Questions tagged [lidr]
R package for Airborne LiDAR Data Manipulation and Visualization in Forestry Applications
307
questions
0
votes
2
answers
22
views
How to export an IDW DTM as a GeoTIFF file in R
I have loaded both raster and lidR packages within RStudio and I am trying to export the IDW DTM files but have been receiving errors about 'format'. I have exported a TIN DTM already however with IDW ...
0
votes
1
answer
48
views
lidR canopy height map has holes/jagged edges
I am trying to create a canopy height map from LIDAR point cloud data (LAS format) but I get some jagged edges/holes in my results (see photo). Is there a parameter I can tweak to fill these in? I ...
- 133
0
votes
1
answer
39
views
Normalizing LAScatalog only outputs one tile
I'm having trouble normalizing a LAScatalog. I wonder whether my methodology is flawed, or if something is possibly wrong with my dataset (a point cloud based on photogrammetry). When I try to ...
- 105
1
vote
1
answer
20
views
How to fill pits for a DEM/CHM when using the LAScatalog engine?
I'm trying to create a DEM/CHM using the LAScatalog engine. I've followed the steps in the lidRbook. In chapter 6 section 6.4 the post processing fills in areas no missing values for single las files ...
- 590
0
votes
0
answers
27
views
Create a buffer on a single LAS file using lidR
I want to create a buffer for a single LAS file in order to test different algorithims for DTM creation on a small scale before scaling up to all my files using LAScatalog.
I know LAScatalog creates a ...
- 590
0
votes
1
answer
15
views
lidR pixel_metrics returning incorrect results with LAScatalog [closed]
This code seems to work correctly when I use it with a single las file
f <- function(x) { # user-defined fucntion
list(mean = mean(x), sd = sd(x))
}
las <- readLAS(<path to las file>)
...
- 1
0
votes
0
answers
15
views
Interactively re-center a lidR plot
Is it possible to move the plot center of a lidR plot from within the plot visualization? For example, I try dragging and using up and down arrows, but it does not move the point cloud's position ...
- 790
0
votes
1
answer
34
views
R LidR Package readlas function with extra features limitations
I'm encountering an issue while working with LAS data generated from the open-source software CloudCompare. I've exported 24 geometric features to a LAS file format(1.4), and I'm experiencing ...
- 61
0
votes
1
answer
25
views
How to calculate voxel metrics for a LAScatalog using lidR?
I'm trying to calculate metrics for a LAScatalog with the voxel_metrics function. This is the code I used:
library(lidR)
ctg <- readLAScatalog("laspath")
voxel_metrics(ctg, ~mean(Z), 4)
...
1
vote
1
answer
51
views
lidR producing error "$ operator not definied for this S4 class" when trying to apply function to lascatalog using catalog_apply
I am trying to write a function to calculate specific metrics which I can write to a data frame and then a .csv file to write 'reports' on each las file in a directory. I have tried the following code:...
0
votes
0
answers
26
views
Can Z output from rasterize_terrain() be made numeric?
I'm updating code to compute height and elevation of tree tops derived from locate_trees(). To do this I also create a DTM from the LAS file. The older grid_terrain() produced a RasterLayer and the ...
- 549
1
vote
1
answer
32
views
Iterating through las directory using lidR in R results in not finding file or not recognising file as .las
I am trying to produce a script which has functions that can produce a list of statistics and writes them to data.frame, which can in turn be written to a csv file if needed. This would be to check ...
0
votes
1
answer
40
views
How do I use autocrop with a complex function for catalog_apply()?
In the case of a complex function, I would like to try the autocrop option, instead of crop inside the function, to resize output from catalog_apply() to the chunk size. In the code below, the ...
- 549
1
vote
1
answer
16
views
How do I use autocrop in a function for catalog_apply()?
I would like to try the autocrop option, instead of crop inside the function, to resize output from catalog_apply() to the chunk size. In the code below, the commented-out code works, but the autocrop ...
- 549
0
votes
1
answer
38
views
Plotting real (normalized) las values on dtm
I am trying to plot a las where I filtered objects, that have a first and a last return simultaneously (objects in the las file), onto a created dtm of the same las. I am able to produce a good result....
- 3
0
votes
1
answer
31
views
lidR: What is "Area" in Cloud_metrics(.stdmetrics)? [closed]
I have plot locations and .las tiles.
I have extracted the point clouds at each of the plots with a 15 meters radius.
It means i now have as many .las files as i have plots.
Then, in a for loop, for ...
0
votes
0
answers
22
views
LAS files not identified in lidR
When I try to upload the las file to work on lidR package it give the following error.
The code I used to upload the file
las <-readLAS("<Sample.las>")
Error in streamLAS.character(...
