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

topology-tool-kit · Jun 27, 2024 · b03fd09 · b03fd09
2 parents dc09123 + 2035bd7
commit b03fd09
Show file tree

Hide file tree

Showing 68 changed files with 8,180 additions and 151 deletions.
diff --git a/.github/workflows/package.yml b/.github/workflows/package.yml
@@ -326,7 +326,7 @@ jobs:
       shell: bash
       run: |
         conda install -c conda-forge "qt>=5.12" boost eigen spectralib zfp \
-          scikit-learn openmp graphviz websocketpp
+          scikit-learn llvm-openmp graphviz websocketpp clangxx
 
     - name: Remove hosted Python
       shell: bash

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -429,7 +429,7 @@ jobs:
       shell: bash
       run: |
         conda install -c conda-forge boost glew eigen spectralib zfp  \
-          scikit-learn openmp graphviz ninja websocketpp sccache=0.4.2 python=3.10 zlib qhull
+          scikit-learn graphviz ninja websocketpp sccache=0.4.2 python=3.10 zlib qhull llvm-openmp clangxx
         # add sccache to PATH
         echo "$CONDA_ROOT/bin" >> $GITHUB_PATH
         # add TTK & ParaView install folders to PATH

diff --git a/CMake/Print.cmake b/CMake/Print.cmake
@@ -15,6 +15,7 @@ function(ttk_print_summary)
     message(STATUS "TTK_ENABLE_SHARED_BASE_LIBRARIES: ${TTK_ENABLE_SHARED_BASE_LIBRARIES}")
     message(STATUS "TTK_ENABLE_SPECTRA: ${TTK_ENABLE_SPECTRA}")
     message(STATUS "TTK_ENABLE_SQLITE3: ${TTK_ENABLE_SQLITE3}")
+    message(STATUS "TTK_ENABLE_TORCH: ${TTK_ENABLE_TORCH}")
     message(STATUS "TTK_ENABLE_WEBSOCKETPP: ${TTK_ENABLE_WEBSOCKETPP}")
     message(STATUS "TTK_ENABLE_ZFP: ${TTK_ENABLE_ZFP}")
     message(STATUS "TTK_ENABLE_ZLIB: ${TTK_ENABLE_ZLIB}")

diff --git a/CMake/config.cmake b/CMake/config.cmake
@@ -153,6 +153,15 @@ endif()
 
 # optional packages
 
+find_package(Torch QUIET)
+if(TORCH_FOUND)
+  option(TTK_ENABLE_TORCH "Enable Torch support" ON)
+  message(STATUS "Found Torch ${TORCH_VERSION} (${TORCH_LIBRARIES})")
+else()
+  option(TTK_ENABLE_TORCH "Enable Torch support" OFF)
+  message(STATUS "Torch not found, disabling Torch support in TTK.")
+endif()
+
 find_package(ZLIB QUIET)
 if(ZLIB_FOUND)
   option(TTK_ENABLE_ZLIB "Enable Zlib support" ON)

diff --git a/CMake/merge_tree_preprocess.xml b/CMake/merge_tree_preprocess.xml
@@ -55,7 +55,7 @@ panel_visibility="advanced">
   </PropertyWidgetDecorator>
   </Hints>
   <Documentation>
-
+    When merging a saddle point that was already merged to other saddle points before, this option allows to consider not the saddle point itself but the farthest saddle among the ones that were already merge to it before. "Farthest" means here the saddle with lowest value for join tree and highest value for split tree.
   </Documentation>
   <BooleanDomain name="bool"/>
 </IntVectorProperty>

diff --git a/core/base/TTKBaseConfig.cmake.in b/core/base/TTKBaseConfig.cmake.in
@@ -17,6 +17,10 @@ if (@TTK_ENABLE_QHULL@ AND @Qhull_FOUND@)
   find_dependency(Qhull REQUIRED)
 endif()
 
+if (@TTK_ENABLE_TORCH@ AND TORCH_FOUND)
+  find_dependency(Torch REQUIRED)
+endif()
+
 if (@TTK_ENABLE_ZFP@ AND NOT @TTK_ENABLE_SHARED_BASE_LIBRARIES@)
   set(ZFP_DIR "@ZFP_DIR@" CACHE PATH "Use TTK ZFP dir" FORCE)
   find_dependency(ZFP REQUIRED @ZFP_DIR@)

diff --git a/core/base/ftmTree/FTMTreeUtils.cpp b/core/base/ftmTree/FTMTreeUtils.cpp
@@ -130,7 +130,8 @@ namespace ttk {
     }
 
     int FTMTree_MT::getNumberOfLeavesFromTree() {
-      auto leaves = this->getLeaves();
+      std::vector<idNode> leaves;
+      this->getLeavesFromTree(leaves);
       return leaves.size();
     }
 
