diff --git a/scripts/Diffraction/isis_powder/abstract_inst.py b/scripts/Diffraction/isis_powder/abstract_inst.py
index 09b5302aa20c976cae48baaf9ac654a176c777a8..320c8a876cc3f02b6aacdd0c9265515d56c91cd1 100644
--- a/scripts/Diffraction/isis_powder/abstract_inst.py
+++ b/scripts/Diffraction/isis_powder/abstract_inst.py
@@ -34,7 +34,7 @@ class AbstractInst(object):
def user_name(self):
return self._user_name
- def _create_vanadium(self, run_details, do_absorb_corrections=True, gen_absorb_correction=False):
+ def _create_vanadium(self, run_details, do_absorb_corrections=True):
"""
Creates a vanadium calibration - should be called by the concrete instrument
:param vanadium_runs: The vanadium run or run in range (depending on instrument) to process
@@ -44,7 +44,7 @@ class AbstractInst(object):
:return: d_spacing focused vanadium group
"""
return calibrate.create_van(instrument=self, run_details=run_details,
- absorb=do_absorb_corrections, gen_absorb=gen_absorb_correction)
+ absorb=do_absorb_corrections)
def _focus(self, run_number_string, do_van_normalisation):
"""
@@ -95,7 +95,7 @@ class AbstractInst(object):
raise NotImplementedError("spline_vanadium_ws must be implemented per instrument")
# Optional overrides
- def _apply_absorb_corrections(self, run_details, van_ws, gen_absorb=False):
+ 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
diff --git a/scripts/Diffraction/isis_powder/gem.py b/scripts/Diffraction/isis_powder/gem.py
index 6dc674a3a58ffad1c3ca52086e6a1f4942920960..0fbecd54cbbf735ab1941b4382224f63e1f0fb99 100644
--- a/scripts/Diffraction/isis_powder/gem.py
+++ b/scripts/Diffraction/isis_powder/gem.py
@@ -1,10 +1,8 @@
from __future__ import (absolute_import, division, print_function)
-import mantid.simpleapi as mantid
-
from isis_powder.abstract_inst import AbstractInst
-from isis_powder.gem_routines import gem_advanced_config, gem_param_mapping
-from isis_powder.routines import InstrumentSettings, RunDetails, yaml_parser
+from isis_powder.gem_routines import gem_advanced_config, gem_algs, gem_param_mapping
+from isis_powder.routines import InstrumentSettings, yaml_parser
class Gem(AbstractInst):
@@ -12,7 +10,7 @@ class Gem(AbstractInst):
basic_config_dict = yaml_parser.open_yaml_file_as_dictionary(kwargs.get("config_file", None))
self._inst_settings = InstrumentSettings.InstrumentSettings(
- attr_mapping=gem_param_mapping.attr_mapping, adv_conf_dict=gem_advanced_config,
+ attr_mapping=gem_param_mapping.attr_mapping, adv_conf_dict=gem_advanced_config.get_all_adv_variables(),
kwargs=kwargs, basic_conf_dict=basic_config_dict)
super(Gem, self).__init__(user_name=self._inst_settings.user_name,
@@ -21,7 +19,6 @@ class Gem(AbstractInst):
self._cached_run_details = None
self._cached_run_number = None
- raise NotImplementedError()
def focus(self, **kwargs):
self._inst_settings.update_attributes(kwargs=kwargs)
@@ -34,13 +31,12 @@ class Gem(AbstractInst):
run_details = self._get_run_details(run_number_string=self._inst_settings.run_in_range)
# Set the run and vanadium run equal
run_details.run_number = run_details.vanadium_run_numbers
- # TODO remove gen absorb_corrections param if we remove it on POLARIS
+
return self._create_vanadium(run_details=run_details,
- do_absorb_corrections=self._inst_settings.do_absorb_corrections,
- gen_absorb_correction=None)
+ do_absorb_corrections=self._inst_settings.do_absorb_corrections)
def _get_run_details(self, run_number_string):
- raise NotImplementedError()
+ return gem_algs.get_run_details(run_number_string=run_number_string, inst_settings=self._inst_settings)
def _generate_auto_vanadium_calibration(self, run_details):
raise NotImplementedError()
@@ -52,7 +48,7 @@ class Gem(AbstractInst):
def _generate_input_file_name(run_number):
raise NotImplementedError()
- def _apply_absorb_corrections(self, run_details, van_ws, gen_absorb=False):
+ def _apply_absorb_corrections(self, run_details, van_ws):
raise NotImplementedError()
def _spline_vanadium_ws(self, focused_vanadium_banks):
diff --git a/scripts/Diffraction/isis_powder/gem_routines/gem_algs.py b/scripts/Diffraction/isis_powder/gem_routines/gem_algs.py
index 5ca40f49ef22f5877498841526d8f1bcbc3502a7..db9e8bbedbcffd042af2eec234c1ea988f5f1a21 100644
