From eaa32fcf1c5735316f7ab26ef41cfaaa5696721e Mon Sep 17 00:00:00 2001
From: Martyn Gigg <martyn.gigg@gmail.com>
Date: Fri, 2 Aug 2019 17:38:52 +0100
Subject: [PATCH] Move vanadium spline/peak masking to abstract instrument
This makes it the default behaviour unless overridden,
like GEM and PEARL.
Refs #23731
---
.../Diffraction/isis_powder/abstract_inst.py | 12 +++-
scripts/Diffraction/isis_powder/gem.py | 4 ++
scripts/Diffraction/isis_powder/hrpd.py | 6 --
.../hrpd_routines/hrpd_advanced_config.py | 1 +
.../hrpd_routines/hrpd_param_mapping.py | 1 +
scripts/Diffraction/isis_powder/polaris.py | 10 ---
.../isis_powder/routines/common.py | 70 ++++++++++++++++---
7 files changed, 76 insertions(+), 28 deletions(-)
diff --git a/scripts/Diffraction/isis_powder/abstract_inst.py b/scripts/Diffraction/isis_powder/abstract_inst.py
index 2c1bc9ee0ec..d5644f8b925 100644
--- a/scripts/Diffraction/isis_powder/abstract_inst.py
+++ b/scripts/Diffraction/isis_powder/abstract_inst.py
@@ -141,9 +141,15 @@ class AbstractInst(object):
:param focused_vanadium_banks: The list processed (and cropped) vanadium banks to take a spline of
:return: The splined vanadium workspaces as a list
"""
- # XXX: Although this could be moved to common if enough instruments spline the same way and have
- # the instrument override the optional behaviour
- raise NotImplementedError("spline_vanadium_ws must be implemented per instrument")
+ if self._inst_settings.masking_file_name is not None:
+ masking_file_path = os.path.join(self.calibration_dir,
+ self._inst_settings.masking_file_name)
+ bragg_mask_list = common.read_masking_file(masking_file_path)
+ focused_vanadium_banks = common.apply_bragg_peaks_masking(focused_vanadium_banks,
+ mask_list=bragg_mask_list)
+ output = common.spline_workspaces(focused_vanadium_spectra=focused_vanadium_banks,
+ num_splines=self._inst_settings.spline_coeff)
+ return output
def _crop_banks_to_user_tof(self, focused_banks):
"""
diff --git a/scripts/Diffraction/isis_powder/gem.py b/scripts/Diffraction/isis_powder/gem.py
index 075ed239dda..262a7c18ad5 100644
--- a/scripts/Diffraction/isis_powder/gem.py
+++ b/scripts/Diffraction/isis_powder/gem.py
@@ -209,6 +209,10 @@ class Gem(AbstractInst):
return self._inst_settings.unit_to_keep
def _spline_vanadium_ws(self, focused_vanadium_banks):
+ """
+ GEM uses a Vanadium-Niobium mix and doesn't need to strip any Vanadium Bragg peaks
+ before splining
+ """
return common.spline_vanadium_workspaces(focused_vanadium_spectra=focused_vanadium_banks,
spline_coefficient=self._inst_settings.spline_coeff)
diff --git a/scripts/Diffraction/isis_powder/hrpd.py b/scripts/Diffraction/isis_powder/hrpd.py
index 14f4cb7be34..748787090f4 100644
--- a/scripts/Diffraction/isis_powder/hrpd.py
+++ b/scripts/Diffraction/isis_powder/hrpd.py
@@ -149,12 +149,6 @@ class HRPD(AbstractInst):
max_crop = middle + right_crop
mantid.MaskBins(InputWorkspace=ws, OutputWorkspace=ws, XMin=min_crop, XMax=max_crop)
- def _spline_vanadium_ws(self, focused_vanadium_banks, instrument_version=''):
- spline_coeff = self._inst_settings.spline_coeff
- output = hrpd_algs.process_vanadium_for_focusing(bank_spectra=focused_vanadium_banks,
- spline_number=spline_coeff)
- return output
-
def _switch_tof_window_inst_settings(self, tof_window):
self._inst_settings.update_attributes(
advanced_config=hrpd_advanced_config.get_tof_window_dict(tof_window=tof_window))
diff --git a/scripts/Diffraction/isis_powder/hrpd_routines/hrpd_advanced_config.py b/scripts/Diffraction/isis_powder/hrpd_routines/hrpd_advanced_config.py
index fc724b05a69..2adac4400ca 100644
--- a/scripts/Diffraction/isis_powder/hrpd_routines/hrpd_advanced_config.py
+++ b/scripts/Diffraction/isis_powder/hrpd_routines/hrpd_advanced_config.py
@@ -64,6 +64,7 @@ window_180_280_params = {
}
file_names = {
+ "vanadium_peaks_masking_file": "VanaPeaks.dat",
"grouping_file_name": "hrpd_new_072_01_corr.cal"
}
diff --git a/scripts/Diffraction/isis_powder/hrpd_routines/hrpd_param_mapping.py b/scripts/Diffraction/isis_powder/hrpd_routines/hrpd_param_mapping.py
index 471d5a8aaaf..02eb39434b1 100644
--- a/scripts/Diffraction/isis_powder/hrpd_routines/hrpd_param_mapping.py
+++ b/scripts/Diffraction/isis_powder/hrpd_routines/hrpd_param_mapping.py
@@ -33,5 +33,6 @@ attr_mapping = \
ParamMapEntry(ext_name="user_name", int_name="user_name"),
ParamMapEntry(ext_name="vanadium_normalisation", int_name="do_van_norm"),
ParamMapEntry(ext_name="vanadium_tof_cropping", int_name="van_tof_cropping"),
+ ParamMapEntry(ext_name="vanadium_peaks_masking_file", int_name="masking_file_name"),
ParamMapEntry(ext_name="window", int_name="tof_window", enum_class=HRPD_TOF_WINDOWS)
]
diff --git a/scripts/Diffraction/isis_powder/polaris.py b/scripts/Diffraction/isis_powder/polaris.py