2
votes
1
answer
60
views
How do I overwrite files in the function pixel_metrics()?
I'm trying to test my pixel_metrics() custom function, and I'm not sure how to overwrite the old file, like the error message suggests in the screenshot. I have added overwrite=TRUE to my function ...
- 105
3
votes
1
answer
52
views
How do I run filter_poi() on a LAScatalog object?
I want to read a LAS catalog, create a DEM, normalize the catalog, and run filter_poi() on the catalog.
My issue is that when I try to run filter_poi(), in the code below, I get the error "...
- 105
1
vote
1
answer
83
views
How can I export a lidR LAScatalog to a shapefile?
I would like to export a lascatalog to a shapefile. It could be done in the past with rgdal but this is being retired.
The error is below.
library(lidR)
library(sf)
ctg <- readLAScatalog(system....
- 549
0
votes
0
answers
78
views
Euclidean distance point Cloud clustering in R lidR
I'm looking for a way to implement the python function filter.clusters from the pdal package in R using the lidR package.
The function clusters pointclouds using the Euclidean distance, a tolerance ...
- 1
3
votes
1
answer
92
views
Classify vegetation by height
Trying to further classify a las catalog that already has buildings, bridges, noise and ground classified. I want to break the unassigned points into vegetation classes by height but can't get it to ...
- 55
1
vote
1
answer
41
views
Create LAS v1.4 from scratch
I want to create a LAS object from scratch with number of returns up to 15 (according to LAS v1.4) like:
data <- data.frame(X = runif(100, 0, 100),
Y = runif(100, 0, 100),
...
- 13
0
votes
0
answers
18
views
rasterize_terrain DTM raster file write error [duplicate]
I am trying to create DTM rasters from a list of LAS files.
Code:
# Create a LAS catalog
LAS_List = readLAScatalog("path", recursive = TRUE)
# Create an output destination to store the DTM ...
- 1,112
0
votes
1
answer
68
views
Create one single DTM raster file from multiple LAS files
This question can be considered an extension of Create a DTM using the TIN algorithm
I am providing multiple LAS files as a catalog list to the rasterize_terrain which breaks the LAS into smaller ...
- 1,112
0
votes
0
answers
30
views
Unexpected artifacts when creating a digital terrain model (DTM) using lidR and gstat libraries in R
I'm using the lidR, raster, sp, and gstat libraries in R to create a Digital Terrain Model (DTM) from LiDAR data. I'm encountering unexpected artifacts in my DTM and I'm unsure why.
Here is my code:
...
- 55
1
vote
1
answer
58
views
Create a DTM using the TIN algorithm
I am trying to create a DTM on a county wide level (so using LAS catalog). The lidRworkbook advises to use a buffer when using the TIN method, however the workbook doesn't show how to do that. So how ...
- 1,112
2
votes
1
answer
69
views
Calculate proportions of all returns, returns between a height interval
I want to calculate, for each pixel, the proportions of returns between 0.5 and 5 m height above ground, compared to the total return count
I have figured out how to do it for the entire las file, but ...
- 68.8k
2
votes
2
answers
192
views
How can I crop a raster (within a function) that is used by catalog_apply() in lidR, using Terra instead of Raster?
I have older code to crop a chunk within a function (to avoid edge effects when later merging CHM tiles together (i.e., edge pixels derived without enough data. The extend of 1 is to avoid little gaps)...
- 549
1
vote
1
answer
39
views
Classify Pointcloud using thematic layer with lidR
I want to use lidR to classify points within a point cloud using a few thematic shapefiles. This includes buildings, vegetation and cars. For this I use the classify_poi function, which works for ...
- 109
1
vote
1
answer
27
views
How to harmonize catalog to target density
My original catalog:
has a mean density of 2.2 points/m2, but some areas have a higher density.
:
> plot(lidR::grid_density(ctg, 1), main = "Density grid 1x1 m ", breaks = c(0,2,3,5,16), ...
- 369
2
votes
1
answer
72
views
negative or null values in custom function
I'm working with the package lidR (v 4.0.3) to extract the tree positions using a custom function but it behaves weirdly. If I use the following, I get an error:
f = function(x) { 0.413 * x^0.5532 }
...
- 305
0
votes
0
answers
31
views
Why clip_roi function in lidR only work with SpatialPolygons and not SpatVector?
Most of the functions from lidR work using SpatVector and SpatRaster from terra package but I obtained this error using clip_roi function
Error in clip_roi(ctg, Extent1) : Geometry type SpatVector not ...
- 147
0
votes
1
answer
51
views
lidR, create table with numberofreturn by returnnumber in catalog
In a LAScatalog we can have the 5th first return, but how can i have this table if there is 7 return like this :
With this code i can generate this table with 4 return :
LASfile <- system.file(&...
