TEST: Create unit tests for all classes where possible (#38)

* ENH: Add unit tests for 8 high-priority classes with no/minimal coverage

Add comprehensive Catch2 unit tests for:
- Matrix3X1<T>: construction, dot, cross, magnitude, normalize, sortAscending, cosTheta, operators (20 tests)
- Matrix3X3<T>: construction, multiply, transpose, determinant, invert, adjoint, col/row, DirectStructureMatrix (23 tests)
- ArrayHelpers<T,K>: splat, multiply, scalarMultiply, scalarDivide, sum, sumofSquares, maxval, absValue, power (13 tests)
- EbsdDataArray<T>: CreateArray, FromStdVector, CopyFromPointer, get/set, components, resize, erase, deepCopy, copyFromArray (23 tests)
- EbsdStringUtils: split (single/multi delimiter, consecutive), specific_split, replace, ltrim, rtrim, trimmed, chop, number, simplified (18 tests)
- EbsdTransform: IdentifyStandardTransformation for TSL, HKL, HEDM, and unknown parameters (6 tests)
- EbsdLibRandom: seeded deterministic output, range checks for real1/real2/real3/res53/int31, init_by_array (9 tests)
- OrientationMath: MetricTensor, RootTensor, Miller-Bravais conversions with round-trip verification (12 tests)

Also documents newly discovered Bug #5: EbsdDataArray::eraseTuples() does not update m_NumTuples.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* ENH: Add unit tests for 9 medium-priority classes (#13-#21)

Add 80 new test cases across 9 test files covering ColorTable/ColorUtilities,
LambertUtilities, ModifiedLambertProjection, ComputeStereographicProjection,
TexturePreset, AngPhase/CtfPhase/EspritPhase, LaueOps subclasses,
ModifiedLambertProjection3D, and OrientationTransformation known-value tests.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* ENH: Add unit tests for 6 low-priority classes (#23-#28) and fix ToolTipGenerator bug

Add 44 new test cases covering ToolTipGenerator, PoleFigureData, CanvasUtilities,
ModifiedLambertProjectionArray, PoleFigureUtilities, and TiffWriter. Fix bug in
ToolTipGenerator::generateHTML() and rowToHTML() where both methods returned an
empty string instead of the stringstream content.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* BUG: Replace M_PI with ebsdlib::constants::k_PiD in LambertUtilitiesTest

M_PI is not defined on Windows without _USE_MATH_DEFINES. Use the
project's own constant to ensure cross-platform compilation.

