Patches to make latest AliceVision (as Sept 13 2021) works with rtabmap library (no crash, all unwrapping methods working)

alicevision_0f6115b.patch

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 3a5c91d30..015421d2f 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -343,7 +343,7 @@ find_package(Eigen3 3.3 REQUIRED)
 if(Eigen3_FOUND OR EIGEN3_FOUND)
   # message(STATUS "EIGEN_INCLUDE_DIR: ${EIGEN_INCLUDE_DIR}")
   # See https://eigen.tuxfamily.org/dox/group__TopicUnalignedArrayAssert.html
-  set(AV_EIGEN_DEFINITIONS -DEIGEN_MAX_ALIGN_BYTES=0 -DEIGEN_MAX_STATIC_ALIGN_BYTES=0)
+  #set(AV_EIGEN_DEFINITIONS -DEIGEN_MAX_ALIGN_BYTES=0 -DEIGEN_MAX_STATIC_ALIGN_BYTES=0)
 else()
   message(FATAL_ERROR " EIGEN NOT FOUND. EIGEN_INCLUDE_DIR: ${EIGEN_INCLUDE_DIR}")
 endif()
diff --git a/src/aliceVision/mesh/Texturing.cpp b/src/aliceVision/mesh/Texturing.cpp
index 7891b146c..e40be063b 100644
--- a/src/aliceVision/mesh/Texturing.cpp
+++ b/src/aliceVision/mesh/Texturing.cpp
@@ -961,7 +961,7 @@ void Texturing::replaceMesh(const std::string& otherMeshPath, bool flipNormals)
     // keep previous mesh/visibilities as reference
     Mesh* refMesh = mesh;
     // set pointers to null to avoid deallocation by 'loadFromObj'
-    mesh->pointsVisibilities.resize(0);
+    //mesh->pointsVisibilities.resize(0);
     mesh = nullptr;
     
     // load input obj file
diff --git a/src/aliceVision/numeric/numeric.hpp b/src/aliceVision/numeric/numeric.hpp
index 1475c13e9..7a187fe05 100644
--- a/src/aliceVision/numeric/numeric.hpp
+++ b/src/aliceVision/numeric/numeric.hpp
@@ -10,17 +10,17 @@
 
 // AliceVision does not support Eigen with alignment,
 // So ensure Eigen is used with the correct flags.
-#ifndef EIGEN_MAX_ALIGN_BYTES
-#error "EIGEN_MAX_ALIGN_BYTES is not defined"
-#elif EIGEN_MAX_ALIGN_BYTES != 0
-#error "EIGEN_MAX_ALIGN_BYTES is defined but not 0"
-#endif
-
-#ifndef EIGEN_MAX_STATIC_ALIGN_BYTES
-#error "EIGEN_MAX_STATIC_ALIGN_BYTES is not defined"
-#elif EIGEN_MAX_STATIC_ALIGN_BYTES != 0
-#error "EIGEN_MAX_STATIC_ALIGN_BYTES is defined but not 0"
-#endif
+//#ifndef EIGEN_MAX_ALIGN_BYTES
+//#error "EIGEN_MAX_ALIGN_BYTES is not defined"
+//#elif EIGEN_MAX_ALIGN_BYTES != 0
+//#error "EIGEN_MAX_ALIGN_BYTES is defined but not 0"
+//#endif
+
+//#ifndef EIGEN_MAX_STATIC_ALIGN_BYTES
+//#error "EIGEN_MAX_STATIC_ALIGN_BYTES is not defined"
+//#elif EIGEN_MAX_STATIC_ALIGN_BYTES != 0
+//#error "EIGEN_MAX_STATIC_ALIGN_BYTES is defined but not 0"
+//#endif
 
 
 //--
diff --git a/src/aliceVision/sfmData/SfMData.cpp b/src/aliceVision/sfmData/SfMData.cpp
index f6822215a..7e4580135 100644
--- a/src/aliceVision/sfmData/SfMData.cpp
+++ b/src/aliceVision/sfmData/SfMData.cpp
@@ -252,6 +252,11 @@ void SfMData::setPose(const View& view, const CameraPose& absolutePose)
   throw std::runtime_error("SfMData::setPose: dependant view pose not part of an initialized rig.");
 }
 
+void SfMData::setAbsolutePose(IndexT poseId, const CameraPose& pose)
+{
+  _poses[poseId] = pose;
+}
+
 
 void SfMData::combine(const SfMData& sfmData)
 {
diff --git a/src/aliceVision/sfmData/SfMData.hpp b/src/aliceVision/sfmData/SfMData.hpp
index 9ea7da88d..8d24d6e7b 100644
--- a/src/aliceVision/sfmData/SfMData.hpp
+++ b/src/aliceVision/sfmData/SfMData.hpp
@@ -24,13 +24,13 @@ namespace aliceVision {
 namespace sfmData {
 
 /// Define a collection of View
-using Views = HashMap<IndexT, std::shared_ptr<View> >;
+using Views = std::map<IndexT, std::shared_ptr<View> >;
 
 /// Define a collection of Pose (indexed by view.getPoseId())
 using Poses = HashMap<IndexT, CameraPose>;
 
