LoadNexusLogs now extends NexusHDF5Descriptor
Allow HDF5 open to handle multiple handlers in NexusHDF5Descriptor

Expose m_fileInfo from NexusFileLoader

To do:
LoadNexusMonitors2

This means we can hide the parsing function that takes an xml string from the public interface and add a friend class to test this.
It also means that getRuns() can be called multiple times with different criteria without having to re-parse the file.

Re #26897

Giovanni Di Siena authored 4 years ago and Gigg, Martyn Anthony committed 4 years ago

In places other substitutions have been made, e.g
Clang does not yet specialize std::shared_ptr for T[]. Vector
has been used instead. The operator[] methods were incorrectly
marked const but returning a non-const reference - this has been fixed.
Refs #25842

Adds a couple of generic functions for requesting data from a journal. The main work is done by a function that takes the file contents as a string so that this can be easily tested. A wrapper function allows the file to first be fetched from a URL constructed for the instrument and cycle.

Also adds a couple of functions for requesting the list of cycles, again with one function taking the file contents and another which finds the URL for the instrument.

Re #26897

Miscellaneous code review comments to add comments, remove redundant brackets
Also added comment to the sample environment concept page to explain where
Mantid will search for the attenuation profile file

Signed-off-by: Steven Hahn <hahnse@ornl.gov>

Signed-off-by: Steven Hahn <hahnse@ornl.gov>

Signed-off-by: Steven Hahn <hahnse@ornl.gov>

Runs clang-tidy pass by ref across the codebase to fix-up various
warnings we are seeing in cppcheck

Hand-fixes some cppcheck warnings, this was work prior to fixing the
cppcheck target.

Signed-off-by: Steven Hahn <hahnse@ornl.gov>

Signed-off-by: Steven Hahn <hahnse@ornl.gov>

Signed-off-by: Steven Hahn <hahnse@ornl.gov>

Signed-off-by: Steven Hahn <hahnse@ornl.gov>

While the primary use of the new attenuation profile file feature is expected
to be via the sample environment xml file, it also makes sense to add it into
any algorithms where the material properties can be specified. So I've added a
new attenuation profile parameter to the SetSampleMaterial and LoadSampleEnvironment
algorithms. The validations on these algorithms means they can't be called using
postional arguments so have inserted the new parameter in the logical place next
to the absorption cross section

Have updated the docs to explain how the attenuation profile file is used

Add feature where an externally generated attenuation profile can be loaded into
the material definition from a .DAT text file. This will override the normal
exp(-alpha*thickness) calculation of the attenuation. The new feature was requested
as part of the absorption calculation for the Pearl instrument where some parts
of the environment are crystalline

Found the lookup\interpolation on the loaded profile was slowing down the absorption
Monte Carlo calculation.
So improved performance of Kernel::Interpolation. Changed it to use vector of pairs
instead of two separate vectors to reduce amount of navigation around vectors

Considered adding feature into AttenuationProfile where I add any interpolated points
into the override attenuation profile to prevent interpolation next iteration of
Monte Carlo simulation. However wasn't convinced this was going to be thread-safe
during the parallel part of the absorption calculation - may revisit this. While doing
this investigation I fixed the following issues with the function Interpolation::AddPoint:

a) it doesn't add the same point twice
b) it reuses the lower_bound function rather than stepping through the vector sequentially

I removed the exception from findIndexOfNextLargerValue because the end()
iterator is a valid result if the x value supplied equals the last x value
already in the vector. Could have left check in for begin() but didn't seem
much point

Finally - the interpolation outside the range is not v good. The data at the extremes
is noisy so we end up extrapolating based on random gradient in extreme 2 points. Need
to either fit or use more points to determine gradient

Also updated class_maker.py

This commit replaces all header guards in DataHandling with #pragma once

Reuse map from NeXus file getEntries prevents creation and destruction
of std::map
addressing clang-format

This commit changes the call of workspace->x(0) to workspace->points(0) because of this I no longer need to check if the workspace is a histogram or not.

re: #27774