BUG: Fixes issues when computing the FZ Quaternion from an input quaternion

.clang-format

@@ -1,12 +1,11 @@
 ---
-Language:        Cpp
-# BasedOnStyle:  LLVM
+Language: Cpp
 # AccessModifierOffset: -2
 # AlignAfterOpenBracket: Align
 # AlignConsecutiveAssignments: false
 # AlignConsecutiveDeclarations: false
 # AlignEscapedNewlinesLeft: false
-# AlignOperands:   true
+# AlignOperands: true
 # AlignTrailingComments: true
 # AllowAllParametersOfDeclarationOnNextLine: true
 # AllowShortBlocksOnASingleLine: false
@@ -20,49 +19,45 @@ AllowShortFunctionsOnASingleLine: false
 AlwaysBreakTemplateDeclarations: true
 # BinPackArguments: true
 # BinPackParameters: true
-BraceWrapping:   
-  AfterClass:      true
+BraceWrapping:
+  AfterClass: true
   AfterControlStatement: true
-  AfterEnum:       true
-  AfterFunction:   true
-  AfterNamespace:  true
+  AfterEnum: true
+  AfterFunction: true
+  AfterNamespace: true
   AfterObjCDeclaration: false
-  AfterStruct:     true
-  AfterUnion:      false
-  BeforeCatch:     false
-  BeforeElse:      true
-  IndentBraces:    false
+  AfterStruct: true
+  AfterUnion: false
+  BeforeCatch: false
+  BeforeElse: true
+  IndentBraces: false
 #BreakBeforeBinaryOperators: None
 BreakBeforeBraces: Custom
 BreakBeforeTernaryOperators: false
 BreakConstructorInitializersBeforeComma: true
-ColumnLimit:     200
-# CommentPragmas:  '^ IWYU pragma:'
+ColumnLimit: 200
+# CommentPragmas: '^ IWYU pragma:'
 # ConstructorInitializerAllOnOneLineOrOnePerLine: false
 ConstructorInitializerIndentWidth: 0
 # ContinuationIndentWidth: 4
 # Cpp11BracedListStyle: true
 # DerivePointerAlignment: false
-# DisableFormat:   false
+# DisableFormat: false
 # ExperimentalAutoDetectBinPacking: false
-# ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
-SortIncludes: true
-#IncludeBlocks: Regroup
-IncludeCategories:
-  - Regex:           '^(<|"(QtCore|QtWidgets|QtGui|QtNetwork)/)'
-    Priority:        5
-  - Regex:           '^"(SIMPL|llvm-c|clang|clang-c)/'
-    Priority:        100
-  - Regex:           '^"(SIMPLib/SIMPLib)'
-    Priority:        90
-  - Regex:           '.*'
-    Priority:        1000
+# ForEachMacros: [ foreach, Q_FOREACH, BOOST_FOREACH ]
+# IncludeCategories: 
+#   - Regex: '^"(llvm|llvm-c|clang|clang-c)/'
+#     Priority: 2
+#   - Regex: '^(<|"(gtest|isl|json)/)'
+#     Priority: 3
+#   - Regex: '.*'
+#     Priority: 1
 # IndentCaseLabels: false
-# IndentWidth:     2
+# IndentWidth: 2
 # IndentWrappedFunctionNames: false
 # KeepEmptyLinesAtTheStartOfBlocks: true
 # MacroBlockBegin: ''
-# MacroBlockEnd:   ''
+# MacroBlockEnd: ''
 # MaxEmptyLinesToKeep: 1
 # NamespaceIndentation: None
 # ObjCBlockIndentWidth: 2
@@ -73,21 +68,22 @@ IncludeCategories:
 # PenaltyBreakFirstLessLess: 120
 # PenaltyBreakString: 1000
 # PenaltyExcessCharacter: 1000000
-# PenaltyReturnTypeOnItsOwnLine: 60
+PenaltyReturnTypeOnItsOwnLine: 100
 PointerAlignment: Left
-# ReflowComments:  true
+# ReflowComments: true
+SortIncludes: true
 # SpaceAfterCStyleCast: false
 # SpaceBeforeAssignmentOperators: true
 SpaceBeforeParens: Never
 # SpaceInEmptyParentheses: false
 # SpacesBeforeTrailingComments: 1
-# SpacesInAngles:  false
+# SpacesInAngles: false
 # SpacesInContainerLiterals: true
 # SpacesInCStyleCastParentheses: false
 # SpacesInParentheses: false
 # SpacesInSquareBrackets: false
-Standard:        Cpp11
-TabWidth:        2
-UseTab:          Never
+SpaceAfterTemplateKeyword: true
+Standard: c++20
+TabWidth: 2
+UseTab: Never
 ...
-

