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Export Mesh

Source: R/export_mesh.R
export_mesh.Rd

Exports a QSM cylinder mesh in various formats

Usage

export_mesh(
  cylinder,
  filename,
  format = "ply",
  radius = NULL,
  color = NULL,
  palette = NULL,
  facets = 6,
  normals = FALSE,
  alpha = NULL
)

Arguments

cylinder

QSM cylinder data frame.

filename

File name and path for exporting. The file extension is automatically added if not present.

format

Mesh file format. Defaults to ply. Supported formats include ply, obj, stl, and blender. format = "blender" exports the mesh in the qsm-blender-addons format.

radius

Radius column name either quoted or unquoted. Defaults to the modified radii.

color

Optional cylinder color parameter. color must be a single hex color string, a grDevices::colors(), a vector of hex colors, or a quoted/unquoted column name. Vectors must have the same length as the cylinder data frame. color = "random" will generate a random color applied to all cylinders. Defaults to branching order.

palette

Optional cylinder color palette for numerical data. Palettes include colourvalues::color_palettes() or a user supplied RGB palette matrix with the length of cylinder. It can also be set to "random" to generate a random palette. If combined with color = "random", each cylinder will have a random, distinct color.

facets

The number of facets in the polygon cross section. Defaults to 6. A higher number of facets improves visual smoothness at the cost of plotting speed, performance and memory.

normals

Export surface normals per vertex. Defaults to FALSE.

alpha

Set the transparency of the cylinders used in the "ply" format. Defaults to 1. 1 is opaque and 0 is fully transparent.

Value

A mesh file

Examples


## Load QSM
file <- system.file("extdata/QSM.mat", package = "rTwig")
qsm <- import_treeqsm(file)
#> Importing TreeQSM
cylinder <- qsm$cylinder
cylinder <- update_cylinders(cylinder)
#> Updating Cylinder Ordering
#> Calculating Total Children
#> Building Cylinder Network
#> Caching Network
#> Verifying Topology
#> Calculating Growth Length
#> Calculating Reverse Branch Order
#> Calculating Branch Segments
#> Calculating Alternate Branch Numbers
#> Calculating Path Metrics

# PLY
filename <- tempfile(pattern = "QSM_ply")
export_mesh(
  cylinder = cylinder,
  filename = filename,
  format = "ply",
  color = "distanceToTwig",
  palette = "viridis",
  normals = TRUE
)
#> Exporting Mesh

# OBJ
filename <- tempfile(pattern = "QSM_obj")
export_mesh(
  cylinder = cylinder,
  filename = filename,
  format = "obj",
  normals = TRUE
)
#> Exporting Mesh

# STL
filename <- tempfile(pattern = "QSM_stl")
export_mesh(
  cylinder = cylinder,
  filename = filename,
  format = "stl",
  normals = TRUE
)
#> Exporting Mesh

# QSM Blender Addons
filename <- tempfile(pattern = "QSM_blender")
export_mesh(
  cylinder = cylinder,
  filename = filename,
  format = "blender",
  normals = TRUE
)
#> Exporting Mesh