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

Author: imikejackson

CLAUDE.md

@@ -0,0 +1,98 @@
+# Project Guidelines for Claude
+
+## Project Overview
+
+### Phase 1
+I would like to add more unit testing to the EbsdLib library. Can we put together a TODO.md file stored in the "Code_Review" directory that lists all the candidate classes to create unit tests for?
+
+### Phase 2
+I would also like to write documentation for this library
+
+### Phase 3
+I would also like to write more example code that shows how to use the library
+
+How should we get stated with these tasks?
+
+## Directory Structure
+- `Source/Ebsdlib/` - Core library 
+- `Source/Apps/` - various test applications
+- `src/Test/` - Test files
+- `cmake/` - CMake configuration
+
+
+## Directories to Ignore
+- `scripts/` - Build/utility scripts
+- `conda/` - Conda packaging
+
+## Coding Standards
+
+### C++ Style (from .clang-format)
+- C++20 standard
+- Allman brace style (braces on new lines for classes, control statements, enums, functions, namespaces, structs, before else)
+- 200 column limit
+- 2-space indentation, no tabs
+- Pointer alignment left (`int* ptr` not `int *ptr`)
+- No space before parentheses
+- Sort includes alphabetically
+- No short functions on single line
+- Always break template declarations
+- Constructor initializers break before comma
+
+### Naming Conventions (from .clang-tidy)
+- C++ header files: `.hpp` extension
+- C++ source files: `.cpp` extension
+- Namespaces: `lower_case`
+- Classes: `CamelCase`
+- Structs: `CamelCase`
+- Class methods: `camelBack`
+- Functions: `camelBack`
+- Variables: `camelBack`
+- Private members: `m_` prefix + `CamelCase` (e.g., `m_MemberVariable`)
+- Global variables: `CamelCase`
+- Global constants: `k_` prefix + `CamelCase` (e.g., `k_DefaultValue`)
+- Local pointers: `camelBack` + `Ptr` suffix (e.g., `dataPtr`)
+- Type aliases: `CamelCase` + `Type` suffix (e.g., `ValueType`)
+- Macros: `UPPER_CASE`
+
+
+## Build System
+- vcpkg for dependency management
+- CMake-based build system
+
+Example configuring the project
+```bash
+cd /Users/mjackson/Workspace1/EbsdLib && cmake --preset EbsdLib-Release
+```
+
+- Build directory is located at "/Users/mjackson/Workspace1/DREAM3D-Build/EbsdLib-Release"
+
+Example building the project
+```bash
+cd /Users/mjackson/Workspace5/DREAM3D-Build/EbsdLib-Release && cmake --build . --target all
+```
+
+- Python anaconda environment 'dream3d' can be used if needed
+
+## Testing
+- Unit tests use the Catch2 framework.
+- Use the `ctest` to run unit tests
+
+### Running Unit Tests
+- Always use `ctest` to run unit tests, NOT the test binary directly
+- The `ctest` command handles test data extraction and cleanup automatically
+- Use the `-R` flag to run specific tests by name pattern
+
+Example - Running a specific test:
+```bash
+cd /Users/mjackson/Workspace5/DREAM3D-Build/EbsdLib-Release && ctest -R "EbsdLib::FillBadData" --verbose
+```
+
+Example - Running all SimplnxCore tests:
+```bash
+cd /Users/mjackson/Workspace5/DREAM3D-Build/EbsdLib-Release && ctest -R "EbsdLib::" --verbose
+```
+
+### Printing debug statements in unit tests
+
+## Additional Notes
+<!-- Add any other project-specific rules here -->

Code_Review/TODO.md

@@ -59,6 +59,12 @@ There are **12 active test files** compiled into a single `EbsdLibUnitTest` exec
 **Severity:** MEDIUM - Tests pass even with wildly incorrect values
 **Issue:** The tolerance check uses `delta < 1.0E6` (one million) instead of `1.0E-6` (one millionth). This means the round-trip conversion tests will pass even if values are off by up to a million, making the tests effectively useless for catching conversion errors.
 
+### Bug 5: `EbsdDataArray::eraseTuples()` - Does not update `m_NumTuples`
+
+**File:** `Source/EbsdLib/Core/EbsdDataArray.cpp:678`
+**Severity:** MEDIUM - `getNumberOfTuples()` returns stale value after eraseTuples
+**Issue:** The `eraseTuples()` method updates `m_Size`, `m_MaxId`, and `m_Array` but never updates `m_NumTuples`. After calling `eraseTuples()`, `getNumberOfTuples()` returns the original tuple count instead of the new (reduced) count. `getSize()` correctly returns the new total element count.
+
 ---
 
 ## Classes Requiring Unit Tests
@@ -70,7 +76,7 @@ These classes have zero or near-zero test coverage and contain non-trivial logic
 #### 1. `EbsdDataArray<T>` - Core data container
 
 - **File:** `Source/EbsdLib/Core/EbsdDataArray.hpp`
-- **Status:** No tests
+- **Status:** **DONE** - `Source/Test/EbsdDataArrayTest.cpp` (23 test cases)
 - **Why:** Core template class used by virtually every reader and computation. Wraps raw arrays with lifecycle management.
 - **Recommended tests:**
   - Construction (default, sized, from existing pointer)
@@ -85,7 +91,7 @@ These classes have zero or near-zero test coverage and contain non-trivial logic
 #### 2. `Matrix3X1<T>` - 3x1 vector operations
 