@@ -249,7 +250,6 @@ namespace ttk {
         std::stringstream ss;
         ss << "problem, there is " << noRoot << " root(s)";
         printErr(ss.str());
-        this->printTree2();
         this->printTree();
       }
       if(this->isNodeAlone(nodeId))
@@ -431,6 +431,25 @@ namespace ttk {
       ss << std::endl;
     }
 
+    std::stringstream FTMTree_MT::printSubTree(idNode subRoot) {
+      std::stringstream ss;
+      ss << "Nodes----------" << std::endl;
+      std::queue<idNode> queue;
+      queue.push(subRoot);
+      while(!queue.empty()) {
+        idNode node = queue.front();
+        queue.pop();
+
+        printNodeSS(node, ss);
+
+        std::vector<idNode> children;
+        this->getChildren(node, children);
+        for(idNode child : children)
+          queue.push(child);
+      }
+      return ss;
+    }
+
     std::stringstream FTMTree_MT::printTree(bool doPrint) {
       std::stringstream ss;
       std::vector<idNode> allRoots;
@@ -440,20 +459,7 @@ namespace ttk {
       for(unsigned int i = 0; i < allRoots.size(); ++i) {
         if(allRoots.size() != 1)
           ss << i << " _ ";
-        ss << "Nodes----------" << std::endl;
-        std::queue<idNode> queue;
-        queue.push(allRoots[i]);
-        while(!queue.empty()) {
-          idNode const node = queue.front();
-          queue.pop();
-
-          printNodeSS(node, ss);
-
-          std::vector<idNode> children;
-          this->getChildren(node, children);
-          for(idNode const child : children)
-            queue.push(child);
-        }
+        ss << this->printSubTree(allRoots[i]).str();
       }
       if(allRoots.size() == 0)
         for(unsigned int i = 0; i < this->getNumberOfNodes(); ++i)

diff --git a/core/base/ftmTree/FTMTree_MT.h b/core/base/ftmTree/FTMTree_MT.h
@@ -775,6 +775,8 @@ namespace ttk {
       template <class dataType>
       std::stringstream printMergedRoot(bool doPrint = true);
 
+      std::stringstream printSubTree(idNode subRoot);
+
       std::stringstream printTree(bool doPrint = true);
 
       std::stringstream printTreeStats(bool doPrint = true);

diff --git a/core/base/ftmTreePP/FTMTreePPUtils.h b/core/base/ftmTreePP/FTMTreePPUtils.h
@@ -29,11 +29,6 @@ namespace ttk {
       std::vector<std::tuple<SimplexId, SimplexId, dataType>> pairs;
       getPersistencePairs<dataType>(tree, pairs);
       for(auto pair : pairs) {
-        if(tree->getNode(std::get<0>(pair))->getOrigin() < std::get<0>(pair)
-           and tree->getNode(std::get<0>(pair))->getOrigin() >= 0)
-          tree->getNode(tree->getNode(std::get<0>(pair))->getOrigin())
-            ->setOrigin(std::get<1>(pair));
-
         tree->getNode(std::get<0>(pair))->setOrigin(std::get<1>(pair));
         tree->getNode(std::get<1>(pair))->setOrigin(std::get<0>(pair));
       }

diff --git a/core/base/mergeTreeAutoencoder/CMakeLists.txt b/core/base/mergeTreeAutoencoder/CMakeLists.txt
@@ -0,0 +1,20 @@
+ttk_add_base_library(mergeTreeAutoencoder
+  SOURCES
+    MergeTreeAutoencoder.cpp
+    MergeTreeAutoencoderUtils.cpp
+    MergeTreeTorchUtils.cpp
+  HEADERS
+    MergeTreeAutoencoder.h
+    MergeTreeAutoencoderUtils.h
+    MergeTreeTorchUtils.h
+  DEPENDS
+    mergeTreePrincipalGeodesics
+    geometry
+)
+
+if(TTK_ENABLE_TORCH)
+  target_include_directories(mergeTreeAutoencoder PUBLIC ${TORCH_INCLUDE_DIRS})
+  target_compile_options(mergeTreeAutoencoder PUBLIC "${TORCH_CXX_FLAGS}")
+  target_link_libraries(mergeTreeAutoencoder PUBLIC "${TORCH_LIBRARIES}")
+  target_compile_definitions(mergeTreeAutoencoder PUBLIC TTK_ENABLE_TORCH)
+endif()