diff --git a/scripts/Diffraction/isis_powder/abstract_inst.py b/scripts/Diffraction/isis_powder/abstract_inst.py
index 57f6b5445641cd514cd3cb2bf6f1e63d619c617d..ad60cb2b4e321c49fc69750fb11e0ebf5762e360 100644
--- a/scripts/Diffraction/isis_powder/abstract_inst.py
+++ b/scripts/Diffraction/isis_powder/abstract_inst.py
@@ -36,7 +36,7 @@ class AbstractInst(object):
def user_name(self):
return self._user_name
- def _create_vanadium(self, run_number_string, do_absorb_corrections=True):
+ def _create_vanadium(self, run_number_string, do_absorb_corrections):
"""
Creates a vanadium calibration - should be called by the concrete instrument
:param run_number_string : The user input string for any run within the cycle
@@ -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):
+ def _focus(self, run_number_string, do_van_normalisation, do_absorb_corrections):
"""
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)
+ instrument=self, absorb=do_absorb_corrections)
# Mandatory overrides
@@ -79,6 +79,15 @@ class AbstractInst(object):
"""
raise NotImplementedError("generate_input_file_name must be implemented per instrument")
+ def _apply_absorb_corrections(self, run_details, ws_to_correct):
+ """
+ Generates absorption corrections to compensate for the container. The overriding instrument
+ should handle the difference between a vanadium workspace and regular workspace
+ :param ws_to_correct: A reference vanadium workspace to match the binning of or correct
+ :return: A workspace containing the corrections
+ """
+ raise NotImplementedError("apply_absorb_corrections Not implemented for this instrument yet")
+
def _generate_output_file_name(self, run_number_string):
"""
Generates the filename which is used to uniquely identify and save the workspace. This should include any
@@ -99,14 +108,6 @@ class AbstractInst(object):
raise NotImplementedError("spline_vanadium_ws must be implemented per instrument")
# Optional overrides
- def _apply_absorb_corrections(self, run_details, van_ws):
- """
- Generates vanadium absorption corrections to compensate for the container
- :param van_ws: A reference vanadium workspace to match the binning of or correct
- :return: A workspace containing the corrections
- """
- raise NotImplementedError("apply_absorb_corrections Not implemented for this instrument yet")
-
def _attenuate_workspace(self, input_workspace):
"""
Applies an attenuation correction to the workspace
diff --git a/scripts/Diffraction/isis_powder/gem.py b/scripts/Diffraction/isis_powder/gem.py
index b73fb7cdbf5f9f09fbf230d653b831c1f1100582..a00b24932f6fdae05ddff0cf3247491dbc8d637a 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, sample_details
+from isis_powder.routines import absorb_corrections, common, instrument_settings, sample_details
class Gem(AbstractInst):
@@ -22,8 +22,9 @@ class Gem(AbstractInst):
def focus(self, **kwargs):
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_norm)
+ return self._focus(
+ run_number_string=self._inst_settings.run_number, do_van_normalisation=self._inst_settings.do_van_norm,
+ do_absorb_corrections=self._inst_settings.do_absorb_corrections)
def create_vanadium(self, **kwargs):
self._inst_settings.update_attributes(kwargs=kwargs)
@@ -62,9 +63,14 @@ class Gem(AbstractInst):
def _generate_input_file_name(run_number):
return _gem_generate_inst_name(run_number=run_number)
- def _apply_absorb_corrections(self, run_details, van_ws):
- return gem_algs.calculate_van_absorb_corrections(ws_to_correct=van_ws,
- multiple_scattering=self._inst_settings.multiple_scattering)
+ def _apply_absorb_corrections(self, run_details, ws_to_correct):
+ if self._is_vanadium:
+ return gem_algs.calculate_van_absorb_corrections(
+ ws_to_correct=ws_to_correct, multiple_scattering=self._inst_settings.multiple_scattering)
+ 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)
def _crop_banks_to_user_tof(self, focused_banks):
return common.crop_banks_using_crop_list(focused_banks, self._inst_settings.focused_cropping_values)
