Adjust seg (#75)

* add unit test for preprocess; remove object contact is really working * inplace segmentation of watershed * seeded watershed * add robin map github repo as submodule since robin_map is not updated in conda-forge * make the priority queue more general to use * update the edit of priority queue * move priority queue to utils * move priority queue back to segmentation since the functions are built in for the edge type * seeded watershed compiles, but runs with core dump error * compilation in macbook pro * unit test for seeded watershed. the correctness of the result is not checked * add segmentation module with 2d seeded watershed * fixed the bug; the code still has a lot of assertion * remove a lot of assertions * test seeded watershed 3d
image-infomatics · Mar 28, 2022 · 3c895c0 · 3c895c0
1 parent e0db485
commit 3c895c0
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Showing 18 changed files with 375 additions and 100 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,4 @@
+*.nfs*
 *.code-workspace
 *.DS_Store
 

diff --git a/.gitmodules b/.gitmodules
@@ -1,3 +1,3 @@
 [submodule "cpp/third-party/robin-map"]
-	path = cpp/third-party/robin-map
-	url = https://github.com/Tessil/robin-map.git
+    path = cpp/third-party/robin-map
+    url = https://github.com/Tessil/robin-map.git
diff --git a/.vscode/c_cpp_properties.json b/.vscode/c_cpp_properties.json
@@ -1,19 +1,39 @@
 {
     "configurations": [
         {
-            "name": "Mac",
+            "name": "centos",
             "includePath": [
-                "~/code/reneu/cpp/include",
-                "~/opt/anaconda3/envs/reneu/include",
-                "~/opt/anaconda3/envs/reneu/include/python3.8",
-                "~/opt/anaconda3/envs/reneu/lib/python3.8/site-packages/numpy/core/include"
+                "${HOME}/code/reneu/cpp/include",
+                "${CONDA_PREFIX}/include/python3.8",
+                "${CONDA_PREFIX}/include",
+                "${CONDA_PREFIX}/lib/python3.8/site-packages/numpy/core/include",
+                "${workspaceFolder}/cpp/third-party/robin-map/include"
             ],
             "defines": [],
             "macFrameworkPath": [],
-            "compilerPath": "/usr/bin/clang",
+            "compilerPath": "/cm/shared/sw/nix/store/hmphldjnv7440cwpv29ph5d5bp3lbxz5-gcc-11.2.0/bin/gcc",
             "cStandard": "c17",
-            "cppStandard": "c++17",
-            "intelliSenseMode": "clang-x64",
+            "cppStandard": "c++20",
+            "intelliSenseMode": "linux-gcc-x64",
+            "configurationProvider": "ms-vscode.cmake-tools"
+        },
+        {
+            "name": "MacOS",
+            "includePath": [
+                "${workspaceFolder}/cpp/include",
+                "${CONDA_PREFIX}/include/python3.8",
+                "${CONDA_PREFIX}/include",
+                "${HOME}/opt/anaconda3/envs/reneu/include",
+                "${CONDA_PREFIX}/lib/python3.8/site-packages/numpy/core/include",
+                "${workspaceFolder}/cpp/third-party/robin-map/include"
+            ],
+            "defines": [],
+            "macFrameworkPath": [
+                "/System/Library/Frameworks"
+            ],
+            "cStandard": "c17",
+            "cppStandard": "c++20",
+            "intelliSenseMode": "macos-clang-x64",
             "configurationProvider": "ms-vscode.cmake-tools"
         }
     ],

diff --git a/cpp/CMakeLists.txt b/cpp/CMakeLists.txt
@@ -2,6 +2,9 @@ cmake_minimum_required(VERSION 3.12.0)
 set(RENEU_VERSION 0.2.0)
 project(libreneu VERSION ${RENEU_VERSION} LANGUAGES CXX)
 
+# add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/third-party/robin-map)
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/third-party/robin-map/include)
+
 set(CMAKE_THREAD_LIBS_INIT "-lpthread")
 set(CMAKE_HAVE_THREADS_LIBRARY 1)
 set(CMAKE_USE_WIN32_THREADS_INIT 0)
@@ -18,7 +21,6 @@ set(xtensor_DIR ${CONDA_PREFIX}/lib/cmake/xtensor)
 set(xtensor-python_DIR ${CONDA_PREFIX}/lib/cmake/xtensor-python)
 set(xtl_DIR ${CONDA_PREFIX}/lib/cmake/xtl)
 
-add_subdirectory(third-party/robin-map)
 
 set(Boost_USE_STATIC_LIBS OFF) 
 set(Boost_USE_MULTITHREADED OFF)  
@@ -35,14 +37,10 @@ if(Boost_NO_SYSTEM_PATH)
 endif(Boost_NO_SYSTEM_PATH)
 find_package(Boost REQUIRED serialization)
 
