| Title: | Rock Mass Structural Analysis from 3D Mesh of Point Cloud |
|---|---|
| Description: | Provides functions to extract joint planes from 3D triangular mesh derived from point cloud and makes data available for structural analysis. |
| Authors: | Riccardo Campana [aut, cre], Jeffrey R. Webber [ctb] |
| Maintainer: | Riccardo Campana <[email protected]> |
| License: | GPL |
| Version: | 1.0 |
| Built: | 2024-11-02 04:42:54 UTC |
| Source: | https://github.com/cran/JFM |
Provides functions to extract joint planes from 3D triangular mesh and makes data available for structural analysis. Below compute_plane_normal function description an example test over all function is done. In your package directory you will find in extdata dir an example of point_cloud.txt file and in test folder two R scripts a test.R file to process point_cloud.txt file and a JFM_workflow.R generic workflow script.
Riccardo Campana <[email protected]>
This function reads a XYZRGB text file, requires a search radius in meters and an output file name to save the resulting mesh. for data format see file in package extdata folder
build_3d_mesh(path2myXYZRGBtxt, search_radius, file_name)build_3d_mesh(path2myXYZRGBtxt, search_radius, file_name)
path2myXYZRGBtxt |
Path to the XYZRGB.txt input file |
search_radius |
Path to the XYZRGB.txt input file |
file_name |
name of the output .ply mesh file |
A 3D triangular mesh
## Not run: path2myXYZRGBtxt<-system.file("extdata", "test.txt", package = "JFM") file_name<- "test" mesh3d<-build_3d_mesh(path2myXYZRGBtxt,0.5,file_name) ## End(Not run)## Not run: path2myXYZRGBtxt<-system.file("extdata", "test.txt", package = "JFM") file_name<- "test" mesh3d<-build_3d_mesh(path2myXYZRGBtxt,0.5,file_name) ## End(Not run)
This function calculates joint orientation with the least square method selecting vertexes of each facet plane
calculate_joints(vertici_tr, indici_tri, normal_from_wild)calculate_joints(vertici_tr, indici_tri, normal_from_wild)
vertici_tr |
list of facets vertexes coordinates ("vb property of mesh3d object") |
indici_tri |
list of facets indexes ("it property of mesh3d object") |
normal_from_wild |
matrix of data resulting from wildfire search |
a matrix of least square plane for each joint
## Not run: mesh3d<-build_3d_mesh(path2myXYZRGBtxt,0.5,file_name) normali_recalc<-Rcpp_wildfire_search(7,normals[,1:3],neighbours) joint_list_Cpp<-calculate_joints(mesh3d,normali_recalc) ## End(Not run)## Not run: mesh3d<-build_3d_mesh(path2myXYZRGBtxt,0.5,file_name) normali_recalc<-Rcpp_wildfire_search(7,normals[,1:3],neighbours) joint_list_Cpp<-calculate_joints(mesh3d,normali_recalc) ## End(Not run)
This function calculates the area of each cluster of facets belonging to the same plane
calculate_joints_area(normal_from_wild)calculate_joints_area(normal_from_wild)
normal_from_wild |
matrix of data resulting from wildfire search |
a list of the area of each plane
## Not run: normali_recalc<-Rcpp_wildfire_search(7,normals[,1:3],neighbours) calculate_joints(mesh3d,normali_recalc) ## End(Not run)## Not run: normali_recalc<-Rcpp_wildfire_search(7,normals[,1:3],neighbours) calculate_joints(mesh3d,normali_recalc) ## End(Not run)
This function returns a matrix of the three component vector of the normal of each facet.
