Giovanni Di Siena authored Mar 31, 2020 and Gigg, Martyn Anthony committed Apr 07, 2020

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

Also updated class_maker.py

reduction.two_theta -> loader.two_theta

no more reduction.two_theta information

Refs #24123

- revert some changes of SpecularReflectionPositionCorrect2 (but keep all const changes)
- add new method addSampleLogs to LoadILLReflectometry, sample log of two theta not complete for user given angle
- use m_sampleAngleName for FIGARO (many occasions in code where this name is used)
- in ReflectometryILLPreprocess(Test):
  - in case of user given two theta: need to write this to the sample logs
  - use loader with fixed two theta and line position to avoid peak fitting and final detector rotation
  - handle LinePosition input properly when moving the detector (only needed if two theta is user given)
  - provide FIGARO's deflection angle (added a method to common since it handles NeXus variable names)
  - import and use numpy.full in PreProcess test to improve the test in terms of shape and type of the values. Get blocksize() outside loop.
  - CalculatePolynomialBackground failed often during testing and it was not easy to adapt the test, deleted background offset and width input properties -> cleanup still tested fully
  - replaced use of getLogData by getProperty

Refs #24123

(the offset was subtracted)

- input validation
- moving detector logic

Refs #24123

Corrected the use of SpecularReflectionPositionCorrect for D17,
- must not RotateAroundSample

I found a difference of about 7.1e-15  between master and this change for the doctest ReflectometryILLConvertToQ for reflected workspaces.

Refs #24123

- PreProcess name changes: BraggAngle -> TwoTheta (a factor of two needs to be taken into account for this change), BeamCentre -> LinePosition (due to FindReflectometryLines naming, still not sure if this name is the best)

- DirectLineWorkspace input for PreProcess

- Test for DirectLineWorkspace

- Documentation + its tests

- Loader: added unit Degrees to sample log reduction.two_theta + tests

Refs #24123

Refs #24123

instead of 1

Refs #24123

Refs #24123

- peak position as workspace index: it is foreseen to change the IDF that spectrum number and workspace index are interchangeable

Refs #24123

Update copyright headers in all files

Squashed commit of the following:

* First version of a script to manage copyright statements

re #23468

* Neatened up script, added comments

re #23488

* move script to tools directory

re #23488

* small script changes and a couple of manual file changes

re #23488

* Minor chnage to whitespace detection in regex

re #23488

* Add an excluded directory

re #23488

* remove a repeasted copyright statement in a file

re #23488

* Don't comsume the comment end if it is on the same line

re #23488

* fix error in new copright parsing

re #23488

* remove double copyrifght entry

re #23488

* Improve handling of old copyrights at the start of comments

re #23488

* remove empty comments re #23488

* exclude gsoapgenerated directories

re #23488

* Sort out greedy line matching re #23488

* improve empty comment removal

re #23488

* improve false positives

re #23488

* impressive speedup by limiting regex matching length

re #23488

* remove evil invisible non ascii character

Also upadte the copyright at the same time

re #23488

* resolve multiple copyrights in a single file

re #23488

* resolve an issue with new statement detection

re #23488

* another unprintable unicode character

re #23488

* pep updates and cmake the new copyright fit clang format

re #23488

* update already done new format headers

re #23488

* wrong type of bracket

re #23488

* Update class_maker and friends

re #23488

* Update all copyright statements

re #23488

* clang format re #23488

* flake8 warnings re #23488

* Flake8 warnings re #23488

* Exclude .cmake.in and rb.in files

re #23488

* replace missing line re #23488

* exclude .py.in files as they are flasely recognized as C++

re #23488

* another setp.py.in re #23488

* another .py.in correction re #23488

* Hopefully the last of the .py.in files re #23488

* resolve utf-8 encoding of python files and changed ABINS checksum

re #23488

* updates to unit tests that reference line numbers

re #23488

* remaining unit test files and other fixes

re #23488

Update to clang-format-5 and reformat the codebase 

Re #22794

Refs #21907

Refs #21907

Thus, intermediate solution!
- D0, D1 not correctly defined in Nexus
- commented out test code and source code for the moment
- use existing methods for D0 and D1 computation

This implementation is necessary for loading reflectometry data since some Nexus entries were moved.

Refs #21907

- doubleFromRun is public now to be used in tests

Refs #21907

Refs #21907

- Added check of units for all tested Nexus entries
- Used try catch to differentiate between the two supported Nexus versions (else loader throws "Unknown property seach object ...")
- Added unit tests for new Nexus file (test data not yet uploaded -> need to be fixed later)
- Added tests for new distance fields which fail (unclear yet if this is an implementation error (likely) or an error in Nexus file)

Refs #21907

Refs #21907

Refs #21907

Refs #21907

Refs #21907

Refs #21907

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