BUG: Misc bug fixes for 3.1.1 release (#53)

.github/workflows/format_pr.yml

@@ -0,0 +1,38 @@
+name: clang-format pr
+
+on:
+  pull_request:
+    branches:
+      - develop
+      - master
+
+jobs:
+  clang_format_pr:
+    runs-on: ubuntu-24.04
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 2
+      - name: Add Problem Matcher
+        uses: ammaraskar/gcc-problem-matcher@a141586609e2a558729b99a8c574c048f7f56204
+      - name: Install clang-format-19
+        run: |
+          sudo apt-get update
+          sudo apt-get install clang-format-19
+          clang-format-19 --version
+      - name: Check Formatting
+        id: check_format
+        continue-on-error: true
+        run: |
+          python3 scripts/clang_format.py --format-version 19 --commits HEAD^ HEAD
+      - name: Apply Formatting
+        if: steps.check_format.outcome != 'success'
+        run: |
+          python3 scripts/clang_format.py --format-version 19 --modify --commits HEAD^ HEAD
+      - name: Add Suggestions
+        if: steps.check_format.outcome != 'success'
+        uses: reviewdog/action-suggester@v1
+        with:
+          tool_name: clang-format
+          fail_level: error

.github/workflows/format_push.yml

@@ -0,0 +1,24 @@
+name: clang-format
+
+on:
+  push:
+    branches:
+      - develop
+      - master
+
+jobs:
+  clang_format:
+    runs-on: ubuntu-24.04
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Add Problem Matcher
+        uses: ammaraskar/gcc-problem-matcher@a141586609e2a558729b99a8c574c048f7f56204
+      - name: Install clang-format-19
+        run: |
+          sudo apt-get update
+          sudo apt-get install clang-format-19
+          clang-format-19 --version
+      - name: Check Formatting
+        run: |
+          python3 scripts/clang_format.py --format-version 19

AGENTS.md

@@ -0,0 +1,9 @@
+# Repository Guidance
+
+EbsdLib is a C++20 CMake library. Follow the checked-in formatter and lint configuration: Allman braces, two-space indentation, left-aligned pointers, and the repository naming conventions.
+
+- Core library code is under `Source/EbsdLib/`; applications are under `Source/Apps/`; tests and CMake support live in their existing repository directories.
+- Configure with `cmake --preset EbsdLib-Release`; verify with the actual CMake build and tests rather than relying on clangd diagnostics alone.
+- Run tests through `ctest`, not test executables directly.
+- For inverse-pole-figure and standard-stereographic-triangle visualization, reuse the LaueOps stereographic mapping. Do not substitute a Lambert eta/chi rectangle.
+- Keep durable architecture and workflow documentation in the repository; do not encode active-branch status or personal machine paths here.

CMakeLists.txt

@@ -37,7 +37,7 @@ option(EbsdLib_BUILD_H5SUPPORT "Build H5Support Library" OFF)
 
 
 # set project's name
-project(EbsdLibProj VERSION 3.1.0)
+project(EbsdLibProj VERSION 3.1.1)
 
 
 # Request C++17 standard, using new CMake variables.

Docs/Index.md

@@ -1,4 +1,4 @@
-# Various Bits of Documentation for EbsdLib
+# Documentation for EbsdLib
 
 EbsdLib is primarily used in the [DREAM3D](https://www.bluequartz.net) family of applications and libraries.
 