-set(RENEU_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
-include_directories(${NUMPY_INCLUDE_DIR} ${RENEU_INCLUDE_DIR} 
-                        ${CONDA_PREFIX}/include ${BOOST_INCLUDEDIR})
-
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Modules)
-set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD 20)
 set(CMAKE_CXX_STANDARD_REQUIRED True)
-set(PYBIND11_CPP_STANDARD  "-std=c++17")
+set(PYBIND11_CPP_STANDARD  "-std=c++20")
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY_DEBUG ${CMAKE_CURRENT_SOURCE_DIR}/../bin)
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY_RELEASE ${CMAKE_CURRENT_SOURCE_DIR}/../bin)
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY_DEBUG ${CMAKE_CURRENT_SOURCE_DIR}/../python/reneu/lib)
@@ -52,14 +50,19 @@ find_package(BLAS REQUIRED)
 find_package(PythonInterp 3 REQUIRED)
 find_package(PythonLibs 3 REQUIRED)
 find_package(Numpy REQUIRED)
-#find_package(Python3 REQUIRED COMPONENTS Numpy)
+# find_package(Python3 REQUIRED COMPONENTS Numpy)
 find_package(pybind11 REQUIRED)
 find_package(xtensor REQUIRED)
 find_package(xtensor-python REQUIRED)
 find_package(xtensor-blas REQUIRED)
-# find_package(tsl REQUIRED)
+#find_package(tsl_robin_map REQUIRED)
+# find_package(tsl-robin-map REQUIRED)
 # find_package(TBB REQUIRED)
 
+set(RENEU_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/include)
+include_directories(${NUMPY_INCLUDE_DIR} ${RENEU_INCLUDE_DIR} 
+                        ${CONDA_PREFIX}/include ${BOOST_INCLUDEDIR})
+
 pybind11_add_module(skeleton ${CMAKE_CURRENT_SOURCE_DIR}/skeleton.cpp)
 pybind11_add_module(segmentation ${CMAKE_CURRENT_SOURCE_DIR}/segmentation.cpp)
 pybind11_add_module(synapse ${CMAKE_CURRENT_SOURCE_DIR}/synapse.cpp)
@@ -71,10 +74,8 @@ target_link_libraries(skeleton PRIVATE ${BLAS_LIBRARIES})
 
 message("boost libarries: ${Boost_LIBRARIES}")
 target_include_directories(segmentation PUBLIC ${NUMPY_INCLUDE_DIR} ${RENEU_INCLUDE_DIR})
-target_link_libraries(segmentation PRIVATE ${Boost_LIBRARIES} tsl::robin_map)
-
-# target_link_libraries(segmentation ${Boost_LIBRARIES} )
-# target_link_libraries(segmentation "${Boost_LIBRARIES}/libboost_serialization.dylib" )
+#target_link_libraries(segmentation PRIVATE ${Boost_LIBRARIES} tsl::robin_map)
+target_link_libraries(segmentation PRIVATE ${Boost_LIBRARIES})
 
 # options
 option(BUILD_TESTS "build test suite" OFF)

diff --git a/cpp/include/reneu/segmentation/preprocess.hpp b/cpp/include/reneu/segmentation/preprocess.hpp
@@ -4,6 +4,7 @@
 
 #include "reneu/type_aliase.hpp"
 #include <xtensor/xview.hpp>
+#include "reneu/utils/print.hpp"
 
 namespace reneu{
 
@@ -15,18 +16,18 @@ void remove_contact_1d(SEG1D seg1d){
         if(seg1d(x)>0 && seg1d(x-1)>0 && seg1d(x)!=seg1d(x-1)){
             seg1d(x) = 0;
             seg1d(x-1) = 0;
-            std::cout<<x<<", ";
+            // std::cout<<x<<", ";
         }
     }
-    std::cout<<std::endl;
+    // std::cout<<std::endl;
 }
 
 /**
  * @brief remove the object boundary voxel if it contacted another object
  * 
  * @param seg the input plain segmentation
  */
-void remove_contact(Segmentation&& seg){
+auto remove_contact(PySegmentation& seg){
     // z direction
     for(std::size_t y=0; y<seg.shape(1); y++){
         for(std::size_t x=0; x<seg.shape(2); x++){
@@ -47,14 +48,7 @@ void remove_contact(Segmentation&& seg){
             remove_contact_1d(xt::view(seg, z, y, xt::all()));
         }
     }
-
-}
-
-auto py_remove_contact(PySegmentation& pySeg){
-    remove_contact(pySeg);
-    // remove_contact(std::forward(pySeg));
-    // return std::forward(pySeg);
-    // return pySeg;
+    // reneu::utils::print_array(seg);
 }
 