compute_facets_normal(vertici_tr, indici_tri)compute_facets_normal(vertici_tr, indici_tri)
vertici_tr |
list of facets vertexes coordinates ("vb property of mesh3d object") |
indici_tri |
list of facets indexes ("it property of mesh3d object") |
matrix of the three component of the normal vector and area of each face
## Not run: indici_tri<-t(mesh3d[['it']]) vertici_tr<-t(mesh3d[["vb"]]) normals<-compute_facets_normal(vertici_tr,indici_tri) ## End(Not run)## Not run: indici_tri<-t(mesh3d[['it']]) vertici_tr<-t(mesh3d[["vb"]]) normals<-compute_facets_normal(vertici_tr,indici_tri) ## End(Not run)
returns the sum of the area of facets belonging to the same plane
tr_area |
a matrix with the first column facet area and second column the ID of plane it belows |
id_fam_no_zero |
the list of planes ID |
the sum of the area of facets belonging to the same plane given tr_area and id_fam_no_zero
returns the least square plane from the vertexes of facets of the same plane (nested in calculate_joints function)
compute_plane_normal(it_id_plane_points, vb_facets, id_fam_no_zero)compute_plane_normal(it_id_plane_points, vb_facets, id_fam_no_zero)
it_id_plane_points |
the "it"property of mesh object binded with ID column of widfire search |
vb_facets |
the vb property of mesh object (vertexes coordinates) |
id_fam_no_zero |
the list of planes ID |
returns the least square plane from the vertexes of facets of the same plane given it_id_plane_points
the list of planes ID id_fam_no_zero, the matrix of vertexes coordinates vb_facets
#This is an example of workflow script in test folder path2myXYZRGBtxt<-system.file("test", "test.txt", package = "JFM") file_name<- "test" mesh3d<-build_3d_mesh(path2myXYZRGBtxt,0.5,paste0(tempdir(),"/",file_name)) vertici_tr<-t(mesh3d[["vb"]]) indici_tri<-t(mesh3d[['it']]) neighbours<-find_neighbours_rcpp(indici_tri) ### find neighbours of each triangle facet using a Rcpp function neighbours<-find_neighbours_rcpp(indici_tri) ### or a hybrid R-Rcpp function #### core number to dedicate to computational processes; check with #### detectCores() function how many cores your pc owns require("parallel") detectCores() ### use only 2 cores no_cores <- 2 neighbours<-findNeighbourFacets(no_cores,indici_tri) ### compute normal of each triangle facet normals<-compute_facets_normal(vertici_tr,indici_tri) ### apply wildfire search normali_recalc<-Rcpp_wildfire_search(7,normals[,1:3],neighbours) ### plot search result and if not satisfied repeat search increasing/decreasing tolerance angle plotrand_col_planes(mesh3d,normali_recalc) ### calculate least square plane for each group of facets joint_list_Cpp<-calculate_joints(vertici_tr,indici_tri,normali_recalc) ### calculate area for each group of facets val_area<-calculate_joints_area(normali_recalc) ### extract pole maxima setting your minimum contour density ### and area to filter data, plot and save them poles_maxima<-plot_joint_poles(normali_recalc,joint_list_Cpp, val_area,paste0(tempdir(),"/",file_name),0.3,1) ##### plot and save great circle of pole maxima azi_dip_maxima<-plot_joint_great_circles(poles_maxima, paste0(tempdir(),"/",file_name)) ### plot colors of pole maxima onto mesh facets plot_maxima2mesh(mesh3d,azi_dip_maxima,normali_recalc,10) remove()#This is an example of workflow script in test folder path2myXYZRGBtxt<-system.file("test", "test.txt", package = "JFM") file_name<- "test" mesh3d<-build_3d_mesh(path2myXYZRGBtxt,0.5,paste0(tempdir(),"/",file_name)) vertici_tr<-t(mesh3d[["vb"]]) indici_tri<-t(mesh3d[['it']]) neighbours<-find_neighbours_rcpp(indici_tri) ### find neighbours of each triangle facet using a Rcpp function neighbours<-find_neighbours_rcpp(indici_tri) ### or a hybrid R-Rcpp function #### core number to dedicate to computational processes; check with #### detectCores() function how many cores your pc owns require("parallel") detectCores() ### use only 2 cores no_cores <- 2 neighbours<-findNeighbourFacets(no_cores,indici_tri) ### compute normal of each triangle facet normals<-compute_facets_normal(vertici_tr,indici_tri) ### apply wildfire search normali_recalc<-Rcpp_wildfire_search(7,normals[,1:3],neighbours) ### plot search result and if not satisfied repeat search increasing/decreasing tolerance angle plotrand_col_planes(mesh3d,normali_recalc) ### calculate least square plane for each group of facets joint_list_Cpp<-calculate_joints(vertici_tr,indici_tri,normali_recalc) ### calculate area for each group of facets val_area<-calculate_joints_area(normali_recalc) ### extract pole maxima setting your minimum contour density ### and area to filter data, plot and save them poles_maxima<-plot_joint_poles(normali_recalc,joint_list_Cpp, val_area,paste0(tempdir(),"/",file_name),0.3,1) ##### plot and save great circle of pole maxima azi_dip_maxima<-plot_joint_great_circles(poles_maxima, paste0(tempdir(),"/",file_name)) ### plot colors of pole maxima onto mesh facets plot_maxima2mesh(mesh3d,azi_dip_maxima,normali_recalc,10) remove()
returns the area of a mesh facet
tr_vertex_coords |
A 3x3 matrix of the coordinates of facet vertexes |
This function finds the rows IDs of neighbours of each mesh facet. It requires a list of facets indexes corresponding to the "it" property of mesh3d object
find_neighbours_rcpp(indici_tr)find_neighbours_rcpp(indici_tr)
indici_tr |
matrix of facets ID the "it" property of a mesh3D |
this function returns the rows IDs of neighbours of each mesh facet given a list of facets indexes indici_tri
indici_tri<-matrix(data = c(1, 2, 3 ,5, 6, 3, 2, 3, 5,7, 8 ,1), nrow = 4,ncol = 3, byrow = TRUE) find_neighbours_rcpp(indici_tri)indici_tri<-matrix(data = c(1, 2, 3 ,5, 6, 3, 2, 3, 5,7, 8 ,1), nrow = 4,ncol = 3, byrow = TRUE) find_neighbours_rcpp(indici_tri)
returns the row indexes of the neighbour facets of a target facet (nested in findNeighbourFacets R function)
find_triangles_rcpp(indici_tr, r)find_triangles_rcpp(indici_tr, r)
indici_tr |
matrix of facets ID the "it" property of a mesh3D |
r |
index of the row of the target facet |
returns the row indexes of the neighbour facets of the facet at r row of indici_tr facet indexes matrix
indici_tri<-matrix(data = c(1, 2, 3 ,5, 6, 3, 2, 3, 5,7, 8 ,1), nrow = 4,ncol = 3, byrow = TRUE) row_index<-1 find_triangles_rcpp (indici_tri,row_index)indici_tri<-matrix(data = c(1, 2, 3 ,5, 6, 3, 2, 3, 5,7, 8 ,1), nrow = 4,ncol = 3, byrow = TRUE) row_index<-1 find_triangles_rcpp (indici_tri,row_index)
This function finds the IDs of each mesh facet It requires number of cores of your pc to use and list of facets indexes corresponding to the "it" property of mesh3d object.
findNeighbourFacets(no_cores, indici_tri)findNeighbourFacets(no_cores, indici_tri)
no_cores |
number of core to use in search computation |
indici_tri |
list of facets indexes ("it property of mesh3d object") |
a matrix of indexes of facets neighbours of target face saved on working dir
## Not run: indici_tri<-t(mesh3d[['it']]) require("parallel") detectCores() no_cores <- detectCores() - 4 ### keep free some cores neighbours<-findNeighbourFacets(no_cores,indici_tri) ## End(Not run)## Not run: indici_tri<-t(mesh3d[['it']]) require("parallel") detectCores() no_cores <- detectCores() - 4 ### keep free some cores neighbours<-findNeighbourFacets(no_cores,indici_tri) ## End(Not run)
returns the coefficients of the least square plane and the relative mean square error
least_square_plane_rcpp(PointsXYZ)least_square_plane_rcpp(PointsXYZ)
PointsXYZ |
matrix of coordinates of point |
returns the coefficients of the least square plane and the relative mean square error of a set of 3d points PointsXYZ
list_xyz<-matrix(data = c(-10.0, -10.0, -15.0 ,10.0, -10.0, -5.0, -10.0, 10.0, 5.0, 10.0, 10.0 ,15.0), nrow = 4,ncol = 3, byrow = TRUE) least_square_plane_rcpp(list_xyz)list_xyz<-matrix(data = c(-10.0, -10.0, -15.0 ,10.0, -10.0, -5.0, -10.0, 10.0, 5.0, 10.0, 10.0 ,15.0), nrow = 4,ncol = 3, byrow = TRUE) least_square_plane_rcpp(list_xyz)
This function loads joint maxima poles, convert them to great circles and plot them on Schmidt stereogram. Data are also saved in working folder.
plot_joint_great_circles(giac_max, file_name)plot_joint_great_circles(giac_max, file_name)
giac_max |
Joint maxima poles returned from plot_joint_poles function |
file_name |
Name of the output data file |
A plot with great circles of joint maxima saved in working dir
## Not run: poles_maxima<-plot_joint_poles(normali_recalc,joint_list_Cpp,val_area,file_name,max_pole,min_area) azi_dip_maxima<-plot_joint_great_circles(poles_maxima, file_name) ## End(Not run)## Not run: poles_maxima<-plot_joint_poles(normali_recalc,joint_list_Cpp,val_area,file_name,max_pole,min_area) azi_dip_maxima<-plot_joint_great_circles(poles_maxima, file_name) ## End(Not run)
This function plots on schmidt stereogram selected joints poles, draws density contour lines and retrieves poles maxima. Selected joints and poles maxima are saved in working folder.