- 189
2
votes
1
answer
47
views
Memory efficient way of using clip_roi for bigger areas
I am trying to clip LAS files from a LAScatalog object based on a polygon boundary (sf object). However, since the area of interest is too big, the clip_roi function might eventually like mid way ...
- 1,112
2
votes
1
answer
61
views
clip_roi dimension error
I am trying to clip LAS files from a catalog object based on a Polygon boundary (sf_object), however, I am getting the following error.
What could be the issue and how can it be fixed?
Error:
...
- 1,112
1
vote
1
answer
36
views
lidR version 4.0.3 lasmetrics disappear and make error
Before lidR v4.0.3 this code return datatable but now lasmetrics is replaced with different part function. How can i transform this code in lidR v 4.0.3 ?
LASfile <- system.file("extdata",...
- 189
1
vote
1
answer
39
views
LidR catalog apply function not return dataframe
Here is my code :
LASfile <- system.file("extdata", "Megaplot.laz", package="lidR")
ctg = readLAScatalog(LASfile)
myMetrics2 <- function(rnu, nor) {
tab <- ...
- 189
0
votes
1
answer
28
views
Pass the whole roi's cloud to use it in plot_metrics()?
I am trying to create a custom plot_metrics function that calculates a series of metrics from the Canopy Heigh Model (CHM) of the points clipped from a catalog.
LASfile <- system.file("extdata&...
- 369
1
vote
1
answer
147
views
Tips for optimizing parallelism with lidR custom metric to be deployed on HPC [closed]
I've read the documentation on parallel computation in lidR in the lidR package documentation (page 73) and am a bit lost about how to optimize or effectively implement parallelism on a high-...
- 25
5
votes
2
answers
607
views
Is there a major drawback of working with compressed LAZ vs. the uncompressed LAS?
Compressed LAS pointclouds (LAZ) are significantly smaller than the uncompressed ones (I observe a compression factor of x4 - x5). Since point clouds are often large files, this is a substantial ...
- 2,334
1
vote
1
answer
38
views
lidR custom grid metric returning raster output mean max values lower than 1 m for mean height bin interval between 0.2-4
I want to calculate the mean height of shrubs layer using the mean height of points between 0.2-4 m above ground but the raster output mean max values never is higher than 1 m which is not make sense ...
- 147
0
votes
1
answer
54
views
lidR custom grid metric returning infinite values
I am trying to calculate the proportion of points 0.3-2.5m above ground relative to the number of ground points + all points up to 2.5m above ground using lidR grid_metrics(). My custom grid_metrics() ...
- 25
2
votes
1
answer
332
views
How to efficiently reproject a LAS point cloud to EPSG:2056 (not known by LAStools)?
I have a large LAS pointcloud in LV03 (EPSG:21781) that I want to reproject to LV95 (EPSG:2056). My approaches so far bear no fruit.
What is a good way to re-project LAS data to a different CRS (...
- 2,334
3
votes
2
answers
250
views
Why is laspy X,Y co-ordinate different to X,Y co-ordinate in lidr
I am working in both r and python to process lidar data with .las format. One thing I have noticed is that the x,y co-ordinate when working with laspy is different than x,y co-ordinate when using lidr....
- 55
2
votes
0
answers
51
views
Can a function that lists various metrics be used in `plot_metrics()`
I'm trying to combine various metrics to use in plot_metrics(). But I get an error when I run it. I tried to follow the answer from here: How to incorporate stdmetrics in gridmetrics function?
Can a ...
- 549
3
votes
1
answer
96
views
lidR: How to configure opt_output_files() for chunk processing of multiple pixel_metrics()?
This is a somewhat conceptual question about how the opt_output_files() function works in lidR. I'm working on a project where I'm calculating a series of custom pixel metrics across a large spatial ...
- 33
0
votes
1
answer
110
views
Clipping LAScatolog with a large polygon shapefile using is extremely slow
I´m using the lidR (Version 4.0.0) package to clip a LAScatalog (with 119 .las files, ~52.9 Gb) using a very large polygon shapefile (~865K buffers with 25m diameter each). I´m stuck in this task ...
- 9
1
vote
1
answer
134
views
Error in "writeOGR" When creating a shapefile from convex hulls
I am working on the segmentation of crown canopy using LiDAR. I want to extract the crowns created after the segmentation as a shapefile. Other documentation and links show that using writeOGR I can ...
- 55
0
votes
0
answers
153
views
lidR: Clipping LAS files with a polygon shapefile using clip_roi
I'm trying to clip a LAScatalog (containing several .las files) with a shapefile (containing multiple polygons). I tried using clip_roi function, however getting an Error: Z only allowed for 3 or ...
- 1