 /// Define a collection of IntrinsicParameter (indexed by view.getIntrinsicId())
-using Intrinsics = HashMap<IndexT, std::shared_ptr<camera::IntrinsicBase> >;
+using Intrinsics = std::map<IndexT, std::shared_ptr<camera::IntrinsicBase> >;
 
 /// Define a collection of landmarks are indexed by their TrackId
 using Landmarks = HashMap<IndexT, Landmark>;
@@ -478,10 +478,7 @@ public:
    * @param[in] poseId The given poseId
    * @param[in] pose The given pose
    */
-  void setAbsolutePose(IndexT poseId, const CameraPose& pose)
-  {
-    _poses[poseId] = pose;
-  }
+  void setAbsolutePose(IndexT poseId, const CameraPose& pose);
 
   /**
    * @brief Erase yhe pose for the given poseId

geogram_8b2ae61.patch

diff --git a/src/lib/geogram/parameterization/mesh_atlas_maker.cpp b/src/lib/geogram/parameterization/mesh_atlas_maker.cpp
index e13f028..5ba7b95 100644
--- a/src/lib/geogram/parameterization/mesh_atlas_maker.cpp
+++ b/src/lib/geogram/parameterization/mesh_atlas_maker.cpp
@@ -176,6 +176,7 @@ namespace {
 	    index_t total_f = mesh_.facets.nb();
 	    index_t param_f = 0;
 	    segment_mesh();
+
 	    for(index_t f: mesh_.facets) {
 		while(chart_[f] >= chart_queue_.size()) {
 		    chart_queue_.push_back(Chart(mesh_, chart_[f]));
@@ -360,7 +361,7 @@ namespace {
 			    index_t f2=mesh_.facet_corners.adjacent_facet(c);
 			    if(
 				f2 != NO_FACET &&
-				chart_[f2] != nb_charts_ &&
+				chart_[f2] == index_t(-1) &&
 				Geom::mesh_unsigned_normal_angle(
 				    mesh_,cur_f,f2) < hard_angles_threshold_
 			    ) {
diff --git a/src/lib/geogram/parameterization/mesh_param_packer.cpp b/src/lib/geogram/parameterization/mesh_param_packer.cpp
index e9841b0..e250874 100755
--- a/src/lib/geogram/parameterization/mesh_param_packer.cpp
+++ b/src/lib/geogram/parameterization/mesh_param_packer.cpp
@@ -1051,20 +1051,20 @@ namespace GEO {
 	vector<Chart> charts;
 	index_t nb_charts=0;
 	for(index_t f: mesh.facets) {
-	    nb_charts = std::max(nb_charts, chart_attr_[f]);
+	    nb_charts = (index_t)std::max((int)nb_charts, (int)chart_attr_[f]);
 	}
 	++nb_charts;
 
 	for(index_t i=0; i<nb_charts; ++i) {
 	    charts.push_back(Chart(mesh, i));
 	}
-	
 	for(index_t f: mesh.facets) {
-	    charts[chart_attr_[f]].facets.push_back(f);
+	    if(chart_attr_[f] != (index_t)-1)
+	        charts[chart_attr_[f]].facets.push_back(f);
 	}
 
 	Logger::out("Packer") << "Packing " << charts.size() << " charts" << std::endl;
-	
+
         // Sanity check
 	for(index_t i=0; i<nb_charts; ++i) {
             if(!chart_is_ok(charts[i], tex_coord_)) {
@@ -1097,6 +1097,7 @@ namespace GEO {
 
 	tex_coord_.unbind();
 	chart_attr_.unbind();
+
     }
 
 
diff --git a/src/lib/geogram/parameterization/mesh_param_validator.cpp b/src/lib/geogram/parameterization/mesh_param_validator.cpp
index 8208e59..c4cd2e0 100644
--- a/src/lib/geogram/parameterization/mesh_param_validator.cpp
+++ b/src/lib/geogram/parameterization/mesh_param_validator.cpp
@@ -182,6 +182,11 @@ namespace GEO {
             } 
         }
 
+        if(facet_scaling.empty()) {
+            printf("chart_scaling failed (chart.id=%d), return NaN\n", chart.id);
+            return NAN;
+        }
+
         // Ignore 1% of the values at each end.
         std::sort(facet_scaling.begin(), facet_scaling.end());
         index_t offset = index_t(double(facet_scaling.size()) * 0.01);
diff --git a/src/lib/geogram/parameterization/mesh_segmentation.cpp b/src/lib/geogram/parameterization/mesh_segmentation.cpp
index 4d53f06..ee03d84 100644
--- a/src/lib/geogram/parameterization/mesh_segmentation.cpp
+++ b/src/lib/geogram/parameterization/mesh_segmentation.cpp
@@ -261,11 +261,16 @@ namespace GEO {
 	    if(chart_id[f] == new_chart_1.id) {
 		new_chart_1.facets.push_back(f);
 		++nb1;
-	    } else {
+	    } else if(chart_id[f] == new_chart_2.id) {
+
 		geo_assert(chart_id[f] == new_chart_2.id);
 		new_chart_2.facets.push_back(f);
 		++nb2;
 	    }
+	    else
+	    {
+	        printf("Ignoring face %d from chart (chart_id = %d) \n", f, chart_id[f]);
+	    }
 	}
 
 	if(verbose) {