 /* 
@@ -119,9 +113,9 @@ void fill_background_with_affinity_guidance2d(
     }
 }
 
-template<class SEG, class AFFS, class AFF_EDGE>
 void fill_background_with_affinity_guidance(
-        SEG& seg, const AFFS& affs, const AFF_EDGE& threshold){
+        PySegmentation& seg, const PyAffinityMap& affs, 
+        const aff_edge_t& threshold){
     for(size_t z = 0; z<seg.shape(0); z++){
         auto seg2d = xt::view(seg, z, xt::all(), xt::all());
         auto affx2d = xt::view(affs, 0, z, xt::all(), xt::all());
@@ -130,9 +124,5 @@ void fill_background_with_affinity_guidance(
     }
 }
 
-auto py_fill_background_with_affinity_guidance(PySegmentation& pySeg, const PyAffinityMap& pyAffs, const aff_edge_t& threshold){
-    fill_background_with_affinity_guidance(pySeg, pyAffs, threshold);
-    return pySeg;
-}
 
 } // namespace reneu
diff --git a/cpp/include/reneu/segmentation/priority_queue.hpp b/cpp/include/reneu/segmentation/priority_queue.hpp
@@ -6,30 +6,11 @@
 
 namespace reneu{
 
-struct EdgeInQueue{
-    segid_t segid0;
-    segid_t segid1;
-    aff_edge_t aff;
-    size_t version;
-
-    // constructor for emplace operation
-    EdgeInQueue(const segid_t& segid0_, const segid_t& segid1_, const aff_edge_t& aff_, const std::size_t& version_):
-        segid0(segid0_), segid1(segid1_), aff(aff_), version(version_){}
-
-    bool operator<(const EdgeInQueue& other) const {
-        return aff < other.aff;
-    }
-};
-// struct LessThanByAff{
-//     bool operator()(const EdgeInQueue& lhs, const EdgeInQueue& rhs) const {
-//         return lhs.aff < rhs.aff;
-//     }
-// };
-// using PriorityQueue = std::priority_queue<EdgeInQueue, std::vector<EdgeInQueue>, std::less<EdgeInQueue>>;
 
+template<class E>
 class PriorityQueue{
 private:
-    std::vector<EdgeInQueue> _edges;
+    std::vector<E> _edges;
 
 public:
     PriorityQueue(): _edges({}) { }

diff --git a/cpp/include/reneu/segmentation/region_graph.hpp b/cpp/include/reneu/segmentation/region_graph.hpp
@@ -30,6 +30,30 @@ namespace reneu{
 
 class RegionGraph;
 
+struct EdgeInHeap{
+    segid_t segid0;
+    segid_t segid1;
+    aff_edge_t aff;
+    size_t version;
+
+    // constructor for emplace operation
+    EdgeInHeap(
+        const segid_t& segid0_, const segid_t& segid1_, 
+        const aff_edge_t& aff_, const std::size_t& version_):
+        segid0(segid0_), segid1(segid1_), aff(aff_), version(version_){}
+
+    bool operator<(const EdgeInHeap& other) const {
+        return aff < other.aff;
+    }
+};
+// struct LessThanByAff{
+//     bool operator()(const EdgeInQueue& lhs, const EdgeInQueue& rhs) const {
+//         return lhs.aff < rhs.aff;
+//     }
+// };
+// using PriorityQueue = std::priority_queue<EdgeInQueue, std::vector<EdgeInQueue>, std::less<EdgeInQueue>>;
+
+
 class RegionEdge{
 public:
 // we use the same type for both value for type stability in the average division. 
@@ -170,7 +194,7 @@ inline void _accumulate_edge(const segid_t& segid0, const segid_t& segid1, const
 
 
 auto _build_priority_queue (const aff_edge_t& threshold) const {
-    PriorityQueue heap;
+    PriorityQueue<EdgeInHeap> heap;
     for(const auto& [segid0, neighbors0] : _segid2neighbor){
         for(const auto& [segid1, edgeIndex] : neighbors0){
             // the connection is bidirectional, 
@@ -192,7 +216,7 @@ auto _build_priority_queue (const aff_edge_t& threshold) const {
 }
 
 auto _merge_segments(segid_t& segid0, segid_t& segid1, const RegionEdge& edge,
-            PriorityQueue& heap, 
+            PriorityQueue<EdgeInHeap>& heap, 
             const aff_edge_t& affinityThreshold){
 
     // always merge object with less neighbors to more neighbors

diff --git a/cpp/include/reneu/segmentation/region_graph_chunk.hpp b/cpp/include/reneu/segmentation/region_graph_chunk.hpp
@@ -65,7 +65,7 @@ inline auto _frozen_neighbor_flag(const segid_t& segid0, const aff_edge_t& thres
 
 
 auto _build_priority_queue (const aff_edge_t& threshold) const {
-    PriorityQueue heap;
+    PriorityQueue<EdgeInHeap> heap;
     for(const auto& [segid0, neighbors0] : _segid2neighbor){
         for(const auto& [segid1, edgeIndex] : neighbors0){
             // the connection is bidirectional,