diff --git a/scripts/Diffraction/isis_powder/pearl.py b/scripts/Diffraction/isis_powder/pearl.py
index 947b7144b3416a6b859bf907d06860b6ee4c47fd..e10e0c7527159a5aa93b200d9fa9ddd27ddee597 100644
--- a/scripts/Diffraction/isis_powder/pearl.py
+++ b/scripts/Diffraction/isis_powder/pearl.py
@@ -23,7 +23,10 @@ class Pearl(AbstractInst):
def focus(self, **kwargs):
self._switch_long_mode_inst_settings(kwargs.get("long_mode"))
self._inst_settings.update_attributes(kwargs=kwargs)
+ # Pearl does not have absorption corrections for a sample
+ do_absorb_corrections = False
return self._focus(run_number_string=self._inst_settings.run_number,
+ do_absorb_corrections=do_absorb_corrections,
do_van_normalisation=self._inst_settings.van_norm)
def create_vanadium(self, **kwargs):
@@ -115,13 +118,19 @@ class Pearl(AbstractInst):
x_max=self._inst_settings.van_tof_cropping[-1])
return cropped_ws
- def _apply_absorb_corrections(self, run_details, van_ws):
- # TODO move this to an instrument param
+ def _apply_absorb_corrections(self, run_details, ws_to_correct):
+ # TODO move generating absorption corrections to an instrument param
gen_absorb = False
if gen_absorb:
- pearl_algs.generate_vanadium_absorb_corrections(van_ws=van_ws)
+ pearl_algs.generate_vanadium_absorb_corrections(van_ws=ws_to_correct)
- return pearl_algs.apply_vanadium_absorb_corrections(van_ws=van_ws, run_details=run_details)
+ if not self._is_vanadium:
+ # This is sample absorption corrections which is not supported on Pearl.
+ # We should not get here as the absorption flag shouldn't do anything whilst focusing on Pearl
+ raise RuntimeError("Cannot run Absorption corrections for a sample on Pearl. Please contact development "
+ "team.")
+
+ return pearl_algs.apply_vanadium_absorb_corrections(van_ws=ws_to_correct, run_details=run_details)
def _switch_long_mode_inst_settings(self, long_mode_on):
self._inst_settings.update_attributes(advanced_config=pearl_advanced_config.get_long_mode_dict(long_mode_on),
diff --git a/scripts/Diffraction/isis_powder/polaris.py b/scripts/Diffraction/isis_powder/polaris.py
index abc010c734e90d1dc01f45fc113bce9de8cdc1a6..8241e0c91ab9da275eec47a02fa0f8edf1a49cb9 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, sample_details
+from isis_powder.routines import absorb_corrections, 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
@@ -26,7 +26,8 @@ class Polaris(AbstractInst):
def focus(self, **kwargs):
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_van_normalisation=self._inst_settings.do_van_normalisation,
+ do_absorb_corrections=self._inst_settings.do_absorb_corrections)
def create_vanadium(self, **kwargs):
self._inst_settings.update_attributes(kwargs=kwargs)
@@ -44,9 +45,14 @@ class Polaris(AbstractInst):
self._sample_details = sample_details_obj
# Overrides
- def _apply_absorb_corrections(self, run_details, van_ws):
- return polaris_algs.calculate_van_absorb_corrections(ws_to_correct=van_ws,
- multiple_scattering=self._inst_settings.multiple_scattering)
+ def _apply_absorb_corrections(self, run_details, ws_to_correct):
+ if self._is_vanadium:
+ return polaris_algs.calculate_van_absorb_corrections(
+ ws_to_correct=ws_to_correct, multiple_scattering=self._inst_settings.multiple_scattering)
+ 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)
@staticmethod
def _can_auto_gen_vanadium_cal():
diff --git a/scripts/Diffraction/isis_powder/routines/calibrate.py b/scripts/Diffraction/isis_powder/routines/calibrate.py
index 2b9d0108fdfe2ae6e999450a8ae54d5b9e5a063b..96e06873fe4faed82bc202f2c2beae0562a050d2 100644
--- a/scripts/Diffraction/isis_powder/routines/calibrate.py
+++ b/scripts/Diffraction/isis_powder/routines/calibrate.py
@@ -21,7 +21,6 @@ def create_van(instrument, run_details, absorb):
input_batching=INPUT_BATCHING.Summed)
input_van_ws = input_van_ws_list[0] # As we asked for a summed ws there should only be one returned
- # TODO where do we subtract empty can on GEM ?