 - **File:** `Source/EbsdLib/Math/Matrix3X1.hpp`
-- **Status:** Only `cosTheta` tested (in QuaternionTest)
+- **Status:** **DONE** - `Source/Test/Matrix3X1Test.cpp` (20 test cases)
 - **Why:** Core math class with known bugs (see Bugs #1 and #2)
 - **Recommended tests:**
   - Construction and element access
@@ -99,7 +105,7 @@ These classes have zero or near-zero test coverage and contain non-trivial logic
 #### 3. `Matrix3X3<T>` - 3x3 matrix operations
 
 - **File:** `Source/EbsdLib/Math/Matrix3X3.hpp`
-- **Status:** Exercised in TextureTest but no assertions on results
+- **Status:** **DONE** - `Source/Test/Matrix3X3Test.cpp` (23 test cases)
 - **Why:** Used in orientation math, coordinate transforms; currently only smoke-tested
 - **Recommended tests:**
   - Construction and element access
@@ -145,7 +151,7 @@ These classes have zero or near-zero test coverage and contain non-trivial logic
 #### 7. `OrientationMath` - Crystallographic math
 
 - **File:** `Source/EbsdLib/Core/OrientationMath.h`
-- **Status:** No direct tests (indirectly exercised by ConvertToFundamentalZoneTest)
+- **Status:** **DONE** - `Source/Test/OrientationMathTest.cpp` (12 test cases)
 - **Why:** Static methods for misorientation calculations, widely used
 - **Recommended tests:**
   - `axisAngletoMatrix()`, `quatsToMatrix()`
@@ -156,7 +162,7 @@ These classes have zero or near-zero test coverage and contain non-trivial logic
 #### 8. `EbsdStringUtils` - String utilities
 
 - **File:** `Source/EbsdLib/Utilities/EbsdStringUtils.hpp`
-- **Status:** No tests
+- **Status:** **DONE** - `Source/Test/EbsdStringUtilsTest.cpp` (18 test cases)
 - **Why:** String parsing utilities used by all readers
 - **Recommended tests:**
   - `split()`, `tokenize()` with various delimiters
@@ -168,7 +174,7 @@ These classes have zero or near-zero test coverage and contain non-trivial logic
 #### 9. `EbsdTransform` - Reference frame transformations
 
 - **File:** `Source/EbsdLib/Core/EbsdTransform.h`
-- **Status:** No tests
+- **Status:** **DONE** - `Source/Test/EbsdTransformTest.cpp` (6 test cases)
 - **Why:** Transforms sample and Euler reference frames; errors here corrupt all downstream analysis
 - **Recommended tests:**
   - Sample reference frame transformations (all axis combinations)
@@ -179,7 +185,7 @@ These classes have zero or near-zero test coverage and contain non-trivial logic
 #### 10. `EbsdLibRandom` - PRNG
 
 - **File:** `Source/EbsdLib/Math/EbsdLibRandom.h`
-- **Status:** No tests
+- **Status:** **DONE** - `Source/Test/EbsdLibRandomTest.cpp` (9 test cases)
 - **Why:** Mersenne Twister wrapper; used for texture generation
 - **Recommended tests:**
   - Seeded deterministic output verification
@@ -189,7 +195,7 @@ These classes have zero or near-zero test coverage and contain non-trivial logic
 #### 11. `ArrayHelpers<T,K>` - Template math helpers
 
 - **File:** `Source/EbsdLib/Math/ArrayHelpers.hpp`
-- **Status:** No tests
+- **Status:** **DONE** - `Source/Test/ArrayHelpersTest.cpp` (13 test cases)
 - **Why:** Static utility methods used in orientation conversions
 - **Recommended tests:**
   - `splat()`, `multiply()`, `scalarMultiply()`
@@ -213,43 +219,43 @@ These classes have zero or near-zero test coverage and contain non-trivial logic
 #### 13. `ColorTable` / `ColorUtilities` - Color handling
 
 - **Files:** `Source/EbsdLib/Utilities/ColorTable.h`, `Source/EbsdLib/Utilities/ColorUtilities.h`
-- **Status:** No direct tests
+- **Status:** **DONE** - `Source/Test/ColorTableTest.cpp` (11 test cases)
 - **Recommended tests:** `RgbColor` helpers, HSV-to-RGB conversion, color component extraction
 
