Files for cubert.example

.devcontainer/devcontainer.json

@@ -0,0 +1,64 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/cpp
+{
+
+
+	// docker build commands are to create the docker image
+	// docker build -t docker_image_name -f dockerfile_name .
+	//docker network is needed to assign ip address to docker container
+	// docker network create --driver bridge --subnet 192.168.200.0/24 my_custom_network
+
+
+	// make sure to uncomment the image that is desired for development
+	"image": "hypertools_sfm:latest" ,
+	// "image": "hypertools_cubert:latest" ,
+	// "image": "hypertools_4_2_cuda:latest" ,
+	// "image": "hypertools_current_opencv:latest" ,
+	// "image": "hypertools_cubert_cuda:latest" ,
+	// "image": "hypertools_cuda_ml:latest" ,
+
+
+	"mounts": [
+
+		// below two mounts are for visualization on windows machine if there are issues with wsl
+		// "source=/run/desktop/mnt/host/wslg/.X11-unix,target=/tmp/.X11-unix,type=bind,consistency=cached",
+		// "source=/run/desktop/mnt/host/wslg,target=/mnt/wslg,type=bind,consistency=cached",
+
+		// below is used for visualization on ubuntu machine if there are issues with visualization
+		// "source=/tmp/.X11-unix,target=/tmp/.X11-unix,type=bind,consistency=cached",
+
+		// below mounts hyperimages in container
+		"source=${localWorkspaceFolder}/../HyperImages,target=/workspaces/HyperImages,type=bind,consistency=cached"
+	  ],
+
+
+	// "remoteEnv": {"DISPLAY":":0"},
+
+	 //below is used when cuda image is being used
+	 /*
+	 "runArgs": [
+	 	"--gpus=all", // used for cuda images
+	 //"--network=host", //used to connect to camera on ubunutu, assumes host has ethernet interface ip of 192.168.20.x, subnet of 255.255.255.0
+	       //testing below for getting camera working with docker in wsl	
+	//	 "-p", "9392:9392", "--network=my_custom_network", "ip=192.168.200.20"
+	       //note: subnet needs to be 255.255.255.0, camera ip is 127.0.0.1	
+	 ],*/
+
+	 "customizations": {
+		// Configure properties specific to VS Code.
+		"vscode": {
+		  // Add the IDs of extensions you want installed when the container is created.
+		  "extensions": [
+			"ms-python.python",
+			"GitHub.copilot",
+			"ms-vscode.cmake-tools",
+			"ms-azuretools.vscode-docker",
+			"streetsidesoftware.code-spell-checker",
+			"ms-vscode.cpptools",
+			"ms-vscode.cpptools-extension-pack"
+
+			]
+		}
+	  }
+
+}

.gitignore

@@ -0,0 +1,43 @@
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+#build directory
+**/build/*
+
+# temp ui 
+*.ui~
+
+*.json
+*.DS_Store
+*.log
+*.pyc

CMakeLists.txt

@@ -1,87 +1,90 @@
 ##############################################################################
 # CMAKE CONFIGURATION
 ##############################################################################
-cmake_minimum_required(VERSION 3.5.1 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.16)
+set(CMAKE_CXX_STANDARD 17)
 
 # set project name
-project(iTree3DMap VERSION 1.0.0)
+project(iTree3DMap C CXX)
 
 # set build type = Debug mode
-set(CMAKE_BUILD_TYPE Release)
-
-message("\n" "=========================================")
-message("Project: ${PROJECT_NAME} ")
-message("=========================================")
+# set(CMAKE_BUILD_TYPE Release)
 
 # set the include directive in the same project folder
-set(CMAKE_INCLUDE_CURRENT_DIR ON)
+# set(CMAKE_INCLUDE_CURRENT_DIR ON)
 
 # set corresponding package directories
-set(OpenCV_DIR /opt/opencv-3.4.1/build)
-set(PCL_DIR /opt/pcl-1.8.1/build)
+find_package(OpenCV REQUIRED)
+find_package(Ceres REQUIRED)
+find_package(PCL REQUIRED)
+find_package(VTK 7.1 REQUIRED)
+
+# set(OpenCV_DIR /opt/opencv-3.4.1/build)
+# set(PCL_DIR /opt/pcl-1.8.1/build)
 
 # set the CMP0074 policy to old behavior (disable warnings)
-cmake_policy(SET CMP0074 OLD)
+# cmake_policy(SET CMP0074 OLD)
 
 # Include dependencies of pcl 1.8.1 in project directorie
-set(CMAKE_MODULE_PATH ${PCL_DIR}/../cmake/Modules)
+# set(CMAKE_MODULE_PATH ${PCL_DIR}/../cmake/Modules)
 