.clang-tidy

@@ -1,31 +1,56 @@
-Checks:          '-*,modernize-use-nullptr,modernize-deprecated-headers,modernize-shrink-to-fit,modernize-use-bool-literals,modernize-use-default-member-init,modernize-use-equals-default,modernize-use-equals-delete,modernize-use-override,modernize-use-equals-default,readability-avoid-const-params-in-decls,readability-braces-around-statements,readability-container-size-empty,readability-delete-null-pointer,readability-else-after-return,readability-implicit-bool-conversion,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-member-init,readability-redundant-smartptr-get,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-simplify-subscript-expr,readability-static-accessed-through-instance,readability-static-definition-in-anonymous-namespace,readability-string-compare,bugprone-unused-return-value'
-WarningsAsErrors: ''
-HeaderFilterRegex: ''
-AnalyzeTemporaryDtors: false
-FormatStyle:     file
-User:            mjackson
+---
+Checks: "-abseil-*,
+  bugprone-*,
+  -boost-*,
+  -cert-*,
+  clang-diagnostic-*,
+  -clang-diagnostic-documentation,
+  clang-analyzer-*,
+  cppcoreguidelines-*,
+  -cppcoreguidelines-avoid-magic-numbers,
+  -darwin-*,
+  -fuchsia-*,
+  -google-*,
+  -hicpp-*,
+  -linuxkernel-*,
+  -llvm-*,
+  misc-*,
+  modernize-*,
+  -modernize-use-trailing-return-type,
+  -modernize-use-nodiscard,
+  -modernize-use-auto,
+  -mpi-*,
+  -objc-*,
+  -openmp-*,
+  performance-*,
+  -portability-*,
+  readability-*,
+  -readability-function-cognitive-complexity,
+  -readability-function-size,
+  -readability-uppercase-literal-suffix,
+  -readability-magic-numbers"
+WarningsAsErrors: '*'
+HeaderFilterRegex: 'simplnx/.*\.hpp'
+FormatStyle: file
 CheckOptions:
-  - key:             google-readability-braces-around-statements.ShortStatementLines
-    value:           '1'
-  - key:             google-readability-function-size.StatementThreshold
-    value:           '800'
-  - key:             google-readability-namespace-comments.ShortNamespaceLines
-    value:           '10'
-  - key:             google-readability-namespace-comments.SpacesBeforeComments
-    value:           '2'
-  - key:             modernize-loop-convert.MaxCopySize
-    value:           '16'
-  - key:             modernize-loop-convert.MinConfidence
-    value:           reasonable
-  - key:             modernize-loop-convert.NamingStyle
-    value:           CamelCase
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-    value:           llvm
-  - key:             modernize-replace-auto-ptr.IncludeStyle
-    value:           llvm
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-    value:           '1'
-  - key:             modernize-use-default-member-init.UseAssignment
-    value:           '1'
-  - key:             modernize-use-nullptr.NullMacros
-    value:           'NULL'
+  cppcoreguidelines-macro-usage.AllowedRegexp: 'SIMPLNX_EXPORT|SIMPLNX_NO_EXPORT|SIMPLNX_DEPRECATED'
+  readability-identifier-naming.IgnoreMainLikeFunctions: 'false'
+  readability-identifier-naming.PrivateMemberPrefix: 'm_'
+  readability-identifier-naming.NamespaceCase: lower_case
+  readability-identifier-naming.ClassCase: CamelCase
+  readability-identifier-naming.ClassMethodCase: camelBack
+  readability-identifier-naming.PrivateMember: CamelCase
+  readability-identifier-naming.PublicMemberCase: CamelCase
+  readability-identifier-naming.StructCase: CamelCase
+  readability-identifier-naming.FunctionCase: camelBack
+  readability-identifier-naming.VariableCase: camelBack
+  readability-identifier-naming.GlobalVariableCase: CamelCase
+  readability-identifier-naming.GlobalConstantCase: CamelCase
+  readability-identifier-naming.GlobalConstantPrefix: 'k_'
+  readability-identifier-naming.GlobalFunctionCase: CamelCase
+  readability-identifier-naming.LocalPointerCase: camelBack
+  readability-identifier-naming.LocalPointerSuffix: 'Ptr'
+  readability-identifier-naming.TypeAliasCase: CamelCase
+  readability-identifier-naming.TypeAliasSuffix: 'Type'
+  readability-identifier-naming.MacroDefinitionCase: UPPER_CASE
+...