 #### 14. `LambertUtilities` - Square-to-sphere mapping
 
 - **File:** `Source/EbsdLib/Utilities/LambertUtilities.h`
-- **Status:** No tests
+- **Status:** **DONE** - `Source/Test/LambertUtilitiesTest.cpp` (4 test cases)
 - **Recommended tests:** Square-to-sphere and sphere-to-square conversions, round-trip consistency, boundary values
 
 #### 15. `ModifiedLambertProjection` - Lambert projection
 
 - **File:** `Source/EbsdLib/Utilities/ModifiedLambertProjection.h`
-- **Status:** No tests
+- **Status:** **DONE** - `Source/Test/ModifiedLambertProjectionTest.cpp` (7 test cases)
 - **Recommended tests:** North/south hemisphere projection, `addInterpolatedValues()`, normalization
 
 #### 16. `ComputeStereographicProjection` - Stereographic projection utilities
 
 - **File:** `Source/EbsdLib/Utilities/ComputeStereographicProjection.h`
-- **Status:** No tests
+- **Status:** **DONE** - `Source/Test/StereographicProjectionTest.cpp` (6 test cases)
 - **Recommended tests:** Stereographic-to-spherical and spherical-to-stereographic round-trips
 
 #### 17. `TexturePreset` - Texture presets
 
 - **File:** `Source/EbsdLib/Texture/TexturePreset.h`
-- **Status:** No tests
+- **Status:** **DONE** - `Source/Test/TexturePresetTest.cpp` (5 test cases)
 - **Recommended tests:** Preset value getters, preset registration
 
 #### 18. `AngPhase` / `CtfPhase` / `EspritPhase` - Phase data classes
 
 - **Files:** `Source/EbsdLib/IO/TSL/AngPhase.h`, `Source/EbsdLib/IO/HKL/CtfPhase.h`, `Source/EbsdLib/IO/BrukerNano/EspritPhase.h`
-- **Status:** CtfPhase partially tested via CtfReaderTest; others untested
+- **Status:** **DONE** - `Source/Test/PhaseTest.cpp` (18 test cases)
 - **Recommended tests:** Construction, getter/setter verification, lattice constant parsing
 
 #### 19. LaueOps subclasses - Enhanced symmetry tests
 
 - **Files:** `Source/EbsdLib/LaueOps/*.h` (11 subclasses)
-- **Status:** FZ tests comprehensive; IPF generation and misorientation calculation only smoke-tested
+- **Status:** **DONE** - `Source/Test/LaueOpsTest.cpp` (11 test cases)
 - **Recommended tests:**
   - `getNumSymOps()` returns expected count for each crystal system
   - `getIPFColor()` with known orientations against reference values
@@ -259,13 +265,13 @@ These classes have zero or near-zero test coverage and contain non-trivial logic
 #### 20. `ModifiedLambertProjection3D<T,K>` - 3D Lambert projection
 
 - **File:** `Source/EbsdLib/Utilities/ModifiedLambertProjection3D.hpp`
-- **Status:** No tests
+- **Status:** **DONE** - `Source/Test/ModifiedLambertProjection3DTest.cpp` (7 test cases)
 - **Recommended tests:** Cube-to-sphere and sphere-to-cube conversions, edge cases at cube boundaries
 
 #### 21. `OrientationTransformation` (namespace) - Conversion functions
 
 - **File:** `Source/EbsdLib/Core/OrientationTransformation.hpp`
-- **Status:** Well-tested via OrientationTest.cpp (round-trip), but not all individual functions are directly tested
+- **Status:** **DONE** - `Source/Test/OrientationTransformationTest.cpp` (11 test cases)
 - **Recommended tests:** Direct tests of each `xx2yy()` function with known analytical values (supplement existing round-trip tests)
 
 #### 22. `H5CtfReader` / `H5AngReader` - HDF5 format readers
@@ -281,37 +287,37 @@ These classes have zero or near-zero test coverage and contain non-trivial logic
 #### 23. `ToolTipGenerator` - HTML tooltip builder
 