 # set cmake for use std c++11 and output executable folder to bin
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-set(EXECUTABLE_OUTPUT_PATH ${CMAKE_BINARY_DIR}/bin)
+# set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++17")
+# set(EXECUTABLE_OUTPUT_PATH ${CMAKE_BINARY_DIR}/bin)
 
 # set turn off the output rule messages of cmake
-set_property(GLOBAL PROPERTY RULE_MESSAGES OFF)
+# set_property(GLOBAL PROPERTY RULE_MESSAGES OFF)
 
 ##############################################################################
 # PACKAGES
 ##############################################################################
-message("Finding packages...")
-
-message("***********************")
-message("OpenCV PACKAGE")
-message("***********************")
-
-set(OpenCV_Components core highgui features2d xfeatures2d calib3d imgcodecs imgproc)
-find_package(OpenCV 3.4.1 REQUIRED PATHS ${OPENCV_DIR} COMPONENTS ${OpenCV_Components})
-if(OpenCV_FOUND)
-    message(STATUS "OpenCV status:")
-    message(STATUS "    version: ${OpenCV_VERSION}")
-else()
-    message(FATAL_ERROR "    ERROR: OpenCV ${OpenCV_VERSION} not found")
-endif()
-
-message("***********************")
-message("Ceres PACKAGE")
-message("***********************")
-
-find_package(Ceres 1.13.0 REQUIRED)
-if(Ceres_FOUND)
-   message(STATUS "Ceres library status:")
-   message(STATUS "    version: ${CERES_VERSION}")
-else()
-   message(FATAL_ERROR "    ERROR: Ceres ${CERES_VERSION} not found")
-endif()
-
-message("***********************")
-message("PCL PACKAGE")
-message("***********************")
-
-find_package(PCL 1.8.1 REQUIRED PATHS ${PCL_DIR})
-if(PCL_FOUND)
-    message(STATUS "PCL library status:")
-    message(STATUS "    version: ${PCL_VERSION}")
-else()
-    message(FATAL_ERROR "    ERROR: PCL not found")
-endif()
+# message("Finding packages...")
+
+# message("***********************")
+# message("OpenCV PACKAGE")
+# message("***********************")
+
+# set(OpenCV_Components core highgui features2d xfeatures2d calib3d imgcodecs imgproc)
+# find_package(OpenCV REQUIRED)
+# if(OpenCV_FOUND)
+#     message(STATUS "OpenCV status:")
+#     message(STATUS "    version: ${OpenCV_VERSION}")
+# else()
+#     message(FATAL_ERROR "    ERROR: OpenCV ${OpenCV_VERSION} not found")
+# endif()
+
+# message("***********************")
+# message("Ceres PACKAGE")
+# message("***********************")
+
+# find_package(Ceres REQUIRED)
+# if(Ceres_FOUND)
+#    message(STATUS "Ceres library status:")
+#    message(STATUS "    version: ${CERES_VERSION}")
+# else()
+#    message(FATAL_ERROR "    ERROR: Ceres ${CERES_VERSION} not found")
+# endif()
+
+# message("***********************")
+# message("PCL PACKAGE")
+# message("***********************")
+
+# find_package(PCL REQUIRED)
+# if(PCL_FOUND)
+#     message(STATUS "PCL library status:")
+#     message(STATUS "    version: ${PCL_VERSION}")
+# else()
+#     message(FATAL_ERROR "    ERROR: PCL not found")
+# endif()
 
 ##############################################################################
 # HEADERS
 ##############################################################################
 include_directories(${OpenCV_INCLUDE_DIRS})
 include_directories(${PCL_INCLUDE_DIRS})
 include_directories(${CERES_INCLUDE_DIRS})
-include(CheckFunctionExists)
+include(${VTK_USE_FILE})
+# include(CheckFunctionExists)
 
 # Use the compile definitions defined in PCL
 #add_definitions(${PCL_DEFINITIONS})
@@ -92,6 +95,7 @@ include(CheckFunctionExists)
 link_directories(${OpenCV_LIBRARIES})
 link_directories(${PCL_LIBRARY_DIRS})
 link_directories(${CERES_LIBRARIES})
+link_directories(${VTK_LIBRARIES})
 
 ##############################################################################
 # SOURCE CODE
@@ -117,11 +121,12 @@ add_executable(${PROJECT_NAME} ${SFM_HEADER} ${SFM_SOURCE} ${SEGMENT_HEADER} ${S
 ##############################################################################
 # TARGET LIBRARIES
 ##############################################################################
-set(OpenCV_LIBRARIES opencv_core opencv_highgui opencv_features2d opencv_calib3d
-                     opencv_imgproc opencv_imgcodecs opencv_xfeatures2d)
+# set(OpenCV_LIBRARIES opencv_core opencv_highgui opencv_features2d opencv_calib3d
+#                      opencv_imgproc opencv_imgcodecs opencv_xfeatures2d)
+
+target_link_libraries(${PROJECT_NAME} ${OpenCV_LIBRARIES} ${PCL_LIBRARIES} ${CERES_LIBRARIES} ${VTK_LIBRARIES})
 