.gitignore

@@ -36,6 +36,7 @@ __pycache__/
 release
 debug
 Test/ProjectTest/Build
+CMakeUserPresets.json
 
 # Python build-related files
 pyebsd/build/

CMakeLists.txt

@@ -15,7 +15,7 @@ set(CMAKE_CXX_EXTENSIONS OFF)
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
 # set project's name
-project(EbsdLibProj VERSION 1.0.39)
+project(EbsdLibProj VERSION 1.0.40)
 
 # ---------- Setup output Directories -------------------------
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY

CMakePresets.json

@@ -27,7 +27,7 @@
             },
             "VCPKG_INSTALLED_DIR": {
                 "type": "STRING",
-                "value": "${sourceDir}/../vcpkg-installed"
+                "value": "${sourceDir}/../vcpkg-installed-ebsd-lib"
             },
             "VCPKG_MANIFEST_INSTALL": {
                 "type": "BOOL",

LaueNotes.md

@@ -6,10 +6,10 @@ There are several LaueOps classes that have incomplete implementations. This doc
 
 ### Texture::CalculateODFData() ###
 
-| | Triclinic | Monoclinic | OrthoRhombic | Tetragonal_Low | Tetragonal_High | Trigonal_Low | Trigonal_High | Hexagonal_Low | Hexagonal_Low | Cubic_Low | Cubic_High |
-|---|-----------|------------|--------------|----------------|-----------------|--------------|---------------|---------------|---------------|-----------|----------|
-| getODFFZRod() | O | O | O | O | O | O | O | O | O | O  | O |
-| getOdfBin()  | O | O | O | O | O | O | O | O | O | O  | O |
+|               | Triclinic | Monoclinic | OrthoRhombic | Tetragonal_Low | Tetragonal_High | Trigonal_Low | Trigonal_High | Hexagonal_Low | Hexagonal_Low | Cubic_Low | Cubic_High |
+|---------------|-----------|------------|--------------|----------------|-----------------|--------------|---------------|---------------|---------------|-----------|------------|
+| getODFFZRod() | O         | O          | O            | O              | O               | O            | O             | O             | O             | O         | O          |
+| getOdfBin()   | O         | O          | O            | O              | O               | O            | O             | O             | O             | O         | O          |
 
 ### StatsGen::GenODFPlotData() ###
 

README.md

@@ -4,27 +4,65 @@ EBSDLib is a C++ Library that can read EBSD Files from OEMs and perform basic EB
 library is to be able to convert between the seven orientation representations that
 are typically used through out materials science and engineering domains.
 
-The DREAM.3D project ( [code repository](http://www.github.com/bluequartzsoftware/DREAM3D) and [web site](https://www.dream3d.io) ) uses this library for all of the EBSD processing.
+The [DREAM.3D](https://dream3d.bluequartz.net) project and [DREAM3D-NX](https://www.dream3d.io) uses this library for all the EBSD processing.
 
-## Supported EBSD OEM Data Files ##
+## Supported EBSD OEM Data FilesDirectionalStatsTest
 
 + EDAX/AMETEK: .ang and HDF5 based file formats
 + Oxford Instruments: .ctf and .h5oina file formats
 + Bruker: HDF5 based file format
 
 Please have a look at the unit tests for examples on using the various readers.
 