--- a/scripts/Diffraction/isis_powder/gem_routines/gem_algs.py
+++ b/scripts/Diffraction/isis_powder/gem_routines/gem_algs.py
@@ -1 +1,38 @@
-from __future__ import (absolute_import, division, print_function)
\ No newline at end of file
+from __future__ import (absolute_import, division, print_function)
+
+import os
+
+from isis_powder.routines import common, RunDetails, yaml_parser
+
+
+def get_run_details(run_number_string, inst_settings):
+ run_number = common.generate_run_numbers(run_number_string=run_number_string)
+ if isinstance(run_number, list):
+ run_number = run_number[0]
+
+ # Get calibration mapping file
+ cycle_map = yaml_parser.get_run_dictionary(run_number_string=run_number_string,
+ file_path=inst_settings.cal_mapping_path)
+ label = cycle_map["label"]
+ offset_file_name = cycle_map["offset_file_name"]
+ empty_runs = cycle_map["empty_run_numbers"]
+ vanadium_runs = cycle_map["vanadium_run_numbers"]
+
+ # For GEM the grouping and offset file are identical
+ calibration_folder = os.path.normpath(os.path.expanduser(inst_settings.calibration_dir))
+ label_calibration_folder = os.path.join(calibration_folder, label)
+
+ offset_file_path = os.path.join(label_calibration_folder, offset_file_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
+ run_details.label = label
+ run_details.vanadium_run_numbers = vanadium_runs
+
+ run_details.grouping_file_path = offset_file_path
+ run_details.offset_file_path = offset_file_path
+
+ return run_details
diff --git a/scripts/Diffraction/isis_powder/gem_routines/gem_param_mapping.py b/scripts/Diffraction/isis_powder/gem_routines/gem_param_mapping.py
index 9721ec1a97e65405e256720d2180b0849ec8523d..e8d965dd642c613d9593db8ea7e02a80d3cfdced 100644
--- a/scripts/Diffraction/isis_powder/gem_routines/gem_param_mapping.py
+++ b/scripts/Diffraction/isis_powder/gem_routines/gem_param_mapping.py
@@ -2,6 +2,7 @@ from __future__ import (absolute_import, division, print_function)
# Maps friendly user name -> script name
attr_mapping = [("calibration_directory", "calibration_dir"),
+ ("calibration_mapping_file", "cal_mapping_path"),
("config_file", "config_file"),
("output_directory", "output_dir"),
("run_in_range", "run_in_range"),
diff --git a/scripts/Diffraction/isis_powder/pearl.py b/scripts/Diffraction/isis_powder/pearl.py
index 69255747f08431f78d95efb42ddad3bf6226dd65..87370343e88cc123641f775f34cd8ebfab8a4527 100644
--- a/scripts/Diffraction/isis_powder/pearl.py
+++ b/scripts/Diffraction/isis_powder/pearl.py
@@ -121,7 +121,9 @@ class Pearl(AbstractInst):
x_max=self._inst_settings.van_tof_cropping[-1])
return cropped_ws
- def _apply_absorb_corrections(self, run_details, van_ws, gen_absorb=False):
+ def _apply_absorb_corrections(self, run_details, van_ws):
+ # TODO move this to an instrument param
+ gen_absorb = False
if gen_absorb:
pearl_algs.generate_vanadium_absorb_corrections(van_ws=van_ws)
diff --git a/scripts/Diffraction/isis_powder/pearl_routines/pearl_algs.py b/scripts/Diffraction/isis_powder/pearl_routines/pearl_algs.py
index 43443ca52767142bb60087469e10e68e66766e8e..2f12d2ddf00bbb0e72bcdf9fd75df4cf6a14307f 100644
--- a/scripts/Diffraction/isis_powder/pearl_routines/pearl_algs.py
+++ b/scripts/Diffraction/isis_powder/pearl_routines/pearl_algs.py
@@ -102,7 +102,7 @@ def get_run_details(run_number_string, inst_settings):
run_details = RunDetails(run_number=first_run_number)
run_details.user_input_run_number = run_number_string
- run_details.calibration_file_path = calibration_file_path
+ run_details.offset_file_path = calibration_file_path
run_details.grouping_file_path = grouping_file_path
run_details.empty_runs = empty_run_numbers
run_details.label = label
diff --git a/scripts/Diffraction/isis_powder/polaris.py b/scripts/Diffraction/isis_powder/polaris.py
index f4ccbeda19717fa136421278382266ef1490416f..f242f0823e09871f7c5a28309d5e2fdb6d0d5879 100644
--- a/scripts/Diffraction/isis_powder/polaris.py
+++ b/scripts/Diffraction/isis_powder/polaris.py
@@ -37,14 +37,12 @@ class Polaris(AbstractInst):
run_details = self._get_run_details(run_number_string=int(self._inst_settings.run_in_range))
run_details.run_number = run_details.vanadium_run_numbers
- # TODO POLARIS doesn't need this flag to gen abs. corrections does PEARL?