index 496cfc40410..2a2e8bd9d05 100644
--- a/scripts/Diffraction/isis_powder/polaris.py
+++ b/scripts/Diffraction/isis_powder/polaris.py
@@ -6,7 +6,6 @@
# SPDX - License - Identifier: GPL - 3.0 +
from __future__ import (absolute_import, division, print_function)
-import os
from isis_powder.routines import absorb_corrections, common, instrument_settings
from isis_powder.abstract_inst import AbstractInst
@@ -134,15 +133,6 @@ class Polaris(AbstractInst):
return self._run_details_cached_obj[run_number_string_key]
- def _spline_vanadium_ws(self, focused_vanadium_spectra, instrument_version=''):
- masking_file_name = self._inst_settings.masking_file_name
- spline_coeff = self._inst_settings.spline_coeff
- masking_file_path = os.path.join(self.calibration_dir, masking_file_name)
- output = polaris_algs.process_vanadium_for_focusing(bank_spectra=focused_vanadium_spectra,
- spline_number=spline_coeff,
- mask_path=masking_file_path)
- return output
-
def _switch_mode_specific_inst_settings(self, mode):
if mode is None and hasattr(self._inst_settings, "mode"):
mode = self._inst_settings.mode
diff --git a/scripts/Diffraction/isis_powder/routines/common.py b/scripts/Diffraction/isis_powder/routines/common.py
index c1915bac8d9..58324df1c28 100644
--- a/scripts/Diffraction/isis_powder/routines/common.py
+++ b/scripts/Diffraction/isis_powder/routines/common.py
@@ -5,7 +5,7 @@
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
from __future__ import (absolute_import, division, print_function)
-from six import iterkeys
+from six import PY2, iterkeys
import warnings
import mantid.kernel as kernel
@@ -13,6 +13,24 @@ import mantid.simpleapi as mantid
from isis_powder.routines.common_enums import INPUT_BATCHING, WORKSPACE_UNITS
+def apply_bragg_peaks_masking(workspaces_to_mask, mask_list):
+ """
+ Mask a series of peaks defined by the lower/upper bounds
+ :param workspaces_to_mask: Mask these workspaces
+ :param mask_list: A list of pairs of peak X min/max for masking
+ :return: A list of masked workspaces
+ """
+ output_workspaces = list(workspaces_to_mask)
+
+ for ws_index, (bank_mask_list, workspace) in enumerate(zip(mask_list, output_workspaces)):
+ output_name = "masked_vanadium-" + str(ws_index + 1)
+ for mask_params in bank_mask_list:
+ output_workspaces[ws_index] = mantid.MaskBins(InputWorkspace=output_workspaces[ws_index],
+ OutputWorkspace=output_name,
+ XMin=mask_params[0], XMax=mask_params[1])
+ return output_workspaces
+
+
def cal_map_dictionary_key_helper(dictionary, key, append_to_error_message=None):
"""
Provides a light wrapper around the dictionary key helper and uses case insensitive lookup.
@@ -460,6 +478,48 @@ def subtract_summed_runs(ws_to_correct, empty_sample_ws_string, instrument, scal
return ws_to_correct
+def read_masking_file(masking_file_path):
+ """
+ Read a masking file in the ISIS powder format:
+
+ # bank N(plus any other comments)
+ peak_min0 peak_max0
+ peak_min1 peak_max1
+ ...
+ # bank M(plus any other comments)
+ peak_min0 peak_max0
+ peak_min1 peak_max1
+ ...
+ :param masking_file_path: The full path to a masking file
+ :return: A list of peak min/max values for each bank
+ """
+ all_banks_masking_list = []
+ bank_masking_list = []
+
+ # Python > 3 requires the encoding to be included so an Angstrom
+ # symbol can be read, I'm assuming all file read here are
+ # `latin-1` which may not be true in the future. Python 2 `open`
+ # doesn't have an encoding option
+ if PY2:
+ encoding = {}
+ else:
+ encoding = {"encoding": "latin-1"}
+ with open(masking_file_path, **encoding) as mask_file:
+ for line in mask_file:
+ if 'bank' in line:
+ # Push back onto new bank
+ if bank_masking_list:
+ all_banks_masking_list.append(bank_masking_list)
+ bank_masking_list = []
+ else:
+ # Parse and store in current list
+ bank_masking_list.append(line.strip().split())
+ # deal with final bank
+ if bank_masking_list:
+ all_banks_masking_list.append(bank_masking_list)
+ return all_banks_masking_list
+
+
def _crop_single_ws_in_tof(ws_to_rebin, x_max, x_min):
"""
Implementation of cropping the single workspace in TOF. First converts to TOF, crops then converts
@@ -542,14 +602,6 @@ def _load_list_of_files(run_numbers_list, instrument, file_ext=None):
return read_ws_list
-def _strip_vanadium_peaks(workspaces_to_strip):
- out_list = []
- for i, ws in enumerate(workspaces_to_strip):
- out_name = ws.name() + "_toSpline-" + str(i+1)
- out_list.append(mantid.StripVanadiumPeaks(InputWorkspace=ws, OutputWorkspace=out_name))
- return out_list
-
-
def _sum_ws_range(ws_list):
"""
Sums a list of workspaces into a single workspace. This will take the name
--
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