-## Orientation Representations ##
-
-| From/To |  Euler  |  Orientation Matrix   |  Axis Angle  |  Rodrigues   |  Quaternion   |  Homochoric  |  Cubochoric  |
-| ------- |-------| ------- |------- |------- |-------  |-------  |------- |
-|Euler|  -   |  X   |  X   |  X   |  X   |  a   | ah   |
-|Orientation Matrix|  X   |  --  |  X   |  e   |  X   |  a   | ah   |
-|Axis Angle|  o   |  X   | --   |  X   |  X   |  X   |  h   |
-|Rodrigues|  o   |  a   |  X   | --   |  a   |  X   |  h   |
-|Quaternion|  X   |  X   |  X   |  X   | --   |  X   |  h   |
-|Homochoric|  ao  |  a   |  X   |  a   |  a   | --   |  X   |
-|Cubochoric| hao  |  ha  |  h   |  ha  | ha   |  X   | --   |
+## Crystallographic Classes
+|  # | Point Group (H–M) | Rotation Point Group | Space Group No(s). | Schoenflies   | Crystal system | Laue class  | Laue Ops         |
+|---:|-------------------|----------------------|--------------------|---------------|----------------|-------------|------------------|
+|  1 | 1                 | 1                    | 1                  | C₁            | Triclinic      | (\bar{1})   | TriclinicOps     |
+|  2 | (\bar{1})         | 1                    | 2                  | C(_i)         | Triclinic      | (\bar{1})   |                  |
+|  3 | 2                 | 2                    | 3–5                | C₂            | Monoclinic     | 2/m         |                  |
+|  4 | m                 | 1                    | 6–9                | C(_s)         | Monoclinic     | 2/m         |                  |
+|  5 | 2/m               | 2                    | 10–15              | C(_{2h})      | Monoclinic     | 2/m         | MonoclinicOps    |
+|  6 | 222               | 222                  | 16–24              | D₂            | Orthorhombic   | mmm         |                  |
+|  7 | mm2               | 2                    | 25–46              | C(_{2v})      | Orthorhombic   | mmm         |                  |
+|  8 | mmm               | 222                  | 47–74              | D(_{2h})      | Orthorhombic   | mmm         | OrthorhombicOps  |
+|  9 | 4                 | 4                    | 75–80              | C₄            | Tetragonal     | 4/m         |                  |
+| 10 | (\bar{4})         | 2                    | 81–82              | S₄            | Tetragonal     | 4/m         |                  |
+| 11 | 4/m               | 4                    | 83–88              | C(_{4h})      | Tetragonal     | 4/m         | TetragonalLowOps |
+| 12 | 422               | 422                  | 89–98              | D₄            | Tetragonal     | 4/mmm       |                  |
+| 13 | 4mm               | 4                    | 99–110             | C(_{4v})      | Tetragonal     | 4/mmm       |                  |
+| 14 | (\bar{4}2m)       | 222                  | 111–122            | D(_{2d})      | Tetragonal     | 4/mmm       |                  |
+| 15 | 4/mmm             | 422                  | 123–142            | D(_{4h})      | Tetragonal     | 4/mmm       | TetragonalOps    |
+| 16 | 3                 | 3                    | 143–146            | C₃            | Trigonal       | (\bar{3})   |                  |
+| 17 | (\bar{3})         | 3                    | 147–148            | C(_{3i}) (S₆) | Trigonal       | (\bar{3})   | TrigonalLowOps   |
+| 18 | 32                | 32                   | 149–155            | D₃            | Trigonal       | (\bar{3}m)  |                  |
+| 19 | 3m                | 3                    | 156–161            | C(_{3v})      | Trigonal       | (\bar{3}m)  |                  |
+| 20 | (\bar{3}m)        | 32                   | 162–167            | D(_{3d})      | Trigonal       | (\bar{3}m)  | TrigonalOps      |
+| 21 | 6                 | 6                    | 168–173            | C₆            | Hexagonal      | 6/m         |                  |
+| 22 | (\bar{6})         | 3                    | 174                | C(_{3h})      | Hexagonal      | 6/m         |                  |
+| 23 | 6/m               | 6                    | 175–176            | C(_{6h})      | Hexagonal      | 6/m         | HexagonalLowOps  |
+| 24 | 622               | 622                  | 177–182            | D₆            | Hexagonal      | 6/mmm       |                  |
+| 25 | 6mm               | 6                    | 183–186            | C(_{6v})      | Hexagonal      | 6/mmm       |                  |
+| 26 | (\bar{6}m2)       | 32                   | 187–190            | D(_{3h})      | Hexagonal      | 6/mmm       |                  |
+| 27 | 6/mmm             | 622                  | 191–194            | D(_{6h})      | Hexagonal      | 6/mmm       | HexagonalOps     |
+| 28 | 23                | 23                   | 195–199            | T             | Cubic          | m(\bar{3})  |                  |
+| 29 | m(\bar{3})        | 23                   | 200–206            | T(_h)         | Cubic          | m(\bar{3})  | CubicLowOps      |
+| 30 | 432               | 432                  | 207–214            | O             | Cubic          | m(\bar{3})m |                  |
+| 31 | (\bar{4}3m)       | 23                   | 215–220            | T(_d)         | Cubic          | m(\bar{3})m |                  |
+| 32 | m(\bar{3})m       | 432                  | 221–230            | O(_h)         | Cubic          | m(\bar{3})m | CubicOps         |
+
+
+## Orientation TransformationsDirectionalStatsTest
+
+| From/To            | Euler | Orientation Matrix | Axis Angle | Rodrigues | Quaternion | Homochoric | Cubochoric | Stereographic |
+|--------------------|-------|--------------------|------------|-----------|------------|------------|------------|---------------|
+| Euler              | -     | X                  | X          | X         | X          | a          | ah         | q             |
+| Orientation Matrix | X     | --                 | X          | e         | X          | a          | ah         | q             |
+| Axis Angle         | o     | X                  | --         | X         | X          | X          | h          | q             |
+| Rodrigues          | o     | a                  | X          | --        | a          | X          | h          | q             |
+| Quaternion         | X     | X                  | X          | X         | --         | X          | h          | q             |
+| Homochoric         | ao    | a                  | X          | a         | a          | --         | X          | q             |
+| Cubochoric         | hao   | ha                 | h          | ha        | ha         | X          | --         | q             |
+| Stereographic      | a     | a                  | X          | X         | a          | X          | hc         | --            |
 