return self._create_vanadium(run_details=run_details,
- do_absorb_corrections=self._inst_settings.do_absorb_corrections,
- gen_absorb_correction=None)
+ do_absorb_corrections=self._inst_settings.do_absorb_corrections)
# Overrides
- def _apply_absorb_corrections(self, run_details, van_ws, gen_absorb=False):
+ def _apply_absorb_corrections(self, run_details, van_ws):
return polaris_algs.calculate_absorb_corrections(ws_to_correct=van_ws,
multiple_scattering=self._inst_settings.multiple_scattering)
diff --git a/scripts/Diffraction/isis_powder/polaris_routines/polaris_algs.py b/scripts/Diffraction/isis_powder/polaris_routines/polaris_algs.py
index ead35de5b755758a9bc0b732fc2ef89fc0029bf5..206153af981da657cf7773ce8a7e5c324f06efb4 100644
--- a/scripts/Diffraction/isis_powder/polaris_routines/polaris_algs.py
+++ b/scripts/Diffraction/isis_powder/polaris_routines/polaris_algs.py
@@ -2,11 +2,11 @@ from __future__ import (absolute_import, division, print_function)
import mantid.simpleapi as mantid
import os
+
from isis_powder.routines import common, yaml_parser
from isis_powder.routines.RunDetails import RunDetails
from isis_powder.polaris_routines import polaris_advanced_config
-
def calculate_absorb_corrections(ws_to_correct, multiple_scattering):
mantid.MaskDetectors(ws_to_correct, SpectraList=list(range(0, 55)))
@@ -46,7 +46,7 @@ def get_run_details(run_number_string, inst_settings):
grouping_full_path = os.path.join(grouping_full_path, inst_settings.grouping_file_name)
in_calib_dir = os.path.join(inst_settings.calibration_dir, label)
- calibration_full_path = os.path.join(in_calib_dir, offset_file_name)
+ offsets_file_full_path = os.path.join(in_calib_dir, offset_file_name)
# Generate the name of the splined file we will either be loading or saving
splined_vanadium_name = _generate_splined_van_filename(chopper_on=inst_settings.chopper_on,
vanadium_run_string=vanadium_runs,
@@ -59,7 +59,7 @@ def get_run_details(run_number_string, inst_settings):
run_details.vanadium_run_numbers = vanadium_runs
run_details.label = label
- run_details.calibration_file_path = calibration_full_path
+ run_details.offset_file_path = offsets_file_full_path
run_details.grouping_file_path = grouping_full_path
run_details.splined_vanadium_file_path = splined_vanadium
diff --git a/scripts/Diffraction/isis_powder/routines/RunDetails.py b/scripts/Diffraction/isis_powder/routines/RunDetails.py
index 9d6a5f9265901925d8be5f8778d87d35ca3baace..b03e87ba945cb334eba7da417341362b99f84748 100644
--- a/scripts/Diffraction/isis_powder/routines/RunDetails.py
+++ b/scripts/Diffraction/isis_powder/routines/RunDetails.py
@@ -14,7 +14,7 @@ class RunDetails(object):
self.empty_runs = None
self.label = None
- self.calibration_file_path = None
+ self.offset_file_path = None
self.grouping_file_path = None
self.splined_vanadium_file_path = None
diff --git a/scripts/Diffraction/isis_powder/routines/calibrate.py b/scripts/Diffraction/isis_powder/routines/calibrate.py
index 3ba7d6d5cf766508732b571e356c74fa916c4c16..f86f3facffc802fa2ff1b7be6ab9f0924969d018 100644
--- a/scripts/Diffraction/isis_powder/routines/calibrate.py
+++ b/scripts/Diffraction/isis_powder/routines/calibrate.py
@@ -6,7 +6,7 @@ import isis_powder.routines.common as common
from isis_powder.routines.common_enums import InputBatchingEnum
-def create_van(instrument, run_details, absorb, gen_absorb):
