ENH: PoleFigure, IPF Color and many other enhancements

.claude/settings.local.json

@@ -0,0 +1,46 @@
+{
+  "permissions": {
+    "allow": [
+      "Bash(ls:*)",
+      "Bash(cmake --build:*)",
+      "Bash(ctest:*)",
+      "Bash(cmake:*)",
+      "Bash(python3:*)",
+      "Bash(ninja -t targets:*)",
+      "Bash(git rm:*)",
+      "Bash(tar:*)",
+      "Bash(test:*)",
+      "Bash(git commit:*)",
+      "Bash(git push:*)",
+      "Bash(/Users/mjackson/Workspace5/DREAM3D-Build/NX-Com-Qt69-Vtk95-Rel/Bin/SimplnxCoreUnitTest:*)",
+      "Bash(/opt/local/cmake-3.30.3-macos-universal/CMake.app/Contents/bin/cmake:*)",
+      "Bash(for f in segment_features_neighbor_scheme_test.tar.gz segment_features_test_data.tar.gz)",
+      "Bash(do /opt/local/cmake-3.30.3-macos-universal/CMake.app/Contents/bin/cmake -E tar xzf \"$f\")",
+      "Bash(done)",
+      "Bash(for f in 6_5_test_data_1_v2.tar.gz segment_features_test_data.tar.gz 6_6_ebsd_segment_features.tar.gz segment_features_neighbor_scheme_test.tar.gz)",
+      "Bash(do echo \"Extracting $f...\")",
+      "Bash(echo:*)",
+      "Bash(for f in 6_5_test_data_1_v2.tar.gz segment_features_test_data.tar.gz segment_features_neighbor_scheme_test.tar.gz)",
+      "Bash(do tar -xzf \"$f\")",
+      "Bash(/Users/mjackson/Workspace5/DREAM3D-Build/NX-Com-Qt69-Vtk95-Rel/Bin/OrientationAnalysisUnitTest:*)",
+      "Bash(xargs sed:*)",
+      "Bash(grep:*)",
+      "Bash(git status:*)",
+      "Bash(git add:*)",
+      "Bash(git push:*)",
+      "Bash(tee:*)",
+      "Bash(git mv:*)",
+      "Bash(perl -pe:*)",
+      "Bash(find:*)",
+      "Bash(perl -pi -e:*)",
+      "Bash(perl -pi -e 's/k_TypeName = \"\"AbstractNodeGeometry0D\"\"/k_TypeName = \"\"INodeGeometry0D\"\"/g':*)",
+      "Bash(gh pr view:*)",
+      "Bash(/opt/local/bin/gh pr view:*)",
+      "WebFetch(domain:github.com)",
+      "Bash(git checkout:*)"
+    ],
+    "deny": [
+      "Bash(rm -rf *)"
+    ]
+  }
+}

CMakeLists.txt

@@ -37,7 +37,7 @@ option(EbsdLib_BUILD_H5SUPPORT "Build H5Support Library" OFF)
 
 
 # set project's name
-project(EbsdLibProj VERSION 2.4.0)
+project(EbsdLibProj VERSION 3.0.0)
 
 
 # Request C++17 standard, using new CMake variables.

Code_Review/compare_ipf_legends_all_laue.m

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+% compare_ipf_legends_all_laue.m
+%
+% Companion to EbsdLib's IPFLegendTest::MTEXCompare_AllLaueClasses.
+%
+% For every Laue class in IPFComparison/, writes two MTEX legends so the
+% pairs can be compared apples-to-apples against the EbsdLib outputs:
+%   ebsdlib_ipf_legend_tsl.png  vs  mtex_ipf_legend_tsl.png
+%   ebsdlib_ipf_legend_nh.png   vs  mtex_ipf_legend_hsv.png
+% The TSL pair uses MTEX's ipfTSLKey; the NH pair uses MTEX's ipfHSVKey,
+% which is the Nolze-Hielscher-style HSV scheme that EbsdLib's
+% NolzeHielscherColorKey is modeled on.
+%
+% Usage:
+%   1. Build and run the EbsdLib unit test first:
+%        cd .../DREAM3D-Build/ebsdlib-Release && \
+%          Bin/EbsdLibUnitTest "ebsdlib::IPFLegendTest::MTEXCompare_AllLaueClasses"
+%   2. Edit `baseDir` below to point at the IPFComparison directory
+%   3. Run this script in MATLAB (MTEX must be on the path: startup_mtex)
+
+
+baseDir = '/Users/mjackson/Workspace7/DREAM3D-Build/ebsdlib-Release/Testing/Temporary/IPFComparison';
+
+if ~exist(baseDir, 'dir')
+    error('baseDir does not exist: %s\nRun the IPFLegendTest MTEXCompare first.', baseDir);
+end
+
+setMTEXpref('xAxisDirection', 'east');
+setMTEXpref('zAxisDirection', 'outOfPlane');
+
+% Map EbsdLib rotation point group -> MTEX crystalSymmetry.
+% Hexagonal/trigonal use X||a to match EbsdLib's X||a* after the 30-degree
+% reciprocal-basis reinterpretation. (MTEX's default is X||a*; using X||a
+% here rotates MTEX 30 degrees to match EbsdLib.)
+laueMap = containers.Map();
+laueMap('432') = crystalSymmetry('m-3m');
+laueMap('23')  = crystalSymmetry('m-3');
+laueMap('622') = crystalSymmetry('6/mmm', [1 1 1.6], 'X||a', 'Z||c*');
+laueMap('6')   = crystalSymmetry('6/m',   [1 1 1.6], 'X||a', 'Z||c*');
+laueMap('422') = crystalSymmetry('4/mmm');
+laueMap('4')   = crystalSymmetry('4/m');
+laueMap('32')  = crystalSymmetry('-3m',   [1 1 1.6], 'X||a', 'Z||c*');
+laueMap('3')   = crystalSymmetry('-3',    [1 1 1.6], 'X||a', 'Z||c*');
+laueMap('222') = crystalSymmetry('mmm');
+laueMap('2')   = crystalSymmetry('2/m');
+laueMap('1')   = crystalSymmetry('-1');
+
+entries = dir(baseDir);
+for e = 1:numel(entries)
+    if ~entries(e).isdir, continue; end
+    name = entries(e).name;
+    if name(1) == '.', continue; end
+    if ~isKey(laueMap, name)
+        fprintf('skipping %s (not in laueMap)\n', name);
+        continue;
+    end
+
+    classDir = fullfile(baseDir, name);
+    cs = laueMap(name);
+
+    % --- TSL pair (compare ebsdlib_ipf_legend_tsl.png vs mtex_ipf_legend_tsl.png) ---
+    try
+        keyTSL = ipfTSLKey(cs);
+    catch
+        warning('ipfTSLKey not available for %s; falling back to ipfHKLKey', name);
+        keyTSL = ipfHKLKey(cs);
+    end
+    fT = figure('Visible', 'off', 'Position', [100 100 600 600]);
+    plot(keyTSL);
+    title(sprintf('MTEX ipfTSLKey %s', name));
+    outTSL = fullfile(classDir, 'tsl_gridded_mtex_ipf_legend.png');
+    outDir = fileparts(outTSL);
+    if ~isfolder(outDir)
+        mkdir(outDir);
+    end
+    %exportgraphics(outTSL, outTSL, 'Resolution', 72);
+    saveas(fT, outTSL);
+    close(fT);
+    fprintf('wrote %s\n', outTSL);
+
+    % --- NH/HSV pair (compare ebsdlib_ipf_legend_nh.png vs mtex_ipf_legend_hsv.png) ---
+    keyHSV = ipfHSVKey(cs);
+    fH = figure('Visible', 'off', 'Position', [100 100 600 600]);
+    plot(keyHSV);
+    title(sprintf('MTEX ipfHSVKey %s', name));
+    outHSV = fullfile(classDir, 'nh_gridded_mtex_ipf_legend.png');
+    %exportgraphics(outHSV, outHSV, 'Resolution', 72);
+    saveas(fH, outHSV);
+    close(fH);
+    fprintf('wrote %s\n', outHSV);
+end
+
+fprintf('\nDone. For each Laue class directory there should now be:\n');
+fprintf('  <class>/ebsdlib_ipf_legend_tsl.png   EbsdLib TSL legend\n');
+fprintf('  <class>/ebsdlib_ipf_legend_nh.png    EbsdLib Nolze-Hielscher legend\n');
+fprintf('  <class>/mtex_ipf_legend_tsl.png       MTEX ipfTSLKey legend\n');
+fprintf('  <class>/mtex_ipf_legend_hsv.png       MTEX ipfHSVKey legend\n');
+fprintf('Compare each pair (TSL <-> TSL, NH <-> HSV) side-by-side.\n');

Code_Review/compare_pole_figure_mtex.m

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+% compare_pole_figure_mtex.m
+%
+% Compares the pole figure produced by EbsdLib's ODFTest against MTEX.
+% Expects a CSV of Bunge Euler angles (phi1, Phi, phi2) in degrees.
+%
+% Usage: edit csvPath below to point at the file written by ODFTest, then run.
+%
+% The ODFTest writes the CSV to:
+%   <EbsdLib build dir>/Testing/Temporary/ODFTest_Eulers_deg.csv
+% e.g. /Users/mjackson/Workspace7/DREAM3D-Build/ebsdlib-Release/Testing/Temporary/ODFTest_Eulers_deg.csv
+
+csvPath = '/Users/mjackson/Workspace7/DREAM3D-Build/ebsdlib-Release/Testing/Temporary/ODFTest_Eulers_deg.csv';
+
+% Load Euler angles
+T = readtable(csvPath);
+eulers_deg = [T.phi1, T.Phi, T.phi2];
+fprintf('Loaded %d Euler triples from %s\n', size(eulers_deg,1), csvPath);
+fprintf('First 3 rows (deg):\n');
+disp(eulers_deg(1:min(3,end), :));
+
+% Crystal symmetry: hexagonal high (6/mmm).
+% Use X||a (real-space a-axis along X) to match EbsdLib's hexagonal
+% direction convention in HexagonalOps.cpp. EbsdLib's (10-10) pole uses
+% direction (sqrt(3)/2, 1/2, 0) and (2-1-10) uses (1, 0, 0), which is the
+% X||a convention. MTEX's default is X||a* (reciprocal), which swaps the
+% labels of the two prismatic pole figures — that is why EbsdLib's (10-10)
+% looks like MTEX's (2-1-10) and vice versa. Switching MTEX to X||a here
+% aligns the labels.
+cs = crystalSymmetry('6/mmm', [1 1 1.6], 'X||a', 'Z||c*');
+% Specimen symmetry: triclinic (no sample symmetry)
+ss = specimenSymmetry('1');
+
+% Build orientations (Bunge convention is MTEX default)
+ori = orientation.byEuler(eulers_deg(:,1)*degree, eulers_deg(:,2)*degree, eulers_deg(:,3)*degree, cs, ss);
+
+% MTEX default plotting: X east (right), Y north (up), Z outOfPlane.
+% These match EbsdLib's pole figure convention after this fix.
+setMTEXpref('xAxisDirection', 'east');
+setMTEXpref('zAxisDirection', 'outOfPlane');
+
+% Miller indices for the pole figures EbsdLib shows: (0001), (10-10), (2-1-10)
+h = [ ...
+    Miller(0, 0, 0, 1, cs), ...
+    Miller(1, 0,-1, 0, cs), ...
+    Miller(2,-1,-1, 0, cs)];
+
+% Plot pole figures as scatter of individual orientations (like EbsdLib discrete PF)
+figure('Name', 'MTEX pole figures for EbsdLib ODFTest Euler sample');
+plotPDF(ori, h, 'MarkerSize', 3, 'upper', 'projection', 'eangle', 'complete');
+title('MTEX: (0001), (10-10), (2-1-10) for EbsdLib ODFTest sample');
+
+% Print a short diagnostic
+fprintf('\n');
+fprintf('Expected for Bunge (180, 90, 0):\n');
+fprintf('  c-axis [0001] in sample frame = +Y, so (0001) cluster at 12:00 (top).\n');
+fprintf('  Centrosymmetric 6/mmm: antipodal [000-1] at 6:00 (bottom) also appears.\n');
+fprintf('  The (0001) pole figure should show clusters at 12:00 and 6:00.\n');

Code_Review/compare_pole_figures_all_laue.m

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+% compare_pole_figures_all_laue.m
+%
+% Companion to EbsdLib's PoleFigureLaueComparisonTest (Source/Test/PoleFigureLaueComparisonTest.cpp).
+%
+% For every Laue class listed in manifest.txt, reads eulers.csv, reconstructs
+% the orientations in MTEX with the matching crystal symmetry, and saves
+% a pole figure PNG named mtex.png next to EbsdLib's ebsdlib.png — so the two
+% images can be compared side-by-side per Laue class.
+%
+% Usage:
+%   1. Run the EbsdLib test first:
+%        cd .../DREAM3D-Build/ebsdlib-Release && \
+%          Bin/EbsdLibUnitTest "ebsdlib::PoleFigureLaueComparisonTest::GenerateAllLaueClasses"
+%   2. Edit `baseDir` below to point at the PoleFigureComparison directory
+%   3. Run this script in MATLAB (MTEX must be on the path; run `startup_mtex` first)
+
+baseDir = '/Users/mjackson/Workspace7/DREAM3D-Build/ebsdlib-Release/Testing/Temporary/PoleFigureComparison';
+
+if ~exist(baseDir, 'dir')
+    error('baseDir does not exist: %s\nRun the PoleFigureLaueComparisonTest first.', baseDir);
+end
+
+% MTEX pole-figure plotting conventions (match EbsdLib after the axis fixes)
+setMTEXpref('xAxisDirection', 'east');
+setMTEXpref('zAxisDirection', 'outOfPlane');
+
+% Map EbsdLib rotation point group → MTEX crystalSymmetry Laue class string
+% plus the 3 Miller-Bravais / Miller indices to plot. EbsdLib now uses
+% X||a* for hexagonal/trigonal crystals (MTEX default).
+laueMap = containers.Map();
+% cubic
+laueMap('432') = struct('cs', crystalSymmetry('m-3m'), ...
+    'h', {{[0 0 1], [0 1 1], [1 1 1]}});
+laueMap('23')  = struct('cs', crystalSymmetry('m-3'), ...
+    'h', {{[0 0 1], [0 1 1], [1 1 1]}});
+% hexagonal
+laueMap('622') = struct('cs', crystalSymmetry('6/mmm', [1 1 1.6]), ...
+    'h', {{[0 0 0 1], [1 0 -1 0], [2 -1 -1 0]}});
+laueMap('6')   = struct('cs', crystalSymmetry('6/m', [1 1 1.6]), ...
+    'h', {{[0 0 0 1], [1 0 -1 0], [1 1 -2 0]}});
+% tetragonal
+laueMap('422') = struct('cs', crystalSymmetry('4/mmm'), ...
+    'h', {{[0 0 1], [1 0 0], [1 1 0]}});
+laueMap('4')   = struct('cs', crystalSymmetry('4/m'), ...
+    'h', {{[0 0 1], [1 0 0], [1 1 0]}});
+% trigonal
+laueMap('32')  = struct('cs', crystalSymmetry('-3m', [1 1 1.6]), ...
+    'h', {{[0 0 0 1], [0 -1 1 0], [1 -1 0 0]}});
+laueMap('3')   = struct('cs', crystalSymmetry('-3', [1 1 1.6]), ...
+    'h', {{[0 0 0 1], [-1 -1 2 0], [2 -1 -1 0]}});
+% orthorhombic
+laueMap('222') = struct('cs', crystalSymmetry('mmm'), ...
+    'h', {{[0 0 1], [1 0 0], [0 1 0]}});
+% monoclinic
+laueMap('2')   = struct('cs', crystalSymmetry('2/m'), ...
+    'h', {{[0 0 1], [1 0 0], [0 1 0]}});
+% triclinic
+laueMap('1')   = struct('cs', crystalSymmetry('-1'), ...
+    'h', {{[0 0 1], [1 0 0], [0 1 0]}});
+
+% Discover all Laue class subdirectories
+entries = dir(baseDir);
+for e = 1:numel(entries)
+    if ~entries(e).isdir, continue; end
+    name = entries(e).name;
+    if name(1) == '.', continue; end
+    if ~isKey(laueMap, name)
+        fprintf('skipping %s (not in laueMap)\n', name);
+        continue;
+    end
+
+    classDir = fullfile(baseDir, name);
+    csvPath = fullfile(classDir, 'pole_figure_input_eulers.csv');
+    if ~exist(csvPath, 'file')
+        fprintf('skipping %s (no pole_figure_input_eulers.csv)\n', name);
+        continue;
+    end
+
+    info = laueMap(name);
+    cs = info.cs;
+    ss = specimenSymmetry('1');
+
+    T = readtable(csvPath);
+    eulers_deg = [T.phi1, T.Phi, T.phi2];
+    ori = orientation.byEuler(eulers_deg(:,1)*degree, eulers_deg(:,2)*degree, eulers_deg(:,3)*degree, cs, ss);
+
+    % Build Miller objects for the 3 pole figures
+    hArr = cell(1, numel(info.h));
+    for k = 1:numel(info.h)
+        idx = info.h{k};
+        if numel(idx) == 4
+            hArr{k} = Miller(idx(1), idx(2), idx(3), idx(4), cs);
+        else
+            hArr{k} = Miller(idx(1), idx(2), idx(3), cs);
+        end
+    end
+    h = [hArr{:}];
+
+    f = figure('Visible', 'off', 'Position', [100 100 700 250]);
+    plotPDF(ori, h, 'MarkerSize', 3, 'upper', 'projection', 'eangle', 'complete');
+    ttl = sprintf('MTEX %s — Euler %.1f, %.1f, %.1f (deg)', name, eulers_deg(1,1), eulers_deg(1,2), eulers_deg(1,3));
+    sgtitle(ttl);
+
+    outPath = fullfile(classDir, 'mtex_pole_figure.png');
+    outDir = fileparts(outPath);
+    if ~isfolder(outDir)
+        mkdir(outDir);
+    end
+    exportgraphics(f, outPath, 'Resolution', 72);
+    close(f);
+    fprintf('wrote %s\n', outPath);
+end
+
+fprintf('\nDone. For each Laue class directory there should now be:\n');
+fprintf('  <class>/eulers.csv      input Euler samples\n');
+fprintf('  <class>/ebsdlib.png     EbsdLib-rendered composite\n');
+fprintf('  <class>/mtex.png        MTEX-rendered composite\n');
+fprintf('Compare the two image files per class to verify convention agreement.\n');

Code_Review/ebsdlib_todo.md

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+# EbsdLib TODO Items
+
+## PUCM
+
+## Tighter spacing for Legend outputs.
+
+Some legends do not take up all the canvas space. Make changes to tighten this up.
+