lidR-LAScatalog-drivers: LAScatalog drivers

In Jean-Romain/lidR: Airborne LiDAR Data Manipulation and Visualization for Forestry Applications

LAScatalog drivers

Description

This document explains how objects are written on disk when processing a LAScatalog. As mentioned in LAScatalog-class, users can set a templated filename to store the outputs on disk instead of in R memory. By defaut LAS objects are stored in .las files with writeLAS, raster objects are stored in .tif files using native write function for raster, stars or terra, ⁠Spatial*⁠ objects are stored in .shp files with after coercion to sf with st_write, sf object are stored to .gpkg files with st_write.data.frame objects are stored in .csv files with fwrite, and other objects are not supported. However, users can modify all these default settings and even add new drivers. This manual page explain how. One may also refer to some unofficial documentation here or here.

Generic form of a driver

A driver is stored in the slot ⁠@output_options⁠ of a LAScatalog. It is a list that contains:

write

A function that receives an object and a path, and writes the object into a file using the path. The function can also have extra options.

extension

A string that gives the file extension.

object

A string that gives the name of the argument used to pass the object to write in the function used to write the object.

path

A string that gives the name of the argument used to pass the path of the file to write in the function used to write the object.

param

A labelled list of extra parameters for the function used to write the object

For example, the driver to write a ⁠Raster*⁠ is

list(
 write = raster::writeRaster,
 extension = ".tif",
 object = "x",
 path = "filename",
 param = list(format = "GTiff"))

And the driver to write a LAS is

list(
 write = lidR::writeLAS,
 extension = ".las",
 object = "las",
 path = "file",
 param = list())

Modify a driver (1/2)

Users can modify the drivers to write different file types than the default. For example, to write in shapefile instead of a GeoPackage, one must change the sf driver:

ctg@output_options$drivers$sf$extension <- ".shp"

To write a ⁠Raster*⁠ in .grd files instead of .tif files one must change the Raster driver:

ctg@output_options$drivers$Raster$extension <- ".grd"
ctg@output_options$drivers$Raster$param$format <- "raster"

To write in .laz files instead of .las files one must change the LAS driver:

ctg@output_options$drivers$LAS$extension <- ".laz"

Add a new driver

The drivers allow LAS, Spatial,⁠sf,⁠ Raster, stars, SpatRaster and data.frame objects to be written. When using the engine (catalog_apply) to build new tools, users may need to be able to write other objects such as a list. To do that users need to add a list element into ⁠@output_options⁠:

ctg@output_options$drivers$list = list(
 write = base::saveRDS,
 object = "object",
 path = "file",
 extension = ".rds",
 param = list(compress = TRUE))

The LAScatalog now has a new driver capable of writing a list.

Modify a driver (2/2)

It is also possible to completely overwrite an existing driver. By default sf objects are written into GeoPackage with st_write. st_write can also wite in GeoJSON and even in SQLlite database objects. But it cannot add data into an existing SQLlite database. Let's create our own driver for a sf. First we need a function able to write and append a sf into a SQLlite database from the object and the path.

dbWrite_sf = function(x, path, name)
{
 x <- sf::st_drop_geometry(x)
 con <- RSQLite::dbConnect(RSQLite::SQLite(), path)
 RSQLite::dbWriteTable(con, name, x, append = TRUE)
 RSQLite::dbDisconnect(con)
}

Then we create the driver. User-defined drivers supersede default drivers:

ctg@output_options$drivers$sf = list(
 write = dbWrite_sf,
 extension = ".sqlite",
 object = "x",
 path = "path",
 param = list(name = "layername"))

Then to be sure that we do not write several .sqlite files, we don't use templated filename.

opt_output_files(ctg) <- paste0(tempdir(), "/mysqlitefile")

And all the sf will be appended in a single database. To preserve the geometry one can

Jean-Romain/lidR documentation built on April 6, 2024, 9:41 p.m.