@@ -27,6 +27,81 @@ Position-space validation across all 11 Laue classes lives in
 
 ---
 
+# Release Notes — EbsdLib 3.1.1
+
+EbsdLib 3.1.1 is the "misorientation analysis + correctness" release. It adds
+tools for calculating and evaluating misorientation distribution functions
+(MDFs), and fixes several long-standing Laue-class fundamental-zone and Schmid
+factor defects inherited from the legacy OrientationLib implementation.
+
+## New features
+
+### Misorientation kernel density estimation
+
+- `MisorientationKDE` accumulates weighted misorientations on the Laue-class MDF
+  fundamental-zone grid and evaluates the resulting density at arbitrary
+  misorientation quaternions.
+- KDE evaluation is symmetrized over the crystal symmetry operators and grain
+  exchange, and is normalized to a mean density of one over SO(3).
+- `computeAngleCurve()` extracts a misorientation-angle distribution together
+  with the corresponding random-reference distribution.
+- Each occupied bin retains the weighted circular mean of its observations as
+  its kernel center. This avoids the low-angle bias caused by snapping narrow
+  kernels to geometric bin centers, particularly for hexagonal phases.
+
+### SO(3) kernel and random-angle reference
+
+- `SO3DeLaValleePoussinKernel` implements the de la Vallée Poussin orientation
+  kernel, including half-width conversion, normalization, and finite support.
+- `random_angle_distribution::Compute()` and `MaxMisorientationAngle()` provide
+  analytical random misorientation-angle distributions and limits for the
+  supported Laue classes.
+
+## Correctness fixes
+
+### Misorientation fundamental-zone folds
+
+- Corrected `getMDFFZRod()` for cubic-low, trigonal, trigonal-low,
+  hexagonal-low, tetragonal, and tetragonal-low symmetry. The corrected folds
+  preserve the misorientation angle and use the proper rotational-symmetry
+  sector for each Laue class.
+- Implemented the previously stubbed triclinic, monoclinic, and orthorhombic
+  folds, so MDF calculations for those phases no longer abort with
+  `method_not_implemented`.
+- Corrected equatorial boundary handling in the hexagonal, trigonal, and
+  tetragonal folds.
+
+### ODF and Schmid-factor calculations
+
+- Fixed the tetragonal-low ODF dimension constant that caused
+  `determineEulerAngles()` to return NaN Euler angles for all sampled bins.
+- Replaced truncated cubic slip-system normalizers with the full-precision
+  `sqrt(3)` and `sqrt(2)` constants, preventing Schmid factors from exceeding
+  the physical maximum of 0.5 because of rounding bias.
+- Initialized every output of the automatic `getSchmidFactorAndSS()` overloads
+  on all code paths. Unsupported Laue classes now return defined zero values
+  instead of stale or indeterminate angle components.
+
+## Validation evidence
+
+- Fundamental-zone tests cover all 11 Laue classes, including symmetry
+  equivalence, angle preservation, idempotence, boundary behavior, and guards
+  against over-folding.
+- Kernel constants and random-angle distributions are checked against MTEX
+  6.1.0 reference values.
+- Cubic and hexagonal MDF angle curves are cross-checked against MTEX, and a
+  correlated 60° about `<111>` (Σ3) distribution guards against regressions
+  that flatten a textured MDF toward the random reference.
+- Schmid-factor tests pre-poison output values to ensure the stub Laue classes
+  explicitly reset every output.
+
+## Maintenance
+
+- Updated the formatting workflows to run for both pull requests and pushes,
+  using clang-format 19.
+
+---
+
 # Release Notes — EbsdLib 3.1.0
 
 EbsdLib 3.1 is the "discrete pole figures + TSL-by-default" release. It builds

Source/EbsdLib/Core/EbsdDataArray.cpp

@@ -52,8 +52,8 @@
 #define EBSD_BYTE_SWAP_32(x) _byteswap_ulong(x)
 #define EBSD_BYTE_SWAP_64(x) _byteswap_uint64(x)
 
-#elif(defined(__clang__) && __has_builtin(__builtin_bswap32) && __has_builtin(__builtin_bswap64)) || (defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3)))
-#if(defined(__clang__) && __has_builtin(__builtin_bswap16)) || (defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 8)))
+#elif (defined(__clang__) && __has_builtin(__builtin_bswap32) && __has_builtin(__builtin_bswap64)) || (defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3)))
+#if (defined(__clang__) && __has_builtin(__builtin_bswap16)) || (defined(__GNUC__) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 8)))
 #define EBSD_BYTE_SWAP_16(x) __builtin_bswap16(x)
 #else
 #define EBSD_BYTE_SWAP_16(x) __builtin_bswap32((x) << 16)

Source/EbsdLib/Core/EbsdLibDLLExport.h

@@ -59,13 +59,13 @@ building on Windows.
 #if defined(EbsdLib_EXPORTS) /* Compiling the EbsdLib DLL/Dylib */
 #if defined(_MSC_VER)        /* MSVC Compiler Case */
 #define EbsdLib_EXPORT __declspec(dllexport)
-#elif(__GNUC__ >= 4) /* GCC 4.x has support for visibility options */
+#elif (__GNUC__ >= 4) /* GCC 4.x has support for visibility options */
 #define EbsdLib_EXPORT __attribute__((visibility("default")))
 #endif
 #else                 /* Importing the DLL into another project */
 #if defined(_MSC_VER) /* MSVC Compiler Case */
 #define EbsdLib_EXPORT __declspec(dllimport)
-#elif(__GNUC__ >= 4) /* GCC 4.x has support for visibility options */
+#elif (__GNUC__ >= 4) /* GCC 4.x has support for visibility options */
 #define EbsdLib_EXPORT __attribute__((visibility("default")))
 #endif
 #endif

Source/EbsdLib/IO/HKL/H5CtfImporter.cpp

@@ -332,7 +332,7 @@ int H5CtfImporter::writeSliceData(hid_t fileId, CtfReader& reader, int z, int ac
       if(nullptr == dataPtr)
       {
         assert(false);
-      }                                            // We are going to crash here. I would rather crash than have bad data
+      } // We are going to crash here. I would rather crash than have bad data
       dataPtr = dataPtr + (actualSlice * dims[0]); // Put the pointer at the proper offset into the larger array
       WRITE_EBSD_DATA_ARRAY(reader, int, gid, name);
     }
@@ -342,7 +342,7 @@ int H5CtfImporter::writeSliceData(hid_t fileId, CtfReader& reader, int z, int ac
       if(nullptr == dataPtr)
       {
         assert(false);
-      }                                            // We are going to crash here. I would rather crash than have bad data
+      } // We are going to crash here. I would rather crash than have bad data
       dataPtr = dataPtr + (actualSlice * dims[0]); // Put the pointer at the proper offset into the larger array
       WRITE_EBSD_DATA_ARRAY(reader, float, gid, name);
     }

Source/EbsdLib/LaueOps/CubicLowOps.cpp

@@ -316,48 +316,26 @@ RodriguesDType CubicLowOps::getMDFFZRod(const RodriguesDType& inRod) const
   double n1 = ax[0];
   double n2 = ax[1], n3 = ax[2], w = ax[3];
 
-  double FZn1 = w, FZn2 = 0.0, FZn3 = 0.0, FZw = 0.0;
+  double FZn1 = 0.0, FZn2 = 0.0, FZn3 = 0.0;
+  double FZw = w;
 
   n1 = fabs(n1);
   n2 = fabs(n2);
   n3 = fabs(n3);
-  if(n1 > n2)
+  // The tetrahedral rotation group only provides the <111> 3-fold axes, so only
+  // cyclic permutations of the axis components are symmetry-equivalent. Rotate
+  // cyclically so the largest component is first; n2/n3 must NOT be sorted.
+  if(n2 >= n1 && n2 >= n3)
   {
-    if(n1 > n3)
-    {
-      FZn1 = n1;
-      if(n2 > n3)
-      {
-        FZn2 = n2, FZn3 = n3;
-      }
-      else
-      {
-        FZn2 = n3, FZn3 = n2;
-      }
-    }
-    else
-    {
-      FZn1 = n3, FZn2 = n1, FZn3 = n2;
-    }
+    FZn1 = n2, FZn2 = n3, FZn3 = n1;
+  }
+  else if(n3 >= n1 && n3 >= n2)
+  {
+    FZn1 = n3, FZn2 = n1, FZn3 = n2;
   }
   else
   {
-    if(n2 > n3)
-    {
-      FZn1 = n2;
-      if(n1 > n3)
-      {
-        FZn2 = n1, FZn3 = n3;
-      }
-      else
-      {
-        FZn2 = n3, FZn3 = n1;
-      }
-    }
-    else
-    {
-      FZn1 = n3, FZn2 = n2, FZn3 = n1;
-    }
+    FZn1 = n1, FZn2 = n2, FZn3 = n3;
   }
 
   return AxisAngleDType(FZn1, FZn2, FZn3, FZw).toRodrigues();

Source/EbsdLib/LaueOps/CubicOps.cpp

@@ -846,25 +846,25 @@ void CubicOps::getSchmidFactorAndSS(double load[3], double& schmidfactor, double
 
   double mag = loadx * loadx + loady * loady + loadz * loadz;
   mag = std::sqrt(mag);
-  theta1 = (loadx + loady + loadz) / (mag * 1.732f);
+  theta1 = (loadx + loady + loadz) / (mag * ebsdlib::constants::k_Sqrt3D);
   theta1 = std::fabs(theta1);
-  theta2 = (loadx + loady - loadz) / (mag * 1.732f);
+  theta2 = (loadx + loady - loadz) / (mag * ebsdlib::constants::k_Sqrt3D);
   theta2 = std::fabs(theta2);
-  theta3 = (loadx - loady + loadz) / (mag * 1.732f);
+  theta3 = (loadx - loady + loadz) / (mag * ebsdlib::constants::k_Sqrt3D);
   theta3 = std::fabs(theta3);
-  theta4 = (-loadx + loady + loadz) / (mag * 1.732f);
+  theta4 = (-loadx + loady + loadz) / (mag * ebsdlib::constants::k_Sqrt3D);
   theta4 = std::fabs(theta4);
-  lambda1 = (loadx + loady) / (mag * 1.414f);
+  lambda1 = (loadx + loady) / (mag * ebsdlib::constants::k_Sqrt2D);
   lambda1 = std::fabs(lambda1);
-  lambda2 = (loadx + loadz) / (mag * 1.414f);
+  lambda2 = (loadx + loadz) / (mag * ebsdlib::constants::k_Sqrt2D);
   lambda2 = std::fabs(lambda2);
-  lambda3 = (loadx - loady) / (mag * 1.414f);
+  lambda3 = (loadx - loady) / (mag * ebsdlib::constants::k_Sqrt2D);
   lambda3 = std::fabs(lambda3);
-  lambda4 = (loadx - loadz) / (mag * 1.414f);
+  lambda4 = (loadx - loadz) / (mag * ebsdlib::constants::k_Sqrt2D);
   lambda4 = std::fabs(lambda4);
-  lambda5 = (loady + loadz) / (mag * 1.414f);
+  lambda5 = (loady + loadz) / (mag * ebsdlib::constants::k_Sqrt2D);
   lambda5 = std::fabs(lambda5);
-  lambda6 = (loady - loadz) / (mag * 1.414f);
+  lambda6 = (loady - loadz) / (mag * ebsdlib::constants::k_Sqrt2D);
   lambda6 = std::fabs(lambda6);
   schmid1 = theta1 * lambda6;
   schmid2 = theta1 * lambda4;

Source/EbsdLib/LaueOps/HexagonalLowOps.cpp

@@ -386,24 +386,14 @@ RodriguesDType HexagonalLowOps::getMDFFZRod(const RodriguesDType& inRod) const
   FZn1 = n1;
   FZn2 = n2;
   FZn3 = n3;
-  if(angle > 30.0)
+  // The 6/m rotation group is only the 6-fold about c (no in-plane 2-folds), so the
+  // axis azimuth folds into a plain 60 degree wedge with no mirror alternation
   {
     n1n2mag = std::sqrt(n1 * n1 + n2 * n2);
-    if(int(angle / 30) % 2 == 0)
-    {
-      FZw = angle - (30.0 * int(angle / 30.0));
-      FZw = FZw * ebsdlib::constants::k_PiOver180D;
-      FZn1 = n1n2mag * std::cos(FZw);
-      FZn2 = n1n2mag * std::sin(FZw);
-    }
-    else
-    {
-      FZw = angle - (30.0 * int(angle / 30.0));
-      FZw = 30.0f - FZw;
-      FZw = FZw * ebsdlib::constants::k_PiOver180D;
-      FZn1 = n1n2mag * std::cos(FZw);
-      FZn2 = n1n2mag * std::sin(FZw);
-    }
+    FZw = std::fmod(static_cast<double>(angle), 60.0);
+    FZw = FZw * ebsdlib::constants::k_PiOver180D;
+    FZn1 = n1n2mag * std::cos(FZw);
+    FZn2 = n1n2mag * std::sin(FZw);
   }
 
   return AxisAngleDType(FZn1, FZn2, FZn3, w).toRodrigues();
@@ -532,6 +522,15 @@ int HexagonalLowOps::getOdfBin(const RodriguesDType& rod) const
 
 void HexagonalLowOps::getSchmidFactorAndSS(double load[3], double& schmidfactor, double angleComps[2], int& slipsys) const
 {
+  // Every output must be defined before the schmid comparison chain below, which only assigns to
+  // them when a candidate beats the incumbent. Without these, schmidfactor was READ uninitialized
+  // by the first `if(schmid1 > schmidfactor)`, and slipsys/angleComps were left untouched whenever
+  // no candidate won.
+  schmidfactor = 0.0;
+  slipsys = 0;
+  angleComps[0] = 0.0;
+  angleComps[1] = 0.0;
+
   double theta1, theta2, theta3, theta4, theta5, theta6, theta7, theta8, theta9;
   double lambda1, lambda2, lambda3, lambda4, lambda5, lambda6, lambda7, lambda8, lambda9, lambda10;
   double schmid1, schmid2, schmid3, schmid4, schmid5, schmid6;