 **LEGEND**: X = Direct mathematical conversion between the representations
 lower case letters denote the conversion uses other more basic conversions. For
@@ -38,13 +76,13 @@ library has selected to align with the AMETEK/EDAX output.
 
 The folder Data/IPF_Legend has premade IPF Legends for all the Laue classes.
 
-## Quaternion Convention ##
+## Quaternion ConventionDirectionalStatsTest
 
-Please also note that by default EbsdLib organizes Quaternions as Vector-Scalar. If your quaternions
-are layed out as Scalar-Vector there is an extra argument to some functions that you
+Please also note that by default EbsdLib organizes Quaternions as Vector-Scalar (X,Y,Z,W). If your quaternions
+are laid out as Scalar-Vector (w,x,y,z) there is an extra argument to some functions that you
 can set to allow the orientation transformations to accept this layout.
 
-## Dependent Libraries ##
+## Dependent LibrariesDirectionalStatsTest
 
 EbsdLib is dependent on:
 
@@ -53,19 +91,19 @@ EbsdLib is dependent on:
 ## Optional Libraries
 
 + HDF5 1.10.4 (HDF5 is optional only if you want the HDF5 functionality)
-+ Qt5 5.15.x (minimum)
++ Qt5 5.15.x (minimum: Optional)
 
-## Rotation Convention ##
+## Rotation ConventionDirectionalStatsTest
 
 By convention this library uses **Passive** rotations
 
-## Citations ##
+## CitationsDirectionalStatsTest
 
 D Rowenhorst, A D Rollett, G S Rohrer, M Groeber, M Jackson, P J Konijnenberg and M De Graef  _et al_ 2015 _Modelling Simul. Mater. Sci. Eng._ **23** 083501
 
 [DOI: https://doi.org/10.1088/0965-0393/23/8/083501](https://doi.org/10.1088/0965-0393/23/8/083501)
 
-## Examples ##
+## ExamplesDirectionalStatsTest
 
 If you want to transform an Euler angle into a Quaternion the following works: