JFM: A package for structural analysis.

Description

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.

Author(s)

Riccardo Campana <riccarl@hotmail.it>

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

Description

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

Usage

Rcpp_wildfire_search(tol_ang, list_of_normals, list_neighbours)

Arguments

Value

the IDs of same joint facets given a tol_angle between facets normal and 3Dmesh list_of_normals and list_neighbours

Examples

## 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)

build_3d_mesh

Description

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

Usage

build_3d_mesh(path2myXYZRGBtxt, search_radius, file_name)

Arguments

Value

A 3D triangular mesh

Examples

## 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)

calculate_joints

Description

This function calculates joint orientation with the least square method selecting vertexes of each facet plane

Usage

calculate_joints(vertici_tr, indici_tri, normal_from_wild)

Arguments

Value

a matrix of least square plane for each joint

Examples

## 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)

calculate_joints_area

Description

This function calculates the area of each cluster of facets belonging to the same plane

Usage

calculate_joints_area(normal_from_wild)

Arguments

Value

a list of the area of each plane

Examples

## Not run: 

normali_recalc<-Rcpp_wildfire_search(7,normals[,1:3],neighbours)

calculate_joints(mesh3d,normali_recalc)


## End(Not run)

compute_facets_normal

Description

This function returns a matrix of the three component vector of the normal of each facet.

Usage

compute_facets_normal(vertici_tr, indici_tri)

Arguments

Value

matrix of the three component of the normal vector and area of each face

Examples

## 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

Description

returns the sum of the area of facets belonging to the same plane

Arguments

Value

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)

Description

returns the least square plane from the vertexes of facets of the same plane (nested in calculate_joints function)

Usage

compute_plane_normal(it_id_plane_points, vb_facets, id_fam_no_zero)

Arguments

Value

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

Examples

 #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

Description

returns the area of a mesh facet

Arguments

findNeighbourFacets

Description

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.

Usage

findNeighbourFacets(no_cores, indici_tri)

Arguments

Value

a matrix of indexes of facets neighbours of target face saved on working dir

Examples

## 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)

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

Description

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

Usage

find_neighbours_rcpp(indici_tr)

Arguments

Value

this function returns the rows IDs of neighbours of each mesh facet given a list of facets indexes indici_tri

Examples

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)

Description

returns the row indexes of the neighbour facets of a target facet (nested in findNeighbourFacets R function)

Usage

find_triangles_rcpp(indici_tr, r)

Arguments

Value

returns the row indexes of the neighbour facets of the facet at r row of indici_tr facet indexes matrix

Examples

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)

returns the coefficients of the least square plane and the relative mean square error

Description

returns the coefficients of the least square plane and the relative mean square error

Usage

least_square_plane_rcpp(PointsXYZ)

Arguments

Value

returns the coefficients of the least square plane and the relative mean square error of a set of 3d points PointsXYZ

Examples

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)

plot_joint_great_circles

Description

This function loads joint maxima poles, convert them to great circles and plot them on Schmidt stereogram. Data are also saved in working folder.

Usage

plot_joint_great_circles(giac_max, file_name)

Arguments

Value

A plot with great circles of joint maxima saved in working dir

Examples

## 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)

plot_joint_poles

Description

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.

Usage

plot_joint_poles(
  normal_from_wild,
  planes_mtx,
  area_ls,
  file_name,
  min_dens,
  plane_area
)

Arguments

Value

A Schmidt density plot with maxima values of joints

Examples

## 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)

plot_maxima2mesh

Description

This funtion plots a coloured mesh facets as great circles plot colours

Usage

plot_maxima2mesh(mesh_tr, planes_max, normal_from_wild, tol_ang_fam)

Arguments

Value

A plot with great circles of joint maxima

Examples

## 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)

plotrand_col_planes

Description

This function returns a 3d plot of mesh where facets of the same plane are of same color.

Usage

plotrand_col_planes(mesh_tr, normal_from_wild)

Arguments

Value

a 3d plot of mesh with facets of the same plane

Examples

## 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

Description

returns the outer product of ab and ac

Usage

rcpp_crossProd(ab, ac)

Arguments

Value

the outer product of ab and ac

Examples

a1<-c(1,2,3)
a2<-c(3,4,5)
rcpp_crossProd(a1,a2)

returns the inner product of ab and ac

Description

returns the inner product of ab and ac

Arguments

Value

the dot product of ab and ac

Examples

a1<-c(1,2,3)
a2<-c(3,4,5)
rcpparma_dotproduct(a1,a2)