plot_joint_poles( normal_from_wild, planes_mtx, area_ls, file_name, min_dens, plane_area )plot_joint_poles( normal_from_wild, planes_mtx, area_ls, file_name, min_dens, plane_area )
normal_from_wild |
the output matrix resulting from wildfire search |
planes_mtx |
the list of joints output from calculate_plane function |
area_ls |
the list of joints area output from calculate_planes_area function |
file_name |
Name of the output data file containing joint poles |
min_dens |
the minimum density pole value to be plotted |
plane_area |
minimum value of joint area to be considered in plot |
A Schmidt density plot with maxima values of joints
## Not run: normali_recalc<-Rcpp_wildfire_search(7,normals[,1:3],neighbours) joint_list_Cpp<-calculate_joints(mesh3d,normali_recalc) val_area<-calculate_joints_area(normali_recalc) file_name<-"my_out_file" max_pole<-0.3 min_area<-1 poles_maxima<-plot_joint_poles(normali_recalc,joint_list_Cpp,val_area,file_name,max_pole,min_area) ## End(Not run)## Not run: normali_recalc<-Rcpp_wildfire_search(7,normals[,1:3],neighbours) joint_list_Cpp<-calculate_joints(mesh3d,normali_recalc) val_area<-calculate_joints_area(normali_recalc) file_name<-"my_out_file" max_pole<-0.3 min_area<-1 poles_maxima<-plot_joint_poles(normali_recalc,joint_list_Cpp,val_area,file_name,max_pole,min_area) ## End(Not run)
This funtion plots a coloured mesh facets as great circles plot colours
plot_maxima2mesh(mesh_tr, planes_max, normal_from_wild, tol_ang_fam)plot_maxima2mesh(mesh_tr, planes_max, normal_from_wild, tol_ang_fam)
mesh_tr |
an object of type mesh3d |
planes_max |
the output of plot_joint_great_circles function |
normal_from_wild |
the output matrix iresulting from wildfire search |
tol_ang_fam |
a tolerance angle to include joints in the same joint set color |
A plot with great circles of joint maxima
## Not run: azi_dip_maxima<-plot_joint_great_circles(poles_maxima, file_name) plot_maxima2mesh(mesh3d,azi_dip_maxima,normali_recalc,10) ## End(Not run)## Not run: azi_dip_maxima<-plot_joint_great_circles(poles_maxima, file_name) plot_maxima2mesh(mesh3d,azi_dip_maxima,normali_recalc,10) ## End(Not run)
This function returns a 3d plot of mesh where facets of the same plane are of same color.
plotrand_col_planes(mesh_tr, normal_from_wild)plotrand_col_planes(mesh_tr, normal_from_wild)
mesh_tr |
an object of type mesh3d |
normal_from_wild |
the output matrix resulting from wildfire search |
a 3d plot of mesh with facets of the same plane
## Not run: mesh3d<-build_3d_mesh(path2myXYZRGBtxt,0.5,file_name) normali_recalc<-Rcpp_wildfire_search(7,normals[,1:3],neighbours) plotrand_col_planes(mesh3d,normali_recalc) ## End(Not run)## Not run: mesh3d<-build_3d_mesh(path2myXYZRGBtxt,0.5,file_name) normali_recalc<-Rcpp_wildfire_search(7,normals[,1:3],neighbours) plotrand_col_planes(mesh3d,normali_recalc) ## End(Not run)
returns the outer product of ab and ac
rcpp_crossProd(ab, ac)rcpp_crossProd(ab, ac)
ab |
a 3D numeric vector |
ac |
a 3D numeric vector |
the outer product of ab and ac
a1<-c(1,2,3) a2<-c(3,4,5) rcpp_crossProd(a1,a2)a1<-c(1,2,3) a2<-c(3,4,5) rcpp_crossProd(a1,a2)
returns a matrix with the 3 components of each face normal vector; the 4th column is the ID of the plane each facet belongs to the 5th colum the area of each facet
Rcpp_wildfire_search(tol_ang, list_of_normals, list_neighbours)Rcpp_wildfire_search(tol_ang, list_of_normals, list_neighbours)
tol_ang |
the maximum angle between facets normal belonging to the same plane |
list_of_normals |
the matrix of the components of each facet normal vector |
list_neighbours |
the matrix of facets ID neighbours of each target facet |
the IDs of same joint facets given a tol_angle between facets normal and 3Dmesh list_of_normals and list_neighbours
## Not run: neighbours<-find_neighbours_rcpp(indici_tri) normals<-compute_facets_normal(vertici_tr,indici_tri) tol_ang<-7 normali_recalc<-Rcpp_wildfire_search(tol_ang,normals[,1:3],neighbours) ## End(Not run)## Not run: neighbours<-find_neighbours_rcpp(indici_tri) normals<-compute_facets_normal(vertici_tr,indici_tri) tol_ang<-7 normali_recalc<-Rcpp_wildfire_search(tol_ang,normals[,1:3],neighbours) ## End(Not run)
returns the inner product of ab and ac
ab |
a 3D numeric vector |
ac |
a 3D numeric vector |
the dot product of ab and ac
a1<-c(1,2,3) a2<-c(3,4,5) rcpparma_dotproduct(a1,a2)a1<-c(1,2,3) a2<-c(3,4,5) rcpparma_dotproduct(a1,a2)