The LoadEventNexus algorithm is run without compression and the events
in the Nexus file are not already sorted by pulse time, the algorithm
is incorrectly labelling them as sorted by pulse time. This change fixes
the problem by always looping through the "used" detectors even if
loading without compression
This problem was causing FilterByTime to incorrectly slice up an event
file by time. A lot of events were assigned to the last second of a run
when slicing by time

Changed screenshot, reworded an entry, amalgamated Algorithms into single section and moved some SliceViewer bugfixes to Algorithms

Reordered SliceViewer bugfixes list, revised note for IPeakFunction.intensityError, grammar check

Updated links, removed obsolete headings, added screenshots, spell check

When run with a sample that is offset from the origin, the calculation
of the beam height and width could result in a beam that didn't overlap
with the sample. This caused an error when running the MonteCarloAbsorption
algorithm
Have added unit test to cover this scenario and have modified the RectangularBeamProfile
class to expose the min\max points on the beam profile to support this

Pass by const reference where possible
Make code cleaner andremove unneccessary include
Update release notes
Add comments to CopySample and SetSample

* mask nans and infs instead of just replacing with 0

* remove irrelevant beam center offset in default q-binning calculation

* fix doc test output

* remove trailing (), check for n_wedges

* use the new stitch in SANSILLAuto

* remove blank doc test

* enable 4th column by default in ascii exports

* made outputbinning per sample

* proper validation for OutputBinning with : as delimiter

* do not complain on dx if it is requested, but doesn't exist

* refactored outputting the wedges

* uncomment the sensitivity outputs

* refactor outputting panels

* also set shape_table to empty for not doing wedges for panels

* check if ws exist before bookkeeping, happens if there is empty token

* swap det 1 and 2 for D22B starting from cyc 212

* chopper att2 for D22 and smarter q interval

* better error when requesting wrong q range

* convert att_value to float

* remove extra flux rescaling

* support kinetic mode for d11b in the loader

* implemented kinetic reduction returning a workspace group

* implemented kinetic (mono) reduction

* guard for workspace group in needs_processing

* handle absent or present 2nd monitor, store durations as the 2nd mon

* round wavelength for kinetic, require alphanum for output

* set the 2nd monitor (a.k.a durations) errors to 0

* added a unit test for kinetic and D33 VTOF

* fix the regression for d16 omega scan, add unit test

* updated sys test reference for SANSILLReduction

* update system test reference for autoprocess, chunk 1

* fix the test name

* update system test references for autoprocess (chunk 2)

* fix the validation ws name in iphiq

* adjust the test of SaveAscii2 when there is no dx

* adjust the doc test

* fixed d11 multi transmission ref following a bug fix in stitch

* fixed D16 gamma scan ref after a fix in stitch

* updated reference of d11 abs scale test

* fixed the inputs in drill process test to match the other sys test

* scale by the flux factor before comparison, due to commit f25a6cd5

* doxygen, removed unneeded include statements

* added a test for D22B cycle 212 onwards

* added release notes for extended algorithms

* fixed the doxygen param issues

The following shapes can be rotated, and the finite ones can be plotted:
Cuboid
Cylinder
HollowCylinder
InfinitePlane
InfiniteCylinder
Hexahedron
TaperedGuide
SliceofCylinderRing

The rotation can be manually set by the user using the rotation tag
Further rotation is added using a goniometer tag, which works with SetGoniometer

CopySample can now copy a shape which can be plotted, but maintains its own
Goniometer angle

Call triangulator directly to render with OpenCascade
This can create shapes such as spheres or cylinders
and can merge shapes

These mainly affect the performance on a debug build but still helpful
to assist in problem identification
Fix a problem in InterpolateLogQuadratic where for point data the
method wasn't handling x values more than halfway past the midpoint
between two points and switch to using std::upper_bound
Pass histogram around rather than workspace now that not relying on
YIndexOfX method
Prime the sample bounding box so there's no race condition in the
multi-threaded part
Create the Track in the return statement of generateInitialTrack to
encourage the return value optimization to happen
Pass the S(Q) histogram around rather than the full workspace
Avoid calling the points() method because the underlying cow_ptr
code involves an std::atomic_load that seems to degrade the performance
when running with a lot of threads
Fix bug in determining detector position (wrong index being used)
Also change the way the seed is determined so the same seed is used for a particular
spectrum regardless of how many other spectra are loaded based on the SpectrumMin and
SpectrumMax settings of Load
Make logging less verbose and some documentation improvements
Also rename InterpolateLogQuadratic to InterpolateGaussian to better
suggest what it's doing
Stop output workspace overwriting existing workspaces
Sort out logic for saving the output group workspace - force use of the ADS since
we're naming the group member workspaces, and also cater for potential name clashes

* added additional param to control max shift

* building blocks for test data generator

* organized components into objects and tests

* updated parameters for b2bexpconvpv defaults

* added appropriate logic for max shift, still need to refactor

* refactored a bit, deobfuscated names

* fixed some unintention text changes

* moved shiftCorrection Calc, changed maxBins calc

* fixed upper bound issue

* apparently some formatting errors slipped through?