 - **File:** `Source/EbsdLib/Utilities/ToolTipGenerator.h`
-- **Status:** No tests
+- **Status:** **DONE** - `Source/Test/ToolTipGeneratorTest.cpp` (8 test cases). Also fixed bug where `generateHTML()` and `rowToHTML()` returned empty strings.
 - **Recommended tests:** `addTitle()`, `addValue()`, output HTML correctness
 
 #### 24. `PoleFigureData` - Data holder
 
 - **File:** `Source/EbsdLib/Utilities/PoleFigureData.h`
-- **Status:** No tests
+- **Status:** **DONE** - `Source/Test/PoleFigureDataTest.cpp` (5 test cases)
 - **Recommended tests:** Construction, getter verification
 
 #### 25. `CanvasUtilities` - Visualization helpers
 
 - **File:** `Source/EbsdLib/Utilities/CanvasUtilities.hpp`
-- **Status:** No tests
+- **Status:** **DONE** - `Source/Test/CanvasUtilitiesTest.cpp` (6 test cases)
 - **Recommended tests:** Only if visual regression testing infrastructure is added
 
 #### 26. `ModifiedLambertProjectionArray` - Array variant
 
 - **File:** `Source/EbsdLib/Utilities/ModifiedLambertProjectionArray.h`
-- **Status:** No tests
+- **Status:** **DONE** - `Source/Test/ModifiedLambertProjectionArrayTest.cpp` (16 test cases)
 - **Recommended tests:** Array construction, element access, resize
 
 #### 27. `PoleFigureUtilities` - Pole figure generation
 
 - **File:** `Source/EbsdLib/Utilities/PoleFigureUtilities.h`
-- **Status:** No tests
+- **Status:** **DONE** - `Source/Test/PoleFigureUtilitiesTest.cpp` (4 test cases)
 - **Recommended tests:** Configuration setup, pole figure generation with known inputs
 
 #### 28. `TiffWriter` - TIFF file output
 
 - **File:** `Source/EbsdLib/Utilities/TiffWriter.h`
-- **Status:** Indirectly tested via IPFLegendTest (only checks return code)
+- **Status:** **DONE** - `Source/Test/TiffWriterTest.cpp` (4 test cases)
 - **Recommended tests:** Write and read-back verification, grayscale and color modes
 
 ---

Source/EbsdLib/Math/Matrix3X1.hpp

@@ -1,5 +1,6 @@
 #pragma once
 
+#include <array>
 #include <cmath>
 #include <memory>
 

Source/EbsdLib/Math/Matrix3X3.hpp

@@ -5,6 +5,7 @@
 
 #include <Eigen/Dense>
 
+#include <array>
 #include <cassert>
 #include <cmath>
 

Source/EbsdLib/Utilities/PoleFigureUtilities.h

@@ -148,7 +148,7 @@ class EbsdLib_EXPORT PoleFigureUtilities
  * @brief The GeneratePoleFigureRgbaImageImpl class is a wrapper around generating the RGBA image (2D UChar Array with 4 Components) from the
  * intensity image. This should be called from a TBB Task
  */
-class GeneratePoleFigureRgbaImageImpl
+class EbsdLib_EXPORT GeneratePoleFigureRgbaImageImpl
 {
 public:
   GeneratePoleFigureRgbaImageImpl(ebsdlib::DoubleArrayType* intensity, PoleFigureConfiguration_t* config, ebsdlib::UInt8ArrayType* rgba);

Source/EbsdLib/Utilities/ToolTipGenerator.cpp

@@ -122,7 +122,7 @@ std::string ToolTipGenerator::generateHTML() const
   ss << rowToHTML(spacer);
   ss << "</tbody></table>\n";
   ss << "</body></html>";
-  return html;
+  return ss.str();
 }
 
 // -----------------------------------------------------------------------------
@@ -144,5 +144,5 @@ std::string ToolTipGenerator::rowToHTML(const RowItem& row) const
     break;
   }
 
-  return html;
+  return ss.str();
 }