corrected_van_ws = common.subtract_summed_runs(ws_to_correct=input_van_ws,
empty_sample_ws_string=run_details.empty_runs,
instrument=instrument)
@@ -32,7 +31,7 @@ def create_van(instrument, run_details, absorb):
aligned_ws = mantid.AlignDetectors(InputWorkspace=corrected_van_ws,
CalibrationFile=run_details.offset_file_path)
if absorb:
- aligned_ws = instrument._apply_absorb_corrections(run_details=run_details, van_ws=aligned_ws)
+ aligned_ws = instrument._apply_absorb_corrections(run_details=run_details, ws_to_correct=aligned_ws)
focused_vanadium = mantid.DiffractionFocussing(InputWorkspace=aligned_ws,
GroupingFileName=run_details.grouping_file_path)
diff --git a/scripts/Diffraction/isis_powder/routines/focus.py b/scripts/Diffraction/isis_powder/routines/focus.py
index a6b2034e09e2defcae765ea028cb83b705ad9559..b7068e1ae12b018de6eadcf5b6fdbd8ff09c3208 100644
--- a/scripts/Diffraction/isis_powder/routines/focus.py
+++ b/scripts/Diffraction/isis_powder/routines/focus.py
@@ -8,17 +8,18 @@ import os
import warnings
-def focus(run_number_string, instrument, perform_vanadium_norm=True):
+def focus(run_number_string, instrument, perform_vanadium_norm, absorb):
input_batching = instrument._get_input_batching_mode()
if input_batching == INPUT_BATCHING.Individual:
- return _individual_run_focusing(instrument, perform_vanadium_norm, run_number_string)
+ 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)
else:
raise ValueError("Input batching not passed through. Please contact development team.")
-def _focus_one_ws(ws, run_number, instrument, perform_vanadium_norm):
+def _focus_one_ws(ws, run_number, instrument, perform_vanadium_norm, absorb):
run_details = instrument._get_run_details(run_number_string=run_number)
if perform_vanadium_norm:
_test_splined_vanadium_exists(instrument, run_details)
@@ -32,6 +33,10 @@ def _focus_one_ws(ws, run_number, instrument, perform_vanadium_norm):
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)
@@ -77,13 +82,13 @@ def _apply_vanadium_corrections(instrument, run_number, input_workspace, perform
return processed_spectra
-def _batched_run_focusing(instrument, perform_vanadium_norm, run_number_string):
+def _batched_run_focusing(instrument, perform_vanadium_norm, run_number_string, absorb):
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)
+ perform_vanadium_norm=perform_vanadium_norm, absorb=absorb)
return output
@@ -98,13 +103,13 @@ def _divide_by_vanadium_splines(spectra_list, spline_file_path):
return output_list
-def _individual_run_focusing(instrument, perform_vanadium_norm, run_number):
+def _individual_run_focusing(instrument, perform_vanadium_norm, run_number, absorb):
# 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,
+ output = _focus_one_ws(ws=ws[0], run_number=run, instrument=instrument, absorb=absorb,
perform_vanadium_norm=perform_vanadium_norm)
return output