-target_link_libraries(${PROJECT_NAME} ${OpenCV_LIBRARIES} ${PCL_LIBRARIES} ${CERES_LIBRARIES})
 
-message("=========================================")
-message("Project: ${PROJECT_NAME} COMPILED WITH CMAKE " ${CMAKE_VERSION})
-message("=========================================")
+# message("=========================================")
+# message("Project: ${PROJECT_NAME} COMPILED WITH CMAKE " ${CMAKE_VERSION})
+# message("=========================================")

Dockerfile

@@ -0,0 +1,16 @@
+FROM hypertools_4_2:latest
+
+RUN apt-get update 
+
+RUN apt-get install -y \
+    python3-pip \
+    libceres-dev 
+
+
+RUN apt update && apt-get update && apt-get install -y \
+    libpcl-dev \
+    libvtk7-dev
+
+    # gdb \
+    # gdbserver
+

README.md

@@ -16,36 +16,33 @@ A simple incremental SFM pipeline for 3D reconstruction of a tree with bundle ad
 
 <img src="./imgs/example.png" align="center" height="500" width="950"><br>
 
-### Resources
 
-* Homepage: <http://opencv.org>
-* Docs: <http://docs.opencv.org/master/>
 
-## Build 
-
-To build use CMake minimum required 3.5.1 : https://github.com/Kitware/CMake
-
-### Prerequisite
-- OpenCV 3.4.1: https://github.com/opencv/opencv/tree/3.4.1
-- PCL 1.8.1: https://github.com/PointCloudLibrary/pcl/tree/pcl-1.8.1
 
 ### Compilation
 * Set "YOUR OWN" PCL Build DIR in CMakeList.txt e.g: **/opt/pcl-1.8.1/build** and save it.
 * Set "YOUR OWN" OpenCV Build DIR in CMakeList.txt e.g: **/opt/opencv-3.4.1/build** and save it.
 * Create a "build" folder
 
-in the main folder:
+in the build folder:
 
-    cd /build  
-    cmake ../
+    cd build/  
+    cmake ..
     make
+    ./iTree3DMap
 
-### Test
-	cd /build/bin
-	./iTree3DMap
 
-*Note:*
-If OpenCV is not installed (just compiled). please set the path to the current build directory in the CMakeList.txt file.
 
 
 
+### debug 
+cmake -DCMAKE_BUILD_TYPE=Debug ..
+make
+file ./iTree3DMap
+apt-get update && apt-get install -y gdb gdbserver
+gdb ./iTree3DMap
+break main  # adds breakpoint
+run
+continue 
+info locals infor args
+quit # quit gdb

main.cpp

@@ -47,7 +47,7 @@ int main(int argc, char **argv){
   STEP X: INPUT IMAGES
   **************************/
   StructFromMotion sf;    
-  bool success = sf.imagesLOAD("/home/daniel/Proyecto-grado-3D-recons-master/data/temple");
+  bool success = sf.imagesLOAD("../data/temple");
   if(not success){
       std::cerr << "Error: set of images is not valid." << std::endl;
       return -1;
@@ -56,7 +56,7 @@ int main(int argc, char **argv){
   /*************************
   STEP X: INPUT CAMERA FILE
   **************************/
-  success = sf.getCameraMatrix("/home/daniel/Proyecto-grado-3D-recons-master/data/temple/camera_calibration_template.xml");
+  success = sf.getCameraMatrix("../data/temple/camera_calibration_template.xml");
   if(not success){
       std::cerr << "Error: camera calibration file is not valid." << std::endl;
       return -1;

src/BundleAdjustment.cpp

@@ -1,4 +1,4 @@
-#include "include/BundleAdjustment.h"
+#include "../include/BundleAdjustment.h"
 #include <ceres/ceres.h>
 #include <ceres/rotation.h>
 

src/DendrometryE.cpp

@@ -1,4 +1,4 @@
-#include "include/DendrometryE.h"
+#include "../include/DendrometryE.h"
 
 void Dendrometry::estimate(pcl::PointCloud<pcl::PointXYZRGB>::Ptr& cloudPCL){
 

src/Segmentation.cpp

@@ -1,4 +1,4 @@
-#include "include/Segmentation.h"
+#include "../include/Segmentation.h"
 
 void Segmentation::color_based_growing_segmentation(){