* better way of getting the bin width

* crop cc spectra to region

* a better way of cropping the cc spectra, courtesy of rosswhitfield

* CrossCorrelateTestData fix for non rhel platforms

* warning fixes, hopefully

* forgot to commit the use of an unused variable

* wip test fixes and changes

* Change to use a simpler function

* Create new workspace with only the reference spectrum

* Add second spectrum with horizontal shift

* merge and modified some cross correlate data

* Fill in the other function types for fake data

* wip debugging test stuff, failing spectrum range

* Change logging method

* Minor refactor to collect methods

* Dynamically get number of spectra

* Fix CrossCorrelateTestData, need to fix hard codes difc/difa/t0 values

* added test cases for the CC of a few spectra in a couple algos

* added to cmake file, allowed me to remove gauss simplex def

* revert, breaks on ubuntu, cant add to cmake without removing simplex

* need these changes back, found a solution

* moved gauss declaration fixes cmake issue

* moved TOF to DSpacing conversion vals/calcs

* added fix for logging, requires newline char

* add dllexport to see if that fixes windows

* remove anon namespace while I look into other solutions

* added release notes for new CrossCorrelate param

* moved new param to end for backwards compatibility

Co-authored-by: Harry Hughes <5n4@ornl.gov>
Co-authored-by: Pete Peterson <petersonpf@ornl.gov>
Co-authored-by: Ross Whitfield <whitfieldre@ornl.gov>

* added additional param to control max shift

* building blocks for test data generator

* organized components into objects and tests

* updated parameters for b2bexpconvpv defaults

* added appropriate logic for max shift, still need to refactor

* refactored a bit, deobfuscated names

* fixed some unintention text changes

* moved shiftCorrection Calc, changed maxBins calc

* fixed upper bound issue

* apparently some formatting errors slipped through?

* better way of getting the bin width

* crop cc spectra to region

* a better way of cropping the cc spectra, courtesy of rosswhitfield

* CrossCorrelateTestData fix for non rhel platforms

* warning fixes, hopefully

* forgot to commit the use of an unused variable

* wip test fixes and changes

* Change to use a simpler function

* Create new workspace with only the reference spectrum

* Add second spectrum with horizontal shift

* merge and modified some cross correlate data

* Fill in the other function types for fake data

* wip debugging test stuff, failing spectrum range

* Change logging method

* Minor refactor to collect methods

* Dynamically get number of spectra

* Fix CrossCorrelateTestData, need to fix hard codes difc/difa/t0 values

* added test cases for the CC of a few spectra in a couple algos

* added to cmake file, allowed me to remove gauss simplex def

* revert, breaks on ubuntu, cant add to cmake without removing simplex

* need these changes back, found a solution

* moved gauss declaration fixes cmake issue

* moved TOF to DSpacing conversion vals/calcs

* added fix for logging, requires newline char

* add dllexport to see if that fixes windows

* remove anon namespace while I look into other solutions

* added release notes for new CrossCorrelate param

* moved new param to end for backwards compatibility

Co-authored-by: Pete Peterson <petersonpf@ornl.gov>
Co-authored-by: Harry Hughes <5n4@ornl.gov>
Co-authored-by: Ross Whitfield <whitfieldre@ornl.gov>

* Re #31429 Fixture, as the problem caused by two values in the

denominator being equal

* Re #31429 cpp paranoid warnings

* Re #31429 fixing typos in the code

* Re #31429 Release notes

* Re #31429 better release notes located in proper place.

* Update comments.

* Avoid repetition of warning message within loop.

* Tidy release notes.

* Add test to recreate bug.

* Add test for leading edge noisy data case

* Remove redundant if statement

* Tighten failure criteria

* Fix linux compiler warnings

* Fix release notes error

Co-authored-by: Tom Hampson <thomas.hampson@stfc.ac.uk>

Add extra unit test to ConvertToDiffractionMDWorkspace3Test to cover
ISIS use case for ConvertToDiffractionMDWorkspace where initial workspace
has units of dSpacing.
Also fix bug in ConvertToMDMinMaxLocal (which is called as a child
algorithm from ConvertToDiffractionMDWorkspace) where there's a mix up
between the workspace index and the detector index used to look up stuff
from the table workspace created by PreprocessDetectorsToMD

Signed-off-by: Jose Borreguero <borreguero@gmail.com>

They have not been used since release 3.8

Signed-off-by: Jose Borreguero <borreguero@gmail.com>

CreateMDWorkspace has parseNames for the input param Names
Now this parser has been added to CreateMDHistoWorkspace