- instrument=self, absorb=do_absorb_corrections)
+ instrument=self, absorb=do_absorb_corrections, sample_details=sample_details)
# Mandatory overrides
diff --git a/scripts/Diffraction/isis_powder/polaris.py b/scripts/Diffraction/isis_powder/polaris.py
index c720dfcd86c..8232bd6c7b4 100644
--- a/scripts/Diffraction/isis_powder/polaris.py
+++ b/scripts/Diffraction/isis_powder/polaris.py
@@ -28,7 +28,8 @@ class Polaris(AbstractInst):
self._inst_settings.update_attributes(kwargs=kwargs)
return self._focus(run_number_string=self._inst_settings.run_number,
do_van_normalisation=self._inst_settings.do_van_normalisation,
- do_absorb_corrections=self._inst_settings.do_absorb_corrections)
+ do_absorb_corrections=self._inst_settings.do_absorb_corrections,
+ sample_details=self._sample_details)
def create_vanadium(self, **kwargs):
self._switch_mode_specific_inst_settings(kwargs.get("mode"))
diff --git a/scripts/Diffraction/isis_powder/routines/absorb_corrections.py b/scripts/Diffraction/isis_powder/routines/absorb_corrections.py
index 47407321d6c..caf8c9241ef 100644
--- a/scripts/Diffraction/isis_powder/routines/absorb_corrections.py
+++ b/scripts/Diffraction/isis_powder/routines/absorb_corrections.py
@@ -85,19 +85,8 @@ def _calculate__cylinder_absorb_corrections(ws_to_correct, multiple_scattering,
def _setup_sample_for_cylinder_absorb_corrections(ws_to_correct, sample_details_obj):
- geometry_json = {'Shape': 'Cylinder',
- 'Height': sample_details_obj.height(), 'Radius': sample_details_obj.radius(),
- 'Center': sample_details_obj.center()}
- material = sample_details_obj.material_object
- # See SetSampleMaterial for documentation on this dictionary
- material_json = {'ChemicalFormula': material.chemical_formula}
- if material.number_density:
- material_json["SampleNumberDensity"] = material.number_density
- if material.absorption_cross_section:
- material_json["AttenuationXSection"] = material.absorption_cross_section
- if material.scattering_cross_section:
- material_json["ScatteringXSection"] = material.scattering_cross_section
-
+ geometry_json = common.generate_sample_geometry(sample_details_obj)
+ material_json = common.generate_sample_material(sample_details_obj)
mantid.SetSample(InputWorkspace=ws_to_correct, Geometry=geometry_json, Material=material_json)
diff --git a/scripts/Diffraction/isis_powder/routines/calibrate.py b/scripts/Diffraction/isis_powder/routines/calibrate.py
index ecf345e7504..9d3a33ca214 100644
--- a/scripts/Diffraction/isis_powder/routines/calibrate.py
+++ b/scripts/Diffraction/isis_powder/routines/calibrate.py
@@ -31,6 +31,9 @@ def create_van(instrument, run_details, absorb):
if absorb:
corrected_van_ws = instrument._apply_absorb_corrections(run_details=run_details,
ws_to_correct=corrected_van_ws)
+ else:
+ # Assume that create_van only uses Vanadium runs
+ mantid.SetSampleMaterial(InputWorkspace=corrected_van_ws, ChemicalFormula='V')
aligned_ws = mantid.AlignDetectors(InputWorkspace=corrected_van_ws,
CalibrationFile=run_details.offset_file_path)
diff --git a/scripts/Diffraction/isis_powder/routines/focus.py b/scripts/Diffraction/isis_powder/routines/focus.py
index 7392910f2ad..cd69aef8ed2 100644
--- a/scripts/Diffraction/isis_powder/routines/focus.py
+++ b/scripts/Diffraction/isis_powder/routines/focus.py
@@ -7,18 +7,19 @@ from isis_powder.routines.common_enums import INPUT_BATCHING
import os
-def focus(run_number_string, instrument, perform_vanadium_norm, absorb):
+def focus(run_number_string, instrument, perform_vanadium_norm, absorb, sample_details=None):
input_batching = instrument._get_input_batching_mode()
if input_batching == INPUT_BATCHING.Individual:
return _individual_run_focusing(instrument=instrument, perform_vanadium_norm=perform_vanadium_norm,
- run_number=run_number_string, absorb=absorb)
+ run_number=run_number_string, absorb=absorb, sample_details=sample_details)
elif input_batching == INPUT_BATCHING.Summed:
- return _batched_run_focusing(instrument, perform_vanadium_norm, run_number_string, absorb=absorb)
+ return _batched_run_focusing(instrument, perform_vanadium_norm, run_number_string, absorb=absorb,
+ sample_details=sample_details)
else:
raise ValueError("Input batching not passed through. Please contact development team.")
-def _focus_one_ws(ws, run_number, instrument, perform_vanadium_norm, absorb):
+def _focus_one_ws(ws, run_number, instrument, perform_vanadium_norm, absorb, sample_details):
run_details = instrument._get_run_details(run_number_string=run_number)
if perform_vanadium_norm:
_test_splined_vanadium_exists(instrument, run_details)
@@ -38,7 +39,12 @@ def _focus_one_ws(ws, run_number, instrument, perform_vanadium_norm, absorb):
# Correct for absorption / multiple scattering if required
if absorb:
input_workspace = instrument._apply_absorb_corrections(run_details=run_details, ws_to_correct=input_workspace)
-
+ else:
+ # Set sample material if specified by the user
+ if sample_details is not None:
+ mantid.SetSample(InputWorkspace=input_workspace,
+ Geometry=common.generate_sample_geometry(sample_details),
+ Material=common.generate_sample_material(sample_details))
# Align
aligned_ws = mantid.AlignDetectors(InputWorkspace=input_workspace,
CalibrationFile=run_details.offset_file_path)
@@ -88,13 +94,14 @@ def _apply_vanadium_corrections(instrument, run_number, input_workspace, perform
return processed_spectra
-def _batched_run_focusing(instrument, perform_vanadium_norm, run_number_string, absorb):
+def _batched_run_focusing(instrument, perform_vanadium_norm, run_number_string, absorb, sample_details):
read_ws_list = common.load_current_normalised_ws_list(run_number_string=run_number_string,
instrument=instrument)
output = None
for ws in read_ws_list:
output = _focus_one_ws(ws=ws, run_number=run_number_string, instrument=instrument,
- perform_vanadium_norm=perform_vanadium_norm, absorb=absorb)
+ perform_vanadium_norm=perform_vanadium_norm, absorb=absorb,
+ sample_details=sample_details)
return output
@@ -109,14 +116,14 @@ def _divide_by_vanadium_splines(spectra_list, spline_file_path):
return output_list
-def _individual_run_focusing(instrument, perform_vanadium_norm, run_number, absorb):
+def _individual_run_focusing(instrument, perform_vanadium_norm, run_number, absorb, sample_details):
# Load and process one by one
run_numbers = common.generate_run_numbers(run_number_string=run_number)
output = None
for run in run_numbers:
ws = common.load_current_normalised_ws_list(run_number_string=run, instrument=instrument)
output = _focus_one_ws(ws=ws[0], run_number=run, instrument=instrument, absorb=absorb,
- perform_vanadium_norm=perform_vanadium_norm)
+ perform_vanadium_norm=perform_vanadium_norm, sample_details=sample_details)
return output
--
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