+def create_van(instrument, run_details, absorb):
van = run_details.vanadium_run_numbers
run_details = instrument._get_run_details(run_number_string=van)
# Always sum a range of inputs as its a vanadium run over multiple captures
@@ -24,7 +24,7 @@ def create_van(instrument, run_details, absorb, gen_absorb):
if absorb:
aligned_ws = _apply_absorb_corrections(instrument=instrument, run_details=run_details,
- van_ws=aligned_ws, gen_absorb=gen_absorb)
+ van_ws=aligned_ws)
focused_vanadium = mantid.DiffractionFocussing(InputWorkspace=aligned_ws,
GroupingFileName=run_details.grouping_file_path)
@@ -55,8 +55,8 @@ def _create_vanadium_splines(focused_spectra, instrument, run_details):
mantid.GroupWorkspaces(InputWorkspaces=splined_ws_list, OutputWorkspace="Van_spline_data")
-def _apply_absorb_corrections(instrument, run_details, van_ws, gen_absorb):
- absorb_ws = instrument._apply_absorb_corrections(run_details, van_ws, gen_absorb=gen_absorb)
+def _apply_absorb_corrections(instrument, run_details, van_ws):
+ absorb_ws = instrument._apply_absorb_corrections(run_details=run_details, van_ws=van_ws)
return absorb_ws
diff --git a/scripts/Diffraction/isis_powder/routines/yaml_parser.py b/scripts/Diffraction/isis_powder/routines/yaml_parser.py
index 476fadbe00c0747648196464ea2d14784dc914fc..54e058d57aa3e50f069c1e1da822996d87c8df6d 100644
--- a/scripts/Diffraction/isis_powder/routines/yaml_parser.py
+++ b/scripts/Diffraction/isis_powder/routines/yaml_parser.py
@@ -12,7 +12,7 @@ def get_run_dictionary(run_number_string, file_path):
run_number_string = run_number_list[0]
config_file = open_yaml_file_as_dictionary(file_path)
- yaml_sanity.calibration_file_sanity_check(config_file)
+ yaml_sanity.calibration_file_sanity_check(config_file, file_path)
run_key = _find_dictionary_key(dict_to_search=config_file, run_number=run_number_string)
if not run_key:
@@ -49,10 +49,15 @@ def _find_dictionary_key(dict_to_search, run_number):
if is_run_range_key_unbounded(key): # Have an unbounded run don't generate numbers
split_key = str(key).split('-')
lower_key_bound = int(split_key[-2])
- if run_number > lower_key_bound:
+ if run_number >= lower_key_bound:
return key
else:
- generated_runs = common.generate_run_numbers(run_number_string=key)
+ try:
+ generated_runs = common.generate_run_numbers(run_number_string=key)
+ except RuntimeError:
+ raise ValueError("Could not parse '" + str(key) + "'\n"
+ "This should be a range of runs in this cycle in the mapping file."
+ " Please check your indentation if this should be within a cycle.")
if run_number in generated_runs:
return key
diff --git a/scripts/Diffraction/isis_powder/routines/yaml_sanity.py b/scripts/Diffraction/isis_powder/routines/yaml_sanity.py
index 4d945b71ae6a19361aecfe3d5dbb9e8faff5780c..8227aecce194a2ffaa8f72f9f0299680d5d18699 100644
--- a/scripts/Diffraction/isis_powder/routines/yaml_sanity.py
+++ b/scripts/Diffraction/isis_powder/routines/yaml_sanity.py
@@ -1,7 +1,11 @@
from __future__ import (absolute_import, division, print_function)
-def calibration_file_sanity_check(yaml_dict):
+def calibration_file_sanity_check(yaml_dict, file_path):
+ # Check that the dictionary has data
+ if not yaml_dict:
+ raise ValueError("YAML dictionary appear to be empty at:\n" + str(file_path))
+
# Check that we only have one unbounded range at maximum
unbound_key_exists = _does_single_unbound_key_exist(yaml_dict)
if unbound_key_exists: