Merge branch 'dev' of https://github.com/topology-tool-kit/ttk into DelRips

Author: julien-tierny

.github/workflows/test-macos.yml

@@ -139,6 +139,7 @@ jobs:
       run: |
         cd ttk-data
         # remove buggy example
+        rm python/harmonicSkeleton.py
         # related issue: https://github.com/topology-tool-kit/ttk/issues/1055
         rm python/nestedTrackingFromOverlap.py
         # tmp removal of mpi example

ChangeLog.md

@@ -1,9 +1,11 @@
 ## TTK - ChangeLog
 =
 ### dev
-- Cycle-aware dimensionality reduction (TopoAE++)
+- Cycle-aware dimensionality reduction (TopoAE++, IEEE TVCG 2026)
 - Distributed computation of persistent homology! (IEEE TPDS 2025)
+- Discrete vector field topology! (IEEE VIS 2024)
 - New backend for TrackingFromFields (critical point based)
+- Stochastic discrete gradient (IEEE VIS 2012)
 - Fast planar Rips filtration persistence computation
 - Migration to ParaView 6
 - CI updates

core/base/common/welcomeMsg.inl

@@ -2,39 +2,37 @@
 // Julien Tierny <[email protected]>
 // January 2020.
 
-// "TTK                   (c) 2025"
+// "TTK                   (c) 2026"
 
 printMsg(
   debug::output::BOLD
-    + " _____ _____ _  __                    __  __    ____   ___ ____  ____"
+    + " _____ _____ _  __                    __  __    ____   ___ ____   __"
     + debug::output::ENDCOLOR,
   debug::Priority::PERFORMANCE,
   debug::LineMode::NEW,
   stream);
 printMsg(debug::output::BOLD
-           + "|_   _|_   _| |/ /                   / /__\\ \\  |___ \\ / _ "
-             "\\___ \\| ___|"
+  + "|_   _|_   _| |/ /                   / /__\\ \\  |___ \\ / _ \\___ \\ / /_"
            + debug::output::ENDCOLOR,
          debug::Priority::PERFORMANCE,
          debug::LineMode::NEW,
          stream);
 printMsg(
   debug::output::BOLD
-    + "  | |   | | | ' /                   | |/ __| |   __) | | | |__) |___ \\"
+    + "  | |   | | | ' /                   | |/ __| |   __) | | | |__) | '_ \\"
     + debug::output::ENDCOLOR,
   debug::Priority::PERFORMANCE,
   debug::LineMode::NEW,
   stream);
 printMsg(
   debug::output::BOLD
-    + "  | |   | | | . \\                   | | (__| |  / __/| |_| / __/ ___) |"
+    + "  | |   | | | . \\                   | | (__| |  / __/| |_| / __/| (_) |"
     + debug::output::ENDCOLOR,
   debug::Priority::PERFORMANCE,
   debug::LineMode::NEW,
   stream);
 printMsg(debug::output::BOLD
-           + "  |_|   |_| |_|\\_\\                  | |\\___| | "
-             "|_____|\\___/_____|____/"
+    + "  |_|   |_| |_|\\_\\                  | |\\___| | |_____|\\___/_____|\\___/"
            + debug::output::ENDCOLOR,
          debug::Priority::PERFORMANCE,
          debug::LineMode::NEW,

core/base/dimensionReduction/DimensionReduction.cpp

@@ -81,23 +81,14 @@ int DimensionReduction::execute(
       ae_CUDA, ae_Deterministic, ae_Seed, NumberOfComponents, ae_Epochs,
       ae_LearningRate, ae_Optimizer, ae_Method, ae_Model, ae_Architecture,
       ae_Activation, ae_BatchSize, ae_BatchNormalization, ae_RegCoefficient,
-      IsInputImages);
+      IsInputImages, ae_PreOptimize, ae_PreOptimizeEpochs);
     tcdr.setDebugLevel(debugLevel_);
     tcdr.setThreadNumber(threadNumber_);
 
     outputEmbedding.resize(NumberOfComponents);
     for(int d = 0; d < NumberOfComponents; d++)
       outputEmbedding[d].resize(nRows);
 
-    if(ae_PreOptimize) {
-      DimensionReduction initDR;
-      initDR.setDebugLevel(debugLevel_);
-      initDR.setInputMethod(ae_PreOptimizeMethod);
-      std::vector<std::vector<double>> latentInitialization;
-      initDR.execute(latentInitialization, inputMatrix, nRows, nColumns);
-      tcdr.setLatentInitialization(latentInitialization);
-    }
-
     tcdr.execute(outputEmbedding, inputMatrix, nRows);
 
     this->printMsg("Computed AE dimension reduction", 1.0, t.getElapsedTime(),

core/base/dimensionReduction/DimensionReduction.h

@@ -66,8 +66,9 @@
 ///
 /// "Topological Autoencoders++: Fast and Accurate Cycle-Aware Dimensionality
 /// Reduction" \n
-/// Mattéo Clémot, Julie Digne, Julien Tierny, \n
-/// arXiv preprint, 2025.
+/// Mattéo Clémot, Julie Digne, Julien Tierny, \n
+/// IEEE Transactions on Visualization and Computer Graphics.
+/// Accepted, to be presented at IEEE VIS 2026.
 
 #pragma once
 
@@ -365,7 +366,7 @@ namespace ttk {
     bool ae_BatchNormalization{true};
     double ae_RegCoefficient{1e-2};
     bool ae_PreOptimize{false};
-    METHOD ae_PreOptimizeMethod{METHOD::PCA};
+    int ae_PreOptimizeEpochs{1000};
 
     // testing
     std::string ModulePath{"default"};

core/base/discreteGradient/CMakeLists.txt

@@ -6,4 +6,5 @@ ttk_add_base_library(discreteGradient
     DiscreteGradient_Template.h
   DEPENDS
     triangulation
+    ftmTree
     )

core/base/discreteGradient/DiscreteGradient.cpp

@@ -249,6 +249,58 @@ int DiscreteGradient::setManifoldSize(
   return 0;
 }
 
+void DiscreteGradient::computeDerivatives(
+  const SimplexId &x,
+  const std::vector<SimplexId> &stencilIds,
+  const std::array<float, 3> &xCoords,
+  const std::vector<std::array<float, 3>> &stencilCoords,
+  double (&grad)[3]) {
+
+  const double *scalars
+    = static_cast<double const *>(this->inputScalarField_.first);
+  if(stencilIds[0] != -1 && stencilIds[1] != -1)
+    grad[0] = -(scalars[stencilIds[0]] - scalars[stencilIds[1]])
+              / std::abs(stencilCoords[0][0] - stencilCoords[1][0]);
+  else if(stencilIds[0] != -1 && stencilIds[1] == -1)
+    grad[0] = -(scalars[stencilIds[0]] - scalars[x])
+              / std::abs(stencilCoords[0][0] - xCoords[0]);
+  else if(stencilIds[1] != -1 && stencilIds[0] == -1)
+    grad[0] = -(scalars[x] - scalars[stencilIds[1]])
+              / std::abs(stencilCoords[1][0] - xCoords[0]);
+  if(stencilIds[2] != -1 && stencilIds[3] != -1)
+    grad[1] = -(scalars[stencilIds[2]] - scalars[stencilIds[3]])
+              / std::abs(stencilCoords[2][1] - stencilCoords[3][1]);
+  else if(stencilIds[2] != -1 && stencilIds[3] == -1)
+    grad[1] = -(scalars[stencilIds[2]] - scalars[x])
+              / std::abs(stencilCoords[2][1] - xCoords[1]);
+  else if(stencilIds[3] != -1 && stencilIds[2] == -1)
+    grad[1] = -(scalars[x] - scalars[stencilIds[3]])
+              / std::abs(stencilCoords[3][1] - xCoords[1]);
+  if(stencilIds[4] != -1 && stencilIds[5] != -1)
+    grad[2] = -(scalars[stencilIds[4]] - scalars[stencilIds[5]])
+              / std::abs(stencilCoords[4][2] - stencilCoords[5][2]);
+  else if(stencilIds[4] != -1 && stencilIds[5] == -1)
+    grad[2] = -(scalars[stencilIds[4]] - scalars[x])
+              / std::abs(stencilCoords[4][2] - xCoords[2]);
+  else if(stencilIds[5] != -1 && stencilIds[4] == -1)
+    grad[2] = -(scalars[x] - scalars[stencilIds[5]])
+              / std::abs(stencilCoords[5][2] - xCoords[2]);
+}
+
+int DiscreteGradient::getCriticalPointMap(
+  const vector<pair<SimplexId, char>> &criticalPoints, vector<char> &isPL) {
+  isPL.resize(numberOfVertices_);
+  std::fill(isPL.begin(), isPL.end(), 0);
+  for(pair<SimplexId, char> criticalPoint : criticalPoints) {
+    const SimplexId criticalPointId = criticalPoint.first;
+    const char criticalPointType = criticalPoint.second;
+
+    isPL[criticalPointId] = criticalPointType;
+  }
+
+  return 0;
+}
+
 #ifdef TTK_ENABLE_MPI
 void DiscreteGradient::setCellToGhost(const int cellDim,
                                       const SimplexId cellId) {